@article {pmid38036425,
year = {2023},
author = {Doolin, ML and Dearing, MD},
title = {Differential effects of two common antiparasitics on microbiota resilience.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiad547},
pmid = {38036425},
issn = {1537-6613},
abstract = {BACKGROUND: Parasitic infections challenge vertebrate health worldwide, and off-target effects of antiparasitic treatments may be an additional obstacle to recovery. However, there have been few investigations of the effects of antiparasitics on the gut microbiome in the absence of parasites.<br><br>METHODS: We investigated whether two common antiparasitics-albendazole and metronidazole-significantly alter the gut microbiome of parasite-free mice. We treated mice with albendazole or metronidazole daily for seven days and sampled the fecal microbiota immediately before and after treatment, and again after a two-week recovery period.<br><br>RESULTS: Albendazole did not immediately change the gut microbiota, while metronidazole decreased microbial richness by 8.5% and significantly changed community structure during treatment. The structural changes caused by metronidazole included depletion of the beneficial family Lachnospiraceae, and predictive metagenomic analysis revealed that these losses likely depressed microbiome metabolic function. Separately, we compared the fecal microbiotas of treatment groups after recovery, and there were minor differences in community structure between the albendazole, metronidazole, and sham-treated control groups.<br><br>CONCLUSIONS: These results suggest that a healthy microbiome is resilient after metronidazole-induced depletions of beneficial gut microbes and albendazole may cause slight, latent shifts in the microbiota but does not deplete healthy gut microbiota diversity.},
}
@article {pmid38036127,
year = {2023},
author = {Zhao, J and Yu, X and Zhang, C and Hou, L and Wu, N and Zhang, W and Wang, Y and Yao, B and Delaplace, P and Tian, J},
title = {Harnessing microbial interactions with rice: Strategies for abiotic stress alleviation in the face of environmental challenges and climate change.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168847},
doi = {10.1016/j.scitotenv.2023.168847},
pmid = {38036127},
issn = {1879-1026},
abstract = {Rice, which feeds more than half of the world's population, confronts significant challenges due to environmental and climatic changes. Abiotic stressors such as extreme temperatures, drought, heavy metals, organic pollutants, and salinity disrupt its cellular balance, impair photosynthetic efficiency, and degrade grain quality. Beneficial microorganisms from rice and soil microbiomes have emerged as crucial in enhancing rice's tolerance to these stresses. This review delves into the multifaceted impacts of these abiotic stressors on rice growth, exploring the origins of the interacting microorganisms and the intricate dynamics between rice-associated and soil microbiomes. We highlight their synergistic roles in mitigating rice's abiotic stresses and outline rice's strategies for recruiting these microorganisms under various environmental conditions, including the development of techniques to maximize their benefits. Through an in-depth analysis, we shed light on the multifarious mechanisms through which microorganisms fortify rice resilience, such as modulation of antioxidant enzymes, enhanced nutrient uptake, plant hormone adjustments, exopolysaccharide secretion, and strategic gene expression regulation, emphasizing the objective of leveraging microorganisms to boost rice's stress tolerance. The review also recognizes the growing prominence of microbial inoculants in modern rice cultivation for their eco-friendliness and sustainability. We discuss ongoing efforts to optimize these inoculants, providing insights into the rigorous processes involved in their formulation and strategic deployment. In conclusion, this review emphasizes the importance of microbial interventions in bolstering rice agriculture and ensuring its resilience in the face of rising environmental challenges.},
}
@article {pmid38036110,
year = {2023},
author = {Kulshrestha, M and Tiwari, M and Tiwari, V},
title = {Bacteriophage therapy against ESKAPE bacterial pathogens: Current status, strategies, challenges, and future scope.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {106467},
doi = {10.1016/j.micpath.2023.106467},
pmid = {38036110},
issn = {1096-1208},
abstract = {The ESKAPE pathogens are the primary threat due to their constant spread of drug resistance worldwide. These pathogens are also regarded as opportunistic pathogens and could potentially cause nosocomial infections. Most of the ESKAPE pathogens have developed resistance to almost all the antibiotics that are used against them. Therefore, to deal with antimicrobial resistance, there is an urgent requirement for alternative non-antibiotic strategies to combat this rising issue of drug-resistant organisms. One of the promissing alternatives to this scenario is implementing bacteriophage therapy. This under-explored mode of treatment in modern medicine has posed several concerns, such as preferable phages for the treatment, impact on the microbiome (or gut microflora), dose optimisation, safety, etc. The review will cover a rationale for phage therapy, clinical challenges, and propose phage therapy as an effective therapeutic against bacterial coinfections during pandemics. This review also addresses the expected uncertainties for administering the phage as a treatment against the ESKAPE pathogens and the advantages of using lytic phage over temperate, the immune response to phages, and phages in combinational therapies. The interaction between bacteria and bacteriophages in humans and countless animal models can also be used to design novel and futuristic therapeutics like personalised medicine or bacteriophages as anti-biofilm agents. Hence, this review explores different aspects of phage therapy and its potential to emerge as a frontline therapy against ESKAPE bacterial pathogen.},
}
@article {pmid38035997,
year = {2023},
author = {Chooi, YC and Zhang, QA and Magkos, F and Ng, M and Michael, N and Wu, X and Volchanskaya, VSB and Lai, X and Wanjaya, ER and Elejalde, U and Goh, CC and Yap, CPL and Wong, LH and Lim, KJ and Velan, SS and Yaligar, J and Muthiah, MD and Chong, YS and Loo, EXL and Eriksson, JG and , and Lim, KLM and Kouk, MSF and Mei Chong, EW and Gani, MA and Li, L and Tay, VHK and Kway, YM and Kumar, M and Sadananthan, SA and Khoo, K and Koh, D and Lim, R and Kang, CW and Sin, KL and Lim, JW},
title = {Effect of an Asian-adapted Mediterranean diet and pentadecanoic acid on fatty liver disease: The TANGO randomized controlled trial.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2023.11.013},
pmid = {38035997},
issn = {1938-3207},
abstract = {BACKGROUND: Weight loss is the most effective treatment for non-alcoholic fatty liver disease (NAFLD). There is evidence that Mediterranean diets rich in unsaturated fatty acids and fiber have beneficial effects on weight homeostasis and metabolic risk factors in individuals with NAFLD. Studies have also shown that higher circulating concentrations of pentadecanoic acid (C15:0) are associated with lower risk for NAFLD.<br><br>OBJECTIVES: To examine the effects of a Mediterranean-like, culturally contextualized Asian diet rich in fiber and unsaturated fatty acids, with or without C15:0 supplementation, in Chinese females with NAFLD.<br><br>METHODS: In a double-blinded, parallel-design, randomized controlled trial, 88 Chinese females with NAFLD were randomized to one of three groups for 12-weeks: diet with C15:0 supplementation (n=31), diet without C15:0 supplementation (n=28), or control (habitual diet and no C15:0 supplementation, n=29). At baseline and after the intervention, body fat percentage, intrahepatic lipid content, muscle and abdominal fat, liver enzymes, cardiometabolic risk factors and gut microbiome were assessed.<br><br>RESULTS: In intention-to-treat analysis, weight reductions of 4.0&#xb1;0.5 kg (5.3%), 3.4&#xb1;0.5 kg (4.5%), and 1.5&#xb1;0.5 kg (2.1%) were achieved in the diet-with-C15:0, diet-without-C15:0, and the control groups, respectively. The proton density fat fraction (PDFF) of the liver decreased by 33%, 30% and 10%, respectively. Both diet groups achieved significantly greater reductions in body weight, liver PDFF, total cholesterol, gamma-glutamyl transferase, and triglyceride concentrations compared to the control group. C15:0 supplementation reduced LDL-cholesterol further, and increased abundance of Bifidobacterium adolescentis. Fat mass, visceral adipose tissue, subcutaneous abdominal adipose tissue (deep and superficial), insulin, glycated hemoglobin and blood pressure decreased significantly in all groups, in parallel with weight loss.<br><br>CONCLUSION: Mild weight loss induced by a Mediterranean-like diet adapted for Asians has multiple beneficial health effects in women with NAFLD. C15:0 supplementation lowers LDL-cholesterol and may cause beneficial shifts in gut microbiome.<br><br>REGISTRATION: clinicaltrials.gov, NCT05259475.},
}
@article {pmid38035991,
year = {2023},
author = {Balasubramanian, S and Haneen, MA and Sharma, G and Perumal, E},
title = {Acute copper oxide nanoparticles exposure alters zebrafish larval microbiome.},
journal = {Life sciences},
volume = {},
number = {},
pages = {122313},
doi = {10.1016/j.lfs.2023.122313},
pmid = {38035991},
issn = {1879-0631},
abstract = {Copper oxide nanoparticles (CuO NPs) are being used in healthcare industries due to its antimicrobial properties. The increased consumption of NPs could lead to the rise of these NPs in the environment affecting the biological systems. Altered microbiome has been correlated to disease pathology in humans as well as xenobiotic toxicity in experimental animal models. However, CuO NPs-induced microbiome alterations in vertebrates have not been reported so far. In this study for the first time, zebrafish larvae at 96 hpf (hours post fertilization) were exposed to CuO NPs for 24 h at 10, 20, and 40 ppm. After exposure, the control and treated larvae were subjected to 16S rRNA amplicon sequencing followed by relative taxa abundance, alpha and beta diversity analysis, single factor analysis, LEfSe, Deseq2, and functional profiling. No significant alteration was detected in the microbial richness and diversity, however, specific taxa constituting the core microbiome such as the phylum Proteobacteria were significantly increased and Bacterioidetes and Firmicutes were decreased in the treated groups, indicating a core microbiota dysbiosis. Further, the family Lachnospiraceae, and genus Syntrophomonas involved in butyrate production and the metabolism of lipids and glucose were significantly altered. In addition, the opportunistic pathogens belonging to order Flavobacteriales were increased in CuO NPs treated groups. Moreover, the taxa involved in host immune response (Shewanella, Delftia, and Bosea) were found to be enriched in CuO NPs exposed larvae. These results indicate that CuO NPs exposure causes alteration in the core microbiota, which could cause colitis or inflammatory bowel disease.},
}
@article {pmid38035748,
year = {2023},
author = {Reynolds, AN and Hood, F and Wilson, R and Ross, A and Neumann, S and Turner, R and Iosua, E and Katare, R and Shahin, A and Kok, ZY and Chan, H and Coffey, S and Mann, J},
title = {Healthy grocery delivery in the usual care for adults recovering from an acute coronary event: protocol for a three-arm randomised controlled trial.},
journal = {BMJ open},
volume = {13},
number = {11},
pages = {e074278},
pmid = {38035748},
issn = {2044-6055},
abstract = {INTRODUCTION: Coronary heart disease is a major contributor to the global burden of disease. Appropriate nutrition is a cornerstone of the prevention and treatment of coronary heart disease; however, barriers including cost and access to recommended foods limits long-term adherence for many. We are conducting, in adults with coronary heart disease, a randomised controlled trial comparing usual care with two dietary interventions in which usual care is augmented by 12 weeks free delivered groceries.<br><br>METHODS AND ANALYSIS: Three hundred adults recovering from an acute coronary event will be recruited from outpatient cardiovascular services in three regions of Aotearoa New Zealand. Participants will be randomly allocated to three arms: usual care (control group), usual care and the free delivery of foods high in dietary fibre or usual care and the free delivery of foods high in unsaturated fats. Interventions duration is 12 weeks, with a further 12 months follow-up. The primary outcome measures are change in low-density lipoprotein (LDL) cholesterol concentration following the intervention, and a cost-effectiveness analysis of healthcare access and social costs in the year after the intervention. A broad range of secondary outcome measures include other blood lipids, anthropometry, glycaemia, inflammatory markers, gut microbiome, dietary biomarkers, food acceptability, dietary change and the facilitators and barriers to dietary change. The trial will determine whether the free provision of groceries known to reduce cardiovascular risk within usual care will be clinically beneficial and justify the cost of doing so. Results may also provide an indication of the relative benefit of foods rich in dietary fibre or unsaturated fats in coronary heart disease management.<br><br>ETHICS AND DISSEMINATION: This trial, The Healthy Heart Study, has Health and Disability Ethics Committee approval (20/NTB/121), underwent M&#x101;ori consultation, and has locality authority to be conducted in Canterbury, Otago and Southland.<br><br>TRIAL REGISTRATION NUMBER: ACTRN12620000689976, U1111-1250-1499.},
}
@article {pmid38035726,
year = {2023},
author = {Zhou, H and Wang, L and Lin, Z and Jiang, C and Chen, X and Wang, K and Liu, L and Shao, L and Pan, J and Li, J and Zhang, D and Wu, J},
title = {Methylglyoxal from gut microbes boosts radiosensitivity and radioimmunotherapy in rectal cancer by triggering endoplasmic reticulum stress and cGAS-STING activation.},
journal = {Journal for immunotherapy of cancer},
volume = {11},
number = {11},
pages = {},
pmid = {38035726},
issn = {2051-1426},
abstract = {BACKGROUND: Preoperative radiation therapy (preRT) is a fundamental aspect of neoadjuvant treatment for rectal cancer (RC), but the response to this treatment remains unsatisfactory. The combination of radiation therapy (RT) and immunotherapy (iRT) presents a promising approach to cancer treatment, though the underlying mechanisms are not yet fully understood. The gut microbiota may influence the response to RT and immunotherapy. Therefore, we aimed to identify the metabolism of gut microbiota to reverse radioresistance and enhance the efficacy of iRT.<br><br>METHODS: Fecal and serum samples were prospectively collected from patients with locally advanced rectal cancer (LARC) who had undergone pre-RT treatment. Candidate gut microbiome-derived metabolites linked with radiosensitization were screened using 16s rRNA gene sequencing and ultrahigh-performance liquid chromatography-mass coupled with mass spectrometry. In vitro and in vivo studies were conducted to assess the radiosensitizing effects of the metabolites including the syngeneic CT26 tumor model and HCT116 xenograft tumor model, transcriptomics and immunofluorescence. The CT26 abscopal effect modeling was employed to evaluate the combined effects of metabolites on iRT.<br><br>RESULTS: We initially discovered the gut microbiota-associated metabolite, methylglyoxal (MG), which accurately predicts the response to preRT (Area Under Curve (AUC) value of 0.856) among patients with LARC. Subsequently, we observed that MG amplifies the RT response in RC by stimulating intracellular reactive oxygen species (ROS) and reducing hypoxia in the tumor in vitro and in vivo. Additionally, our study demonstrated that MG amplifies the RT-induced activation of the cyclic guanosine monophosphate AMP synthase-stimulator of interferon genes pathway by elevating DNA double-strand breaks. Moreover, it facilitates immunogenic cell death generated by ROS-mediated endoplasmic reticulum stress, consequently leading to an increase in CD8[+] T and natural killer cells infiltrated in the tumor immune microenvironment. Lastly, we discovered that the combination of anti-programmed cell death protein 1 (anti-PD1) therapy produced long-lasting complete responses in all irradiated tumor sites and half of the non-irradiated ones.<br><br>CONCLUSIONS: Our research indicates that MG shows promise as a radiosensitizer and immunomodulator for RC. Furthermore, we propose that combining MG with iRT has great potential for clinical practice.},
}
@article {pmid38035660,
year = {2023},
author = {Luise, D and Correa, F and Negrini, C and Virdis, S and Mazzoni, M and Dalcanale, S and Trevisi, P},
title = {Blend of natural and natural identical essential oil compounds as a strategy to improve the gut health of weaning pigs.},
journal = {Animal : an international journal of animal bioscience},
volume = {17},
number = {12},
pages = {101031},
doi = {10.1016/j.animal.2023.101031},
pmid = {38035660},
issn = {1751-732X},
abstract = {Weaning is one of the most critical phases in pig's life, often leading to postweaning diarrhoea (PWD). Zinc oxide (ZnO), at pharmacological doses, has been largely used to prevent PWD; however, due to antimicrobial co-resistant and environmental pollution issues, the EU banned its use in June 2022. Natural or natural identical components of essential oils and their mixture with organic acids are possible alternatives studied for their antimicrobial, anti-inflammatory and antioxidant abilities. This study aimed to evaluate the effect of two blends of natural or natural identical components of essential oils and organic acids compared to ZnO on health, performance, and gut health of weaned pigs. At weaning (d0), 96 piglets (7 058 ± 895 g) were assigned to one of four treatments balanced for BW and litter: CO (control treatment), ZnO (2 400 mg/kg ZnO from d0 to d14); Blend1 (cinnamaldehyde, ajowan and clove essential oils, 1 500 mg/kg feed); Blend2 (cinnamaldehyde, eugenol and short- and medium-chain fatty acids, 2 000 mg/kg feed). Pigs were weighed weekly until d35. Faeces were collected at d13 and d35 for microbiota (v3-v4 regions of the 16 s rRNA gene) and Escherichia coli (E. coli) count analysis. At d14 and d35, eight pigs/treatment were slaughtered; pH was recorded on intestinal contents and jejunal samples were collected for morphological and gene expression analysis. From d7-d14, the Blend2 had a lower average daily gain (ADG) than CO and ZnO (P < 0.05). ZnO and Blend1 never differed in ADG and feed intake. At d14, ZnO had a lower caecum pH than all other treatments. The CO treatment had a higher abundance of haemolytic E. coli than Blend1 (P = 0.01). At d13, the ZnO treatment had a lower alpha diversity (P < 0.01) and a different microbial beta diversity (P < 0.001) compared to the other treatments. At d13, the ZnO treatment was characterised by a higher abundance of Prevotellaceae_NK3B31_group (Linear Discriminant Analysis (LDA) score = 4.5, P = 0.011), Parabacteroides (LDA score = 4.5, P adj. = 0.005), the CO was characterised by Oscillospiraceae UCG-005 (LDA score = 4.3, P adj. = 0.005), Oscillospiraceae NK4A214_group (LDA score = 4.2, P adj. = 0.02), the Blend2 was characterised by Megasphaera (LDA score = 4.1, P adj. = 0.045), and Ruminococcus (LDA score = 3.9, P adj. = 0.015) and the Blend1 was characterised by Christensenellaceae_R-7_group (LDA score = 4.6, P adj. < 0.001) and Treponema (LDA score = 4.5, P adj. < 0.001). In conclusion, Blend1 allowed to maintain the gut health of postweaning piglets through modulation of the gut microbiome, the reduction of haemolytic E. coli while Blend2 did not help piglets.},
}
@article {pmid38035522,
year = {2023},
author = {Nguyen, AH and Oh, S},
title = {Side effects of the addition of an adsorbent for the nitrification performance of a microbiome in the treatment of an antibiotic mixture.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {133034},
doi = {10.1016/j.jhazmat.2023.133034},
pmid = {38035522},
issn = {1873-3336},
abstract = {This work determined the effect of biochar (BC) as an adsorbent on the nitrifying microbiome in regulating the removal, transformation, fate, toxicity, and potential environmental consequences of an antibiotic mixture containing oxytetracycline (OTC) and sulfamethoxazole (SMX). Despite the beneficial role of BC as reported in the literature, the present study revealed side effects for the nitrifying microbiome and its functioning arising from the presence of BC. Long-term monitoring revealed severe disruption to nitratation via the inhibition of both nitrite oxidizers (e.g., Nitrospira defluvii) and potential comammox species (e.g., Ca. Nitrospira nitrificans). Byproducts (BPs) more toxic than the parent compounds were found to persist at a high relative abundance, particularly in the presence of BC. Quantitative structure-activity relationship modeling determined that the physicochemical properties of the toxic BPs significantly differed from those of OTC and SMX. The results suggested that the BPs tended to mobilize and accumulate on the surface of the solids in the system (i.e., the BC and biofilm), disrupting the nitrifiers growing at the interface. Collectively, this study provides novel insights, demonstrating that the addition of adsorbents to biological systems may not necessarily be beneficial; rather, they may generate side effects for specific bacteria that have important ecosystem functions.},
}
@article {pmid38035404,
year = {2023},
author = {Lindner, BG and Gerhardt, K and Feistel, DJ and Rodriguez-R, LM and Hatt, JK and Konstantinidis, KT},
title = {A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection.},
journal = {International journal of food microbiology},
volume = {410},
number = {},
pages = {110488},
doi = {10.1016/j.ijfoodmicro.2023.110488},
pmid = {38035404},
issn = {1879-3460},
abstract = {Metagenomics, i.e., shotgun sequencing of the total microbial community DNA from a sample, has become a mature technique but its application to pathogen detection in clinical, environmental, and food samples is far from common or standardized. In this review, we summarize ongoing developments in metagenomic sequence analysis that facilitate its wider application to pathogen detection. We examine theoretical frameworks for estimating the limit of detection for a particular level of sequencing effort, current approaches for achieving species and strain analytical resolution, and discuss some relevant modern tools for these tasks. While these recent advances are significant and establish metagenomics as a powerful tool to provide insights not easily attained by culture-based approaches, metagenomics is unlikely to emerge as a widespread, routine monitoring tool in the near future due to its inherently high detection limits, cost, and inability to easily distinguish between viable and non-viable cells. Instead, metagenomics seems best poised for applications involving special circumstances otherwise challenging for culture-based and molecular (e.g., PCR-based) approaches such as the de novo detection of novel pathogens, cases of co-infection by more than one pathogen, and situations where it is important to assess the genomic composition of the pathogenic population(s) and/or its impact on the indigenous microbiome.},
}
@article {pmid38035339,
year = {2023},
author = {Li, K and Deng, J and Zhang, C and Lai, G and Xie, B and Zhong, X},
title = {Gut microbiome dysbiosis in men who have sex with men increases HIV infection risk through immunity homeostasis alteration.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1260068},
pmid = {38035339},
issn = {2235-2988},
abstract = {OBJECTIVES: Recent studies pointed out that gut microbiome dysbiosis in HIV infection was possibly confounded in men who have sex with men (MSM), but there is a lack of evidence. It also remained unclear how MSM-associated gut microbiome dysbiosis affected human health. This study aimed to compare the differences in gut microbiome changes between HIV and MSM and reveal the potential impacts of MSM-associated gut microbiome dysbiosis on the immune system.<br><br>METHODS: We searched available studies based on the PubMed database, and all gut microbiome changes associated with HIV infection and MSM were extracted from the enrolled studies. The gutMgene database was used to identify the target genes and metabolites of the gut microbiome. Bioinformatic technology and single-cell RNA sequencing data analysis were utilized to explore the impacts of these gut microbiome changes on human immunity.<br><br>RESULTS: The results showed significant overlaps between the gut microbiome associated with HIV and that of MSM. Moreover, bioinformatic analysis revealed that gut microbiome dysbiosis in MSM had an impact on several pathways related to immunity, including the IL-17 signaling pathway and Th17 cell differentiation. Additionally, target genes of MSM-associated gut microbiome were found to be highly expressed in monocytes and lymphocytes, suggesting their potential regulatory role in immune cells. Furthermore, we found that MSM-associated gut microbiome could produce acetate and butyrate which were reported to increase the level of inflammatory factors.<br><br>CONCLUSION: In conclusion, this study highlighted that MSM-associated gut microbiome dysbiosis might increase the risk of HIV acquisition by activating the immune system. Further studies are expected to elucidate the mechanism by which gut microbiome dysbiosis in MSM modulates HIV susceptibility.},
}
@article {pmid38035338,
year = {2023},
author = {Van Dingenen, L and Segers, C and Wouters, S and Mysara, M and Leys, N and Kumar-Singh, S and Malhotra-Kumar, S and Van Houdt, R},
title = {Dissecting the role of the gut microbiome and fecal microbiota transplantation in radio- and immunotherapy treatment of colorectal cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1298264},
pmid = {38035338},
issn = {2235-2988},
abstract = {Colorectal cancer (CRC) is one of the most commonly diagnosed cancers and poses a major burden on the human health worldwide. At the moment, treatment of CRC consists of surgery in combination with (neo)adjuvant chemotherapy and/or radiotherapy. More recently, immune checkpoint blockers (ICBs) have also been approved for CRC treatment. In addition, recent studies have shown that radiotherapy and ICBs act synergistically, with radiotherapy stimulating the immune system that is activated by ICBs. However, both treatments are also associated with severe toxicity and efficacy issues, which can lead to temporary or permanent discontinuation of these treatment programs. There's growing evidence pointing to the gut microbiome playing a role in these issues. Some microorganisms seem to contribute to radiotherapy-associated toxicity and hinder ICB efficacy, while others seem to reduce radiotherapy-associated toxicity or enhance ICB efficacy. Consequently, fecal microbiota transplantation (FMT) has been applied to reduce radio- and immunotherapy-related toxicity and enhance their efficacies. Here, we have reviewed the currently available preclinical and clinical data in CRC treatment, with a focus on how the gut microbiome influences radio- and immunotherapy toxicity and efficacy and if these treatments could benefit from FMT.},
}
@article {pmid38035128,
year = {2024},
author = {Martinez, R and Mayur, O and Pagani, K and Lukac, D and McGee, JS},
title = {Topical tretinoin alters skin microbiota in patients with mild acne.},
journal = {JAAD international},
volume = {14},
number = {},
pages = {1-3},
pmid = {38035128},
issn = {2666-3287},
}
@article {pmid38035090,
year = {2023},
author = {Gu, J and Zhang, J and Liu, Q and Xu, S},
title = {Neurological risks of COVID-19 in women: the complex immunology underpinning sex differences.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1281310},
pmid = {38035090},
issn = {1664-3224},
abstract = {The COVID-19 pandemic has uncovered many mysteries about SARS-CoV-2, including its potential to trigger abnormal autoimmune responses. Emerging evidence suggests women may face higher risks from COVID-induced autoimmunity manifesting as persistent neurological symptoms. Elucidating the mechanisms underlying this female susceptibility is now imperative. We synthesize key insights from existing studies on how COVID-19 infection can lead to immune tolerance loss, enabling autoreactive antibodies and lymphocyte production. These antibodies and lymphocytes infiltrate the central nervous system. Female sex hormones like estrogen and X-chromosome mediated effects likely contribute to dysregulated humoral immunity and cytokine profiles among women, increasing their predisposition. COVID-19 may also disrupt the delicate immunological balance of the female microbiome. These perturbations precipitate damage to neural damage through mechanisms like demyelination, neuroinflammation, and neurodegeneration - consistent with the observed neurological sequelae in women. An intentional focus on elucidating sex differences in COVID-19 pathogenesis is now needed to inform prognosis assessments and tailored interventions for female patients. From clinical monitoring to evaluating emerging immunomodulatory therapies, a nuanced women-centered approach considering the hormonal status and immunobiology will be vital to ensure equitable outcomes. Overall, deeper insights into the apparent female specificity of COVID-induced autoimmunity will accelerate the development of solutions mitigating associated neurological harm.},
}
@article {pmid38035082,
year = {2023},
author = {Deng, WY and Chen, WJ and Zhong, HJ and Wu, LH and He, XX},
title = {Washed microbiota transplantation: a case report of clinical success with skin and gut microbiota improvement in an adolescent boy with atopic dermatitis.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1275427},
pmid = {38035082},
issn = {1664-3224},
abstract = {Atopic dermatitis (AD) is a chronic, recurrent inflammatory disease characterized by itching. The gut microbiome can help maintain skin immune homeostasis by regulating innate and adaptive immunity. Here, we report a case of AD in a 15-year-old adolescent boy who benefited from washed microbiota transplantation (WMT). WMT was performed for three courses, with each course lasting for three consecutive days and an interval of one month between two courses. Clinical assessments were conducted at each WMT course, and skin, blood, and stool samples were collected for microbial analysis. After three months of WMT treatment, the boy's itchiness was effectively controlled: his skin showed noticeable improvement, with reduced Staphylococcus aureus in the skin lesions. The scores of SCORAD (SCORing Atopic Dermatitis), EASI (Eczema Area and Severity Index), NRS (Numerical Rating Scale), and DLQI (Dermatology Life Quality Index) significantly decreased compared to the baseline. Serum levels of eosinophil ratio, tumor necrotic factor-α, and interleukin-6 also reduced to the normal levels. There was a significant decrease in S. aureus in the skin lesions. Additionally, the intestinal flora became more diverse, and the abundance of Bifidobacterium species, significantly increased after WMT. No adverse events were reported during the treatment and the 1-year follow-up period. This case report provides direct clinical evidence for WMT as a novel promising treatment strategy for AD, and preliminary experimental data suggests the existence of an intestinal-skin axis in terms of the gut microbiota and the skin immune homeostasis.},
}
@article {pmid38034829,
year = {2023},
author = {Monleón-Getino, A and Pujol-Muncunill, G and Méndez Viera, J and Álvarez Carnero, L and Sanseverino, W and Paytuví-Gallart, A and Martín de Carpí, J},
title = {A pilot study of the use of the oral and faecal microbiota for the diagnosis of ulcerative colitis and Crohn's disease in a paediatric population.},
journal = {Frontiers in pediatrics},
volume = {11},
number = {},
pages = {1220976},
pmid = {38034829},
issn = {2296-2360},
abstract = {Crohn's disease (CD) and ulcerative colitis (UC) are chronic inflammatory bowel diseases (IBD) that affect the gastrointestinal tract. Changes in the microbiome and its interaction with the immune system are thought to play a key role in their development. The aim of this study was to determine whether metagenomic analysis is a feasible non-invasive diagnostic tool for IBD in paediatric patients. A pilot study of oral and faecal microbiota was proposed with 36 paediatric patients divided in three cohorts [12 with CD, 12 with UC and 12 healthy controls (HC)] with 6 months of follow-up. Finally, 30 participants were included: 13 with CD, 11 with UC and 8 HC (6 dropped out during follow-up). Despite the small size of the study population, a differential pattern of microbial biodiversity was observed between IBD patients and the control group. Twenty-one bacterial species were selected in function of their discriminant accuracy, forming three sets of potential markers of IBD. Although IBD diagnosis requires comprehensive medical evaluation, the findings of this study show that faecal metagenomics or a reduced set of bacterial markers could be useful as a non-invasive tool for an easier and earlier diagnosis.},
}
@article {pmid38034672,
year = {2023},
author = {Oyeyemi, BF and Kaur, US and Paramraj, A and Chintamani, and Tandon, R and Kumar, A and Bhavesh, NS},
title = {Microbiome analysis of saliva from oral squamous cell carcinoma (OSCC) patients and tobacco abusers with potential biomarkers for oral cancer screening.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e21773},
pmid = {38034672},
issn = {2405-8440},
abstract = {Oral squamous cell carcinoma (OSCC) is the most common type of oral cancer and accounts for about 95% of all head and neck cancers with high mortality, usually at a late stage. Dysbiosis in the oral microbiome can lead to chronic inflammatory responses and may predispose to the development and progression of OSCC. Tobacco abuse plays an essential role in oral microbiome dysregulation and OSCC pathogenesis. We used 16S rRNA gene amplicon next-generation sequencing to examine microbial signatures unique to saliva from OSCC patients, tobacco abusers (TA) and controls (n = 10 for each group) to elucidate oral microbiome changes associated with tobacco abuse and OSCC. Overall, the oral microbiome compositions of class Betaproteobacteria and Epsilonproteobacteria, order Neisseriales, Burkholderiales and Campylobacterales, family Burkholderiaceae and Campylobacteraceae and genera Campylobacter and Leptotrichia revealed significant differences among OSCC patients, TA and control. Our preliminary pilot study not only serves as a basis for future studies with large sample size but also gives an indication of microbiome-based potential non-invasive biomarkers for early screening and monitoring of oral carcinogenesis transition due to tobacco abuse.},
}
@article {pmid38034657,
year = {2023},
author = {Fu, J and Liang, Y and Shi, Y and Yu, D and Wang, Y and Chen, P and Liu, S and Lu, F},
title = {HuangQi ChiFeng decoction maintains gut microbiota and bile acid homeostasis through FXR signaling to improve atherosclerosis.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e21935},
pmid = {38034657},
issn = {2405-8440},
abstract = {Huangqi Chifeng Decoction (HQCFT), a traditional Chinese medicine preparation, has long been used to treat cardiovascular and cerebrovascular diseases. However, the mechanism of the beneficial effect of HQCFT on atherosclerosis remains to be explored. In this work, to investigate the effects of HQCFT on bile acid (BA) metabolism and the gut microbiome in atherosclerosis, ApoE[-/-] mice were fed a with high-fat diet for 16 weeks to establish the AS model. HQCFT(1.95 g kg[-1] and 3.9 g kg[-1] per day) was administered intragastrically for 8 weeks to investigate the regulatory effects of HQCFT on gut microbiota and bile acid metabolism and to inhibit the occurrence and development of AS induced by a high-fat diet. Histopathology, liver function and blood lipids were used to assess whether HQCFT can reduce plaque area, regulate lipid levels and alleviate liver steatosis in AS mice. In addition, 16S rDNA sequencing was used to screen the gut microbiota structure, and ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC‒MS/MS) was used to determine the bile acid profile. The mRNA and protein expression levels of bile acid metabolism were detected by RT‒PCR and WB to find the potential correlation. Results: HQCFT can regulate gut microbiota disorders, which was achieved by increasing gut microbiota diversity and altering Proteobacteria, Desulfobacterota, Deferribacteres, Rodentibacter, Parasutterella, and Mucispirillum interference abundance to improve AS-induced gut microbiota. HQCFT can also adjust the content of bile acids (TCA, LCA, DCA, TDCA, TLCA, UDCA, etc.), regulate bile acid metabolism, relieve liver fat accumulation, and inhibit the process of AS. In addition, HQCFT can restore the abnormal metabolism of bile acid caused by AS by regulating the expression of farnesoid X receptor (FXR), liver X receptor α (LXRα), ABCA1, ABCG1 and CYP7A1. Conclusion: HQCFT may play a part in the prevention of atherosclerosis by inhibiting the FXR/LXRα axis, increasing the expression of CYP7A1 in the liver, and regulating the interaction between the gut microbiota and bile acid metabolism.},
}
@article {pmid38034621,
year = {2023},
author = {Jiang, W and Lu, G and Qiao, T and Yu, X and Luo, Q and Tong, J and Fan, S and Chai, L and Gao, D and Wang, R and Deng, C and Lv, Z and Li, D},
title = {Integrated microbiome and metabolome analysis reveals a distinct microbial and metabolic signature in Graves' disease and hypothyroidism.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e21463},
pmid = {38034621},
issn = {2405-8440},
abstract = {Recent studies reveal that imbalanced microbiota is related to thyroid diseases. However, studies on the alterations in fecal metabolites in Graves' disease and clinical hypothyroidism patients are insufficient. Here, we identified 21 genera and 53 metabolites that were statistically significant among Graves' disease patients, hypothyroidism patients, and controls integrating microbiome and untargeted metabolome analysis. Disease groups revealed a decreased abundance in butyrate-producing microbiota and an increased abundance in potentially pathogenic microbiota. Lipids molecules were the major differential metabolites identified in all fecal samples. Network analysis recognized that microbiota may affect thyroid function by targeting specific metabolites. We further identified specific microbiota and metabolites that could distinguish Graves' disease patients, hypothyroidism patients, and controls. Our study reveals a distinct microbial and metabolic signature in hypothyroidism patients and Graves' disease patients and further validates the potential role of microbiota in thyroid diseases, providing new ideas for future research into the etiology and clinical intervention of thyroid diseases.},
}
@article {pmid38034569,
year = {2023},
author = {Xia, K and Feng, Z and Zhang, X and Zhou, Y and Zhu, H and Yao, Q},
title = {Potential functions of the shared bacterial taxa in the citrus leaf midribs determine the symptoms of Huanglongbing.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1270929},
pmid = {38034569},
issn = {1664-462X},
abstract = {INSTRUCTION: Citrus is a globally important fruit tree whose microbiome plays a vital role in its growth, adaptability, and resistance to stress.<br><br>METHODS: With the high throughput sequencing of 16S rRNA genes, this study focused on analyzing the bacterial community, especially in the leaf midribs, of healthy and Huanglongbing (HLB)-infected plants.<br><br>RESULTS: We firstly identified the shared bacterial taxa in the midribs of both healthy and HLB-infected plants, and then analyzed their functions. Results showed that the shared bacterial taxa in midribs belonged to 62 genera, with approximately 1/3 of which modified in the infected samples. Furthermore, 366 metabolic pathways, 5851 proteins, and 1833 enzymes in the shared taxa were predicted. Among these, three metabolic pathways and one protein showed significant importance in HLB infection. With the random forest method, six genera were identified to be significantly important for HLB infection. Notably, four of these genera were also among the significantly different shared taxa. Further functional characterization of these four genera revealed that Pseudomonas and Erwinia likely contributed to plant defense against HLB, while Streptomyces might have implications for plant defense against HLB or the pathogenicity of Candidatus Liberibacter asiaticus (CLas).<br><br>DISCCUSION: Overall, our study highlights that the functions of the shared taxa in leaf midribs are distinguished between healthy and HLB-infected plants, and these microbiome-based findings can contribute to the management and protection of citrus crops against CLas.},
}
@article {pmid38034470,
year = {2023},
author = {Mukhi, S and Dhanashree, B and Srikantiah, RM and Manjrekar, P and Harish, S},
title = {Evaluation of Minimum Inhibitory Concentration of Heavy Metals Contained in Packaging Material Digest on Prominent Gut Microbiota.},
journal = {International journal of food science},
volume = {2023},
number = {},
pages = {3840795},
pmid = {38034470},
issn = {2314-5765},
abstract = {Several scientific investigations have revealed that the leaching of metals from packaging material into the packed food is an unavoidable process. Hence, this study is aimed at investigating the effect of leached heavy metals from food packing materials on normal human gut flora. We analysed the effect of vanadium, arsenic, cadmium, and mercury present in digested packaging materials (DPM) on standard strains of Escherichia coli ATCC 25923, Pseudomonas aeruginosa ATCC 27853, Klebsiella pneumoniae ATCC 70063, and Enterococcus faecalis ATCC 29212. The minimum inhibitory concentration (MIC) of laboratory-grade heavy metal salts and heavy metals present in DPM was determined by the agar dilution method. For all four bacteria, the MIC of cadmium and arsenic in the DPM was 7 μg/ml and 1.6 μg/ml, respectively. The MIC of mercury in DPM was 1.6 μg/ml for E. coli, K. pneumoniae, and E. faecalis and 1.4 μg/ml for P. aeruginosa. MIC of vanadium for E. coli, P. aeruginosa, and E. faecalis was 2.2 μg/ml, and for K. pneumoniae was 2.0 μg/ml. The difference in MICs of heavy metals in DPMs and heavy metal salts was not statistically significant. MICs were within CODEX-specified permissible levels. Though heavy metals in packaging material have not shown a deleterious effect on representative human gut flora, there is scope to study their effect on the gut microbiome. Thus, understanding the risk of heavy metal ingestion through unknown sources and avoiding any possible ingestion is crucial to preventing chronic diseases.},
}
@article {pmid38034007,
year = {2023},
author = {Abuqwider, J and Corrado, A and Scidà, G and Lupoli, R and Costabile, G and Mauriello, G and Bozzetto, L},
title = {Gut microbiome and blood glucose control in type 1 diabetes: a systematic review.},
journal = {Frontiers in endocrinology},
volume = {14},
number = {},
pages = {1265696},
pmid = {38034007},
issn = {1664-2392},
abstract = {OBJECTIVE: The risk of developing micro- and macrovascular complications is higher for individuals with type 1 diabetes (T1D). Numerous studies have indicated variations in gut microbial composition between healthy individuals and those with T1D. These changes in the gut ecosystem may lead to inflammation, modifications in intestinal permeability, and alterations in metabolites. Such effects can collectively impact the metabolic regulation system, thereby influencing blood glucose control. This review aims to explore the relationship between the gut microbiome, inflammation, and blood glucose parameters in patients with T1D.<br><br>METHODS: Google Scholar, PubMed, and Web of Science were systematically searched from 2003 to 2023 using the following keywords: "gut microbiota," "gut microbiome," "bacteria," "T1D," "type 1 diabetes," "autoimmune diabetes," "glycemic control," "glucose control," "HbA1c," "inflammation," "inflammatory," and "cytokine." The examination has shown 18,680 articles with relevant keywords. After the exclusion of irrelevant articles, seven observational papers showed a distinct gut microbial signature in T1D patients.<br><br>RESULTS: This review shows that, in T1D patients, HbA1c level was negatively correlated with abundance of Prevotella, Faecalibacterium, and Ruminococcaceae and positively correlated with abundance of Dorea formicigenerans, Bacteroidetes, Lactobacillales, and Bacteriodes. Instead, Bifidobacteria was negatively correlated with fasting blood glucose. In addition, there was a positive correlation between Clostridiaceae and time in range. Furthermore, a positive correlation between inflammatory parameters and gut dysbiosis was revealed in T1D patients.<br><br>CONCLUSION: We draw the conclusion that the gut microbiome profiles of T1D patients and healthy controls differ. Patients with T1D may experience leaky gut, bacterial translocation, inflammation, and poor glucose management due to microbiome dysbiosis. Direct manipulation of the gut microbiome in humans and its effects on gut permeability and glycemic control, however, have not been thoroughly investigated. Future research should therefore thoroughly examine other potential pathophysiological mechanisms in larger studies.},
}
@article {pmid38033919,
year = {2023},
author = {Bautista-Becerril, B and Budden, KF and Falfán-Valencia, R},
title = {Editorial: Microbiota and asthma.},
journal = {Frontiers in allergy},
volume = {4},
number = {},
pages = {1297425},
pmid = {38033919},
issn = {2673-6101},
}
@article {pmid38033643,
year = {2023},
author = {Centeno-Martinez, RE and Klopp, RN and Koziol, J and Boerman, JP and Johnson, TA},
title = {Dynamics of the nasopharyngeal microbiome of apparently healthy calves and those with clinical symptoms of bovine respiratory disease from disease diagnosis to recovery.},
journal = {Frontiers in veterinary science},
volume = {10},
number = {},
pages = {1297158},
pmid = {38033643},
issn = {2297-1769},
abstract = {INTRODUCTION: Bovine respiratory disease (BRD) is a multifactorial disease complex in which bacteria in the upper respiratory tract play an important role in disease development. Previous studies have related the presence of four BRD-pathobionts (Mycoplasma bovis, Histophilus somni, Pasteurella multocida, and Mannheimia haemolytica) in the upper respiratory tract to BRD incidence and mortalities in the dairy and beef cattle industry, but these studies typically only use one time point to compare the abundance of BRD-pathobionts between apparently healthy and BRD-affected cattle. The objective of this study was to characterize the longitudinal development of the nasopharyngeal (NP) microbiome from apparently healthy calves, and in calves with clinical signs of BRD, the microbiota dynamics from disease diagnosis to recovery.<br><br>METHODS: Deep nasopharyngeal swabs were taken from all calves immediately after transport (day 0). If a calf was diagnosed with BRD (n = 10), it was sampled, treated with florfenicol or tulathromycin, and sampled again 1, 5, and 10 days after antibiotic administration. Otherwise, healthy calves (n = 20) were sampled again on days 7 and 14. Bacterial community analysis was performed through 16S rRNA gene amplicon sequencing.<br><br>RESULTS: The NP microbiome of the healthy animals remained consistent throughout the study, regardless of time. The NP microbiota beta diversity and community composition was affected by tulathromycin or florfenicol administration. Even though BRD-pathobionts were identified by 16S rRNA gene sequencing in BRD-affected animals, no difference was observed in their relative abundance between the BRD-affected and apparently healthy animals. The abundance of BRD-pathobionts was not predictive of disease development while the relative abundance of BRD pathobionts was unique to each BRD-affected calf. Interestingly, at the end of the study period, the genera Mycoplasma was the most abundant genus in the healthy group, while Lactobacillus was the most abundant genus in the animals that recovered from BRD.<br><br>DISCUSSION: This study highlights that injected antibiotics seem to improve the NP microbiome composition (higher abundance of Lactobacillus and lower abundance of Mycoplasma), and that the relative abundance of BRD-pathobionts differs between individual calves but is not strongly predictive of BRD clinical signs, indicating that additional factors are likely important in the clinical progression of BRD.},
}
@article {pmid38033611,
year = {2023},
author = {Lin, Y and Lourenco, JM and Olukosi, OA},
title = {Effects of xylanase, protease, and xylo-oligosaccharides on growth performance, nutrient utilization, short chain fatty acids, and microbiota in Eimeria-challenged broiler chickens fed high fiber diet.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {15},
number = {},
pages = {430-442},
pmid = {38033611},
issn = {2405-6383},
abstract = {A 21-d experiment was conducted to study the effect of xylanase, protease, and xylo-oligosaccharides on growth performance, nutrient utilization, gene expression of nutrient transporters, cecal short-chain fatty acids (SCFA), and cecal microbiota profile of broilers challenged with mixed Eimeria spp. The study utilized 392 zero-d-old male broiler chicks allocated to 8 treatments in a 4 × 2 factorial arrangement, as follows: corn-soybean meal diet with no enzyme (Con); Con plus xylanase alone (XYL); Con plus xylanase combined with protease (XYL + PRO); or Con plus xylo-oligosaccharides (XOS); with or without Eimeria challenge. Diets were based on a high-fiber (100 g/kg soluble fibers and 14 g/kg insoluble fibers) basal diet. At d 15, birds in challenged treatment were gavaged with a solution containing Eimeria maxima, Eimeria acervulina, and Eimeria tenella oocysts. At d 21, birds were sampled. Eimeria depressed (P < 0.01) growth performance and nutrient utilization, whereas supplementation had no effect. There were significant Eimeria × supplementation interactions for the sugar transporters GLUT5 (P = 0.02), SGLT1 (P = 0.01), SGLT4 (P < 0.01), and peptide transporter PepT1 (P < 0.01) in jejunal mucosa. Eimeria challenge increased the expression of GM-CSF2 (P < 0.01) and IL-17 (P = 0.04) but decreased (P = 0.03) IL-1β expression in the cecal tonsil. Eimeria × supplementation interactions for cecal acetate, butyrate, and total SCFA showed that concentrations increased or tended to be greater in the supplemented treatments, but only in non-challenged birds. Birds challenged with Eimeria spp. had higher concentrations of isobutyrate (P < 0.01), isovalerate (P < 0.01), and valerate (P = 0.02) in cecal content. Eimeria challenge significantly (P < 0.01) decreased the microbial richness and diversity, and increased (P < 0.01) the proportion of Anaerostipes butyraticus, Bifidobacterium pseudolongum, and Lactobacillus pontis. In conclusion, Eimeria infection depressed growth performance, nutrient utilization with regulating nutrient transporters. Furthermore, Eimeria challenge shifted the microbial profile and reduced microbial richness and diversity. On the other hand, enzyme supplementation showed limited benefits, which included increased concentrations of SCFA.},
}
@article {pmid38033603,
year = {2023},
author = {Yuan, L and Zhu, C and Gu, F and Zhu, M and Yao, J and Zhu, C and Li, S and Wang, K and Hu, P and Zhang, Y and Cai, D and Liu, HY},
title = {Lactobacillus johnsonii N5 from heat stress-resistant pigs improves gut mucosal immunity and barrier in dextran sodium sulfate-induced colitis.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {15},
number = {},
pages = {210-224},
pmid = {38033603},
issn = {2405-6383},
abstract = {Developing effective strategies to prevent diarrhea and associated-gut disorders in mammals has gained great significance. Owing to the many health benefits provided by the commensal microbiota of the intestinal tract, such as against environmental perturbation, we explored the host phenotype-associated microbes and their probiotic potential. Based on the observations that the chronic heat stress-exposed weaned piglets present as heat stress-susceptible (HS-SUS) or heat stress-resistant (HS-RES) individuals, we confirmed the phenotypic difference between the two on growth performance (P < 0.05), diarrhea index (P < 0.001), intestinal heat shock protein 70 (HSP70) regulation (P < 0.01), and inflammatory responses (P < 0.01). By comparing the gut microbiome using 16S rRNA gene sequencing and KEGG functional analysis, we found that Lactobacillus johnsonii exhibited significantly higher relative abundance in the HS-RES piglets than in the HS-SUS ones (P < 0.05). Further experiments using a mouse model for chemical-induced inflammation and intestinal injury demonstrated that oral administration of a representative L. johnsonii N5 (isolated from the HS-RES piglets) ameliorated the clinical and histological signs of colitis while suppressing intestinal pro-inflammatory cytokines TNF-α and IL-6 production (P < 0.05). We found that N5 treatment enhanced tight junction proteins ZO-1 and occludin and cytoprotective HSP70 levels under physiological condition and restored their mucosal expressions in colitis (P < 0.05). In support of the high production of the anti-inflammatory cytokine IL-10, N5 promoted the intestinal Peyer's patches MHCII[+] and CD103[+] dendritic cell populations (P < 0.05), increased the regulatory T (Treg) cell numbers (P < 0.05), and decreased the Th17 population and its IL-17a production under physiological condition and during colitis (P < 0.01). Our results shed light on understanding the interaction between commensal Lactobacillus and the host health, and provide L. johnsonii N5 as an alternative to antibiotics for preventing diarrhea and intestinal diseases.},
}
@article {pmid38033594,
year = {2023},
author = {Fujita, H and Ushio, M and Suzuki, K and Abe, MS and Yamamichi, M and Okazaki, Y and Canarini, A and Hayashi, I and Fukushima, K and Fukuda, S and Kiers, ET and Toju, H},
title = {Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1261137},
pmid = {38033594},
issn = {1664-302X},
abstract = {Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).},
}
@article {pmid38033589,
year = {2023},
author = {Liu, Z and Liu, X},
title = {Gut microbiome, metabolome and alopecia areata.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1281660},
pmid = {38033589},
issn = {1664-302X},
abstract = {Alopecia areata (AA) is a type of dermatological disease characterized by rapid and non-scarring hair loss of the scalp or body skin that may be related to genetic, immunological and physiological factors. It is now believed that AA is associated with oxidative stress, autoimmune disease, neuropsychological factors, pathogens, immune checkpoint inhibitors and microecological imbalance under the premise of host genetic susceptibility. In recent years, studies have revealed the significant role of the gut microbiome or metabolome in many aspects of human health. Diverse studies have revealed that the gut microbiome and metabolome have an important influence on skin conditions. This review highlights the relationship between AA and the gut microbiome or metabolome to provide novel directions for the prevention, clinical diagnosis and treatment of AA.},
}
@article {pmid38033568,
year = {2023},
author = {Seo, JY and You, SW and Gu, KN and Kim, H and Shin, JG and Leem, S and Hwang, BK and Kim, Y and Kang, NG},
title = {Longitudinal study of the interplay between the skin barrier and facial microbiome over 1 year.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1298632},
pmid = {38033568},
issn = {1664-302X},
abstract = {Skin is a diverse ecosystem that provides a habitat for microorganisms. The skin condition and the skin microbiome interact each other under diverse environmental conditions. This study was conducted on 10 study participants for a one-year, from September 2020 to August 2021, to investigate the variability of skin microbiome and skin biophysical parameters [TEWL, hydration, and elasticity (R5)] according to season, and to understand the interplay between skin microbiome and skin characteristics. We identified that Cutibacterium, Corynebacterium, Staphyloccocus, unclassified genus within Neisseriaceae, and Streptococcus were major skin microbial taxa at the genus level, and fluctuated with the seasons. Cutibacterium was more abundant in winter, while Corynebacterium, Staphylococcus, and Streptococcus were more abundant in summer. Notably, Cutibacterium and skin barrier parameter, TEWL, exhibited a co-decreasing pattern from winter to summer and showed a significant association between Cutibacterium and TEWL. Furthermore, functional profiling using KEGG provided clues on the impact of Cutibacterium on the host skin barrier. This study enhances our understanding of the skin microbiome and its interplay with skin characteristics and highlights the importance of seasonal dynamics in shaping skin microbial composition.},
}
@article {pmid38033481,
year = {2023},
author = {Bai, J and Wei, JQ and Tian, Q and Xue, F and Zhang, W and He, H},
title = {The impact of electroacupuncture on anxiety-like behavior and gut microbiome in a mouse model of chronic restraint stress.},
journal = {Frontiers in behavioral neuroscience},
volume = {17},
number = {},
pages = {1292835},
pmid = {38033481},
issn = {1662-5153},
abstract = {INTRODUCTION: Electroacupuncture (EA) is a beneficial physiotherapy approach for addressing neuropsychiatric disorders. Nevertheless, the impact of EA on the gut microbiome in relation to anxiety disorders remains poorly understood.<br><br>METHODS: To address this gap, we conducted a study using a chronic restraint stress (CRS) mouse model to investigate the anti-anxiety outcome of EA and its influence on gut microbiota. Our research involved behavioral tests and comprehensive sequencing of full-length 16S rRNA microbiomes.<br><br>RESULTS: Our findings revealed that CRS led to significant anxiety-like behaviors and an imbalance in the gut microbiota. Specifically, we identified 13 species that exhibited changes associated with anxiety-like behaviors. Furthermore, EA partially alleviated both behaviors related to anxiety and the dysbiosis induced by CRS.<br><br>DISCUSSION: In summary, this study sheds light on the alterations in gut microbiota species resulting from CRS treatment and brings new light into the connection between EA's anti-anxiety effects and the gut microbiota.},
}
@article {pmid38032916,
year = {2023},
author = {Sondo, M and Wonni, I and Koïta, K and Rimbault, I and Barro, M and Tollenaere, C and Moulin, L and Klonowska, A},
title = {Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0287084},
pmid = {38032916},
issn = {1932-6203},
abstract = {Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.},
}
@article {pmid38032828,
year = {2023},
author = {Micks, E and Reed, S and Mitchell, C},
title = {The Postmenopausal Vaginal Microbiome and Genitourinary Syndrome of Menopause.},
journal = {Clinical obstetrics and gynecology},
volume = {},
number = {},
pages = {},
pmid = {38032828},
issn = {1532-5520},
abstract = {This review summarizes our current understanding of associations of the postmenopausal vaginal microbiome with genitourinary syndrome of menopause. We review the normal postmenopausal microbiota, examine the association of the microbiome with vulvovaginal symptoms, describe microbial communities associated with physical and laboratory findings, and report the impact of different treatments for genitourinary syndrome of menopause on microbiota and symptom improvement. Postmenopausal vaginal symptoms have an underlying pathophysiology that has not been fully elucidated. Estrogen treatment may not be sufficient to relieve symptoms of vaginal discomfort in all postmenopausal individuals. In addition, other interventions targeted at changing the microbiota or pH do not consistently improve symptom severity.},
}
@article {pmid38032704,
year = {2023},
author = {Lednovich, KR and Gough, S and Priyadarshini, M and Pandya, N and Nnyamah, C and Xu, K and Wicksteed, B and Mishra, S and Jain, S and Zapater, JL and Cordoba-Chacon, J and Yadav, H and Layden, B},
title = {Intestinal FFA2 promotes obesity by altering food intake in Western diet-fed mice.},
journal = {The Journal of endocrinology},
volume = {},
number = {},
pages = {},
doi = {10.1530/JOE-23-0184},
pmid = {38032704},
issn = {1479-6805},
abstract = {Short-chain fatty acids (SCFAs) are key nutrients that play a diverse set of roles in physiological function, including regulating metabolic homeostasis. Generated through the fermentation of dietary fibers in the distal colon by the gut microbiome, SCFAs and their effects are partially mediated by their cognate receptors, including free fatty acid receptor 2 (FFA2). FFA2 is highly expressed in the intestinal epithelial, where its putative functions are controversial, with numerous in vivo studies relying on global knockout mouse models to characterize intestine-specific roles of the receptor. Here, we used the Villin-Cre mouse line to generate a novel, intestine-specific knockout mouse model for FFA2 (Vil-FFA2) to investigate receptor function within the intestine. Because dietary changes are known to affect the composition of the gut microbiome, and can thereby alter SCFA production, we performed an obesogenic challenge on male Vil-FFA2 mice and their littermate controls (FFA2-floxed, FFA2fl/fl) to identify physiological changes on a high-fat, high-sugar "Western diet" (WD) compared to a low-fat control diet (CD). We found that the WD-fed Vil-FFA2 mice were transiently protected from the obesogenic effects of the WD, and had lower fat mass and improved glucose homeostasis compared to the WD-fed FFA2fl/fl control group during the first half of the study. Additionally, major differences in respiratory exchange ratio and energy expenditure were observed in the WD-fed Vil-FFA2 mice, and food intake was found to be significantly reduced at multiple points in the study. Taken together, this study uncovers a novel role of intestinal FFA2 in mediating the development of obesity.},
}
@article {pmid38032526,
year = {2023},
author = {Dong, X and Deng, L and Su, Y and Han, X and Yao, S and Wu, W and Cao, J and Tian, L and Bai, Y and Wang, G and Ren, W},
title = {Curcumin alleviates traumatic brain injury induced by gas explosion through modulating gut microbiota and suppressing the LPS/TLR4/MyD88/NF-κB pathway.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {38032526},
issn = {1614-7499},
support = {U2004102//National Natural Science Foundation of China/ ; U1904209//National Natural Science Foundation of China/ ; 232102311071//Henan Provincial Science and Technology Research Project/ ; 202300410312//Natural Science Foundation of Henan Province/ ; },
abstract = {Gas explosions (GE) are a prevalent and widespread cause of traumatic brain injury (TBI) in coal miners. However, the impact and mechanism of curcumin on GE-induced TBI in rats remain unclear. In this study, we simulated GE-induced TBI in rats and administered curcumin orally at a dose of 100 mg/kg every other day for 7 days to modulate the gut microbiota in TBI rats. We employed 16S rRNA sequencing and LC-MS/MS metabolomic analysis to investigate changes in the intestinal flora and its metabolic profile. Additionally, we utilized ELISA, protein assays, and immunohistochemistry to assess neuroinflammatory signaling molecules for validation. In a rat TBI model, GE resulted in weight loss, pathological abnormalities, and cortical hemorrhage. Treatment with curcumin significantly mitigated histological abnormalities and microscopic mitochondrial structural changes in brain tissue. Furthermore, curcumin treatment markedly ameliorated GE-induced brain dysfunction by reducing the levels of several neuroinflammatory signaling molecules, including neuron-specific enolase, interleukin (IL)-1β, IL-6, and cryptothermic protein 3. Notably, curcumin reshaped the gut microbiome by enhancing evenness, richness, and composition. Prevotella_9, Alloprevotella, Bacilli, Lactobacillales, Proteobacteria, and Gammaproteobacteria were identified as prominent members of the gut microbiota, increasing the linear discriminant analysis scores and specifically enhancing the abundance of bacteria involved in the nuclear factor (NF)-κB signaling pathway, such as Lachnospiraceae and Roseburia. Additionally, there were substantial alterations in serum metabolites associated with metabolic NF-κB signaling pathways in the model group. Curcumin administration reduced serum lipopolysaccharide levels and downregulated downstream Toll-like receptor (TLR)4/myeloid differentiation primary response 88 (MyD88)/NF-κB signaling. Furthermore, curcumin alleviated GE-induced TBI in rats by modulating the gut microbiota and its metabolites. Based on these protective effects, curcumin may exert its influence on the gut microbiota and the TLR4/MyD88/NF-κB signaling pathways to ameliorate GE-induced TBI.},
}
@article {pmid38032332,
year = {2023},
author = {Zawadzka-Głos, L},
title = {Microbiota and antibiotic therapy in rhinosinusitis.},
journal = {Otolaryngologia polska = The Polish otolaryngology},
volume = {77},
number = {5},
pages = {36-42},
doi = {10.5604/01.3001.0053.8709},
pmid = {38032332},
issn = {2300-8423},
mesh = {Humans ; *Sinusitis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; *Microbiota ; *Nasal Polyps ; },
abstract = {Rhinosinusitis is one of the most frequently diagnosed diseases in patients seeking medical consultation. Sinusitis is a heterogeneous group of diseases and can be acute or chronic. The current state of knowledge on rhinosinusitis is presented in the recommendations of the European Position Paper on Rhinosynusitis and Nasal Polyps 2020 (EPOS 2020). More and more attention is paid to the condition of the microbiota in the context of inflammatory changes in the sinuses. There is also a negative effect of excessively prescribed antibiotics on the increase in bacterial resistance to drugs and significant changes in the disturbance in the composition of the microbiota during antibiotic therapy. Since the most common etiology of acute sinusitis is viral, the use of antibiotics in uncomplicated sinusitis is unjustified. New therapeutic solutions are sought, including the use of herbal medicines. The EPOS 2020 document recommends the use of BNO 1016 in uncomplicated acute rhinosinusitis. New models of treatment also take into account the use of biological drugs, especially in the treatment of chronic rhinosinusitis.},
}
@article {pmid38032239,
year = {2023},
author = {Bowen, M and Farag, IF and Main, CR and Biddle, JF},
title = {Reference library for microbial source tracking in the mid-Atlantic United States.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0067423},
doi = {10.1128/MRA.00674-23},
pmid = {38032239},
issn = {2576-098X},
abstract = {Microbial source tracking can determine fecal contamination but requires a relevant, sizable reference library for analysis. We provide a reference library of 100+ fecal microbiome samples relevant to mid-Atlantic United States ecosystems. Included are wild and domesticated fauna, wastewater, and septic samples applicable to Delaware source tracking studies.},
}
@article {pmid38032203,
year = {2023},
author = {Tahiri, M and Johnsrud, C and Steffensen, IL},
title = {Evidence and hypotheses on adverse effects of the food additives carrageenan (E 407)/processed Eucheuma seaweed (E 407a) and carboxymethylcellulose (E 466) on the intestines: a scoping review.},
journal = {Critical reviews in toxicology},
volume = {},
number = {},
pages = {1-51},
doi = {10.1080/10408444.2023.2270574},
pmid = {38032203},
issn = {1547-6898},
abstract = {This scoping review provides an overview of publications reporting adverse effects on the intestines of the food additives carrageenan (CGN) (E 407)/processed Eucheuma seaweed (PES) (E 407a) and carboxymethylcellulose (CMC) (E 466). It includes evidence from human, experimental mammal and in vitro research publications, and other evidence. The databases Medline, Embase, Scopus, Web of Science Core Collection, Cochrane Database of Systematic Reviews and Epistemonikos were searched without time limits, in addition to grey literature. The publications retrieved were screened against predefined criteria. From two literature searches, 2572 records were screened, of which 224 records were included, as well as 38 records from grey literature, making a total of 262 included publications, 196 on CGN and 101 on CMC. These publications were coded and analyzed in Eppi-Reviewer and data gaps presented in interactive maps. For CGN, five, 69 and 33 research publications on humans, experimental mammals and in vitro experiments were found, further separated as degraded or native (non-degraded) CGN. For CMC, three human, 20 animal and 14 in vitro research publications were obtained. The most studied adverse effects on the intestines were for both additives inflammation, the gut microbiome, including fermentation, intestinal permeability, and cancer and metabolic effects, and immune effects for CGN. Further studies should focus on native CGN, in the form and molecular weight used as food additive. For both additives, randomized controlled trials of sufficient power and with realistic dietary exposure levels of single additives, performed in persons of all ages, including potentially vulnerable groups, are needed.},
}
@article {pmid38031529,
year = {2023},
author = {Sanders, WB},
title = {The disadvantages of current proposals to redefine lichens: A comment on Hawksworth &amp; Grube (2020): 'Lichens redefined as complex ecosystems'.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19321},
pmid = {38031529},
issn = {1469-8137},
}
@article {pmid38031491,
year = {2023},
author = {Kim, SH and Choi, Y and Oh, J and Lim, EY and Lee, JE and Song, EJ and Nam, YD and Kim, H},
title = {Associations among the Duodenal Ecosystem, Gut Microbiota, and Nutrient Intake in Functional Dyspepsia.},
journal = {Gut and liver},
volume = {},
number = {},
pages = {},
doi = {10.5009/gnl230130},
pmid = {38031491},
issn = {2005-1212},
abstract = {BACKGROUND/AIMS: : Functional dyspepsia (FD) has long been regarded as a syndrome because its pathophysiology is multifactorial. However, recent reports have provided evidence that changes in the duodenal ecosystem may be the key. This study aimed to identify several gastrointestinal factors and biomarkers associated with FD, specifically changes in the duodenal ecosystem that may be key to understanding its pathophysiology.<br><br>METHODS: : In this case-control study, 28 participants (12 with FD and 16 healthy control individuals) were assessed for dietary nutrients, gastrointestinal symptom severity, immunological status of the duodenal mucosa, and microbiome composition from oral, duodenal, and fecal samples. Integrated data were analyzed using immunohistochemistry, real-time polymerase chain reaction, 16S rRNA sequencing, and network analysis.<br><br>RESULTS: : Duodenal mucosal inflammation and impaired expression of tight junction proteins were confirmed in patients with FD. The relative abundance of duodenal Streptococcus (p=0.014) and reductions in stool Butyricicoccus (p=0.047) were confirmed. These changes in the gut microbiota were both correlated with symptom severity. Changes in dietary micronutrients, such as higher intake of valine, were associated with improved intestinal barrier function and microbiota.<br><br>CONCLUSIONS: : This study emphasizes the relationships among dietary nutrition, oral and gut microbiota, symptoms of FD, impaired function of the duodenal barrier, and inflammation. Assessing low-grade inflammation or increased permeability in the duodenal mucosa, along with changes in the abundance of stool Butyricicoccus, is anticipated to serve as effective biomarkers for enhancing the objectivity of FD diagnosis and monitoring.},
}
@article {pmid38031487,
year = {2023},
author = {Hawksworth, DL and Grube, M},
title = {Reflections on lichens as ecosystems.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19418},
pmid = {38031487},
issn = {1469-8137},
}
@article {pmid38031339,
year = {2023},
author = {Kamenova, S and de Muinck, EJ and Veiberg, V and Utsi, TA and Steyaert, SMJG and Albon, SD and Loe, LE and Trosvik, P},
title = {Gut microbiome biogeography in reindeer supersedes millennia of ecological and evolutionary separation.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiad157},
pmid = {38031339},
issn = {1574-6941},
abstract = {Ruminants are dependent on their gut microbiomes for nutrient extraction from plant diets. However, knowledge about the composition, diversity, function, and spatial structure of gut microbiomes, especially in wild ruminants, is limited, largely because analysis has been restricted to faeces or the rumen. In two geographically separated reindeer subspecies, 16S rRNA gene amplicon sequencing revealed strong spatial structuring, and pronounced differences in microbial diversity of at least 33 phyla across the stomach, small intestine, and large intestine (including faeces). The main structural feature was the Bacteroidota to Firmicutes ratio, which declined from the stomachs to the large intestine, likely reflecting functional adaptation. Metagenome shotgun sequencing also revealed highly significant structuring in the relative occurrence of carbohydrate-active enzymes (CAZymes). CAZymes were enriched in the rumen relative to the small and large intestine. Interestingly, taxonomic diversity was highest in the large intestine, suggesting an important and understudied role for this organ. Despite the two study populations being separated by an ocean and six millennia of evolutionary history, gut microbiome structuring was remarkably consistent. Our study suggests a strong selection for gut microbiome biogeography along the gastrointestinal tract in reindeer subspecies.},
}
@article {pmid38031252,
year = {2023},
author = {Crossland, NA and Beck, S and Tan, WY and Lo, M and Mason, JB and Zhang, C and Guo, W and Crott, JW},
title = {Fecal microbiota transplanted from old mice promotes more colonic inflammation, proliferation, and tumor formation in azoxymethane-treated A/J mice than microbiota originating from young mice.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2288187},
doi = {10.1080/19490976.2023.2288187},
pmid = {38031252},
issn = {1949-0984},
abstract = {Aging is a strong risk factor for colorectal cancer (CRC). It is well established that gut microbial dysbiosis can play a role in the etiology of CRC. Although the composition of the gut microbial community changes with age and is reported to become more pro-inflammatory, it is unclear whether such changes are also pro-tumorigenic for the colon. To address this gap, we conducted fecal microbiota transplants (FMT) from young (DY, ~6 wk) and old (DO, ~72 wk) donor mice into young (8 wk) recipient mice that were pre-treated with antibiotics. After initiating tumorigenesis with azoxymethane, recipients were maintained for 19 wk during which time they received monthly FMT boosters. Compared to recipients of young donors (RY), recipients of old donors (RO) had an approximately 3-fold higher prevalence of histologically confirmed colon tumors (15.8 vs 50%, Chi2 P = .03), approximately 2-fold higher proliferating colonocytes as well as significantly elevated colonic IL-6, IL-1β and Tnf-α. Transcriptomics analysis of the colonic mucosa revealed a striking upregulation of mitochondria-related genes in the RO mice, a finding corroborated by increased mitochondrial abundance. Amongst the differences in fecal microbiome observed between DY and DO mice, the genera Ruminoclostridium, Lachnoclostridium and Marvinbryantia were more abundant in DY mice while the genera Bacteroides and Akkermansia were more abundant in DO mice. Amongst recipients, Ruminoclostridium and Lachnoclostridium were higher in RY mice while Bacteroides was higher in RO mice. Differences in fecal microbiota were observed between young and old mice, some of which persisted upon transplant into recipient mice. Recipients of old donors displayed significantly higher colonic proliferation, inflammation and tumor abundance compared to recipients of young donors. These findings support an etiological role for altered gut microbial communities in the increased risk for CRC with increasing age and establishes that such risk can be transmitted between individuals.},
}
@article {pmid38031142,
year = {2023},
author = {Holm, JB and France, MT and Gajer, P and Ma, B and Brotman, RM and Shardell, M and Forney, L and Ravel, J},
title = {Integrating compositional and functional content to describe vaginal microbiomes in health and disease.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {259},
pmid = {38031142},
issn = {2049-2618},
support = {R01-NR015495/NR/NINR NIH HHS/United States ; },
abstract = {BACKGROUND: A Lactobacillus-dominated vaginal microbiome provides the first line of defense against adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this gap, we developed metagenomic community state types (mgCSTs) which use metagenomic sequences to describe and define vaginal microbiomes based on both composition and functional potential.<br><br>RESULTS: MgCSTs are categories of microbiomes classified using taxonomy and the functional potential encoded in their metagenomes. MgCSTs reflect unique combinations of metagenomic subspecies (mgSs), which are assemblages of bacterial strains of the same species, within a microbiome. We demonstrate that mgCSTs are associated with demographics such as age and race, as well as vaginal pH and Gram stain assessment of vaginal smears. Importantly, these associations varied between mgCSTs predominated by the same bacterial species. A subset of mgCSTs, including three of the six predominated by Gardnerella vaginalis mgSs, as well as mgSs of L. iners, were associated with a greater likelihood of bacterial vaginosis diagnosed by Amsel clinical criteria. This L. iners mgSs, among other functional features, encoded enhanced genetic capabilities for epithelial cell attachment that could facilitate cytotoxin-mediated cell lysis. Finally, we report a mgSs and mgCST classifier for which source code is provided and may be adapted for use by the microbiome research community.<br><br>CONCLUSIONS: MgCSTs are a novel and easily implemented approach to reduce the dimension of complex metagenomic datasets while maintaining their functional uniqueness. MgCSTs enable the investigation of multiple strains of the same species and the functional diversity in that species. Future investigations of functional diversity may be key to unraveling the pathways by which the vaginal microbiome modulates the protection of the genital tract. Importantly, our findings support the hypothesis that functional differences between vaginal microbiomes, including those that may look compositionally similar, are critical considerations in vaginal health. Ultimately, mgCSTs may lead to novel hypotheses concerning the role of the vaginal microbiome in promoting health and disease, and identify targets for novel prognostic, diagnostic, and therapeutic strategies to improve women's genital health. Video Abstract.},
}
@article {pmid38031016,
year = {2023},
author = {Li, P and Jiang, J and Li, Y and Lan, Y and Yang, F and Wang, J and Xie, Y and Xiong, F and Wu, J and Liu, H and Fan, Z},
title = {Metagenomic analysis reveals distinct changes in the gut microbiome of obese Chinese children.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {721},
pmid = {38031016},
issn = {1471-2164},
support = {No. 2023YFS0034 and 2020YFS0109//the Science and Technology Bureau of Sichuan Province/ ; No. KL119//the Clinical Discipline Development Fund of West China Second Hospital, Sichuan University/ ; SCU2022D022//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: The prevalence of obese children in China is increasing, which poses a great challenge to public health. Gut microbes play an important role in human gut health, and changes in gut status are closely related to obesity. However, how gut microbes contribute to obesity in children remains unclear. In our study, we performed shotgun metagenomic sequencing of feces from 23 obese children, 8 overweight children and 22 control children in Chengdu, Sichuan, China.<br><br>RESULTS: We observed a distinct difference in the gut microbiome of obese children and that of controls. Compared with the controls, bacterial pathogen Campylobacter rectus was significantly more abundant in obese children. In addition, functional annotation of microbial genes revealed that there might be gut inflammation in obese children. The guts of overweight children might belong to the transition state between obese and control children due to a gradient in relative abundance of differentially abundant species. Finally, we compared the gut metagenomes of obese Chinese children and obese Mexican children and found that Trichuris trichiura was significantly more abundant in the guts of obese Mexican children.<br><br>CONCLUSIONS: Our results contribute to understanding the changes in the species and function of intestinal microbes in obese Chinese children.},
}
@article {pmid38030903,
year = {2023},
author = {Lutz, S and Bodenhausen, N and Hess, J and Valzano-Held, A and Waelchli, J and Deslandes-Hérold, G and Schlaeppi, K and van der Heijden, MGA},
title = {Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi.},
journal = {Nature microbiology},
volume = {8},
number = {12},
pages = {2277-2289},
pmid = {38030903},
issn = {2058-5276},
support = {GRS-072/17//Gebert R&#xfc;f Stiftung (Gebert R&#xfc;f Foundation)/ ; GRS-088/20//Gebert R&#xfc;f Stiftung (Gebert R&#xfc;f Foundation)/ ; GRS-072/17//Gebert R&#xfc;f Stiftung (Gebert R&#xfc;f Foundation)/ ; 40IN40_215832 / 1//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 40IN40_215832 / 1//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 40IN40_215832 / 1//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {Alternative solutions to mineral fertilizers and pesticides that reduce the environmental impact of agriculture are urgently needed. Arbuscular mycorrhizal fungi (AMF) can enhance plant nutrient uptake and reduce plant stress; yet, large-scale field inoculation trials with AMF are missing, and so far, results remain unpredictable. We conducted on-farm experiments in 54 fields in Switzerland and quantified the effects on maize growth. Growth response to AMF inoculation was highly variable, ranging from -12% to +40%. With few soil parameters and mainly soil microbiome indicators, we could successfully predict 86% of the variation in plant growth response to inoculation. The abundance of pathogenic fungi, rather than nutrient availability, best predicted (33%) AMF inoculation success. Our results indicate that soil microbiome indicators offer a sustainable biotechnological perspective to predict inoculation success at the beginning of the growing season. This predictability increases the profitability of microbiome engineering as a tool for sustainable agricultural management.},
}
@article {pmid38030898,
year = {2023},
author = {Gancz, AS and Farrer, AG and Nixon, MP and Wright, S and Arriola, L and Adler, C and Davenport, ER and Gully, N and Cooper, A and Britton, K and Dobney, K and Silverman, JD and Weyrich, LS},
title = {Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain.},
journal = {Nature microbiology},
volume = {8},
number = {12},
pages = {2315-2325},
pmid = {38030898},
issn = {2058-5276},
support = {DGE1255832//National Science Foundation (NSF)/ ; DGE1255832//National Science Foundation (NSF)/ ; },
abstract = {The prevalence of chronic, non-communicable diseases has risen sharply in recent decades, especially in industrialized countries. While several studies implicate the microbiome in this trend, few have examined the evolutionary history of industrialized microbiomes. Here we sampled 235 ancient dental calculus samples from individuals living in Great Britain (∼2200 BCE to 1853 CE), including 127 well-contextualized London adults. We reconstructed their microbial history spanning the transition to industrialization. After controlling for oral geography and technical biases, we identified multiple oral microbial communities that coexisted in Britain for millennia, including a community associated with Methanobrevibacter, an anaerobic Archaea not commonly prevalent in the oral microbiome of modern industrialized societies. Calculus analysis suggests that oral hygiene contributed to oral microbiome composition, while microbial functions reflected past differences in diet, specifically in dairy and carbohydrate consumption. In London samples, Methanobrevibacter-associated microbial communities are linked with skeletal markers of systemic diseases (for example, periostitis and joint pathologies), and their disappearance is consistent with temporal shifts, including the arrival of the Second Plague Pandemic. This suggests pre-industrialized microbiomes were more diverse than previously recognized, enhancing our understanding of chronic, non-communicable disease origins in industrialized populations.},
}
@article {pmid38030815,
year = {2023},
author = {Zhang, N and Zhu, W and Zhang, S and Liu, T and Gong, L and Wang, Z and Zhang, W and Cui, Y and Wu, Q and Li, J and Yu, H and El-Omar, EM and Hao, J and Lu, W},
title = {A Novel Bifidobacterium/Klebsiella Ratio in Characterization Analysis of the Gut and Bile Microbiota of CCA Patients.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {5},
pmid = {38030815},
issn = {1432-184X},
abstract = {Cholangiocarcinoma (CCA) is a serious health problem worldwide. The gut and bile microbiota have not been clearly characterized in patients with CCA, and better noninvasive diagnostic approaches for CCA need to be established. The aim of this study was to investigate the characteristics of the gut and bile microbiota in CCA patients. Forty-two CCA patients and 16 healthy normal controls (HNCs) were enrolled. DNA was extracted from fecal and bile samples and subjected to 16S rRNA gene analysis. We found that there were significant differences in the species diversity, structure, and composition of the microbial communities between the CCA group and the HNC grouAt the phylum level, compared with that in the HNC group, the relative abundance of Firmicutes and Actinobacteriota was significantly decreased in the CCA group, whereas Proteobacteria and Bacteroidota were significantly enriched. The Firmicutes/Bacteroidota (F/B) ratio significantly decreased in the CCA group compared to the HNC grouThe relative abundance of Klebsiella in the CCA group was significantly higher than that in the HNC group, while the relative abundance of Bifidobacterium was significantly decreased. The Bifidobacterium/Klebsiella (B/K) ratio was established as a novel biomarker and was found to be significantly decreased in the CCA group compared with the HNC grouOur findings provide evidence supporting the use of Klebsiella and Bifidobacterium as noninvasive intestinal microbiomarkers for improving the diagnosis of CCA.},
}
@article {pmid38030736,
year = {2023},
author = {Gajecka, M and Gutaj, P and Jaskiewicz, K and Rydzanicz, M and Szczapa, T and Kaminska, D and Kosewski, G and Przyslawski, J and Ploski, R and Wender-Ozegowska, E},
title = {Effects of maternal type 1 diabetes and confounding factors on neonatal microbiomes.},
journal = {Diabetologia},
volume = {},
number = {},
pages = {},
pmid = {38030736},
issn = {1432-0428},
support = {PSNC-534//Poznan Supercomputing and Networking Center/ ; Professor Artur Czy&#x17c;yk' Scientific Grant 2015//Polish Diabetes Association/ ; Professor Artur Czy&#x17c;yk' Scientific Grant 2017//Polish Diabetes Association/ ; 502-01-01110142-05618//Uniwersytet Medyczny im. Karola Marcinkowskiego w Poznaniu/ ; 502-14-03301402-09911//Uniwersytet Medyczny im. Karola Marcinkowskiego w Poznaniu/ ; },
abstract = {AIMS/HYPOTHESIS: Body niche-specific microbiota in maternal-neonatal dyads from gravidae with type 1 diabetes have not been quantitatively and functionally examined. Similarly, the impact of pregnancy-specific factors, such as the presence of comorbidities known to occur more frequently among gravidae with type 1 diabetes, including Caesarean delivery, as well as antibiotic prophylaxis, level of glycaemic control during each trimester of pregnancy and insulin administration, has not been adequately considered. The aims of this study were to characterise the maternal and neonatal microbiomes, assess aspects of microbiota transfer from the maternal microbiomes to the neonatal microbiome and explore the impact of type 1 diabetes and confounding factors on the microbiomes.<br><br>METHODS: In this observational case-control study, we characterised microbiome community composition and function using 16S rRNA amplicon sequencing in a total of 514 vaginal, rectal and ear-skin swabs and stool samples derived from 92 maternal-neonatal dyads (including 50 gravidae with type 1 diabetes) and in-depth clinical metadata from throughout pregnancy and delivery.<br><br>RESULTS: Type 1 diabetes-specific microbiota were identified among gravidae with type 1 diabetes and their neonates. Neonatal microbiome profiles of ear-skin swabs and stool samples were established, indicating the taxa more prevalent among neonates born to mothers with type 1 diabetes compared with neonates born to control mothers. Without taking into account the type 1 diabetes status of mothers, both delivery mode and intrapartum antibiotic prophylaxis were found to have an influence on neonatal microbiota composition (both p=0.001). In the logistic regression analysis involving all confounding variables, neonatal ear-skin microbiome variation was explained by maternal type 1 diabetes status (p=0.020) and small for gestational age birthweight (p=0.050). Moreover, in women with type 1 diabetes, a relationship was found between HbA1c levels >55 mmol/mol (>7.2%) measured in the first trimester of pregnancy and neonatal ear-skin microbiota composition (p=0.008). In the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) assessment, pathways concerning carbohydrate biosynthesis were predicted as key elements of the microbial functional profiles dysregulated in type 1 diabetes. Additionally, in SourceTracker analysis, we found that, on average, 81.0% of neonatal microbiota was attributed to maternal sources. An increase in the contribution of maternal rectum microbiota and decrease in the contribution of maternal cervix microbiota were found in ear-skin samples of vaginally delivered neonates of mothers with type 1 diabetes compared with neonates born to control mothers (83.2% vs 59.5% and 0.7% vs 5.2%, respectively).<br><br>CONCLUSIONS/INTERPRETATION: These findings indicate that, in addition to maternal type 1 diabetes, glycaemic dysregulation before/in the first trimester of pregnancy, mode of delivery and intrapartum antibiotic prophylaxis may contribute to the inoculation and formation of the neonatal microbiomes.<br><br>DATA AVAILABILITY: The BioProject (PRJNA961636) and associated SRA metadata are available at http://www.ncbi.nlm.nih.gov/bioproject/961636 . Processed data on probiotic supplementation and the PICRUSt analysis are available in the Mendeley Data Repository (https://doi.org/10.17632/g68rwnnrfk.1).},
}
@article {pmid38030652,
year = {2023},
author = {Bacci, G and Meriggi, N and Cheng, CLY and Ng, KH and Iannucci, A and Mengoni, A and Cavalieri, D and Cannicci, S and Fratini, S},
title = {Species-specific gill's microbiome of eight crab species with different breathing adaptations.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {21033},
pmid = {38030652},
issn = {2045-2322},
support = {207080320.088562.26020.430.01//Hong Kong Government/ ; 260008686.088562.26000.400.01//TUYF Charitable Trust funds, Hong Kong/ ; CN00000033//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; },
abstract = {Transitions to physically different environments, such as the water-to-land transition, proved to be the main drivers of relevant evolutionary events. Brachyuran crabs evolved remarkable morphological, behavioral, and physiological adaptations to terrestrial life. Terrestrial species evolved new respiratory structures devoted to replace or support the gills, a multifunctional organ devoted to gas exchanges, ion-regulation and nitrogen excretion. It was hypothesized that microorganisms associated with respiratory apparatus could have facilitated the processes of osmoregulation, respiration, and elimination of metabolites along this evolutionary transition. To test if crab species with different breathing adaptations may host similar microbial communities on their gills, we performed a comparative targeted-metagenomic analysis, selecting two marine and six terrestrial crabs belonging to different families and characterised by different breathing adaptations. We analysed anterior and posterior gills separately according to their different and specific roles. Regardless of their terrestrial or marine adaptations, microbial assemblages were strongly species-specific indicating a non-random association between the host and its microbiome. Significant differences were found in only two terrestrial species when considering posterior vs. anterior gills, without any association with species-specific respiratory adaptations. Our results suggest that all the selected species are strongly adapted to the ecological niche and specific micro-habitat they colonise.},
}
@article {pmid38030540,
year = {2023},
author = {Holers, VM},
title = {Are there causal mucosal drivers in the preclinical development of rheumatoid arthritis?.},
journal = {Seminars in arthritis and rheumatism},
volume = {},
number = {},
pages = {152324},
doi = {10.1016/j.semarthrit.2023.152324},
pmid = {38030540},
issn = {1532-866X},
abstract = {BACKGROUND: The causal pathways which drive the development of seropositive rheumatoid arthritis (RA) are incompletely understood, especially in the period of time prior to the first development of signs and symptoms of joint involvement. That asymptomatic period, designated herein as pre-RA, is characterized by the presence of RA-related autoantibodies for many years and is the subject of an increasing number of studies as well as a focus of efforts to prevent the onset of clinically apparent arthritis.<br><br>OBJECTIVES: To review the potential causal pathways in pre-RA by examining results of studies which evaluate the systemic peripheral blood and mucosal alterations that have been identified in individuals who are genetically at-risk, and/or who elaborate RA-related autoantibodies, and are defined as in a pre-RA period.<br><br>METHODS: Published studies by the author and his colleagues, as well as publications by other groups, which describe the presence of biomarkers at mucosal sites and in the blood were reviewed. From these studies, a hypothesis related to the presence of pre-RA causal drivers was constructed.<br><br>RESULTS: The author and his colleagues, as well as other groups, have shown that there are multiple mucosal sites, primarily gut, lung and oral/peridontial, which appear in subsets of individuals in the pre-RA to exhibit inflammation and/or the presence of local production of IgA and IgG RA-related autoantibodies, including anti-citrullinated protein antibodies (ACPA). These findings are reviewed herein. There remain a large number of unanswered questions, though, related to the immune mechanisms that are operative at each site, as well as how these local findings evolve to causal systemic autoimmunity and eventually inflammatory arthritis.<br><br>AUTHOR'S CONCLUSIONS: Comprehensive natural history studies are required to understand how multiple mucosal sites which appear to be involved in pre-RA are causally involved in the development of arthritis. Questions remain as to whether there are independent, serially involved, or inter-related causal immune pathways originating from these sites. In addition, the microbiota which may be involved in local immune inflammation and autoantibody production should be identified and characterized.},
}
@article {pmid38030382,
year = {2023},
author = {Song, CH and Kim, N and Nam, RH and Choi, SI and Jang, JY and Kim, EH and Choi, J and Choi, Y and Yoon, H and Lee, SM},
title = {The Possible Preventative Role of Lactate- and Butyrate-Producing Bacteria in Colorectal Carcinogenesis.},
journal = {Gut and liver},
volume = {},
number = {},
pages = {},
doi = {10.5009/gnl230385},
pmid = {38030382},
issn = {2005-1212},
abstract = {BACKGROUND/AIMS: : The gut microbiome has emerged as a key player that mechanistically links various risk factors to colorectal cancer (CRC) etiology. However, the role of the gut microbiome in CRC pathogenesis remains unclear. This study aimed to characterize the gut microbiota in healthy controls (HCs) and patients with colorectal adenoma (AD) and CRC in subgroups based on sex and age.<br><br>METHODS: : Study participants who visited the hospital for surveillance of CRC or gastrointestinal symptoms were prospectively enrolled, and the gut microbiome was analyzed based on fecal samples.<br><br>RESULTS: : In terms of HC-AD-CRC sequence, commensal bacteria, including lactate-producing (Streptococcus salivarius) and butyrate-producing (Faecalibacterium prausnitzii, Anaerostipes hadrus, and Eubacterium hallii) bacteria, were more abundant in the HC group than in the AD and CRC groups. In the sex comparison, the female HC group had more lactate-producing bacteria (Bifidobacterium adolescentis, Bifidobacterium catenulatum, and Lactobacillus ruminis) than the male HC group. In age comparison, younger subjects had more butyrate-producing bacteria (Agathobaculum butyriciproducens and Blautia faecis) than the older subjects in the HC group. Interestingly, lactate-producing bacteria (B. catenulatum) were more abundant in females than males among younger HC group subjects. However, these sex- and age-dependent differences were not observed in the AD and CRC groups.<br><br>CONCLUSIONS: : The gut microbiome, specifically lactate- and butyrate-producing bacteria, which were found to be abundant in the HC group, may play a role in preventing the progression of CRC. In particular, lactate-producing bacteria, which were found to be less abundant in healthy male controls may contribute to the higher incidence of CRC in males.},
}
@article {pmid38030126,
year = {2023},
author = {Ahsan, T and Tian, PC and Gao, J and Wang, C and Liu, C and Huang, YQ},
title = {Effects of microbial agent and microbial fertilizer input on soil microbial community structure and diversity in a peanut continuous cropping system.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2023.11.028},
pmid = {38030126},
issn = {2090-1224},
abstract = {INTRODUCTION: The soil harbors a diverse array of microorganisms, and these are essential components of terrestrial ecosystems. The presence of microorganisms in the soil, particularly in the rhizosphere, is closely linked to plant growth and soil fertility.<br><br>OBJECTIVE: The primary objective of this study is to assess the potential advantages of integrating microbial inoculants with compound fertilizer in enhancing peanut yield.<br><br>METHODS: We utilized Illumina MiSeq high-throughput sequencing technology to conduct our investigation. The experimental design consists of four treatment groups: compound fertilizers (CF), compound fertilizers supplemented with microbial agents (CF+MA), compound fertilizers supplemented with microbial fertilizers (CF+MF), and compound fertilizers supplemented with both microbial agents and microbial fertilizers (CF+MM).<br><br>RESULTS: The experimental results demonstrated a significant increase in peanut yield upon application of CF+MA, CF+MF, and CF+MM treatments. During the blossom stage and pod-setting stage, the soil's catalase, urease, and acid phosphatase activities were significantly increased in the CF+MA, and CF+MM treatments compared to the CF treatment. The application of CF+MA resulted in an increase in bacterial richness in the rhizosphere soil of peanuts, as indicated by the sequencing results. The application of CF+MA, CF+MF, and CF+MM resulted in a reduction of fungal diversity. Proteobacteria, Actinobacteria, and Acidobacteria were the dominant bacterial phyla, while Ascomycota and Basidiomycota were the dominant phyla in the fungal component of the rhizosphere soil microbiome across all experimental treatments.<br><br>CONCLUSION: Microbial agents and fertilizers modify the peanut rhizosphere soil's microbial community structure, as per our findings. The abundance of potentially beneficial bacteria (Bradyrhizobium, Rhizobium, and Burkholderia) and fungi (Trichoderma and Cladophialophora) could increase, while pathogenic fungi (Penicillium and Fusarium) decreased, thereby significantly promoting plant growth and yield of peanut.},
}
@article {pmid38030048,
year = {2023},
author = {Gong, X and Ma, Y and Deng, X and Li, A and Li, X and Kong, X and Liu, Y and Liu, X and Guo, K and Yang, Y and Li, Z and Wei, H and Zhou, D and Hong, Z},
title = {Intestinal dysbiosis exacerbates susceptibility to the anti-NMDA receptor encephalitis-like phenotype by changing blood brain barrier permeability and immune homeostasis.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2023.11.030},
pmid = {38030048},
issn = {1090-2139},
abstract = {Changes in the intestinal microbiota have been observed in patients with anti-N-methyl-D-aspartate receptor encephalitis (NMDARE). However, whether and how the intestinal microbiota is involved in the pathogenesis of NMDARE susceptibility needs to be demonstrated. Here, we first showed that germ-free (GF) mice that underwent fecal microbiota transplantation (FMT) from NMDARE patients, whose fecal microbiota exhibited low short-chain fatty acid content, decreased abundance of Lachnospiraceae, and increased abundance of Verrucomicrobiota, Akkermansia, Parabacteroides, Oscillospirales, showed significant behavioral deficits. Then, these FMT mice were actively immunized with an amino terminal domain peptide from the GluN1 subunit (GluN1356-385) to mimic the pathogenic process of NMDARE. We found that FMT mice showed an increased susceptibility to an encephalitis-like phenotype characterized by more clinical symptoms, greater pentazole (PTZ)-induced susceptibility to seizures, and higher levels of T2 weighted image (T2WI) hyperintensities following immunization. Furthermore, mice with dysbiotic microbiota had impaired blood-brain barrier integrity and a proinflammatory condition. In NMDARE-microbiota recipient mice, the levels of Evan's blue (EB) dye extravasation increased, ZO-1 and claudin-5 expression decreased, and the levels of proinflammatory cytokines (IL-1, IL-6, IL-17, TNF-α and LPS) increased. Finally, significant brain inflammation, mainly in hippocampal and cortical regions, with modest neuroinflammation, immune cell infiltration, and reduced expression of NMDA receptors were observed in NMDARE microbiota recipient mice following immunization. Overall, our findings demonstrated that intestinal dysbiosis increased NMDARE susceptibility, suggesting a new target for limiting the occurrence of the severe phenotype of NMDARE.},
}
@article {pmid38030004,
year = {2023},
author = {Liu, Y and Deng, G and Liu, H and Chen, P and Pan, Y and Chen, L and Chen, H and Zhang, G},
title = {Seasonal variations of airborne microbial diversity in waste transfer stations and preventive effect on Streptococcus pneumoniae induced pulmonary inflammation.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168888},
doi = {10.1016/j.scitotenv.2023.168888},
pmid = {38030004},
issn = {1879-1026},
abstract = {Environment, location, and season are important factors that influence the microbiological community, yet, little research on airborne microorganisms in waste transfer stations (WTSs). Here, the airborne bacterial and fungal communities at four WTSs during different seasons were analyzed by high-throughput sequencing. The bacteria were isolated by cultural method and screened bacterium alleviate inflammation induced by Streptococcus pneumoniae (Spn) by regulating gut microbiome. The results revealed that collected bioaerosols from the WTSs varied significantly by location and season. Proteobacteria and Pseudomonadota are prevalent in summer and winter, respectively. Ascomycota was predominant in two seasons. Hazard quotients for adults from four WTSs were below one. Three selected potential probiotics were formulated into a microbial preparation with a carrier that effectively prevented inflammation in bacterial and animal experiments. The expression levels of interleukin-1β, interleukin-6, and tumor necrosis factor-α in Pre group (0.11, 0.17, and 0.48-fold) were significantly lower than Spn group (2.75, 1.71, and 5.01-fold). These mechanisms are associated with changes in gut microbiota composition and short-chain fatty acids (SCFAs) levels, such as affecting Lachnospiraceae lachnospira abundance and acetic acid content. This study provides insights into the potential application of probiotics derived from WTSs as an alternative approach to preventing respiratory infections.},
}
@article {pmid38029942,
year = {2023},
author = {Xie, Z and Zhou, J and Zhang, X and Li, Z},
title = {Clinical potential of microbiota in thyroid cancer therapy.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {1870},
number = {2},
pages = {166971},
doi = {10.1016/j.bbadis.2023.166971},
pmid = {38029942},
issn = {1879-260X},
abstract = {Thyroid cancer is one of the most common tumors of the endocrine system because of its rapid and steady increase in incidence and prevalence. In recent years, a growing number of studies have identified a key role for the gut, thyroid tissue and oral microbiota in the regulation of metabolism and the immune system. A growing body of evidence has conclusively demonstrated that the microbiota influences tumor formation, prevention, diagnosis, and treatment. We provide extensive information in which oral, gut, and thyroid microbiota have an effect on thyroid cancer development in this review. In addition, we thoroughly discuss the various microbiota species, their potential functions, and the underlying mechanisms for thyroid cancer. The microbiome offers a unique opportunity to improve the effectiveness of immunotherapy and radioiodine therapy thyroid cancer by maintaining the right type of microbiota, and holds great promise for improving clinical outcomes and quality of life for thyroid cancer patients.},
}
@article {pmid38029921,
year = {2023},
author = {Lian, V and Hinrichs, H and Young, M and Faerber, A and Özler, O and Xie, Y and Ballentine, SJ and Tarr, PI and Davidson, NO and Thompson, MD},
title = {MATERNAL OBESOGENIC DIET ATTENUATES MICROBIOME DEPENDENT OFFSPRING WEANING REACTION WITH WORSENING OF STEATOTIC LIVER DISEASE.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2023.11.006},
pmid = {38029921},
issn = {1525-2191},
abstract = {The mechanisms by which maternal obesity increases the susceptibility to steatotic liver disease (SLD) in offspring are incompletely understood and models using different maternal obesogenic diets (MODEs) display phenotypic variability, likely reflecting the influence of timing and diet composition. Here we compare three maternal obesogenic diets using standardized exposure times to identify differences in offspring disease progression. We found that the severity of hepatic inflammation and fibrosis in offspring depends on the composition of maternal obesogenic diet. Offspring cecal microbiome composition was shifted in all MODE groups relative to control. Decreased alpha-diversity in some MODE offspring with shifts in abundance of multiple genera suggestive of delayed maturation of the microbiome. Next we demonstrated that the weaning reaction typically characterized by a spike in intestinal expression of Tnfa and Ifng is attenuated in MODE offspring in an early microbiome dependent manner shown using cross-fostering. Cross-fostering also switched the severity of disease progression in offspring dependent on the diet of the fostering dam. These results identify maternal diet composition and timing of exposure as modifiers in mediating transmissible changes in the microbiome. These changes in the early microbiome alter a critical window during weaning that drives susceptibility to progressive liver disease in offspring.},
}
@article {pmid38029741,
year = {2023},
author = {Meyer, KM and Muscettola, IE and Vasconcelos, ALS and Sherman, JK and Metcalf, CJE and Lindow, SE and Koskella, B},
title = {Conspecific versus heterospecific transmission shapes host specialization of the phyllosphere microbiome.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2023.11.002},
pmid = {38029741},
issn = {1934-6069},
abstract = {In disease ecology, pathogen transmission among conspecific versus heterospecific hosts is known to shape pathogen specialization and virulence, but we do not yet know if similar effects occur at the microbiome level. We tested this idea by experimentally passaging leaf-associated microbiomes either within conspecific or across heterospecific plant hosts. Although conspecific transmission results in persistent host-filtering effects and more within-microbiome network connections, heterospecific transmission results in weaker host-filtering effects but higher levels of interconnectivity. When transplanted onto novel plants, heterospecific lines are less differentiated by host species than conspecific lines, suggesting a shift toward microbiome generalism. Finally, conspecific lines from tomato exhibit a competitive advantage on tomato hosts against those passaged on bean or pepper, suggesting microbiome-level host specialization. Overall, we find that transmission mode and previous host history shape microbiome diversity, with repeated conspecific transmission driving microbiome specialization and repeated heterospecific transmission promoting microbiome generalism.},
}
@article {pmid38029703,
year = {2023},
author = {Liu, H and Feng, X and Wang, D and Liu, L and Liu, Y and Liu, B and Zhu, L and Zhang, C and Yang, W},
title = {Altered metabolome and microbiome features provide clues in predicting recurrence of ulcerative colitis.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {239},
number = {},
pages = {115864},
doi = {10.1016/j.jpba.2023.115864},
pmid = {38029703},
issn = {1873-264X},
abstract = {PURPOSE: Many studies have shown that the imbalance of the intestinal flora and metabolite can lead to the development of ulcerative colitis (UC), but their role in recurrent-UC is still unclear. We studied the intestinal flora and metabolites associated with recurrent-UC to elucidate the mechanism and biomarkers of recurrent-UC.<br><br>METHODS: Ulcerative colitis (UC) models in active, remission, and recurrence stages were established, and the abundance of intestinal flora was determined by 16&#xa0;S rRNA sequencing. The changes in the metabolites present in feces and serum were analyzed by UPLC-MS/MS.<br><br>RESULTS: We identified 24 metabolites in feces and serum, which might be used as diagnostic and predictive biomarkers of recurrent-UC. The dominant flora of recurrent-UC included Romboutsia, UCG-005, etc. The results of a network analysis found that long-chain fatty acids and phenylalanine were strongly correlated with Firmicutes and Proteobacteria, which indicated that the recurrence of UC might be closely related to metabolites and microorganisms.<br><br>CONCLUSION: The changes in intestinal microbiota and metabolites are closely related to the development of UC. Microbiota is an important inducer of UC, which can regulate metabolites through the 'microorganism-gut-metabolite' axis. It may provide a new method for the prediction and treatment of UC.},
}
@article {pmid38029586,
year = {2023},
author = {Fan, Y and Keerthisinghe, TP and Nian, M and Cao, X and Chen, X and Yang, Q and Sampathkumar, K and Loo, JSC and Ng, KW and Demokritou, P and Fang, M},
title = {Comparative secretome metabolic dysregulation by six engineered dietary nanoparticles (EDNs) on the simulated gut microbiota.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {133003},
doi = {10.1016/j.jhazmat.2023.133003},
pmid = {38029586},
issn = {1873-3336},
abstract = {The potential use of engineered dietary nanoparticles (EDNs) in diet has been increasing and poses a risk of exposure. The effect of EDNs on gut bacterial metabolism remains largely unknown. In this study, liquid chromatography-mass spectrometry (LC-MS) based metabolomics was used to reveal significantly altered metabolites and metabolic pathways in the secretome of simulated gut microbiome exposed to six different types of EDNs (Chitosan, cellulose nanocrystals (CNC), cellulose nanofibrils (CNF) and polylactic-co-glycolic acid (PLGA); two inorganic EDNs including TiO2 and SiO2) at two dietary doses. We demonstrated that all six EDNs can alter the composition in the secretome with distinct patterns. Chitosan, followed by PLGA and SiO2, has shown the highest potency in inducing the secretome change with major pathways in tryptophan and indole metabolism, bile acid metabolism, tyrosine and phenol metabolism. Metabolomic alterations with clear dose response were observed in most EDNs. Overall, phenylalanine has been shown as the most sensitive metabolites, followed by bile acids such as chenodeoxycholic acid and cholic acid. Those metabolites might be served as the representative metabolites for the EDNs-gut bacteria interaction. Collectively, our studies have demonstrated the sensitivity and feasibility of using metabolomic signatures to understand and predict EDNs-gut microbiome interaction.},
}
@article {pmid38029543,
year = {2023},
author = {Ohkubo, T and Matsumoto, Y and Sasaki, H and Kinoshita, K and Ogasawara, Y and Sugita, T},
title = {Citrobacter koseri inhibits the growth of Staphylococcus epidermidis by suppressing iron utilization.},
journal = {Biochemical and biophysical research communications},
volume = {691},
number = {},
pages = {149277},
doi = {10.1016/j.bbrc.2023.149277},
pmid = {38029543},
issn = {1090-2104},
abstract = {The human skin microbiome consists of many species of bacteria, including Staphylococcus aureus and S. epidermidis. Individuals with atopic dermatitis (AD) have an increased relative abundance of S. aureus, which exacerbates the inflammation of AD. Although S. epidermidis, a main component of healthy skin microbiota, inhibits the growth of S. aureus, the balance between S. epidermidis and S. aureus is disrupted in the skin of individuals with AD. In this study, we found that Citrobacter koseri isolated from patients with AD produces substances that inhibit the growth of S. epidermidis. Heat-treated culture supernatant (CS) of C. koseri inhibited the growth of S. epidermidis but not S. aureus. The genome of C. koseri has gene clusters related to siderophores and the heat-treated CS of C. koseri contained a high concentration of siderophores compared with the control medium. The inhibitory activity of C. koseri CS against the growth of S. epidermidis was decreased by the addition of iron, but not copper or zinc. Deferoxamine, an iron-chelating agent, also inhibited the growth of S. epidermidis, but not that of S. aureus. These findings suggest that C. koseri inhibits the growth of S. epidermidis by interfering with its iron utilization.},
}
@article {pmid38029490,
year = {2023},
author = {Thomas, S and Lappin, DF and Bennett, D and Nile, C and Riggio, MP},
title = {Elevated pro-inflammatory cytokines and chemokines in saliva of cats with feline odontoclastic resorptive lesion.},
journal = {Research in veterinary science},
volume = {166},
number = {},
pages = {105092},
doi = {10.1016/j.rvsc.2023.105092},
pmid = {38029490},
issn = {1532-2661},
abstract = {Feline odontoclastic resorptive lesion (FORL) is an inflammatory oral disease of unknown aetiopathogenesis that affects between 20% to 75% of cats. Twenty immune-associated molecules were measured in saliva of 25 healthy and 40 cats with FORL using a multiplex assay. No statistically significant differences were observed in the levels of these proteins between the healthy group and the diseased group of cats. A two-step cluster analysis of the oral microbiome and salivary cytokine data identified two subgroups of cats with FORL: FORL-1 (subset of cats with a less diverse oral microbiome) and FORL-2 (diseased cats with a microbiome similar to that of healthy animals). The level of some key proinflammatory cytokines (IL-1β, IL-12p40) and chemokines (IL-8, RANTES, KC) were significantly higher in the FORL-1 subgroup than in the FORL-2 subgroup and the healthy group. In addition, TNF-α levels were greater in the FORL-1 subgroup than in the FORL-2 subgroup. These increases in pro-inflammatory cytokines and chemokines indicate active ongoing inflammation that may promote the osteoclastic/odontoclastic activity associated with FORL.},
}
@article {pmid38029259,
year = {2023},
author = {Ogai, K and Nana, BC and Lloyd, YM and Arios, JP and Jiyarom, B and Awanakam, H and Esemu, LF and Hori, A and Matsuoka, A and Nainu, F and Megnekou, R and Leke, RGF and Ekali, GL and Okamoto, S and Kuraishi, T},
title = {Skin microbiome profile in people living with HIV/AIDS in Cameroon.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1211899},
pmid = {38029259},
issn = {2235-2988},
abstract = {The presence of pathogens and the state of diseases, particularly skin diseases, may alter the composition of human skin microbiome. HIV infection has been reported to impair gut microbiome that leads to severe consequences. However, with cutaneous manifestations, that can be life-threatening, due to the opportunistic pathogens, little is known whether HIV infection might influence the skin microbiome and affect the skin homeostasis. This study catalogued the profile of skin microbiome of healthy Cameroonians, at three different skin sites, and compared them to the HIV-infected individuals. Taking advantage on the use of molecular assay coupled with next-generation sequencing, this study revealed that alpha-diversity of the skin microbiome was higher and beta-diversity was altered significantly in the HIV-infected Cameroonians than in the healthy ones. The relative abundance of skin microbes such as Micrococcus and Kocuria species was higher and Cutibacterium species was significantly lower in HIV-infected people, indicating an early change in the human skin microbiome in response to the HIV infection. This phenotypical shift was not related to the number of CD4 T cell count thus the cause remains to be identified. Overall, these data may offer an important lead on the role of skin microbiome in the determination of cutaneous disease state and the discovery of safe pharmacological preparations to treat microbial-related skin disorders.},
}
@article {pmid38029257,
year = {2023},
author = {Liu, H and Hu, Q and Yan, Q and Hao, Z and Liang, C},
title = {Alterations in urinary microbiota composition in urolithiasis patients: insights from 16S rRNA gene sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1266446},
pmid = {38029257},
issn = {2235-2988},
abstract = {OBJECTIVES: To investigate the urinary microbiota composition in urolithiasis patients compared to healthy controls and to identify potential microbial markers and their association with clinical parameters.<br><br>METHODS: A total of 66 samples, comprising 45 from urolithiasis patients and 21 from healthy controls, were analyzed. 16S rRNA gene sequencing was employed to determine the microbiota composition. Various statistical and bioinformatics tools, including ANOVA, PCoA, and LEfSe, were utilized to analyze the sequencing data and identify significant differences in microbial abundance.<br><br>RESULTS: No significant demographic differences were observed between the two groups. Post-quality control, clean tags ranged from 60,979 to 68,736. Significant differences in &#x3b1;-diversity were observed between the two groups. &#x3b2;-diversity analysis revealed distinct clustering of the urinary microbiota in urolithiasis patients and controls. Notably, Ruminococcaceae was predominant in urolithiasis samples, while Proteobacteria was more prevalent in healthy samples. Lactobacillus was significantly overrepresented in samples from healthy females.<br><br>CONCLUSION: The urinary microbiota composition in urolithiasis patients is distinct from that of healthy controls. Specific microbial taxa, such as Ruminococcaceae and Proteobacteria, could serve as potential biomarkers for urolithiasis. The findings pave the way for further exploration of the role of microbiota in urolithiasis and the development of microbiome-based therapeutic strategies.},
}
@article {pmid38029244,
year = {2023},
author = {Zong, Y and Wang, X and Wang, J},
title = {Research progress on the correlation between gut microbiota and preeclampsia: microbiome changes, mechanisms and treatments.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1256940},
pmid = {38029244},
issn = {2235-2988},
abstract = {Preeclampsia is a specific disease during pregnancy and is a significant factor in the increased mortality in perinatal women. Gut microbiota, an intricate and abundant microbial community in the digestive tract, is crucial for host metabolism, immunity, and nutrient absorption. The onset and progression of preeclampsia are closely correlated with the changes in maternal gut microbiota. Research purpose was to compile the existing bits of present scientific data and to close the gap in the knowledge of changes in gut microbiota in preeclampsia and their association with preeclampsia. We searched studies from two electronic databases (PubMed and Web of Science) included from 2014 to 2023. This review is divided into three parts. In the first part, the author elaborates longitudinal differences of maternal gut microbiota during different gestation periods. In the second part, we discuss that gut microbiota can lead to the occurrence of preeclampsia by systemic immune response, influencing the release of active peptides, short-chain fatty acids, trimethylamine-N-oxide (TMAO) and other metabolites, vascular factors and Microorganism-immune axis. In the third part, we proposed that a high-fiber diet combined with drugs and microecological regulators may be therapeutic in enhancing or preventing the emergence and evolution of preeclampsia, which needs further exploration. Although the pathogenesis of preeclampsia is still nebulous and there is no clear and valid clinical treatment, our study provides new ideas for the pathogenesis, prevention and treatment of preeclampsia.},
}
@article {pmid38029238,
year = {2023},
author = {Nie, Q and Wan, X and Tao, H and Yang, Q and Zhao, X and Liu, H and Hu, J and Luo, Y and Shu, T and Geng, R and Gu, Z and Fan, F and Liu, Z},
title = {Multi-function screening of probiotics to improve oral health and evaluating their efficacy in a rat periodontitis model.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1261189},
pmid = {38029238},
issn = {2235-2988},
abstract = {The oral cavity is the second most microbially rich region of the human body, and many studies have shown that there is a strong association between microorganisms and oral health. Some pathogenic bacteria produce biofilms and harmful metabolites in the mouth that may cause oral problems such as oral malodor, periodontitis, and dental caries. Altering the oral microbiota by using probiotics may alleviate oral health problems. Thus, using multi-function screening, we aimed to identify probiotics that can significantly improve oral health. The main parameters were the inhibition of pathogenic bacteria growth, inhibition of biofilm formation, reduction in the production of indole, H2S, and NH3 metabolites that cause halitosis, increase in the production of H2O2 to combat harmful bacteria, and co-aggregation with pathogens to prevent their adhesion and colonization in the oral cavity. Tolerance to cholic acid and choline was also assessed. Bifidobacterium animalis ZK-77, Lactobacillus salivarius ZK-88, and Streptococcus salivarius ZK-102 had antibacterial activity and inhibited biofilm production to prevent caries. They also improved the oral malodor parameter, H2S, NH3, and indole production. The selected probiotics (especially L. salivarius ZK-88) alleviated the inflammation in the oral cavity of rats with periodontitis. The analysis of the gingival crevicular fluid microbiome after probiotic intervention showed that B. animalis ZK-77 likely helped to restore the oral microbiota and maintain the oral microecology. Next, we determined the best prebiotics for each candidate probiotic in order to obtain a formulation with improved effects. We then verified that a probiotics/prebiotic combination (B. animalis ZK-77, L. salivarius ZK-88, and fructooligosaccharides) significantly improved halitosis and teeth color in cats. Using whole-genome sequencing and acute toxicity mouse experiments involving the two probiotics, we found that neither probiotic had virulence genes and they had no significant effects on the growth or development of mice, indicating their safety. Taking the results together, B. animalis ZK-77 and L. salivarius ZK-88 can improve oral health, as verified by in vivo and in vitro experiments. This study provides a reference for clinical research and also provides new evidence for the oral health benefits of probiotics.},
}
@article {pmid38029215,
year = {2023},
author = {Jin, X and Xiao, J and Lu, C and Ma, W and Fan, Y and Xue, X and Xia, Y and Chen, N and Liu, J and Pei, X},
title = {Breastmilk microbiome changes associated with lactational mastitis and treatment with dandelion extract.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1247868},
pmid = {38029215},
issn = {1664-302X},
abstract = {INTRODUCTION: Dandelion (Pugongying) is one of the most frequently used Chinese herbs for treating lactational mastitis (LM). Pugongying granules, a patented medication primarily comprised of dandelion extract, have been approved by CFDA for LM treatment in China. The aims of this study were to investigate the etiology of LM and the mechanism by which Pugongying granules decrease LM symptoms, with a particular focus on the microbial communities found in breastmilk.<br><br>METHODS: Participants were recruited from a previously performed randomized controlled trial (Identifier: NCT03756324, ClinicalTrials.gov). Between 2019 and 2020, women diagnosed with unilateral LM at the Beijing University of Chinese Medicine Third Affiliated Hospital were enrolled. In total, 42 paired breastmilk samples from the healthy and affected breasts of the participants were collected. Additionally, 37 paired pre- and post-treatment breastmilk samples from the affected breast were collected from women who received a 3-day course of either Pugongying granules (20 women) or cefdinir (17 women). Clinical outcomes [e.g., body temperature, visual analogue scale (VAS) score for breast pain, the percentage of neutrophils (NE%)] were analyzed pre- and post-treatment, and the breastmilk samples were subjected to 16S rRNA gene sequencing to analyze the alpha and beta diversities and identify significant bacteria. Finally, the relationship between microorganisms and clinical outcomes was analyzed.<br><br>RESULTS: There was no significant difference in fever and pain between the Pugongying group and cefdinir group. The most prevalent bacterial genera in breastmilk were Streptococcus and Staphylococcus. Compared to healthy breastmilk, microbial diversity was reduced in affected breastmilk, and there was a higher relative abundance of Streptococcus. After Pugongying treatment, there was an increase in microbial diversity with significantly higher abundance of Corynebacterium. A negative correlation was found between Corynebacterium, VAS score, and NE%. Treatment with cefdinir did not affect microbial diversity. Taken together, our results show a correlation between LM and reduced microbial diversity, as well as an increased abundance of Streptococcus in affected breastmilk.<br><br>CONCLUSION: Pugongying granules enhanced microbial diversity in breastmilk samples. Given the substantial variation in individual microbiomes, identifying specific species of Streptococcus and Corynebacterium associated with LM may provide additional insight into LM pathogenesis and treatment.},
}
@article {pmid38029194,
year = {2023},
author = {Smith, JC and Varriano, S and Roach, K and Snipes, Z and Dawson, JL and Shealy, J and Dunn, LL and Snyder, WE and Shariat, NW},
title = {Prevalence and molecular characterization of Salmonella isolated from wild birds in fresh produce environments.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1272916},
pmid = {38029194},
issn = {1664-302X},
abstract = {Wild birds pose a difficult food safety risk to manage because they can avoid traditional wildlife mitigation strategies, such as fences. Birds often use agricultural fields and structures as foraging and nesting areas, which can lead to defecation on crops and subsequent transfer of foodborne pathogens. To assess the food safety risk associated with these events, wild bird feces were collected from produce fields across the southeastern United States during the 2021 and 2022 growing seasons. In total 773 fecal samples were collected from 45 farms across Florida, Georgia, South Carolina, and Tennessee, and 2.1% (n = 16) of samples were Salmonella-positive. Importantly, 75% of Salmonella were isolated from moist feces, showing reduced Salmonella viability when feces dry out. 16S microbiome analysis showed that presence of culturable Salmonella in moist feces correlated to a higher proportion of the Enterobacteriaceae family. From the Salmonella-positive samples, 62.5% (10/16) contained multi-serovar Salmonella populations. Overall, 13 serovars were detected, including six most commonly attributed to human illness (Enteriditis, Newport, Typhimurium, Infantis, Saintpaul, and Muenchen). PCR screening identified an additional 59 Salmonella-positive fecal samples, which were distributed across moist (n = 44) and dried feces (n = 15). On-farm point counts and molecular identification from fecal samples identified 57 bird species, including for 10 Salmonella-positive fecal samples. Overall, there was a low prevalence of Salmonella in fecal samples, especially in dried feces, and we found no evidence of Salmonella transmission to proximal foliage or produce. Fecal samples collected in farms close together shared highly related isolates by whole genome sequencing and also had highly similar Salmonella populations with comparable relative frequencies of the same serovars, suggesting the birds acquired Salmonella from a common source.},
}
@article {pmid38029189,
year = {2023},
author = {Zhang, X and Luo, X and Tian, L and Yue, P and Li, M and Liu, K and Zhu, D and Huang, C and Shi, Q and Yang, L and Xia, Z and Zhao, J and Ma, Z and Li, J and Leung, JW and Lin, Y and Yuan, J and Meng, W and Li, X and Chen, Y},
title = {The gut microbiome dysbiosis and regulation by fecal microbiota transplantation: umbrella review.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1286429},
pmid = {38029189},
issn = {1664-302X},
abstract = {BACKGROUND: Gut microbiome dysbiosis has been implicated in various gastrointestinal and extra-gastrointestinal diseases, but evidence on the efficacy and safety of fecal microbiota transplantation (FMT) for therapeutic indications remains unclear.<br><br>METHODS: The gutMDisorder database was used to summarize the associations between gut microbiome dysbiosis and diseases. We performed an umbrella review of published meta-analyses to determine the evidence synthesis on the efficacy and safety of FMT in treating various diseases. Our study was registered in PROSPERO (CRD42022301226).<br><br>RESULTS: Gut microbiome dysbiosis was associated with 117 gastrointestinal and extra-gastrointestinal. Colorectal cancer was associated with 92 dysbiosis. Dysbiosis involving Firmicutes (phylum) was associated with 34 diseases. We identified 62 published meta-analyses of FMT. FMT was found to be effective for 13 diseases, with a 95.56% cure rate (95% CI: 93.88-97.05%) for recurrent Chloridoids difficile infection (rCDI). Evidence was high quality for rCDI and moderate to high quality for ulcerative colitis and Crohn's disease but low to very low quality for other diseases.<br><br>CONCLUSION: Gut microbiome dysbiosis may be implicated in numerous diseases. Substantial evidence suggests FMT improves clinical outcomes for certain indications, but evidence quality varies greatly depending on the specific indication, route of administration, frequency of instillation, fecal preparation, and donor type. This variability should inform clinical, policy, and implementation decisions regarding FMT.},
}
@article {pmid38029184,
year = {2023},
author = {Ye, L and Zhang, B and Zhang, L and Yang, X and Tan, W and Zhang, X and Li, X},
title = {Pathogenic invasive microbes Trichoderma pleuroticola transform bacterial and fungal community diversity in Auricularia cornea crop production system.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1263982},
pmid = {38029184},
issn = {1664-302X},
abstract = {Pathogenic invasion of Trichoderma pleuroticola profoundly altered microflora in the Auricularia cornea crop production system, impacting diversity and composition in both artificial bed-log and fruiting bodies. A more complex ecological network between the diseased and healthy bodies. Researchers still have poor knowledge about how the important agricultural relationship between the composition of the microbiome of the artificial bed-log and the fruiting bodies is infected by the pathogenic invasive microbes T. pleuroticola, but this knowledge is crucial if we want to use or improve it. Here, we investigated 8 groups (48 biological samples) across 5 growth stages of the A. cornea production system using metagenomic technology. Diseased and healthy fruiting bodies exhibited distinct microbial compositions, while core members in artificial bed-logs remained stable. Core microbiota analysis highlighted Pseudomonas and Pandoraea bacterial genera, as well as Sarocladium, Cephalotrichum, Aspergillus, and Mortierella fungal genera as biomarker species after the bodies were treated with the pathogenic invasive microbes T. pleuroticola. In diseased bodies, these core members upregulated pathways including polymyxin resistance, L-arginine degradation II, superpathway of L-arginine and L-ornithine degradation, glucose degradation (oxidative), glucose and glucose-1-phosphate degradation, promoting fruit spoilage. Our data confirm that T. pleuroticola plays an important role in the early stages of disease development in the A. cornea crop generation system. The exposed volatile core microbiome may play an important role in accelerating T. pleuroticola-induced decay of fruiting bodies.},
}
@article {pmid38029177,
year = {2023},
author = {Rempfert, KR and Kraus, EA and Nothaft, DB and Dildar, N and Spear, JR and Sepúlveda, J and Templeton, AS},
title = {Intact polar lipidome and membrane adaptations of microbial communities inhabiting serpentinite-hosted fluids.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1198786},
pmid = {38029177},
issn = {1664-302X},
abstract = {The generation of hydrogen and reduced carbon compounds during serpentinization provides sustained energy for microorganisms on Earth, and possibly on other extraterrestrial bodies (e.g., Mars, icy satellites). However, the geochemical conditions that arise from water-rock reaction also challenge the known limits of microbial physiology, such as hyperalkaline pH, limited electron acceptors and inorganic carbon. Because cell membranes act as a primary barrier between a cell and its environment, lipids are a vital component in microbial acclimation to challenging physicochemical conditions. To probe the diversity of cell membrane lipids produced in serpentinizing settings and identify membrane adaptations to this environment, we conducted the first comprehensive intact polar lipid (IPL) biomarker survey of microbial communities inhabiting the subsurface at a terrestrial site of serpentinization. We used an expansive, custom environmental lipid database that expands the application of targeted and untargeted lipodomics in the study of microbial and biogeochemical processes. IPLs extracted from serpentinite-hosted fluid communities were comprised of >90% isoprenoidal and non-isoprenoidal diether glycolipids likely produced by archaeal methanogens and sulfate-reducing bacteria. Phospholipids only constituted ~1% of the intact polar lipidome. In addition to abundant diether glycolipids, betaine and trimethylated-ornithine aminolipids and glycosphingolipids were also detected, indicating pervasive membrane modifications in response to phosphate limitation. The carbon oxidation state of IPL backbones was positively correlated with the reduction potential of fluids, which may signify an energy conservation strategy for lipid synthesis. Together, these data suggest microorganisms inhabiting serpentinites possess a unique combination of membrane adaptations that allow for their survival in polyextreme environments. The persistence of IPLs in fluids beyond the presence of their source organisms, as indicated by 16S rRNA genes and transcripts, is promising for the detection of extinct life in serpentinizing settings through lipid biomarker signatures. These data contribute new insights into the complexity of lipid structures generated in actively serpentinizing environments and provide valuable context to aid in the reconstruction of past microbial activity from fossil lipid records of terrestrial serpentinites and the search for biosignatures elsewhere in our solar system.},
}
@article {pmid38029176,
year = {2023},
author = {Jain, U and Poltronieri, P and Fusco, V and Primiceri, E},
title = {Editorial: Latest perspective on microbes detection: from laboratory to on-spot sensor.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1302805},
doi = {10.3389/fmicb.2023.1302805},
pmid = {38029176},
issn = {1664-302X},
}
@article {pmid38029169,
year = {2023},
author = {Nguyen, TQ and Martínez-Álvaro, M and Lima, J and Auffret, MD and Rutherford, KMD and Simm, G and Dewhurst, RJ and Baima, ET and Roehe, R},
title = {Identification of intestinal and fecal microbial biomarkers using a porcine social stress model.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1197371},
pmid = {38029169},
issn = {1664-302X},
abstract = {Understanding the relationships between social stress and the gastrointestinal microbiota, and how they influence host health and performance is expected to have many scientific and commercial implementations in different species, including identification and improvement of challenges to animal welfare and health. In particular, the study of the stress impact on the gastrointestinal microbiota of pigs may be of interest as a model for human health. A porcine stress model based on repeated regrouping and reduced space allowance during the last 4 weeks of the finishing period was developed to identify stress-induced changes in the gut microbiome composition. The application of the porcine stress model resulted in a significant increase in salivary cortisol concentration over the course of the trial and decreased growth performance and appetite. The applied social stress resulted in 32 bacteria being either enriched (13) or depleted (19) in the intestine and feces. Fecal samples showed a greater number of microbial genera influenced by stress than caecum or colon samples. Our trial revealed that the opportunistic pathogens Treponema and Clostridium were enriched in colonic and fecal samples from stressed pigs. Additionally, genera such as Streptococcus, Parabacteroides, Desulfovibrio, Terrisporobacter, Marvinbryantia, and Romboutsia were found to be enriched in response to social stress. In contrast, the genera Prevotella, Faecalibacterium, Butyricicoccus, Dialister, Alloprevotella, Megasphaera, and Mitsuokella were depleted. These depleted bacteria are of great interest because they synthesize metabolites [e.g., short-chain fatty acids (SCFA), in particular, butyrate] showing beneficial health benefits due to inhibitory effects on pathogenic bacteria in different animal species. Of particular interest are Dialister and Faecalibacterium, as their depletion was identified in a human study to be associated with inferior quality of life and depression. We also revealed that some pigs were more susceptible to pathogens as indicated by large enrichments of opportunistic pathogens of Clostridium, Treponema, Streptococcus and Campylobacter. Generally, our results provide further evidence for the microbiota-gut-brain axis as indicated by an increase in cortisol concentration due to social stress regulated by the hypothalamic-pituitary-adrenal axis, and a change in microbiota composition, particularly of bacteria known to be associated with pathogenicity and mental health diseases.},
}
@article {pmid38029159,
year = {2023},
author = {Huang, B and Khan, MZ and Chen, Y and Liang, H and Kou, X and Wang, X and Ren, W and Wang, C and Zhang, Z},
title = {Yeast polysaccharide supplementation: impact on lactation, growth, immunity, and gut microbiota in Dezhou donkeys.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1289371},
pmid = {38029159},
issn = {1664-302X},
abstract = {INTRODUCTION: The Dezhou donkey, a prominent Chinese breed, is known for its remarkable size, rapid growth, and resilience to tough feeding conditions, and disease resistance. These traits are crucial in meeting the growing demand for Ejiao and donkey meat. Yeast polysaccharide (YPS), a functional polysaccharide complex known for its immune-enhancing and growth-promoting properties in livestock and poultry, remains relatively understudied in donkeys.<br><br>OBJECTIVES: This study aimed to investigate the impact of YPS supplementation on lactating and growing Dezhou donkey jennies and foals.<br><br>MATERIALS AND METHODS: Twelve 45-day-old Dezhou donkey foals and their jennies, matched for body weight and age, were randomly allocated to two dietary groups: a control group receiving a basal diet and an experimental group receiving the basal diet supplemented with 10&#x2009;g/pen of YPS. The experiment was conducted over a 23-day period, during which donkey foals and lactating jennies were co-housed.<br><br>RESULTS AND DISCUSSION: The findings revealed that YPS supplementation had no adverse effects on milk production or composition in Dezhou donkey jennies but significantly increased feed intake. Additionally, YPS was associated with increased plasma glucose and creatinine concentrations in foals, while tending to decrease alkaline phosphatase, white blood cell count, red blood cell count, and hemoglobin levels (p&#x2009;<&#x2009;0.10). Immune indices demonstrated that YPS supplementation elevated the levels of immunoglobulin A (IgA) and immunoglobulin G (IgG) in jennies (p&#x2009;<&#x2009;0.05) and increased complement component C4 concentrations in foals (p&#x2009;<&#x2009;0.05). Moreover, YPS positively influenced the fecal microbiome, promoting the abundance of beneficial microorganisms such as Lactobacillus and Prevotella in donkey foals and Terriporobacter and Cellulosilyticum in jennies, all of which contribute to enhanced feed digestion. Additionally, YPS induced alterations in the plasma metabolome for both jennies and foals, with a predominant presence of lipids and lipid-like molecules. Notably, YPS increased the concentrations of specific lipid metabolites, including 13,14-Dihydro PGF2a, 2-Isopropylmalic acid, 2,3-Dinor-TXB2, Triterpenoids, Taurocholic acid, and 3b-Allotetrahydrocortisol, all of which are associated with improved animal growth.<br><br>CONCLUSION: In conclusion, this study suggests that dietary supplementation of YPS enhances feed intake, boosts immunity by increasing immunoglobulin levels, stimulates the growth-promoting gut microbiota (Lactobacillus and Prevotella), and exerts no adverse effects on the metabolism of both Dezhou donkey jennies and foals.},
}
@article {pmid38029157,
year = {2023},
author = {Liu, M and Ding, J and Lu, M},
title = {Influence of symbiotic bacteria on the susceptibility of Plagiodera versicolora to Beauveria bassiana infection.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1290925},
pmid = {38029157},
issn = {1664-302X},
abstract = {The symbiotic bacterial microbiota of insects has been shown to play essential roles in processes related to physiology, metabolism, and innate immunity. In this study, the symbiotic microbiome of Plagiodera versicolora at different developmental stages was analyzed using 16S rRNA high-throughput sequencing. The result showed that symbiotic bacteria community in P. versicolora was primarily made up of Actinobacteriota, Proteobacteria, Firmicutes, Bacteroidota, and Dependentiae. The bacterial composition among different age individuals were highly diverse, while 65 core genera were distributed in all samples which recommend core bacterial microbiome. The 8 species core bacteria were isolated from all samples, and all of them were classified as Pseudomonas sp. Among them, five species have been proven to promote the vegetable growth of Beauveria bassiana. Moreover, the virulence of B. bassiana against nonaxenic larvae exceeded B. bassiana against axenic larvae, and the introduction of the Pseudomonas sp. to axenic larvae augmented the virulence of fungi. Taken together, our study demonstrates that the symbiotic bacteria of P. versicolora are highly dissimilar, and Pseudomonas sp. core bacteria can promote host infection by entomopathogenic fungus. This result emphasizes the potential for harnessing these findings in the development of effective pest management strategies.},
}
@article {pmid38029153,
year = {2023},
author = {Wu, C and Lower, BA and Moreira, R and Dorantes, D and Le, T and Giurgiu, C and Shi, Y and van der Donk, WA},
title = {Investigation into the mechanism of action of the antimicrobial peptide epilancin 15X.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1247222},
pmid = {38029153},
issn = {1664-302X},
abstract = {Addressing the current antibiotic-resistance challenge would be aided by the identification of compounds with novel mechanisms of action. Epilancin 15X, a lantibiotic produced by Staphylococcus epidermidis 15 × 154, displays antimicrobial activity in the submicromolar range against a subset of pathogenic Gram-positive bacteria. S. epidermidis is a common member of the human skin or mucosal microbiota. We here investigated the mechanism of action of epilancin 15X. The compound is bactericidal against Staphylococcus carnosus as well as Bacillus subtilis and appears to kill these bacteria by membrane disruption. Structure-activity relationship studies using engineered analogs show that its conserved positively charged residues and dehydroamino acids are important for bioactivity, but the N-terminal lactyl group is tolerant of changes. Epilancin 15X treatment negatively affects fatty acid synthesis, RNA translation, and DNA replication and transcription without affecting cell wall biosynthesis. The compound appears localized to the surface of bacteria and is most potent in disrupting the membranes of liposomes composed of negatively charged membrane lipids in a lipid II independent manner. Epilancin 15X does not elicit a LiaRS response in B. subtilis but did upregulate VraRS in S. carnosus. Treatment of S. carnosus or B. subtilis with epilancin 15X resulted in an aggregation phenotype in microscopy experiments. Collectively these studies provide new information on epilancin 15X activity.},
}
@article {pmid38029152,
year = {2023},
author = {Huang, Z and He, X and Zhang, C and Zhang, M and Wang, J and Hou, Y and Wang, D and Yao, S and Yu, Q and Ji, K},
title = {Microbial communities and functions changed in rhizosphere soil of Pinus massoniana provenances with different carbon storage.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1264670},
pmid = {38029152},
issn = {1664-302X},
abstract = {INTRODUCTION: The average carbon storage of Pinus massoniana is much higher than the average carbon storage of Chinese forests, an important carbon sink tree species in subtropical regions of China. However, there are few studies on the differences in rhizosphere microorganisms of P. massoniana with different carbon storages.<br><br>METHODS: To clarify the relationships between plant carbon storage level, environmental parameters and microbial community structure, we identified three carbon storage levels from different P. massoniana provenances and collected rhizosphere soil samples. We determined chemical properties of soil, extracellular enzyme activity, and microbial community structures at different carbon storage levels and examined how soil factors affect rhizosphere microorganisms under different carbon storage levels.<br><br>RESULTS: The results revealed that soil organic carbon (SOC), nitrate nitrogen (NO3[-]-N), ammonium nitrogen (NH4[+]-N) contents all increased with increasing carbon storage levels, while pH decreased accordingly. In contrast, the available phosphorus (AP) content did not change significantly. The soil AP content was within the range of 0.91&#x2009;~&#x2009;1.04&#x2009;mg/kg. The microbial community structure of P. massoniana changed with different carbon storage, with Acidobacteria (44.27%), Proteobacteria (32.57%), and Actinobacteria (13.43%) being the dominant bacterial phyla and Basidiomycota (73.36%) and Ascomycota (24.64%) being the dominant fungal phyla across the three carbon storage levels. Soil fungi were more responsive to carbon storage than bacteria in P. massoniana. C/N, NH4[+]-N, NO3[-]-N, and SOC were the main drivers (p&#x2009;<&#x2009;0.05) of changes in rhizosphere microbial communities.<br><br>DISCUSSION: The results revealed that in the rhizosphere there were significant differences in soil carbon cycle and microorganism nutrient preferences at different carbon storages of P. massoniana provenance, which were significantly related to the changes in rhizosphere microbial community structure. Jiangxi Anyuan (AY) provenance is more suitable for the construction of high carbon storage plantation.},
}
@article {pmid38029138,
year = {2023},
author = {Portugal, A and Liu, X and Pyzik, A and Trovão, J},
title = {Editorial: Microbiomes of art and their importance in preserving cultural heritage.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1321133},
doi = {10.3389/fmicb.2023.1321133},
pmid = {38029138},
issn = {1664-302X},
}
@article {pmid38029137,
year = {2023},
author = {Qian, X and Fu, Z and Diao, C and Zhang, W and Tao, W and Hu, J and Zhang, S and Zhao, D},
title = {Genetic causal relationship between gut microbiome and psoriatic arthritis: a bidirectional two-sample Mendelian randomization study.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1265786},
pmid = {38029137},
issn = {1664-302X},
abstract = {BACKGROUND: Several observational studies have suggested a potential relationship between gut microbiome and psoriatic arthritis (PsA). However, the causality of this relationship still remains unclear. We aim to explore if the specific gut microbiome is causally associated with PsA at the genetic level and offer valuable insights into the etiology of PsA.<br><br>METHODS: In this study, we employed a bidirectional two-sample Mendelian randomization (MR) analysis to investigate the causal effects of the gut microbiome on PsA. Publicly accessible genome-wide association study summary data of gut microbiome were obtained from the MiBioGen consortium (n&#x2009;=&#x2009;14,306), while the summary statistics of psoriatic arthropathies were sourced from the FinnGen consortium R8 release data (2,776 cases and 221,323 controls). The primary analytical method employed was inverse variance weighted (IVW), complemented by supplementary methods including MR-Egger, weighted median, weighted mode, maximum likelihood, MR-PRESSO, and cML-MA. Reverse MR analysis was performed on the bacteria that were found to be causally associated with PsA in forward MR analysis. Cochran's IVW Q statistic was utilized to assess the heterogeneity of instrumental variables among the selected single nucleotide polymorphisms.<br><br>RESULTS: IVW estimates revealed that Ruminococcaceae_UCG-002 (odds ratio (OR)&#x2009;=&#x2009;0.792, 95% confidence interval (CI), 0.643-0.977, p =&#x2009;0.029) exhibited a protective effect on PsA. Conversely, Blautia (OR&#x2009;=&#x2009;1.362, 95% CI, 1.008-1.842, p =&#x2009;0.044), Eubacterium_fissicatena_group (OR&#x2009;=&#x2009;1.28, 95% CI, 1.075-1.524, p =&#x2009;0.006), and Methanobrevibacter (OR&#x2009;=&#x2009;1.31, 95% CI, 1.059-1.621, p =&#x2009;0.013) showed a positive correlation with the risk of PsA. No significant heterogeneity, horizontal pleiotropy, or outliers were observed, and the results of the MR analysis remained unaffected by any single nucleotide polymorphisms. According to the results of reverse MR analysis, no significant causal effect of PsA was found on gut microbiome.<br><br>CONCLUSION: This study establishes for the first time a causal relationship between the gut microbiome and PsA, providing potential valuable strategies for the prevention and treatment of PsA. Further randomized controlled trials are urgently warranted to support the targeted protective mechanisms of probiotics on PsA.},
}
@article {pmid38029135,
year = {2023},
author = {Maingi, FM and Akutse, KS and Ajene, IJ and Omolo, KM and Khamis, FM},
title = {Immunological responses and gut microbial shifts in Phthorimaea absoluta exposed to Metarhizium anisopliae isolates under different temperature regimes.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1258662},
pmid = {38029135},
issn = {1664-302X},
abstract = {The invasive tomato leaf miner, Phthorimaea absoluta, is conventionally controlled through chemical insecticides. However, the rise of insecticide resistance has necessitated sustainable and eco-friendly alternatives. Entomopathogenic fungi (EPF) have shown potential due to their ability to overcome resistance and have minimal impact on non-target organisms. Despite this potential, the precise physiological mechanisms by which EPF acts on insect pests remain poorly understood. To attain a comprehensive understanding of the complex physiological processes that drive the successful control of P. absoluta adults through EPF, we investigated the impacts of different Metarhizium anisopliae isolates (ICIPE 665, ICIPE 20, ICIPE 18) on the pest's survival, cellular immune responses, and gut microbiota under varying temperatures. The study unveiled that ICIPE 18 caused the highest mortality rate among P. absoluta moths, while ICIPE 20 exhibited the highest significant reduction in total hemocyte counts after 10 days at 25°C. Moreover, both isolates elicited notable shifts in P. absoluta's gut microbiota. Our findings revealed that ICIPE 18 and ICIPE 20 compromised the pest's defense and physiological functions, demonstrating their potential as biocontrol agents against P. absoluta in tomato production systems.},
}
@article {pmid38029134,
year = {2023},
author = {Lartey, I and Benucci, GMN and Marsh, TL and Bonito, GM and Melakeberhan, H},
title = {Characterizing microbial communities associated with northern root-knot nematode (Meloidogyne hapla) occurrence and soil health.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1267008},
pmid = {38029134},
issn = {1664-302X},
abstract = {The northern root-knot nematode (Meloidogyne hapla) causes extensive damage to agricultural crops globally. In addition, M. hapla populations with no known genetic or morphological differences exhibit parasitic variability (PV) or reproductive potential based on soil type. However, why M. hapla populations from mineral soil with degraded soil health conditions have a higher PV than populations from muck soil is unknown. To improve our understanding of soil bio-physicochemical conditions in the environment where M. hapla populations exhibited PV, this study characterized the soil microbial community and core- and indicator-species structure associated with M. hapla occurrence and soil health conditions in 15 Michigan mineral and muck vegetable production fields. Bacterial and fungal communities in soils from where nematodes were isolated were characterized with high throughput sequencing of 16S and internal transcribed spacer (ITS) rDNA. Our results showed that M. hapla-infested, as well as disturbed and degraded muck fields, had lower bacterial diversity (observed richness and Shannon) compared to corresponding mineral soil fields or non-infested mineral fields. Bacterial and fungal community abundance varied by soil group, soil health conditions, and/or M. hapla occurrence. A core microbial community was found to consist of 39 bacterial and 44 fungal sub-operational taxonomic units (OTUs) across all fields. In addition, 25 bacteria were resolved as indicator OTUs associated with M. hapla presence or absence, and 1,065 bacteria as indicator OTUs associated with soil health conditions. Out of the 1,065 bacterial OTUs, 73.9% indicated stable soil health, 8.4% disturbed, and 0.4% degraded condition; no indicators were common to the three categories. Collectively, these results provide a foundation for an in-depth understanding of the environment where M. hapla exists and conditions associated with parasitic variability.},
}
@article {pmid38029126,
year = {2023},
author = {Shah, T and Hou, Y and Jiang, J and Shah, Z and Wang, Y and Li, Q and Xu, X and Wang, Y and Wang, B and Xia, X},
title = {Comparative analysis of the intestinal microbiome in Rattus norvegicus from different geographies.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1283453},
pmid = {38029126},
issn = {1664-302X},
abstract = {Rat species Rattus norvegicus, also known as the brown street rat, is the most abundant mammal after humans in urban areas, where they co-exist with humans and domestic animals. The reservoir role of R. norvegicus of zoonotic pathogens in cities among rodent-borne diseases that could endanger the lives of humans and other mammals. Therefore, understanding the normal microbiome of R. norvegicus is crucial for understanding and preventing zoonotic pathogen transmission to humans and animals. We investigated the intestinal microbiome of free-living R. norvegicus collected from the Ruili, Nujiang, and Lianhe regions of Yunnan, China, using 16S rRNA gene sequence analysis. Proteobacteria, followed by Firmicutes, and Bacteroidetes were abundant in the intestines of R. norvegicus; however, bacterial compositions varied significantly between samples from different locations. Following a similar trend, Gammaproteobacteria, Bacilli, and Clostridia were among the top bacterial classes in most intestinal samples. The situation differed slightly for the Lianhe and Nujiang samples, although Phyla Bacteroidota and Spirochaetota were most prevalent. The Alpha diversity, Chao1, and Simpson indexes revealed microbial richness among the R. norvegicus samples. A slight variation was observed among the samples collected from Ruili, Nujiang, and Lianhe. At species levels, several opportunistic and zoonotic bacterial pathogens, including Lactococcus garvieae, Uruburuella suis, Bartonella australis, Clostridium perfringens, Streptococcus azizii, Vibrio vulnificus, etc., were revealed in the R. norvegicus intestines, implying the need for a regular survey to monitor and control rodent populations. In conclusion, we explored diverse microbial communities in R. norvegicus intestines captured from different regions. Further, we identified several opportunistic and potential bacterial pathogens, which still need to be tested for their underlying pathogenesis. The findings of our current study should be considered a warning to the health authorities to implement rat control and surveillance strategies globally.},
}
@article {pmid38029121,
year = {2023},
author = {Alvarado-Peña, N and Galeana-Cadena, D and Gómez-García, IA and Mainero, XS and Silva-Herzog, E},
title = {The microbiome and the gut-lung axis in tuberculosis: interplay in the course of disease and treatment.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1237998},
pmid = {38029121},
issn = {1664-302X},
abstract = {Tuberculosis is a chronic infectious disease caused by Mycobacterium tuberculosis (MTB) that remains a significant global health challenge. The extensive use of antibiotics in tuberculosis treatment, disrupts the delicate balance of the microbiota in various organs, including the gastrointestinal and respiratory systems. This gut-lung axis involves dynamic interactions among immune cells, microbiota, and signaling molecules from both organs. The alterations of the microbiome resulting from anti-TB treatment can significantly influence the course of tuberculosis, impacting aspects such as complete healing, reinfection, and relapse. This review aims to provide a comprehensive understanding of the gut-lung axis in the context of tuberculosis, with a specific focus on the impact of anti-TB treatment on the microbiome.},
}
@article {pmid38029119,
year = {2023},
author = {Moore, GG and Chalivendra, S and Mack, BM and Gilbert, MK and Cary, JW and Rajasekaran, K},
title = {Microbiota of maize kernels as influenced by Aspergillus flavus infection in susceptible and resistant inbreds.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1291284},
pmid = {38029119},
issn = {1664-302X},
abstract = {BACKGROUND: Nearly everything on Earth harbors a microbiome. A microbiome is a community of microbes (bacteria, fungi, and viruses) with potential to form complex networks that involve mutualistic and antagonistic interactions. Resident microbiota on/in an organism are determined by the external environment, both biotic and abiotic, and the intrinsic adaptability of each organism. Although the maize microbiome has been characterized, community changes that result from the application of fungal biocontrol strains, such as non-aflatoxigenic Aspergillus flavus, have not.<br><br>METHODS: We silk channel inoculated field-grown maize separately with a non-aflatoxigenic biocontrol strain (K49), a highly toxigenic strain (Tox4), and a combination of both A. flavus strains. Two maize inbreds were treated, A. flavus-susceptible B73 and A. flavus-resistant CML322. We then assessed the impacts of A. flavus introduction on the epibiota and endobiota of their maize kernels.<br><br>RESULTS: We found that the native microbial communities were significantly affected, irrespective of genotype or sampled tissue. Overall, bacteriomes exhibited greater diversity of genera than mycobiomes. The abundance of certain genera was unchanged by treatment, including genera of bacteria (e.g., Enterobacter, Pantoea) and fungi (e.g., Sarocladium, Meyerozyma) that are known to be beneficial, antagonistic, or both on plant growth and health.<br><br>CONCLUSION: Beneficial microbes like Sarocladium that responded well to A. flavus biocontrol strains are expected to enhance biocontrol efficacy, while also displacing/antagonizing harmful microbes.},
}
@article {pmid38029106,
year = {2023},
author = {Ying, ZH and Mao, CL and Xie, W and Yu, CH},
title = {Postbiotics in rheumatoid arthritis: emerging mechanisms and intervention perspectives.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1290015},
pmid = {38029106},
issn = {1664-302X},
abstract = {Rheumatoid arthritis (RA) is a prevalent chronic autoimmune disease that affects individuals of all age groups. Recently, the association between RA and the gut microbiome has led to the investigation of postbiotics as potential therapeutic strategies. Postbiotics refer to inactivated microbial cells, cellular components, or their metabolites that are specifically intended for the microbiota. Postbiotics not only profoundly influence the occurrence and development of RA, but they also mediate various inflammatory pathways, immune processes, and bone metabolism. Although they offer a variety of mechanisms and may even be superior to more conventional "biotics" such as probiotics and prebiotics, research on their efficacy and clinical significance in RA with disruptions to the intestinal microbiota remains limited. In this review, we provide an overview of the concept of postbiotics and summarize the current knowledge regarding postbiotics and their potential use in RA therapy. Postbiotics show potential as a viable adjunctive therapy option for RA.},
}
@article {pmid38029089,
year = {2023},
author = {Krishnamurthy, HK and Pereira, M and Bosco, J and George, J and Jayaraman, V and Krishna, K and Wang, T and Bei, K and Rajasekaran, JJ},
title = {Gut commensals and their metabolites in health and disease.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1244293},
pmid = {38029089},
issn = {1664-302X},
abstract = {PURPOSE OF REVIEW: This review comprehensively discusses the role of the gut microbiome and its metabolites in health and disease and sheds light on the importance of a holistic approach in assessing the gut.<br><br>RECENT FINDINGS: The gut microbiome consisting of the bacteriome, mycobiome, archaeome, and virome has a profound effect on human health. Gut dysbiosis which is characterized by perturbations in the microbial population not only results in gastrointestinal (GI) symptoms or conditions but can also give rise to extra-GI manifestations. Gut microorganisms also produce metabolites (short-chain fatty acids, trimethylamine, hydrogen sulfide, methane, and so on) that are important for several interkingdom microbial interactions and functions. They also participate in various host metabolic processes. An alteration in the microbial species can affect their respective metabolite concentrations which can have serious health implications. Effective assessment of the gut microbiome and its metabolites is crucial as it can provide insights into one's overall health.<br><br>SUMMARY: Emerging evidence highlights the role of the gut microbiome and its metabolites in health and disease. As it is implicated in GI as well as extra-GI symptoms, the gut microbiome plays a crucial role in the overall well-being of the host. Effective assessment of the gut microbiome may provide insights into one's health status leading to more holistic care.},
}
@article {pmid37539715,
year = {2023},
author = {Berenson, CS and Lashner, B and Korman, LY and Hohmann, E and Deshpande, A and Louie, TJ and Sims, M and Pardi, D and Kraft, CS and Wang, EEL and Cohen, SH and Feuerstadt, P and Oneto, C and Misra, B and Pullman, J and De, A and Memisoglu, A and Lombardi, DA and Hasson, BR and McGovern, BH and von Moltke, L and Lee, CH},
title = {Prevalence of Comorbid Factors in Patients With Recurrent Clostridioides difficile Infection in ECOSPOR III, a Randomized Trial of an Oral Microbiota-Based Therapeutic.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {77},
number = {11},
pages = {1504-1510},
doi = {10.1093/cid/ciad448},
pmid = {37539715},
issn = {1537-6591},
support = {//Seres Therapeutics/ ; },
abstract = {BACKGROUND: Although comorbidities are risk factors for recurrent Clostridioides difficile infection (rCDI), many clinical trials exclude patients with medical conditions such as malignancy or immunosuppression. In a phase 3, double-blind, placebo-controlled, randomized trial (ECOSPOR III), fecal microbiota spores, live (VOWST, Seres Therapeutics; hereafter "VOS," formerly SER-109), an oral microbiota therapeutic, significantly reduced the risk of rCDI at week 8. We evaluated the efficacy of VOS compared with placebo in patients with comorbidities and other risk factors for rCDI.<br><br>METHODS: Adults with rCDI were randomized to receive VOS or placebo (4 capsules daily for 3 days) following standard-of-care antibiotics. In this post hoc analysis, the rate of rCDI through week 8 was assessed in VOS-treated participants compared with placebo for subgroups including (i) Charlson comorbidity index (CCI) score category (0, 1-2, 3-4, &#x2265;5); (ii) baseline creatinine clearance (<30, 30-50, >50 to 80, or >80 mL/minute); (iii) number of CDI episodes, inclusive of the qualifying episode (3 and &#x2265;4); (iv) exposure to non-CDI-targeted antibiotics after dosing; and (v) acid-suppressing medication use at baseline.<br><br>RESULTS: Of 281 participants screened, 182 were randomized (59.9% female; mean age, 65.5 years). Comorbidities were common with a mean overall baseline age-adjusted CCI score of 4.1 (4.1 in the VOS arm and 4.2 in the placebo arm). Across all subgroups analyzed, VOS-treated participants had a lower relative risk of recurrence compared with placebo.<br><br>CONCLUSIONS: In this post hoc analysis, VOS reduced the risk of rCDI compared with placebo, regardless of baseline characteristics, concomitant medications, or comorbidities.},
}
@article {pmid38029086,
year = {2023},
author = {Yang, J and He, Y and Liao, X and Hu, J and Li, K},
title = {Does postoperative pulmonary infection correlate with intestinal flora following gastric cancer surgery? - a nested case-control study.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1267750},
doi = {10.3389/fmicb.2023.1267750},
pmid = {38029086},
issn = {1664-302X},
abstract = {INTRODUCTION: The primary objective of this study was to investigate the potential correlation between gut microbes and postoperative pulmonary infection in gastric cancer patients. Additionally, we aimed to deduce the mechanism of differential functional genes in disease progression to gain a better understanding of the underlying pathophysiology.<br><br>METHODS: A nested case-control study design was utilized to enroll patients with gastric cancer scheduled for surgery at West China Hospital of Sichuan University. Patients were categorized into two groups, namely, the pulmonary infection group and the control group, based on the development of postoperative pulmonary infection. Both groups were subjected to identical perioperative management protocols. Fecal samples were collected 24&#x2009;h postoperatively and upon pulmonary infection diagnosis, along with matched controls. The collected samples were subjected to 16S rDNA and metagenomic analyses, and clinical data and blood samples were obtained for further analysis.<br><br>RESULTS: A total of 180 fecal specimens were collected from 30 patients in both the pulmonary infection and control groups for 16S rDNA analysis, and 3 fecal samples from each group were selected for metagenomic analysis. The study revealed significant alterations in the functional genes of the intestinal microbiome in patients with postoperative pulmonary infection in gastric cancer, primarily involving Klebsiella, Enterobacter, Ruminococcus, and Collinsella. During postoperative pulmonary infection, gut flora and inflammatory factors were found to be associated with the lipopolysaccharide synthesis pathway and short-chain fatty acid (SCFA) synthesis pathway.<br><br>DISCUSSION: The study identified enriched populations of Klebsiella, Escherella, and intestinal bacteria during pulmonary infection following gastric cancer surgery. These bacteria were found to regulate the lipopolysaccharide synthesis pathway, contributing to the initiation and progression of pulmonary infections. Inflammation modulation in patients with postoperative pulmonary infection may be mediated by short-chain fatty acids. The study also revealed that SCFA synthesis pathways were disrupted, affecting inflammation-related immunosuppression pathways. By controlling and maintaining intestinal barrier function, SCFAs may potentially reduce the occurrence of pulmonary infections after gastric cancer surgery. These findings suggest that targeting the gut microbiome and SCFA synthesis pathways may be a promising approach for preventing postoperative pulmonary infections in gastric cancer patients.},
}
@article {pmid38029085,
year = {2023},
author = {Cronin, P and McCarthy, S and Hurley, C and Ghosh, TS and Cooney, JC and Tobin, AM and Murphy, M and O'Connor, EM and Shanahan, F and O'Toole, PW},
title = {Comparative diet-gut microbiome analysis in Crohn's disease and Hidradenitis suppurativa.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1289374},
doi = {10.3389/fmicb.2023.1289374},
pmid = {38029085},
issn = {1664-302X},
abstract = {INTRODUCTION: The chronic inflammatory skin disease Hidradenitis suppurativa (HS) is strongly associated with Crohn's Disease (CD). HS and CD share clinical similarities and similar inflammatory pathways are upregulated in both conditions. Increased prevalence of inflammatory disease in industrialised nations has been linked to the Western diet. However, gut microbiota composition and diet interaction have not been compared in HS and CD.<br><br>METHODS: Here we compared the fecal microbiota (16S rRNA gene amplicon sequencing) and habitual diet of previously reported subjects with HS (n&#x2009;=&#x2009;55), patients with CD (n&#x2009;=&#x2009;102) and controls (n&#x2009;=&#x2009;95).<br><br>RESULTS AND DISCUSSION: Patients with HS consumed a Western diet similar to patients with CD. Meanwhile, habitual diet in HS and CD was significantly different to controls. Previously, we detected differences in microbiota composition among patients with HS from that of controls. We now show that 40% of patients with HS had a microbiota configuration similar to that of CD, characterised by the enrichment of pathogenic genera (Enterococcus, Veillonella and Escherichia_Shigella) and the depletion of putatively beneficial genera (Faecalibacterium). The remaining 60% of patients with HS harboured a normal microbiota similar to that of controls. Antibiotics, which are commonly used to treat HS, were identified as a co-varying with differences in microbiota composition. We examined the levels of several inflammatory markers highlighting that growth-arrest specific 6 (Gas6), which has anti-inflammatory potential, were significantly lower in the 40% of patients with HS who had a CD microbiota configuration. Levels of the pro-inflammatory cytokine IL-12, which is a modulator of intestinal inflammation in CD, were negatively correlated with the abundance of health-associated genera in patients with HS. In conclusion, the fecal microbiota may help identify patients with HS who are at greater risk for development of CD.},
}
@article {pmid38029083,
year = {2023},
author = {Khairunisa, BH and Heryakusuma, C and Ike, K and Mukhopadhyay, B and Susanti, D},
title = {Evolving understanding of rumen methanogen ecophysiology.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1296008},
doi = {10.3389/fmicb.2023.1296008},
pmid = {38029083},
issn = {1664-302X},
abstract = {Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.},
}
@article {pmid38029079,
year = {2023},
author = {Koepper, S and Clark, KF and McClure, JT and Revie, CW and Stryhn, H and Thakur, KK},
title = {Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1245818},
doi = {10.3389/fmicb.2023.1245818},
pmid = {38029079},
issn = {1664-302X},
abstract = {The shell microbial community of lobsters-a key factor in the development of epizootic shell disease (ESD)-is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state.},
}
@article {pmid38029074,
year = {2023},
author = {Frąszczak, K and Barczyński, B and Siwiec, R and Kondracka, A and Malm, A and Kotarski, J and Witt, E and Korona-Głowniak, I},
title = {The analysis of Lactobacillus spp. distribution in the vaginal microbiota of Polish women with abnormal Pap smear result.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1257587},
doi = {10.3389/fmicb.2023.1257587},
pmid = {38029074},
issn = {1664-302X},
abstract = {INTRODUCTION: A healthy vaginal microbiota is represented mainly by Lactobacillus spp. and plays a vital role in maintaining the functional balance in the vaginal environment. Scientists have drawn attention to possible correlations between the vaginal microbiome and gynecological neoplasms. Several recent studies have shown a potential link between the vaginal microbiome and the risk of developing cervical cancer from human papillomavirus (HPV) infection. This study aimed to compare the prevalence and abundance of various lactic acid bacteria species (LABs) in vaginal swabs from healthy controls and patients with abnormal Pap smear results.<br><br>METHODS: The study included 100 women (79 patients with abnormal cervical Pap smear results and 21 controls) from whom vaginal swabs were collected. Real-time quantitative PCR was used to determine seven lactic acid bacteria (LAB) species and their quantities.<br><br>RESULTS: Most patients were colonized by two Lactobacillus species, primarily Lactobacillus gasseri (93%) and L. crispatus (83%). Patient age and place of residence were associated with the diversity of LAB in the vaginal microbiota. The abundance of L. delbrueckii in the vaginal microbiota increased, whereas the abundance of L. gasseri abundance decreased, with patient age. Lactobacillus acidophilus and Limosilactobacillus fermentum were significantly more often detected in patients living in rural versus urban areas. Statistical analysis did not show any significant differences in LAB between groups of patients with various changes on smear tests.<br><br>DISCUSSION: The degree of dysplastic changes in the endothelium or the presence of a group of atypical cervical stratified epithelial cells was not associated with significant changes in the studied vaginal bacteria.},
}
@article {pmid38029073,
year = {2023},
author = {Xie, Q and Hu, B},
title = {Effects of gut microbiota on prostatic cancer: a two-sample Mendelian randomization study.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1250369},
doi = {10.3389/fmicb.2023.1250369},
pmid = {38029073},
issn = {1664-302X},
abstract = {AIM: Recent observational and small-sample case-control studies have shown a relationship between gut microbiota composition and prostatic cancer (PCa). Nevertheless, the causal association between gut microbiota and PCa is still unclear. Herein, we used the Mendelian randomization (MR) method to explore the potential causal relationship between gut microbiota and PCa.<br><br>METHODS: In this two-sample MR study, data were extracted from the summary statistics of gut microbiota from the largest available genome-wide association study meta-analysis conducted by the MiBioGen consortium (n = 14,306) and the Dutch Microbiome Project (n = 8,208). Summary statistics for PCa were obtained from the FinnGen consortium release data (n = 95,213). Inverse variance weighted (IVW), MR-Egger, strength test (F), and MR-PRESSO were used to examine the potential causal association between gut microbiota and PCa. Cochran's Q statistics were used to quantify the heterogeneity of instrumental variables.<br><br>RESULTS: IVW estimates suggested that the relative abundance of Akkermansia muciniphila (odds ratio [OR] = 0.7926, 95% confidence interval [CI]: 0.6655-0.9440) and Bacteroides salyersiae (OR = 0.9023, 95% CI: 0.8262-0.9853) were negatively associated with the odds of PCa, while that of Eubacterium biforme (OR = 1.1629, 95% CI: 1.0110-1.3376) was positively associated with the odds of PCa. In addition, we explored these relationships among patients without other cancers and similarly found that the relative abundance of Akkermansia muciniphila, Bacteroides salyersiae, and Eubacterium biforme were linked to PCa (all P < 0.05).<br><br>CONCLUSION: Gut microbiota potentially influenced the occurrence of PCa. Our findings may provide some new ideas for researching the methods of PCa prevention. In addition, further studies are needed to explore the causal association and specific underlying mechanisms between gut microbiota and PCa.},
}
@article {pmid38029072,
year = {2023},
author = {Dreyer, A and Lenz, C and Groß, U and Bohne, W and Zautner, AE},
title = {Characterization of Campylobacter jejuni proteome profiles in co-incubation scenarios.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1247211},
doi = {10.3389/fmicb.2023.1247211},
pmid = {38029072},
issn = {1664-302X},
abstract = {In dynamic microbial ecosystems, bacterial communication is a relevant mechanism for interactions between different microbial species. When C. jejuni resides in the intestine of either avian or human hosts, it is exposed to diverse bacteria from the microbiome. This study aimed to reveal the influence of co-incubation with Enterococcus faecalis, Enterococcus faecium, or Staphylococcus aureus on the proteome of C. jejuni 81-176 using data-independent-acquisition mass spectrometry (DIA-MS). We compared the proteome profiles during co-incubation with the proteome profile in response to the bile acid deoxycholate (DCA) and investigated the impact of DCA on proteomic changes during co-incubation, as C. jejuni is exposed to both factors during colonization. We identified 1,375 proteins by DIA-MS, which is notably high, approaching the theoretical maximum of 1,645 proteins. S. aureus had the highest impact on the proteome of C. jejuni with 215 up-regulated and 230 down-regulated proteins. However, these numbers are still markedly lower than the 526 up-regulated and 516 down-regulated proteins during DCA exposure. We identified a subset of 54 significantly differentially expressed proteins that are shared after co-incubation with all three microbial species. These proteins were indicative of a common co-incubation response of C. jejuni. This common proteomic response partly overlapped with the DCA response; however, several proteins were specific to the co-incubation response. In the co-incubation experiment, we identified three membrane-interactive proteins among the top 20 up-regulated proteins. This finding suggests that the presence of other bacteria may contribute to increased adherence, e.g., to other bacteria but eventually also epithelial cells or abiotic surfaces. Furthermore, a conjugative transfer regulon protein was typically up-expressed during co-incubation. Exposure to both, co-incubation and DCA, demonstrated that the two stressors influenced each other, resulting in a unique synergistic proteomic response that differed from the response to each stimulus alone. Data are available via ProteomeXchange with identifier PXD046477.},
}
@article {pmid38028745,
year = {2023},
author = {Kural-Rendon, C and Ford, NE and Wagner, MR},
title = {Interactions with fungi vary among Tripsacum dactyloides genotypes from across a precipitation gradient.},
journal = {AoB PLANTS},
volume = {15},
number = {6},
pages = {plad072},
doi = {10.1093/aobpla/plad072},
pmid = {38028745},
issn = {2041-2851},
abstract = {Plant-associated microbes, specifically fungal endophytes, augment the ability of many grasses to adapt to extreme environmental conditions. Tripsacum dactyloides (Eastern gamagrass) is a perennial, drought-tolerant grass native to the tallgrass prairies of the central USA. The extent to which the microbiome of T. dactyloides contributes to its drought tolerance is unknown. Ninety-seven genotypes of T. dactyloides were collected from native populations across an east-west precipitation gradient in Kansas, Oklahoma and Texas, and then grown together in a common garden for over 20 years. Root and leaf samples were visually examined for fungal density. Because fungal endophytes confer drought-tolerant capabilities to their host plants, we expected to find higher densities of fungal endophytes in plants from western, drier regions, compared to plants from eastern, wetter regions. Results confirmed a negative correlation between endophyte densities in roots and precipitation at the genotype's original location (r = -0.21 P = 0.04). Our analyses reveal that the host genotype's origin along the precipitation gradient predicts the absolute abundance of symbionts in the root, but not the relative abundances of particular organisms or the overall community composition. Overall, these results demonstrate that genetic variation for plant-microbe interactions can reflect historical environment, and reinforce the importance of considering plant genotype in conservation and restoration work in tallgrass prairie ecosystems.},
}
@article {pmid38028558,
year = {2023},
author = {O'Shaughnessy, R and Common, J and Gutowska-Owsiak, D},
title = {Editorial: Novel aspects of the immunological and structural barrier of the epidermis.},
journal = {Frontiers in molecular biosciences},
volume = {10},
number = {},
pages = {1324920},
doi = {10.3389/fmolb.2023.1324920},
pmid = {38028558},
issn = {2296-889X},
}
@article {pmid38028206,
year = {2023},
author = {Chai, J and Long, X and Wu, P and Wang, J and Wu, X and Tu, Z and Wei, M and Guo, Z and Zhang, T and Chen, L},
title = {Lactobacillus sp. participated in the adaptation of Rongchang piglets to cold stress.},
journal = {Veterinarni medicina},
volume = {68},
number = {10},
pages = {392-402},
doi = {10.17221/54/2023-VETMED},
pmid = {38028206},
issn = {0375-8427},
abstract = {Rongchang piglets were easily induced to cold stress and diarrhoea in the winter when raised in an open hog house. However, they also gradually recovered under mid-cold stress. Other studies have suggested gut microbiome might be involved in the host energy metabolism to relieve stress. To study how to adapt Rongchang piglets to cold stress by gut microbiome, thirty Rongchang piglets were randomly divided into a mild cold stress group and a control group for 30 consecutive days. The findings revealed that the piglets had low growth performance and a high diarrhoea rate and mortality rate during the first half of the cold treatment, but subsequently stabilised. The level of cortisol (COR) also displayed a similar trend. In the mild cold stress group, the relative abundance of Muribaculaceae significantly increased on day 15, and the predominant bacterial on day 30 was Lactobacillus sp. Our results indicated that the Rongchang piglet's production performance and health were impaired at the start of the mild cold stress. However, as time passed, the body could progressively adapt to the low temperature, and Lactobacillus sp. participated in this process. This study provides new insight into how to alleviate health damage caused by cold stress.},
}
@article {pmid38028014,
year = {2023},
author = {Liu, W and Peng, L and Chen, L and Wan, J and Lou, S and Yang, T and Shen, Z},
title = {Skin microbial dysbiosis is a characteristic of systemic drug-related intertriginous and flexural exanthema-like lesions induced by EGFR inhibitor.},
journal = {Heliyon},
volume = {9},
number = {11},
pages = {e21690},
doi = {10.1016/j.heliyon.2023.e21690},
pmid = {38028014},
issn = {2405-8440},
abstract = {OBJECTIVES: To investigate the characteristics of the skin microbiome in severe afatinib-induced skin toxicity.<br><br>METHODS: Body site-matched skin surface samples were collected from the lesions on seven flexural sites of one lung cancer (Patient 1) with serious systemic drug-related intertriginous and flexural exanthema (SDRIFE)-like toxicity induced by EGFR-TKI and three healthy age/sex matched controls for whole metagenomics sequencing analysis. Lung cancer Patient 1 and Patient 2 were prescribed minocycline and followed up.<br><br>RESULTS: In SDRIFE-like toxicities induced by afatinib, lesion microbiota richness (ACE and Chao1 index: p&#xa0;<&#xa0;0.001) and diversity (Shannon's and Simpson's diversity indices: p&#xa0;<&#xa0;0.01) were reduced. Similarly, the beta diversity analysis (R&#xa0;=&#xa0;1, p&#xa0;=&#xa0;0.002 for ANOSIM) showed that the apparent difference in the microbiota composition was statistically significant. The microbial taxa composition in the patient showed an increased abundance of pathogenic bacteria and a decreased abundance of commensal bacteria. LEfSe analysis identified strong bacterial pathogenicity in the patient, while healthy controls exhibited enrichment in several pathways that are beneficial for skin commensal bacteria and skin physiology, including key amino acid metabolism, energy/lipid/glycan biosynthesis/metabolism, and cofactors/vitamins biosynthesis. Ultimately, the patients experienced significant improvement with minocycline.<br><br>CONCLUSION: Microbial dysbiosis is a characteristic of severe SDRIFE-like toxicity induced by afatinib.},
}
@article {pmid38027512,
year = {2023},
author = {Barton, JR and Londregan, AK and Alexander, TD and Entezari, AA and Covarrubias, M and Waldman, SA},
title = {Enteroendocrine cell regulation of the gut-brain axis.},
journal = {Frontiers in neuroscience},
volume = {17},
number = {},
pages = {1272955},
doi = {10.3389/fnins.2023.1272955},
pmid = {38027512},
issn = {1662-4548},
abstract = {Enteroendocrine cells (EECs) are an essential interface between the gut and brain that communicate signals about nutrients, pain, and even information from our microbiome. EECs are hormone-producing cells expressed throughout the gastrointestinal epithelium and have been leveraged by pharmaceuticals like semaglutide (Ozempic, Wegovy), terzepatide (Mounjaro), and retatrutide (Phase 2) for diabetes and weight control, and linaclotide (Linzess) to treat irritable bowel syndrome (IBS) and visceral pain. This review focuses on role of intestinal EECs to communicate signals from the gut lumen to the brain. Canonically, EECs communicate information about the intestinal environment through a variety of hormones, dividing EECs into separate classes based on the hormone each cell type secretes. Recent studies have revealed more diverse hormone profiles and communication modalities for EECs including direct synaptic communication with peripheral neurons. EECs known as neuropod cells rapidly relay signals from gut to brain via a direct communication with vagal and primary sensory neurons. Further, this review discusses the complex information processing machinery within EECs, including receptors that transduce intraluminal signals and the ion channel complement that govern initiation and propagation of these signals. Deeper understanding of EEC physiology is necessary to safely treat devastating and pervasive conditions like irritable bowel syndrome and obesity.},
}
@article {pmid38027267,
year = {2023},
author = {Francis, D and Chawla, A and LaComb, JF and Markarian, K and Robertson, CE and Frank, DN and Gathungu, GN},
title = {Gastroesophageal reflux and PPI exposure alter gut microbiota in very young infants.},
journal = {Frontiers in pediatrics},
volume = {11},
number = {},
pages = {1254329},
doi = {10.3389/fped.2023.1254329},
pmid = {38027267},
issn = {2296-2360},
abstract = {IMPORTANCE: Infants with symptomatic Gastroesophageal reflux are treated with pharmacological therapy that includes proton pump inhibitors (PPI) with clinical improvement. The alterations to gut microbiome profiles in comparison to infants without reflux is not known.<br><br>OBJECTIVE: To determine the effect of PPI therapy on gut bacterial richness, diversity, and proportions of specific taxa in infants when compared to infants not exposed to acid suppressive therapy.<br><br>This cohort study was conducted at the Stony Brook Hospital in Stony Brook, NY between February 2016, and June 2019. Infants meeting inclusion criteria were enrolled in a consecutive fashion.<br><br>RESULTS: A total of 76 Infants were recruited and 60 were enrolled in the study, Twenty nine infants met clinical criteria for reflux and were treated with PPI therapy: median [IQR] gestation: 38.0 weeks [34.7-39.6 weeks]; median [IQR] birthweight: 2.95&#x2005;Kg [2.2-3.4]; 14 [46.7%] male) and 29 infant were healthy controls median [IQR] gestation: 39.1 weeks [38-40 weeks]; median [IQR] birthweight: 3.3&#x2005;Kg [2.2-3.4]; 17 [58.6%] male); 58 stool samples from 58 infants were analyzed. There were differences in Shannon diversity between the reflux and control groups. The reflux group that was exposed to PPI therapy had increased relative abundance of a diverse set of genera belonging to the phylum Firmicutes. On the other hand, the control group microbiota was dominated by Bifidobacterium, and a comparatively lower level of enrichment and abundance of microbial taxa was observed in this group of infants.<br><br>CONCLUSIONS AND RELEVANCE: We observed significant differences in both &#x3b1;- and &#x3b2;-diversity of the microbiome, when the two groups of infants were compared. The microbiome in the reflux group had more bacterial taxa and the duration of PPIs exposure was clearly associated with the diversity and abundance of gut microbes. These findings suggest that PPI exposure among infants results in early enrichment of the intestinal microbiome.},
}
@article {pmid38027226,
year = {2023},
author = {Tang, J and Han, Y and Pei, L and Gu, W and Qiu, R and Wang, S and Ma, Q and Gan, Y and Tang, M},
title = {Comparative analysis of the rhizosphere microbiome and medicinally active ingredients of Atractylodes lancea from different geographical origins.},
journal = {Open life sciences},
volume = {18},
number = {1},
pages = {20220769},
doi = {10.1515/biol-2022-0769},
pmid = {38027226},
issn = {2391-5412},
abstract = {This study aimed to explore the important role of the rhizosphere microbiome in the quality of Atractylodes lancea (Thunb.) DC. (A. lancea). The rhizosphere microbial community of A. lancea at two sampling sites was studied using metagenomic technology. The results of α-diversity analysis showed that the rhizosphere microbial richness and diversity were higher in the Maoshan area. The higher abundance of core microorganisms of the rhizosphere, especially Penicillium and Streptomyces, in the Maoshan area compared with those in the Yingshan area might be an important factor affecting the yield of A. lancea. Redundancy analysis illustrated that the available phosphorus had a significant effect on the rhizosphere microbial community structure of A. lancea. We also showed that the plant-microbe and microbe-microbe interactions were closer in the Maoshan area than in the Yingshan area, and Streptomyces were the main contributors to the potential functional difference between the two regions. A. lancea in the Maoshan area had a high content of atractylodin and atractylon, which might be related to the enhanced abundance of Streptomyces, Candidatus-Solibacter, and Frankia. Taken together, this study provided theoretical insights into the interaction between medicinal plants and the rhizosphere microbiome and provides a valuable reference for studying beneficial microbes of A. lancea.},
}
@article {pmid38027221,
year = {2023},
author = {Nie, D and Li, C and Zhang, Y},
title = {PitNETs and the gut microbiota: potential connections, future directions.},
journal = {Frontiers in endocrinology},
volume = {14},
number = {},
pages = {1255911},
doi = {10.3389/fendo.2023.1255911},
pmid = {38027221},
issn = {1664-2392},
abstract = {The role of the gut microbiome has been widely discussed in numerous works of literature. The biggest concern is the association of the gut microbiome with the central nervous system through the microbiome-brain-gut axis in the past ten years. As more and more research has been done on the relationship between the disease of the central nervous system and gut microbes. This fact is being revealed that gut microbes seem to play an important role from the onset and progression of the disease to clinical symptoms, and new treatments. As a special tumor of the central nervous system, pituitary neuroendocrine tumors (PitNETs)are closely related to metabolism, endocrinology, and immunity. These factors are the vectors through which intestinal microbes interact with the central nervous system. However, little is known about the effects of gut microbes on the PitNET. In this review, the relationship of gut microbiota in PitNETs is introduced, the potential effects of the gut-brain axis in this relationship are analyzed, and future research directions are presented.},
}
@article {pmid38027173,
year = {2023},
author = {Aghajanova, L and Altmäe, S and Sokalska, A},
title = {Editorial: Uterine factors associated with fertility impairment.},
journal = {Frontiers in endocrinology},
volume = {14},
number = {},
pages = {1307237},
doi = {10.3389/fendo.2023.1307237},
pmid = {38027173},
issn = {1664-2392},
}
@article {pmid38027009,
year = {2023},
author = {Feng, Y and Xu, D},
title = {Short-chain fatty acids are potential goalkeepers of atherosclerosis.},
journal = {Frontiers in pharmacology},
volume = {14},
number = {},
pages = {1271001},
doi = {10.3389/fphar.2023.1271001},
pmid = {38027009},
issn = {1663-9812},
abstract = {Short-chain fatty acids (SCFAs) are metabolites produced by gut bacteria and play a crucial role in various inflammatory diseases. Increasing evidence suggests that SCFAs can improve the occurrence and progression of atherosclerosis. However, the molecular mechanisms through which SCFAs regulate the development of atherosclerosis have not been fully elucidated. This review provides an overview of the research progress on SCFAs regarding their impact on the risk factors and pathogenesis associated with atherosclerosis, with a specific focus on their interactions with the endothelium and immune cells. These interactions encompass the inflammation and oxidative stress of endothelial cells, the migration of monocytes/macrophages, the lipid metabolism of macrophages, the proliferation and migration of smooth muscle cells, and the proliferation and differentiation of Treg cells. Nevertheless, the current body of research is insufficient to comprehensively understand the full spectrum of SCFAs' mechanisms of action. Therefore, further in-depth investigations are imperative to establish a solid theoretical foundation for the development of clinical therapeutics in this context.},
}
@article {pmid38026977,
year = {2023},
author = {Zhou, J and Liu, J and Lin, Q and Shi, L and Zeng, Z and Guan, L and Ma, Y and Zeng, Y and Zhong, S and Xu, L},
title = {Characteristics of the gut microbiome and metabolic profile in elderly patients with sarcopenia.},
journal = {Frontiers in pharmacology},
volume = {14},
number = {},
pages = {1279448},
doi = {10.3389/fphar.2023.1279448},
pmid = {38026977},
issn = {1663-9812},
abstract = {Introduction: There is growing evidence of research indicating that the gut microbiota is involved in the development of sarcopenia. Nevertheless, there exists a notable deficiency in comprehension concerning the connection between irregularities in the intestinal microbiome and metabolic processes in older individuals suffering from sarcopenia. Methods: To analyze fecal samples obtained from a cohort of 30 older patients diagnosed with sarcopenia as well as 30 older patients without sarcopenia, this study employed 16S rDNA sequencing and liquid chromatography-mass spectrometry (LC-MS)-based non-targeted metabolomics profiling techniques. Results: As a result, we found that 29 genera and 172 metabolites were significantly altered in the sarcopenic patients. Among them, Blautia, Lachnospiraceae_unclassified, and Subdoligranulum were the bacteria with a potential diagnostic value for sarcopenia diagnosis. Correlation analysis between clinical indices and these gut bacteria suggested that the IL-6 level was negatively correlated with Blautia. Function prediction analysis demonstrated that 17 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways differ significantly between sarcopenic and non-sarcopenic patients. The primary classes of metabolites identified in the study included lipids and lipid-like molecules, organic acids and derivatives, and organoheterocyclic compounds. KEGG enrichment analysis showed that purine metabolism, arginine and proline metabolism, alanine, aspartate, and glutamate metabolism, butanoate metabolism, and histidine metabolism may contribute to the development of sarcopenia. The correlation study on gut microbiota and metabolites found that Lachnospiraceae_unclassified was positively associated with seven metabolites that were more abundant in the non-sarcopenia group and negatively correlated with three metabolites that were more abundant in the sarcopenia group. In addition, Subdoligranulum was positively correlated with seven metabolites that were lacking in sarcopenia and negatively correlated with two metabolites that were enriching in sarcopenia. Moreover, Blautia was positively associated with xanthosine. Discussion: We conducted a study on the intestinal microbiota and metabolic profile of elderly individuals with sarcopenia, offering a comprehensive analysis of the overall ecosystem. Through this investigation, we were able to validate existing research on the gut-muscle axis and further investigate potential pathogenic processes and treatment options for sarcopenia.},
}
@article {pmid38026796,
year = {2023},
author = {Pohlin, F and Frei, C and Meyer, LCR and Roch, FF and Quijada, NM and Conrady, B and Neubauer, V and Hofmeyr, M and Cooper, D and Stalder, G and Wetzels, SU},
title = {Capture and transport of white rhinoceroses (Ceratotherium simum) cause shifts in their fecal microbiota composition towards dysbiosis.},
journal = {Conservation physiology},
volume = {11},
number = {1},
pages = {coad089},
doi = {10.1093/conphys/coad089},
pmid = {38026796},
issn = {2051-1434},
abstract = {Translocations of Rhinocerotidae are commonly performed for conservation purposes but expose the animals to a variety of stressors (e.g. prolonged fasting, confinement, novel environment, etc.). Stress may change the composition of gut microbiota, which can impact animal health and welfare. White rhinoceroses in particular can develop anorexia, diarrhea and enterocolitis after translocation. The aim of this study was to investigate the associations of age, sex and translocation on the rhinoceros' fecal bacterial microbiota composition. fecal samples were collected from rhinoceroses at capture (n = 16) and after a >30-hour road transport (n = 7). DNA was isolated from these samples and submitted for 16S rRNA V3-V4 phylotyping. Alpha diversity indices of the rhinoceros' fecal microbiota composition of different age, sex and before and after transport were compared using non-parametric statistical tests and beta diversity indices using Permutational Multivariate Analysis Of Variance (PERMANOVA). Resulting P-values were alpha-corrected (Padj.). Alpha and beta diversity did not differ between rhinoceroses of different age and sex. However, there was a significant difference in beta diversity between fecal samples collected from adult animals at capture and after transport. The most abundant bacterial phyla in samples collected at capture were Firmicutes and Bacteroidetes (85.76%), represented by Lachnospiraceae, Ruminococcaceae and Prevotellaceae families. The phyla Proteobacteria (Padj. = 0.009) and Actinobacteria (Padj. = 0.012), amongst others, increased in relative abundance from capture to after transport encompassing potentially pathogenic bacterial families such as Enterobacteriaceae (Padj. = 0.018) and Pseudomonadaceae (Padj. = 0.022). Important commensals such as Spirochaetes (Padj. = 0.009), Fibrobacteres (Padj. = 0.018) and Lachnospiraceae (Padj. = 0.021) decreased in relative abundance. These results indicate that the stressors associated with capture and transport cause an imbalanced fecal microbiota composition in white rhinoceroses that may lead to potentially infectious intestinal disorders. This imbalance may result from recrudescence of normally innocuous pathogens, increased shedding of pathogens or increased vulnerability to new pathogens.},
}
@article {pmid38026235,
year = {2023},
author = {McCall, KD and Walter, D and Patton, A and Thuma, JR and Courreges, MC and Palczewski, G and Goetz, DJ and Bergmeier, S and Schwartz, FL},
title = {Anti-Inflammatory and Therapeutic Effects of a Novel Small-Molecule Inhibitor of Inflammation in a Male C57BL/6J Mouse Model of Obesity-Induced NAFLD/MAFLD.},
journal = {Journal of inflammation research},
volume = {16},
number = {},
pages = {5339-5366},
doi = {10.2147/JIR.S413565},
pmid = {38026235},
issn = {1178-7031},
abstract = {PURPOSE: Non-alcoholic fatty liver disease (NAFLD), recently renamed metabolic (dysfunction) associated fatty liver disease (MAFLD), is the most common chronic liver disease in the United States. Presently, there is an intense and ongoing effort to identify and develop novel therapeutics for this disease. In this study, we explored the anti-inflammatory activity of a new compound, termed IOI-214, and its therapeutic potential to ameliorate NAFLD/MAFLD in male C57BL/6J mice fed a high fat (HF) diet.<br><br>METHODS: Murine macrophages and hepatocytes in culture were treated with lipopolysaccharide (LPS) &#xb1; IOI-214 or DMSO (vehicle), and RT-qPCR analyses of inflammatory cytokine gene expression were used to assess IOI-214's anti-inflammatory properties in vitro. Male C57BL/6J mice were also placed on a HF diet and treated once daily with IOI-214 or DMSO for 16 weeks. Tissues were collected and analyzed to determine the effects of IOI-214 on HF diet-induced NAFL D/MAFLD. Measurements such as weight, blood glucose, serum cholesterol, liver/serum triglyceride, insulin, and glucose tolerance tests, ELISAs, metabolomics, Western blots, histology, gut microbiome, and serum LPS binding protein analyses were conducted.<br><br>RESULTS: IOI-214 inhibited LPS-induced inflammation in macrophages and hepatocytes in culture and abrogated HF diet-induced mesenteric fat accumulation, hepatic inflammation and steatosis/hepatocellular ballooning, as well as fasting hyperglycemia without affecting insulin resistance or fasting insulin, cholesterol or TG levels despite overall obesity in vivo in male C57BL/6J mice. IOI-214 also decreased systemic inflammation in vivo and improved gut microbiota dysbiosis and leaky gut.<br><br>CONCLUSION: Combined, these data indicate that IOI-214 works at multiple levels in parallel to inhibit the inflammation that drives HF diet-induced NAFLD/MAFLD, suggesting that it may have therapeutic potential for NAFLD/MAFLD.},
}
@article {pmid38026003,
year = {2023},
author = {Beretta, S and Apparicio, M and Toniollo, GH and Cardozo, MV},
title = {The importance of the intestinal microbiota in humans and dogs in the neonatal period.},
journal = {Animal reproduction},
volume = {20},
number = {3},
pages = {e20230082},
doi = {10.1590/1984-3143-AR2023-0082},
pmid = {38026003},
issn = {1984-3143},
abstract = {The neonatal period represents a critical stage for the establishment and development of the gut microbiota, which profoundly influences the future health trajectory of individuals. This review examines the importance of intestinal microbiota in humans and dogs, aiming to elucidate the distinct characteristics and variations in the composition between these two species. In humans, the intestinal microbiota contributes to several crucial physiological processes, including digestion, nutrient absorption, immune system development, and modulation of host metabolism. Dysbiosis, an imbalance or disruption of the gut microbial community, has been linked to various disorders, such as inflammatory bowel disease, obesity, and even neurological conditions. Furthermore, recent research has unveiled the profound influence of the gut-brain axis, emphasizing the bidirectional communication between the gut microbiota and the central nervous system, impacting cognitive function and mental health. Similarly, alterations in the canine intestinal microbiota have been associated with gastrointestinal disorders, including chronic enteropathy, such as inflammatory bowel disease, food allergies, and ulcerative histiocytic colitis. However, our understanding of the intricacies and functional significance of the intestinal microbiota in dogs remains limited. Understanding the complex dynamics of the intestinal microbiota in both humans and dogs is crucial for devising effective strategies to promote health and manage disease. Moreover, exploring the similarities and differences in the gut microbial composition between these two species can facilitate translational research, potentially leading to innovative therapeutic interventions and strategies to enhance the well-being of both humans and dogs.},
}
@article {pmid38025771,
year = {2023},
author = {Shadid, ILC and Lee-Sarwar, K and Lu, Z and Yadama, A and Laranjo, N and Carey, V and O'Connor, GT and Zeiger, RS and Bacharier, L and Guchelaar, HJ and Liu, YY and Litonjua, AA and Weiss, ST and Mirzakhani, H},
title = {Early life gut microbiome in children following spontaneous preterm birth and maternal preeclampsia.},
journal = {iScience},
volume = {26},
number = {12},
pages = {108311},
doi = {10.1016/j.isci.2023.108311},
pmid = {38025771},
issn = {2589-0042},
abstract = {The early life microbiome plays an important role in developmental and long-term health outcomes. However, it is unknown whether adverse pregnancy complications affect the offspring's gut microbiome postnatally and in early years. In a longitudinal cohort with a five-year follow-up of mother-child pairs affected by preeclampsia (PE) or spontaneous preterm birth (sPTB), we evaluated offspring gut alpha and beta diversity as well as taxa abundances considering factors like breastfeeding and mode of delivery. Our study highlights a trend where microbiome diversity exhibits comparable development across adverse and normal pregnancies. However, specific taxa at genus level emerge with distinctive abundances, showing enrichment and/or depletion over time in relation to PE or sPTB. These findings underscore the potential for certain adverse pregnancy complications to induce alterations in the offspring's microbiome over the course of early life. The implications of these findings on the immediate and long-term health of offspring should be investigated in future studies.},
}
@article {pmid38025767,
year = {2023},
author = {Sun, H and Su, X and Liu, Y and Li, G and Du, Q},
title = {Roseburia intestinalis relieves intrahepatic cholestasis of pregnancy through bile acid/FXR-FGF15 in rats.},
journal = {iScience},
volume = {26},
number = {12},
pages = {108392},
doi = {10.1016/j.isci.2023.108392},
pmid = {38025767},
issn = {2589-0042},
abstract = {Previous research has demonstrated significant differences in intestinal flora between pregnant women with intrahepatic cholestasis of pregnancy (ICP) and healthy pregnant women. The objective of our study is to identify the key bacteria involved in ICP rats and explore the underlying mechanism. We established an ICP rat model and collected rat feces for metagenomic sequencing and found that Roseburia intestinalis (R.I) is the key bacteria in ICP. Transplantation of R.I improved phenotypes associated with ICP through the bile acid/farnesoid X receptor-fibroblast growth factor 15 (FXR-FGF15) signaling pathway. We used the FXR antagonist Z-Guggulsterone (Z-Gu) to verify the key role of FXR in ICP and found that Z-Gu reversed the benefits of R.I on ICP rats. Our research highlights the important role of intestinal flora in the pathogenesis of ICP and provides a novel approach for its treatment.},
}
@article {pmid38025669,
year = {2023},
author = {Kim, HY and Kim, TH and Shin, JH and Cho, K and Ha, HK and Lee, A and Kim, YJ},
title = {Navigating the microbial community in the trachea-oropharynx of breast cancer patients with or without neoadjuvant chemotherapy (NAC) via endotracheal tube: has NAC caused any change?.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16366},
doi = {10.7717/peerj.16366},
pmid = {38025669},
issn = {2167-8359},
abstract = {BACKGROUND: We compare the diversity and niche specificity of the microbiome in the trachea-oropharynx microbiome of malignant breast neoplasm with or without neoadjuvant chemotherapy (NAC) via NGS analysis.<br><br>METHODS: We prospectively collected a total of 40 endotracheal tubes intubated from subjects, of whom 20 with NAC treated breast cancer (NAC group) and 20 with breast cancer without NAC (Non-NAC group). We generated 16S rRNA-based microbial profiles in IlluminaTM platform and alpha diversity indices were compared between groups. For the comparison of taxa abundance, linear discriminant analysis effect size method with Kruskal-Wallis test was used. The distribution of variables between the two groups was compared using the Mann-Whitney test. For beta diversity analysis, PERMANOVA was used.<br><br>RESULTS: Among the diversity indices, the NAC group showed significantly lower Chao1, Inverse Simpson, and Shannon indices than the Non-NAC group. The three most frequent taxa of all two groups were Streptococcus (20.4%), followed by Veillonella (11.9%), and Prevorella (10.4%). This order was the same in NAC and non-NAC groups.<br><br>CONCLUSION: Here, we provide the first comparison data of the respiratory tract microbiome of breast cancer patients with or without NAC via NGS analysis. This study ultimately seeks to contribute to future studies on the lower respiratory tract in cancer patients with cytotoxic chemotherapy by establishing reliable control data.},
}
@article {pmid38025434,
year = {2023},
author = {Hall, CV and Radford-Smith, G and Savage, E and Robinson, C and Cocchi, L and Moran, RJ},
title = {Brain signatures of chronic gut inflammation.},
journal = {Frontiers in psychiatry},
volume = {14},
number = {},
pages = {1250268},
doi = {10.3389/fpsyt.2023.1250268},
pmid = {38025434},
issn = {1664-0640},
abstract = {Gut inflammation is thought to modify brain activity and behaviour via modulation of the gut-brain axis. However, how relapsing and remitting exposure to peripheral inflammation over the natural history of inflammatory bowel disease (IBD) contributes to altered brain dynamics is poorly understood. Here, we used electroencephalography (EEG) to characterise changes in spontaneous spatiotemporal brain states in Crohn's Disease (CD) (n = 40) and Ulcerative Colitis (UC) (n = 30), compared to healthy individuals (n = 28). We first provide evidence of a significantly perturbed and heterogeneous microbial profile in CD, consistent with previous work showing enduring and long-standing dysbiosis in clinical remission. Results from our brain state assessment show that CD and UC exhibit alterations in the temporal properties of states implicating default-mode network, parietal, and visual regions, reflecting a shift in the predominance from externally to internally-oriented attentional modes. We investigated these dynamics at a finer sub-network resolution, showing a CD-specific and highly selective enhancement of connectivity between the insula and medial prefrontal cortex (mPFC), regions implicated in cognitive-interoceptive appraisal mechanisms. Alongside overall higher anxiety scores in CD, we also provide preliminary support to suggest that the strength of chronic interoceptive hyper-signalling in the brain co-occurs with disease duration. Together, our results demonstrate that a long-standing diagnosis of CD is, in itself, a key factor in determining the risk of developing altered brain network signatures.},
}
@article {pmid38025161,
year = {2023},
author = {Chowdhary, A and Van Gelder, RN and Sundararajan, M},
title = {Methodologic Considerations for Studying the Ocular Surface Microbiome.},
journal = {Ophthalmology science},
volume = {3},
number = {4},
pages = {100408},
doi = {10.1016/j.xops.2023.100408},
pmid = {38025161},
issn = {2666-9145},
abstract = {UNLABELLED: The ocular surface microbiome, unlike that of the skin or gut, has not been well characterized. Culture experiments historically suggested a nearly sterile ocular surface, but initial application of molecular methods such as 16S ribosomal RNA and high-throughput sequencing demonstrated a surprisingly rich ocular surface microbiome. However, a major limitation in studying such a low-biomass niche is the potential for artifactual results when amplification-based techniques such as ribosomal polymerase chain reaction and shotgun sequencing are used. It will be essential to establish standards across the field for sample collection, positive and negative controls, and limitation of contamination in both the laboratory setting and computational analysis. New developments in ocular microbiome research, including the generation of reference reagents and fluoroscopic imaging techniques, provide improved means to validate sequencing results and to visualize complex interactions between host cells and bacteria. Through more thorough characterization of the ocular surface microbiome, the connections between a dysregulated surface and ophthalmic disease may be better understood.<br><br>FINANCIAL DISCLOSURES: Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.},
}
@article {pmid38024855,
year = {2023},
author = {Mao, Z and Hui, H and Zhao, X and Xu, L and Qi, Y and Yin, L and Qu, L and Han, L and Peng, J},
title = {Protective effects of dioscin against Parkinson's disease via regulating bile acid metabolism through remodeling gut microbiome/GLP-1 signaling.},
journal = {Journal of pharmaceutical analysis},
volume = {13},
number = {10},
pages = {1153-1167},
doi = {10.1016/j.jpha.2023.06.007},
pmid = {38024855},
issn = {2214-0883},
abstract = {It is necessary to explore potent therapeutic agents via regulating gut microbiota and metabolism to combat Parkinson's disease (PD). Dioscin, a bioactive steroidal saponin, shows various activities. However, its effects and mechanisms against PD are limited. In this study, dioscin dramatically alleviated neuroinflammation and oxidative stress, and restored the disorders of mice induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). 16 S rDNA sequencing assay demonstrated that dioscin reversed MPTP-induced gut dysbiosis to decrease Firmicutes-to-Bacteroidetes ratio and the abundances of Enterococcus, Streptococcus, Bacteroides and Lactobacillus genera, which further inhibited bile salt hydrolase (BSH) activity and blocked bile acid (BA) deconjugation. Fecal microbiome transplantation test showed that the anti-PD effect of dioscin was gut microbiota-dependent. In addition, non-targeted fecal metabolomics assays revealed many differential metabolites in adjusting steroid biosynthesis and primary bile acid biosynthesis. Moreover, targeted bile acid metabolomics assay indicated that dioscin increased the levels of ursodeoxycholic acid, tauroursodeoxycholic acid, taurodeoxycholic acid and β-muricholic acid in feces and serum. In addition, ursodeoxycholic acid administration markedly improved the protective effects of dioscin against PD in mice. Mechanistic test indicated that dioscin significantly up-regulated the levels of takeda G protein-coupled receptor 5 (TGR5), glucagon-like peptide-1 receptor (GLP-1R), GLP-1, superoxide dismutase (SOD), and down-regulated NADPH oxidases 2 (NOX2) and nuclear factor-kappaB (NF-κB) levels. Our data indicated that dioscin ameliorated PD phenotype by restoring gut dysbiosis and regulating bile acid-mediated oxidative stress and neuroinflammation via targeting GLP-1 signal in MPTP-induced PD mice, suggesting that the compound should be considered as a prebiotic agent to treat PD in the future.},
}
@article {pmid38024851,
year = {2023},
author = {Ravi, A and Marietta, EV and Alexander, JA and Murray, JA and Katzka, DA},
title = {H influenzae LPS colocalization with Toll-like receptor 4 in eosinophilic esophagitis.},
journal = {The journal of allergy and clinical immunology. Global},
volume = {2},
number = {4},
pages = {100151},
doi = {10.1016/j.jacig.2023.100151},
pmid = {38024851},
issn = {2772-8293},
abstract = {BACKGROUND: Patients with eosinophilic esophagitis (EoE) have a unique esophageal microbiome with increased presence of Haemophilus influenzae, but its role in the disease is unclear.<br><br>OBJECTIVE: Microbiome-derived bacterial LPS activation of Toll-like receptors (TLR) is a potential mechanism for inducing inflammation in other chronic inflammatory diseases, but it has not been studied in EoE. Our aim was therefore to study microbiome-derived bacterial LPS activation of TLRs in EoE.<br><br>METHODS: We studied 10 patients with active EoE, 9 patients with inactive EoE, and 10 control patients. Esophageal biopsy samples from the controls, patients with active EoE (>15 eosinophils/hpf), and patients with inactive EoE were immunostained for the presence of H influenzae LPS, presence of TLR4, and colocalization of LPS and TLR4. Staining intensity was measured by using confocal laser microscopy and scored on a scale from 0 to 3 as the average score assigned by 2 blinded observers.<br><br>RESULTS: H influenzae LPS was detected by positive staining in 20 of the 29 patients (69.0%), including 9 of the 10 patients with active EoE (90.0%), 8 of the 9 patients with inactive EoE (89.9%), and 3 of the 10 controls (30%); its level was greater in the patients with active EoE than in the controls (P&#xa0;= .063). TLR4 was detected by positive staining in 19 of the 29 patients (65.5%), including 9 of the 10 patients with active EoE (90.0%), 4 of the 9 patients with inactive EoE (44.4%), and 6 of the 10 controls (60.0%); its level was higher in the patients with active EoE than in those with inactive EoE (P&#xa0;= .096). The result of testing for colocalization of LPS and TLR4 was positive in 8 of 10 patients with active EoE (80.0%), 1 of 9 patients with inactive EoE (11.1%), and 1 of 10 control patients (10.0%), with greater colocalization of H influenzae LPS and TLR4 staining density in the samples from patients with active EoE than in the controls or the patients with inactive EoE (P&#xa0;= .009 and P&#xa0;= .018, respectively).<br><br>CONCLUSION: Esophageal microbiome-rich H influenzae LPS colocalizes to TLR4 in active EoE. These data lend further support to a role for the esophageal microbiome in modulating the activity of EoE.},
}
@article {pmid38024475,
year = {2023},
author = {Zhao, W and Lei, J and Ke, S and Chen, Y and Xiao, J and Tang, Z and Wang, L and Ren, Y and Alnaggar, M and Qiu, H and Shi, W and Yin, L and Chen, Y},
title = {Fecal microbiota transplantation plus tislelizumab and fruquintinib in refractory microsatellite stable metastatic colorectal cancer: an open-label, single-arm, phase II trial (RENMIN-215).},
journal = {EClinicalMedicine},
volume = {66},
number = {},
pages = {102315},
doi = {10.1016/j.eclinm.2023.102315},
pmid = {38024475},
issn = {2589-5370},
abstract = {BACKGROUND: Immunotherapy has revolutionized the treatment of cancer. However, microsatellite stable (MSS) metastatic colorectal cancer (mCRC) shows a low response to PD-1 inhibitors. Antiangiogenic therapy can enhance anti-PD-1 efficacy, but it still cannot meet clinical needs. Increasing evidence supported a close relationship between gut microbiome and anti-PD-1 efficacy. This study aimed to explore the efficacy and safety of the combination of fecal microbiota transplantation (FMT) and tislelizumab and fruquintinib in refractory MSS mCRC.<br><br>METHODS: In the phase II trial, MSS mCRC patients were administered FMT plus tislelizumab and fruquintinib as a third-line or above treatment. The primary endpoint was progression-free survival (PFS). Secondary endpoints were overall survival (OS), objective response rate (ORR), disease control rate (DCR), duration of response (DoR), clinical benefit rate (CBR), safety and quality of life. Feces and peripheral blood were collected for exploratory biomarker analysis. This study is registered with Chictr.org.cn, identifier ChiCTR2100046768.<br><br>FINDINGS: From May 10, 2021 to January 17, 2022, 20 patients were enrolled. Median follow-up was 13.7 months. Median PFS was 9.6 months (95% CI 4.1-15.1). Median OS was 13.7 months (95% CI 9.3-17.7). Median DoR was 8.1 months (95% CI 1.7-10.6). ORR was 20% (95% CI 5.7-43.7). DCR was 95% (95% CI 75.1-99.9). CBR was 60% (95% CI 36.1-80.9). Nineteen patients (95%) experienced at least one treatment-related adverse event (TRAE). Six patients (30%) had grade 3-4 TRAEs, with the most common being albuminuria (10%), urine occult blood (10%), fecal occult blood (10%), hypertension (5%), hyperglycemia (5%), liver dysfunction (5%), hand-foot skin reaction (5%), and hypothyroidism (5%). No treatment-related deaths occurred. Responders had a high-abundance of Proteobacteria and Lachnospiraceae family and a low-abundance of Actinobacteriota and Bifidobacterium. The treatment did not change the structure of peripheral blood TCR repertoire. However, the expanded TCRs exhibited the characteristics of antigen-driven responses in responders.<br><br>INTERPRETATION: FMT plus tislelizumab and fruquintinib as third-line or above treatment showed improved survival and manageable safety in refractory MSS mCRC, suggesting a valuable new treatment option for this patient population.<br><br>FUNDING: This study was supported by the National Natural Science Foundation of China (82102954 to Wensi Zhao) and the Special Project of Central Government for Local Science and Technology Development of Hubei Province (ZYYD2020000169 to Yongshun Chen).},
}
@article {pmid38024360,
year = {2023},
author = {Baek, GH and Kim, YJ and Lee, Y and Jung, SC and Seo, HW and Kim, JS},
title = {Prebiotic potential of green banana flour: impact on gut microbiota modulation and microbial metabolic activity in a murine model.},
journal = {Frontiers in nutrition},
volume = {10},
number = {},
pages = {1249358},
doi = {10.3389/fnut.2023.1249358},
pmid = {38024360},
issn = {2296-861X},
abstract = {INTRODUCTION: Green banana flour can be used as a prebiotic due to its ability to promote gut health and provide several health benefits. In this study, we investigated whether feeding mice green banana flour at different doses would alter intestinal microbiota composition.<br><br>METHODS: We fed C57BL/6N mice either a Low-dose (500 mg/kg/day) or High-dose (2000 mg/kg/day) of green banana flour daily for 3 weeks, and fecal samples were collected on days 0, 14, and 21 for microbiota analysis.<br><br>RESULTS: Our results showed that the composition of intestinal microbiota was significantly altered by day 21, regardless of the dose. Notably, the consumption of green banana flour increased the presence of beneficial bacteria, including Coriobacteriaceae_UCG-002, Turicibacter, Parasutterella, Gastranaerophilales_ge, and RF39_ge. These changes in the intestinal microorganisms were accompanied by increased biological processes such as amino acid biosynthesis and secondary metabolite biosynthesis. Conversely, the consumption of green banana flour resulted in a decrease in biological processes related to carbohydrate degradation, glycerol degradation, and similar functions.<br><br>DISCUSSION: These results emphasize the potential of green banana flour as a prebiotic that can benefit the gut microbiome.},
}
@article {pmid38024319,
year = {2023},
author = {Wojciechowska, O and Costabile, A and Kujawska, M},
title = {The gut microbiome meets nanomaterials: exposure and interplay with graphene nanoparticles.},
journal = {Nanoscale advances},
volume = {5},
number = {23},
pages = {6349-6364},
doi = {10.1039/d3na00696d},
pmid = {38024319},
issn = {2516-0230},
abstract = {Graphene-based nanoparticles are widely applied in many technology and science sectors, raising concerns about potential health risks. Emerging evidence suggests that graphene-based nanomaterials may interact with microorganisms, both pathogens and commensal bacteria, that dwell in the gut. This review aims to demonstrate the current state of knowledge on the interplay between graphene nanomaterials and the gut microbiome. In this study, we briefly overview nanomaterials, their usage and the characteristics of graphene-based nanoparticles. We present and discuss experimental data from in vitro studies, screening tests on small animals and rodent experiments related to exposure and the effects of graphene nanoparticles on gut microbiota. With this in mind, we highlight the reported crosstalk between graphene nanostructures, the gut microbial community and the host immune system in order to shed light on the perspective to bear on the biological interactions. The studies show that graphene-based material exposure is dosage and time-dependent, and different derivatives present various effects on host bacteria cells. Moreover, the route of graphene exposure might influence a shift in the gut microbiota composition, including the alteration of functions and diversity and abundance of specific phyla or genera. However, the mechanism of graphene-based nanomaterials' influence on gut microbiota is poorly understood. Accordingly, this review emphasises the importance of studies needed to establish the most desirable synthesis methods, types of derivatives, properties, and safety aspects mainly related to the routes of exposure and dosages of graphene-based nanomaterials.},
}
@article {pmid38024144,
year = {2023},
author = {Senaratne, NLM and Chong, CW and Yong, LS and Yoke, LF and Gopinath, D},
title = {Impact of waterpipe smoking on the salivary microbiome.},
journal = {Frontiers in oral health},
volume = {4},
number = {},
pages = {1275717},
doi = {10.3389/froh.2023.1275717},
pmid = {38024144},
issn = {2673-4842},
abstract = {BACKGROUND: While oral mirobial dysbiosis due to tobacco smoking has been studied thoroughly, there is limited data on the effect of waterpipe smoking on the oral microbiome. This study aims to compare the salivary microbiome between waterpipe smokers and non-smokers.<br><br>MATERIALS AND METHODS: Unstimulated saliva samples were collected from 60 participants, 30 smokers and 30 non-smokers in Kuala Lumpur and Klang Valley, Malaysia. DNA extraction was performed using the Qiagen DNA mini kit, and the 16S rRNA bacterial gene was amplified and sequenced using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and the alpha and beta diversity of the bacterial community was assessed. Significantly differentiated taxa were identified using LEfSe analysis, while differentially expressed pathways were identified using MaAsLin2.<br><br>RESULTS: A significant compositional change (beta diversity) was detected between the two groups (PERMANOVA P&#x2009;<&#x2009;0.05). Specifically, the levels of phylum Firmicutes and genus Streptococcus were elevated in smokers, whereas phylum Proteobacteria and genus Haemophilus were depleted compared to non-smokers. At the species level, Streptococcus oralis, Streptococcus salivarius, and Streptococcus gingivalis were enriched in smokers. We observed significant differences in the abundance of thirty-seven microbial metabolic pathways between waterpipe smokers and non-smokers. The microbial pathways enriched in smokers were those implicated in polymer degradation and amino acid metabolism.<br><br>CONCLUSION: The taxonomic and metabolic profile of the salivary microbiome in waterpipe smokers compared to healthy controls exhibited a paradigm shift, thus, implying an alteration in the homeostatic balance of the oral cavity posing unique challenges for oral health.},
}
@article {pmid38024036,
year = {2023},
author = {Dewi, DAR and Perdiyana, A and Wiliantari, NM and Nadhira, F and Arkania, N and Salsabila, CA and Allun, CV and Allatib, A and Dewantara, K},
title = {Managing the Skin Microbiome as a New Bacteriotherapy for Inflammatory Atopic Dermatitis.},
journal = {Cureus},
volume = {15},
number = {11},
pages = {e48803},
doi = {10.7759/cureus.48803},
pmid = {38024036},
issn = {2168-8184},
abstract = {The microbiome, comprising various bacteria, assumes a significant role in the immune system's maturation and maintaining bodily homeostasis. Alterations in the microbial composition can contribute to the initiation and progression of inflammation. Recent studies reveal that changes in microbial composition and function, known as dysbiosis in the skin and gut, have been associated with altered immunological responses and skin barrier disruption. These changes are implicated in the development of several skin diseases, such as atopic dermatitis (AD). This review examines research demonstrating the potential of microbiome repair as a therapeutic approach to reduce the effect of inflammatory processes in the skin during atopic dermatitis. This way, corticosteroids in atopic dermatitis therapy can be reduced or even replaced with treatments focusing on controlling the skin microbiome. This study used scientific literature from recognized platforms, including PubMed, Scopus, Google Scholar, and ScienceDirect, covering publications from 2013 to 2023. The primary aim of this study was to assess the efficacy of skin microbiome management in treating atopic dermatitis. This study concludes that physicians must comprehensively understand the microbiome's involvement in atopic dermatitis, including its pathophysiological implications and its relevance to therapeutic interventions.},
}
@article {pmid38023904,
year = {2023},
author = {Fu, X and Huang, Y and Fu, Q and Qiu, Y and Zhao, J and Li, J and Wu, X and Yang, Y and Liu, H and Yang, X and Chen, H},
title = {Critical transition of soil microbial diversity and composition triggered by plant rhizosphere effects.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1252821},
doi = {10.3389/fpls.2023.1252821},
pmid = {38023904},
issn = {1664-462X},
abstract = {Over the years, microbial community composition in the rhizosphere has been extensively studied as the most fascinating topic in microbial ecology. In general, plants affect soil microbiota through rhizodeposits and changes in abiotic conditions. However, a consensus on the response of microbiota traits to the rhizosphere and bulk soils in various ecosystems worldwide regarding community diversity and structure has not been reached yet. Here, we conducted a meta-analysis of 101 studies to investigate the microbial community changes between the rhizosphere and bulk soils across various plant species (maize, rice, vegetables, other crops, herbaceous, and woody plants). Our results showed that across all plant species, plant rhizosphere effects tended to reduce the rhizosphere soil pH, especially in neutral or slightly alkaline soils. Beta-diversity of bacterial community was significantly separated between into rhizosphere and bulk soils. Moreover, r-strategists and copiotrophs (e.g. Proteobacteria and Bacteroidetes) enriched by 24-27% in the rhizosphere across all plant species, while K-strategists and oligotrophic (e.g. Acidobacteria, Gemmatimonadete, Nitrospirae, and Planctomycetes) decreased by 15-42% in the rhizosphere. Actinobacteria, Firmicutes, and Chloroflexi are also depleted by in the plant rhizosphere compared with the bulk soil by 7-14%. The Actinobacteria exhibited consistently negative effect sizes across all plant species, except for maize and vegetables. In Firmicutes, both herbaceous and woody plants showed negative responses to rhizosphere effects, but those in maize and rice were contrarily enriched in the rhizosphere. With regards to Chloroflexi, apart from herbaceous plants showing a positive effect size, the plant rhizosphere effects were consistently negative across all other plant types. Verrucomicrobia exhibited a significantly positive effect size in maize, whereas herbaceous plants displayed a negative effect size in the rhizosphere. Overall, our meta-analysis exhibited significant changes in microbial community structure and diversity responding to the plant rhizosphere effects depending on plant species, further suggesting the importance of plant rhizosphere to environmental changes influencing plants and subsequently their controls over the rhizosphere microbiota related to nutrient cycling and soil health.},
}
@article {pmid38023867,
year = {2023},
author = {Cardoni, M and Mercado-Blanco, J},
title = {Confronting stresses affecting olive cultivation from the holobiont perspective.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1261754},
doi = {10.3389/fpls.2023.1261754},
pmid = {38023867},
issn = {1664-462X},
abstract = {The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.},
}
@article {pmid38023855,
year = {2023},
author = {Jia, J and Chen, L and Yu, W and Cai, S and Su, S and Xiao, X and Tang, X and Jiang, X and Chen, D and Fang, Y and Wang, J and Luo, X and Li, J and Huang, Y and Su, J},
title = {The novel nematicide chiricanine A suppresses Bursaphelenchus xylophilus pathogenicity in Pinus massoniana by inhibiting Aspergillus and its secondary metabolite, sterigmatocystin.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1257744},
doi = {10.3389/fpls.2023.1257744},
pmid = {38023855},
issn = {1664-462X},
abstract = {INTRODUCTION: Pine wilt disease (PWD) is responsible for extensive economic and ecological damage to Pinus spp. forests and plantations worldwide. PWD is caused by the pine wood nematode (PWN, Bursaphelenchus xylophilus) and transmitted into pine trees by a vector insect, the Japanese pine sawyer (JPS, Monochamus alternatus). Host infection by PWN will attract JPS to spawn, which leads to the co-existence of PWN and JPS within the host tree, an essential precondition for PWD outbreaks. Through the action of their metabolites, microbes can manipulate the co-existence of PWN and JPS, but our understanding on how key microorganisms engage in this process remains limited, which severely hinders the exploration and utilization of promising microbial resources in the prevention and control of PWD.<br><br>METHODS: In this study we investigated how the PWN-associated fungus Aspergillus promotes the co-existence of PWN and JPS in the host trees (Pinus massoniana) via its secondary metabolite, sterigmatocystin (ST), by taking a multi-omics approach (phenomics, transcriptomics, microbiome, and metabolomics).<br><br>RESULTS: We found that Aspergillus was able to promote PWN invasion and pathogenicity by increasing ST biosynthesis in the host plant, mainly by suppressing the accumulation of ROS (reactive oxygen species) in plant tissues that could counter PWN. Further, ST accumulation triggered the biosynthesis of VOC (volatile organic compounds) that attracts JPS and drives the coexistence of PWN and JPS in the host plant, thereby encouraging the local transmission of PWD. Meanwhile, we show that application of an Aspergillus inhibitor (chiricanine A treatment) results in the absence of Aspergillus and decreases the in vivo ST amount, thereby sharply restricting the PWN development in host. This further proved that Aspergillus is vital and sufficient for promoting PWD transmission.<br><br>DISCUSSION: Altogether, these results document, for the first time, how the function of Aspergillus and its metabolite ST is involved in the entire PWD transmission chain, in addition to providing a novel and long-term effective nematicide for better PWD control in the field.},
}
@article {pmid38023844,
year = {2023},
author = {Shahid, I and Brunetto, G and Ricachenevsky, FK},
title = {Editorial: Capacity of the zinc mobilizing microbiome for climate-smart &amp; sustainable agriculture.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1323144},
doi = {10.3389/fpls.2023.1323144},
pmid = {38023844},
issn = {1664-462X},
}
@article {pmid38023837,
year = {2023},
author = {Oldstone-Jackson, C and Huang, F and Bergelson, J},
title = {Microbe-associated molecular pattern recognition receptors have little effect on endophytic Arabidopsis thaliana microbiome assembly in the field.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1276472},
doi = {10.3389/fpls.2023.1276472},
pmid = {38023837},
issn = {1664-462X},
abstract = {Plant microbiome structure affects plant health and productivity. A limited subset of environmental microbes successfully establishes within plant tissues, but the forces underlying this selectivity remain poorly characterized. Transmembrane pattern recognition receptors (PRRs), used by plants to detect microbe-associated molecular patterns (MAMPs), are strong candidates for achieving this selectivity because PRRs can potentially interact with many members of the microbiome. Indeed, MAMPs found in many microbial taxa, including beneficials and commensals, can instigate a robust immune response that affects microbial growth. Surprisingly, we found that MAMP-detecting PRRs have little effect on endophytic bacterial and fungal microbiome structure in the field. We compared the microbiomes of four PRR knockout lines of Arabidopsis thaliana to wild-type plants in multiple tissue types over several developmental stages and detected only subtle shifts in fungal, but not bacterial, β-diversity in one of the four PRR mutants. In one developmental stage, lore mutants had slightly altered fungal β-diversity, indicating that LORE may be involved in plant-fungal interactions in addition to its known role in detecting certain bacterial lipids. No other effects of PRRs on α-diversity, microbiome variability, within-individual homogeneity, or microbial load were found. The general lack of effect suggests that individual MAMP-detecting PRRs are not critical in shaping the endophytic plant microbiome. Rather, we suggest that MAMP-detecting PRRs must either act in concert and/or are individually maintained through pleiotropic effects or interactions with coevolved mutualists or pathogens. Although unexpected, these results offer insights into the role of MAMP-detecting PRRs in plant-microbe interactions and help direct future efforts to uncover host genetic elements that control plant microbiome assembly.},
}
@article {pmid38023592,
year = {2023},
author = {Yun, HM and Hyun, S},
title = {Role of gut commensal bacteria in juvenile developmental growth of the host: insights from Drosophila studies.},
journal = {Animal cells and systems},
volume = {27},
number = {1},
pages = {329-339},
doi = {10.1080/19768354.2023.2282726},
pmid = {38023592},
issn = {1976-8354},
abstract = {The gut microbiome plays a crucial role in maintaining health in a variety of organisms, from insects to humans. Further, beneficial symbiotic microbes are believed to contribute to improving the quality of life of the host. Drosophila is an optimal model for studying host-commensal microbe interactions because it allows for convenient manipulation of intestinal microbial composition. Fly microbiota has a simple taxonomic composition and can be cultivated and genetically tracked. This permits functional studies and analyses of the molecular mechanisms underlying their effects on host physiological processes. In this context, we briefly introduce the principle of juvenile developmental growth in Drosophila. Then, we discuss the current understanding of the molecular mechanisms underlying the effects of gut commensal bacteria, such as Lactiplantibacillus plantarum and Acetobacter pomorum, in the fly gut microbiome on Drosophila juvenile growth, including specific actions of gut hormones and metabolites in conserved cellular signaling systems, such as the insulin/insulin-like (IIS) and the target of rapamycin (TOR) pathways. Given the similarities in tissue function/structure, as well as the high conservation of physiological systems between Drosophila and mammals, findings from the Drosophila model system will have significant implications for understanding the mechanisms underlying the interaction between the host and the gut microbiome in metazoans.},
}
@article {pmid38023425,
year = {2023},
author = {Arce-Cordero, JA and Liu, T and Monteiro, HF and Jeong, KC and Faciola, AP},
title = {Megasphaera elsdenii and Saccharomyces cerevisiae as direct fed microbials and their impact on ruminal microbiome during an acute acidosis challenge in continuous culture.},
journal = {Translational animal science},
volume = {7},
number = {1},
pages = {txad123},
doi = {10.1093/tas/txad123},
pmid = {38023425},
issn = {2573-2102},
abstract = {Our objective was to evaluate the effects of combinations of Saccharomyces cerevisiae and Megasphaera elsdenii as direct-fed microbials (DFM) on ruminal microbiome during an acute acidosis challenge in a continuous culture system. Treatments provided a DFM dose of 1 × 10[8] colony-forming unit (CFU)/mL, as follows: control (no DFM), YM1 (S. cerevisiae and M. elsdenii strain 1), YM2 (S. cerevisiae and M. elsdenii strain 2), and YMM (S. cerevisiae and half of the doses of M. elsdenii strains 1 and 2). We conducted four experimental periods of 11 d, which consisted of non-acidotic days (1 to 8) and acidotic challenge days (9 to 11) to establish acute ruminal acidosis conditions with a common basal diet containing 12% neutral detergent fiber and 58% starch. Treatments were applied from days 8 to 11, and samples of liquid and solid-associated bacteria were collected on days 9 to 11. Overall, 128 samples were analyzed by amplification of the V4 region of bacterial 16S rRNA, and data were analyzed with R and SAS for alpha and beta diversity, taxa relative abundance, and correlation of taxa abundance with propionate molar proportion. We observed a lower bacterial diversity (Shannon index, P = 0.02) when YM1 was added to the diet in comparison to the three other treatments. Moreover, compared to control, addition of YM1 to the diet increased relative abundance of phylum Proteobacteria (P = 0.05) and family Succinivibrioceae (P = 0.05) in the solid fraction and tended to increase abundance of family Succinivibrioceae (P = 0.10) and genus Succinivibrio (P = 0.09) in the liquid fraction. Correlation analysis indicated a positive association between propionate molar proportion and relative abundance of Proteobacteria (r = 0.36, P = 0.04) and Succinivibrioceae (r = 0.36, P = 0.05) in the solid fraction. The inclusion of YM1 in high-grain diets with a high starch content resulted in greater abundance of bacteria involved in succinate synthesis which may have provided the substrate for the greater propionate synthesis observed.},
}
@article {pmid38023381,
year = {2023},
author = {Ji, Z and Lu, X and Xue, M and Fan, Y and Tian, J and Dong, L and Zhu, C and Wen, H and Jiang, M},
title = {The probiotic effects of host-associated Bacillus velezensis in diets for hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂).},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {15},
number = {},
pages = {114-125},
doi = {10.1016/j.aninu.2023.08.004},
pmid = {38023381},
issn = {2405-6383},
abstract = {This study was to evaluate the potential of a host-associated Bacillus velezensis as a probiotic for hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂). Diets (B0 to B5) containing 0, 0.90 × 10[8], 0.80 × 10[9], 0.85 × 10[10], 0.90 × 10[11], 0.83 × 10[12] CFU/kg B. velezensis YFI-E109 were fed to the fish with initial weight (3.07 ± 0.08 g) in a recirculating aquaculture system for six weeks with three replicates, respectively. Probiotic effects were analyzed based on growth, body composition, liver and gut morphology, gut microbiome, and liver metabolome. Analysis of the bacterial genome has shown that the most abundant genes in B. velezensis YFI-E109 were distributed in carbohydrate and amino acid metabolism. Fish in groups B3 and B4 had better growth performance, and higher intestinal amylase (AMS) and lipase (LPS) activities compared with other groups (P < 0.05). Fish in groups B0 and B5 showed significant liver damage, while this status improved in group B3. The liver malondialdehyde (MDA) content in group B3 was lower than that in other groups (P < 0.05). The abundance of Mycoplasma, Ralstonia and Acinetobacter was significantly reduced in B3 and B5 compared to B0. The amino acid and carbohydrate metabolism pathways were enriched in group B3 compared with group B0. In conclusion, dietary B. velezensis YFI-E109 supplementation has the potential to improve growth, liver metabolism, and liver and gut health, and reshape the gut microbiome of hybrid yellow catfish. Excessive B. velezensis YFI-E109 reduced the prebiotic effects. The recommended dietary supplementation of B. velezensis YFI-E109 is 0.31 × 10[10] to 0.77 × 10[11] CFU/kg for hybrid yellow catfish according to the quadratic regression method by plotting specific growth rate (SGR), feed conversion ratio (FCR), MDA and activities of AMS against dietary B. velezensis YFI-E109 levels.},
}
@article {pmid38023315,
year = {2023},
author = {Awad, A and Pena, R},
title = {An improved method for extraction of soil fungal mycelium.},
journal = {MethodsX},
volume = {11},
number = {},
pages = {102477},
doi = {10.1016/j.mex.2023.102477},
pmid = {38023315},
issn = {2215-0161},
abstract = {Fungal mycelium is a major component of the soil microbiome. The soil hyphosphere represents a complex and dynamic niche for specific microorganisms, where multitrophic interactions occur, affecting ecosystem processes. However, extracting fungal mycelium from the soil to enable its taxonomical, chemical, and structural characterisation is challenging in the absence of a fast, efficient, and low-cost procedure. In this study, an old method (Bingle and Paul 1985), based on successive soil wet filtrations and density gradient centrifugation, was improved and tested in three different soil types (silty clay, silty clay loam, and loamy sand). The improved method reduced the number of filtrations by about five times and the centrifugation time from 40 min to 1 min. It avoided using any chemical substance which may impair further chemical analyses or DNA isolation and amplification. The method efficiency was about 50 % in the clay and 23 % in the sandy soils. However, a pre-step consisting of removing the fine-root fragments and other debris under the stereomicroscope may increase the method efficiency to more than 65 %, independent of the soil type.•A simple, efficient, and low-cost method suitable for extracting soil mycelium from a large number of samples.•The protocol includes successive soil wet filtrations and sucrose gradient centrifugation.•The method efficiency increases if the fine-root fragments and other debris are previously removed from the soil.},
}
@article {pmid38023290,
year = {2023},
author = {Chorbińska, J and Krajewski, W and Nowak, &#x141; and Bardowska, K and Żebrowska-Różańska, P and Łaczmański, &#x141; and Pacyga-Prus, K and Górska, S and Małkiewicz, B and Szydełko, T},
title = {Is the Urinary and Gut Microbiome Associated With Bladder Cancer?.},
journal = {Clinical Medicine Insights. Oncology},
volume = {17},
number = {},
pages = {11795549231206796},
doi = {10.1177/11795549231206796},
pmid = {38023290},
issn = {1179-5549},
abstract = {BACKGROUND: Microbiome dysbiosis plays a role in the pathogenesis of many urological diseases, including bladder cancer (BC). The aim of the study was to compare the urinary and gut microbiota of patients with BC with a healthy control (HC) group.<br><br>METHODS: The study group included patients hospitalized in 2020 to 2021 with diagnosed BC and HC. Prior to the transurethral resection of bladder tumor, patients collected their urine and stool which was then subjected to 16S rRNA gene sequencing.<br><br>RESULTS: Overall, 25 patients were enrolled in the study: 18 in the BC group and 7 in the HC group. Analysis of the urine and stool microbiome showed no statistically significant differences between patients with BC and HC in alpha diversity, beta diversity, and difference in taxa relative abundance. Detailed analysis of urine and stool microbiome depending on patient- and tumor-related characteristics also showed no statistically significant differences in alpha diversity and beta diversity. Differences in abundance (ANCOM) were noted in both types of samples in patients with BC. In the urine test, genus Lactobacillus was more common in patients with a positive history of Bacillus Calmette-Gu&#xe9;rin (BCG) therapy, while genus Howardella and the strain Streptococcus anginosus were more common in women. In stool samples, abundance of phylum Desulfobacterota was most abundant in Grade G1 and least in G2. Class Alphaproteobacteria, order Rhodospirillales, order Flavobacteriales, and family Flavobacteriaceae were more common in women.<br><br>CONCLUSIONS: The microbiome of urine and stool of patients with BC does not differ significantly from that of HC; however, its composition in patients with BC varies according to the patient's sex.},
}
@article {pmid38023193,
year = {2023},
author = {Thu, MS and Pongpirul, K},
title = {Response: Commentary: Human gut, breast, and oral microbiome in breast cancer: A systematic review and meta-analysis.},
journal = {Frontiers in oncology},
volume = {13},
number = {},
pages = {1279862},
doi = {10.3389/fonc.2023.1279862},
pmid = {38023193},
issn = {2234-943X},
}
@article {pmid38022878,
year = {2023},
author = {Hadžić, E and Starcevic, A and Rupčić, T and Zucko, J and Čvrljak, T and Renko, I and Knjaz, D and Novak, D},
title = {Effects of Soluble Dietary Fibre on Exercise Performance and Perception of Fatigue in Young Basketball Players.},
journal = {Food technology and biotechnology},
volume = {61},
number = {3},
pages = {389-401},
doi = {10.17113/ftb.61.03.23.8124},
pmid = {38022878},
issn = {1330-9862},
abstract = {RESEARCH BACKGROUND: In this study, we investigated the effects of soluble dietary fibre on improving neuromuscular and cardiovascular endurance and perception of fatigue in a closely monitored group of basketball players. Prebiotics have been sidelined in sports nutrition and their effect on performance remains poorly investigated and understood.<br><br>EXPERIMENTAL APPROACH: Eighteen healthy male basketball players were divided into two groups; one received 17 g/day of soluble dietary fibre (Nutriose&#xae;) for four weeks and the other group received placebo. Their morphological characteristics, neuromuscular and cardiovascular endurance, and rating of perceived exertion according to the rating of perceived exertion (RPE) scale were assessed. Measurements were taken before supplementation and after four weeks of supplementation. Faecal samples were collected from all participants immediately before and after the supplementation period, their total DNA extracted and sent for amplicon sequencing.<br><br>RESULTS AND CONCLUSIONS: In this study, fibre had no statistically significant effect on the vertical-type explosive power, no statistically significant effect on sprint-type explosive power, nor on aerobic and anaerobic endurance in the experimental group. Soluble fibre had a statistically significant effect on reducing the rating of perceived exertion of basketball players during the competitive part of the season (RPE 7.27&#xb1;0.04 versus 8.82&#xb1;0.81). This was confirmed by two-way ANOVA with replication, which showed that within-group interaction (p=0.0193), before and after dietary intake (p=0.0049), and between-group interaction before and after dietary intake (p=0.0313) had a significant effect on the result. The overall conclusion of the study is that soluble dietary fibre supplementation does not improve neuromuscular and cardiovascular endurance over a 4-week period. However, fibre supplementation could have a significant effect on reducing the rating of perceived exertion, as shown by the statistics. Both amplicon sequencing and subsequent bioinformatics results suggest that this could be the result of the beneficial effect on the intestinal microbiota and its metabolites.<br><br>This work highlights the importance of prebiotics in sports nutrition. Dietary fibre has been a neglected component of sports nutrition. This study demonstrated a statistically significant positive effect on the perception of fatigue, highlighting the need for further studies in this direction.},
}
@article {pmid38022823,
year = {2023},
author = {Shin, D and Kim, J and Lee, JH and Kim, JI and Oh, YM},
title = {Profiling of Microbial Landscape in Lung of Chronic Obstructive Pulmonary Disease Patients Using RNA Sequencing.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {18},
number = {},
pages = {2531-2542},
doi = {10.2147/COPD.S426260},
pmid = {38022823},
issn = {1178-2005},
abstract = {PURPOSE: The aim of the study was to use RNA sequencing (RNA-seq) data of lung from chronic obstructive pulmonary disease (COPD) patients to identify the bacteria that are most commonly detected. Additionally, the study sought to investigate the differences in these infections between normal lung tissues and those affected by COPD.<br><br>PATIENTS AND METHODS: We re-analyzed RNA-seq data of lung from 99 COPD patients and 93 non-COPD smokers to determine the extent to which the metagenomes differed between the two groups and to assess the reliability of the metagenomes. We used unmapped reads in the RNA-seq data that were not aligned to the human reference genome to identify more common infections in COPD patients.<br><br>RESULTS: We identified 18 bacteria that exhibited significant differences between the COPD and non-COPD smoker groups. Among these, Yersinia enterocolitica was found to be more than 30% more abundant in COPD. Additionally, we observed difference in detection rate based on smoking history. To ensure the accuracy of our findings and distinguish them from false positives, we double-check the metagenomic profile using Basic Local Alignment Search Tool (BLAST). We were able to identify and remove specific species that might have been misclassified as other species in Kraken2 but were actually Staphylococcus aureus, as identified by BLAST analysis.<br><br>CONCLUSION: This study highlighted the method of using unmapped reads, which were not typically used in sequencing data, to identify microorganisms present in patients with lung diseases such as COPD. This method expanded our understanding of the microbial landscape in COPD and provided insights into the potential role of microorganisms in disease development and progression.},
}
@article {pmid38022690,
year = {2023},
author = {Meng, D and Ai, S and Spanos, M and Shi, X and Li, G and Cretoiu, D and Zhou, Q and Xiao, J},
title = {Exercise and microbiome: From big data to therapy.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {5434-5445},
doi = {10.1016/j.csbj.2023.10.034},
pmid = {38022690},
issn = {2001-0370},
abstract = {Exercise is a vital component in maintaining optimal health and serves as a prospective therapeutic intervention for various diseases. The human microbiome, comprised of trillions of microorganisms, plays a crucial role in overall health. Given the advancements in microbiome research, substantial databases have been created to decipher the functionality and mechanisms of the microbiome in health and disease contexts. This review presents an initial overview of microbiomics development and related databases, followed by an in-depth description of the multi-omics technologies for microbiome. It subsequently synthesizes the research pertaining to exercise-induced modifications of the microbiome and diseases that impact the microbiome. Finally, it highlights the potential therapeutic implications of an exercise-modulated microbiome in intestinal disease, obesity and diabetes, cardiovascular disease, and immune/inflammation-related diseases.},
}
@article {pmid38022618,
year = {2023},
author = {Goyvaerts, C and Engeland, CE and Van der Jeught, K},
title = {Editorial: Rising stars in cancer immunity and immunotherapy 2022.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1326374},
doi = {10.3389/fimmu.2023.1326374},
pmid = {38022618},
issn = {1664-3224},
}
@article {pmid38022592,
year = {2023},
author = {Alizadeh, M and Shojadoost, B and Boodhoo, N and Raj, S and Sharif, S},
title = {Molecular and cellular characterization of immunity conferred by lactobacilli against necrotic enteritis in chickens.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1301980},
doi = {10.3389/fimmu.2023.1301980},
pmid = {38022592},
issn = {1664-3224},
abstract = {Necrotic enteritis is an important enteric disease of poultry that can be controlled with in-feed antibiotics. However, with the concerns over antimicrobial resistance, there is an increased interest in the use of alternatives. Probiotics are one of the alternatives that have gained considerable attention due to their antimicrobial and immunomodulatory activities. Therefore, in the present study, we evaluated the effects of two different Lactobacillus species alone or as a cocktail on prevention of necrotic enteritis. Day-old male broiler chickens were divided into five groups and on days 1, 8, 15, and 22, birds in groups 2 and 3 received 1×10[8] colony forming units (CFU) of L. johnsonii and L. reuteri, respectively. Group 4 received probiotic cocktails containing both bacteria (10[8] CFU/bird) and the negative and positive control groups did not receive any lactobacilli. Starting on day 23 post-hatch, birds in all groups (except the negative control group) were orally challenged twice per day with 3×10[8] CFU of a pathogenic C. perfringens strain for 3 days. Tissue and cecal samples were collected before and after challenge to assess gene expression, lymphocyte subsets determination, and microbiome analysis. On day 26 of age, lesion scoring was performed. The results demonstrated that the group that received the lactobacilli cocktail had significantly reduced lesion scores compared to the positive control group. In addition, the expression of interleukin (IL)-12 in the jejunum and CXC motif chemokine ligand 8 (CXCL8), IL-13, and IL-17 in the ileum were downregulated in the group that received the lactobacilli cocktail when compared to the positive control. Treating chickens with the lactobacilli cocktail prior to challenge enhanced the percentage of CD3[-]CD8[+] cells and Bu-1[+]IgY[+] B cells in the ileum and increased the frequency of monocyte/macrophages, CD3[-]CD8[+] cells, Bu-1[+]IgM[+], and Bu-1[+]IgY[+] B cells in the jejunum. Treatment with the lactobacilli cocktail reduced the relative expression of Gamma-Protobacteria and Firmicutes compared to the positive control group. In conclusion, the results presented here suggest that treatment with the lactobacilli cocktail containing L. johnsonii and L. reuteri reduced necrotic enteritis lesions in the small intestine of chickens, possibly through the modulation of immune responses.},
}
@article {pmid38022583,
year = {2023},
author = {Liu, X and van Beek, N and Cepic, A and Andreani, NA and Chung, CJ and Hermes, BM and Yilmaz, K and Benoit, S and Drenovska, K and Gerdes, S and Gläser, R and Goebeler, M and Günther, C and von Georg, A and Hammers, CM and Holtsche, MM and Hübner, F and Kiritsi, D and Schauer, F and Linnenmann, B and Huilaja, L and Tasanen-Määttä, K and Vassileva, S and Zillikens, D and Sadik, CD and Schmidt, E and Ibrahim, S and Baines, JF},
title = {The gut microbiome in bullous pemphigoid: implications of the gut-skin axis for disease susceptibility.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1212551},
doi = {10.3389/fimmu.2023.1212551},
pmid = {38022583},
issn = {1664-3224},
abstract = {Bullous pemphigoid (BP) is an autoimmune blistering disease that primarily affects the elderly. An altered skin microbiota in BP was recently revealed. Accumulating evidence points toward a link between the gut microbiota and skin diseases; however, the gut microbiota composition of BP patients remains largely underexplored, with only one pilot study to date, with a very limited sample size and no functional profiling of gut microbiota. To thoroughly investigate the composition and function of the gut microbiota in BP patients, and explore possible links between skin conditions and gut microbiota, we here investigated the gut microbiota of 66 patients (81.8% firstly diagnosed) suffering from BP and 66 age-, sex-, and study center-matched controls (CL) with non-inflammatory skin diseases (132 total participants), using 16S rRNA gene and shotgun sequencing data. Decreased alpha-diversity and an overall altered gut microbial community is observed in BP patients. Similar trends are observed in subclassifications of BP patients, including first diagnoses and relapsed cases. Furthermore, we observe a set of BP disease-associated gut microbial features, including reduced Faecalibacterium prausnitzii and greater abundance of pathways related to gamma-aminobutyric acid (GABA) metabolism in BP patients. Interestingly, F. prausnitzii is a well-known microbiomarker of inflammatory diseases, which has been reported to be reduced in the gut microbiome of atopic dermatitis and psoriasis patients. Moreover, GABA plays multiple roles in maintaining skin health, including the inhibition of itching by acting as a neurotransmitter, attenuating skin lesions by balancing Th1 and Th2 levels, and maintaining skin elasticity by increasing the expression of type I collagen. These findings thus suggest that gut microbiota alterations present in BP may play a role in the disease, and certain key microbes and functions may contribute to the link between gut dysbiosis and BP disease activity. Further studies to investigate the underlying mechanisms of the gut-skin interaction are thus clearly warranted, which could aid in the development of potential therapeutic interventions.},
}
@article {pmid38022571,
year = {2023},
author = {Liu, X and Wang, X and Zhang, P and Fang, Y and Liu, Y and Ding, Y and Zhang, W},
title = {Intestinal homeostasis in the gut-lung-kidney axis: a prospective therapeutic target in immune-related chronic kidney diseases.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1266792},
doi = {10.3389/fimmu.2023.1266792},
pmid = {38022571},
issn = {1664-3224},
abstract = {In recent years, the role of intestinal homeostasis in health has received increasing interest, significantly improving our understanding of the complex pathophysiological interactions of the gut with other organs. Microbiota dysbiosis, impaired intestinal barrier, and aberrant intestinal immunity appear to contribute to the pathogenesis of immune-related chronic kidney diseases (CKD). Meanwhile, the relationship between the pathological changes in the respiratory tract (e.g., infection, fibrosis, granuloma) and immune-related CKD cannot be ignored. The present review aimed to elucidate the new underlying mechanism of immune-related CKD. The lungs may affect kidney function through intestinal mediation. Communication is believed to exist between the gut and lung microbiota across long physiological distances. Following the inhalation of various pathogenic factors (e.g., particulate matter 2.5 mum or less in diameter, pathogen) in the air through the mouth and nose, considering the anatomical connection between the nasopharynx and lungs, gut microbiome regulates oxidative stress and inflammatory states in the lungs and kidneys. Meanwhile, the intestine participates in the differentiation of T cells and promotes the migration of various immune cells to specific organs. This better explain the occurrence and progression of CKD caused by upper respiratory tract precursor infection and suggests the relationship between the lungs and kidney complications in some autoimmune diseases (e.g., anti-neutrophil cytoplasm antibodies -associated vasculitis, systemic lupus erythematosus). CKD can also affect the progression of lung diseases (e.g., acute respiratory distress syndrome and chronic obstructive pulmonary disease). We conclude that damage to the gut barrier appears to contribute to the development of immune-related CKD through gut-lung-kidney interplay, leading us to establish the gut-lung-kidney axis hypothesis. Further, we discuss possible therapeutic interventions and targets. For example, using prebiotics, probiotics, and laxatives (e.g., Rhubarb officinale) to regulate the gut ecology to alleviate oxidative stress, as well as improve the local immune system of the intestine and immune communication with the lungs and kidneys.},
}
@article {pmid38022530,
year = {2023},
author = {Vietsch, EE and Latifi, D and Verheij, M and van der Oost, EWA and de Wilde, RF and Haen, R and van den Boom, AL and Koerkamp, BG and Doornebosch, PG and van Verschuer, VMT and Ooms, AHAG and Mohammad, F and Willemsen, M and Aerts, JGJV and Krog, RT and de Miranda, NFCC and van den Bosch, TPP and Mueller, YM and Katsikis, PD and van Eijck, CHJ},
title = {B cell immune profiles in dysbiotic vermiform appendixes of pancreatic cancer patients.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1230306},
doi = {10.3389/fimmu.2023.1230306},
pmid = {38022530},
issn = {1664-3224},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest solid tumors and is resistant to immunotherapy. B cells play an essential role in PDAC progression and immune responses, both locally and systemically. Moreover, increasing evidence suggests that microbial compositions inside the tumor, as well as in the oral cavity and the gut, are important factors in shaping the PDAC immune landscape. However, the gut-associated lymphoid tissue (GALT) has not previously been explored in PDAC patients. In this study, we analyzed healthy vermiform appendix (VA) from 20 patients with PDAC and 32 patients with colon diseases by gene expression immune profiling, flow cytometry analysis, and microbiome sequencing. We show that the VA GALT of PDAC patients exhibits markers of increased inflammation and cytotoxic cell activity. In contrast, B cell function is decreased in PDAC VA GALT based on gene expression profiling; B cells express significantly fewer MHC class II surface receptors, whereas plasma cells express the immune checkpoint molecule HLA-G. Additionally, the vermiform appendix microbiome of PDAC patients is enriched with Klebsiella pneumoniae, Bifidobacterium animalis, and Adlercreutzia equolifaciens, while certain commensals are depleted. Our findings may suggest impaired B cell function within the GALT of PDAC patients, which could potentially be linked to microbial dysbiosis. Additional investigations are imperative to validate our observations and explore these potential targets of future therapies.},
}
@article {pmid38022505,
year = {2023},
author = {Lawal, SA and Voisin, A and Olof, H and Bording-Jorgensen, M and Armstrong, H},
title = {Diversity of the microbiota communities found in the various regions of the intestinal tract in healthy individuals and inflammatory bowel diseases.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1242242},
doi = {10.3389/fimmu.2023.1242242},
pmid = {38022505},
issn = {1664-3224},
abstract = {The severe and chronic inflammatory bowel diseases (IBD), Crohn disease and ulcerative colitis, are characterized by persistent inflammation and gut damage. There is an increasing recognition that the gut microbiota plays a pivotal role in IBD development and progression. However, studies of the complete microbiota composition (bacteria, fungi, viruses) from precise locations within the gut remain limited. In particular, studies have focused primarily on the bacteriome, with available methods limiting evaluation of the mycobiome (fungi) and virome (virus). Furthermore, while the different segments of the small and large intestine display different functions (e.g., digestion, absorption, fermentation) and varying microenvironment features (e.g., pH, metabolites), little is known about the biogeography of the microbiota in different segments of the intestinal tract or how this differs in IBD. Here, we highlight evidence of the differing microbiota communities of the intestinal sub-organs in healthy and IBD, along with method summaries to improve future studies.},
}
@article {pmid38022043,
year = {2023},
author = {Kaliamoorthy, S and Priya Sayeeram, S and SundarRaj, S and Balakrishnan, J and Nagarajan, M and Samidorai, A},
title = {Investigating the Association Between Fusobacterium nucleatum and Oral Squamous Cell Carcinoma: A Pilot Case-Control Study on Tissue Samples.},
journal = {Cureus},
volume = {15},
number = {10},
pages = {e47238},
doi = {10.7759/cureus.47238},
pmid = {38022043},
issn = {2168-8184},
abstract = {Background Fusobacterium nucleatum (F. nucleatum) has been increasingly linked to oral squamous cell carcinoma (OSCC), prompting this study to explore its presence using polymerase chain reaction (PCR) and evaluate its clinical significance. Methods In this pilot case-control study, 12 OSCC tissue samples and 12 non-cancerous oral mucosal tissue samples were analyzed. Total RNA extraction and complementary DNA (cDNA) synthesis were performed using Trizol-based methods, followed by PCR amplification and gel electrophoresis. The clinical characteristics of participants and PCR results were recorded. Results Among the OSCC tissue samples, three out of 12 tested positive for F. nucleatum, while none of the control samples showed its presence. The detection rate of F. nucleatum in OSCC was 25%. Gel analysis confirmed specific amplicon amplification, and ImageJ software enabled copy number quantification. Discussion Our findings support previous research indicating a potential association between F. nucleatum and OSCC. Understanding the etiological significance of F. nucleatum in OSCC has clinical implications, including early detection, risk stratification, and prognostication. However, the limited sample size and the need for further research to elucidate underlying mechanisms are acknowledged. Conclusion This pilot study provides initial evidence of F. nucleatum's presence in a subset of OSCC samples, supporting its potential association with oral cancer. Detecting F. nucleatum in OSCC tissues holds promise for future research and clinical applications as a diagnostic and prognostic biomarker. Understanding its role in oral carcinogenesis will facilitate the development of targeted therapeutic strategies. Larger studies are warranted to validate these findings and investigate the precise mechanisms involved.},
}
@article {pmid38021696,
year = {2023},
author = {Algrafi, AS and Jamal, AA and Ismaeel, DM},
title = {Microbiota as a New Target in Cancer Pathogenesis and Treatment.},
journal = {Cureus},
volume = {15},
number = {10},
pages = {e47072},
doi = {10.7759/cureus.47072},
pmid = {38021696},
issn = {2168-8184},
abstract = {The microbial ecosystem of humans is an integral part of human health and disease. A significant percentage of tumors worldwide are thought to be microbially induced. The relationship between cancer and microbes is complex. In this article review, we aim to give an overview of human microbiota and its role in carcinogenesis, emphasize the relation between microbiota and cancer immunity, and highlight its role in the future of cancer therapy. The term microbiota refers to the collection of microorganisms that are located in an individual, whereas the total genome of these microorganisms is referred to as the microbiome. The microbiota in humans has many physiological functions. The microbiota within the gut lumen has a profound effect on the local and systemic immune system. The immune system can change the gut microbiota. Microbiota may induce carcinogenesis by several mechanisms. It also affects tumor progression. Thus, microbiota modulation may aid in the prevention and treatment of cancer. Intentionally introducing microorganisms into the oncological patient is assumed to mobilize the immune system to become able to, at least, limit the development of cancer. Microbes are used as vectors which are carriers of particular antineoplastic agents that reduce the side effects of chemotherapy. Inflammation and tumor microenvironment play an essential role in promoting chemo-resistance. There is now considerable evidence, both in humans as well as in laboratory animals, that the commensal microbiota has important effects on carcinogenesis, tumor growth, and therapy response.},
}
@article {pmid38021670,
year = {2023},
author = {Sharma, N and Chakole, S and Wandile, B},
title = {Uncovering the Cardiovascular Threat: A Comprehensive Examination of Liver Fibrosis and Subclinical Atherosclerosis in Non-alcoholic Fatty Liver Disease.},
journal = {Cureus},
volume = {15},
number = {10},
pages = {e46946},
doi = {10.7759/cureus.46946},
pmid = {38021670},
issn = {2168-8184},
abstract = {Non-alcoholic fatty liver disease (NAFLD) has emerged as a global epidemic intricately linked to the rising tide of obesity and metabolic syndrome. This comprehensive review delves into the complex web of relationships between NAFLD, liver fibrosis, and subclinical atherosclerosis, shedding light on their interplay, shared risk factors, and clinical implications. NAFLD encompasses a spectrum of liver conditions, from the benign non-alcoholic fatty liver (NAFL) to the more severe non-alcoholic steatohepatitis (NASH), characterized by inflammation and hepatocellular injury. Central to the discussion is the insidious development of liver fibrosis, the ominous harbinger of progressive liver damage, cirrhosis, and hepatocellular carcinoma. The increasing prevalence of NAFLD, now affecting a quarter of the global population, poses a significant public health challenge. Its association with obesity, insulin resistance, and metabolic syndrome highlights the multifactorial nature of this disease. However, NAFLD's repercussions extend beyond the liver. This review unveils a potent connection between NAFLD and subclinical atherosclerosis, the early precursor to cardiovascular disease. Individuals with NAFLD face an elevated risk of atherosclerosis, even without traditional cardiovascular risk factors. The intricate link between these two conditions is illuminated through shared pathophysiological pathways, including systemic inflammation, insulin resistance, and dyslipidemia. Understanding the interplay between liver fibrosis and subclinical atherosclerosis has profound clinical implications. Patients with advanced fibrosis or cirrhosis are not only at risk of liver-related complications but also of cardiovascular events. This necessitates a holistic approach to patient care, with lifestyle modifications and pharmacological interventions simultaneously managing both conditions. Physicians must prioritize early detection and collaborate across disciplines to provide comprehensive care. Looking ahead, the future holds promising avenues of research. Emerging areas include genetics and precision medicine, microbiome research, and epigenetics, which may unveil new therapeutic targets. Innovations in diagnostics and therapeutics, such as non-invasive biomarkers and combination therapies, offer hope for more effective management. Long-term outcomes and survivorship research will provide insights into the lasting impact of interventions. In conclusion, this review underscores the imperative of addressing liver fibrosis and atherosclerosis in the context of NAFLD. It is a call to action for healthcare professionals, researchers, and policymakers to work collaboratively, promote early detection, and advance our understanding of these interconnected conditions. By doing so, we can enhance patient outcomes and chart a course toward a healthier future for those grappling with NAFLD and its intricate web of consequences.},
}
@article {pmid38021562,
year = {2023},
author = {Antony, MA and Patel, S and Verma, V and Kant, R},
title = {The Role of Gut Microbiome Supplementation in COVID-19 Management.},
journal = {Cureus},
volume = {15},
number = {10},
pages = {e46960},
doi = {10.7759/cureus.46960},
pmid = {38021562},
issn = {2168-8184},
abstract = {COVID-19, which is caused by the RNA virus, SARS-CoV-2, mainly affects the respiratory system and has a varied clinical presentation. However, several studies have shown that COVID-19 can also affect the gastrointestinal (GI) system. Patients can experience various GI symptoms, such as vomiting and diarrhea, and the virus has been detected in the stool samples of patients hospitalized with COVID-19. There have also been rare reports of COVID-19 presenting with isolated GI symptoms and lack of respiratory symptoms, and the virus has also been detected for prolonged periods in the fecal samples of COVID-19 patients. Major alterations in the gut microbiome in the form of depletion of beneficial organisms and an abundance of pathogenic organisms have been reported in the fecal samples of hospitalized COVID-19 patients. Although the US FDA has approved several drugs to manage COVID-19, their efficacy remains modest. So, there is a constant ongoing effort to investigate novel treatment options for COVID-19. Health supplements like probiotics, prebiotics, postbiotics, and synbiotics have been popularly known for their various health benefits. In this review, we have summarized the current literature, which shows the potential benefit of these health supplements to mitigate and/or prevent the clinical presentation of COVID-19.},
}
@article {pmid38021395,
year = {2023},
author = {Mohsen Hammad, DB and Abdulazeez Alhamad, O and Mahdy Obiad Khzal, A and Mahdi Muslim Alameedy, F},
title = {Molecular Characterisation of Blood Microbiome in Patients with Ankylosing Spondylitis and Healthy Controls.},
journal = {Medical journal of the Islamic Republic of Iran},
volume = {37},
number = {},
pages = {84},
doi = {10.47176/mjiri.37.84},
pmid = {38021395},
issn = {1016-1430},
abstract = {BACKGROUND: In human and animal studies, ankylosing spondylitis (AS) has been increasingly linked to changes in the microbial inhabitants in the human body (microbiome). These studies have primarily now concentrated on the microbial communities that live in the gastrointestinal tract. However, evidence suggests that various molecular techniques can be used to detect microbial DNA in blood circulation. This DNA might be an unknown reservoir of biomarkers with the potential to track alterations in the microbiomes of remote locations, such as the gut. To this end, we compared the presence and identity of microbial DNA in blood samples taken from ankylosing spondylitis patients to healthy control subjects by amplifying and sequencing the bacterial 16S rRNA variable region four.<br><br>METHODS: The study's design is a case study based on the presence and identity of bacterial DNA in the blood of Ankylosing spondylitis (AS) patients (n = 10) and healthy control subjects (n = 10) was investigated by amplifying and sequencing the bacterial 16S rRNA gene. Blood concentrations of the cytokines TNF alpha, IL-17A, and IL-23 were determined by the Human Magnetic Luminex Screening, and data were analysed using an Unpaired T-test.<br><br>RESULTS: Using PCR amplification, 8 of 10 AS patients (80%) and 8 of 10 healthy control samples (80%) had microbial 16S rRNA in their blood. At the phylum level, Proteobacteria (Control = 48.5%, AS = 52%), Firmicutes (Control = 27.8%, AS = 26.1%), Actinobacteria (Control = 15.4%, AS = 10.7%), and Bacteroidetes (Control = 6.5%, AS = 10%) dominated the blood microbiome. A two-tailed Mann-Whitney test found that Ankylosing Spondylitis was associated with significantly elevated Bacteroides (P < 0.05), Prevotella (P < 0.001), and Micrococcus (P < 0.01), and significantly reduced levels of Corynebacterium 1 (P < 0.001), Gemella (P < 0.01), and Alloprevotella (P < 0.05), compared to healthy controls. Additionally, it was shown that the presence of the Prevotella genus was highly positively correlated with higher levels of TNF-alpha (P < 0.05; r = 0.8) in AS patients' blood.<br><br>CONCLUSION: This article reveals that a blood microbiome exists in healthy individuals and identifies particular taxa modulated in disease. These blood-derived signatures indicate that this field needs more research and may be helpful as disease biomarkers.},
}
@article {pmid38021257,
year = {2023},
author = {Chen, G and Yuan, Y and Tang, S and Yang, Z and Wu, Q and Liang, Z and Chen, S and Li, W and Lv, X and Ni, L},
title = {Comparative analysis of microbial communities and volatile flavor components in the brewing of Hongqu rice wines fermented with different starters.},
journal = {Current research in food science},
volume = {7},
number = {},
pages = {100628},
doi = {10.1016/j.crfs.2023.100628},
pmid = {38021257},
issn = {2665-9271},
abstract = {As one of the quintessential representatives of Chinese rice wine, Hongqu rice wine is brewed with glutinous rice as the main raw material and Hongqu (Gutian Qu or Wuyi Qu) as the fermentation starter. The present study aimed to investigate the impact of Hongqu on the volatile compositions and the microbial communities in the traditional production of Gutian Hongqu rice wine (GT) and Wuyi Hongqu rice wine (WY). Through the OPLS-DA analysis, 3-methylbutan-1-ol, isobutanol, ethyl lactate, ethyl acetate, octanoic acid, diethyl succinate, phenylethyl alcohol, hexanoic acid and n-decanoic acid were identified as the characteristic volatile flavor components between GT and WY. Microbiome analysis revealed significant enrichments of Lactobacillus, Pediococcus, Aspergillus and Hyphopichia in WY brewing, whereas Monascus, Saccharomyces, Pantoea, and Burkholderia-Caballeronia-Paraburkholderia were significantly enriched in GT brewing. Additionally, correlation analysis showed that Saccharomyces, Lactobacillus, Weissella and Pediococcus were significantly positively correlated wih most characteristic volatile components. Conversely, Picha, Monascus, Franconibacter and Kosakonia showed significant negative correlations with most of the characteristic volatile components. Furthermore, bioinformatical analysis indicated that the gene abundances for enzymes including glucan 1,4-alpha-glucosidase, carboxylesterase, alcohol dehydrogenase, dihydroxy-acid dehydratase and branched-chain-amino-acid transaminase were significantly higher in WY compared to GT. This finding explains the higher content of higher alcohols and characteristic esters in WY relative to GT. Collectively, this study provides a theoretical basis for improving the flavor profile of Hongqu rice wine and establishing a solid scientific foundation for the sustainable development of Hongqu rice wine industry.},
}
@article {pmid38020871,
year = {2023},
author = {Li, D and Xia, W and Cui, X and Zhao, M and Huang, K and Wang, X and Shen, J and Chen, H and Zhu, L},
title = {The putatively high-altitude adaptation of macaque monkeys: Evidence from the fecal metabolome and gut microbiome.},
journal = {Evolutionary applications},
volume = {16},
number = {10},
pages = {1708-1720},
doi = {10.1111/eva.13595},
pmid = {38020871},
issn = {1752-4571},
abstract = {Animals living in high-altitude environments, such as the Tibetan Plateau, must face harsh environmental conditions (e.g., hypoxia, cold, and strong UV radiation). These animals' physiological adaptations (e.g., increased red cell production and turnover rate) might also be associated with the gut microbial response. Bilirubin is a component of red blood cell turnover or destruction and is excreted into the intestine and reduced to urobilinoids and/or urobilinogen by gut bacteria. Here, we found that the feces of macaques living in high-altitude regions look significantly browner (with a high concentration of stercobilin, a component from urobilinoids) than those living in low-altitude regions. We also found that gut microbes involved in urobilinogen reduction (e.g., beta-glucuronidase) were enriched in the high-altitude mammal population compared to the low-altitude population. Moreover, the spatial-temporal change in gut microbial function was more profound in the low-altitude macaques than in the high-altitude population, which might be attributed to profound changes in food resources in the low-altitude regions. Therefore, we conclude that a high-altitude environment's stress influences living animals and their symbiotic microbiota.},
}
@article {pmid38020771,
year = {2023},
author = {Lee, EH and Kim, GH and Park, HK and Kang, HJ and Park, YK and Lee, HA and Hong, CH and Moon, SY and Kang, W and Oh, HS and Yoon, HJ and Choi, SH and Jeong, JH},
title = {Effects of the multidomain intervention with nutritional supplements on cognition and gut microbiome in early symptomatic Alzheimer's disease: a randomized controlled trial.},
journal = {Frontiers in aging neuroscience},
volume = {15},
number = {},
pages = {1266955},
doi = {10.3389/fnagi.2023.1266955},
pmid = {38020771},
issn = {1663-4365},
abstract = {BACKGROUND: The SoUth Korean study to PrEvent cognitive impaiRment and protect BRAIN health through lifestyle intervention in at-risk elderly people (SUPERBRAIN) is a part of the World-Wide Finnish Geriatric Intervention Study to Prevent Cognitive Impairment and Disability (WW-FINGERS) network. This study aimed to demonstrate the effects of the SUPERBRAIN-based multidomain intervention with nutritional supplements in amyloid positive emission tomography (PET) proven early symptomatic Alzheimer's disease patients.<br><br>METHODS: Forty-six participants who were diagnosed with mild cognitive impairment or mild dementia and were positive in the amyloid PET study randomized into three groups: group A, the multidomain intervention with nutritional supplements; group B, nutritional supplements only; and a control group. The primary outcome was a change in the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) total scale index score after an 8-week intervention. Secondary outcomes, including gut microbiome data, were also analyzed.<br><br>RESULTS: The RBANS total scale index score improved significantly in group A compared with group B (p&#x2009;<&#x2009;0.032) and compared with the control group (p&#x2009;<&#x2009;0.001). After intervention, beta diversity of the gut microbiome between group A and the control group increased, and patients in group A were more enriched with Bifidobacterium.<br><br>CONCLUSION: SUPERBRAIN-based multidomain intervention with nutritional supplements improves cognition and gut microbiota in patients with early symptomatic Alzheimer's disease who were amyloid-positive by PET.},
}
@article {pmid38020719,
year = {2023},
author = {Lin, K and Dong, C and Zhao, B and Zhou, B and Yang, L},
title = {Glucagon-like peptide-1 receptor agonist regulates fat browning by altering the gut microbiota and ceramide metabolism.},
journal = {MedComm},
volume = {4},
number = {6},
pages = {e416},
doi = {10.1002/mco2.416},
pmid = {38020719},
issn = {2688-2663},
abstract = {Studies have shown that antidiabetic drugs can alter the gut microbiota. The hypoglycemic effects of the drugs can be attributed in part to certain species in the gut microbiome that help the drugs work more effectively. In addition, increasing energy expenditure via the induction of adipose tissue browning has become an appealing strategy to treat obesity and associated metabolic complications. Currently, glucagon-like peptide-1 receptor agonist (GLP-1 RA) treatment for metabolic disorders such as obesity and type 2 diabetes has been widely studied. To determine the mechanism of a long-acting GLP-1 RA affects adipose tissue browning and the gut microbiome, we treated high-fat diet mice with GLP-1 RA and demonstrated that the drug can regulate adipose tissue browning. 16S rRNA and untargeted metabolomics assays suggested that it increased the abundance of bacterium Lactobacillus reuteri and decreased serum ceramide levels in mice. L. reuteri was negatively correlated with ceramide. We found that the mechanism of ceramide decline was alkaline ceramidase 2 (Acer2) overexpression. Moreover, L. reuteri can play a therapeutic synergistic role with GLP-1 RA, suggesting that gut microbiota can be used as a part of the treatment of diabetes.},
}
@article {pmid38020524,
year = {2023},
author = {Liss, MA and Reveles, KR and Tipton, CD and Gelfond, J and Tseng, T},
title = {Comparative Effectiveness Randomized Clinical Trial Using Next-generation Microbial Sequencing to Direct Prophylactic Antibiotic Choice Before Urologic Stone Lithotripsy Using an Interprofessional Model.},
journal = {European urology open science},
volume = {57},
number = {},
pages = {74-83},
doi = {10.1016/j.euros.2023.09.008},
pmid = {38020524},
issn = {2666-1683},
abstract = {BACKGROUND: Next-generation sequencing (NGS) methods for microbial profiling have increased sensitivity to detect urinary pathogens.<br><br>OBJECTIVE: To determine whether NGS microbial profiling can be used to guide antibiotic prophylaxis and reduce infection compared with the standard of care.<br><br>A prospective randomized controlled clinical trial of patients undergoing urologic stone interventions at an academic health center from December 2019 to January 2022 was conducted. Urine was collected at the preoperative visit for standard culture and intervention NGS diagnostics. Evaluable patients were culture negative, met 2-wk follow-up, and did not cancel surgery. Of 240 individuals (control&#xa0;=&#xa0;121, intervention&#xa0;=&#xa0;119), 83 control and 74 intervention patients were evaluable.<br><br>INTERVENTION: Microbial findings (paired quantitative polymerase chain reaction and NGS) were sent to an infectious disease pharmacist to recommend prophylactic antimicrobial regimen.<br><br>The primary outcome was postoperative urinary infection within the follow-up period (Fisher's exact test). The primary outcome was analyzed by modified intent-to-treat (mITT) and per-protocol analyses. Secondary endpoints considered included positive culture concordance, antibiotic use, and adverse events. Additional post hoc analyses investigated factors contributing to infection (univariate logistic regression).<br><br>RESULTS AND LIMITATIONS: The intervention significantly reduced postsurgical urinary infection risk by 7.1% (-0.73%, 15%) compared with the standard of care in the mITT analysis (1.4% vs 8.4%, p&#xa0;=&#xa0;0.045) or by 8.5% (0.88%, 16%) compared with the per-protocol analysis (0% vs 8.5%, p&#xa0;=&#xa0;0.032). NGS-guided treatment altered the distribution of antibiotics used (p&#xa0;=&#xa0;0.025), and antibiotics poorly matched with NGS findings were associated with increased infection odds (odds ratio [OR]&#xa0;=&#xa0;5.9, p&#xa0;=&#xa0;0.046). Women were at greater odds to develop infection (OR&#xa0;=&#xa0;10, p&#xa0;=&#xa0;0.03) and possessed differentiated microbial profiles (p&#xa0;<&#xa0;0.001).<br><br>CONCLUSIONS: Urinary microbial NGS-guided antibiotic prophylaxis before endoscopic urologic stone lithotripsy improves antibiotic selection to reduce healthcare-associated urinary infections; however, treatment efficacy may be limited by the ability to adhere to the recommended protocol.<br><br>PATIENT SUMMARY: We investigated whether microbial DNA sequencing could improve the selection of antibiotics before kidney stone surgery in patients not known to have any bacteria in the urine on standard culture. We found that using microbe DNA to guide antibiotic choices decreased postoperative infection rate and may encourage individualized use of available antibiotics.},
}
@article {pmid38020300,
year = {2023},
author = {Liu, W and Li, Z and Li, X and Cao, H and Jiang, H and Niu, Q and Hu, B},
title = {Influence of tumor mycobiome on cancer pathogenesis (Review).},
journal = {Oncology letters},
volume = {26},
number = {6},
pages = {541},
doi = {10.3892/ol.2023.14128},
pmid = {38020300},
issn = {1792-1082},
abstract = {Cancer tissues harbor a large microbiome. There is growing evidence that the tumor microbiome is significantly correlated with the prognosis of cancer patients, but the exact underlying mechanisms have remained elusive. Although the tumor mycobiome is less abundant than the biome of bacteria, it is prevalent in most cancers in humans. The present review describes in detail the impact of the tumor mycobiome on cancer pathogenesis. The tumor mycobiome promotes tumor progression and metastasis by affecting the human immune system, maintaining a pro-inflammatory environment, producing aflatoxins, attenuating cell adhesion mechanisms and fungal-bacterial interactions. Furthermore, the tumor mycobiome likewise has great potential for cancer prevention, diagnosis and treatment.},
}
@article {pmid38020222,
year = {2023},
author = {Arakkal Thaiparambil, N and Radhakrishnan, V},
title = {Role of formulated bacterial consortia in biofortifying tomato fruits with nutrients: A nutritional, genomic and metagenomic analysis.},
journal = {Saudi journal of biological sciences},
volume = {30},
number = {12},
pages = {103851},
doi = {10.1016/j.sjbs.2023.103851},
pmid = {38020222},
issn = {1319-562X},
abstract = {Nutrient deficiencies are a major problem that is prone to affect millions of people around the globe. Biofortification, a process of enriching nutrients in staple food crops is an effective method to tackle this malnutrition-associated disorder. Tomato (Solanum lycopersicum) is a globally consumed crop and therefore is a suitable candidate for biofortification. Many plant growth-promoting bacteria are reported to have the ability to enhance nutrient content in plants. In the present study, we have investigated the ability of two bacterial consortia (consortia-1 -co-culturing Lysinibacillus sp. strain VITKC-5 and Acinetobacter Sp. strain VITKC_6; and consortia-2 -co-culturing Lysinibacillus sp. strain VITKC-5 and Enterobacter sp. strain VITVLC-4) in the nutrient enrichment of tomato fruits. The results were then correlated with the elevated expression of nutrient transporter genes. Furthermore, the effect of these bacterial formulations on the indigenous microbiome has also been evaluated through metagenomic analysis. The application of bacterial formulations significantly improved the nutrient content when compared to the control (untreated) group. These findings advocate that PGPB-assisted biofortification has the potential to alleviate nutrient deficiency in humans.},
}
@article {pmid38020091,
year = {2023},
author = {Kim, MG and Cho, WY and Chung, SM and Choi, YE and Fang, Y and Park, MS and Park, SJ and Ko, YS and Lee, HY and Yang, J and Oh, SW and Jo, SK},
title = {Altered gut microbiome plays an important role in AKI to CKD transition in aged mice.},
journal = {Frontiers in medicine},
volume = {10},
number = {},
pages = {1238960},
doi = {10.3389/fmed.2023.1238960},
pmid = {38020091},
issn = {2296-858X},
abstract = {INTRODUCTION: This study investigated the role of renal-intestinal crosstalk in the transition from acute kidney injury (AKI) to chronic kidney disease (CKD) in elderly individuals.<br><br>METHODS: Using young and aged mice, we induced bilateral ischemia-reperfusion injury (IRI) and compared intestinal and kidney inflammation over 28&#x2009;days. To determine the role of the microbiome in gut-kidney crosstalk, we analyzed the microbiome of fecal samples of the young vs. aged mice and examined the effects of probiotic supplementation.<br><br>RESULTS: In the post-IRI recovery phase, prolonged intestinal and renal inflammation along with dysbiosis were evident in aged vs. younger mice that was associated with severe renal dysfunction and fibrosis progression in aged mice. Probiotic supplementation with Bifidobacterium bifidum BGN4 and Bifidobacterium longum BORI alleviated intestinal inflammation but not intestinal leakage, characterized by decreased inflammatory cytokine levels and decreased infiltration of macrophages, neutrophils, and Th17 cells. This was associated with improved M1-dominant renal inflammation and ultimately improved renal function and fibrosis, suggesting that renal-intestinal crosstalk in aged mice contributes to the transition from AKI to CKD.<br><br>DISCUSSION: Our study findings suggest that exacerbation of chronic inflammation through the gut-kidney axis might be an important mechanism in the transition from AKI to CKD in the elderly.},
}
@article {pmid38019934,
year = {2023},
author = {Agarwal, K and Choudhury, B and Robinson, LS and Morrill, SR and Bouchibiti, Y and Chilin-Fuentes, D and Rosenthal, SB and Fisch, KM and Peipert, JF and Lebrilla, CB and Allsworth, JE and Lewis, AL and Lewis, WG},
title = {Resident microbes shape the vaginal epithelial glycan landscape.},
journal = {Science translational medicine},
volume = {15},
number = {724},
pages = {eabp9599},
doi = {10.1126/scitranslmed.abp9599},
pmid = {38019934},
issn = {1946-6242},
abstract = {Epithelial cells are covered in carbohydrates (glycans). This glycan coat or "glycocalyx" interfaces directly with microbes, providing a protective barrier against potential pathogens. Bacterial vaginosis (BV) is a condition associated with adverse health outcomes in which bacteria reside in direct proximity to the vaginal epithelium. Some of these bacteria, including Gardnerella, produce glycosyl hydrolase enzymes. However, glycans of the human vaginal epithelial surface have not been studied in detail. Here, we elucidate key characteristics of the "normal" vaginal epithelial glycan landscape and analyze the impact of resident microbes on the surface glycocalyx. In human BV, glycocalyx staining was visibly diminished in electron micrographs compared to controls. Biochemical and mass spectrometric analysis showed that, compared to normal vaginal epithelial cells, BV cells were depleted of sialylated N- and O-glycans, with underlying galactose residues exposed on the surface. Treatment of primary epithelial cells from BV-negative women with recombinant Gardnerella sialidases generated BV-like glycan phenotypes. Exposure of cultured VK2 vaginal epithelial cells to recombinant Gardnerella sialidase led to desialylation of glycans and induction of pathways regulating cell death, differentiation, and inflammatory responses. These data provide evidence that vaginal epithelial cells exhibit an altered glycan landscape in BV and suggest that BV-associated glycosidic enzymes may lead to changes in epithelial gene transcription that promote cell turnover and regulate responses toward the resident microbiome.},
}
@article {pmid38019873,
year = {2023},
author = {Bar, O and Sudhof, LS and Yockey, LJ and Bergerat, A and Moriel, N and Andrews, E and Ananthakrishnan, AN and Xavier, RJ and Yassour, M and Mitchell, CM},
title = {Comparison of vaginal microbiota between women with inflammatory bowel disease and healthy controls.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0284709},
doi = {10.1371/journal.pone.0284709},
pmid = {38019873},
issn = {1932-6203},
abstract = {BACKGROUND: The gut microbiota in patients with inflammatory bowel disease are perturbed in both composition and function. The vaginal microbiome and its role in the reproductive health of women with inflammatory bowel disease is less well described.<br><br>OBJECTIVE: We aim to compare the vaginal microbiota of women with inflammatory bowel disease to healthy controls.<br><br>METHODS: Women with inflammatory bowel disease enrolled in a longitudinal cohort study provided self-collected vaginal swabs. Healthy controls underwent provider-collected vaginal swabs at routine gynecologic exams. All participants completed surveys on health history, vulvovaginal symptoms and gastrointestinal symptoms, if applicable. Microbiota were characterized by sequencing the V4 region of the 16S rRNA gene. Associations between patient characteristics and microbial community composition were evaluated by PERMANOVA and Principal Components Analysis. Lactobacillus dominance of the microbial community was compared between groups using chi-square and Poisson regression.<br><br>RESULTS: The cohort included 54 women with inflammatory bowel disease (25 Ulcerative colitis, 25 Crohn's Disease) and 26 controls. A majority, 72 (90%) were White; 17 (31%) with inflammatory bowel disease and 7 (27%) controls were postmenopausal. The composition of the vaginal microbiota did not vary significantly by diagnosis or severity of inflammatory bowel disease but did vary by menopausal status (p = 0.042). There were no significant differences in Shannon Diversity Index between healthy controls and women with IBD in premenopausal participants. There was no difference in proportion of Lactobacillus dominance according to diagnosis in premenopausal participants. A subgroup of postmenopausal women with Ulcerative colitis showed a significant higher alpha diversity and a lack of Lactobacillus dominance in the vaginal microbiome.<br><br>CONCLUSIONS: Menopausal status had a larger impact on vaginal microbial communities than inflammatory bowel disease diagnosis or severity.},
}
@article {pmid38019089,
year = {2023},
author = {Muñoz, E and Fuentes, F and Felmer, R and Arias, ME and Yeste, M},
title = {Effects of reactive oxygen and nitrogen species stress on male fertility.},
journal = {Antioxidants &amp; redox signaling},
volume = {},
number = {},
pages = {},
doi = {10.1089/ars.2022.0163},
pmid = {38019089},
issn = {1557-7716},
abstract = {SIGNIFICANCE: In recent decades, male fertility has been severely reduced worldwide. The causes underlying this decline are multifactorial and include, among others, genetic alterations, changes in the microbiome, and the impact of environmental pollutants. Such factors have in common that they can dysregulate physiological levels of reactive species of oxygen (ROS) and nitrogen (RNS) in the patient, generating oxidative and nitrosative stress that impairs fertility.<br><br>RECENT ADVANCES: Recent studies have delved into other factors involved in the dysregulation of ROS and RNS levels, such as diet, obesity, persistent infections, environmental pollutants and gut microbiota, thus leading to new strategies to solve male fertility problems, such as consuming prebiotics to regulate gut flora or treating psychological conditions.<br><br>CRITICAL ISSUES: The pathways where ROS or RNS may be involved as modulators are still under investigation. Moreover, the extent to which treatments can rescue male infertility as well as whether they may have side effects remain, in most cases, to be elucidated. For example, it is known that prescription of antioxidants to treat nitrosative stress can alter sperm chromatin condensation, which makes DNA more exposed to ROS and RNS, and may thus affect fertilization and early embryo development.<br><br>FUTURE DIRECTIONS: The involvement of extracellular vesicles, which might play a crucial role in cell communication during spermatogenesis and epididymal maturation, and the relevance of other factors like sperm epigenetic signatures should be envisaged in the future.},
}
@article {pmid38018983,
year = {2023},
author = {Panyod, S and Wu, W-K and Hu, M-Y and Huang, H-S and Chen, R-A and Chen, Y-H and Shen, T-CD and Ho, C-T and Liu, C-J and Chuang, H-L and Huang, C-C and Wu, M-S and Sheen, L-Y},
title = {Healthy diet intervention reverses the progression of NASH through gut microbiota modulation.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0186823},
doi = {10.1128/spectrum.01868-23},
pmid = {38018983},
issn = {2165-0497},
abstract = {The link between gut microbiota and diet is crucial in the development of non-alcoholic steatohepatitis (NASH). This study underscores the essential role of a healthy diet in preventing and treating NASH by reversing obesity, lipidemia, and gut microbiota dysbiosis. Moreover, the supplementation of functional food or drug to the diet can provide additional advantages by inhibiting hepatic inflammation through the modulation of the hepatic inflammasome signaling pathway and partially mediating the gut microbiota and lipopolysaccharide signaling pathway. This study highlights the importance of adopting healthy dietary habits in treating NASH and proposes that supplementing with ginger essential oil or obeticholic acid may offer additional benefits. Nonetheless, further clinical studies are necessary to validate these findings.},
}
@article {pmid38018965,
year = {2023},
author = {Ottesen, A and Kocurek, B and Deaver, C and Chiesa, O and Cohen, R and Reed, E and Commichaux, S and Mammel, M and McDermott, P and Strain, E and Myers, M},
title = {Fecal microbiomes of laboratory beagles receiving antiparasitic formulations in an experimental setting.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0086023},
doi = {10.1128/MRA.00860-23},
pmid = {38018965},
issn = {2576-098X},
abstract = {Here, we describe the fecal microbiome of laboratory beagles in a non-invasive experiment designed to contrast in vivo versus in vitro bioequivalence in response to antiparasitic drug administration. The experiment provided a unique opportunity to evaluate metagenomic profiles of canine feces before and after anti-parasitic drug exposure.},
}
@article {pmid38018964,
year = {2023},
author = {Nguyen, VH and Sharon, BM and Shipman, BM and Zimmern, PE and De Nisco, NJ},
title = {Complete genomes of Limosilactobacillus portuensis and Limosilactobacillus vaginalis isolated from the urine of postmenopausal women.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0088323},
doi = {10.1128/MRA.00883-23},
pmid = {38018964},
issn = {2576-098X},
abstract = {There is frequent evidence that Limosilactobacillus vaginalis colonizes female genitourinary tracts but few reports of Limosilactobacillus portuensis. Their role in urinary tract infection (UTI) is unclear. We present the first complete genome of L. portuensis and a complete genome of L. vaginalis isolated from postmenopausal women with varying UTI histories.},
}
@article {pmid38018859,
year = {2023},
author = {Ramamoorthy, S and Pena, M and Ghosh, P and Liao, Y-Y and Paret, M and Jones, JB and Potnis, N},
title = {Transcriptome profiling of type VI secretion system core gene tssM mutant of Xanthomonas perforans highlights regulators controlling diverse functions ranging from virulence to metabolism.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0285223},
doi = {10.1128/spectrum.02852-23},
pmid = {38018859},
issn = {2165-0497},
abstract = {T6SS has received attention due to its significance in mediating interorganismal competition through contact-dependent release of effector molecules into prokaryotic and eukaryotic cells. Reverse-genetic studies have indicated the role of T6SS in virulence in a variety of plant pathogenic bacteria, including the one studied here, Xanthomonas. However, it is not clear whether such effect on virulence is merely due to a shift in the microbiome-mediated protection or if T6SS is involved in a complex virulence regulatory network. In this study, we conducted in vitro transcriptome profiling in minimal medium to decipher the signaling pathways regulated by tssM-i3* in X. perforans AL65. We show that TssM-i3* regulates the expression of a suite of genes associated with virulence and metabolism either directly or indirectly by altering the transcription of several regulators. These findings further expand our knowledge on the intricate molecular circuits regulated by T6SS in phytopathogenic bacteria.},
}
@article {pmid38018836,
year = {2023},
author = {Bishu, S and Ginnebaugh, B and Chu, J and Levy, BH and , },
title = {Microbiome-Based Therapeutics in Digestive Diseases: What They Are and How Are They Regulated.},
journal = {Clinical and translational gastroenterology},
volume = {14},
number = {11},
pages = {e00636},
doi = {10.14309/ctg.0000000000000636},
pmid = {38018836},
issn = {2155-384X},
}
@article {pmid38018203,
year = {2023},
author = {Meda, A and Fredrick, F and Rathod, U and Shah, P and Jain, R},
title = {Cardiovascular Manifestations in Inflammatory Bowel Disease.},
journal = {Current cardiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.2174/011573403X256094231031074753},
pmid = {38018203},
issn = {1875-6557},
abstract = {Inflammatory bowel disease is a group of long-term systemic inflammatory disorders affecting the gastrointestinal tract, including Crohn's disease and ulcerative colitis, which may be associated with an increased risk of developing extraintestinal manifestations, including cardiovascular disease, thereby decreasing the quality of life. Pathophysiological changes associated with inflammatory bowel disease include alterations of the microbiome, endotoxemia, and changes to glucose and lipid metabolism. Inflammatory bowel disease patients have higher carotid intima-media thickness, lower flow-mediated dilatation, and increased carotid-femoral pulse wave velocity, which are markers of elevated cardiovascular risk. In addition, inflammatory bowel disease patients are at an increased risk for developing venous and arterial thrombotic events due to a hypercoagulable state caused by thrombocytosis and coagulation system activation. To reduce the risk of developing cardiovascular disease, lifestyle modifications, such as smoking cessation, dietary changes, and increased physical activity alongside management with appropriate medication, should be considered. This research paper examines how inflammatory bowel disease can influence the risk of cardiovascular complications and the involvement of drug therapy. Methods: PubMed was searched using keywords, such as inflammatory bowel disease, Crohn's disease, ulcerative colitis, cardiovascular disease, pericarditis, thromboembolism, and many more. Relevant literature up to March 2023 has been examined and summarized, which consisted of data from various clinical trials, meta-analyses, retrospective/prospective cohort studies, and current guidelines.},
}
@article {pmid38018189,
year = {2023},
author = {Zheng, Y and Liu, J and Beeraka, NM and Manogaran, P and Vikram P R, H and Yn, LD and Suhail, SM and Pradeepkumar, B and Sinelnikov, MY and Greeshma, MV and P A, M and Mp, N and Bannimath, G and Zhao, J and Fan, R},
title = {Inflammation and Stem Cell Stochasticity of HPV-induced Cervical Cancer: Epigenetics Based Biomarkers through Microbiome and Metabolome for Personalized Medicine: A Systematic Review.},
journal = {Current medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298673257429231108072717},
pmid = {38018189},
issn = {1875-533X},
abstract = {BACKGROUND: Chemoresistance by stemness in HPV-induced cervical carcinogenesis has significant implications for the overall disease-specific survival of the patients. To date, there are no reports related to the implications of significant aspects of inflammation and microbiome-- mediated epigenetics in cervical cancers.<br><br>OBJECTIVE: The current systematic review delineates the significant aspects of the inflammation-related pathophysiology, cervical cancer diagnosis based on the HPV-indued stemness, and microbiome- mediated epigenetic markers to develop personalized therapies to target the stemness-acquired indefinitely dividing cancer stem cells.<br><br>METHODS: We performed a systematic review without a meta- analysis. We searched several public databases, such as Pubmed, ReleMed, National Library of Medicine, and Scopus, related to inflammation, metabolomics, microbiome-mediated epigenetic markers, and HPV-induced stemness.<br><br>RESULTS AND CONCLUSION: The review significantly described the correlation between microbial inflammation and stem cell stochasticity of HPV-Induced cervical cancer and the expression of epigenetics- based biomarkers through microbiome and metabolome to foster the cervical cancer progression. These are major risk factors that can cause cervical dysplasia with substantial therapy resistance in cervical cancer patients. The qualitative and quantitative examination of the spatial transcriptomic expression of these stemness markers in the dividing cervical cancer stem cells has significant implications in the clinical sector to develop early personalized medicine to prevent cervical precancerous lesions depending on the prognosis of the cervical cancer patients. Mainly, the combinatorial regimen of current therapeutic modalities, along with microbiome-related therapies with future landscape of epigenetics-modulated therapies, may enhance overall disease-specific survival by modulating the stochastic dynamics of basal epithelial cells across the cervical region.},
}
@article {pmid38018103,
year = {2023},
author = {Xu, CCY and Lemoine, J and Albert, A and Whirter, &#xc9;M and Barrett, RDH},
title = {Community assembly of the human piercing microbiome.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2011},
pages = {20231174},
doi = {10.1098/rspb.2023.1174},
pmid = {38018103},
issn = {1471-2954},
abstract = {Predicting how biological communities respond to disturbance requires understanding the forces that govern their assembly. We propose using human skin piercings as a model system for studying community assembly after rapid environmental change. Local skin sterilization provides a 'clean slate' within the novel ecological niche created by the piercing. Stochastic assembly processes can dominate skin microbiomes due to the influence of environmental exposure on local dispersal, but deterministic processes might play a greater role within occluded skin piercings if piercing habitats impose strong selection pressures on colonizing species. Here we explore the human ear-piercing microbiome and demonstrate that community assembly is predominantly stochastic but becomes significantly more deterministic with time, producing increasingly diverse and ecologically complex communities. We also observed changes in two dominant and medically relevant antagonists (Cutibacterium acnes and Staphylococcus epidermidis), consistent with competitive exclusion induced by a transition from sebaceous to moist environments. By exploiting this common yet uniquely human practice, we show that skin piercings are not just culturally significant but also represent ecosystem engineering on the human body. The novel habitats and communities that skin piercings produce may provide general insights into biological responses to environmental disturbances with implications for both ecosystem and human health.},
}
@article {pmid38018034,
year = {2023},
author = {Chen, Y and Lu, Y and Wang, T and Wu, J and Yu, B},
title = {Changes in Gut Microbiota at 1-60 Days in 92 Preterm Infants in a Neonatal Intensive Care Unit Using 16S rRNA Gene Sequencing.},
journal = {Medical science monitor : international medical journal of experimental and clinical research},
volume = {29},
number = {},
pages = {e941560},
doi = {10.12659/MSM.941560},
pmid = {38018034},
issn = {1643-3750},
abstract = {BACKGROUND Neonatal gut diversity is influenced by birth conditions and probiotic/antibiotic use. The gut microbiota affects brain development, immunity, and risk of diseases. Preterm infants, especially in neonatal intensive care units (NICUs), have different gut flora from full-term infants, suggesting in utero microbial colonization. This study examined gut microbiota changes in 92 NICU preterm infants in China. MATERIAL AND METHODS We collected data on 92 preterm infants admitted to the NICU immediately after birth, and fecal samples were collected on days 1, 3, 7, 14, 21, 28, and 60. We analyzed changes in intestinal bacteria through 16S rRNA sequencing, predicted the change in gut microbiota function over time, and compared the effects of main feeding modality on the intestinal bacteria of preterm infants. RESULTS At the phylum level, the top 5 phyla in total accounted for 99.69% of the abundance, in decreasing order of abundance: Proteobacteria, Firmicutes, Actinobacteria, Tenericutes, and Bacteroidetes. At the genus level, the top 10 genera in terms of abundance accounted for a total of 90.90%, in decreasing order of abundance: Pseudomonas, Staphylococcus, Klebsiella, Escherichia-Shigella, unclassified Enterobacteriaceae, Staphylococcus, Clostridium-sensu-stricto-1, Streptococcus, Sphingomonas, and Ureaplasma. The abundance of Proteobacteria and Pseudomonas showed a decreasing trend at first, reached a minimum at day 14, and then an increasing trend, while the opposite trend was observed for Firmicutes. The metabolic function of the bacterial community changed greatly at different time points. The abundance of Proteobacteria at the phylum level and Streptococcus at the genus level in formula-fed infants were significantly higher than in breast-fed infants. CONCLUSIONS Between 1 and 60 days, the gut microbiome in preterm infants in the NICU changed with changes in feeding patterns, with the main gut bacteria being from the phyla, Proteobacteria, and Pseudomonas.},
}
@article {pmid38017662,
year = {2023},
author = {Brushett, S and Gacesa, R and Vich Vila, A and Brandao Gois, MF and Andreu-Sánchez, S and Swarte, JC and Klaassen, MAY and Collij, V and Sinha, T and Bolte, LA and Wu, J and Swertz, M and de Kroon, MLA and Reijneveld, SA and Wijmenga, C and Weersma, RK and Fu, J and van Loo, HM and Kurilshikov, A and Zhernakova, A},
title = {Gut feelings: the relations between depression, anxiety, psychotropic drugs and the gut microbiome.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2281360},
doi = {10.1080/19490976.2023.2281360},
pmid = {38017662},
issn = {1949-0984},
abstract = {The gut microbiome is involved in the bi-directional relationship of the gut - brain axis. As most studies of this relationship are small and do not account for use of psychotropic drugs (PTDs), we explored the relations of the gut microbiome with several internalizing disorders, while adjusting for PTDs and other relevant medications, in 7,656 Lifelines participants from the Northern Netherlands (5,522 controls and 491 participants with at least one internalizing disorder). Disorders included dysthymia, major depressive disorder (MDD), any depressive disorder (AnyDep: dysthymia or MDD), generalized anxiety disorder (GAD) and any anxiety disorder (AnyAnx: GAD, social phobia and panic disorder). Compared to controls, 17 species were associated with depressive disorders and 3 were associated with anxiety disorders. Around 90% of these associations remained significant (FDR <0.05) after adjustment for PTD use, suggesting that the disorders, not PTD use, drove these associations. Negative associations were observed for the butyrate-producing bacteria Ruminococcus bromii in participants with AnyDep and for Bifidobacterium bifidum in AnyAnx participants, along with many others. Tryptophan and glutamate synthesis modules and the 3,4-Dihydroxyphenylacetic acid synthesis module (related to dopamine metabolism) were negatively associated with MDD and/or dysthymia. After additional adjustment for functional gastrointestinal disorders and irritable bowel syndrome, these relations remained either statistically (FDR <0.05) or nominally (P < 0.05) significant. Overall, multiple bacterial species and functional modules were associated with internalizing disorders, including gut - brain relevant components, while associations to PTD use were moderate. These findings suggest that internalizing disorders rather than PTDs are associated with gut microbiome differences relative to controls.},
}
@article {pmid38017581,
year = {2023},
author = {Lin, D and Hong, J and Sanogo, B and Du, S and Xiang, S and Hui, JH and Ding, T and Wu, Z and Sun, X},
title = {Core gut microbes Cloacibacterium and Aeromonas associated with different gastropod species could be persistently transmitted across multiple generations.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {267},
pmid = {38017581},
issn = {2049-2618},
support = {82202560, 82161160343 and 82272361//the National Natural Science Foundation of China/ ; 82202560, 82161160343 and 82272361//the National Natural Science Foundation of China/ ; 82202560, 82161160343 and 82272361//the National Natural Science Foundation of China/ ; 22qntd4813//the Fundamental Research Funds for the Central Universities/ ; NPRC-2019-194-30//the National Parasitic Resource Center of China and the Ministry of Science and Technology/ ; N_CUHK401/21//the NSFC/RGC Joint Research Scheme/ ; 2022B1111030002//the R&amp;D Program in Key Areas of Guangdong Province/ ; 20201192//the 6th Nuclear Energy R&amp;D Project/ ; B12003//the 111 Project/ ; 2020YFC1200100, 2020YFC1200103, 2021YFC2300800 and 2016YFC1200500//the National Key R&amp;D Program of China/ ; 2021B1212040017//the Science and Technology Planning Project of Guangdong Province/ ; },
abstract = {BACKGROUND: Studies on the gut microbiota of animals have largely focused on vertebrates. The transmission modes of commensal intestinal bacteria in mammals have been well studied. However, in gastropods, the relationship between gut microbiota and hosts is still poorly understood. To gain a better understanding of the composition of gut microbes and their transmission routes in gastropods, a large-scale and long-term experiment on the dynamics and transmission modes of gut microbiota was conducted on freshwater snails.<br><br>RESULTS: We analyzed 244 microbial samples from the digestive tracts of freshwater gastropods and identified Proteobacteria and Bacteroidetes as dominant gut microbes. Aeromonas, Cloacibacterium, and Cetobacterium were identified as core microbes in the guts, accounting for over 50% of the total sequences. Furthermore, both core bacteria Aeromonas and Cloacibacterium, were shared among 7 gastropod species and played an important role in determining the gut microbial community types of both wild and cultured gastropods. Analysis of the gut microbiota at the population level, including wild gastropods and their offspring, indicated that a proportion of gut microbes could be consistently vertically transmitted inheritance, while the majority of the gut microbes resulted from horizontal transmission. Comparing cultured snails to their wild counterparts, we observed an increasing trend in the proportion of shared microbes and a decreasing trend in the number of unique microbes among wild gastropods and their offspring reared in a cultured environment. Core gut microbes, Aeromonas and Cloacibacterium, remained persistent and dispersed from wild snails to their offspring across multiple generations. Interestingly, under cultured environments, the gut microbiota in wild gastropods could only be maintained for up to 2 generations before converging with that of cultured snails. The difference observed in gut bacterial metabolism functions was associated with this transition. Our study also demonstrated that the gut microbial compositions in gastropods are influenced by developmental stages and revealed the presence of Aeromonas and Cloacibacterium throughout the life cycle in gastropods. Based on the dynamics of core gut microbes, it may be possible to predict the health status of gastropods during their adaptation to new environments. Additionally, gut microbial metabolic functions were found to be associated with the adaptive evolution of gastropods from wild to cultured environments.<br><br>CONCLUSIONS: Our findings provide novel insights into the dynamic processes of gut microbiota colonization in gastropod mollusks and unveil the modes of microbial transmission within their guts. Video Abstract.},
}
@article {pmid38017526,
year = {2023},
author = {Poulsen, JS and Macêdo, WV and Bonde, T and Nielsen, JL},
title = {Energetically exploiting lignocellulose-rich residues in anaerobic digestion technologies: from bioreactors to proteogenomics.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {16},
number = {1},
pages = {183},
pmid = {38017526},
issn = {2731-3654},
support = {NNF16OC0021818//Novo Nordisk Fonden/ ; NNF16OC0021818//Novo Nordisk Fonden/ ; },
abstract = {The biogas produced through anaerobic digestion (AD) of renewable feedstocks is one of the promising alternatives to replace fossil-derived energy. Even though lignocellulosic biomass is the most abundant biomass on earth, only a small fraction is being used towards resources recovery, leaving a great potential unexploited. In this study, the combination of state-of-art genomic techniques and engineered systems were used to further advance the knowledge on biogas production from lignocellulosic-rich residues and the microbiome involved in the anaerobic digestion hereof. A long-term adapted anaerobic microbiome capable of degrading wheat straw as the sole substrate was investigated using protein stable isotope probing (protein-SIP). The results indicated that a diverse microbial community, primarily composed of Firmicutes and Methanogens, played crucial roles in cellulose degradation and methane production. Notably, Defluviitoga tunisiensis, Syntrophothermus lipocalidus, and Pelobacter carbinolicus were identified as direct metabolizers of cellulose, while Dehalobacterium assimilated labelled carbon through cross-feeding. This study provides direct evidence of primary cellulose degraders and sheds light on their genomic composition. By harnessing the potential of lignocellulosic biomass and understanding the microbial communities involved, we can promote sustainable biogas production, contributing to energy security and environmental preservation.},
}
@article {pmid38017525,
year = {2023},
author = {Bakker, JW and Begemann, HLM and Fonville, M and Esser, HJ and de Boer, WF and Sprong, H and Koenraadt, CJM},
title = {Differential associations of horizontally and vertically transmitted symbionts on Ixodes ricinus behaviour and physiology.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {443},
pmid = {38017525},
issn = {1756-3305},
abstract = {BACKGROUND: Ixodes ricinus ticks are infected with a large diversity of vertically and horizontally transmitted symbionts. While horizontally transmitted symbionts rely on a vertebrate host for their transmission, vertically transmitted symbionts rely more on the survival of their invertebrate host for transmission. We therefore hypothesized horizontally transmitted symbionts to be associated with increased tick activity to increase host contact rate and vertically transmitted symbionts to be associated with higher tick weight and lipid fraction to promote tick survival.<br><br>METHODS: We used a behavioural assay to record the questing activity of I. ricinus ticks. In addition, we measured weight and lipid fraction and determined the presence of ten symbiont species in these ticks using qPCR, of which six were vertically transmitted and four horizontally transmitted.<br><br>RESULTS: Vertically transmitted symbionts (e.g. Midichloria mitochondrii) were associated with an increase in tick weight, whereas horizontally transmitted symbionts (e.g. Borrelia burgdorferi sensu lato) were often associated with lower weight and lipid fraction of ticks. Moreover, horizontally transmitted symbionts (e.g. B. burgdorferi s.l.) were associated with increased tick activity, which may benefit pathogen transmission and increases tick-borne disease hazard.<br><br>CONCLUSIONS: Our study shows that horizontally and vertically transmitted symbionts differentially influence the behaviour and physiology of I. ricinus and warrants future research to study the underlying mechanisms and effects on transmission dynamics of tick-borne pathogens.},
}
@article {pmid38017392,
year = {2023},
author = {Jensen, MG and Svraka, L and Baez, E and Lund, M and Poehlein, A and Brüggemann, H},
title = {Species- and strain-level diversity of Corynebacteria isolated from human facial skin.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {366},
pmid = {38017392},
issn = {1471-2180},
support = {LF-OC-21-000826//LEO Fondet/ ; },
abstract = {BACKGROUND: Sequencing of the human skin microbiome revealed that Corynebacterium is an ubiquitous and abundant bacterial genus on human skin. Shotgun sequencing further highlighted the microbial "dark matter" of the skin microbiome, consisting of microorganisms, including corynebacterial species that were not cultivated and genome-sequenced so far. In this pilot project, facial human skin swabs of 13 persons were cultivated to selectively obtain corynebacteria. 54 isolates were collected and 15 of these were genome-sequenced and the pan-genome was determined. The strains were biochemically characterized and antibiotic susceptibility testing (AST) was performed.<br><br>RESULTS: Among the 15 sequenced strains, nine different corynebacterial species were found, including two so far undescribed species, tentatively named "Corynebacterium vikingii" and "Corynebacterium borealis", for which closed genome sequences were obtained. Strain variability beyond the species level was determined in biochemical tests, such as the variable presence of urease activity and the capacity to ferment different sugars. The ability to grow under anaerobic conditions on solid agar was found to be species-specific. AST revealed resistances to clindamycin in seven strains. A Corynebacterium pseudokroppenstedtii strain showed additional resistance towards beta-lactam and fluoroquinolone antibiotics; a chromosomally located 17&#xa0;kb gene cluster with five antibiotic resistance genes was found in the closed genome of this strain.<br><br>CONCLUSIONS: Taken together, this pilot study identified an astonishing diversity of cutaneous corynebacterial species in a relatively small cohort and determined species- and strain-specific individualities regarding biochemical and resistance profiles. This further emphasizes the need for cultivation-based studies to be able to study these microorganisms in more detail, in particular regarding their host-interacting and, potentially, -beneficial and/or -detrimental properties.},
}
@article {pmid38017389,
year = {2023},
author = {Tsakmaklis, A and Farowski, F and Zenner, R and Lesker, TR and Strowig, T and Schlößer, H and Lehmann, J and von Bergwelt-Baildon, M and Mauch, C and Schlaak, M and Knuever, J and Schweinsberg, V and Heinzerling, LM and Vehreschild, MJGT},
title = {TIGIT[+] NK cells in combination with specific gut microbiota features predict response to checkpoint inhibitor therapy in melanoma patients.},
journal = {BMC cancer},
volume = {23},
number = {1},
pages = {1160},
pmid = {38017389},
issn = {1471-2407},
support = {70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; },
abstract = {BACKGROUND: Composition of the intestinal microbiota has been correlated to therapeutic efficacy of immune checkpoint inhibitors (ICI) in various cancer entities including melanoma. Prediction of the outcome of such therapy, however, is still unavailable. This prospective, non-interventional study was conducted in order to achieve an integrated assessment of the connection between a specific intestinal microbiota profile and antitumor immune response to immune checkpoint inhibitor therapy (anti-PD-1 and/or anti-CTLA-4) in melanoma patients.<br><br>METHODS: We assessed blood and stool samples of 29 cutaneous melanoma patients who received immune checkpoint inhibitor therapy. For functional and phenotypical immune analysis, 12-color flow cytometry and FluoroSpot assays were conducted. Gut microbiome was analyzed with shotgun metagenomics sequencing. To combine clinical, microbiome and immune variables, we applied the Random Forest algorithm.<br><br>RESULTS: A total of 29 patients was analyzed in this study, among whom 51.7% (n&#x2009;=&#x2009;15) reached a durable clinical benefit. The Immune receptor TIGIT is significantly upregulated in T cells (p&#x2009;=&#x2009;0.0139) and CD56[high] NK cells (p&#x2009;=&#x2009;0.0037) of responders. Several bacterial taxa were associated with response (e.g. Ruminococcus torques) or failure (e.g. Barnesiella intestinihominis) to immune therapy. A combination of two microbiome features (Barnesiella intestinihominis and the Enterobacteriaceae family) and one immune feature (TIGIT[+] CD56[high] NK cells) was able to predict response to ICI already at baseline (AUC&#x2009;=&#x2009;0.85; 95% CI: 0.841-0.853).<br><br>CONCLUSIONS: Our results reconfirm a link between intestinal microbiota and response to ICI therapy in melanoma patients and furthermore point to TIGIT as a promising target for future immunotherapies.},
}
@article {pmid38016991,
year = {2023},
author = {Auger, L and Bouslama, S and Deschamps, MH and Vandenberg, G and Derome, N},
title = {Author Correction: Absence of microbiome triggers extensive changes in the transcriptional profile of Hermetia illucens during larval ontogeny.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20959},
doi = {10.1038/s41598-023-48023-6},
pmid = {38016991},
issn = {2045-2322},
}
@article {pmid38016587,
year = {2023},
author = {Yuan, X and Wu, D and Zhang, D and He, C and Wang, Z and Xu, W and Shou, N and Fu, K and Yue, M and Zhang, X and Shi, Z},
title = {Combining microbiome and pseudotargeted metabolomics revealed the alleviative mechanism of Cupriavidus sp. WS2 on the cadmium toxicity in Vicia unijuga A.Br.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {123040},
doi = {10.1016/j.envpol.2023.123040},
pmid = {38016587},
issn = {1873-6424},
abstract = {Cadmium (Cd) pollution is one of the most severe toxic metals pollution in grassland. Vicia unijuga (V. unijuga) A.Br. planted nearby the grassland farming are facing the risk of high Cd contamination. Here, we investigated the beneficial effects of a highly Cd tolerant rhizosphere bacterium, Cupriavidus sp. WS2, on Cd contaminated V. unijuga. Through plot experiments, we set up four groups of treatments: the control group (without WS2 or Cd), the Cd group (with only Cd addition), the WS2 group (with only WS2 addition), and the WS2/Cd group (with WS2 and Cd addition), and analyzed the changes in physiological indicators, rhizosphere microorganisms, and stem and leaf metabolites of V. unijuga. Results of physiological indicators indicated that Cupriavidus sp. WS2 had strong absorption and accumulation capacity of Cd, exogenous addition of strain WS2 remarkably decreased the Cd concentrations, and increased the plant heights, the biomass, the total protein concentrations, the chlorophyll contents and the photosynthetic rate in stems and leaves of V. unijuga under Cd stress. Cd treatment increased the abundance of Cd tolerant bacterial genera in rhizosphere microbiome, but these genera were down-regulated in the WS2/Cd group. Pseudotargeted metabolomic results showed that six common differential metabolites associated with antioxidant stress were increased after co-culture with WS2. In addition, WS2 activated the antioxidant system including glutathione (GSH) and catalase (CAT), reduced the contents of oxidative stress markers including malondialdehyde (MDA) and hydrogen peroxide (H2O2) in V. unijuga under Cd stress. Taken together, this study revealed that Cupriavidus sp.WS2 alleviated the toxicity of V. unijuga under Cd exposure by activating the antioxidant system, increasing the antioxidant metabolites, and reducing the oxidative stress markers.},
}
@article {pmid38016577,
year = {2023},
author = {He, X and Zhou, HX and Fu, X and Ni, KD and Lin, AZ and Zhang, LT and Yin, HH and Jiang, Q and Zhou, X and Meng, YW and Liu, JY},
title = {Metabolomics study reveals increased deoxycholic acid contributes to deoxynivalenol-mediated intestinal barrier injury.},
journal = {Life sciences},
volume = {336},
number = {},
pages = {122302},
doi = {10.1016/j.lfs.2023.122302},
pmid = {38016577},
issn = {1879-0631},
abstract = {AIMS: Deoxynivalenol (DON), namely vomitoxin, is one of the most prevalent fungal toxins in cereal crops worldwide. However, the underlying toxic mechanisms of DON remain largely unknown.<br><br>MAIN METHODS: DON exposure-caused changes in the murine plasma metabolome and gut microbiome were investigated by an LC-MS/MS-based nontargeted metabolomics approach and sequencing of 16S rRNA in fecal samples, respectively. Cellular models were then used to validate the findings from the metabolomics study.<br><br>KEY FINDINGS: DON exposure increased intestinal barrier permeability evidenced by its-mediated decrease in colonic Claudin 5 and E-cadherin, as well as increases in colonic Ifn-&#x3b3;, Cxcl9, Cxcl10, and Cxcr3. Furthermore, DON exposure resulted in a significant increase in murine plasma levels of deoxycholic acid (DCA). Also, DON exposure led to gut microbiota dysbiosis, which was associated with DON exposure-caused increase in plasma DCA. In addition, we found not only DON but also DCA dose-dependently caused a significant increase in the levels of IFN-&#x3b3;, CXCL9, CXCL10, and/or CXCR3, as well as a significant decrease in the expression levels of Claudin 5 and/or E-cadherin in the human colonic epithelial cells (NCM460).<br><br>SIGNIFICANCE: DON-mediated increase in DCA contributes to DON-caused intestinal injury. DCA may be a potential therapeutic target for DON enterotoxicity.},
}
@article {pmid38016505,
year = {2023},
author = {Li, S and Chen, T and Zhou, Y and Li, X},
title = {Palmitic acid and trans-4-hydroxy-3-methoxycinnamate, the active ingredients of Yaobishu formula, reduce inflammation and pain by regulating gut microbiota and metabolic changes after lumbar disc herniation to activate autophagy and the Wnt/β-catenin pathway.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {},
number = {},
pages = {166972},
doi = {10.1016/j.bbadis.2023.166972},
pmid = {38016505},
issn = {1879-260X},
abstract = {The imbalance in gut microbiota triggers an inflammatory response that spreads from the gut to the discs and is associated with lumbar disc herniation (LDH). In this study, we investigated the mechanism of palmitic acid (PA) and trans-4-hydroxy-3-methoxycinnamic acid (THMC) on microbiota, metabolic homeostasis, and autophagy after LDH. The LDH rat model was established by puncturing the exposed intervertebral disc. 16S rDNA was used to assess the gut microbiome composition. The microbial metabolites were analyzed by UPLC-MS. The mechanism of PA and THMC in LDH was explored by fecal microbiota transplantation (FMT). We found that Yaobishu, PA, THMC, and the positive control drug Celebrex attenuated intervertebral disc damage in LDH rats and downregulated TRPV1, IL-1β, and IL-18 expression. In addition, Yaobishu reduced Oscillospirales and Ruminococcaceae abundances after LDH. PA increased Bacilli's abundance while decreasing Negativicutes and Ruminococcaceae abundances. Metabolomics showed that Yaobishu increased 2-hexanone, methyl isobutyl ketone, 2-methylpentan-3-one, and nonadecanoic acid levels but decreased pantetheine and urocanate levels. PA and THMC reduced uridine and urocanate levels. Yaobishu, PA, and THMC activated autophagy and the Wnt/β-catenin pathway in LDH rats. Moreover, antibiotics abrogated these effects. FMT-PA and FMT-THMC activated autophagy and decreased IL-1β, IL-18, Wnt1, β-catenin, and TRPV1 expression. FMT-PA and FMT-THMC partially reversed the effects of 3-MA. Taken together, our data suggest that Yaobishu, PA, and THMC relieve inflammation and pain by remodeling the gut microbiota and restoring metabolic homeostasis after LDH to activate autophagy and the Wnt/β-catenin pathway, which provide a new therapeutic target for LDH in the clinic.},
}
@article {pmid38016486,
year = {2023},
author = {Chen, H and Peng, L and Wang, Z and He, Y and Zhang, X},
title = {Exploring the causal relationship between periodontitis and gut microbiome: Unveiling the oral-gut and gut-oral axes through bidirectional Mendelian randomization.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.13906},
pmid = {38016486},
issn = {1600-051X},
support = {CSTB2022NSCQ-MSX0084//the Natural Science Foundation Project of Chongqing, China/ ; 81700982//National Natural Science Foundation of China/ ; ZQNYXGDRCGZS2019004//the Chongqing Medical Reserve Talent Studio for Young People/ ; },
abstract = {AIM: This Mendelian randomization (MR) study was performed to explore the potential bidirectional causal relationship between the gut microbiome (GM) and periodontitis.<br><br>MATERIALS AND METHODS: We used genetic instruments from the genome-wide association study of European descent for periodontitis from the GeneLifestyle Interactions in Dental Endpoints (GLIDE) consortium (17,353 cases and 28,210 controls) and the FinnGen consortium (4434 cases and 259,234 controls) to investigate the causal relationship with GM (the MiBioGen consortium, 18,340 samples), and vice versa. Several MR techniques, which include inverse variance weighting (IVW), MR-Egger, weighted median, simple mode and weighted mode approaches, were employed to investigate the causal relationship between the exposures and the outcomes. Cochran's Q-test was performed to detect heterogeneity. The MR-Egger regression intercept and MR pleiotropy residual sum and outlier test (MR-PRESSO) were conducted to test potential horizontal pleiotropy. Leave-one-out sensitivity analyses were used to assess the stabilities of single nucleotide polymorphisms (SNPs). Finally, the IVW results from the two databases were analysed using meta-analysis.<br><br>RESULTS: We confirmed three potential causal relationships between GM taxa and periodontitis at the genus level. Among them, the genera Alistipes and Holdemanella were genetically associated with an increased risk of periodontitis. In reverse, periodontitis may lead to a decreased abundance of the genus Ruminococcaceae UCG014.<br><br>CONCLUSIONS: The demonstration of a causal link between GM and periodontitis provides compelling evidence, highlighting the interconnectivity and interdependence of the gut-oral and oral-gut axes.},
}
@article {pmid38016408,
year = {2023},
author = {Li, J and Li, Y and Xiao, H and Li, W and Ye, F and Wang, L and Li, Y and Wang, C and Wu, Y and Xuan, R and Huang, Y and Huang, J},
title = {The intestinal microflora diversity of aboriginal chickens in Jiangxi province, China.},
journal = {Poultry science},
volume = {103},
number = {2},
pages = {103198},
doi = {10.1016/j.psj.2023.103198},
pmid = {38016408},
issn = {1525-3171},
abstract = {Intestinal microbiota can coevolve with host to form symbiotic relationship and be participated in the regulation of host physiological function. At present, there is no clear explanation on the effect of intestinal microflora in Jiangxi aboriginal chickens. Here, we investigated the association between gut microbiota and host genome of Jiangxi local chickens using 16S rRNA sequencing and genome-wide association studies (GWAS). The results showed that the breeds and genders had important effects on the intestinal microbiota of chickens. A total of 28 SNPs in 14 regions of the chicken genome were related to the relative abundance of microorganisms in 5 genera: Clostridium_sensu_stricto_1, Enterococcus, Gallibacterium, Turicibacter, and Rikenellaceae_RC9_gut_group. A total of 17 candidate genes were identified composition of chicken microbiome and show an association between the host genome and the chicken intestinal microbiota, which also unveiled the diversity of intestinal microbes in Jiangxi chickens. Given the correlation between chicken genome and intestinal microbe found in the present study, a new idea for the protection of aboriginal chicken genetic resources in China could be provided.},
}
@article {pmid38016379,
year = {2023},
author = {Kavita, and Om, H and Chand, U and Kushawaha, PK},
title = {Postbiotics: An alternative and innovative intervention for the therapy of inflammatory bowel disease.},
journal = {Microbiological research},
volume = {279},
number = {},
pages = {127550},
doi = {10.1016/j.micres.2023.127550},
pmid = {38016379},
issn = {1618-0623},
abstract = {Inflammatory Bowel Disease (IBD) is a persistent gastrointestinal (GI) tract inflammatory disease characterized by downregulated mucosal immune activities and a disrupted microbiota environment in the intestinal lumen. The involvement of bacterium postbiotics as mediators between the immune system and gut microbiome could be critical in determining why host-microbial relationships are disrupted in IBD. Postbiotics including Short-chain fatty acids (SCFAs), Organic acids, Proteins, Vitamins, Bacteriocins, and Tryptophan (Trp) are beneficial bioactive compounds formed via commensal microbiota in the gut environment during the fermentation process that can be used to improve consumer health. The use of metabolites or fragments from microorganisms can be a very attractive treatment and prevention technique in modern medicine. Postbiotics are essential in the immune system's development since they alter the barrier tightness, and the gut ecology and indirectly shape the microbiota's structure. As a result, postbiotics may be beneficial in treating or preventing various diseases, even some for which there is no effective causative medication. Postbiotics may be a promising tool for the treatment of IBD in individuals of all ages, genders, and even geographical locations. Direct distribution of postbiotics may provide a new frontier in microbiome-based therapy for IBD since it allows both the management of host homeostasis and the correction of the negative implications of dysbiosis. Further studies of the biological effects of these metabolites are expected to reveal innovative applications in medicine and beyond. This review attempts to explore the possible postbiotic-based interventions for the treatment of IBD.},
}
@article {pmid38016374,
year = {2023},
author = {Wang, P and Zhang, S and Qi, C and Wang, C and Zhu, Z and Shi, L and Cheng, L and Zhang, X},
title = {Blood microbial analyses reveal long-term effects of SARS-CoV-2 infection on patients who recovered from COVID-19.},
journal = {Computers in biology and medicine},
volume = {168},
number = {},
pages = {107721},
doi = {10.1016/j.compbiomed.2023.107721},
pmid = {38016374},
issn = {1879-0534},
abstract = {OBJECTIVE: Few symptoms persist for a long time after patients recover from COVID-19, called "long COVID". We explored the potential microbial risk factors for COVID-19 for a deeper understanding and assistance in the follow-up treatment of these sequelae.<br><br>METHODS: Microbiome re-annotation was performed using whole blood RNA-Seq data collected from recovered COVID-19 patients and healthy controls at multiple time points. Subsequently, a series of downstream analyses were conducted to reveal the microbial characteristics of patients who recovered from SARS-CoV-2 infection.<br><br>RESULTS: The blood microbiome at 12 weeks post-infection was most evidently disturbed, including an increasing ratio of Bacillota/Bacteroidota and a higher microbial alpha diversity. In addition, a group of pathogenic microbes at 12 weeks post-infection were identified, including Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa, which were positively associated with host genes involved in immune regulatory and olfactory transduction pathways. Several microbes, such as Streptococcus pneumoniae were associated with infiltrating immune cells, such as M2 macrophages.<br><br>CONCLUSION: This study provides insights into the relationship between the blood microbiome and COVID-19 sequelae. Several pathogenic microbes were enriched in recovered COVID-19 patients and thus affected host genes participating in the immune and olfactory transduction pathways, which play critical roles in COVID-19 sequelae.},
}
@article {pmid38016319,
year = {2023},
author = {Xu, H and Wang, J and Wang, Q and Tu, W and Jin, Y},
title = {Co-exposure to polystyrene microplastics and cypermethrin enhanced the effects on hepatic phospholipid metabolism and gut microbes in adult zebrafish.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {133051},
doi = {10.1016/j.jhazmat.2023.133051},
pmid = {38016319},
issn = {1873-3336},
abstract = {Microplastics (MPs) can absorb environmental pollutants from the aquatic environment to cause mixed toxicity, which has received widespread attention. However, studies on the joint effects of MPs and insecticides are limited. As one of the most widely used pyrethroids, there was a large amount of residual cypermethrin (CYP) in water due to insufficient decomposition. Here, adult female zebrafish were exposed to MPs, CYP, and their mixtures for 21 days, respectively. After exposures, the MPs and CYP caused tissue damage to the liver. Hepatic triglyceride (TG) level increased significantly after MPs + CYP exposure, and the expression of genes about glycolipids metabolism was significantly altered. Furthermore, metabolome results suggested that MPs + CYP exposure resulted in increased content of some glycerophospholipid, affecting phospholipid metabolism-related pathways. In addition, through 16 s rDNA sequencing, it was found that MPs + CYP led to significant changes in the proportion of dominant phyla. Interestingly, Cetobacterium which increased in CYP and the co-exposure group was positively correlated with most lipid metabolites. Our results suggested that co-exposure to MPs and CYP enhanced the disturbances in hepatic phospholipid metabolism by affecting the gut microbial composition, while these changes were not observed in separate treatment groups. These results emphasized the importance of studying the joint toxicity of MPs and insecticides.},
}
@article {pmid38016315,
year = {2023},
author = {Gao, FZ and He, LY and He, LX and Bai, H and Zhang, M and Chen, ZY and Qiao, LK and Liu, YS and Ying, GG},
title = {Swine farming shifted the gut antibiotic resistome of local people.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {133082},
doi = {10.1016/j.jhazmat.2023.133082},
pmid = {38016315},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) are prevalent in the livestock environment, but little is known about impacts of animal farming on the gut antibiotic resistome of local people. Here we conducted metagenomic sequencing to investigate gut microbiome and resistome of residents in a swine farming village as well as environmental relevance by comparing with a nearby non-farming village. Results showed a shift of gut microbiome towards unhealthy status in the residents of swine farming village, with an increased abundance and diversity in pathogens and ARGs. The resistome composition in human guts was more similar with that in swine feces and air than that in soil and water. Mobile gene elements were closely associated with the prevalence of gut resistome. Some plasmid-borne ARGs were colocalized in similar genetic contexts in gut and environmental samples. Metagenomic binning obtained 47 ARGs-carrying families in human guts, and therein Enterobacteriaceae posed the highest threats in antibiotic resistance and virulence. Several ARGs-carrying families were shared by gut and environmental samples (mainly in swine feces and air), and the ARGs were evolutionarily conservative within genera. The findings highlight that swine farming can shape gut resistome of local people with close linkage to farm environmental exposures.},
}
@article {pmid38016313,
year = {2023},
author = {Kim, MS and Lee, YH and Lee, Y and Jeong, H and Wang, M and Wang, DZ and Lee, JS},
title = {Multigenerational effects of elevated temperature on host-microbiota interactions in the marine water flea Diaphanosoma celebensis exposed to micro- and nanoplastics.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {132877},
doi = {10.1016/j.jhazmat.2023.132877},
pmid = {38016313},
issn = {1873-3336},
abstract = {Rising ocean temperatures are driving unprecedented changes in global marine ecosystems. Meanwhile, there is growing concern about microplastic and nanoplastic (MNP) contamination, which can endanger marine organisms. Increasing ocean warming (OW) and plastic pollution inevitably cause marine organisms to interact with MNPs, but relevant studies remain sparse. Here, we investigated the interplay between ocean warming and MNP in the marine water flea Diaphanosoma celebensis. We found that combined exposure to MNPs and OW induced reproductive failure in the F2 generation. In particular, the combined effects of OW and MNPs on the F2 generation were associated with key genes related to reproduction and stress response. Moreover, populations of predatory bacteria were significantly larger under OW and MNP conditions during F2 generations, suggesting a potential link between altered microbiota and host fitness. These results were supported by a host transcriptome and microbiota interaction analysis. This research sheds light on the complex interplay between environmental stressors, their multigenerational effects on marine organisms, and the function of the microbiome.},
}
@article {pmid38016224,
year = {2023},
author = {Ke, Y and Sun, W and Xue, Y and Zhu, Y and Yan, S and Xie, S},
title = {Effects of treatments and distribution on microbiome and antibiotic resistome from source to tap water in three Chinese geographical regions based on metagenome assembly.},
journal = {Water research},
volume = {249},
number = {},
pages = {120894},
doi = {10.1016/j.watres.2023.120894},
pmid = {38016224},
issn = {1879-2448},
abstract = {Antibiotic resistance genes (ARGs) represent emerging environmental pollutants that present health risks. Drinking water supply systems (DWSSs), including sources to tap water, play crucial roles in the dissemination and propagation of ARGs. However, there was a paucity of knowledge on the relative abundance, diversity, mobility, and pathogenic hosts of ARGs in DWSSs from source to tap. Therefore, the effects of treatments and distributions on the microbial community and ARGs from three geographical regions (downstream areas of the Yellow, Yangtze, and Pearl Rivers) were elucidated in the present study. Treatment processes lowered the complexity of the microbial community network, whereas transportation increased it. The assembly mechanisms of the microbial community and antibiotic resistome were primarily driven by stochastic processes. Distribution greatly increased the contribution of stochastic processes. Multidrug ARGs (for example, multidrug transporter and adeJ) and bacitracin ARG (bacA) were the primary mobile ARGs in drinking water, as identified by the metagenomic assembly. Achromobacter xylosoxidans, Acinetobacter calcoaceticus, and Acinetobacter junii harbored diverse multidrug ARGs and mobile genetic elements (MGEs) (recombinases, integrases, and transposases) as potential pathogens and were abundant in the disinfected water. Environmental factors, including pH, chlorine, latitude, longitude, and temperature, influenced the ARG abundance by directly regulating the MGEs and microbial community diversity. This study provides critical information on the fate, mobility, host pathogenicity, and driving factors of ARGs in drinking water, which is conducive to ARG risk assessment and management to provide high-quality drinking water to consumers.},
}
@article {pmid38016221,
year = {2023},
author = {Zhang, X and Wang, Y and Jiao, P and Zhang, M and Deng, Y and Jiang, C and Liu, XW and Lou, L and Li, Y and Zhang, XX and Ma, L},
title = {Microbiome-functionality in anaerobic digesters: A critical review.},
journal = {Water research},
volume = {249},
number = {},
pages = {120891},
doi = {10.1016/j.watres.2023.120891},
pmid = {38016221},
issn = {1879-2448},
abstract = {Microbially driven anaerobic digestion (AD) processes are of immense interest due to their role in the biovalorization of biowastes into renewable energy resources. The function-versatile microbiome, interspecies syntrophic interactions, and trophic-level metabolic pathways are important microbial components of AD. However, the lack of a comprehensive understanding of the process hampers efforts to improve AD efficiency. This study presents a holistic review of research on the microbial and metabolic "black box" of AD processes. Recent research on microbiology, functional traits, and metabolic pathways in AD, as well as the responses of functional microbiota and metabolic capabilities to optimization strategies are reviewed. The diverse ecophysiological traits and cooperation/competition interactions of the functional guilds and the biomanipulation of microbial ecology to generate valuable products other than methane during AD are outlined. The results show that AD communities prioritize cooperation to improve functional redundancy, and the dominance of specific microbes can be explained by thermodynamics, resource allocation models, and metabolic division of labor during cross-feeding. In addition, the multi-omics approaches used to decipher the ecological principles of AD consortia are summarized in detail. Lastly, future microbial research and engineering applications of AD are proposed. This review presents an in-depth understanding of microbiome-functionality mechanisms of AD and provides critical guidance for the directional and efficient bioconversion of biowastes into methane and other valuable products.},
}
@article {pmid38016191,
year = {2023},
author = {Zhang, Y and Zhan, J and Ma, C and Liu, W and Huang, H and Yu, H and Christie, P and Li, T and Wu, L},
title = {Root-associated bacterial microbiome shaped by root selective effects benefits phytostabilization by Athyrium wardii (Hook.).},
journal = {Ecotoxicology and environmental safety},
volume = {269},
number = {},
pages = {115739},
doi = {10.1016/j.ecoenv.2023.115739},
pmid = {38016191},
issn = {1090-2414},
abstract = {The root-associated microbiome assembly substantially promotes (hyper)accumulator plant growth and metal accumulation and is influenced by multiple factors, especially host species and environmental stress. Athyrium wardii (Hook.) is a phytostabilizer that grows in lead (Pb)-zinc (Zn) mine tailings and shows high root Pb accumulation. However, there remains little information on the assembly of the root-associated microbiome of A. wardii and its role in phytostabilization. A field study investigated the structural and functional variation in the root-associated bacterial microbiome of Athyrium wardii (Hook.) exposed to different levels of contamination in Pb-Zn mine tailings. The root compartment dominated the variation in the root-associated bacterial microbiome but the levels of contaminants showed less impact. Bacterial co-occurrence was enhanced in the rhizosphere soil and rhizoplane but tended to be much simpler in the endosphere in terms of network complexity and connectivity. This indicates that the microbial community assembly of A. wardii was non-random and shaped by root selective effects. Proteobacteria, Chloroflexi, Actinobacteria, Cyanobacteria, and Acidobacteriota were generally the dominant bacterial phyla. The genera Crossiella and Bradyrhizobium were enriched in the rhizosphere and cyanobacterial genera were enriched in the endosphere, demonstrating substantial advantages to plant survival and adaptation in the harsh mine environment. Functional categories involved in amino acid and carbohydrate metabolism were abundant in the rhizosphere soil, thus contributing to metal solubility and bioavailability in the rhizosphere. Membrane transporters, especially ATP-binding cassette transporters, were enriched in the endosphere, indicating a potential role in metal tolerance and transportation in A. wardii. The study shows substantial variation in the structure and function of microbiomes colonizing different compartments, with the rhizosphere and endophytic microbiota potentially involved in plant metal tolerance and accumulation during phytostabilization.},
}
@article {pmid38016054,
year = {2023},
author = {Ilinskaya, ON and Gafarova, LF and Kurdy, W and Kolpakov, AI and Yakovleva, GY},
title = {[Microbiome of therapeutic muds used in Tatarstan].},
journal = {Voprosy kurortologii, fizioterapii, i lechebnoi fizicheskoi kultury},
volume = {100},
number = {5},
pages = {27-35},
doi = {10.17116/kurort202310005127},
pmid = {38016054},
issn = {0042-8787},
abstract = {UNLABELLED: Therapeutic muds (peloids), which are widely used for body healing, improve metabolism and have antibacterial, anti-inflammatory and analgesic effects due to enrichment with necessary microelements and biological active substances. However, the microbiological component of these effects is not well studied.<br><br>OBJECTIVE: To characterize the microbiome of therapeutic muds, used in the Tatarstan Republic, by identifying spectrum of cultivated microorganisms, using molecular analysis of bacterial communities, and by determining their biodiversity and functional potential based on revealed genetic determinants.<br><br>MATERIAL AND METHODS: The study design of 5 peloids samples (local sapropels and peat deposits of swamp; 3 samples of Crimean sulfide muds) included three main techniques: isolation and taxonomic determination of cultivated microorganisms by time-of-flight mass-spectrometry; molecular analysis of peloids bacterial communities by 16S RNA high-throughput sequencing; identification of functional profiles of communities by their genetic determinant using Global Mapper tool on iVikodak platform.<br><br>RESULTS: Experimental studies have confirmed the safety of examined peloids, where non-pathogenic cultivated bacteria belonging mainly to Bacillus and Rhodococcus genera were dominant. Metagenomic analysis showed that Firmicutes, Proteobacteria and Actinobacteria were predominant in all samples in different ratios. It has been established, that there is both the internal biodiversity of each sample and difference between them. The functional profile of microbial communities was determined based on the identification of bacterial genes. It has been revealed that all communities have an ability to synthesize antibiotics, as well as to decompose dangerous xenobiotics - polyaromatic hydrocarbons, cyclic compounds, and dioxins.<br><br>CONCLUSION: Various microbial communities, which were identified in the therapeutic muds, contribute both to the clearance of toxicants in the peloids and to the antibacterial properties of the latter. The obtained priority results create a fundamental basis for the subsequent study of the role of peloids' microbiome of different origin in their healing action.},
}
@article {pmid38015769,
year = {2023},
author = {Najmanová, L and Vídeňská, P and Cahová, M},
title = {Corrigendum for: Healthy Microbiome - a Mere Idea or a Sound Concept?.},
journal = {Physiological research},
volume = {72},
number = {5},
pages = {684},
pmid = {38015769},
issn = {1802-9973},
abstract = {List of changes: On the basis of author's request the publisher of Physiological Research decided to change the license of the article to CC BY license.},
}
@article {pmid38015713,
year = {2023},
author = {Agrawal, P and Kaur, J and Singh, J and Rasane, P and Sharma, K and Bhadariya, V and Kaur, S and Kumar, V},
title = {Genetics, Nutrition, and Health: A New Frontier in Disease Prevention.},
journal = {Journal of the American Nutrition Association},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/27697061.2023.2284997},
pmid = {38015713},
issn = {2769-707X},
abstract = {The field of nutrition research has traditionally focused on the effects of macronutrients and micronutrients on the body. However, it has become evident that individuals have unique genetic makeups that influence their response to food. Nutritional genomics, which includes nutrigenetics and nutrigenomics, explores the interaction between an individual's genetic makeup, diet, and health outcomes. Nutrigenetics studies the impact of genetic variation on an individual's response to dietary nutrients, while nutrigenomics investigates how dietary components affect gene regulation and expression. These disciplines seek to understand the impact of diet on the genome, transcriptome, proteome, and metabolome. It provides insights into the mechanisms underlying the effect of diet on gene expression. Nutrients can cause the modification of genetic expression through epigenetic changes, such as DNA methylation and histone modifications. The aim of nutrigenomics is to create personalized diets based on the unique metabolic profile of an individual, gut microbiome, and genetic makeup to prevent diseases and promote health. Nutrigenomics has the potential to revolutionize the field of nutrition by combining the practicality of personalized nutrition with knowledge of genetic factors underlying health and disease. Thus, nutrigenomics offers a promising approach to improving health outcomes (in terms of disease prevention) through personalized nutrition strategies based on an individual's genetic and metabolic characteristics.},
}
@article {pmid38015634,
year = {2023},
author = {Gurczynski, SJ and Lipinski, JH and Strauss, JY and Alam, S and Huffnagle, GB and Ranjan, P and Kennedy, LH and Moore, BB and O'Dwyer, DN},
title = {Horizontal transmission of gut microbiota attenuates mortality in lung fibrosis.},
journal = {JCI insight},
volume = {},
number = {},
pages = {},
doi = {10.1172/jci.insight.164572},
pmid = {38015634},
issn = {2379-3708},
abstract = {Pulmonary fibrosis is a chronic and often fatal disease. The pathogenesis is characterized by aberrant repair of lung parenchyma resulting in loss of physiological homeostasis, respiratory failure and death. The immune response in pulmonary fibrosis is dysregulated. The gut microbiome is a key regulator of immunity. The role of the gut microbiome in regulating the pulmonary immunity in lung fibrosis is poorly understood. Here, we determine the impact of gut microbiota on pulmonary fibrosis in C57BL/6 mice derived from different vendors (C57BL/6J and C57BL/6NCrl). We use germ free models, fecal microbiota transplantation and cohousing to transmit gut microbiota. Metagenomic studies of feces establish keystone species between sub-strains. Pulmonary fibrosis is microbiota dependent in C57BL/6 mice. Gut microbiota are distinct by β diversity (PERMANOVA P<0.001) and α diversity (P<0.0001). Mortality and lung fibrosis are attenuated in C57BL/6NCrl mice. Elevated CD4+ IL-10+ T cells and lower IL-6 occur in C57BL/6NCrl mice. Horizontal transmission of microbiota by cohousing attenuates mortality in C57BL/6J mice and promotes a transcriptionally altered pulmonary immunity. Temporal changes in lung and gut microbiota demonstrates that gut microbiota contribute largely to immunological phenotype. Key regulatory gut microbiota contribute to lung fibrosis generating rationale for human studies.},
}
@article {pmid38015339,
year = {2023},
author = {Brar, B and Kumar, R and Sharma, D and Sharma, AK and Thakur, K and Mahajan, D and Kumar, R},
title = {Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India.},
journal = {Journal, genetic engineering &amp; biotechnology},
volume = {21},
number = {1},
pages = {147},
pmid = {38015339},
issn = {2090-5920},
abstract = {BACKGROUND: The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge.<br><br>RESULTS: To explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S3 sampling site (94%). Bacteroidetes phylum was found to be second abundant in S1 and S2 site, whereas Actinobacteria was second dominant in sampling site S3. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S2 and S3 respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances.<br><br>CONCLUSION: Baner river's metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S3 reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section.},
}
@article {pmid38015302,
year = {2023},
author = {Kavyani, B and Ahn, SB and Missailidis, D and Annesley, SJ and Fisher, PR and Schloeffel, R and Guillemin, GJ and Lovejoy, DB and Heng, B},
title = {Dysregulation of the Kynurenine Pathway, Cytokine Expression Pattern, and Proteomics Profile Link to Symptomology in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS).},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {38015302},
issn = {1559-1182},
abstract = {Dysregulation of the kynurenine pathway (KP) is believed to play a significant role in neurodegenerative and cognitive disorders. While some evidence links the KP to myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), further studies are needed to clarify the overall picture of how inflammation-driven KP disturbances may contribute to symptomology in ME/CFS. Here, we report that plasma levels of most bioactive KP metabolites differed significantly between ME/CFS patients and healthy controls in a manner consistent with their known contribution to symptomology in other neurological disorders. Importantly, we found that enhanced production of the first KP metabolite, kynurenine (KYN), correlated with symptom severity, highlighting the relationship between inflammation, KP dysregulation, and ME/CFS symptomology. Other significant changes in the KP included lower levels of the downstream KP metabolites 3-HK, 3-HAA, QUIN, and PIC that could negatively impact cellular energetics. We also rationalized KP dysregulation to changes in the expression of inflammatory cytokines and, for the first time, assessed levels of the iron (Fe)-regulating hormone hepcidin that is also inflammation-responsive. Levels of hepcidin in ME/CFS decreased nearly by half, which might reflect systemic low Fe levels or possibly ongoing hypoxia. We next performed a proteomics screen to survey for other significant differences in protein expression in ME/CFS. Interestingly, out of the seven most significantly modulated proteins in ME/CFS patient plasma, 5 proteins have roles in maintaining gut health, which considering the new appreciation of how gut microbiome and health modulates systemic KP could highlight a new explanation of symptomology in ME/CFS patients and potential new prognostic biomarker/s and/or treatment avenues.},
}
@article {pmid38015063,
year = {2023},
author = {Zhu, R and Gao, Y and Dong, J and Li, Z and Ren, Z},
title = {The changes of gut microbiota and metabolites in different drug-induced liver injuries.},
journal = {Journal of medical microbiology},
volume = {72},
number = {11},
pages = {},
doi = {10.1099/jmm.0.001778},
pmid = {38015063},
issn = {1473-5644},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Chemical and Drug Induced Liver Injury ; Multiomics ; },
abstract = {The increasing incidence of drug-induced liver injury (DILI) has become a major concern. Gut microbiota, as another organ of the human body, has been studied in various tumors, cardiovascular metabolic diseases, inflammatory bowel disease and human immunity. The studies mentioned above have confirmed its important impact on the occurrence and development of DILI. The gut-liver axis explains the close relationship between the gut and the liver, and it may be a pathway by which gut microbes contribute to DILI. In addition, the interaction between drugs and gut microbes affects both separately, which in turn may have positive or negative effects on the body, including DILI. There are both common and specific changes in liver injury caused by different drugs. The alteration of metabolites in DILI is also a new direction of therapeutic exploration. The application of microbiomics, metabolomics and other multi-omics to DILI has also explored new ideas for DILI. In this review, we conclude the alterations of gut microbes and metabolites under different DILI, and the significance of applying gut microbiome-metabolomics to DILI, so as to explore the metabolic characteristics of DILI and possible novel metabolic biomarkers.},
}
@article {pmid38014976,
year = {2023},
author = {Zhuang, Y and Guo, W and Cui, K and Tu, Y and Diao, Q and Zhang, N and Bi, Y and Ma, T},
title = {Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0131423},
doi = {10.1128/spectrum.01314-23},
pmid = {38014976},
issn = {2165-0497},
abstract = {Yaks, as ruminants inhabiting high-altitude environments, possess a distinct rumen microbiome and are resistant to extreme living conditions. This study investigated the microbiota, resistome, and functional gene profiles in the rumen of yaks fed milk or milk replacer (MR), providing insights into the regulation of the rumen microbiome and the intervention of antimicrobial resistance in yaks through dietary methods. The abundance of Prevotella members increased significantly in response to MR. Tetracycline resistance was the most predominant. The rumen of yaks contained multiple antimicrobial resistance genes (ARGs) originating from different bacteria, which could be driven by MR, and these ARGs displayed intricate and complex interactions. MR also induced changes in functional genes. The enzymes associated with fiber degradation and butyrate metabolism were activated and showed close correlations with Prevotella members and butyrate concentration. This study allows us to deeply understand the ruminal microbiome and ARGs of yaks and their relationship with rumen bacteria in response to different milk sources.},
}
@article {pmid38014962,
year = {2023},
author = {Ren, W and Penttilä, R and Kasanen, R and Asiegbu, FO},
title = {Interkingdom and intrakingdom interactions in the microbiome of Heterobasidion fruiting body and associated decayed woody tissues.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0140623},
doi = {10.1128/aem.01406-23},
pmid = {38014962},
issn = {1098-5336},
abstract = {We applied macro- (forest stand and forest management) and micro-scale (bacterial and fungal community) analyses for a better understanding of the Heterobasidion pathosystem and associated wood decay process. The core microbiome, as defined by hierarchy analysis and a consistent model, and environmental factors correlation with the community assembly were found to be novel.},
}
@article {pmid38014951,
year = {2023},
author = {LaReau, JC and Hyde, J and Brackney, DE and Steven, B},
title = {Introducing an environmental microbiome to axenic Aedes aegypti mosquitoes documents bacterial responses to a blood meal.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0095923},
doi = {10.1128/aem.00959-23},
pmid = {38014951},
issn = {1098-5336},
abstract = {The blood meal of the female mosquito serves as a nutrition source to support egg development, so is an important aspect of its biology. Yet, the roles the microbiome may play in blood digestion are poorly characterized. We employed axenic mosquitoes to investigate how the microbiome differs between mosquitoes reared in the insectary versus mosquitoes that acquire their microbiome from the environment. Environmental microbiomes were more diverse and showed larger temporal shifts over the course of blood digestion. Importantly, only bacteria from the environmental microbiome performed hemolysis in culture, pointing to functional differences between bacterial populations. These data highlight that taxonomic differences between the microbiomes of insectary-reared and wild mosquitoes are potentially also related to their functional ecology. Thus, axenic mosquitoes colonized with environmental bacteria offer a way to investigate the role of bacteria from the wild in mosquito processes such as blood digestion, under controlled laboratory conditions.},
}
@article {pmid38014935,
year = {2023},
author = {Shimpi, GG and De la Vega, P and Bentlage, B},
title = {Complete genome sequence of Brachybacterium sp. GU-2 (Actinomycetota), isolated from the massive coral Porites lobata.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0085523},
doi = {10.1128/MRA.00855-23},
pmid = {38014935},
issn = {2576-098X},
abstract = {Brachybacterium sp. GU-2 was isolated from the hard coral Porites lobata found in Apra Harbor, Guam, Micronesia. This genome sequence will be beneficial to understand the role of actinomycetes in coral holobionts. The Brachybacterium genome contains several gene clusters for bioactive compounds, including antibiotics.},
}
@article {pmid38014746,
year = {2023},
author = {Fountain-Jones, NM and Giraud, T and Zinger, L and Bik, H and Creer, S and Videvall, E},
title = {Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.17223},
pmid = {38014746},
issn = {1365-294X},
abstract = {The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning, and disentangling non-bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.},
}
@article {pmid38014621,
year = {2023},
author = {Romberg, N and Le Coz, C},
title = {Common variable immunodeficiency, cross currents, and prevailing winds.},
journal = {Immunological reviews},
volume = {},
number = {},
pages = {},
doi = {10.1111/imr.13291},
pmid = {38014621},
issn = {1600-065X},
support = {//Jeffrey Modell Foundation/ ; },
abstract = {Common variable immunodeficiency (CVID) is a heterogenous disease category created to distinguish late-onset antibody deficiencies from early-onset diseases like agammaglobulinemia or more expansively dysfunctional combined immunodeficiencies. Opinions vary on which affected patients should receive a CVID diagnosis which confuses clinicians and erects reproducibility barriers for researchers. Most experts agree that CVID's most indeliable feature is defective germinal center (GC) production of isotype-switched, affinity-maturated antibodies. Here, we review the biological factors contributing to CVID-associated GC dysfunction including genetic, epigenetic, tolerogenic, microbiome, and regulatory abnormalities. We also discuss the consequences of these biological phenomena to the development of non-infectious disease complications. Finally, we opine on topics and lines of investigation we think hold promise for expanding our mechanistic understanding of this protean condition and for improving the lives of affected patients.},
}
@article {pmid38014521,
year = {2023},
author = {Du, C and Zuo, F and Cao, Y and Zang, Y},
title = {Anti-diabetic effects of natural and modified 'Ganzhou' navel orange peel pectin on type 2 diabetic mice via gut microbiota.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d3fo04118b},
pmid = {38014521},
issn = {2042-650X},
abstract = {Pectin, a kind of dietary fiber, has attracted much attention owing to its beneficial effect on human health in recent years. In this study, the effects of both 'Ganzhou' navel orange peel pectin (GOP) and modified GOP (MGOP) on type 2 diabetes (T2DM) were investigated. The results indicated that GOP and MGOP intervention had positive effects on T2DM in C57BL/6 mice. After modification, pectin can be changed into low methoxy pectin (LMP) and the content of GalA can increase, which endow MGOP with significant effects on improving lipid metabolism (TC, TG, and LDL-C decreased by 30.46%, 50%, and 37.56%, respectively, and HDL-C increased by 56%) and OGTT, further reducing insulin resistance (insulin decreased by 74.35%). In addition, MGOP was superior to GOP in improving oxidative stress (GSH and GSH-Px increased by 52.05% and 29.08% respectively, and MDA decreased by 84.02%), inhibiting inflammation and promoting SCFA synthesis. 16S rRNA analysis showed that MGOP changed the composition of intestinal microbiota in diabetic mice, decreased the abundance of Alistipes, Helicobacter and Oscillibacter, and increased the relative abundance of Dubosiella, Akkermansiaceae, and Atopobiaceae. The phenotypes of the gut microbiome also changed accordingly, which showed that MGOP significantly inhibited the growth of Gram-negative bacteria and potential pathogenic bacteria and reversed the related complications. Taken together, our findings revealed that MGOP intake regulated lipid metabolism and oxidative stress and improved the gut health of mice, with promising effects against T2DM and related complications.},
}
@article {pmid38014449,
year = {2023},
author = {Engevik, MA and Thapa, S and Lillie, I and Yacyshyn, MB and Yacyshyn, B and Percy, AJ and Chace, D and Horvath, TD},
title = {Repurposing dried blood spot (DBS) device technology to examine bile acid profiles in human dried fecal spot (DFS) samples.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00188.2023},
pmid = {38014449},
issn = {1522-1547},
support = {K01K123195-01//HHS | NIH | NIDDK | Division of Diabetes, Endocrinology, and Metabolic Diseases (DEM)/ ; },
abstract = {Dried blood spot (DBS) analysis has existed for >50 years, but application of this technique to fecal analysis remains limited. To address whether dried fecal spots (DFS) could be used to measure fecal bile acids, we collected feces from five subjects for each of the following cohorts: i) healthy individuals, ii) individuals with diarrhea, and iii) Clostridioides difficile-infected patients. Homogenized fecal extracts were loaded onto quantitative DBS (qDBS) devices, dried overnight, and shipped to the bioanalytical lab at ambient temperature. For comparison, source fecal extracts were shipped on dry ice and stored frozen. After four months, frozen fecal extracts and ambient DFS samples were processed and subjected to targeted LC-MS/MS-based metabolomics with stable isotope-labeled standards. We observed no differences in the bile acid levels measured between the traditional extraction and the qDBS-based DFS methods. This pilot data demonstrate that DFS-based analysis is feasible and warrants further development for fecal compounds and microbiome applications.},
}
@article {pmid38014294,
year = {2023},
author = {Pereira, FC and Ge, X and Kristensen, JM and Kirkegaard, RH and Maritsch, K and Zhu, Y and Decorte, M and Hausmann, B and Berry, D and Wasmund, K and Schintlmeister, A and Boettcher, T and Cheng, JX and Wagner, M},
title = {The Parkinson's drug entacapone disrupts gut microbiome homeostasis via iron sequestration.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.12.566429},
pmid = {38014294},
abstract = {Increasing evidence shows that many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, much less is known about the mechanisms by which drugs target the microbiome and how drugs affect microbial function. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single cell chemical imaging to investigate the impact of two widely prescribed nervous system targeted drugs on the gut microbiome. Ex vivo supplementation of physiologically relevant concentrations of entacapone or loxapine succinate to faecal samples significantly impacted the abundance of up to one third of the microbial species present. Importantly, we demonstrate that the impact of these drugs on microbial metabolism is much more pronounced than their impact on abundances, with low concentrations of drugs reducing the activity, but not the abundance of key microbiome members like Bacteroides, Ruminococcus or Clostridium species. We further demonstrate that entacapone impacts the microbiome due to its ability to complex and deplete available iron, and that microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Remarkably, entacapone-induced iron starvation selected for iron-scavenging organisms carrying antimicrobial resistance and virulence genes. Collectively, our study unveils the impact of two under-investigated drugs on whole microbiomes and identifies metal sequestration as a mechanism of drug-induced microbiome disturbance.},
}
@article {pmid38014241,
year = {2023},
author = {Frith, ME and Kashyap, PC and Linden, DR and Theriault, B and Chang, EB},
title = {Microbiota-dependent early life programming of gastrointestinal motility.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.08.566304},
pmid = {38014241},
abstract = {Gastrointestinal microbes modulate peristalsis and stimulate the enteric nervous system (ENS), whose development, as in the central nervous system (CNS), continues into the murine postweaning period. Given that adult CNS function depends on stimuli received during critical periods of postnatal development, we hypothesized that adult ENS function, namely motility, depends on microbial stimuli during similar critical periods. We gave fecal microbiota transplantation (FMT) to germ-free mice at weaning or as adults and found that only the mice given FMT at weaning recovered normal transit, while those given FMT as adults showed limited improvements. RNAseq of colonic muscularis propria revealed enrichments in neuron developmental pathways in mice exposed to gut microbes earlier in life, while mice exposed later - or not at all - showed exaggerated expression of inflammatory pathways. These findings highlight a microbiota-dependent sensitive period in ENS development, pointing to potential roles of the early life microbiome in later life dysmotility.},
}
@article {pmid38014162,
year = {2023},
author = {Subramanian, P and Romero-Soto, HN and Stern, DB and Maxwell, GL and Levy, S and Hourigan, SK},
title = {Delivery mode impacts gut bacteriophage colonization during infancy.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.13.23298307},
pmid = {38014162},
abstract = {BACKGROUND: Cesarean section delivery is associated with altered early-life bacterial colonization and later adverse inflammatory and immune health outcomes. Although gut bacteriophages can alter gut microbiome composition and impact host immune responses, little is known about how delivery mode impacts bacteriophage colonization over time. To begin to address this we examined how delivery mode affected bacteriophage colonization over the first two years of life.<br><br>RESULTS: Shotgun metagenomic sequencing was conducted on 272 serial stool samples from 55 infants, collected at 1-2 days of life and 2, 6, 12 and 24 months. 33/55 (60%) infants were born by vaginal delivery. DNA viruses were identified, and by host inference, 94% of the viral sequences were found to be bacteriophages. Alpha diversity of the virome was increased in vaginally delivered infants compared to cesarean section delivered infants at 2 months (Shannon index, p=0.022). Beta diversity significantly differed by delivery mode at 2, 6, and 12 months when stratified by peripartum antibiotic use (Bray-Curtis dissimilarity, all p<0.05). Significant differentially abundant predicted bacteriophage hosts by delivery mode were seen at all time points. Moreover, there were differences in predicted bacteriophage functional gene abundances up to 24 months by delivery mode. Many of the functions considered to play a role in host response were increased in vaginal delivery.<br><br>CONCLUSIONS: Clear differences in bacteriophage composition and function were seen by delivery mode over the first two years of life. Given that phages are known to affect host immune response, our results suggest that future investigation into how delivery mode may lead to adverse inflammatory outcomes should not only include bacterial microbial colonization but also the potential role of bacteriophages and transkingdom interactions.},
}
@article {pmid38014088,
year = {2023},
author = {Gundogan, K and Nellis, MM and Ozer, NT and Ergul, SS and Sahin, GG and Temel, S and Yuksel, RC and Teeny, S and Alvarez, JA and Sungur, M and Jones, DP and Ziegler, TR},
title = {High-Resolution Plasma Metabolomics and Thiamine Status in Critically Ill Adult Patients.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-3597052/v1},
pmid = {38014088},
abstract = {Thiamine (Vitamin B1) is an essential micronutrient and a co-factor for metabolic functions related to energy metabolism. We determined the association between whole blood thiamine pyrophosphate (TPP) concentrations and plasma metabolites using high resolution metabolomics in critically ill patients. Methods Cross-sectional study performed in Erciyes University Hospital, Kayseri, Turkey and Emory University, Atlanta, GA, USA. Participants were ≥ 18 years of age, with an expected length of ICU stay longer than 48 hours, receiving furosemide therapy for at least 6 months before ICU admission. Results Blood for TPP and metabolomics was obtained on the day of ICU admission. Whole blood TPP concentrations were measured using high-performance liquid chromatography (HPLC). Liquid chromatography/mass spectrometry was used for plasma high-resolution metabolomics. Data was analyzed using regression analysis of TPP levels against all plasma metabolomic features in metabolome-wide association studies. We also compared metabolomic features from patients in the highest TPP concentration tertile to patients in the lowest TPP tertile as a secondary analysis. We enrolled 76 participants with a median age of 69 (range, 62.5-79.5) years. Specific metabolic pathways associated with whole blood TPP levels, using both regression and tertile analysis, included pentose phosphate, fructose and mannose, branched chain amino acid, arginine and proline, linoleate, and butanoate pathways. Conclusions Plasma high-resolution metabolomics analysis showed that whole blood TPP concentrations are significantly associated with metabolites and metabolic pathways linked to the metabolism of energy, amino acids, lipids, and the gut microbiome in adult critically ill patients.},
}
@article {pmid38014044,
year = {2023},
author = {Elovitz, M and Anton, L and Cristancho, A and Ferguson, B and Joseph, A and Ravel, J},
title = {Vaginal microbes alter epithelial transcriptomic and epigenomic modifications providing insight into the molecular mechanisms for susceptibility to adverse reproductive outcomes.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-3580132/v1},
pmid = {38014044},
abstract = {The cervicovaginal microbiome is highly associated with women's health with microbial communities dominated by Lactobacillus spp. being considered optimal. Conversely, a lack of lactobacilli and a high abundance of strict and facultative anaerobes including Gardnerella vaginalis , have been associated with adverse reproductive outcomes. However, the molecular pathways modulated by microbe interactions with the cervicovaginal epithelia remain unclear. Using RNA-sequencing, we characterize the in vitro cervicovaginal epithelial transcriptional response to different vaginal bacteria and their culture supernatants. We showed that G. vaginalis upregulated genes were associated with an activated innate immune response including anti-microbial peptides and inflammasome pathways, represented by NLRP3-mediated increases in caspase-1, IL-1β and cell death. Cervicovaginal epithelial cells exposed to L. crispatus showed limited transcriptomic changes, while exposure to L. crispatus culture supernatants resulted in a shift in the epigenomic landscape of cervical epithelial cells. ATAC-sequencing confirmed epigenetic changes with reduced chromatin accessibility. This study reveals new insight into host-microbe interactions in the lower reproductive tract and suggest potential therapeutic strategies leveraging the vaginal microbiome to improve reproductive health.},
}
@article {pmid38014043,
year = {2023},
author = {Aparicio, A and Sun, Z and Gold, DR and Litonjua, AA and Weiss, ST and Lee-Sarwar, K and Liu, YY},
title = {Genotype-microbiome-metabolome associations in early childhood, and their link to BMI and childhood obesity.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.13.23298467},
pmid = {38014043},
abstract = {The influence of genotype on defining the human gut microbiome has been extensively studied, but definite conclusions have not yet been found. To fill this knowledge gap, we leverage data from children enrolled in the Vitamin D Antenatal Asthma Reduction Trial (VDAART) from 6 months to 8 years old. We focus on a pool of 12 genes previously found to be associated with the gut microbiome in independent studies, establishing a Bonferroni corrected significance level of p-value < 2.29 × 10 [-6] . We identified significant associations between SNPs in the FHIT gene (known to be associated with obesity and type 2 diabetes) and obesity-related microbiome features, and the children's BMI through their childhood. Based on these associations, we defined a set of SNPs of interest and a set of taxa of interest. Taking a multi-omics approach, we integrated plasma metabolome data into our analysis and found simultaneous associations among children's BMI, the SNPs of interest, and the taxa of interest, involving amino acids, lipids, nucleotides, and xenobiotics. Using our association results, we constructed a quadripartite graph where each disjoint node set represents SNPs in the FHIT gene, microbial taxa, plasma metabolites, or BMI measurements. Network analysis led to the discovery of patterns that identify several genetic variants, microbial taxa and metabolites as new potential markers for obesity, type 2 diabetes, or insulin resistance risk.},
}
@article {pmid38014007,
year = {2023},
author = {Mah, JC and Lohmueller, KE and Garud, N},
title = {Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.09.566454},
pmid = {38014007},
abstract = {Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their population demographic histories and their distributions of fitness effects (DFE) of new mutations. Here, we infer the demographic histories and DFEs of 27 of the most highly prevalent and abundant commensal gut microbial species in North Americans over timescales exceeding human generations using a collection of lineages inferred from a panel of healthy hosts. We find overall reductions in genetic variation among commensal gut microbes sampled from a Western population relative to an African rural population. Additionally, some species in North American microbiomes display contractions in population size and others expansions, potentially occurring at several key historical moments in human history. DFEs across species vary from highly to mildly deleterious, with accessory genes experiencing more drift compared to core genes. Within genera, DFEs tend to be more congruent, reflective of underlying phylogenetic relationships. Taken together, these findings suggest that human commensal gut microbes have distinct evolutionary histories, possibly reflecting the unique roles of individual members of the microbiome.},
}
@article {pmid38013050,
year = {2023},
author = {Okawa, Y and Sasagawa, S and Kato, H and Johnson, TA and Nagaoka, K and Kobayashi, Y and Hayashi, A and Shibayama, T and Maejima, K and Tanaka, H and Miyano, S and Shibahara, J and Nishizuka, S and Hirano, S and Seto, Y and Iwaya, T and Kakimi, K and Yasuda, T and Nakagawa, H},
title = {Immuno-genomic analysis reveals eosinophilic feature and favorable prognosis of female non-smoking esophageal squamous cell carcinomas.},
journal = {Cancer letters},
volume = {},
number = {},
pages = {216499},
doi = {10.1016/j.canlet.2023.216499},
pmid = {38013050},
issn = {1872-7980},
abstract = {Most of esophageal squamous cell carcinoma (ESCC) develop in smoking males in Japan, but the genomic etiology and immunological characteristics of rare non-smoking female ECSS remain unclear. To elucidate the genomic and immunological features of ESCC in non-smoking females, we analyzed whole-genome or transcriptome sequencing data from 94 ES CCs, including 20 rare non-smoking female cases. In addition, 31,611 immune cells were extracted from four ESCC tissues and subject to single-cell RNA-seq. We compared their immuno-genomic and microbiome profiles between non-smoking female and smoking ESCCs. Non-smoking females showed much better prognosis. Whole-genome sequencing analysis showed no significant differences in driver genes or copy number alterations depending on smoking status. The mutational signature specifically observed in non-smoking females ESCC could be attributed to aging. Immune profiling from RNA-seq revealed that ESCC in non-smoking females had high tumor microenvironment signatures and a high abundance of eosinophils with a favorable prognosis. Single-cell RNA-sequencing of intratumor immune cells revealed gender differences of eosinophils and their activation in female cases. ESCCs in non-smoking females have age-related mutational signatures and gender-specific tumor immune environment with eosinophils, which is likely to contribute to their favorable prognosis.},
}
@article {pmid38013035,
year = {2023},
author = {Dong, W and Zhou, R and Li, X and Yan, H and Zheng, J and Peng, N and Zhao, S},
title = {Effect of simplified inoculum agent on performance and microbiome during cow manure-composting at industrial-scale.},
journal = {Bioresource technology},
volume = {393},
number = {},
pages = {130097},
doi = {10.1016/j.biortech.2023.130097},
pmid = {38013035},
issn = {1873-2976},
abstract = {A simplified inoculum agent, only comprising Bacillus subtilis and Aspergillus niger, was utilized for industrial-scale cow-manure composting to investigate its impact on composting performance and microbiome. Inoculants elevated the average and peak temperatures by up to 7 and 10 °C, respectively, during the thermophilic stage, reduced organic matter content, and raised germination index. Inoculation also extended the period of composting above 50 °C from 12 to 26 days. Sequencing unveiled significant shifts in microbial diversity, composition, and function. Aspergillus thrived during the mesophilic phase, potentially initiating composting, whereas Bacillus, Lysinibacillus, and Clostridium were enriched during the thermophilic stage. Metagenomic sequencing revealed an increased abundance of carbohydrate-active enzymes and glycometabolism-related genes responsible for lignocellulose degradation and heat generation after inoculation. These enriched microbes and functional genes contributed to organic matter degradation and temperature maintenance during thermophilic stage, expediting composting. This suggests the effectiveness of this simplified inoculum in industrial-level cow-manure composting.},
}
@article {pmid38012967,
year = {2023},
author = {Zhao, J and Duan, G and Zhu, D and Li, J and Zhu, Y},
title = {Microbial-influenced pesticide removal co-occurs with antibiotic resistance gene variation in soil-earthworm-maize system.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {123010},
doi = {10.1016/j.envpol.2023.123010},
pmid = {38012967},
issn = {1873-6424},
abstract = {Within human-influenced landscapes, pesticides cooccur with a variety of antibiotic stressors. However, the relationship between pesticides removal process and antibiotic resistance gene variation are not well understood. This study explored pesticide (topramezone, TPZ) and antibiotic (polymyxin E, PME) co-contamination using liquid chromatography-tandem mass spectrometry (LC-MS/MS), bacterial-16 S rRNA sequencing and high-throughput quantitative polymerase chain reaction (HT-qPCR) in a soil-earthworm-maize system. After incubating soil for 28 days with TPZ and PME (10 mg kg[-1] dry weight), earthworm weight-gain, mortality rates, and maize plant weight-gain only differed slightly, but height-gain significantly decreased. PME significantly increased TPZ-removal in the soil. Accumulation of TPZ in earthworm's tissues may pose potential risks in the food chain. Combined pollution altered the microbial community structure and increased the abundance of functional microorganisms involved in aromatic compound degradation. Furthermore, maize rhizosphere can raise resistance genes, however earthworms can reduce resistance genes. Co-contamination increased absolute abundance of mobile genetic elements (MGEs) in bulk-soil samples, antibiotic resistance genes (ARGs) in skin samples and number of ARGs in bulk-soil samples, while decreased absolute abundance of transposase gene in bulk-soil samples and number of ARGs in rhizosphere-soil samples. Potential hosts harbouring ARGs may be associated with the antagonistic effect during resistance and detoxification of TPZ and PMB co-occurrence. These findings provide insights into the mechanism underlining pesticide removal regarding occurrence of ARGs in maize agroecosystem.},
}
@article {pmid38012609,
year = {2023},
author = {Lai, TT and Liou, CW and Tsai, YH and Lin, YY and Wu, WL},
title = {Butterflies in the gut: the interplay between intestinal microbiota and stress.},
journal = {Journal of biomedical science},
volume = {30},
number = {1},
pages = {92},
pmid = {38012609},
issn = {1423-0127},
support = {112-2628-B-006-013-//National Science and Technology Council/ ; 110-2320-B-006-018-MY3//National Science and Technology Council/ ; 111-2314-B-006-008//National Science and Technology Council/ ; 110-2926-I-006-001-MY4//National Science and Technology Council/ ; 110-2314-B-006-114//Ministry of Science and Technology, Taiwan/ ; 109-2314-B-006-046//Ministry of Science and Technology, Taiwan/ ; 107-2320-B-006-072-MY3//Ministry of Science and Technology, Taiwan/ ; },
mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; *Butterflies ; },
abstract = {Psychological stress is a global issue that affects at least one-third of the population worldwide and increases the risk of numerous psychiatric disorders. Accumulating evidence suggests that the gut and its inhabiting microbes may regulate stress and stress-associated behavioral abnormalities. Hence, the objective of this review is to explore the causal relationships between the gut microbiota, stress, and behavior. Dysbiosis of the microbiome after stress exposure indicated microbial adaption to stressors. Strikingly, the hyperactivated stress signaling found in microbiota-deficient rodents can be normalized by microbiota-based treatments, suggesting that gut microbiota can actively modify the stress response. Microbiota can regulate stress response via intestinal glucocorticoids or autonomic nervous system. Several studies suggest that gut bacteria are involved in the direct modulation of steroid synthesis and metabolism. This review provides recent discoveries on the pathways by which gut microbes affect stress signaling and brain circuits and ultimately impact the host's complex behavior.},
}
@article {pmid38012587,
year = {2023},
author = {Alyousef, YM and Piotrowski, S and Alonaizan, FA and Alsulaiman, A and Alali, AA and Almasood, NN and Vatte, C and Hamilton, L and Gandla, D and Lad, H and Robinson, FL and Cyrus, C and Meng, RC and Dowdell, A and Piening, B and Keating, BJ and Al-Ali, AK},
title = {Oral microbiota analyses of paediatric Saudi population reveals signatures of dental caries.},
journal = {BMC oral health},
volume = {23},
number = {1},
pages = {935},
pmid = {38012587},
issn = {1472-6831},
mesh = {Male ; Child ; Female ; Humans ; *Dental Caries/genetics ; Saudi Arabia ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Saliva ; },
abstract = {BACKGROUND: Oral microbiome sequencing has revealed key links between microbiome dysfunction and dental caries. However, these efforts have largely focused on Western populations, with few studies on the Middle Eastern communities. The current study aimed to identify the composition and abundance of the oral microbiota in saliva samples of children with different caries levels using machine learning approaches.<br><br>METHODS: Oral microbiota composition and abundance were identified in 250 Saudi participants with high dental caries and 150 with low dental caries using 16&#xa0;S rRNA sequencing on a NextSeq 2000 SP flow cell (Illumina, CA) using 250&#xa0;bp paired-end reads, and attempted to build a classifier using random forest models to assist in the early detection of caries.<br><br>RESULTS: The ADONIS test results indicate that there was no significant association between sex and Bray-Curtis dissimilarity (p&#x2009;~&#x2009;0.93), but there was a significant association with dental caries status (p&#x2009;~&#x2009;0.001). Using an alpha level of 0.05, five differentially abundant operational taxonomic units (OTUs) were identified between males and females as the main effect along with four differentially abundant OTUs between high and low dental caries. The mean metrics for the optimal hyperparameter combination using the model with only differentially abundant OTUs were: Accuracy (0.701); Matthew's correlation coefficient (0.0509); AUC (0.517) and F1 score (0.821) while the mean metrics for random forest model using all OTUs were:0.675; 0.054; 0.611 and 0.796 respectively.<br><br>CONCLUSION: The assessment of oral microbiota samples in a representative Saudi Arabian population for high and low metrics of dental caries yields signatures of abundances and diversity.},
}
@article {pmid38012477,
year = {2023},
author = {Zhang, K and Ji, J and Li, N and Yin, Z and Fan, G},
title = {Integrated Metabolomics and Gut Microbiome Analysis Reveals the Efficacy of a Phytochemical Constituent in the Management of Ulcerative Colitis.},
journal = {Molecular nutrition &amp; food research},
volume = {},
number = {},
pages = {e2200578},
doi = {10.1002/mnfr.202200578},
pmid = {38012477},
issn = {1613-4133},
support = {2019KJ076//Tianjin Municipal Education Commission/ ; },
abstract = {SCOPE: Cinnamaldehyde (CAH), a phytochemical constituent isolated from cinnamon, is gaining attention due to its nutritional and medicinal benefits. This study aimed to investigate the potential role of CAH in the treatment of ulcerative colitis (UC).<br><br>METHODS AND RESULTS: Integrated metabolomics and gut microbiome analysis are performed for 2,4,6-trinitrobenzenesulfonic acid (TNBS) induced UC rats. The effect of CAH on colonic inflammation, lipid peroxidation, metabolic profiles, and gut microbiota is systematically explored. It finds that CAH improves the colitis-related symptoms, decreases disease activity index, increases the colon length and body weight, and alleviates histologic inflammation of UC rats. These therapeutic effects of CAH are due to suppression of inflammation and lipid peroxidation. Moreover, multi-omics analysis reveals that CAH treatment cause changes in plasma metabolome and gut microbiome in UC rats. CAH regulates lipid metabolic processes, especially phosphatidylcholines, lysophosphatidylcholines, and polyunsaturated fatty acids. Meanwhile, CAH modulates the gut microbial structure by restraining pathogenic bacteria (such as Helicobacter) and increasing probiotic bacteria (such as Bifidobacterium and Lactobacillus).<br><br>CONCLUSIONS: These results indicate that CAH exerts a beneficial role in UC by synergistic modulating the balance in gut microbiota and the associated metabolites, and highlights the nutritional and medicinal value of CAH in UC management.},
}
@article {pmid38012463,
year = {2023},
author = {Hart, NH and Wallen, MP and Farley, MJ and Haywood, D and Boytar, AN and Secombe, K and Joseph, R and Chan, RJ and Kenkhuis, MF and Buffart, LM and Skinner, TL and Wardill, HR},
title = {Exercise and the gut microbiome: implications for supportive care in cancer.},
journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer},
volume = {31},
number = {12},
pages = {724},
pmid = {38012463},
issn = {1433-7339},
abstract = {PURPOSE: Growing recognition of the gut microbiome as an influential modulator of cancer treatment efficacy and toxicity has led to the emergence of clinical interventions targeting the microbiome to enhance cancer and health outcomes. The highly modifiable nature of microbiota to endogenous, exogenous, and environmental inputs enables interventions to promote resilience of the gut microbiome that have rapid effects on host health, or response to cancer treatment. While diet, probiotics, and faecal microbiota transplant are primary avenues of therapy focused on restoring or protecting gut function in people undergoing cancer treatment, the role of physical activity and exercise has scarcely been examined in this population.<br><br>METHODS: A narrative review was conducted to explore the nexus between cancer care and the gut microbiome in the context of physical activity and exercise as a widely available and clinically effective supportive care strategy used by cancer survivors.<br><br>RESULTS: Exercise can facilitate a more diverse gut microbiome and functional metabolome in humans; however, most physical activity and exercise studies have been conducted in healthy or athletic populations, primarily using aerobic exercise modalities. A scarcity of exercise and microbiome studies in cancer exists.<br><br>CONCLUSIONS: Exercise remains an attractive avenue to promote microbiome health in cancer survivors. Future research should elucidate the various influences of exercise modalities, intensities, frequencies, durations, and volumes to explore dose-response relationships between exercise and the gut microbiome among cancer survivors, as well as multifaceted approaches (such as diet and probiotics), and examine the influences of exercise on the gut microbiome and associated symptom burden prior to, during, and following cancer treatment.},
}
@article {pmid38012292,
year = {2023},
author = {Wang, LJ and Jin, YL and Pei, WL and Li, JC and Zhang, RL and Wang, JJ and Lin, W},
title = {Amuc_1100 pretreatment alleviates acute pancreatitis in a mouse model through regulating gut microbiota and inhibiting inflammatory infiltration.},
journal = {Acta pharmacologica Sinica},
volume = {},
number = {},
pages = {},
pmid = {38012292},
issn = {1745-7254},
abstract = {Amuc_1100 is a membrane protein from Akkermansia muciniphila, which has been found to play a role in host immunological homeostasis in the gastrointestinal tract by activating TLR2 and TLR4. In this study we investigated the effects and underlying mechanisms of Amuc_1100 on acute pancreatitis (AP) induced in mice by intraperitoneal injection of caerulein and lipopolysaccharide (LPS). The mice were treated with the protein Amuc_1100 (3 μg, i.g.) for 20 days before caerulein injection. Cecal contents of the mice were collected for 16S rRNA sequencing. We found that pretreatment with Amuc_1100 significantly alleviated AP-associated pancreatic injury, reduced serum amylase and lipase. Amuc_1100 pretreatment significantly inhibited the expression of proinflammatory cytokines (TNF-α, IL-1β, IFN-γ and IL-6) in spleen and pancreas through inhibiting NF-κB signaling pathway. Moreover, Amuc_1100 pretreatment significantly decreased the inflammatory infiltration, accompanied by the reduction of Ly6C[+] macrophages and neutrophils in the spleen of AP mice. Gut microbiome analysis showed that the abundance of Bacteroidetes, Proteobacteria, Desulfobacterota and Campilobacterota was decreased, while the proportion of Firmicutes and Actinobacteriota was increased in AP mice pretreated with Amuc_1100. We further demonstrated that Amuc_1100 pretreatment restored the enrichment of tryptophan metabolism, which was mediated by intestinal flora. These results provide new evidence that Amuc_1100 lessens the severity of AP through its anti-inflammatory properties with a reduction of macrophages and neutrophil infiltration, as well as its regulation of the composition of intestinal flora and tryptophan metabolism.},
}
@article {pmid38012110,
year = {2023},
author = {Zou, X and Nakura, Y and Kawaguchi, H and Nishiumi, F and Wu, HN and Yanagihara, I},
title = {Comparison of databases useful for the analysis of vaginal microbiota in Japanese women using next-generation sequencing data (QIIME 2 software).},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxad283},
pmid = {38012110},
issn = {1365-2672},
abstract = {AIMS: Approximately 10% of children are born prematurely, and bacterial vaginosis during pregnancy is associated with preterm delivery. Highly accurate species-level vaginal microflora analysis helps control bacteria-induced preterm birth. Therefore, we aimed to conduct a bioinformatic analysis of gene sequences using 16S databases and compare their efficacy in comprehensively identifying potentially pathogenic vaginal microbiota in Japanese women.<br><br>METHODS AND RESULTS: The 16s rRNA databases, Silva, Greengenes, and basic local alignment search tool (BLAST) were compared to determine whether the classification quality could be improved using the V3-V4 region next-generation sequencing (NGS) sequences. It was found that NGS data were aligned using the BLAST database with the QIIME 2 platform, whose classification quality was higher than that of Silva, and the combined Silva and Greengenes databases based on the mutual complementarity of the two databases.<br><br>CONCLUSIONS: The reference database selected during the bioinformatic processing influenced the recognized sequence percentage, taxonomic rankings, and accuracy. This study showed that the BLAST database was the best choice for NGS data analysis of Japanese women's vaginal microbiota.},
}
@article {pmid38011708,
year = {2023},
author = {Moody, M and Sawyer, R},
title = {Is There a Community Microbial Community? A Comparison of Pathogens Between Two Hospital Surgical Intensive Care Units in a Single City.},
journal = {Surgical infections},
volume = {},
number = {},
pages = {},
doi = {10.1089/sur.2023.069},
pmid = {38011708},
issn = {1557-8674},
abstract = {Background: Nosocomial and health-care-associated infections drive increased healthcare costs and negatively affect patient outcomes. The human microbiome has been heavily explored in recent years with incomplete data regarding hospital-specific and community-specific microbial communities. Although bacterial species differ between intensive care units in the same hospital, it is unclear if they differ between similar units in similar hospitals in the same community. Our hypothesis is that pathogens in surgical intensive care units (SICUs) are distinct between hospitals, even in the same community. Methods: From 2017 to 2021, data were collected prospectively from the SICUs of two 400-bed hospitals located three miles apart in the same city (Hospital A and Hospital B). Infections defined using U.S. Centers for Disease Control and Prevention (CDC) criteria were recorded for trauma and general surgery patients, as well as patient demographics, Acute Physiology and Chronic Health Evaluation (APACHE) II score, and causative organism. Results: Overall, Escherichia coli was the most commonly isolated pathogen in Hospital A, whereas Staphylococcus aureus was most commonly isolated at Hospital B. Enterococci were more common in Hospital A, and Haemophilus influenzae and Enterobacter spp. were more common in Hospital B. After stratification between trauma and non-trauma patients, however, these differences disappeared, with the exception of more overall gram-positive organisms and fewer gram-negative organisms among Hospital A trauma patients compared to Hospital B. There were no differences in rates of isolation of either fungi or resistant bacteria between hospitals. Conclusions: At a species level, admission diagnosis appears to be a greater determinant of pathogen isolation than hospital when comparing similar intensive care units (ICUs) in the same geographic area, but a larger body of data is needed to flesh out a distinct microbial map of the organisms occupying a certain geographic region. Further areas for investigation include comparison between hospital units, specific anatomic sites, and ICU versus floor patients.},
}
@article {pmid38011635,
year = {2023},
author = {Choueiry, F and Gold, A and Xu, R and Zhang, S and Zhu, J},
title = {Secondary-Electrospray Ionization Mass Spectrometry-Based Online Analyses of Mouse Volatilome Uncover Gut Microbiome-Dictated Metabolic Changes in the Host.},
journal = {Journal of the American Society for Mass Spectrometry},
volume = {},
number = {},
pages = {},
doi = {10.1021/jasms.3c00304},
pmid = {38011635},
issn = {1879-1123},
abstract = {The symbiotic relationship between the gut microbial population is capable of regulating numerous aspects of host physiology, including metabolism. Bacteria can modulate the metabolic processes of the host by feeding on nutritional components within the lumen and releasing bioactive components into circulation. Endogenous volatile organic compound (VOC) synthesis is dependent on the availability of precursors found in mammalian metabolism. Herein, we report that microbial-mediated metabolic influences can alter the host volatilome and the prominent volatile changes can be uncovered by a novel volatile analysis technique named secondary electrospray ionization mass spectrometry. Mice were subjected to an antibiotic cocktail to deplete the microbiome and then inoculated with either single strain bacteria or fecal matter transplantation (FMT) to replete the microbial population in the gut. VOC sampling was achieved by using an advanced secondary electrospray ionization (SESI) source that directly mounted onto a Thermo Q-Exactive high-resolution mass spectrometer (HRMS). A principal component analysis summarizing the volatile profiles of the mice revealed independent clustering of each strain of the FMT-inoculated groups, suggesting unique volatile profiles. The Mummichog algorithm uncovered phenylalanine metabolism as a significantly altered metabolic profile in the volatilome of the microbiome-repleted mice. Our results indicated that the systemic metabolic changes incurred by the host are translated to unique volatile profiles correlated to the diversity of the microbial population colonized within the host. It is thus possible to take advantage of SESI-HRMS-based platforms for noninvasive screening of VOCs to determine the contribution of various microbial colonization within human gut that may impact host health.},
}
@article {pmid38011171,
year = {2023},
author = {Tomita, S and Kuroda, K and Narihiro, T},
title = {A small step to discover candidate biological control agents from preexisting bioresources by using novel nonribosomal peptide synthetases hidden in activated sludge metagenomes.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0294843},
pmid = {38011171},
issn = {1932-6203},
abstract = {Biological control agents (BCAs), beneficial organisms that reduce the incidence or severity of plant disease, have been expected to be alternatives to replace chemical pesticides worldwide. To date, BCAs have been screened by culture-dependent methods from various environments. However, previously unknown BCA candidates may be buried and overlooked because this approach preferentially selects only easy-to-culture microbial lineages. To overcome this limitation, as a small-scale test case, we attempted to explore novel BCA candidates by employing the shotgun metagenomic information of the activated sludge (AS) microbiome, which is thought to contain unutilized biological resources. We first performed genome-resolved metagenomics for AS taken from a municipal sewage treatment plant and obtained 97 nonribosomal peptide synthetase (NRPS)/polyketide synthase (PKS)-related gene sequences from 43 metagenomic assembled bins, most of which were assigned to the phyla Proteobacteria and Myxococcota. Furthermore, these NRPS/PKS-related genes are predicted to be novel because they were genetically dissimilar to known NRPS/PKS gene clusters. Of these, the condensation domain of the syringomycin-related NRPS gene cluster was detected in Rhodoferax- and Rhodocyclaceae-related bins, and its homolog was found in previously reported AS metagenomes as well as the genomes of three strains available from the microbial culture collections, implying their potential BCA ability. Then, we tested the antimicrobial activity of these strains against phytopathogenic fungi to investigate the potential ability of BCA by in vitro cultivation and successfully confirmed the actual antifungal activity of three strains harboring a possibly novel NRPS gene cluster. Our findings provide a possible strategy for discovering novel BCAs buried in the environment using genome-resolved metagenomics.},
}
@article {pmid38011083,
year = {2023},
author = {Chalifour, BN and Elder, LE and Li, J},
title = {Diversity of gut microbiome in Rocky Mountainsnail across its native range.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0290292},
pmid = {38011083},
issn = {1932-6203},
abstract = {The animal gut microbiome is often a key requirement for host nutrition, digestion, and immunity, and can shift in relation to host geography and environmental factors. However, ecological drivers of microbiome community assembly across large geographic ranges have rarely been examined in invertebrates. Oreohelix strigosa (Rocky Mountainsnail) is a widespread land snail found in heterogeneous environments across the mountainous western United States. It is ideally suited for biogeography studies due to its broad distribution, low migration, and low likelihood of passive transport via other animals. This study aims to uncover large-scale geographic shifts in the composition of O. strigosa gut microbiomes by using 16S rRNA gene sequencing on samples from across its native range. Additionally, we elucidate smaller-scale microbiome variation using samples collected only within Colorado. Results show that gut microbiomes vary significantly across broad geographic ranges. Several possible ecological drivers, including soil and vegetation composition, habitat complexity, habitat type, and human impact, collectively explained 27% of the variation across Coloradan O. strigosa gut microbiomes. Snail gut microbiomes show more similarity to vegetation than soil microbiomes. Gut microbial richness was highest in the rocky habitats and increased significantly in the most disturbed habitats (low complexity, high human impact), potentially indicating signs of dysbiosis in the snails' gut microbiomes. These small-scale environmental factors may be driving changes in O. strigosa gut microbiome composition seen across large-scale geography. This knowledge will also help us better understand how microbial associations influence species survival in diverse environments and aid wildlife conservation efforts.},
}
@article {pmid38010921,
year = {2023},
author = {Fenneman, AC and Boulund, U and Collard, D and Galenkamp, H and Zwinderman, A and van der Born, BJ and van der Spek, AH and Fliers, E and Rampanelli, E and Blaser, M and Nieuwdorp, M},
title = {Comparative Analysis of Taxonomic and Functional Gut Microbiota Profiles in Relation to Seroconversion of Thyroid Peroxidase Antibodies in Euthyroid Participants.},
journal = {Thyroid : official journal of the American Thyroid Association},
volume = {},
number = {},
pages = {},
doi = {10.1089/thy.2023.0346},
pmid = {38010921},
issn = {1557-9077},
abstract = {BACKGROUND: Previous studies have reported gut microbiome alterations in Hashimoto's autoimmune thyroiditis (HT) patients. Yet, it is unknown whether an aberrant microbiome is present before clinical disease onset in participants susceptible to HT or whether it reflects the effects of the disease itself. Here, we report for the first time a comprehensive characterization of the taxonomic and functional profiles of the gut microbiota in euthyroid seropositive and seronegative participants. Our primary goal was to determine taxonomic and functional signatures of the intestinal microbiota associated with serum thyroid peroxidase antibodies (TPOAb) antibodies. A secondary aim was to determine whether different ethnicities warrant distinct reference intervals for accurate interpretation of serum thyroid biomarkers.<br><br>METHODS: In this cross-sectional study, euthyroid participants with (N=159) and without (N=1,309) TPOAb were selected from the multi-ethnic (European Dutch, Moroccan, and Turkish) HEalthy Life In an Urban Setting (HELIUS) cohort. Fecal microbiota composition was profiled using 16S rRNA sequencing. Differences between the groups were analyzed based on overall composition (alpha and beta diversity), as well as differential abundance of microbial taxa and functional pathways using multiple differential abundance tools.<br><br>RESULTS: Overall composition showed a substantial overlap between the two groups (p>0.05 for alpha-diversity; p=0.39 for beta-diversity), indicating that TPOAb-seropositivity does not significantly differentiate gut microbiota composition and diversity. Interestingly, TPOAb-status accounted for only a minor fraction (0.07%) of microbiome variance (p=0.545). Further exploration of taxonomic differences identified 138 taxa nominally associated with TPOAb-status. Among these, thirteen taxa consistently demonstrated nominal significance across three additional differential abundance methods, alongside notable associations within various functional pathways. Furthermore, we showed that ethnicity-specific reference intervals for serum thyroid biomarkers are not required, as no significant disparities in serum thyroid markers were found among the three ethnic groups residing in an iodine-replete area (p>0.05 for TSH, fT4, and TPOAb).<br><br>CONCLUSION: These findings suggest that there is no robust difference in gut microbiome between individuals with or without TPOAb in terms of alpha and beta-diversity. Nonetheless, several taxa were identified with nominal significance related to TPOAb presence. Further research is required to determine whether these changes indeed imply a higher risk of overt HT.},
}
@article {pmid38010886,
year = {2023},
author = {Garrett, S and Asada, MC and Sun, J},
title = {Axin1's mystique in manipulating microbiome amidst colitis.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2286674},
doi = {10.1080/19490976.2023.2286674},
pmid = {38010886},
issn = {1949-0984},
abstract = {Classically, Axin1 is considered a regulator of Wnt/β-catenin signaling. However, Axin1's roles in host-microbial interactions have been unknown. Our recent study has demonstrated that deletion of intestinal epithelial Axin1 in epithelial cells and Paneth cells protects the host against colitis by enhancing Akkermansia muciniphila. Loss of intestinal epithelial or Paneth cell Axin1 results in increased Wnt/β-catenin signaling, proliferation, and cell migration. This is associated with morphologically altered goblet and Paneth cells, including increased Muc2 and decreased lysozyme. Axin1 deletion specifically enriched Akkermansia muciniphila. Akkermansia muciniphila in Axin1 knockout mice is the driver of protection against DSS-induced inflammation. Here, we feature several significant conceptual changes, such as differences between Axin1 and Axin2, Axin1 in innate immunity and microbial homeostasis, and Axin1 reduction of Akkermansia muciniphila. We discuss an important trend in the field related to Paneth cells and tissue-specific Axin1 manipulation of microbiome in health and inflammation.},
}
@article {pmid38010871,
year = {2023},
author = {Jinato, T and Sikaroodi, M and Fagan, A and Sterling, RK and Lee, H and Puri, P and Davis, BC and Fuchs, M and Gavis, E and Gillevet, PM and Bajaj, JS},
title = {Alterations in gut virome are associated with cognitive function and minimal hepatic encephalopathy cross-sectionally and longitudinally in cirrhosis.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2288168},
doi = {10.1080/19490976.2023.2288168},
pmid = {38010871},
issn = {1949-0984},
abstract = {Cognitive dysfunction due to minimal hepatic encephalopathy (MHE) adversely impacts patients with cirrhosis and more precise therapies are needed. Gut-brain axis changes are therapeutic targets, but prior studies have largely focused on bacterial changes. Our aim was to determine linkages between individual cognitive testing results and bacteria with the virome using a cross-sectional and longitudinal approach. We included cross-sectional (n = 138) and longitudinal analyses (n = 36) of patients with cirrhosis tested using three cognitive modalities, which were psychometric hepatic encephalopathy score (PHES), inhibitory control test (ICT), Stroop, and all three. Stool metagenomics with virome and bacteriome were analyzed studied cross-sectionally and in a subset followed for development/reversal of MHE repeated at 6 months (longitudinally only using PHES). Cross-sectional: We found no significant changes in α/β diversity in viruses or bacteria regardless of cognitive testing. Cognitively impaired patients were more likely to have higher relative abundance of bacteriophages linked with Streptococcus, Faecalibacterium, and Lactobacillus, which were distinct based on modality. These were also linked with cognition on correlation networks. Longitudinally, 27 patients remained stable while 9 changed their MHE status. Similar changes in phages that are linked with Streptococcus, Faecalibacterium, and Lactobacillus were seen. These phages can influence ammonia, lactate, and short-chain fatty acid generation, which are neuro-active. In conclusion, we found linkages between bacteriophages and cognitive function likely due to impact on bacteria that produce neuroactive metabolites cross-sectionally and longitudinally. These findings could help explore bacteriophages as options to influence treatment for MHE in cirrhosis.},
}
@article {pmid38010793,
year = {2023},
author = {Li, H and Liu, C and Huang, S and Wang, X and Cao, M and Gu, T and Ou, X and Pan, S and Lin, Z and Wang, X and Zhu, Y and Jing, J},
title = {Multi-omics analyses demonstrate the modulating role of gut microbiota on the associations of unbalanced dietary intake with gastrointestinal symptoms in children with autism spectrum disorder.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2281350},
doi = {10.1080/19490976.2023.2281350},
pmid = {38010793},
issn = {1949-0984},
abstract = {Our previous work revealed that unbalanced dietary intake was an important independent factor associated with constipation and gastrointestinal (GI) symptoms in children with autism spectrum disorder (ASD). Growing evidence has shown the alterations in the gut microbiota and gut microbiota-derived metabolites in ASD. However, how the altered microbiota might affect the associations between unbalanced diets and GI symptoms in ASD remains unknown. We analyzed microbiome and metabolomics data in 90 ASD and 90 typically developing (TD) children based on 16S rRNA and untargeted metabolomics, together with dietary intake and GI symptoms assessment. We found that there existed 11 altered gut microbiota (FDR-corrected P-value <0.05) and 397 altered metabolites (P-value <0.05) in children with ASD compared with TD children. Among the 11 altered microbiota, the Turicibacter, Coprococcus 1, and Lachnospiraceae FCS020 group were positively correlated with constipation (FDR-corrected P-value <0.25). The Eggerthellaceae was positively correlated with total GI symptoms (FDR-corrected P-value <0.25). More importantly, three increased microbiota including Turicibacter, Coprococcus 1, and Eggerthellaceae positively modulated the associations of unbalanced dietary intake with constipation and total GI symptoms, and the decreased Clostridium sp. BR31 negatively modulated their associations in ASD children (P-value <0.05). Together, the altered microbiota strengthens the relationship between unbalanced dietary intake and GI symptoms. Among the altered metabolites, ten metabolites derived from microbiota (Turicibacter, Coprococcus 1, Eggerthellaceae, and Clostridium sp. BR31) were screened out, enriched in eight metabolic pathways, and were identified to correlate with constipation and total GI symptoms in ASD children (FDR-corrected P-value <0.25). These metabolomics findings further support the modulating role of gut microbiota on the associations of unbalanced dietary intake with GI symptoms. Collectively, our research provides insights into the relationship between diet, the gut microbiota, and GI symptoms in children with ASD.},
}
@article {pmid38010636,
year = {2023},
author = {Gladyshev, NS and Baram, DV and Gorbunova, AV and Krivolapov, YA},
title = {[Transcriptome analysis of tissue microbiota diversity in tumor and non-tumor lymph nodes].},
journal = {Arkhiv patologii},
volume = {85},
number = {6},
pages = {26-30},
doi = {10.17116/patol20238506126},
pmid = {38010636},
issn = {0004-1955},
abstract = {BACKGROUND: Metagenomic studies in recent years have demonstrated that all tissues of the human body studied by genomic and transcriptomic sequencing methods, both in pathological processes and in normality, contain fragments of DNA and RNA from a variety of microorganisms. The composition of tissue microbiota and its relationship with development of pathological changes are still poorly understood, despite increasing number of studies in this area every year. In this study, gene expression of the lymph node microbiome in reactive follicular hyperplasia and follicular lymphoma was investigated.<br><br>OBJECTIVE: To study expression of lymph node microbiome genes in reactive follicular hyperplasia and follicular lymphoma.<br><br>MATERIAL AND METHODS: The work included 38 biopsy samples of lymph nodes with follicular lymphoma of different cytological subtypes and 10 biopsy samples of lymph nodes with reactive follicular hyperplasia. Verification of diagnosis was carried out using standard histological, histochemical and immunohistochemical methods. Using sequencing method, the transcriptome was examined. Statistical analysis and data visualization were performed using the R programming language (version 4.2.1).<br><br>RESULTS: Tumor lymph nodes are characterized by large Simpson and Shannon alpha diversity values (p-value = 0.026465 and p-value = 0.007122, respectively). Two clusters were discovered, characterized by different levels of relative abundance of microorganisms.<br><br>CONCLUSION: It has been proven that diversity of microorganisms present in tumor tissue and their number are statistically significantly higher than corresponding indicators in the lymph nodes with follicular hyperplasia.},
}
@article {pmid38010368,
year = {2023},
author = {Yeo, XY and Chae, WR and Lee, HU and Bae, HG and Pettersson, S and Grandjean, J and Han, W and Jung, S},
title = {Nuanced contribution of gut microbiome in the early brain development of mice.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2283911},
doi = {10.1080/19490976.2023.2283911},
pmid = {38010368},
issn = {1949-0984},
abstract = {The complex symbiotic relationship between the mammalian body and gut microbiome plays a critical role in the health outcomes of offspring later in life. The gut microbiome modulates virtually all physiological functions through direct or indirect interactions to maintain physiological homeostasis. Previous studies indicate a link between maternal/early-life gut microbiome, brain development, and behavioral outcomes relating to social cognition. Here we present direct evidence of the role of the gut microbiome in brain development. Through magnetic resonance imaging (MRI), we investigated the impact of the gut microbiome on brain organization and structure using germ-free (GF) mice and conventionalized mice, with the gut microbiome reintroduced after weaning. We found broad changes in brain volume in GF mice that persist despite the reintroduction of gut microbes at weaning. These data suggest a direct link between the maternal gut or early-postnatal microbe and their impact on brain developmental programming.},
}
@article {pmid38010361,
year = {2023},
author = {Nori, SRC and McGuire, TK and Lawton, EM and McAuliffe, FM and Sinderen, DV and Walsh, CJ and Cotter, PD and Feehily, C},
title = {Profiling of vaginal Lactobacillus jensenii isolated from preterm and full-term pregnancies reveals strain-specific factors relating to host interaction.},
journal = {Microbial genomics},
volume = {9},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001137},
pmid = {38010361},
issn = {2057-5858},
abstract = {Each year, 15 million infants are born preterm (<37 weeks gestation), representing the leading cause of mortality for children under the age of five. Whilst there is no single cause, factors such as maternal genetics, environmental interactions, and the vaginal microbiome have been associated with an increased risk of preterm birth. Previous studies show that a vaginal microbiota dominated by Lactobacillus is, in contrast to communities containing a mixture of genera, associated with full-term birth. However, this binary principle does not fully consider more nuanced interactions between bacterial strains and the host. Here, through a combination of analyses involving genome-sequenced isolates and strain-resolved metagenomics, we identify that L. jensenii strains from preterm pregnancies are phylogenetically distinct from strains from full-term pregnancies. Detailed analysis reveals several genetic signatures that distinguish preterm birth strains, including genes predicted to be involved in cell wall synthesis, and lactate and acetate metabolism. Notably, we identify a distinct gene cluster involved in cell surface protein synthesis in our preterm strains, and profiling the prevalence of this gene cluster in publicly available genomes revealed it to be predominantly present in the preterm-associated clade. This study contributes to the ongoing search for molecular biomarkers linked to preterm birth and opens up new avenues for exploring strain-level variations and mechanisms that may contribute to preterm birth.},
}
@article {pmid38010168,
year = {2023},
author = {Ye, H and Ghosh, TS and Hueston, CM and Vlckova, K and Golubeva, AV and Hyland, NP and O'Toole, PW},
title = {Engraftment of aging-related human gut microbiota and the effect of a seven-species consortium in a pre-clinical model.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2282796},
doi = {10.1080/19490976.2023.2282796},
pmid = {38010168},
issn = {1949-0984},
abstract = {Human aging is characterized by gut microbiome alteration and differential loss of gut commensal species associated with the onset of frailty. The administration of cultured commensal strains to replenish lost taxa could potentially promote healthy aging. To investigate the interaction of whole microbiomes and administered strains, we transplanted gut microbiota from a frail or healthy elderly subject into germ-free mice. We supplemented the frail-donor recipient group with a defined consortium of taxa (the "S7") that we identified by analyzing healthy aging subjects in our previous studies and whose abundance correlated with health-promoting dietary intervention. Inoculation with a frail or a healthy donor microbiome resulted in differential microbiota compositions in murine recipients 5 weeks post-transplantation. Fecal acetate levels were significantly higher in healthy donor recipient mice than in frail donor recipient mice after 4 weeks. However, the frailty-related phenotype was not replicated in recipient mice with single-dose microbiota transplantation from a healthy and a frail donor. Five S7 species colonized successfully in germ-free mice, with a relatively high abundance of Barnesiella intestinihominis and Eubacterium rectale. The engraftment of five S7 species in germ-free mice increased fecal acetate levels and reduced colon permeability and plasma TNF-ɑ concentration. Supplementation with the S7 in frail-microbiota recipient mice did not increase alpha-diversity but significantly increased the abundance of Barnesiella intestinihominis. S7 supplementation showed the potential for improving spatial reference memory in frail-microbiota recipient mice. Collectively, these data highlight the challenge of elderly microbiota engraftment in the germ-free mouse model but show promise for modulating the gut microbiome of frail elderly subjects by administering an artificial gut microbe consortium associated with healthy aging.},
}
@article {pmid38010080,
year = {2023},
author = {Luoto, R and Pärtty, A and Vogt, JK and Rautava, S and Isolauri, E},
title = {Reversible aberrancies in gut microbiome of moderate and late preterm infants: results from a randomized, controlled trial.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2283913},
doi = {10.1080/19490976.2023.2283913},
pmid = {38010080},
issn = {1949-0984},
abstract = {The aim of this study was to obtain insight into the composition and function of the deviant gut microbiome throughout infancy in children born moderately and late preterm and their response to microbiome modulation. We characterized the longitudinal development of the gut microbiome from birth to the age of 12 months by metagenomic sequencing in 43 moderate and late preterm children participating in a randomized, controlled trial (ClinicalTrials.gov/no.NCT00167700) assessing the impact of a probiotic (Lactobacillus rhamnosus GG, ATCC 53,103, currently Lacticaseibacillus rhamnosus GG) and a prebiotic (galacto-oligosaccharide and polydextrose mixture, 1:1) intervention as compared to a placebo administered from 3 to 60 days of life. In addition, 9 full-term, vaginally delivered, breast-fed infants, who remained healthy long-term were included as references. Significant differences in taxonomy, but not in functional potential, were found when comparing the gut microbiome composition of preterm and full-term infants during the first month of life. However, the gut microbiome of preterm infants resembled that of full-term infants by 6 months age. Probiotic and prebiotic treatments were found to mitigate the shift in the microbiome of preterm infants by accelerating Bifidobacteria-dominated gut microbiome in beta diversity analysis. This study provides intriguing information regarding the establishment of the gut microbiome in children born moderately and late preterm, representing the majority of children born preterm. Specific pro- and prebiotics may reverse the proinflammatory gut microbiome composition during the vulnerable period, when the microbiome is low in resilience and susceptible to environmental exposure and simultaneously promotes immunological and metabolic maturation.},
}
@article {pmid38010059,
year = {2023},
author = {Zhong, J and Xiong, D and Liu, Y and Yuan, S},
title = {Association of antibiotic exposure with survival in patients with extensive-stage small cell lung cancer receiving immune checkpoint inhibitor therapy.},
journal = {Thoracic cancer},
volume = {},
number = {},
pages = {},
doi = {10.1111/1759-7714.15172},
pmid = {38010059},
issn = {1759-7714},
support = {NSFC82073345//National Natural Science Foundation of China/ ; //Taishan Scholars Program to Shuanghu Yuan/ ; 202019060//Jinan Clinical Medicine Science and Technology Innovation Plan/ ; ZR202209010002//Natural Science Innovation and Development Joint Foundation of Shandong Province/ ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have dramatically shifted the therapeutic paradigm of extensive-stage small cell lung cancer (ES-SCLC). Antibiotic (ATB) exposure before or during ICI therapy can harm the integrity of the gut microbiome and lead to intestinal dysbiosis, which has a profoundly negative impact on the treatment response for various malignancies. Whether this is applicable to ES-SCLC remains unclear.<br><br>METHODS: We retrospectively reviewed the electronic medical records of all patients diagnosed with ES-SCLC who were treated with ICI-based immunotherapies from July 2019 to December 2020 at Shandong Cancer Hospital and Institute, China. Outcomes with the use of ATBs before or after the first infusion of ICI, including progression-free survival (PFS) and overall survival (OS), were investigated using the Kaplan-Meier method. Multivariate analyses were also conducted using a Cox proportional hazards model.<br><br>RESULTS: A total of 214 patients were included, among whom 41 (19.2%) received ATBs within 2&#x2009;months before or after the first initiation of ICI therapy and were assigned to the ATB group. The ATB group showed a shorter median PFS (4.3 vs. 6.3&#x2009;months; HR&#x2009;=&#x2009;1.43, 95% CI: 0.97-2.11; p&#x2009;=&#x2009;0.043) and a significantly shorter median OS (6.9 vs. 13&#x2009;months; HR&#x2009;=&#x2009;1.47, 95% CI: 0.98-2.20; p&#x2009;=&#x2009;0.033) than the non-ATB group. In the multivariate analysis, ATB exposure was markedly associated with worse PFS (HR&#x2009;=&#x2009;1.47, 95% CI: 1.03-2.09, p&#x2009;=&#x2009;0.035) and OS (HR&#x2009;=&#x2009;1.46, 95% CI: 1.01-2.11, p&#x2009;=&#x2009;0.043).<br><br>CONCLUSIONS: Our results demonstrate that ATB exposure was significantly associated with worse survival in ES-SCLC patients who received ICI therapy.},
}
@article {pmid38009922,
year = {2023},
author = {Tsitouras, A and Al-Ghussain, N and Butcher, J and Stintzi, A and Delatolla, R},
title = {The microbiome of two strategies for ammonia removal with the sequencing batch moving bed biofilm reactor treating cheese production wastewater.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0150723},
doi = {10.1128/aem.01507-23},
pmid = {38009922},
issn = {1098-5336},
abstract = {Cheese production facilities must abide by sewage discharge bylaws that prevent overloading municipal water resource recovery facilities, eutrophication, and toxicity to aquatic life. Compact treatment systems can permit on-site treatment of cheese production wastewater; however, competition between heterotrophs and nitrifiers impedes the implementation of the sequencing batch moving bed biofilm reactor (SB-MBBR) for nitrification from high-carbon wastewaters. This study demonstrates that a single SB-MBBR is not feasible for nitrification when operated with anerobic and aerobic cycling for carbon and phosphorous removal from cheese production wastewater, as nitrification does not occur in a single reactor. Thus, two reactors in series are recommended to achieve nitrification from cheese production wastewater in SB-MBBRs. These findings can be applied to pilot and full-scale SB-MBBR operations. By demonstrating the potential to implement partial nitrification in the SB-MBBR system, this study presents the possibility of implementing partial nitrification in the SB-MBBR, resulting in the potential for more sustainable treatment of nitrogen from cheese production wastewater.},
}
@article {pmid38009901,
year = {2023},
author = {Szaleniec, J and Bezshapkin, V and Krawczyk, A and Kopera, K and Zapała, B and Gosiewski, T and Kosciolek, T},
title = {Determinants of the microbiome spatial variability in chronic rhinosinusitis.},
journal = {Rhinology},
volume = {},
number = {},
pages = {},
doi = {10.4193/Rhin22.423},
pmid = {38009901},
issn = {0300-0729},
abstract = {BACKGROUND: The sinus microbiome in patients with chronic rhinosinusitis (CRS) is considered homogenous across the sinonasal cavity. The middle nasal meatus is the recommended sampling site for 16S rRNA sequencing. However, individuals with unusually high between-site variability between the middle meatus and the sinuses were identified in previous studies. This study aimed to identify which factors determine increased microbial heterogeneity between sampling sites in the sinuses.<br><br>METHODOLOGY: In this cross-sectional study samples for 16S rRNA sequencing were obtained from the middle meatus, the maxillary and the frontal sinus in 50 patients with CRS. The microbiome diversity between sampling sites was analysed in relation to the size of the sinus ostia and clinical metadata.<br><br>RESULTS: In approximately 15% of study participants, the differences between sampling sites within one patient were greater than between the patient and other individuals. Contrary to a popular hypothesis, obstruction of the sinus ostium resulted in decreased dissimilarity between the sinus and the middle meatus. The dissimilarity between the sampling sites was patient-specific: greater between-sinus differences were associated with greater meatus-sinus differences, regardless of the drainage pathway patency. Decreased spatial variability was observed in patients with nasal polyps and extensive mucosal changes in the sinuses.<br><br>CONCLUSIONS: Sampling from the middle meatus is not universally representative of the sinus microbiome. The differences between sites cannot be predicted from the patency of communication pathways between them.},
}
@article {pmid38009763,
year = {2023},
author = {Szymanski, EA and Turner, M},
title = {Metaphors as design tools for microbial consortia: An analysis of recent peer-reviewed literature.},
journal = {Microbial biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-7915.14366},
pmid = {38009763},
issn = {1751-7915},
support = {2042475//Division of Social and Economic Sciences/ ; },
abstract = {Single engineered microbial species cannot always conduct complex transformations, while complex, incompletely defined microbial consortia have heretofore been suited to a limited range of tasks. As biodesigners bridge this gap with intentionally designed microbial communities, they will, intentionally or otherwise, build communities that embody particular ideas about what microbial communities can and should be. Here, we suggest that metaphors-ideas about what microbial communities are like-are therefore important tools for designing synthetic consortia-based bioreactors. We identify a range of metaphors currently employed in peer-reviewed microbiome research articles, characterizing each through its potential structural implications and distinctive imagery. We present this metaphor catalogue in the interest of, first, making metaphors visible as design choices, second, enabling deliberate experimentation with them towards expanding the potential design space of the field, and third, encouraging reflection on the goals and values they embed.},
}
@article {pmid38009697,
year = {2023},
author = {Molina, MA and Melchers, WJG},
title = {Methodological and analytical challenges in microbiome-HPV association studies.},
journal = {Journal of medical virology},
volume = {95},
number = {11},
pages = {e29260},
doi = {10.1002/jmv.29260},
pmid = {38009697},
issn = {1096-9071},
}
@article {pmid38009508,
year = {2023},
author = {Cameron, O and Neves, JF and Gentleman, E},
title = {Listen to Your Gut: Key Concepts for Bioengineering Advanced Models of the Intestine.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2302165},
doi = {10.1002/advs.202302165},
pmid = {38009508},
issn = {2198-3844},
support = {MR/X008789/1/MRC_/Medical Research Council/United Kingdom ; NC/X002497/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NC/X002497/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; },
abstract = {The intestine performs functions central to human health by breaking down food and absorbing nutrients while maintaining a selective barrier against the intestinal microbiome. Key to this barrier function are the combined efforts of lumen-lining specialized intestinal epithelial cells, and the supportive underlying immune cell-rich stromal tissue. The discovery that the intestinal epithelium can be reproduced in vitro as intestinal organoids introduced a new way to understand intestinal development, homeostasis, and disease. However, organoids reflect the intestinal epithelium in isolation whereas the underlying tissue also contains myriad cell types and impressive chemical and structural complexity. This review dissects the cellular and matrix components of the intestine and discusses strategies to replicate them in vitro using principles drawing from bottom-up biological self-organization and top-down bioengineering. It also covers the cellular, biochemical and biophysical features of the intestinal microenvironment and how these can be replicated in vitro by combining strategies from organoid biology with materials science. Particularly accessible chemistries that mimic the native extracellular matrix are discussed, and bioengineering approaches that aim to overcome limitations in modelling the intestine are critically evaluated. Finally, the review considers how further advances may extend the applications of intestinal models and their suitability for clinical therapies.},
}
@article {pmid38009223,
year = {2023},
author = {Yu, J and Youngson, NA and Laybutt, DR and Morris, MJ and Leigh, SJ},
title = {Complementary yet divergent effects of exercise and an exercise mimetic on microbiome in high-fat diet-induced obesity.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00066.2023},
pmid = {38009223},
issn = {1531-2267},
support = {//Rebecca Cooper Foundation Grant/ ; //DHAC | National Health and Medical Research Council (NHMRC)/ ; //Department of Education and Training | Australian Research Council (ARC)/ ; //Australian Government Research Training Program/ ; //Australian Government Research Training Program/ ; },
abstract = {Exercise is beneficial for obesity, partially through increased mitochondrial activity and raised nicotinamide adenine dinucleotide, a coenzyme critical for mitochondrial function and metabolism. Recent work has shown that increasing the availability of nicotinamide adenine dinucleotide through pharmacological means improves metabolic health in rodent models of diet induced obesity, and that the effect of these supplements when administered orally may be modulated by the gut microbiome. The gut microbiome is altered by both diet and exercise, and is thought to contribute to some aspects of high-fat diet-induced metabolic dysfunction. We examined the independent and combined effects of treadmill exercise and nicotinamide mononucleotide (NMN) supplementation on the gut microbiome of female C57Bl6/J mice chronically fed a high-fat diet. We showed that 8 weeks of treadmill exercise, oral-administered NMN or combined therapy exert unique effects on gut microbiome composition without changing bacterial species richness. Exercise and NMN exerted additive effects on microbiota composition, and NMN partially or fully restored predicted microbial functions, specifically carbohydrate and lipid metabolism, to control levels. Further research is warranted to better understand the mechanisms underpinning the interactions between exercise and oral NAD[+] precursor supplementation on gut microbiome.},
}
@article {pmid38009162,
year = {2023},
author = {Farooqi, MS and Podury, S and Crowley, G and Javed, U and Li, Y and Liu, M and Kwon, S and Grunig, G and Khan, AR and Francois, F and Nolan, A},
title = {Noninvasive, MultiOmic, and Multicompartmental Biomarkers of Reflux Disease: A Systematic Review.},
journal = {Gastro hep advances},
volume = {2},
number = {4},
pages = {608-620},
pmid = {38009162},
issn = {2772-5723},
support = {R01 HL119326/HL/NHLBI NIH HHS/United States ; U01 OH011300/OH/NIOSH CDC HHS/United States ; U01 OH011855/OH/NIOSH CDC HHS/United States ; U01 OH012069/OH/NIOSH CDC HHS/United States ; },
abstract = {BACKGROUND AND AIMS: Gastroesophageal reflux disease (GERD) is a prevalent gastrointestinal disorder that may complicate conditions such as obstructive airway disease. Our group has identified predictive biomarkers of GERD in particulate exposed first responders with obstructive airway disease. In addition, GERD diagnosis and treatment is costly and invasive. In light of these clinical concerns, we aimed to systematically review studies identifying noninvasive, multiOmic, and multicompartmental biomarkers of GERD.<br><br>METHODS: A systematic review of PubMed and Embase was performed using keywords focusing on reflux disease and biomarkers and registered with PROSPERO. We included original human studies in English, articles focusing on noninvasive biomarkers of GERD published after December 31, 2009. GERD subtypes (non-erosive reflux disease and erosive esophagitis) and related conditions (Barrett's Esophagus [BE] and Esophageal Adenocarcinoma). Predictive measures were synthesized and risk of bias assessed (Newcastle-Ottawa Scale).<br><br>RESULTS: Initial search identified n = 238 studies andn 13 articles remained after applying inclusion/exclusion criteria. Salivary pepsin was the most studied biomarker with significant sensitivity and specificity for GERD. Serum assessment showed elevated levels of Tumor Necrosis Factor-alpha in both GERD and Barrett's. Exhaled breath volatile sulfur compounds and acetic acid were associated with GERD. Oral Microbiome: Models with Lautropia, Streptococcus, and Bacteroidetes showed the greatest discrimination between BE and controls vs Lautropia; ROCAUC 0.94 (95% confidence interval; 0.85-1.00).<br><br>CONCLUSION: Prior studies identified significant multiOmic, multicompartmental noninvasive biomarker risks for GERD and BE. However, studies have a high risk of bias and the reliability and accuracy of the biomarkers identified are greatly limited, which further highlights the need to discover and validate clinically relevant noninvasive biomarkers of GERD.},
}
@article {pmid38009054,
year = {2023},
author = {Zahra, A and Menon, R and Bento, GFC and Selim, J and Taylor, BD and Vincent, KL and Pyles, RB and Richardson, LS},
title = {Validation of vaginal microbiome proxies for in vitro experiments that biomimic Lactobacillus-dominant vaginal cultures.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {90},
number = {6},
pages = {e13797},
doi = {10.1111/aji.13797},
pmid = {38009054},
issn = {1600-0897},
support = {K12HD052023//NIH/NICHD/ ; //Building Interdisciplinary Research Careers in Women's Health Program-BIRCWH; Berenson, PI/ ; //National Institutes of Health/Office of the Director (OD)/National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01HD100729-01S1//Eunice Kennedy Shriver National Institute of Child Health &amp; Human Development (NICHD)/ ; //Institute for Translational Sciences/ ; UL1&#xa0;TR001439//Clinical and Translational Science/ ; //National Center for Advancing Translational Sciences at the National Institutes of Health (NIH)/ ; },
mesh = {Female ; Humans ; Lactobacillus/physiology ; Tumor Necrosis Factor-alpha/metabolism ; Interleukin-6/metabolism ; Interleukin-8/metabolism ; Vagina/microbiology ; *Vaginosis, Bacterial/microbiology ; Bacteria ; Anti-Inflammatory Agents ; *Microbiota ; },
abstract = {The vaginal microbiome includes diverse microbiota dominated by Lactobacillus [L.] spp. that protect against infections, modulate inflammation, and regulate vaginal homeostasis. Because it is challenging to incorporate vaginal microbiota into in vitro models, including organ-on-a-chip systems, we assessed microbial metabolites as reliable proxies in addition to traditional vaginal epithelial cultures (VECs). Human immortalized VECs cultured on transwells with an air-liquid interface generated stratified cell layers colonized by transplanted healthy microbiomes (L. jensenii- or L. crispatus-dominant) or a community representing bacterial vaginosis (BV). After 48-h, a qPCR array confirmed the expected donor community profiles. Pooled apical and basal supernatants were subjected to metabolomic analysis (untargeted mass spectrometry) followed by ingenuity pathways analysis (IPA). To determine the bacterial metabolites' ability to recreate the vaginal microenvironment in vitro, pooled bacteria-free metabolites were added to traditional VEC cultures. Cell morphology, viability, and cytokine production were assessed. IPA analysis of metabolites from colonized samples contained fatty acids, nucleic acids, and sugar acids that were associated with signaling networks that contribute to secondary metabolism, anti-fungal, and anti-inflammatory functions indicative of a healthy vaginal microbiome compared to sterile VEC transwell metabolites. Pooled metabolites did not affect cell morphology or induce cell death (∼5.5%) of VEC cultures (n = 3) after 72-h. However, metabolites created an anti-inflammatory milieu by increasing IL-10 production (p = .06, T-test) and significantly suppressing pro-inflammatory IL-6 (p = .0001), IL-8 (p = .009), and TNFα (p = .0007) compared to naïve VEC cultures. BV VEC conditioned-medium did not affect cell morphology nor viability; however, it induced a pro-inflammatory environment by elevating levels of IL-6 (p = .023), IL-8 (p = .031), and TNFα (p = .021) when compared to L.-dominate microbiome-conditioned medium. VEC transwells provide a suitable ex vivo system to support the production of bacterial metabolites consistent with the vaginal milieu allowing subsequent in vitro studies with enhanced accuracy and utility.},
}
@article {pmid38008735,
year = {2023},
author = {Xiao, X and Cui, Y and Lu, H and Wang, J and Yang, J and Liu, L and Liu, Z and Peng, X and Cao, H and Liu, X and Wei, X},
title = {Strontium ranelate enriched Ruminococcus albus in the gut microbiome of Sprague-Dawley rats with postmenopausal osteoporosis.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {365},
pmid = {38008735},
issn = {1471-2180},
support = {2018QDJZR12//Cultivating Project for Young Scholar at Hubei University of Medicine/ ; 2015QDJZR06//Cultivating Project for Young Scholar at Hubei University of Medicine/ ; JC2022002//Innovation Research Program for Graduates of Basic Medical College, Hubei University of Medicine/ ; AD18281029//Guangxi Natural Science Foundation/ ; WJ2021M052//Hubei Provincial Health and Health Commission Funded Projects/ ; WJ2019Q025//Hubei Provincial Health and Health Commission Funded Projects/ ; },
mesh = {Humans ; Female ; Rats ; Animals ; Rats, Sprague-Dawley ; *Osteoporosis, Postmenopausal/drug therapy/metabolism ; *Gastrointestinal Microbiome ; Ruminococcus ; Lycopene/therapeutic use ; RNA, Ribosomal, 16S/genetics ; *Osteoporosis/drug therapy/metabolism ; },
abstract = {BACKGROUND: Gut microbiome is critical to our human health and is related to postmenopausal osteoporosis (PMO). Strontium ranelate (SrR) is an anti-osteoporosis oral drug that can promote osteoblast formation and inhibit osteoclast formation. However, the effect of SrR on gut microbiome has been rarely studied. Therefore, we investigated the effect of oral SrR on gut microbiome and metabolic profiles.<br><br>RESULTS: In this study, we used ovariectomized (OVX) Sprague-Dawley rats to construct a PMO model and applied oral SrR for 6 weeks. The relative abundance of intestinal microbiome was investigated by 16S rRNA metagenomic sequencing. Ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) was used to analyze changes in metabolites of intestinal contents. Results demonstrated that 6-week oral SrR alleviated osteoporosis and significantly changed the composition of the gut microbiome and metabolic profiles of OVX rats. Ruminococcus, Akkermansia and Oscillospira were significantly enriched in the gut of OVX rats after 6-week oral SrR. Especially, the species R. albus showed the greatest importance by a random forest classifier between OVX and OVX_Sr group. The enrichment of R. albus in the gut was positively correlated with bone mineral density and the accumulation of lycopene and glutaric acid, which also significantly elevated after oral SrR.<br><br>CONCLUSIONS: We discovered that oral SrR can improve bone health while stimulate the accumulation of gut microbe R. albus and metabolites (lycopene and glutaric acid). The results suggested possible connections between oral SrR and the gut-bone axis, which may provide new insight into the treatment/prevention of osteoporosis.},
}
@article {pmid38008696,
year = {2023},
author = {Foppa, C and Rizkala, T and Repici, A and Hassan, C and Spinelli, A},
title = {Microbiota and IBD: Current knowledge and future perspectives.},
journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.dld.2023.11.015},
pmid = {38008696},
issn = {1878-3562},
abstract = {Inflammatory Bowel Disease (IBD) is a chronic relapsing-remitting disease with a remarkable increase in incidence worldwide and a substantial disease burden. Although the pathophysiology is not fully elucidated yet an aberrant immune reaction against the intestinal microbiota and the gut microbial dysbiosis have been identified to play a major role. The composition of gut microbiota in IBD patients is distinct from that of healthy individuals, with certain organisms predominating over others. Differences in the microbial dysbiosis have been also observed between Crohn Disease (CD) and Ulcerative Colitis (UC). A disruption of the microbiota's balance can lead to inflammation and intestinal damage. Microbiota composition in IBD can be affected both by endogenous (i.e., interaction with the immune system and intestinal epithelial cells) and exogenous (i.e., medications, surgery, diet) factors. The complex interplay between the gut microbiota and IBD is an area of great interest for understanding disease pathogenesis and developing new treatments. The purpose of this review is to summarize the latest evidence on the role of microbiota in IBD pathogenesis and to explore possible future areas of research.},
}
@article {pmid38008300,
year = {2023},
author = {Gakis, G and Angelopoulos, I and Panagoulias, I and Mouzaki, A},
title = {Current knowledge on multiple sclerosis pathophysiology, disability progression assessment and treatment options, and the role of autologous hematopoietic stem cell transplantation.},
journal = {Autoimmunity reviews},
volume = {},
number = {},
pages = {103480},
doi = {10.1016/j.autrev.2023.103480},
pmid = {38008300},
issn = {1873-0183},
abstract = {Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS) that affects nearly 2.8 million people each year. MS distinguishes three main types: relapsing-remitting MS (RRMS), secondary progressive MS (SPMS) and primary progressive MS (PPMS). RRMS is the most common type, with the majority of patients eventually progressing to SPMS, in which neurological development is constant, whereas PPMS is characterized by a progressive course from disease onset. New or additional insights into the role of effector and regulatory cells of the immune and CNS systems, Epstein-Barr virus (EBV) infection, and the microbiome in the pathophysiology of MS have emerged, which may lead to the development of more targeted therapies that can halt or reverse neurodegeneration. Depending on the type and severity of the disease, various disease-modifying therapies (DMTs) are currently used for RRMS/SPMS and PPMS. As a last resort, and especially in highly active RRMS that does not respond to DMTs, autologous hematopoietic stem cell transplantation (AHSCT) is performed and has shown good results in reducing neuroinflammation. Nevertheless, the question of its potential role in preventing disability progression remains open. The aim of this review is to provide a comprehensive update on MS pathophysiology, assessment of MS disability progression and current treatments, and to examine the potential role of AHSCT in preventing disability progression.},
}
@article {pmid38007891,
year = {2023},
author = {Solanki, MK and Joshi, NC and Singh, PK and Singh, SK and Santoyo, G and Basilio de Azevedo, LC and Kumar, A},
title = {From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity.},
journal = {Microbiological research},
volume = {279},
number = {},
pages = {127553},
doi = {10.1016/j.micres.2023.127553},
pmid = {38007891},
issn = {1618-0623},
abstract = {The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.},
}
@article {pmid38007617,
year = {2023},
author = {Umarje, SC and Banerjee, SK},
title = {Non-traditional approaches for control of antibiotic resistance.},
journal = {Expert opinion on biological therapy},
volume = {},
number = {},
pages = {1-23},
doi = {10.1080/14712598.2023.2279644},
pmid = {38007617},
issn = {1744-7682},
abstract = {INTRODUCTION: The drying up of antibiotic pipeline has necessitated the development of alternative therapeutic strategies to control the problem of antimicrobial resistance (AMR) that is expected to kill 10-million people annually by 2050. Newer therapeutic approaches address the shortcomings of traditional small-molecule antibiotics - the lack of specificity, evolvability, and susceptibility to mutation-based resistance. These 'non-traditional' molecules are biologicals having a complex structure and mode(s) of action that makes them resilient to resistance.<br><br>AREAS COVERED: This review aims to provide information about the non-traditional drug development approaches to tackle the problem of antimicrobial resistance, from the pre-antibiotic era to the latest developments. We have covered the molecules under development in the clinic with literature sourced from reviewed scholarly articles, official company websites involved in innovation of concerned therapeutics, press releases from the regulatory bodies, and clinical trial databases.<br><br>EXPERT OPINION: Formal introduction of non-traditional therapies in general practice can be quick and feasible only if supported with companion diagnostics and used in conjunction with established therapies. Owing to relatively higher development costs, non-traditional therapeutics require more funding as well as well as clarity in regulatory and clinical path. We are hopeful these issues are adequately addressed before AMR develops into a pandemic.},
}
@article {pmid38007500,
year = {2023},
author = {Matthews, JL and Hoch, L and Raina, JB and Pablo, M and Hughes, DJ and Camp, EF and Seymour, JR and Ralph, PJ and Suggett, DJ and Herdean, A},
title = {Symbiodiniaceae photophysiology and stress resilience is enhanced by microbial associations.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20724},
pmid = {38007500},
issn = {2045-2322},
mesh = {Animals ; *Anthozoa/physiology ; Photosynthesis ; Temperature ; Bacteria ; Photosystem II Protein Complex ; *Dinoflagellida/physiology ; Symbiosis ; },
abstract = {Symbiodiniaceae form associations with extra- and intracellular bacterial symbionts, both in culture and in symbiosis with corals. Bacterial associates can regulate Symbiodiniaceae fitness in terms of growth, calcification and photophysiology. However, the influence of these bacteria on interactive stressors, such as temperature and light, which are known to influence Symbiodiniaceae physiology, remains unclear. Here, we examined the photophysiological response of two Symbiodiniaceae species (Symbiodinium microadriaticum and Breviolum minutum) cultured under acute temperature and light stress with specific bacterial partners from their microbiome (Labrenzia (Roseibium) alexandrii, Marinobacter adhaerens or Muricauda aquimarina). Overall, bacterial presence positively impacted Symbiodiniaceae core photosynthetic health (photosystem II [PSII] quantum yield) and photoprotective capacity (non-photochemical quenching; NPQ) compared to cultures with all extracellular bacteria removed, although specific benefits were variable across Symbiodiniaceae genera and growth phase. Symbiodiniaceae co-cultured with M. aquimarina displayed an inverse NPQ response under high temperatures and light, and those with L. alexandrii demonstrated a lowered threshold for induction of NPQ, potentially through the provision of antioxidant compounds such as zeaxanthin (produced by Muricauda spp.) and dimethylsulfoniopropionate (DMSP; produced by this strain of L. alexandrii). Our co-culture approach empirically demonstrates the benefits bacteria can deliver to Symbiodiniaceae photochemical performance, providing evidence that bacterial associates can play important functional roles for Symbiodiniaceae.},
}
@article {pmid38007124,
year = {2023},
author = {You, W and An, Q and Guo, D and Huang, Z and Guo, L and Chen, Z and Xu, H and Wang, G and Weng, Y and Ma, Z and Chen, X and Hong, F and Zhao, R},
title = {Exploration of risk analysis and elimination methods for a Cr(VI)-removal recombinant strain through a biosafety assessment in mice.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168743},
doi = {10.1016/j.scitotenv.2023.168743},
pmid = {38007124},
issn = {1879-1026},
abstract = {Though recombinant strains are increasingly recognized for their potential in heavy metal remediation, few studies have evaluated their safety. Moreover, biosafety assessments of fecal-oral pathway exposure at country as well as global level have seldom analyzed the health risks of exposure to microorganisms from a microscopic perspective. The present study aimed to predict the long-term toxic effects of recombinant strains by conducting a subacute toxicity test on the chromium-removal recombinant strain 3458 and analyzing the gut microbiome. The available disinfection methods were also evaluated. The results showed that strain 3458 induced liver damage and affected renal function and lipid metabolism at 1.0 × 10[11] CFU/mL, which may be induced by its carrier strain, pET-28a. Strain 3458 poses the risk of increasing the number of pathogenic bacteria under prolonged exposure. When 500 mg L[-1] chlorine-containing disinfectant or 250 mg L[-1] chlorine dioxide disinfectant was added for 30 min, the sterilization rate exceeded 99.9 %. These findings suggest that existing wastewater disinfection methods can effectively sterilize strain 3458, ensuring its application value. The present study can serve a reference for the biosafety evaluation of the recombinant strain through exposure to the digestive tract and its feasibility for application in environmental pollution remediation.},
}
@article {pmid38007081,
year = {2023},
author = {Tinkov, AA and Skalny, AV and Domingo, JL and Samarghandian, S and Kirichuk, AA and Aschner, M},
title = {A review of the epidemiological and laboratory evidence of the role of aluminum exposure in pathogenesis of cardiovascular diseases.},
journal = {Environmental research},
volume = {242},
number = {},
pages = {117740},
doi = {10.1016/j.envres.2023.117740},
pmid = {38007081},
issn = {1096-0953},
abstract = {The objective of the present study was to review the epidemiological and laboratory evidence on the role of aluminum (Al) exposure in the pathogenesis of cardiovascular diseases. Epidemiological data demonstrated an increased incidence of cardiovascular diseases (CVD), including hypertension and atherosclerosis in occupationally exposed subjects and hemodialysis patients. In addition, Al body burden was found to be elevated in patients with coronary heart disease, hypertension, and dyslipidemia. Laboratory studies demonstrated that Al exposure induced significant ultrastructural damage in the heart, resulting in electrocardiogram alterations in association with cardiomyocyte necrosis and apoptosis, inflammation, oxidative stress, inflammation, and mitochondrial dysfunction. In agreement with the epidemiological findings, laboratory data demonstrated dyslipidemia upon Al exposure, resulting from impaired hepatic lipid catabolism, as well as promotion of low-density lipoprotein oxidation. Al was also shown to inhibit paraoxonase 1 activity and to induce endothelial dysfunction and adhesion molecule expression, further promoting atherogenesis. The role of Al in hypertension was shown to be mediated by up-regulation of NADPH-oxidase, inhibition of nitric oxide bioavailability, and stimulation of renin-angiotensin-aldosterone system. It has been also demonstrated that Al exposure targets cerebral vasculature, which may be considered a link between Al exposure and cerebrovascular diseases. Findings from other tissues lend support that ferroptosis, pyroptosis, endoplasmic reticulum stress, and modulation of gut microbiome and metabolome are involved in the development of CVD upon Al exposure. A better understanding of the role of the cardiovascular system as a target for Al toxicity will be useful for risk assessment and the development of treatment and prevention strategies.},
}
@article {pmid38007045,
year = {2023},
author = {Lin, CS and Chen, TC and Verhoeff, MC and Lobbezoo, F and Trulsson, M and Fuh, JL},
title = {An Umbrella Review on the Association between Factors of Oral Health and Cognitive Dysfunction.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {102128},
doi = {10.1016/j.arr.2023.102128},
pmid = {38007045},
issn = {1872-9649},
abstract = {An increasing number of systematic reviews and meta-analyses have been published on the association between oral health and cognitive dysfunction, also known as oral-cognitive links. However, there is great diversity in the oral and cognitive factors included in these studies, with different opinions for clinical practice drawn from the evidence. To understand which oral and cognitive factors are involved in those associations, we conducted an umbrella review of 28 systematic reviews, including 12 meta-analyses, on oral-cognitive links. We found that (a) periodontal diseases, oral microbiome, and dementia were frequently studied, while other factors, such as mastication and mild cognitive impairment, were less commonly investigated, and (b) severe deterioration of oral health, such as severe periodontitis or extensive tooth loss, was strongly associated with cognitive dysfunction, rather than the presence of oral diseases alone. In conclusion, the diversity of oral and cognitive factors included in the review studies reflects the complexity of oral-cognitive links. Clarifying the factors helps to form evidence-based clinical advice for healthcare.},
}
@article {pmid38007009,
year = {2023},
author = {Ravindran, DR and Kannan, S and Marudhamuthu, M},
title = {Fabrication and characterisation of human gut microbiome derived exopolysaccharide mediated silver nanoparticles - An in-vitro and in-vivo approach of Bio-Pm-AgNPs targeting Vibrio cholerae.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {128406},
doi = {10.1016/j.ijbiomac.2023.128406},
pmid = {38007009},
issn = {1879-0003},
abstract = {Utilising bacteria to produce silver nanoparticles was highly favoured due to its ability to minimise costs and mitigate any potential negative environmental impact. Exopolysaccharides (EPS) extracted from the human gut microbe have demonstrated remarkable efficacy in combating various bacterial infections. Exopolysaccharide (EPS), a naturally occurring biomolecule found in the human gut isolate Proteus mirabilis DMTMMR-11, was characterised using analytical techniques such as Fourier transform infrared spectroscopy (FTIR), [1]H-nuclear magnetic resonance, [13]C-nuclear magnetic resonance (NMR), and chemical composition analysis, which confirms the presence of carbohydrates (81.03 ± 0.23), proteins (4.22 ± 1.2), uronic acid (12.1 ± 0.12), and nucleic acid content (2.44 ± 0.15) in exopolysaccharide. The one factor at a time (OFAT) and response surface methodology (RSM) - central composite design (CCD) approaches were used to optimise the production of Bio-Pm-AgNPs, leading to an increase in yield of up to 1.86 g/L. The Bio-Pm-AgNPs were then subjected to Fourier transform infrared spectroscopy (FTIR) which determines the functional groups, X-ray diffractometer confers that Bio-Pm-AgNPs are crystalline in nature, field emission-scanning electron microscopy (FE-SEM) reveals the morphology of Bio-Pm-AgNPs, energy dispersive X-ray spectroscopy (EDX) confirms the presence of elements like Ag, C and O, high-resolution transmission electron microscopy (HR-TEM) determines that the Bio-Pm-AgNPs are sphere-shaped at 75 nm. Dynamic light scattering (DLS) and zeta potential analysis were also carried out to reveal the physiological nature of Bio-Pm-AgNPs. Bio-Pm-AgNPs have a promising effect on the inhibitory mechanism of Vibrio cholerae cells at a MIC concentration of 20 μg/ml which significantly affects cellular respiration and energy metabolism through glycolysis and TCA cycles by deteriorating the enzyme responsible for ATP and NADH utilisation. The action of Bio-Pm-AgNPs reduces the purity and concentration of nucleic acids, which leads to higher DNA damage. In-vivo analysis reveals that the treatment of Bio-Pm-AgNPs decreased the colonisation of V. cholerae and improved the survival rates in C. elegans.},
}
@article {pmid38006809,
year = {2023},
author = {Wu, J and Zhang, HL and Guo, S and Li, X and Dong, T and Zhu, Y and Tsim, KWK},
title = {Acori Tatarinowii Rhizoma prevents the fluoxetine-induced multiple-drug resistance of Escherichia coli against antibiotics.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {123},
number = {},
pages = {155232},
doi = {10.1016/j.phymed.2023.155232},
pmid = {38006809},
issn = {1618-095X},
abstract = {BACKGROUND: In treating depression, the residual anti-depressant in gut interacts with the microbiome, leading to the appearance of multiple drug resistant (MDR) mutants, which poses a challenge for the treatment of infectious complications. Strategy is needed to combat this issue. Acori Tatarinowii Rhizoma (ATR, rhizome of Acorus tatarinowii Schott, Araceae), a traditional Chinese medicine, has been widely used for treatment of neurological disorders and gastrointestinal digestive disease in China. Here, ATR was demonstrated an excellent MDR-preventing effect in fluoxetine-induced Escherichia coli (E. coli).<br><br>AIM OF THE STUDY: This study aimed to reveal the effective role of ATR and its signaling cascades involved in preventing fluoxetine-induced MDR.<br><br>MATERIALS AND METHODS: The water extract of ATR was co-applied with sub-minimum inhibitory concentration (100&#xa0;mg/l) of fluoxetine in E. coli to evaluate its anti-MDR potential. Formation of reactive oxygen species (ROS) and expression of MDR-related genes in bacteria were measured by dichloro-dihydro-fluorescein diacetate assay and real-time PCR, respectively. Two fluorescent dyes, 1-N-phenylnapthylamine and 3,3'-dipropylthiadicarbocyanine were used to analyze the outer membrane permeability and inner membrane depolarization of E. coli. The accumulation of fluoxetine in the treated E. coli was determined via HPLC. The active fraction of ATR was identified.<br><br>RESULTS: The water extract of ATR significantly decreased the number of MDR mutants induced by fluoxetine and had half effective concentrations (EC50) of 55.5&#xa0;&#x3bc;g/ml and 16.8&#xa0;&#x3bc;g/ml for chloramphenicol and tetracycline, respectively. ATR robustly reversed the fluoxetine-induced superoxide response and membrane damage in E. coli. In addition, the inclusion of ATR significantly reduced the accumulation of fluoxetine in E. coli. After further fractionation, the polysaccharide of ATR was demonstrated as the fraction with the most significant anti-MDR activity.<br><br>CONCLUSIONS: This is the first report to investigate the MDR-preventing effect of ATR. The results of this study proposed ATR as an excellent herbal product to prevent MDR issues, as induced by fluoxetine, with the potential to reduce the side effects during the drug therapy of depression.},
}
@article {pmid38006744,
year = {2023},
author = {Elgart, M and Zhang, Y and Zhang, Y and Yu, B and Kim, Y and Zee, PC and Gellman, MD and Boerwinkle, E and Daviglus, ML and Cai, J and Redline, S and Burk, RD and Kaplan, R and Sofer, T},
title = {Anaerobic pathogens associated with OSA may contribute to pathophysiology via amino-acid depletion.},
journal = {EBioMedicine},
volume = {98},
number = {},
pages = {104891},
doi = {10.1016/j.ebiom.2023.104891},
pmid = {38006744},
issn = {2352-3964},
abstract = {BACKGROUND: The human microbiome is linked to multiple metabolic disorders such as obesity and diabetes. Obstructive sleep apnoea (OSA) is a common sleep disorder with several metabolic risk factors. We investigated the associations between the gut microbiome composition and function, and measures of OSA severity in participants from a prospective community-based cohort study: the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).<br><br>METHODS: Bacterial-Wide Association Analysis (BWAS) of gut microbiome measured via metagenomics with OSA measures was performed adjusting for clinical, lifestyle and co-morbidities. This was followed by functional analysis of the OSA-enriched bacteria. We utilized additional metabolomic and transcriptomic associations to suggest possible mechanisms explaining the microbiome effects on OSA.<br><br>FINDINGS: Several uncommon anaerobic human pathogens were associated with OSA severity. These belong to the Lachnospira, Actinomyces, Kingella and Eubacterium genera. Functional analysis revealed enrichment in 49 processes including many anaerobic-related ones. Severe OSA was associated with the depletion of the amino acids glycine and glutamine in the blood, yet neither diet nor gene expression revealed any changes in the production or consumption of these amino acids.<br><br>INTERPRETATION: We show anaerobic bacterial communities to be a novel component of OSA pathophysiology. These are established in the oxygen-poor environments characteristic of OSA. We hypothesize that these bacteria deplete certain amino acids required for normal human homeostasis and muscle tone, contributing to OSA phenotypes. Future work should test this hypothesis as well as consider diagnostics via anaerobic bacteria detection and possible interventions via antibiotics and amino-acid supplementation.<br><br>FUNDING: Described in methods.},
}
@article {pmid38006743,
year = {2023},
author = {Wei, J and Yang, Z and Li, J and Zhang, Y and Zhang, W and Doherty, M and Yang, T and Yang, Y and Li, H and Wang, Y and Wu, Z and Li, C and Lei, G and Zeng, C},
title = {Association between gut microbiome-related metabolites and symptomatic hand osteoarthritis in two independent cohorts.},
journal = {EBioMedicine},
volume = {98},
number = {},
pages = {104892},
doi = {10.1016/j.ebiom.2023.104892},
pmid = {38006743},
issn = {2352-3964},
abstract = {BACKGROUND: Since gut microbiome dysbiosis can cause inflammatory disorders by affecting host metabolism, we postulate that the gut microbiome and related metabolites could play a role in hand osteoarthritis. We characterised gut microbiome-related metabolites in people with symptomatic hand osteoarthritis (SHOA) in two independent cohorts.<br><br>METHODS: Using data collected from a large-sample community-based observational study (discovery cohort), we assessed the relations of the microbial function and plasma key metabolites related to altered microbial function with SHOA. Finally, we verified the relations of plasma metabolites to SHOA in an independent observational study (validation cohort).<br><br>FINDINGS: In the discovery cohort (n&#xa0;=&#xa0;1359), compared to those without SHOA, participants with SHOA had significantly altered microbial functions related to tryptophan metabolism (Q&#xa0;=&#xa0;0.025). Therefore we measured the plasma tryptophan metabolites and found that participants with SHOA had higher levels of 5-hydroxyindoleacetic acid (odds ratio [OR]&#xa0;=&#xa0;1.25, 95% confidence interval [CI]: 1.09-1.42) and 5-hydroxytryptophol (OR&#xa0;=&#xa0;1.13, 95% CI: 1.04-1.23), but lower levels of indole-3-lactic acid (ILA) (OR&#xa0;=&#xa0;0.85, 95% CI: 0.72-1.00), skatole (OR&#xa0;=&#xa0;0.93, 95% CI: 0.88-0.99) and 3-hydroxyanthranilic acid (OR&#xa0;=&#xa0;0.90, 95% CI: 0.85-0.96). Findings from the validation cohort (n&#xa0;=&#xa0;142) verified that lower levels of ILA were related to SHOA (OR&#xa0;=&#xa0;0.70, 95% CI: 0.53-0.92).<br><br>INTERPRETATION: Alterations of the microbial function of tryptophan biosynthesis and tryptophan metabolites, especially lower levels of ILA, are associated with SHOA. These findings suggest the role of the microbiome and tryptophan metabolites in developing of SHOA and may contribute to future translational opportunities.<br><br>FUNDING: National Key Research and Development Plan and National Natural Science Foundation of China.},
}
@article {pmid38006691,
year = {2023},
author = {Hes, C and Desilets, A and Tonneau, M and El Ouarzadi, O and De Figueiredo Sousa, M and Bahig, H and Filion, &#xc9; and Nguyen-Tan, PF and Christopoulos, A and Benlaïfaoui, M and Derosa, L and Alves Costa Silva, C and Ponce, M and Malo, J and Belkad, W and Charpentier, D and Aubin, F and Hamilou, Z and Jamal, R and Messaoudene, M and Soulières, D and Routy, B},
title = {Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma.},
journal = {Oral oncology},
volume = {148},
number = {},
pages = {106623},
doi = {10.1016/j.oraloncology.2023.106623},
pmid = {38006691},
issn = {1879-0593},
abstract = {OBJECTIVES: Chemoradiation (CRT) in patients with locally advanced head and neck squamous cell cancer (HNSCC) is associated with significant toxicities, including mucositis. The gut microbiome represents an emerging hallmark of cancer and a potentially important biomarker for CRT-related adverse events. This prospective study investigated the association between the gut microbiome composition and CRT-related toxicities in patients with HNSCC, including mucositis.<br><br>MATERIALS AND METHODS: Stool samples from patients diagnosed with locally advanced HNSCC were prospectively collected prior to CRT initiation and analyzed using shotgun metagenomic sequencing to evaluate gut microbiome composition at baseline. Concurrently, clinicopathologic data, survival outcomes and the incidence and grading of CRT-emergent adverse events were documented in all patients.<br><br>RESULTS: A total of 52 patients were included, of whom 47 had baseline stool samples available for metagenomic analysis. Median age was 62, 83&#xa0;% patients were men and 54&#xa0;% had stage III-IV disease. All patients developed CRT-induced mucositis, including 42&#xa0;% with severe events (i.e. CTCAE v5.0 grade&#xa0;&#x2265;&#xa0;3) and 25&#xa0;% who required enteral feeding. With a median follow-up of 26.5 months, patients with severe mucositis had shorter overall survival (HR&#xa0;=&#xa0;3.3, 95&#xa0;%CI 1.0-10.6; p&#xa0;=&#xa0;0.02) and numerically shorter progression-free survival (HR&#xa0;=&#xa0;2.8, 95&#xa0;%CI, 0.8-9.6; p&#xa0;=&#xa0;0.09). The gut microbiome beta-diversity of patients with severe mucositis differed from patients with grades 1-2 mucositis (p&#xa0;=&#xa0;0.04), with enrichment in Mediterraneibacter (Ruminococcus gnavus) and Clostridiaceae family members, including Hungatella hathewayi. Grade 1-2 mucositis was associated with enrichment in Eubacterium rectale, Alistipes putredinis and Ruminococcaceae family members. Similar bacterial profiles were observed in patients who required enteral feeding.<br><br>CONCLUSION: Patients who developed severe mucositis had decreased survival and enrichment in specific bacteria associated with mucosal inflammation. Interestingly, these same bacteria have been linked to immune checkpoint inhibitor resistance.},
}
@article {pmid38006569,
year = {2023},
author = {Aminu, S and Ascandari, A and Laamarti, M and Safdi, NEH and El Allali, A and Daoud, R},
title = {Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-25},
doi = {10.1080/1040841X.2023.2282447},
pmid = {38006569},
issn = {1549-7828},
abstract = {The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.},
}
@article {pmid38006554,
year = {2024},
author = {Walker, T},
title = {Detection of Natural Wolbachia Strains in Anopheles Mosquitoes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2739},
number = {},
pages = {205-218},
pmid = {38006554},
issn = {1940-6029},
mesh = {Animals ; Humans ; *Anopheles/genetics ; *Wolbachia/genetics ; In Situ Hybridization, Fluorescence ; Mosquito Vectors ; *Malaria ; },
abstract = {Wolbachia is an endosymbiotic bacterium that naturally infects many insect species, including mosquitoes that transmit human diseases. Wolbachia strains have been shown to inhibit the transmission of both arboviruses and malaria Plasmodium parasites. The existence of natural strains in wild Anopheles (An.) mosquitoes, the vectors of malaria parasites, in an endosymbiotic relationship is still to be fully determined. Although Wolbachia has been reported to be present in wild populations of the An. gambiae complex, the primary vectors of malaria in Sub-Saharan Africa, Wolbachia DNA sequence density and infection frequencies are low. As most studies have used highly sensitive nested PCR as the only detection method, more robust evidence is required to determine whether Wolbachia strains are established as endosymbionts in Anopheles species. Techniques such as fluorescent in situ hybridization, microbiome sequencing, and Wolbachia whole genome sequencing have provided concrete evidence for genuine Wolbachia strains in two mosquito species: An. moucheti and An. demeilloni. In this chapter, the current methodology used to determine if resident strains exist in Anopheles mosquitoes will be reviewed, including both PCR- and non-PCR-based protocols.},
}
@article {pmid38006513,
year = {2023},
author = {Subbaiyan, R and Ganesan, A and Varadharajan, V and Jeyachandran, PR and Thangavel, H},
title = {Formulation and validation of probioticated foxtail millet laddu as a source of antioxidant for biological system using response surface methodology.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {38006513},
issn = {1678-4405},
abstract = {Probiotics play a critical role in supporting a healthy gut microbiome, which significantly impacts overall health and well-being. While there has been an increase in the availability of probiotic foods in recent years, there may still be limited options and accessibility in certain regions. This study focused on formulating a traditional Indian sweet called laddu enriched with millet and Lactobacillus acidophilus. The formulation of laddu ingredients was optimized using Design Expert software to create an optimal product for testing. The probiotic Lactobacillus acidophilus culture was incorporated into the laddu in three forms: lyophilized, microencapsulated powder, and natural curd. The probiotic foxtail laddu was selected based on specific criteria such as color, odor, and texture. The nutritional analysis revealed that the laddu contained approximately 64.46 g of carbohydrates, 15.13 g of protein, and 5.06 g of fat per 100 g of laddu. A microbial count analysis was performed over a two-month storage period to assess the viability of the incorporated Lactobacillus acidophilus. The results showed that the lyophilized and microencapsulated culture demonstrated good viability, with counts of 6.10 ± 0.09 log CFU/g and 7.43 ± 0.02 log CFU/g, respectively, when stored at 4 °C. In comparison, storage at room temperature resulted in counts of 5.41 ± 0.08 log CFU/g and 6.97 ± 0.02 log CFU/g at the end of the storage period. Based on the findings, the probiotic millet laddu developed in this study has the potential to be a value-added food product that can enhance the overall health of consumers. Incorporating probiotics into traditional food items like laddu offers a convenient and enjoyable way to promote gut health and improve the product's nutritional value.},
}
@article {pmid38006392,
year = {2023},
author = {Zhou, P and Yan, H and Zhang, Y and Qi, R and Zhang, H and Liu, J},
title = {Growth performance, bile acid profile, fecal microbiome and serum metabolomics of growing-finishing pigs fed diets with bile acids supplementation.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skad393},
pmid = {38006392},
issn = {1525-3163},
abstract = {The present experiment was conducted to determine the effect of bile acids (BAs) supplementation on growth performance, BAs profile, fecal microbiome, and serum metabolomics in growing-finishing pigs. A total of 60 pigs [Duroc × (Landrace ×Yorkshire)] with an average body weight of 27.0 ± 1.5 kg were selected and allotted into one of 2 groups (castrated male to female ratio = 1:1), with 10 replicates per treatment and 3 pigs per replicate. The 2 treatments were the control group (Control) and a porcine bile extract supplemented group dosed at 0.5 g/kg feed (BA). After a 16-wk treatment, growth performance, BAs profiles in serum and feces and fecal microbial composition were determined. An untargeted metabolomics approach using gas chromatography with a time-of-flight mass spectrometer (GC-TOF-MS) was conducted to identify the metabolic pathways and associated metabolites in the serum of pigs. We found that BAs supplementation had no effect on the growth performance of the growing-finishing pig. However, it tended to increase the gain to feed ratio for the whole period (P = 0.07). Bile acids supplementation resulted in elevated serum concentrations of secondary BAs (SBA), including hyodeoxycholic acid (HDCA), glycoursodeoxycholic acid (GUDCA), and tauro-hyodeoxycholic acid (THDCA), as well as fecal concentration of HDCA (P < 0.05). Fecal microbiota analysis revealed no differences in alpha and beta diversity indices or the relative abundance of Operational Taxonomic Units (OTUs) at both phylum and genus levels between groups. Metabolic pathway analysis revealed that the differential metabolites between Control and BA groups mainly involved in purine metabolism, ether lipid metabolism, glycerophospholipid metabolism, and amino sugar and nucleotide sugar metabolism, as well as primary bile acid biosynthesis. Our findings indicate that BAs supplementation tended to improve the feed efficiency, and significantly altered the BA profile in the serum and feces of growing-finished pigs, regardless of any changes in the gut microbial composition. The altered metabolic pathways could potentially play a vital role in improving the feed efficiency of growing-finished pigs with BAs supplementation.},
}
@article {pmid38006234,
year = {2023},
author = {Yadav, A and Ahlawat, S and Sharma, KK},
title = {Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxad280},
pmid = {38006234},
issn = {1365-2672},
abstract = {Metagenome sequencing techniques revolutionized the field of gut microbiome study. However, it is equipped with experimental and computational biases which affect the downstream analysis results. Also, live microbial strains is needed for a better understanding of host-microbial crosstalks and for designing next-generation treatment therapies based on probiotic strains and postbiotic molecules. Conventional culturing methodologies are insufficient to get the dark gut matter on the plate; therefore, there is an urgent need to propose novel culturing methods that can fill the limitations of metagenomic. The current work aims to provide a consolidated evaluation of the available methods for host-microbe interaction with an emphasis on in vitro culturing of gut microbes using organoids, gut on a chip, and gut bioreactor. Further, the knowledge of microbial crosstalk in the gut helps us to identify core microbiota, and key metabolites that will aid in designing culturing media and co-culturing systems for gut microbiome study. After the deeper mining of the current culturing methods, we recommend that 3-D printed intestinal cells in a multistage continuous flow reactor equipped with an extended organoid system might be a good practical choice for gut microbiota-based studies.},
}
@article {pmid38005959,
year = {2023},
author = {Balieiro Neto, G and Engracia Filho, JR and Budino, FEL and Freitas, AWP and Soares, WVB},
title = {Effects of High-Biotin Sample Interference on Antibody Concentrations in Sandwich Immunoassays.},
journal = {Vaccines},
volume = {11},
number = {11},
pages = {},
pmid = {38005959},
issn = {2076-393X},
abstract = {The use of antimicrobial growth promoters (AGPs) is banned because of problems associated with drug residues in animal products and increased bacterial resistance. The immunization of chickens with specific antigens is a promising strategy for generating specific antibodies that can target a wide range of antibiotic-resistant bacteria and can be used as an alternative to antibiotics. Immunoglobulin Y (IgY) antibodies in a polyclonal antibody (pAb) format, when administered orally, modulate the ruminal microbiome and maintain animal health and performance; however, there are concerns pertaining to protein impurities and biotin concentrations in the samples. Signal amplification strategies involving the noncovalent interaction of biotin with streptavidin is extensively used in diagnosis and scientific research, particularly in enzyme-linked immunosorbent assays (ELISAs). However, the high concentrations of biotin in samples, especially in those derived from rich sources such as egg yolk, can pose challenges and potentially harm the accuracy of diagnostic tests and protein concentration measurements. This study aimed to evaluate the influence of biotin on the measurement of IgY in freeze-dried egg yolk samples obtained from immunized laying hens using immunoassays with biotin-avidin/streptavidin. The detection of IgY in yolk samples using ELISA with streptavidin-biotin binding could lead to misdiagnosis due to biotin interference; the level of interference varies with the specific assay conditions and the concentration of biotin in the yolk samples. An ELISA without streptavidin-biotin binding is advisable to avoid interactions between biotin and target proteins, prevent biotin interference with the results, and achieve more reliable and accurate results.},
}
@article {pmid38005873,
year = {2023},
author = {Borase, H and Shukla, D},
title = {The Interplay of Genital Herpes with Cellular Processes: A Pathogenesis and Therapeutic Perspective.},
journal = {Viruses},
volume = {15},
number = {11},
pages = {},
pmid = {38005873},
issn = {1999-4915},
support = {R01AI139768//National Institute of Health/ ; },
mesh = {Humans ; *Herpes Genitalis/drug therapy/pathology ; Herpesvirus 2, Human/physiology ; Autophagy ; Antiviral Agents/pharmacology/therapeutic use ; *Herpes Simplex/drug therapy ; },
abstract = {Genital herpes, primarily caused by herpes simplex virus-2 (HSV-2), remains a pressing global health concern. Its remarkable ability to intertwine with cellular processes, from harnessing host machinery for replication to subverting antiviral defenses like autophagy and programmed cell death, exemplifies the intricate interplay at the heart of its pathogenesis. While the biomedical community has extensively researched antiviral interventions, the efficiency of these strategies in managing HSV-2 remains suboptimal. Recognizing this, attention has shifted toward leveraging host cellular components to regulate HSV-2 replication and influence the cell cycle. Furthermore, innovative interventional strategies-including drug repurposing, microbivacs, connecting the host microbiome, and exploiting natural secondary metabolites-are emerging as potential game changers. This review summarizes the key steps in HSV-2 pathogenesis and newly discovered cellular interactions, presenting the latest developments in the field, highlighting existing challenges, and offering a fresh perspective on HSV-2's pathogenesis and the potential avenues for its treatment by targeting cellular proteins and pathways.},
}
@article {pmid38004827,
year = {2023},
author = {Kim, J and Koh, H},
title = {MiTree: A Unified Web Cloud Analytic Platform for User-Friendly and Interpretable Microbiome Data Mining Using Tree-Based Methods.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004827},
issn = {2076-2607},
support = {2021R1C1C1013861//National Research Foundation of Korea/ ; },
abstract = {The advent of next-generation sequencing has greatly accelerated the field of human microbiome studies. Currently, investigators are seeking, struggling and competing to find new ways to diagnose, treat and prevent human diseases through the human microbiome. Machine learning is a promising approach to help such an effort, especially due to the high complexity of microbiome data. However, many of the current machine learning algorithms are in a "black box", i.e., they are difficult to understand and interpret. In addition, clinicians, public health practitioners and biologists are not usually skilled at computer programming, and they do not always have high-end computing devices. Thus, in this study, we introduce a unified web cloud analytic platform, named MiTree, for user-friendly and interpretable microbiome data mining. MiTree employs tree-based learning methods, including decision tree, random forest and gradient boosting, that are well understood and suited to human microbiome studies. We also stress that MiTree can address both classification and regression problems through covariate-adjusted or unadjusted analysis. MiTree should serve as an easy-to-use and interpretable data mining tool for microbiome-based disease prediction modeling, and should provide new insights into microbiome-based diagnostics, treatment and prevention. MiTree is an open-source software that is available on our web server.},
}
@article {pmid38004817,
year = {2023},
author = {Parigi, TL and Vieujean, S and Paridaens, K and Dalgaard, K and Peyrin-Biroulet, L and Danese, S},
title = {Efficacy, Safety, and Concerns on Microbiota Modulation, Antibiotics, Probiotics, and Fecal Microbial Transplant for Inflammatory Bowel Disease and Other Gastrointestinal Conditions: Results from an International Survey.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004817},
issn = {2076-2607},
abstract = {The gut microbiota play a pivotal role in human health. Dysbiosis, alterations in microbiota composition and function, is associated with gastrointestinal disorders, including inflammatory bowel disease (IBD). This international survey aimed to assess physicians' experiences, perceptions, and practices related to microbiome modulation for gastrointestinal conditions, with a focus on IBD. Results from 142 healthcare professionals, predominantly gastroenterologists, confirmed a consensus on the relevance of the gut microbiota in IBD pathogenesis. However, the utilization of microbial composition analysis and probiotics in clinical practice was limited, primarily due to the lack of standardized guidelines and supporting evidence. Physicians held conflicting views on antibiotics, recognizing their potential for inducing remission but also causing flares in IBD. Respondents also had varying opinions on the efficacy of fecal microbiota transplantation (FMT) for different gastrointestinal conditions, with higher confidence in FMT effectiveness for irritable bowel syndrome with diarrhea, pouchitis, and ulcerative colitis. Concerns on FMT included uncertainty about effect duration, administration intervals, and conflicting evidence. Donor selection was believed to be a crucial factor in FMT outcomes. This survey highlights the need for further research and evidence-based guidelines to optimize the use of microbiome-based therapies in clinical practice. As our understanding of the gut microbiome continues to evolve, these insights will contribute to more informed and personalized approaches to managing gastrointestinal disorders.},
}
@article {pmid38004804,
year = {2023},
author = {Borrel, G and Fadhlaoui, K and Ben Hania, W and Gaci, N and Pehau-Arnaudet, G and Chaudhary, PP and Vandekerckove, P and Ballet, N and Alric, M and O'Toole, PW and Fardeau, ML and Ollivier, B and Brugère, JF},
title = {Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004804},
issn = {2076-2607},
support = {NA/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {The methanogenic strain Mx-05[T] was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05[T] were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05[T] required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05[T] grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L[-1] NaCl (optimum 0.12 mol.L[-1] NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05[T] as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05[T] (JCM 31474T).},
}
@article {pmid38004800,
year = {2023},
author = {Maddock, D and Brady, C and Denman, S and Arnold, D},
title = {Bacteria Associated with Acute Oak Decline: Where Did They Come From? We Know Where They Go.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004800},
issn = {2076-2607},
support = {BB/T010886/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Acute oak decline is a high-impact disease causing necrotic lesions on the trunk, crown thinning and the eventual death of oak. Four bacterial species are associated with the lesions-Brenneria goodwinii, Gibbsiella quercinecans, Rahnella victoriana and Lonsdalea Britannica-although an epi-/endophytic lifestyle has also been suggested for these bacteria. However, little is known about their environmental reservoirs or their pathway to endophytic colonisation. This work aimed to investigate the ability of the four AOD-associated bacterial species to survive for prolonged periods within rhizosphere soil, leaves and acorns in vitro, and to design an appropriate method for their recovery. This method was trialled on field samples related to healthy and symptomatic oaks. The in vitro study showed that the majority of these species could survive for at least six weeks within each sample type. Results from the field samples demonstrated that R. victoriana and G. quercinecans appear environmentally widespread, indicating multiple routes of endophytic colonisation might be plausible. B. goodwinii and L. britannica were only identified from acorns from healthy and symptomatic trees, indicating they may be inherited members of the endophytic seed microbiome and, despite their ability to survive outside of the host, their environmental occurrence is limited. Future research should focus on preventative measures targeting the abiotic factors of AOD, how endophytic bacteria shift to a pathogenic cycle and the identification of resilient seed stock that is less susceptible to AOD.},
}
@article {pmid38004795,
year = {2023},
author = {Wallen-Russell, C and Pearlman, N and Wallen-Russell, S and Cretoiu, D and Thompson, DC and Voinea, SC},
title = {A Catastrophic Biodiversity Loss in the Environment Is Being Replicated on the Skin Microbiome: Is This a Major Contributor to the Chronic Disease Epidemic?.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004795},
issn = {2076-2607},
abstract = {There has been a catastrophic loss of biodiversity in ecosystems across the world. A similar crisis has been observed in the human gut microbiome, which has been linked to "all human diseases affecting westernized countries". This is of great importance because chronic diseases are the leading cause of death worldwide and make up 90% of America's healthcare costs. Disease development is complex and multifactorial, but there is one part of the body's interlinked ecosystem that is often overlooked in discussions about whole-body health, and that is the skin microbiome. This is despite it being a crucial part of the immune, endocrine, and nervous systems and being continuously exposed to environmental stressors. Here we show that a parallel biodiversity loss of 30-84% has occurred on the skin of people in the developed world compared to our ancestors. Research has shown that dysbiosis of the skin microbiome has been linked to many common skin diseases and, more recently, that it could even play an active role in the development of a growing number of whole-body health problems, such as food allergies, asthma, cardiovascular diseases, and Parkinson's, traditionally thought unrelated to the skin. Damaged skin is now known to induce systemic inflammation, which is involved in many chronic diseases. We highlight that biodiversity loss is not only a common finding in dysbiotic ecosystems but also a type of dysbiosis. As a result, we make the case that biodiversity loss in the skin microbiome is a major contributor to the chronic disease epidemic. The link between biodiversity loss and dysbiosis forms the basis of this paper's focus on the subject. The key to understanding why biodiversity loss creates an unhealthy system could be highlighted by complex physics. We introduce entropy to help understand why biodiversity has been linked with ecosystem health and stability. Meanwhile, we also introduce ecosystems as being governed by "non-linear physics" principles-including chaos theory-which suggests that every individual part of any system is intrinsically linked and implies any disruption to a small part of the system (skin) could have a significant and unknown effect on overall system health (whole-body health). Recognizing the link between ecosystem health and human health allows us to understand how crucial it could be to maintain biodiversity across systems everywhere, from the macro-environment we inhabit right down to our body's microbiome. Further, in-depth research is needed so we can aid in the treatment of chronic diseases and potentially change how we think about our health. With millions of people currently suffering, research to help mitigate the crisis is of vital importance.},
}
@article {pmid38004791,
year = {2023},
author = {Thamm, M and Reiß, F and Sohl, L and Gabel, M and Noll, M and Scheiner, R},
title = {Solitary Bees Host More Bacteria and Fungi on Their Cuticle than Social Bees.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004791},
issn = {2076-2607},
support = {ID73253//Bayerisches Staatsministerium f&#xfc;r Umwelt und Verbraucherschutz/ ; },
abstract = {Bees come into contact with bacteria and fungi from flowering plants during their foraging trips. The Western honeybee (Apis mellifera) shows a pronounced hygienic behavior with social interactions, while the solitary red mason bee (Osmia bicornis) lacks a social immune system. Since both visit the same floral resources, it is intriguing to speculate that the body surface of a solitary bee should harbor a more complex microbiome than that of the social honeybee. We compared the cuticular microbiomes of A. mellifera (including three European subspecies) and O. bicornis for the first time by bacterial 16S rRNA and fungal ITS gene-based high-throughput amplicon sequencing. The cuticular microbiome of the solitary O. bicornis was significantly more complex than that of the social A. mellifera. The microbiome composition of A. mellifera subspecies was very similar. However, we counted significantly different numbers of fungi and a higher diversity in the honeybee subspecies adapted to warmer climates. Our results suggest that the cuticular microbiome of bees is strongly affected by visited plants, lifestyle and adaptation to temperature, which have important implications for the maintenance of the health of bees under conditions of global change.},
}
@article {pmid38004785,
year = {2023},
author = {Zheng, W and Guan, Y and Wu, B},
title = {Effects of Yupingfeng Polysaccharides as Feed Supplement on Immune Function and Intestinal Microbiome in Chickens.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004785},
issn = {2076-2607},
support = {2019B030301010//Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding/ ; },
abstract = {The health of chicks is closely related to their productivity. Yupingfeng polysaccharide (YPF-P) is a kind of water-soluble polysaccharide extracted from Yupingfeng powder; it has high pharmacological activity and can be used as a potential substitute for antibiotics to improve the health of chicks. This study aimed to investigate the effects of YPF-P on immune performance, the duodenum, and the cecal microflora of chicks. All chickens (4224) were randomly distributed into four groups (eight replicas/group, 132 hens/replica). The control group was fed a basal diet (0 g/kg YPF-P), while the experimental groups were fed basal diets supplemented with 1, 2, or 4 g/kg YPF-P. The results showed that YPF-P significantly increased the thymus index (p < 0.05). The content of total antioxidant capacity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), immunoglobulin A (IgA), and IgG and immunoglobulin M (IgM) was upregulated in the serum by YPF-P (p < 0.05). YPF-P decreased the content of malondialdehyde (MDA) (p < 0.05). Further, 16S rRNA sequencing showed that 2 g/kg YPF-P modulated the predominant duodenum and cecal microbial community structure, which increased the number of Faecalibacterium, Megamonas, Bacteroides, Alistipes, NK4A214_group, and Enterococcus. In conclusion, YPF-P ameliorated the growth performance of chicks by regulating serum immune and antioxidant balance, as well as the intestinal microbiota.},
}
@article {pmid38004775,
year = {2023},
author = {Santiago, JM and Hallman, LM and Fox, JP and Pitino, M and Shatters, RG and Cano, LM and Rossi, L},
title = {Impacts of Oak Mulch Amendments on Rhizosphere Microbiome of Citrus Trees Grown in Florida Flatwood Soils.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004775},
issn = {2076-2607},
support = {#2019-38640-29878//United States Department of Agriculture/ ; #2020-70029-33176//United States Department of Agriculture/ ; UF/IFAS A.H. Krezdorn Memorial Fund//University of Florida/ ; },
abstract = {Rhizosphere interactions are an understudied component of citrus production. This is even more important in Florida flatwood soils, which pose significant challenges in achieving sustainable and effective fruit production due to low natural fertility and organic matter. Citrus growers apply soil amendments, including oak mulch, to ameliorate their soil conditions. Thus, the aim of this research was to evaluate the effects of oak mulch on citrus nutrient uptake, soil characteristics, and rhizosphere composition. The plant material consisted of 'Valencia' sweet orange (Citrus × sinensis) trees grafted on 'US-812' (C. reticulata × C. trifoliata) rootstock. The experiment consisted of two treatments, which included trees treated with oak mulch (300 kg of mulch per plot) and a control. The soil and leaf nutrient contents, soil pH, cation exchange capacity, moisture, temperature, and rhizosphere bacterial compositions were examined over the course of one year (spring and fall 2021). During the spring samplings, the citrus trees treated with oak mulch resulted in significantly greater soil Zn and Mn contents, greater soil moisture, and greater rhizosphere bacterial diversity compared to the control, while during the fall samplings, only a greater soil moisture content was observed in the treated trees. The soil Zn and Mn content detected during the spring samplings correlated with the significant increases in the diversity of the rhizosphere bacterial community composition. Similarly, the reduced rates of leaching and evaporation (at the soil surface) of oak mulch applied to Florida sandy soils likely played a large role in the significant increase in moisture and nutrient retention.},
}
@article {pmid38004761,
year = {2023},
author = {Do, KH and Ko, SH and Kim, KB and Seo, K and Lee, WK},
title = {Comparative Study of Intestinal Microbiome in Patients with Ulcerative Colitis and Healthy Controls in Korea.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004761},
issn = {2076-2607},
support = {2021RIS-001//National Research Foundation of Korea/ ; },
abstract = {Ulcerative colitis (UC) poses a contemporary medical challenge, with its exact cause still eluding researchers. This is due to various factors, such as the rising incidence, diagnostic complexities, and difficulties associated with its management. We compared the intestinal microbiome of patients with UC to that of healthy controls to determine the qualitative and quantitative changes associated with UC that occur in the intestinal microbiota. The intestinal bacterial abundance in 40 Korean patients with UC and 25 healthy controls was assayed using via next-generation sequencing. There were five major phyla in both groups: Firmicutes (UC patients: 51.12%; healthy controls: 46.90%), Bacteroidota (UC patients: 37.04%; healthy controls: 40.34%), Proteobacteria (UC patients: 6.01%; healthy controls: 11.05%), Actinobacteriota (UC patients: 5.71%; healthy controls: 1.56%), and Desulfobacteriota (UC patients: 0.13%; healthy controls: 0.14%). Firmicutes was more prevalent in patients with UC (51.12%) compared to that of healthy controls (46.90%). Otherwise, Bacteroidota was more prevalent in healthy controls (40.34%) compared to patients with UC (37.04%). Although there was no significant difference, our results showed a substantially lower gut microbiome diversity in patients with UC (mean: 16.5; 95% confidence interval (CI) = 14.956-18.044) than in healthy controls (mean: 17.84; 95% CI = 15.989-19.691), the beta diversity and the flora structure of the microbiome in patients with UC differed from those in healthy controls. This will be helpful for the development of new treatment options and lay the groundwork for future research on UC. To understand the disease mechanism, it is essential to define the different types of microbes in the guts of patients with UC.},
}
@article {pmid38004758,
year = {2023},
author = {Yan, P and Luo, S and Guo, L and Wang, X and Ren, X and Lv, J and Chen, Y and Lin, X and Chen, J and Wang, R},
title = {Unraveling Intestinal Microbial Shifts in ESRD and Kidney Transplantation: Implications for Disease-Related Dysbiosis.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004758},
issn = {2076-2607},
support = {82070766//National Natural Science Foundation of China/ ; 2022RC147//Medical Health Science and Technology Project of Zhejiang Provincial Health Commission/ ; LQ23H050003//Zhejiang Provincial Natural Science Foundation of China/ ; },
abstract = {The composition of the gut microbiome is profoundly influenced by the accumulation of toxins in end-stage renal disease (ESRD) and specific medical treatments during kidney transplantation (KT). However, variations in results may arise due to factors such as genetics, dietary habits, and the strategy of anti-rejection therapy. Therefore, we conducted a 16S rRNA sequencing study to characterize intestinal microbiomes by using 75 fecal specimens obtained from 25 paired Chinese living donors (LDs) of kidneys and recipients before and after KT. Surprisingly, similar enterotypes were observed between healthy LDs and ESRD recipients. Nonetheless, following KT, the fecal communities of recipients exhibited distinct clustering, which was primarily characterized by Escherichia-Shigella and Streptococcus at the genus level, along with a reduction in the diversity of microbiota. To further explore the characteristics of gut microorganisms in early rejection episodes, two recipients with biopsy-proven borderline changes during follow-up were enrolled in a preliminary sub-cohort study. Our findings reveal a comparable construction of gut microbiota between ESRD patients and their healthy relatives while also highlighting the significant impact of KT on gut microbial composition.},
}
@article {pmid38004757,
year = {2023},
author = {Aryee, G and Luecke, SM and Dahlen, CR and Swanson, KC and Amat, S},
title = {Holistic View and Novel Perspective on Ruminal and Extra-Gastrointestinal Methanogens in Cattle.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004757},
issn = {2076-2607},
support = {N/A//North Dakota Agricultural Experiment Station/ ; },
abstract = {Despite the extensive research conducted on ruminal methanogens and anti-methanogenic intervention strategies over the last 50 years, most of the currently researched enteric methane (CH4) abatement approaches have shown limited efficacy. This is largely because of the complex nature of animal production and the ruminal environment, host genetic variability of CH4 production, and an incomplete understanding of the role of the ruminal microbiome in enteric CH4 emissions. Recent sequencing-based studies suggest the presence of methanogenic archaea in extra-gastrointestinal tract tissues, including respiratory and reproductive tracts of cattle. While these sequencing data require further verification via culture-dependent methods, the consistent identification of methanogens with relatively greater frequency in the airway and urogenital tract of cattle, as well as increasing appreciation of the microbiome-gut-organ axis together highlight the potential interactions between ruminal and extra-gastrointestinal methanogenic communities. Thus, a traditional singular focus on ruminal methanogens may not be sufficient, and a holistic approach which takes into consideration of the transfer of methanogens between ruminal, extra-gastrointestinal, and environmental microbial communities is of necessity to develop more efficient and long-term ruminal CH4 mitigation strategies. In the present review, we provide a holistic survey of the methanogenic archaea present in different anatomical sites of cattle and discuss potential seeding sources of the ruminal methanogens.},
}
@article {pmid38004753,
year = {2023},
author = {Mathlouthi, NEH and Belguith, I and Yengui, M and Oumarou Hama, H and Lagier, JC and Ammar Keskes, L and Grine, G and Gdoura, R},
title = {The Archaeome's Role in Colorectal Cancer: Unveiling the DPANN Group and Investigating Archaeal Functional Signatures.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004753},
issn = {2076-2607},
abstract = {BACKGROUND AND AIMS: Gut microbial imbalances are linked to colorectal cancer (CRC), but archaea's role remains underexplored. Here, using previously published metagenomic data from different populations including Austria, Germany, Italy, Japan, China, and India, we performed bioinformatic and statistical analysis to identify archaeal taxonomic and functional signatures related to CRC.<br><br>METHODS: We analyzed published fecal metagenomic data from 390 subjects, comparing the archaeomes of CRC and healthy individuals. We conducted a biostatistical analysis to investigate the relationship between Candidatus Mancarchaeum acidiphilum (DPANN superphylum) and other archaeal species associated with CRC. Using the Prokka tool, we annotated the data focusing on archaeal genes, subsequently linking them to CRC and mapping them against UniprotKB and GO databases for specific archaeal gene functions.<br><br>RESULTS: Our analysis identified enrichment of methanogenic archaea in healthy subjects, with an exception for Methanobrevibacter smithii, which correlated with CRC. Notably, CRC showed a strong association with archaeal species, particularly Natrinema sp. J7-2, Ferroglobus placidus, and Candidatus Mancarchaeum acidiphilum. Furthermore, the DPANN archaeon exhibited a significant correlation with other CRC-associated archaea (p < 0.001). Functionally, we found a marked association between MvhB-type polyferredoxin and colorectal cancer. We also highlighted the association of archaeal proteins involved in the biosynthesis of leucine and the galactose metabolism process with the healthy phenotype.<br><br>CONCLUSIONS: The archaeomes of CRC patients show identifiable alterations, including a decline in methanogens and an increase in Halobacteria species. MvhB-type polyferredoxin, linked with CRC and species like Candidatus Mancarchaeum acidiphilum, Natrinema sp. J7-2, and Ferroglobus placidus emerge as potential archaeal biomarkers. Archaeal proteins may also offer gut protection, underscoring archaea's role in CRC dynamics.},
}
@article {pmid38004740,
year = {2023},
author = {Ossa-Trujillo, C and Taylor, EA and Sarwar, F and Vinasco, J and Jordan, ER and Buitrago, JAG and Hagevoort, GR and Lawhon, SD and Piñeiro, JM and Galloway-Peña, J and Norman, KN and Scott, HM},
title = {Two-Dose Ceftiofur Treatment Increases Cephamycinase Gene Quantities and Fecal Microbiome Diversity in Dairy Cows Diagnosed with Metritis.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004740},
issn = {2076-2607},
support = {2016-68003- 24607//United States Department of Agriculture/ ; },
abstract = {Antimicrobial resistance is a significant concern worldwide; meanwhile, the impact of 3rd generation cephalosporin (3GC) antibiotics on the microbial communities of cattle and resistance within these communities is largely unknown. The objectives of this study were to determine the effects of two-dose ceftiofur crystalline-free acid (2-CCFA) treatment on the fecal microbiota and on the quantities of second-and third-generation cephalosporin, fluoroquinolone, and macrolide resistance genes in Holstein-Friesian dairy cows in the southwestern United States. Across three dairy farms, 124 matched pairs of cows were enrolled in a longitudinal study. Following the product label regimen, CCFA was administered on days 0 and 3 to cows diagnosed with postpartum metritis. Healthy cows were pair-matched based on lactation number and calving date. Fecal samples were collected on days 0, 6, and 16 and pooled in groups of 4 (n = 192) by farm, day, and treatment group for community DNA extraction. The characterization of community DNA included real-time PCR (qPCR) to quantify the following antibiotic resistance genes: blaCMY-2, blaCTX-M, mphA, qnrB19, and the highly conserved 16S rRNA back-calculated to gene copies per gram of feces. Additionally, 16S rRNA amplicon sequencing and metagenomics analyses were used to determine differences in bacterial community composition by treatment, day, and farm. Overall, blaCMY-2 gene copies per gram of feces increased significantly (p ≤ 0.05) in the treated group compared to the untreated group on day 6 and remained elevated on day 16. However, blaCTX-M, mphA, and qnrB19 gene quantities did not differ significantly (p ≥ 0.05) between treatment groups, days, or farms, suggesting a cephamycinase-specific enhancement in cows on these farms. Perhaps unexpectedly, 16S rRNA amplicon metagenomic analyses showed that the fecal bacterial communities from treated animals on day 6 had significantly greater (p ≤ 0.05) alpha and beta diversity than the untreated group. Two-dose ceftiofur treatment in dairy cows with metritis elevates cephamycinase gene quantities among all fecal bacteria while paradoxically increasing microbial diversity.},
}
@article {pmid38004716,
year = {2023},
author = {Ahmed, RO and Ali, A and Leeds, T and Salem, M},
title = {Fecal Microbiome Analysis Distinguishes Bacterial Taxa Biomarkers Associated with Red Fillet Color in Rainbow Trout.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004716},
issn = {2076-2607},
support = {2021-67015-33388, 2023-67015-39742//National Institute of Food and Agriculture/ ; CRIS Project 8082-31000-013//United States Department of Agriculture, Agricultural Research Service/ ; },
abstract = {The characteristic reddish-pink fillet color of rainbow trout is an important marketing trait. The gastrointestinal microbiome is vital for host health, immunity, and nutrient balance. Host genetics play a crucial role in determining the gut microbiome, and the host-microbiome interaction impacts the host's phenotypic expression. We hypothesized that fecal microbiota could be used to predict fillet color in rainbow trout. Fish were fed Astaxanthin-supplemented feed for six months, after which 16s rDNA sequencing was used to investigate the fecal microbiome composition in rainbow trout families with reddish-pink fillet coloration (red fillet group, average saturation index = 26.50 ± 2.86) compared to families with pale white fillet color (white fillet group, average saturation index = 21.21 ± 3.53). The linear discriminant analysis effect size (LEFse) tool was used to identify bacterial biomarkers associated with fillet color. The alpha diversity measure shows no difference in the red and white fillet groups. Beta diversity principal component analysis showed clustering of the samples along the white versus red fillet group. The red fillet group has enrichment (LDA score > 1.5) of taxa Leuconostoc lactis, Corynebacterium variabile, Jeotgalicoccus halotolerans, and Leucobacter chromiireducens. In contrast, the white fillet group has an enriched presence of mycoplasma, Lachnoclostridium, and Oceanobacillus indicireducens. The enriched bacterial taxa in the red fillet group have probiotic functions and can generate carotenoid pigments. Bacteria taxa enriched in the white fillet group are either commensal, parasitic, or capable of reducing indigo dye. The study identified specific bacterial biomarkers differentially abundant in fish families of divergent fillet color that could be used in genetic selection to improve feed carotenoid retention and reddish-pink fillet color. This work extends our understanding of carotenoid metabolism in rainbow trout through the interaction between gut microbiota and fillet color.},
}
@article {pmid38004715,
year = {2023},
author = {Bourumeau, W and Tremblay, K and Jourdan, G and Girard, C and Laprise, C},
title = {Bacterial Biomarkers of the Oropharyngeal and Oral Cavity during SARS-CoV-2 Infection.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004715},
issn = {2076-2607},
support = {2021-HQ-000051//Fonds de recherche du Qu&#xe9;bec - sant&#xe9; (FRQS) and Public Health Agency of Canada/ ; },
abstract = {(1) Background: Individuals with COVID-19 display different forms of disease severity and the upper respiratory tract microbiome has been suggested to play a crucial role in the development of its symptoms. (2) Methods: The present study analyzed the microbial profiles of the oral cavity and oropharynx of 182 COVID-19 patients compared to 75 unaffected individuals. The samples were obtained from gargle screening samples. 16S rRNA amplicon sequencing was applied to analyze the samples. (3) Results: The present study shows that SARS-CoV-2 infection induced significant differences in bacterial community assemblages, with Prevotella and Veillonella as biomarkers for positive-tested people and Streptococcus and Actinomyces for negative-tested people. It also suggests a state of dysbiosis on the part of the infected individuals due to significant differences in the bacterial community in favor of a microbiome richer in opportunistic pathogens. (4) Conclusions: SARS-CoV-2 infection induces dysbiosis in the upper respiratory tract. The identification of these opportunistic pathogenic biomarkers could be a new screening and prevention tool for people with prior dysbiosis.},
}
@article {pmid38004705,
year = {2023},
author = {Mancilla, VJ and Braden-Kuhle, PN and Brice, KN and Mann, AE and Williams, MT and Zhang, Y and Chumley, MJ and Barber, RC and White, SN and Boehm, GW and Allen, MS},
title = {A Synthetic Formula Amino Acid Diet Leads to Microbiome Dysbiosis, Reduced Colon Length, Inflammation, and Altered Locomotor Activity in C57BL/6J Mice.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004705},
issn = {2076-2607},
support = {S21MD012472/MD/NIMHD NIH HHS/United States ; R25GM125587/GM/NIGMS NIH HHS/United States ; },
abstract = {The effects of synthetic, free-amino acid diets, similar to those prescribed as supplements for (phenylketonuria) PKU patients, on gut microbiota and overall health are not well understood. In the current, multidisciplinary study, we examined the effects of a synthetically-derived, low-fiber, amino acid diet on behavior, cognition, gut microbiome composition, and inflammatory markers. A cohort of 20 male C57BL/6J mice were randomly assigned to either a standard or synthetic diet (n = 10) at post-natal day 21 and maintained for 13 weeks. Sequencing of the 16S rRNA gene from fecal samples revealed decreased bacterial diversity, increased abundance of bacteria associated with disease, such as Prevotella, and a downward shift in gut microbiota associated with fermentation pathways in the synthetic diet group. Furthermore, there were decreased levels of short chain fatty acids and shortening of the colon in mice consuming the synthetic diet. Finally, we measured TNF-α, IL-6, and IL-10 in serum, the hippocampus, and colon, and found that the synthetic diet significantly increased IL-6 production in the hippocampus. These results demonstrate the importance of a multidisciplinary approach to future diet and microbiome studies, as diet not only impacts the gut microbiome composition but potentially systemic health as well.},
}
@article {pmid38004678,
year = {2023},
author = {Mondal, S and Somani, J and Roy, S and Babu, A and Pandey, AK},
title = {Insect Microbial Symbionts: Ecology, Interactions, and Biological Significance.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004678},
issn = {2076-2607},
support = {BT/PR45283/NER/95/1919/2022//Department of Biotechnology/ ; },
abstract = {The guts of insect pests are typical habitats for microbial colonization and the presence of bacterial species inside the gut confers several potential advantages to the insects. These gut bacteria are located symbiotically inside the digestive tracts of insects and help in food digestion, phytotoxin breakdown, and pesticide detoxification. Different shapes and chemical assets of insect gastrointestinal tracts have a significant impact on the structure and makeup of the microbial population. The number of microbial communities inside the gastrointestinal system differs owing to the varying shape and chemical composition of digestive tracts. Due to their short generation times and rapid evolutionary rates, insect gut bacteria can develop numerous metabolic pathways and can adapt to diverse ecological niches. In addition, despite hindering insecticide management programs, they still have several biotechnological uses, including industrial, clinical, and environmental uses. This review discusses the prevalent bacterial species associated with insect guts, their mode of symbiotic interaction, their role in insecticide resistance, and various other biological significance, along with knowledge gaps and future perspectives. The practical consequences of the gut microbiome and its interaction with the insect host may lead to encountering the mechanisms behind the evolution of pesticide resistance in insects.},
}
@article {pmid38004667,
year = {2023},
author = {Kalnina, I and Gudra, D and Silamikelis, I and Viksne, K and Roga, A and Skinderskis, E and Fridmanis, D and Klovins, J},
title = {Variations in the Relative Abundance of Gut Bacteria Correlate with Lipid Profiles in Healthy Adults.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004667},
issn = {2076-2607},
support = {"Investigation of interaction of smoked dietary products with gut microbiota" Agreement Nr. 1.1.1.2/VIAA/1/16/128//European Regional Development Fund "On Implementation of Activity 1.1.1.2 "Post-doctoral Research Aid"/ ; },
abstract = {The gut microbiome is a versatile system regulating numerous aspects of host metabolism. Among other traits, variations in the composition of gut microbial communities are related to blood lipid patterns and hyperlipidaemia, yet inconsistent association patterns exist. This study aims to assess the relationships between the composition of the gut microbiome and variations in lipid profiles among healthy adults. This study used data and samples from 23 adult participants of a previously conducted dietary intervention study. Circulating lipid measurements and whole-metagenome sequences of the gut microbiome were derived from 180 blood and faecal samples collected from eight visits distributed across an 11-week study. Lipid-related variables explained approximately 4.5% of the variation in gut microbiome compositions, with higher effects observed for total cholesterol and high-density lipoproteins. Species from the genera Odoribacter, Anaerostipes, and Parabacteroides correlated with increased serum lipid levels, whereas probiotic species like Akkermansia muciniphila were more abundant among participants with healthier blood lipid profiles. An inverse correlation with serum cholesterol was also observed for Massilistercora timonensis, a player in regulating lipid turnover. The observed correlation patterns add to the growing evidence supporting the role of the gut microbiome as an essential regulator of host lipid metabolism.},
}
@article {pmid38004642,
year = {2023},
author = {Smith, ML and Weitz, KK and Thompson, AM and Jansson, JK and Hofmockel, KS and Lipton, MS},
title = {Real-Time and Rapid Respiratory Response of the Soil Microbiome to Moisture Shifts.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004642},
issn = {2076-2607},
abstract = {Microbial response to changing environmental factors influences the fate of soil organic carbon, and drought has been shown to affect microbial metabolism and respiration. We hypothesized that the access of microbes to different carbon pools in response to dry-rewet events occurs sequentially at different rates. We amended desiccated soils with [13]C-labeled glucose and measured the rates of [12]CO2 and [13]CO2 respiration in real time after rewetting. Using these differentiated [12]CO2 and [13]CO2 respiration rate soils after rewetting, we were able to deduce when microbes are accessing different pools of carbon. Immediately upon rewetting, respiration of [12]CO2 occurred first, with negligible [13]CO2 respiration. Appreciable metabolism and respiration of the added [13]C glucose did not occur until 15 min after rewetting. We conclude that, while all carbon pools are being accessed in the first 9 h after rewetting, the rate and timing at which new and existing carbon pools are being accessed varies. Within this study, using stable isotope-labeled substrates to discern which carbon pools are metabolized first uniquely illustrates how microorganisms access different carbon pools which has implications into understanding how carbon metabolism can further affect climate, carbon sequestration, and soil health.},
}
@article {pmid38004641,
year = {2023},
author = {Zhao, R and Fajardo, J and Shen, GX},
title = {Influence of Brown or Germinated Brown Rice Supplementation on Fecal Short-Chain Fatty Acids and Microbiome in Diet-Induced Insulin-Resistant Mice.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004641},
issn = {2076-2607},
support = {OG-3-15-4889-GS//Diabetes Canada/ ; },
abstract = {Intake of whole grain foods is associated with improving metabolic profile compared to refined grain products, but the underlying mechanism remains unclear. The present study examined the effects of brown rice (BRR) or germinated brown rice (GBR) supplementation on fecal short-chain fatty acids (SCFAs), and relationship with gut microbiota, metabolism and inflammation in high fat (HF)-diet-fed mice. The results demonstrated that an HF diet supplemented with BRR or GBR comparably increased the abundance of fecal isobutyric acid compared to that in mice receiving HF+white rice (WHR) diet (p < 0.01). The abundance of valeric acid in HF+GBR-diet-fed mice was higher than those receiving HF+WHR diet (p < 0.05). The abundances of fecal isobutyric acid negatively correlated with fasting plasma glucose, insulin, cholesterol, triglycerides, tumor necrosis factor-α, plasminogen activator inhibit-1, monocyte chemotactic protein-1 and homeostatic model assessment of insulin resistance (p < 0.01). The abundance of valeric acids negatively correlated with insulin resistance (p < 0.05). The abundances of isobutyric acid positively correlated with Lactobacillus, but negatively correlated with Dubosiella genus bacteria (p < 0.05). The findings demonstrated that the increases in SCFAs in the feces of BRR and GBR-treated mice were associated with improvements in gut microbiome, metabolic and inflammatory profile, which may contribute to the antidiabetic and anti-inflammatory effects of the whole grains in HF-diet-fed mice.},
}
@article {pmid38004350,
year = {2023},
author = {Ren, Y and Ciwang, R and Wang, J and Mehmood, K and Ataya, FS and Li, K},
title = {Effect of Different Feeds on the Fungi Microbiome of Suffolk Crossed with Tibetan Sheep.},
journal = {Life (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
pmid = {38004350},
issn = {2075-1729},
support = {XZ202101ZD0001N//Major projects for the Tibet Autonomous Region/ ; },
abstract = {The gut microbiome plays an important role in the metabolism, nutrient absorption and immunocompetency of animals. The dynamics of the microbiota can be influenced by modulatory factors that involve nutrition, environment, health, diseases, etc. Few reports have been documented regarding the effects of different feeds on the fungi microbiome of Suffolk crossed with Tibetan sheep. A total of 30 Suffolk crossed with Tibetan sheep (ST sheep) were selected for the study and randomly divided into five equal groups (n = 6): AZ, BZ, CZ, DZ and EZ. Group AZ was fed with alfalfa and oat grass, whereas group BZ was fed with mixture of concentrated feed, alfalfa and oat grass. Groups CZ, DZ and EZ were fed with concentrated feed #1, #2 and #3, respectively. All experimental animals were fed twice a day for four months, and rectum samples were collected for microbiota analysis. Results revealed that 2,781,461 raw reads and 2,333,239 clean reads were achieved in the ST sheep. When compared with the sheep of groups AZ and BZ (164), the shared amplicon sequence variants (ASVs) between AZ and CZ (109), AZ (113) and DZ (118) as well as AZ along with EZ were fewer. Conspicuous different phyla (8) and genera (56) were examined and compared with free-range sheep in AZ. Genera including Xeromyces, Kazachstania, Cordyceps, Rhodotorula, Pichia, Spor, etc. were found higher in animals in the CZ, DZ and EZ groups. The results of this study provide new insights regarding the effects of different feeds on the fungi microbiome of sheep farmed on the plateau. We concluded that the differences in feed in Suffolk crossed with Tibetan sheep altered their gut microbiota.},
}
@article {pmid37961388,
year = {2023},
author = {Karim, S and Zenzal, TJ and Beati, L and Sen, R and Adegoke, A and Kumar, D and Downs, LP and Keko, M and Nussbaum, A and Becker, DJ and Moore, FR},
title = {Ticks without borders: Microbial communities of immature Neotropical tick species parasitizing migratory landbirds along northern Gulf of Mexico.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37961388},
support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; },
abstract = {The long-distance, seasonal migrations of birds make them an effective ecological bridge for the movement of ticks. The introduction of exotic tick species to new geographical regions can lead to the emergence of novel tick-borne pathogens or the re-emergence of previously eradicated ones. This study assessed the prevalence of exotic tick species parasitizing resident, short-distance, and long-distance songbirds during spring and autumn at stopover sites in the northern Gulf of Mexico using the mitochondrial 12S rDNA gene. Birds were captured for tick collection from six different sites from late August to early November in both 2018 and 2019. The highest number of ticks were collected in the 2019 season. Most ticks were collected off the Yellow-breasted Chat (Icteria virens) and Common Yellowthroat (Geothlypis trichas), and 54% of the total ticks collected were from Grand Chenier, LA. A high throughput 16S ribosomal RNA sequencing approach was followed to characterize the microbial communities and identify pathogenic microbes in all tick samples. Tick microbial communities, diversity, and community structure were determined using quantitative insight into microbial ecology (QIIME). The sparse correlations for compositional data (SparCC) approach was then used to construct microbial network maps and infer microbial correlations. A total of 421 individual ticks in the genera Amblyomma, Haemaphysalis, and Ixodes were recorded from 28 songbird species, of which Amblyomma and Amblyomma longirostre was the most abundant tick genus and species, respectively. Microbial profiles showed that Proteobacteria was the most abundant phylum. The most abundant bacteria include the pathogenic Rickettsia and endosymbiont Francisella, Candidatus Midichloria, and Spiroplasma. BLAST analysis and phylogenetic reconstruction of the Rickettsia sequences revealed the highest similarities to pathogenic spotted and non-spotted fever groups, including R. buchneri, R. conorii, R. prowazekii, R. bellii, R. australis, R. parkeri, R. monacensis, and R. monteiroi. Permutation multivariate analysis of variance revealed that the relative abundance of Francisella and Rickettsia drives microbial patterns across the tick genera. We also observed a higher percentage of positive correlations in microbe-microbe interactions among members of the microbial communities. Network analysis suggested a negative correlation between a) Francisella and Rickettsia and, b) Francisella and Cutibacterium. Lastly, mapping the distributions of bird species parasitized during spring migrations highlighted geographic hotspots where migratory songbirds could disperse ticks and their pathogens at stopover sites or upon arrival to their breeding grounds, the latter showing means dispersal distances from 421-5003 kilometers. These findings strongly highlight the potential role of migratory birds in the epidemiology of tick-borne pathogens.},
}
@article {pmid38004243,
year = {2023},
author = {Hong, L and Huang, Y and Han, J and Li, S and Zhang, L and Jiang, S and Zhou, Q and Cao, X and Yu, W and Yang, Y and Hong, S and Zhou, Y and Yan, W and Cao, Y},
title = {Dynamics and Crosstalk between Gut Microbiota, Metabolome, and Fecal Calprotectin in Very Preterm Infants: Insights into Feeding Intolerance.},
journal = {Nutrients},
volume = {15},
number = {22},
pages = {},
pmid = {38004243},
issn = {2072-6643},
support = {2021YFC2701800//National Key Research and Development Program of China/ ; 2021YFC2701801//National Key Research and Development Program of China/ ; 2016ZB0101//Key Developing Discipline of the Shanghai Municipal Health Commission (Pediatrics)/ ; },
abstract = {BACKGROUND: Feeding intolerance (FI) is a significant concern in the care of preterm infants, impacting their growth and development. We previously reported that FI is linked to lower fecal calprotectin (FC) levels. This study aims to explore the postnatal dynamics and interplay between microbiota, metabolic profiles, and host immunity in preterm infants with and without FI.<br><br>METHODS: Infants with gestational age <32 weeks or birth weight <1500 g were enrolled at the Children's Hospital of Fudan University between January 2018 and October 2020. Weekly fecal samples were analyzed for bacterial profiling, metabolome, and calprotectin levels, exploring their longitudinal development and interrelationships.<br><br>RESULTS: Of the 118 very preterm infants studied, 48 showed FI. These infants experienced an interrupted microbial-immune trajectory, particularly at 3-4 weeks of age, marked by a reduced bacterial abundance, alpha diversity, and FC levels. Metabolic changes in FI were pronounced between 3 and 6 weeks. Pantothenic acid and two polyamine metabolites were closely associated with bacterial abundance and FC levels and negatively correlated with the duration to attain full enteral feeding.<br><br>CONCLUSIONS: FI infants demonstrated compromised microbiome-immune interactions, potentially influenced by specific metabolites. This research underscored the importance of early microbial and metabolic development in the pathogenesis of FI in very preterm infants.},
}
@article {pmid38004216,
year = {2023},
author = {Dębińska, A and Sozańska, B},
title = {Dietary Polyphenols-Natural Bioactive Compounds with Potential for Preventing and Treating Some Allergic Conditions.},
journal = {Nutrients},
volume = {15},
number = {22},
pages = {},
pmid = {38004216},
issn = {2072-6643},
abstract = {In light of the constantly increasing prevalence of allergic diseases, changes in dietary patterns have been suggested as a plausible environmental explanation for the development and progression of these diseases. Nowadays, much attention has been paid to the development of dietary interventions using natural substances with anti-allergy activities. In this respect, dietary polyphenols have been studied extensively as one of the most prominent natural bioactive compounds with well-documented anti-inflammatory, antioxidant, and immunomodulatory properties. This review aims to discuss the mechanisms underlying the potential anti-allergic actions of polyphenols related to their ability to reduce protein allergenicity, regulate immune response, and gut microbiome modification; however, these issues need to be elucidated in detail. This paper reviews the current evidence from experimental and clinical studies confirming that various polyphenols such as quercetin, curcumin, resveratrol, catechins, and many others could attenuate allergic inflammation, alleviate the symptoms of food allergy, asthma, and allergic rhinitis, and prevent the development of allergic immune response. Conclusively, dietary polyphenols are endowed with great anti-allergic potential and therefore could be used either for preventive approaches or therapeutic interventions in relation to allergic diseases. Limitations in studying and widespread use of polyphenols as well as future research directions are also discussed.},
}
@article {pmid38004205,
year = {2023},
author = {Lundtorp Olsen, C and Massarenti, L and Vendius, VFD and Gürsoy, UK and Van Splunter, A and Bikker, FJ and Gürsoy, M and Damgaard, C and Markvart, M and Belstrøm, D},
title = {Probiotics Partly Suppress the Impact of Sugar Stress on the Oral Microbiota-A Randomized, Double-Blinded, Placebo-Controlled Trial.},
journal = {Nutrients},
volume = {15},
number = {22},
pages = {},
pmid = {38004205},
issn = {2072-6643},
support = {1044-00093B//Innovation Fund Denmark/ ; Not possible//ADM Denmark A/S/ ; },
abstract = {The aim was to test if probiotics counteract oral dysbiosis during 14 days of sugar stress and subsequently help restore oral homeostasis. Eighty healthy individuals received either probiotics (n = 40) or placebo lozenges (n = 40) for 28 days and rinsed with a 10% sucrose solution 6-8 times during the initial 14 days of the trial. Saliva and supragingival samples were collected at baseline, day 14, and day 28. Saliva samples were analyzed for levels of pro-inflammatory cytokines, albumin, and salivary enzyme activity. The supragingival microbiota was characterized according to the Human Oral Microbiome Database. After 14 days of sugar stress, the relative abundance of Porphyromonas species was significantly higher (p = 0.03) and remained significantly elevated at day 28 in the probiotic group compared to the placebo group (p = 0.004). At day 28, the relative abundance of Kingella species was significantly higher in the probiotic group (p = 0.03). Streptococcus gordinii and Neisseria elongata were associated with the probiotic group on day 28, while Streptococcus sobrinus was associated with the placebo group on day 14 and day 28. On day 28, the salivary albumin level was significantly lower in the probiotic group. The present study demonstrates a potential stabilizing effect on the supragingival microbiota mediated by consumption of probiotics during short-term sugar stress.},
}
@article {pmid38004198,
year = {2023},
author = {Suta, S and Ophakas, S and Manosan, T and Honwichit, O and Charoensiddhi, S and Surawit, A and Pongkunakorn, T and Pumeiam, S and Mongkolsucharitkul, P and Pinsawas, B and Sutheeworapong, S and Puangsombat, P and Khoomrung, S and Mayurasakorn, K},
title = {Influence of Prolonged Whole Egg Supplementation on Insulin-like Growth Factor 1 and Short-Chain Fatty Acids Product: Implications for Human Health and Gut Microbiota.},
journal = {Nutrients},
volume = {15},
number = {22},
pages = {},
pmid = {38004198},
issn = {2072-6643},
support = {PRP6105022310, PRP6505030460//Agricultural Research Development Agency/ ; 17108//Mahidol University/ ; },
abstract = {The gut microbiota exert a profound influence on human health and metabolism, with microbial metabolites playing a pivotal role in shaping host physiology. This study investigated the impact of prolonged egg supplementation on insulin-like growth factor 1 (IGF-1) and circulating short-chain fatty acids (SCFAs). In a subset of a cluster-randomized trial, participants aged 8-14 years were randomly assigned into three groups: (1) Whole Egg (WE)-consuming 10 additional eggs per week [n = 24], (2) Protein Substitute (PS)-consuming yolk-free egg substitute equivalent to 10 eggs per week [n = 25], and (3) Control Group (C) [n = 26]. At week 35, IGF-1 levels in WE significantly increased (66.6 ± 27.7 ng/mL, p < 0.05) compared to C, with positive SCFA correlations, except acetate. Acetate was stable in WE, increasing in PS and C. Significant propionate differences occurred between WE and PS (14.8 ± 5.6 μmol/L, p = 0.010). WE exhibited notable changes in the relative abundance of the Bifidobacterium and Prevotella genera. Strong positive SCFA correlations were observed with MAT-CR-H4-C10 and Libanicoccus, while Roseburia, Terrisporobacter, Clostridia_UCG-014, and Coprococcus showed negative correlations. In conclusion, whole egg supplementation improves growth factors that may be related to bone formation and growth; it may also promote benefits to gut microbiota but may not affect SCFAs.},
}
@article {pmid38004180,
year = {2023},
author = {Zhou, J and Ho, V},
title = {Role of Baseline Gut Microbiota on Response to Fiber Intervention in Individuals with Irritable Bowel Syndrome.},
journal = {Nutrients},
volume = {15},
number = {22},
pages = {},
pmid = {38004180},
issn = {2072-6643},
support = {Investigator Initiated Funding Scheme//Nestl&#xe9; Foundation/ ; },
abstract = {Irritable bowel syndrome (IBS) is one of the most prevalent functional gut disorders in the world. Partially hydrolyzed guar gum, a low-viscosity soluble fiber, has shown promise in the management of IBS-related symptoms. In this study, we aimed to determine if an individual's baseline gut microbiota impacted their response to a partially hydrolyzed guar gum intervention. Patients diagnosed with IBS undertook a 90-day intervention and follow-up. IBS symptom severity, tolerability, quality-of-life, and fecal microbiome composition were recorded during this study. Patients with normal microbiota diversity (Shannon index ≥ 3) showed significant improvements to IBS symptom scores, quality-of-life, and better tolerated the intervention compared to patients with low microbiota diversity (Shannon index < 3). Our findings suggest that an individual's baseline microbiome composition exerts a substantial influence on their response to fiber intervention. Future investigations should explore a symbiotic approach to the treatment of IBS.},
}
@article {pmid38004139,
year = {2023},
author = {Song, S and Shon, J and Yang, WR and Kang, HB and Kim, KH and Park, JY and Lee, S and Baik, SY and Lee, KR and Park, YJ},
title = {Short-Term Effects of Weight-Loss Meal Replacement Programs with Various Macronutrient Distributions on Gut Microbiome and Metabolic Parameters: A Pilot Study.},
journal = {Nutrients},
volume = {15},
number = {22},
pages = {},
pmid = {38004139},
issn = {2072-6643},
support = {2021R1A2C2012578//National Research Foundation of Korea/ ; },
abstract = {It has emerged the gut microbiome is crucially linked to metabolic health and obesity. Macronutrient distribution has been discussed as a key parameter in weight-loss programs, but little is known about its impact on the gut microbiome. We investigated the effects of weight-loss meal replacement programs with different macronutrient ratios on the gut microbiota and metabolic parameters in subjects with overweight and obesity. Three low-calorie meal replacement programs with different ratios of carbohydrates, proteins, and lipids were designed: a balanced diet (Group B, 60:15:30), a high-lipid-low-carbohydrate diet (Group F, 35:20:55), and a protein-enriched diet (Group P, 40:25:35). Sixty overweight or obese participants were provided with the meals twice daily for 3 weeks. In all groups, diet intervention resulted in reduced body weight and BMI. The relative abundance of Bacteroidetes and Firmicutes phyla decreased and increased, respectively, which increased the Firmicutes/Bacteroidetes (F/B) ratio in all subjects, particularly in Groups B and P. Alpha- and beta-diversity were augmented at the phylum level in Group P. In conclusion, short-term interventions with weight-loss meal replacement programs increased butyrate-producing bacteria and the F/B ratio. Moreover, the protein-enriched diet significantly increased alpha- and beta-diversity compared to the balanced diet and the high-lipid-low-carbohydrate diet.},
}
@article {pmid38004133,
year = {2023},
author = {Wang, C and Zhu, H and Cheng, Y and Guo, Y and Zhao, Y and Qian, H},
title = {Aqueous Extract of Brassica rapa L.'s Impact on Modulating Exercise-Induced Fatigue via Gut-Muscle Axis.},
journal = {Nutrients},
volume = {15},
number = {22},
pages = {},
pmid = {38004133},
issn = {2072-6643},
support = {Nos. 2020YFC1606800//The Wuxi Taihu Lake Talent Plan, National Key Research and Development Program of China/ ; 2022YFF1101103//The National Key Research and Development Program of China/ ; Q202150//The Youth Talent Project of Wuxi Health Commission/ ; },
abstract = {Exercise-induced fatigue is a common physiological response to prolonged physical activity, often associated with changes in gut microbiota and metabolic responses. This study investigates the potential role of Brassica rapa L. in modulating these responses. Using an animal model subjected to chronic exercise-induced stress, we explored the effects of Brassica rapa L. on fatigue-related biomarkers, energy metabolism genes, inflammatory responses, intestinal integrity, and gut microbiota composition. Our findings revealed that Brassica rapa L. exhibits significant antioxidant activity and effectively modulates physiological responses to fatigue. It influences gene expression related to the tricarboxylic acid (TCA) cycle in muscle tissue through the AMPK/PGC-1α/TFAM signaling pathway. Furthermore, Brassica rapa L. has been found to alleviate inflammation by inhibiting lipopolysaccharide (LPS) infection and suppressing the activation of the NF-κB pathway. It also maintains intestinal integrity and controls Gram-negative bacterial growth. A correlation analysis identified several pathogenic bacteria linked with inflammation and energy metabolism, as well as beneficial probiotic bacteria associated with improved energy metabolism and reduced inflammation. These findings underscore Brassica rapa L.'s potential for managing prolonged exercise-induced fatigue, paving the way for future therapeutic applications. The results highlight its impact on gut microbiota modulation and its role in nutrition science and sports medicine.},
}
@article {pmid38004131,
year = {2023},
author = {Gao, X and Yin, P and Ren, Y and Yu, L and Tian, F and Zhao, J and Chen, W and Xue, Y and Zhai, Q},
title = {Predicting Personalized Diets Based on Microbial Characteristics between Patients with Superficial Gastritis and Atrophic Gastritis.},
journal = {Nutrients},
volume = {15},
number = {22},
pages = {},
pmid = {38004131},
issn = {2072-6643},
support = {32122067//National Natural Science Foundation of China/ ; 32021005//National Natural Science Foundation of China/ ; BK20200084//Natural Science Foundation of Jiangsu Province/ ; ZDRC039//Key Talents Project of "Strengthening Health through Science and Education" of Wuxi Health and Family Planning Commission/ ; LGY2018016//Top Talents Project of "Six-one Project" for High-level Health Talents in Jiangsu Province/ ; },
abstract = {BACKGROUND: gastritis is a common stomach disease with a high global incidence and can potentially develop into gastric cancer. The treatment of gastritis focuses on medication or diets based on national guidelines. However, the specific diet that can alleviate gastritis remains largely unknown.<br><br>METHODS: we propose a microbiota-directed dietary strategy that investigates potential food factors using microbial exogenous metabolites. Given the current lack of understanding of the repeatable characteristics of gastric microbiota, we conducted a meta-analysis to identify the features of gastric bacteria. Local samples were collected as validation cohorts. Furthermore, RevEcoR was employed to identify bacteria's exogenous metabolites, and FooDB was used to retrieve foods that can target specific bacteria.<br><br>RESULTS: Bacteroides, Weissella, Actinomyces, Atopobium, Oribacterium, Peptostreptococcus, and Rothia were biomarkers between superficial gastritis (SG) and atrophic gastritis (AG) (AG_N) without H. pylori infection, whereas Bacillus, Actinomyces, Cutibacterium, Helicobacter, Novosphingobium, Pseudomonas, and Streptococcus were signatures between SG and AG (AG_P) with H. pylori infection. According to the exogenous metabolites, adenosyloobalamin, soybean, common wheat, dates, and barley were regarded as potential candidates for AG_N treatment, while gallate was regarded as a candidate for AG_P treatment.<br><br>CONCLUSIONS: this study firstly profiled the gastric microbiota of AG and SG with or without H. pylori and provided a recommended diet for global AG according to exogenous metabolites.},
}
@article {pmid38004128,
year = {2023},
author = {He, S and Lin, F and Hu, X and Pan, P},
title = {Gut Microbiome-Based Therapeutics in Critically Ill Adult Patients-A Narrative Review.},
journal = {Nutrients},
volume = {15},
number = {22},
pages = {},
pmid = {38004128},
issn = {2072-6643},
support = {z047-02//The national key clinical specialist construction programs of China/ ; },
abstract = {The gut microbiota plays a crucial role in the human microenvironment. Dysbiosis of the gut microbiota is a common pathophysiological phenomenon in critically ill patients. Therefore, utilizing intestinal microbiota to prevent complications and improve the prognosis of critically ill patients is a possible therapeutic direction. The gut microbiome-based therapeutics approach focuses on improving intestinal microbiota homeostasis by modulating its diversity, or treating critical illness by altering the metabolites of intestinal microbiota. There is growing evidence that fecal microbiota transplantation (FMT), selective digestive decontamination (SDD), and microbiota-derived therapies are all effective treatments for critical illness. However, different treatments are appropriate for different conditions, and more evidence is needed to support the selection of optimal gut microbiota-related treatments for different diseases. This narrative review summarizes the curative effects and limitations of microbiome-based therapeutics in different critically ill adult patients, aiming to provide possible directions for gut microbiome-based therapeutics for critically ill patients such as ventilator-associated pneumonia, sepsis, acute respiratory distress syndrome, and COVID-19, etc.},
}
@article {pmid38004098,
year = {2023},
author = {López-Montoya, P and Rivera-Paredez, B and Palacios-González, B and Morán-Ramos, S and López-Contreras, BE and Canizales-Quinteros, S and Salmerón, J and Velázquez-Cruz, R},
title = {Dietary Patterns Are Associated with the Gut Microbiome and Metabolic Syndrome in Mexican Postmenopausal Women.},
journal = {Nutrients},
volume = {15},
number = {22},
pages = {},
pmid = {38004098},
issn = {2072-6643},
support = {Grant numbers: 7876, 87783, 262233, 26267M, SALUD-2010-01-139796, SALUD-2011-01-161930, and CB-2013-01-221628//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; Proyecto FPIS2023-INMEGEN-5251//"Financiamiento de Proyectos de Investigaci&#xf3;n para la Salud" (FPIS) 2023/ ; },
abstract = {Postmenopausal women are at an increased risk of developing metabolic syndrome (MetS) due to hormonal changes and lifestyle factors. Gut microbiota (GM) have been linked to the development of MetS, and they are influenced by dietary habits. However, the interactions between dietary patterns (DP) and the GM of postmenopausal women, as well as their influence on MetS, still need to be understood. The present study evaluated the DP and microbiota composition of postmenopausal Mexican women with MetS and those in a control group. Diet was assessed using a food frequency questionnaire, and the GM were profiled using 16S rRNA gene sequencing. Greater adherence to a "healthy" DP was significantly associated with lower values of MetS risk factors. GM diversity was diminished in women with MetS, and it was negatively influenced by an "unhealthy" DP. Moreover, a higher intake of fats and proteins, as well as lower amounts of carbohydrates, showed a reduction in some of the short-chain fatty acid-producing genera in women with MetS, as well as increases in some harmful bacteria. Furthermore, Roseburia abundance was positively associated with dietary fat and waist circumference, which may explain 7.5% of the relationship between this macronutrient and MetS risk factors. These findings suggest that GM and diet interactions are important in the development of MetS in postmenopausal Mexican women.},
}
@article {pmid38004014,
year = {2023},
author = {Biţă, CE and Scorei, IR and Vreju, AF and Muşetescu, AE and Mogoşanu, GD and Biţă, A and Dinescu, VC and Dinescu, &#x15e;C and Criveanu, C and Bărbulescu, AL and Florescu, A and Ciurea, PL},
title = {Microbiota-Accessible Boron-Containing Compounds in Complex Regional Pain Syndrome.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {59},
number = {11},
pages = {},
pmid = {38004014},
issn = {1648-9144},
support = {POCU/993/6/13/153178//European Social Fund within the Sectorial Operational Program Human Capital 2014-2020/ ; },
abstract = {The microbiota-gut-brain axis has garnered increasing attention in recent years for its role in various health conditions, including neuroinflammatory disorders like complex regional pain syndrome (CRPS). CRPS is a debilitating condition characterized by chronic neuropathic pain, and its etiology and pathophysiology remain elusive. Emerging research suggests that alterations in the gut microbiota composition and function could play a significant role in CRPS development and progression. Our paper explores the implications of microbiota in CRPS and the potential therapeutic role of boron (B). Studies have demonstrated that individuals with CRPS often exhibit dysbiosis, with imbalances in beneficial and pathogenic gut bacteria. Dysbiosis can lead to increased gut permeability and systemic inflammation, contributing to the chronic pain experienced in CRPS. B, an essential trace element, has shown promise in modulating the gut microbiome positively and exerting anti-inflammatory effects. Recent preclinical and clinical studies suggest that B supplementation may alleviate neuropathic pain and improve CRPS symptoms by restoring microbiota balance and reducing inflammation. Our review highlights the complex interplay between microbiota, inflammation, and neuropathic pain in CRPS and underscores the potential of B as a novel therapeutic approach to target the microbiota-gut-brain axis, offering hope for improved management of this challenging condition.},
}
@article {pmid38003917,
year = {2023},
author = {Ispas, S and Tuta, LA and Botnarciuc, M and Ispas, V and Staicovici, S and Ali, S and Nelson-Twakor, A and Cojocaru, C and Herlo, A and Petcu, A},
title = {Metabolic Disorders, the Microbiome as an Endocrine Organ, and Their Relations with Obesity: A Literature Review.},
journal = {Journal of personalized medicine},
volume = {13},
number = {11},
pages = {},
pmid = {38003917},
issn = {2075-4426},
abstract = {UNLABELLED: The etiology of metabolic disorders, such as obesity, has been predominantly associated with the gut microbiota, which is acknowledged as an endocrine organ that plays a crucial role in modulating energy homeostasis and host immune responses. The presence of dysbiosis has the potential to impact the functioning of the intestinal barrier and the gut-associated lymphoid tissues by allowing the transit of bacterial structural components, such as lipopolysaccharides. This, in turn, may trigger inflammatory pathways and potentially lead to the onset of insulin resistance. Moreover, intestinal dysbiosis has the potential to modify the production of gastrointestinal peptides that are linked to the feeling of fullness, hence potentially leading to an increase in food consumption. In this literature review, we discuss current developments, such as the impact of the microbiota on lipid metabolism as well as the processes by which its changes led to the development of metabolic disorders. Several methods have been developed that could be used to modify the gut microbiota and undo metabolic abnormalities.<br><br>METHODS: After researching different databases, we examined the PubMed collection of articles and conducted a literature review.<br><br>RESULTS: After applying our exclusion and inclusion criteria, the initial search yielded 1345 articles. We further used various filters to narrow down our titles analysis and, to be specific to our study, selected the final ten studies, the results of which are included in the Results section.<br><br>CONCLUSIONS: Through gut barrier integrity, insulin resistance, and other influencing factors, the gut microbiota impacts the host's metabolism and obesity. Although the area of the gut microbiota and its relationship to obesity is still in its initial stages of research, it offers great promise for developing new therapeutic targets that may help prevent and cure obesity by restoring the gut microbiota to a healthy condition.},
}
@article {pmid38003905,
year = {2023},
author = {Fawaz, A and Ferraresi, A and Isidoro, C},
title = {Systems Biology in Cancer Diagnosis Integrating Omics Technologies and Artificial Intelligence to Support Physician Decision Making.},
journal = {Journal of personalized medicine},
volume = {13},
number = {11},
pages = {},
pmid = {38003905},
issn = {2075-4426},
abstract = {Cancer is the second major cause of disease-related death worldwide, and its accurate early diagnosis and therapeutic intervention are fundamental for saving the patient's life. Cancer, as a complex and heterogeneous disorder, results from the disruption and alteration of a wide variety of biological entities, including genes, proteins, mRNAs, miRNAs, and metabolites, that eventually emerge as clinical symptoms. Traditionally, diagnosis is based on clinical examination, blood tests for biomarkers, the histopathology of a biopsy, and imaging (MRI, CT, PET, and US). Additionally, omics biotechnologies help to further characterize the genome, metabolome, microbiome traits of the patient that could have an impact on the prognosis and patient's response to the therapy. The integration of all these data relies on gathering of several experts and may require considerable time, and, unfortunately, it is not without the risk of error in the interpretation and therefore in the decision. Systems biology algorithms exploit Artificial Intelligence (AI) combined with omics technologies to perform a rapid and accurate analysis and integration of patient's big data, and support the physician in making diagnosis and tailoring the most appropriate therapeutic intervention. However, AI is not free from possible diagnostic and prognostic errors in the interpretation of images or biochemical-clinical data. Here, we first describe the methods used by systems biology for combining AI with omics and then discuss the potential, challenges, limitations, and critical issues in using AI in cancer research.},
}
@article {pmid38003898,
year = {2023},
author = {Loperfido, A and Cavaliere, C and Begvarfaj, E and Ciofalo, A and D'Erme, G and De Vincentiis, M and Greco, A and Millarelli, S and Bellocchi, G and Masieri, S},
title = {The Impact of Antibiotics and Steroids on the Nasal Microbiome in Patients with Chronic Rhinosinusitis: A Systematic Review According to PICO Criteria.},
journal = {Journal of personalized medicine},
volume = {13},
number = {11},
pages = {},
pmid = {38003898},
issn = {2075-4426},
abstract = {BACKGROUND: The nasal microbiome represents the main environmental factor of the inflammatory process in chronic rhinosinusitis (CRS). Antibiotics and steroids constitute the mainstay of CRS therapies. However, their impact on microbial communities needs to be better understood. This systematic review summarizes the evidence about antibiotics' and steroids' impact on the nasal microbiota in patients with CRS.<br><br>METHODS: The search strategy was conducted in accordance with the PRISMA guidelines for systematic reviews. The authors searched all papers in the three major medical databases (PubMed, Scopus, and Cochrane Library) using the PICO tool (population, intervention, comparison, and outcomes). The search was carried out using a combination of the key terms "Microbiota" or "Microbiome" and "Chronic Rhinosinusitis".<br><br>RESULTS: Overall, 402 papers were identified, and after duplicate removal (127 papers), excluding papers off-topic (154) and for other structural reasons (110), papers were assessed for eligibility; finally, only 11 papers were included and summarized in the present systematic review. Some authors used only steroids, other researchers used only antibiotics, and others used both antibiotics and steroids. With regard to the use of steroids as exclusive medical treatment, topical mometasone and budesonide were investigated. With regard to the use of antibiotics as exclusive medical treatments, clarithromycin, doxycycline, roxithromycin, and amoxicillin clavulanate were investigated. Regarding the use of both antibiotics and steroids, two associations were investigated: systemic prednisone combined with amoxicillin clavulanate and topical budesonide combined with azithromycin.<br><br>CONCLUSIONS: The impact that therapies can have on the nasal microbiome of CRS patients is very varied. Further studies are needed to understand the role of the nasal microbiome, prevent CRS, and improve therapeutic tools for personalized medicine tailored to the individual patient.},
}
@article {pmid38003804,
year = {2023},
author = {Alsholi, DM and Yacoub, GS and Rehman, AU and Ullah, H and Khan, AI and Deng, T and Siddiqui, NZ and Alioui, Y and Farooqui, NA and Elkharti, M and Li, Y and Wang, L and Xin, Y},
title = {Lactobacillus rhamnosus Attenuates Cisplatin-Induced Intestinal Mucositis in Mice via Modulating the Gut Microbiota and Improving Intestinal Inflammation.},
journal = {Pathogens (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
pmid = {38003804},
issn = {2076-0817},
support = {2019GBJ011630//Chinese Scholarship Council grant number/ ; 31600614, 82072953//the National Nature Science Foundation of China/ ; 2023JJ12SN029//Dalian Science and Technology Innovation Fund Application Foundation Project/ ; 2021-MS-287//Liaoning Natural Science Foundation Program/ ; 2021RJ12//Dalian outstanding young scientific and technological talents/ ; },
abstract = {Lactobacillus rhamnosus (LBS) is a well-documented probiotic strain in oncology and has a pivotal role in clinical applications. Here, we have investigated the protective effect of Lactobacillus rhamnosus on intestinal mucositis induced by cisplatin (CP) and explored the underlying mechanisms targeting inflammatory proteins, as well as the histological changes in the intestinal tissue of mice, in addition, the bacterial strains that may be related to the health-enhancing properties. BALB/c mice were pre-treated with or without LBS via oral gavage, followed by mucositis induction with cisplatin. Our results revealed that the LBS-treated groups significantly attenuated proinflammatory cytokine levels (IL-1β, IL-6, and TNF-α) compared to the CP group. Furthermore, LBS mitigated the damaged tight junction integrity caused by CP via up-regulating the levels of claudin, occludin, ZO-1, and mucin-2 protein (MUC-2). Finally, the 16S rRNA fecal microbiome genomic analysis showed that LBS administration enhanced the growth of beneficial bacteria, i.e., Firmicutes and Lachnospiraceae, while the relative abundance of the opportunistic bacteria Bacteroides and Proteobacteria decreased. Collectively, LBS was found to beneficially modulate microbial composition structure and functions and enrich the ecological diversity in the gut.},
}
@article {pmid38003787,
year = {2023},
author = {Thompson, MEH and Shrestha, A and Rinne, J and Limay-Rios, V and Reid, L and Raizada, MN},
title = {The Cultured Microbiome of Pollinated Maize Silks Shifts after Infection with Fusarium graminearum and Varies by Distance from the Site of Pathogen Inoculation.},
journal = {Pathogens (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
pmid = {38003787},
issn = {2076-0817},
support = {054810//Grain Farmers of Ontario/ ; 030356, 030564//Ministry of Agriculture, Food and Rural Affairs/ ; 401424, 401663, 400924//Natural Sciences and Engineering Research Council/ ; },
abstract = {Styles transmit pollen-derived sperm nuclei from pollen to ovules, but also transmit environmental pathogens. The microbiomes of styles are likely important for reproduction/disease, yet few studies exist. Whether style microbiome compositions are spatially responsive to pathogens is unknown. The maize pathogen Fusarium graminearum enters developing grain through the style (silk). We hypothesized that F. graminearum treatment shifts the cultured transmitting silk microbiome (TSM) compared to healthy silks in a distance-dependent manner. Another objective of the study was to culture microbes for future application. Bacteria were cultured from husk-covered silks of 14 F. graminearum-treated diverse maize genotypes, proximal (tip) and distal (base) to the F. graminearum inoculation site. Long-read 16S sequences from 398 isolates spanned 35 genera, 71 species, and 238 OTUs. More bacteria were cultured from F. graminearum-inoculated tips (271 isolates) versus base (127 isolates); healthy silks were balanced. F. graminearum caused a collapse in diversity of ~20-25% across multiple taxonomic levels. Some species were cultured exclusively or, more often, from F. graminearum-treated silks (e.g., Delftia acidovorans, Klebsiella aerogenes, K. grimontii, Pantoea ananatis, Stenotrophomonas pavanii). Overall, the results suggest that F. graminearum alters the TSM in a distance-dependent manner. Many isolates matched taxa that were previously identified using V4-MiSeq (core and F. graminearum-induced), but long-read sequencing clarified the taxonomy and uncovered greater diversity than was initially predicted (e.g., within Pantoea). These isolates represent the first comprehensive cultured collection from pathogen-treated maize silks to facilitate biocontrol efforts and microbial marker-assisted breeding.},
}
@article {pmid38003760,
year = {2023},
author = {Soldati, KR and Jiang, Y and Brandt, BW and Exterkate, RAM and Buijs, MJ and Nazmi, K and Kaman, WE and Cheng, L and Bikker, FJ and Crielaard, W and Zandim-Barcelos, DL and Deng, DM},
title = {Differential Modulation of Saliva-Derived Microcosm Biofilms by Antimicrobial Peptide LL-31 and D-LL-31.},
journal = {Pathogens (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
pmid = {38003760},
issn = {2076-0817},
abstract = {Microbiome modulation, aiming to restore a health-compatible microbiota, is a novel strategy to treat periodontitis. This study evaluated the modulation effects of antimicrobial peptide LL-31 and its D-enantiomer (D-LL-31) on saliva-derived microcosm biofilms, spiked with or without Porphyromonas gingivalis. To this end, one-day-old biofilms were incubated for 24 h with biofilm medium alone, or medium containing 40 µM LL-31 or D-LL-31, after which biofilms were grown for 5 days. Biofilms were assessed at 1 day and 5 days after intervention for the total viable cell counts, dipeptidyl peptidase IV (DPP4) activity, P. gingivalis amount (by qPCR) and microbial composition (by sequencing). The results showed that D-LL-31, not LL-31, significantly reduced the total viable cell counts, the P. gingivalis amount, and the DPP4 activity of the biofilms spiked with P. gingivalis, but only at 1 day after intervention. In the biofilms spiked with P. gingivalis, D-LL-31 tended to reduce the α-diversity and the compositional shift of the biofilms in time as compared to the control and LL-31 groups. In conclusion, D-LL-31 showed a better performance than LL-31 in biofilm modulation. The biofilm modulation function of the peptides could be impaired when the biofilms were in a severely dysbiotic state.},
}
@article {pmid38003752,
year = {2023},
author = {Garrigós, M and Garrido, M and Panisse, G and Veiga, J and Martínez-de la Puente, J},
title = {Interactions between West Nile Virus and the Microbiota of Culex pipiens Vectors: A Literature Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
pmid = {38003752},
issn = {2076-0817},
support = {PID2020-118205GB-I00//Ministerio Espa&#xf1;ol de Ciencia e Innovaci&#xf3;n/ ; PRE2021-098544//Ministerio Espa&#xf1;ol de Ciencia e Innovaci&#xf3;n/ ; FJC2021-048057-I//Ministerio Espa&#xf1;ol de Ciencia e Innovaci&#xf3;n/ ; Mar&#xed;a Zambrano//Ministerio Espa&#xf1;ol de Universidades/ ; Margarita Salas//Ministerio Espa&#xf1;ol de Universidades/ ; P21_00049//Junta de Andaluc&#xed;a, Consejer&#xed;a de Universidad, Investigaci&#xf3;n e Innovaci&#xf3;n/ ; },
abstract = {The flavivirus West Nile virus (WNV) naturally circulates between mosquitoes and birds, potentially affecting humans and horses. Different species of mosquitoes play a role as vectors of WNV, with those of the Culex pipiens complex being particularly crucial for its circulation. Different biotic and abiotic factors determine the capacity of mosquitoes for pathogen transmission, with the mosquito gut microbiota being recognized as an important one. Here, we review the published studies on the interactions between the microbiota of the Culex pipiens complex and WNV infections in mosquitoes. Most articles published so far studied the interactions between bacteria of the genus Wolbachia and WNV infections, obtaining variable results regarding the directionality of this relationship. In contrast, only a few studies investigate the role of the whole microbiome or other bacterial taxa in WNV infections. These studies suggest that bacteria of the genera Serratia and Enterobacter may enhance WNV development. Thus, due to the relevance of WNV in human and animal health and the important role of mosquitoes of the Cx. pipiens complex in its transmission, more research is needed to unravel the role of mosquito microbiota and those factors affecting this microbiota on pathogen epidemiology. In this respect, we finally propose future lines of research lines on this topic.},
}
@article {pmid38003692,
year = {2023},
author = {Maslennikov, R and Poluektova, E and Zolnikova, O and Sedova, A and Kurbatova, A and Shulpekova, Y and Dzhakhaya, N and Kardasheva, S and Nadinskaia, M and Bueverova, E and Nechaev, V and Karchevskaya, A and Ivashkin, V},
title = {Gut Microbiota and Bacterial Translocation in the Pathogenesis of Liver Fibrosis.},
journal = {International journal of molecular sciences},
volume = {24},
number = {22},
pages = {},
doi = {10.3390/ijms242216502},
pmid = {38003692},
issn = {1422-0067},
abstract = {Cirrhosis is the end result of liver fibrosis in chronic liver diseases. Studying the mechanisms of its development and developing measures to slow down and regress it based on this knowledge seem to be important tasks for medicine. Currently, disorders of the gut-liver axis have great importance in the pathogenesis of cirrhosis. However, gut dysbiosis, which manifests as increased proportions in the gut microbiota of Bacilli and Proteobacteria that are capable of bacterial translocation and a decreased proportion of Clostridia that strengthen the intestinal barrier, occurs even at the pre-cirrhotic stage of chronic liver disease. This leads to the development of bacterial translocation, a process by which those microbes enter the blood of the portal vein and then the liver tissue, where they activate Kupffer cells through Toll-like receptor 4. In response, the Kupffer cells produce profibrogenic cytokines, which activate hepatic stellate cells, stimulating their transformation into myofibroblasts that produce collagen and other elements of the extracellular matrix. Blocking bacterial translocation with antibiotics, probiotics, synbiotics, and other methods could slow down the progression of liver fibrosis. This was shown in a number of animal models but requires further verification in long-term randomized controlled trials with humans.},
}
@article {pmid38003647,
year = {2023},
author = {Angelova, IY and Kovtun, AS and Averina, OV and Koshenko, TA and Danilenko, VN},
title = {Unveiling the Connection between Microbiota and Depressive Disorder through Machine Learning.},
journal = {International journal of molecular sciences},
volume = {24},
number = {22},
pages = {},
doi = {10.3390/ijms242216459},
pmid = {38003647},
issn = {1422-0067},
support = {20-14-00132//Russian Science Foundation/ ; },
abstract = {In the last few years, investigation of the gut-brain axis and the connection between the gut microbiota and the human nervous system and mental health has become one of the most popular topics. Correlations between the taxonomic and functional changes in gut microbiota and major depressive disorder have been shown in several studies. Machine learning provides a promising approach to analyze large-scale metagenomic data and identify biomarkers associated with depression. In this work, machine learning algorithms, such as random forest, elastic net, and You Only Look Once (YOLO), were utilized to detect significant features in microbiome samples and classify individuals based on their disorder status. The analysis was conducted on metagenomic data obtained during the study of gut microbiota of healthy people and patients with major depressive disorder. The YOLO method showed the greatest effectiveness in the analysis of the metagenomic samples and confirmed the experimental results on the critical importance of a reduction in the amount of Faecalibacterium prausnitzii for the manifestation of depression. These findings could contribute to a better understanding of the role of the gut microbiota in major depressive disorder and potentially lead the way for novel diagnostic and therapeutic strategies.},
}
@article {pmid38003531,
year = {2023},
author = {Šešelja, K and Bazina, I and Vrecl, M and Farger, J and Schicht, M and Paulsen, F and Baus Lončar, M and Pirman, T},
title = {Tff3 Deficiency Differentially Affects the Morphology of Male and Female Intestines in a Long-Term High-Fat-Diet-Fed Mouse Model.},
journal = {International journal of molecular sciences},
volume = {24},
number = {22},
pages = {},
doi = {10.3390/ijms242216342},
pmid = {38003531},
issn = {1422-0067},
support = {IP-06-2016-2717//Croatian Science Foundation/ ; 2014-2020//European Structural Found (financial support for Ph.D student)/ ; German project No. 57448642//Bilateral Croatian -Germany project of student exchange/ ; P4-0097//Slovenian Research Agency/ ; P4-0053//Slovenian Research Agency/ ; },
abstract = {Trefoil factor family protein 3 (Tff3) protects the gastrointestinal mucosa and has a complex mode of action in different tissues. Here, we aimed to determine the effect of Tff3 deficiency on intestinal tissues in a long-term high-fat-diet (HFD)-fed model. A novel congenic strain without additional metabolically relevant mutations (Tff3-/-/C57Bl6NCrl strain, male and female) was used. Wild type (Wt) and Tff3-deficient mice of both sexes were fed a HFD for 36 weeks. Long-term feeding of a HFD induces different effects on the intestinal structure of Tff3-deficient male and female mice. For the first time, we found sex-specific differences in duodenal morphology. HFD feeding reduced microvilli height in Tff3-deficient females compared to that in Wt females, suggesting a possible effect on microvillar actin filament dynamics. These changes could not be attributed to genes involved in ER and oxidative stress, apoptosis, or inflammation. Tff3-deficient males exhibited a reduced cecal crypt depth compared to that of Wt males, but this was not the case in females. Microbiome-related short-chain fatty acid content was not affected by Tff3 deficiency in HFD-fed male or female mice. Sex-related differences due to Tff3 deficiency imply the need to consider both sexes in future studies on the role of Tff in intestinal function.},
}
@article {pmid38003489,
year = {2023},
author = {Pai, AH and Wang, YW and Lu, PC and Wu, HM and Xu, JL and Huang, HY},
title = {Gut Microbiome-Estrobolome Profile in Reproductive-Age Women with Endometriosis.},
journal = {International journal of molecular sciences},
volume = {24},
number = {22},
pages = {},
doi = {10.3390/ijms242216301},
pmid = {38003489},
issn = {1422-0067},
support = {CMRPG3G1981, CMRPG3K0782//Linkou Chang Gung Memorial Hospital/ ; },
abstract = {Microbiota is associated with our bodily functions and microenvironment. A healthy, balanced gut microbiome not only helps maintain mucosal integrity, prevents translocation of bacterial content, and contributes to immune status, but also associates with estrogen metabolism. Gut dysbiosis and estrobolome dysfunction have hence been linked to certain estrogen-dependent diseases, including endometriosis. While prior studies on microbiomes and endometriosis have shown conflicting results, most of the observed microbial differences are seen in the genital tract. This case-control study of reproductive-age women utilizes their fecal and urine samples for enzymatic, microbial, and metabolic studies to explore if patients with endometriosis have distinguishable gut microbiota or altered estrogen metabolism. While gut β-glucuronidase activities, microbial diversity, and abundance did not vary significantly between patients with or without endometriosis, fecal samples of patients with endometriosis were more enriched by the Erysipelotrichia class and had higher folds of four estrogen/estrogen metabolites. Further studies are needed to elucidate what these results imply and whether there indeed is an association or causation between gut microbiota and endometriosis.},
}
@article {pmid38003359,
year = {2023},
author = {Siebieszuk, A and Sejbuk, M and Witkowska, AM},
title = {Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping.},
journal = {International journal of molecular sciences},
volume = {24},
number = {22},
pages = {},
doi = {10.3390/ijms242216169},
pmid = {38003359},
issn = {1422-0067},
abstract = {The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.},
}
@article {pmid38003317,
year = {2023},
author = {Liu, L and Mahalak, KK and Bobokalonov, JT and Narrowe, AB and Firrman, J and Lemons, JMS and Bittinger, K and Hu, W and Jones, SM and Moustafa, AM},
title = {Impact of Ivermectin on the Gut Microbial Ecosystem.},
journal = {International journal of molecular sciences},
volume = {24},
number = {22},
pages = {},
doi = {10.3390/ijms242216125},
pmid = {38003317},
issn = {1422-0067},
support = {In-House Project 8072-41000-108-00-D//United States Department of Agriculture/ ; },
abstract = {Ivermectin is a an anti-helminthic that is critical globally for both human and veterinary care. To the best of our knowledge, information available regarding the influence of ivermectin (IVM) on the gut microbiota has only been collected from diseased donors, who were treated with IVM alone or in combination with other medicines. Results thus obtained were influenced by multiple elements beyond IVM, such as disease, and other medical treatments. The research presented here investigated the impact of IVM on the gut microbial structure established in a Triple-SHIME[®] (simulator of the human intestinal microbial ecosystem), using fecal material from three healthy adults. The microbial communities were grown using three different culture media: standard SHIME media and SHIME media with either soluble or insoluble fiber added (control, SF, ISF). IVM introduced minor and temporary changes to the gut microbial community in terms of composition and metabolite production, as revealed by 16S rRNA amplicon sequencing analysis, flow cytometry, and GC-MS. Thus, it was concluded that IVM is not expected to induce dysbiosis or yield adverse effects if administered to healthy adults. In addition, the donor's starting community influences the relationship between IVM and the gut microbiome, and the soluble fiber component in feed could protect the gut microbiota from IVM; an increase in short-chain fatty acid production was predicted by PICRUSt2 and detected with IVM treatment.},
}
@article {pmid38003306,
year = {2023},
author = {Xiong, Q and Yang, J and Ni, S},
title = {Microbiome-Mediated Protection against Pathogens in Woody Plants.},
journal = {International journal of molecular sciences},
volume = {24},
number = {22},
pages = {},
doi = {10.3390/ijms242216118},
pmid = {38003306},
issn = {1422-0067},
support = {2022YFD2201900, 2021YDF22011202//National Key Research and Development Program/ ; 32122056, 42011045, 31600512//National Natural Science Foundation of China/ ; CX-21-3045//Jiangsu Agriculture Science and Technology Independent Innovation Fund/ ; 2021M691605//China Postdoctoral Science Foundation/ ; 2021K641C//Postdoctoral Science Foundation of Jiangsu Province/ ; SJCX23_0350//Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; 2022NFUSPITP0364&#xff0c;202310298135Y//Students Practice Innovation and Training Program of Nanjing Forestry University/ ; },
abstract = {Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.},
}
@article {pmid38003242,
year = {2023},
author = {Hardman, SJ and Shackley, FM and Ugonna, K and Darton, TC and Rigby, AS and Bogaert, D and Binkowska, JM and Condliffe, AM},
title = {Seasonal Azithromycin Use in Paediatric Protracted Bacterial Bronchitis Does Not Promote Antimicrobial Resistance but Does Modulate the Nasopharyngeal Microbiome.},
journal = {International journal of molecular sciences},
volume = {24},
number = {22},
pages = {},
doi = {10.3390/ijms242216053},
pmid = {38003242},
issn = {1422-0067},
support = {1589//Sir Halley Stewart Trust/ ; ANTSRG 03/2018//Antibiotic Research UK/ ; NIHR200636//Florey Institute AMR Research Capital Funding/ ; 50059609//Bassetlaw Fellowship Scheme/ ; },
abstract = {Protracted bacterial bronchitis (PBB) causes chronic wet cough for which seasonal azithromycin is increasingly used to reduce exacerbations. We investigated the impact of seasonal azithromycin on antimicrobial resistance and the nasopharyngeal microbiome. In an observational cohort study, 50 children with PBB were enrolled over two consecutive winters; 25/50 at study entry were designated on clinical grounds to take azithromycin over the winter months and 25/50 were not. Serial nasopharyngeal swabs were collected during the study period (12-20 months) and cultured bacterial isolates were assessed for antimicrobial susceptibility. 16S rRNA-based sequencing was performed on a subset of samples. Irrespective of azithromycin usage, high levels of azithromycin resistance were found; 73% of bacteria from swabs in the azithromycin group vs. 69% in the comparison group. Resistance was predominantly driven by azithromycin-resistant S. pneumoniae, yet these isolates were mostly erythromycin susceptible. Analysis of 16S rRNA-based sequencing revealed a reduction in within-sample diversity in response to azithromycin, but only in samples of children actively taking azithromycin at the time of swab collection. Actively taking azithromycin at the time of swab collection significantly contributed to dissimilarity in bacterial community composition. The discrepancy between laboratory detection of azithromycin and erythromycin resistance in the S. pneumoniae isolates requires further investigation. Seasonal azithromycin for PBB did not promote antimicrobial resistance over the study period, but did perturb the microbiome.},
}
@article {pmid38003202,
year = {2023},
author = {Clough, J and Schwab, S and Mikac, K},
title = {Gut Microbiome Profiling of the Endangered Southern Greater Glider (Petauroides volans) after the 2019-2020 Australian Megafire.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {22},
pages = {},
doi = {10.3390/ani13223583},
pmid = {38003202},
issn = {2076-2615},
support = {Regional Bushfire Recovery for Multiregional Species and Strategic Projects Program (2021-2022)//Australian Department of Industry, Science, Energy and Resources/ ; },
abstract = {Studying the gut microbiome can provide valuable insights into animal health and inform the conservation management of threatened wildlife. Gut microbiota play important roles in regulating mammalian host physiology, including digestion, energy metabolism and immunity. Dysbiosis can impair such physiological processes and compromise host health, so it is essential that the gut microbiome be considered in conservation planning. The southern greater glider (Petauroides volans) is an endangered arboreal marsupial that faced widespread habitat fragmentation and population declines following the 2019-2020 Australian bushfire season. This study details baseline data on the gut microbiome of this species. The V3-V4 region of the 16S rRNA gene was amplified from scats collected from individuals inhabiting burnt and unburnt sites across southeastern Australia and sequenced to determine bacterial community composition. Southern greater glider gut microbiomes were characterised by high relative abundances of Firmicutes and Bacteroidota, which is consistent with that reported for other marsupial herbivores. Significant differences in gut microbial diversity and community structure were detected among individuals from different geographic locations. Certain microbiota and functional orthologues were also found to be significantly differentially abundant between locations. The role of wildfire in shaping southern greater glider gut microbiomes was shown, with some significant differences in the diversity and abundance of microbiota detected between burnt and unburnt sites. Overall, this study details the first data on greater glider (Petauroides) gut microbiomes, laying the foundation for future studies to further explore relationships between microbial community structure, environmental stressors and host health.},
}
@article {pmid38003162,
year = {2023},
author = {Anderson, JG and Rojas, CA and Scarsella, E and Entrolezo, Z and Jospin, G and Hoffman, SL and Force, J and MacLellan, RH and Peak, M and Shope, BH and Tsugawa, AJ and Ganz, HH},
title = {The Oral Microbiome across Oral Sites in Cats with Chronic Gingivostomatitis, Periodontal Disease, and Tooth Resorption Compared with Healthy Cats.},
journal = {Animals : an open access journal from MDPI},
volume = {13},
number = {22},
pages = {},
doi = {10.3390/ani13223544},
pmid = {38003162},
issn = {2076-2615},
abstract = {Feline chronic gingivostomatitis (FCGS) is a chronic mucosal and gingival inflammatory disease in which pathogenesis remains unclear. Interactions between the host inflammatory process, the host immune response, and the oral microbiome are implicated in this pathogenesis. To begin to understand this disease and the impact of the microbiome to host inflammatory disease states, we collected sterile noninvasive plaque biofilm samples from ten distinct sites within the oral cavity in cats with stomatitis (n = 12), healthy cats (n = 9), and cats with tooth resorption or periodontitis (n = 11). Analysis of full-length 16S rRNA gene sequences indicated that the microbiomes of cats with FCGS presented marked dysbiosis at multiple oral sites. Additionally, microbiome beta diversity varied with oral condition, indicating that stomatitis, periodontitis, and/or tooth resorption influence the microbiome differently. Lastly, we found that the microbiomes of swabs taken from the oral cavity were comparable to those taken from plaque using endodontic paper points, validating this as another sampling method. Collectively, our work furthers our understanding of the dysbiosis and composition of bacteria in the oral microbiome in FCGS, with hopes of contributing to the prevention, diagnosis, and treatment of this challenging condition in felines.},
}
@article {pmid38002951,
year = {2023},
author = {Diao, F and Li, Y and Gao, X and Luo, J and Zhu, X and Wang, L and Zhang, K and Li, D and Ji, J and Cui, J},
title = {Response of the Propylea japonica Microbiota to Treatment with Cry1B Protein.},
journal = {Genes},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/genes14112008},
pmid = {38002951},
issn = {2073-4425},
abstract = {Propylea japonica (Thunberg) (Coleoptera: Coccinellidae) is a dominant natural enemy of insect pests in farmland ecosystems. It also serves as an important non-target insect for environmental safety evaluations of transgenic crops. Widespread planting of transgenic crops may result in direct or indirect exposure of P. japonica to recombinant Bacillus thuringiensis (Bt) protein, which may in turn affect the biological performance of this natural enemy by affecting the P. japonica microflora. However, the effects of Bt proteins (such as Cry1B) on the P. japonica microbiota are currently unclear. Here, we used a high-throughput sequencing method to investigate differences in the P. japonica microbiota resulting from treatment with Cry1B compared to a sucrose control. The results demonstrated that the P. japonica microbiome was dominated by Firmicutes at the phylum level and by Staphylococcus at the genus level. Within-sample (α) diversity indices demonstrated a high degree of consistency between the microbial communities of P. japonica treated with the sucrose control and those treated with 0.25 or 0.5 mg/mL Cry1B. Furthermore, there were no significant differences in the abundance of any taxa after treatment with 0.25 mg/mL Cry1B for 24 or 48 h, and treatment with 0.5 mg/mL Cry1B for 24 or 48 h led to changes only in Staphylococcus, a member of the phylum Firmicutes. Treatment with a high Cry1B concentration (1.0 mg/mL) for 24 or 48 h caused significant changes in the abundance of specific taxa (e.g., Gemmatimonades, Patescibacteria, Thauera, and Microbacterium). However, compared with the control, most taxa remained unchanged. The statistically significant differences may have been due to the stimulatory effects of treatment with a high concentration of Cry1B. Overall, the results showed that Cry1B protein could alter endophytic bacterial community abundance, but not composition, in P. japonica. The effects of Bt proteins on endophytes and other parameters in non-target insects require further study. This study provides data support for the safety evaluation of transgenic plants.},
}
@article {pmid38002943,
year = {2023},
author = {Li, G and Yang, L and Chen, J and Zhang, X},
title = {Robust Differential Abundance Analysis of Microbiome Sequencing Data.},
journal = {Genes},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/genes14112000},
pmid = {38002943},
issn = {2073-4425},
support = {R01GM144351/NH/NIH HHS/United States ; },
abstract = {It is well known that the microbiome data are ridden with outliers and have heavy distribution tails, but the impact of outliers and heavy-tailedness has yet to be examined systematically. This paper investigates the impact of outliers and heavy-tailedness on differential abundance analysis (DAA) using the linear models for the differential abundance analysis (LinDA) method and proposes effective strategies to mitigate their influence. The presence of outliers and heavy-tailedness can significantly decrease the power of LinDA. We investigate various techniques to address outliers and heavy-tailedness, including generalizing LinDA into a more flexible framework that allows for the use of robust regression and winsorizing the data before applying LinDA. Our extensive numerical experiments and real-data analyses demonstrate that robust Huber regression has overall the best performance in addressing outliers and heavy-tailedness.},
}
@article {pmid38002858,
year = {2023},
author = {Bettag, J and Goldenberg, D and Carter, J and Morfin, S and Borsotti, A and Fox, J and ReVeal, M and Natrop, D and Gosser, D and Kolli, S and Jain, AK},
title = {Gut Microbiota to Microglia: Microbiome Influences Neurodevelopment in the CNS.},
journal = {Children (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/children10111767},
pmid = {38002858},
issn = {2227-9067},
abstract = {The brain is traditionally viewed as an immunologically privileged site; however, there are known to be multiple resident immune cells that influence the CNS environment and are reactive to extra-CNS signaling. Microglia are an important component of this system, which influences early neurodevelopment in addition to modulating inflammation and regenerative responses to injury and infection. Microglia are influenced by gut microbiome-derived metabolites, both as part of their normal function and potentially in pathological patterns that may induce neurodevelopmental disabilities or behavioral changes. This review aims to summarize the mounting evidence indicating that, not only is the Gut-Brain axis mediated by metabolites and microglia throughout an organism's lifetime, but it is also influenced prenatally by maternal microbiome and diet, which holds implications for both early neuropathology and neurodevelopment.},
}
@article {pmid38002796,
year = {2023},
author = {Wong, PY and Yip, C and Lemberg, DA and Day, AS and Leach, ST},
title = {Evolution of a Pathogenic Microbiome.},
journal = {Journal of clinical medicine},
volume = {12},
number = {22},
pages = {},
doi = {10.3390/jcm12227184},
pmid = {38002796},
issn = {2077-0383},
abstract = {The process of microbiome development arguably begins before birth. Vertical transmission of bacteria from the mother to the infant is a keystone event in microbiome development. Subsequent to birth, the developing microbiome is vulnerable to influence from a wide range of factors. Additionally, the microbiome can influence the health and development of the host infant. This intricate interaction of the gastrointestinal microbiome and the host has been described as both symbiotic and dysbiotic. Defining these terms, a symbiotic microbiome is where the microbiome and host provide mutual benefit to each other. A pathogenic microbiome, or more precisely a gastrointestinal microbiome associated with disease, is increasing described as dysbiotic. This review seeks to investigate the factors that contribute to evolving a disease-causing or 'dysbiotic' microbiome. This review covers the development of the gastrointestinal microbiome in infants, the interaction of the microbiome with the host, and its contribution to host immunity and investigates specific features of the gastrointestinal microbiome that are associated with disease.},
}
@article {pmid38002788,
year = {2023},
author = {Velho, RV and Werner, F and Mechsner, S},
title = {Endo Belly: What Is It and Why Does It Happen?-A Narrative Review.},
journal = {Journal of clinical medicine},
volume = {12},
number = {22},
pages = {},
doi = {10.3390/jcm12227176},
pmid = {38002788},
issn = {2077-0383},
abstract = {Endometriosis is a chronic inflammatory disease where endometrial-like lesions settle outside the uterus, resulting in extensive inflammatory reactions. It is a complex disease that presents with a range of symptoms, with pain and infertility being the most common. Along with severe dysmenorrhea, cyclic and acyclic lower abdominal pain, cyclic dysuria and dyschezia, dyspareunia, and infertility, there are also nonspecific complaints that can cause confusion and make endometriosis the chameleon among gynecological diseases. These symptoms include unspecific intestinal complaints, cyclic diarrhea, but also constipation, nausea, vomiting, and stomach complaints. It appears that in addition to general bowel symptoms, there are also specific symptoms related to endometriosis such as cyclic bloating of the abdomen, known as endo belly. During the second half of the menstrual cycle leading up to menstruation, the abdomen becomes increasingly bloated causing discomfort and pain due to elevated sensitivity of the intestinal wall. Patients with endometriosis exhibit a reduced stretch pain threshold of the intestinal wall. Here, we review the endo belly, for the first time, pathophysiology and the influence of other diseases (such as irritable bowel syndrome-IBS), microbiome, hormonal levels, inflammation, and diet on the presentation of this condition.},
}
@article {pmid38002515,
year = {2023},
author = {Kulkarni, MS and Miller, BC and Mahani, M and Mhaskar, R and Tsalatsanis, A and Jain, S and Yadav, H},
title = {Poor Oral Health Linked with Higher Risk of Alzheimer's Disease.},
journal = {Brain sciences},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/brainsci13111555},
pmid = {38002515},
issn = {2076-3425},
abstract = {Alzheimer's disease (AD) is a multifactorial neurodegenerative disease characterized by cognitive and behavioral changes in older adults. Emerging evidence suggests poor oral health is associated with AD, but there is a lack of large-scale clinical studies demonstrating this link. Herein, we used the TriNetX database to generate clinical cohorts and assess the risk of AD and survival among >30 million de-identified subjects with normal oral health (n = 31,418,814) and poor oral health (n = 1,232,751). There was a greater than two-fold increase in AD risk in the poor oral health cohort compared to the normal oral health group (risk ratio (RR): 2.363, (95% confidence interval: 2.326, 2.401)). To reduce potential bias, we performed retrospective propensity score matching for age, gender, and multiple laboratory measures. After matching, the cohorts had no significant differences in survival probability. Furthermore, when comparing multiple oral conditions, diseases related to tooth loss were the most significant risk factor for AD (RR: 3.186, (95% CI: 3.007, 3.376)). Our results suggest that oral health may be important in AD risk, regardless of age, gender, or laboratory measures. However, more large-scale cohort studies are necessary to validate these findings and further evaluate links between oral health and AD.},
}
@article {pmid38002290,
year = {2023},
author = {Saha, S and Boesch, C and Maycock, J and Wood, S and Do, T},
title = {Sweet Orange Juice Processing By-Product Extracts: A Caries Management Alternative to Chlorhexidine.},
journal = {Biomolecules},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/biom13111607},
pmid = {38002290},
issn = {2218-273X},
abstract = {Dental caries is one of the most prevalent chronic diseases globally in both children and adults. This study investigated the potential of industrial sweet orange waste extracts (ISOWE) as a substitute for chlorhexidine (CHX) in managing dental caries. First, the cytotoxicity of ISOWE (40, 80, 120 mg/mL) and CHX (0.1 and 0.2%) on buccal epithelial cells was determined. ISOWE exhibited no overall toxicity, whereas CHX strongly affected cell viability. The combination of ISOWE and CHX significantly enhanced cell proliferation compared to CHX alone. Next, the antimicrobial efficacy of ISOWE, CHX, and their combination was assessed against a 7-day complex biofilm model inoculated with oral samples from human volunteers. CHX exhibited indiscriminate antimicrobial action, affecting both pathogenic and health-associated oral microorganisms. ISOWE demonstrated lower antimicrobial efficacy than CHX but showed enhanced efficacy against pathogenic species while preserving the oral microbiome's balance. When applied to a cariogenic biofilm, the combined treatment of ISOWE with 0.1% CHX showed similar efficacy to 0.2% CHX treatment alone. Overall, the findings suggest that ISOWE is a promising natural anti-cariogenic agent with lower toxicity and enhanced selectivity for pathogenic species compared to CHX.},
}
@article {pmid38002184,
year = {2023},
author = {Tang, Z and Zhan, L and He, R and Zhou, Y and Tang, Q and Liu, Z and Zhang, S and Liu, A},
title = {Hepatoprotective Effect of Tea Composite Solid Beverage on Alcohol-Caused Rat Liver Injury.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {22},
pages = {},
doi = {10.3390/foods12224126},
pmid = {38002184},
issn = {2304-8158},
support = {2022YFE011120 &amp; 2021YFD1601104//National Key R&amp;D Project/ ; 2021NK1020-3//Key R&amp;D Project of Hunan Province/ ; No. 2021JJ40251//Natural Science Foundation of Hunan Province Youth Fund/ ; },
abstract = {Alcoholic liver disease (ALD) remains a major cause of liver-related morbidity and mortality worldwide. Tea polyphenols (TPs) possess strong antioxidant activity; cassia seed extract (CSE) has the effect of brightening the eyes; and Ampelopsis grossedentata extract (AGE) has the function of protecting the liver. However, the synergistic hepatoprotective effect of TP, AGE and CSE as a joint formulation is unknown. This study aimed to investigate the role of a tea solid beverage, composed of TP, AGE and CSE, on chronic alcoholic liver injury in rats and its underlying mechanisms via the analysis of transcriptomics and gut microbiota. The histopathological findings revealed that the tea solid beverage could reduce the production of fat vacuoles and inflammatory cell infiltration. Additionally, the tea solid beverage was found to effectively relieve the increase in the AST (from 424.85 U/L to 180.17 U/L), ALT (from 139.95 U/L to 85.88 U/L) and LDH (from 21.16 U/L to 13.35 U/L) enzyme activities and the expression of the inflammatory factors TNF-α (from 394.02 pg/mL to 214.44 pg/mL) and IL-6 (from 208.46 pg/mL to 116.59 pg/mL) caused by alcohol consumption. Further, it significantly enhanced the GSH concentration (from 4.53 pg/mL to 8.08 pg/mL) and SOD activity (from 84.70 U/mL to 156.94 U/mL) and decreased the MDA (from 58.61 mmol/mL to 36.58 mmol/mL) and TG (from 7.07 mmol/L to 3.43 mmol/L)) concentrations in the liver of rats. The analysis and identification of transcriptomics showed that the tea solid beverage intervention primarily protected the liver of rats with chronic alcoholic injury by up-regulating the differential gene Hmgcs1 in order to increase the synthesis of ketone bodies and by down-regulating the differential gene Pfkfb1 for the purpose of decreasing the glucose metabolism. Additionally, it was found that the tea solid beverage could significantly change the composition of intestinal flora in drinking rats by regulating mineral absorption, the pathways of bile secretion, the adipocytokine signaling pathway and the peroxisome balance of the intestinal flora, in order to protect alcohol-drinking rats' livers. In conclusion, the tea solid beverage, consisting of TP, AGE and CSE, is a functional drink that prevents ketone metabolism, glucose metabolism and microbiome disorders induced by alcohol intake.},
}
@article {pmid38002033,
year = {2023},
author = {Altamura, S and Pietropaoli, D and Lombardi, F and Del Pinto, R and Ferri, C},
title = {An Overview of Chronic Kidney Disease Pathophysiology: The Impact of Gut Dysbiosis and Oral Disease.},
journal = {Biomedicines},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/biomedicines11113033},
pmid = {38002033},
issn = {2227-9059},
support = {DK042191-S1/NH/NIH HHS/United States ; },
abstract = {Chronic kidney disease (CKD) is a severe condition and a significant public health issue worldwide, carrying the burden of an increased risk of cardiovascular events and mortality. The traditional factors that promote the onset and progression of CKD are cardiometabolic risk factors like hypertension and diabetes, but non-traditional contributors are escalating. Moreover, gut dysbiosis, inflammation, and an impaired immune response are emerging as crucial mechanisms in the disease pathology. The gut microbiome and kidney disease exert a reciprocal influence commonly referred to as "the gut-kidney axis" through the induction of metabolic, immunological, and endocrine alterations. Periodontal diseases are strictly involved in the gut-kidney axis for their impact on the gut microbiota composition and for the metabolic and immunological alterations occurring in and reciprocally affecting both conditions. This review aims to provide an overview of the dynamic biological interconnections between oral health status, gut, and renal pathophysiology, spotlighting the dynamic oral-gut-kidney axis and raising whether periodontal diseases and gut microbiota can be disease modifiers in CKD. By doing so, we try to offer new insights into therapeutic strategies that may enhance the clinical trajectory of CKD patients, ultimately advancing our quest for improved patient outcomes and well-being.},
}
@article {pmid38001930,
year = {2023},
author = {Boicean, A and Birlutiu, V and Ichim, C and Brusnic, O and Onișor, DM},
title = {Fecal Microbiota Transplantation in Liver Cirrhosis.},
journal = {Biomedicines},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/biomedicines11112930},
pmid = {38001930},
issn = {2227-9059},
abstract = {The human gastrointestinal tract houses a diverse array of probiotic and pathogenic bacteria and any alterations in this microbial composition can exert a significant influence on an individual's well-being. It is well-established that imbalances in the gut microbiota play a pivotal role in the development of liver diseases. In light of this, a new adjuvant therapy for liver diseases could be regulating the intestinal microbiota. Through fecal microbiota transplantation, patients whose microbiomes are compromised are treated with stool from healthy donors in an attempt to restore a normal microbiome and alleviate their symptoms. A review of cross-sectional studies and case reports suggests that fecal microbiota transplants may offer effective treatment for chronic liver diseases. Adding to the potential of this emerging therapy, recent research has indicated that fecal microbiota transplantation holds promise as a therapeutic approach specifically for liver cirrhosis. By introducing a diverse range of beneficial microorganisms into the gut, this innovative treatment aims to address the microbial imbalances often observed in cirrhotic patients. While further validation is still required, these preliminary findings highlight the potential impact of fecal microbiota transplantation as a novel and targeted method for managing liver cirrhosis. We aimed to summarize the current state of understanding regarding this procedure, as a new therapeutic method for liver cirrhosis, as well as to explain its clinical application and future potential.},
}
@article {pmid38001694,
year = {2023},
author = {Maghsoudi, H and Sheikhnia, F and Sitarek, P and Hajmalek, N and Hassani, S and Rashidi, V and Khodagholi, S and Mir, SM and Malekinejad, F and Kheradmand, F and Ghorbanpour, M and Ghasemzadeh, N and Kowalczyk, T},
title = {The Potential Preventive and Therapeutic Roles of NSAIDs in Prostate Cancer.},
journal = {Cancers},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/cancers15225435},
pmid = {38001694},
issn = {2072-6694},
abstract = {Prostate cancer (PC) is the second most common type of cancer and the leading cause of death among men worldwide. Preventing the progression of cancer after treatments such as radical prostatectomy, radiation therapy, and hormone therapy is a major concern faced by prostate cancer patients. Inflammation, which can be caused by various factors such as infections, the microbiome, obesity and a high-fat diet, is considered to be the main cause of PC. Inflammatory cells are believed to play a crucial role in tumor progression. Therefore, nonsteroidal anti-inflammatory drugs along with their effects on the treatment of inflammation-related diseases, can prevent cancer and its progression by suppressing various inflammatory pathways. Recent evidence shows that nonsteroidal anti-inflammatory drugs are effective in the prevention and treatment of prostate cancer. In this review, we discuss the different pathways through which these drugs exert their potential preventive and therapeutic effects on prostate cancer.},
}
@article {pmid38001645,
year = {2023},
author = {Tu, SM and Aydin, AM and Maraboyina, S and Chen, Z and Singh, S and Gokden, N and Langford, T},
title = {Stem Cell Origin of Cancer: Clinical Implications for Cancer Immunity and Immunotherapy.},
journal = {Cancers},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/cancers15225385},
pmid = {38001645},
issn = {2072-6694},
abstract = {A simple way to understand the immune system is to separate the self from non-self. If it is self, the immune system tolerates and spares. If it is non-self, the immune system attacks and destroys. Consequently, if cancer has a stem cell origin and is a stem cell disease, we have a serious problem and a major dilemma with immunotherapy. Because many refractory cancers are more self than non-self, immunotherapy may become an uphill battle and pyrrhic victory in cancer care. In this article, we elucidate cancer immunity. We demonstrate for whom, with what, as well as when and how to apply immunotherapy in cancer care. We illustrate that a stem cell theory of cancer affects our perspectives and narratives of cancer. Without a pertinent theory about cancer's origin and nature, we may unwittingly perform misdirected cancer research and prescribe misguided cancer treatments. In the ongoing saga of immunotherapy, we are at a critical juncture. Because of the allure and promises of immunotherapy, we will be treating more patients not immediately threatened by their cancer. They may have more to lose than to gain, if we have a misconception and if we are on a wrong mission with immunotherapy. According to the stem cell theory of cancer, we should be careful with immunotherapy. When we do not know or realize that cancer originates from a stem cell and has stem-ness capabilities, we may cause more harm than good in some patients and fail to separate the truth from the myth about immunotherapy in cancer care.},
}
@article {pmid38001408,
year = {2023},
author = {Chen, C and Zhang, Y and Yao, X and Yan, Q and Li, S and Zhong, Q and Liu, Z and Tang, F and Liu, C and Li, H and Zhu, D and Lan, W and Ling, Y and Lu, D and Xu, H and Ning, Q and Wang, Y and Jiang, Z and Zhang, Q and Gu, G and Sun, L and Wang, N and Wang, G and Zhang, A and Ullah, H and Sun, W and Ma, W},
title = {Characterizations of the multi-kingdom gut microbiota in Chinese patients with gouty arthritis.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {363},
pmid = {38001408},
issn = {1471-2180},
support = {Support [2020]4Y155//Science and Technology Program of Guizhou Province/ ; Platform and talent [2020]2202//Science and Technology Program of Guizhou Province/ ; 82260894//National Natural Science Foundation of China/ ; 81902037//National Natural Science Foundation of China/ ; GZEYK-B[2021]2//Scientific Research Project of the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine/ ; },
abstract = {OBJECTIVE: The gut microbial composition has been linked to metabolic and autoimmune diseases, including arthritis. However, there is a dearth of knowledge on the gut bacteriome, mycobiome, and virome in patients with gouty arthritis (GA).<br><br>METHODS: We conducted a comprehensive analysis of the multi-kingdom gut microbiome of 26 GA patients and 28 healthy controls, using whole-metagenome shotgun sequencing of their stool samples.<br><br>RESULTS: Profound alterations were observed in the gut bacteriome, mycobiome, and virome of GA patients. We identified 1,117 differentially abundant bacterial species, 23 fungal species, and 4,115 viral operational taxonomic units (vOTUs). GA-enriched bacteria included Escherichia coli_D GENOME144544, Bifidobacterium infantis GENOME095938, Blautia_A wexlerae GENOME096067, and Klebsiella pneumoniae GENOME147598, while control-enriched bacteria comprised Faecalibacterium prausnitzii_G GENOME147678, Agathobacter rectalis GENOME143712, and Bacteroides_A plebeius_A GENOME239725. GA-enriched fungi included opportunistic pathogens like Cryptococcus neoformans GCA_011057565, Candida parapsilosis GCA_000182765, and Malassezia spp., while control-enriched fungi featured several Hortaea werneckii subclades and Aspergillus fumigatus GCA_000002655. GA-enriched vOTUs mainly attributed to Siphoviridae, Myoviridae, Podoviridae, and Microviridae, whereas control-enriched vOTUs spanned 13 families, including Siphoviridae, Myoviridae, Podoviridae, Quimbyviridae, Phycodnaviridae, and crAss-like. A co-abundance network revealed intricate interactions among these multi-kingdom signatures, signifying their collective influence on the disease. Furthermore, these microbial signatures demonstrated the potential to effectively discriminate between patients and controls, highlighting their diagnostic utility.<br><br>CONCLUSIONS: This study yields crucial insights into the characteristics of the GA microbiota that may inform future mechanistic and therapeutic investigations.},
}
@article {pmid38000818,
year = {2023},
author = {Weber, AM and Barbazza, S and Fauzi, MD and Rachmadewi, A and Zuhrina, R and Putri, FK and Campos Ponce, M and Hoeven, MV and Rimbawan, R and Nasution, Z and Giriwono, PE and Wieringa, FT and Soekarjo, DD and Ryan, EP},
title = {Solutions to Enhance Health with Alternative Treatments (SEHAT) protocol: a double-blinded randomised controlled trial for gut microbiota-targeted treatment of severe acute malnutrition using rice bran in ready-to-use therapeutic foods in Indonesia.},
journal = {BMJ open},
volume = {13},
number = {11},
pages = {e076805},
doi = {10.1136/bmjopen-2023-076805},
pmid = {38000818},
issn = {2044-6055},
abstract = {INTRODUCTION: Current formulations of ready-to-use therapeutic foods (RUTFs) to treat severe acute malnutrition (SAM) in children focus on nutrient density and quantity. Less attention is given to foods targeting gut microbiota metabolism and mucosal barrier functions. Heat-stabilised rice bran contains essential nutrients, prebiotics, vitamins and unique phytochemicals that have demonstrated favourable bioactivity to modulate gut microbiota composition and mucosal immunity. This study seeks to examine the impact of RUTF with rice bran on the microbiota during SAM treatment, recovery and post-treatment growth outcomes in Jember, Indonesia. Findings are expected to provide insights into rice bran as a novel food ingredient to improve SAM treatment outcomes.<br><br>METHODS AND ANALYSIS: A total of 200 children aged 6-59 months with uncomplicated SAM (weight-for-height z-scores (WHZ) <-3, or mid-upper arm circumference (MUAC) <115&#x2009;mm or having bilateral pitting oedema +/++) or approaching SAM (WHZ<-2.5) will be enrolled in a double-blinded, randomised controlled trial. Children in the active control arm will receive a locally produced RUTF; those in the intervention arm will receive the local RUTF with 5% rice bran. Children will receive daily RUTF treatment for 8 weeks and be monitored for 8 weeks of follow-up. Primary outcomes include the effectiveness of RUTF as measured by changes in weight, WHO growth z-scores, MUAC and morbidity. Secondary outcomes include modulation of the gut microbiome and dried blood spot metabolome, the percentage of children recovered at weeks 8 and 12, and malnutrition relapse at week 16. An intention-to-treat analysis will be conducted for each outcome.<br><br>ETHICS AND DISSEMINATION: The findings of this trial will be submitted to peer-reviewed journals and will be presented at relevant conferences. Ethics approval obtained from the Medical and Health Research Ethical Committee at the Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Madain Yogyakarta Ref. No.: KE/FK/0546/EC/2022 and KE/FK/0703/EC/2023 and from Colorado State University IRB#1823, OHRP FWA00000647.<br><br>TRIAL REGISTRATION NUMBER: NCT05319717.},
}
@article {pmid38000743,
year = {2023},
author = {Reiß, F and Kiefer, N and Purahong, W and Borken, W and Kalkhof, S and Noll, M},
title = {Active soil microbial composition and proliferation are directly affected by the presence of biocides from building materials.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168689},
doi = {10.1016/j.scitotenv.2023.168689},
pmid = {38000743},
issn = {1879-1026},
abstract = {Combinations of biocides are commonly added to building materials to prevent microbial growth and thereby cause degradation of the façades. These biocides reach the environment by leaching from façades posing an environmental risk. Although ecotoxicity to the aquatic habitat is well established, there is hardly any data on the ecotoxicological effects of biocides on the soil habitat. This study aimed to characterize the effect of the biocides terbutryn, isoproturon, octhilinone, and combinations thereof on the total and active soil microbial community composition and functions. Total soil microbial community was retrieved directly from the nucleic acid extracts, while the DNA of the active soil microbial community was separated after bromodeoxyuridine labeling. Bacterial 16S rRNA gene and fungal transcribed spacer region gene-based amplicon sequencing was carried out for both active and total, while gene copy numbers were quantified only for the total soil microbial community. Additionally, soil respiration and physico-chemical parameters were analyzed to investigate overall soil microbial activity. The bacterial and fungal gene copy numbers were significantly affected by single biocides and combined biocide soil treatment but not soil respiration and physico-chemical parameters. Moreover, results showed that single and combined biocide treatment only had minor effects on the total soil microbiome. While the total soil microbiome experienced only minor effects from single and combined biocide treatment, the active soil microbiome was significantly impacted in its diversity, richness, composition, and functional patterns. The active bacterial richness was more sensitive than fungi. However, the adverse effects of the biocide combination treatments on soil bacterial richness were highly dependent on the identities of the biocide combination. Our results demonstrate that the presence of biocides frequently used in building materials affects the active soil microbiome. Thereby, the approach described herein can be used as an ecotoxicological measure for the effect on complex soil environments in future studies.},
}
@article {pmid38001502,
year = {2023},
author = {Li, P and Hong, J and Yuan, Z and Huang, Y and Wu, M and Ding, T and Wu, Z and Sun, X and Lin, D},
title = {Gut microbiota in parasite-transmitting gastropods.},
journal = {Infectious diseases of poverty},
volume = {12},
number = {1},
pages = {105},
pmid = {38001502},
issn = {2049-9957},
support = {2020YFC1200100//the National Key R&amp;D Program of China/ ; 2020YFC1200103//the National Key R&amp;D Program of China/ ; 2021YFC2300800//the National Key R&amp;D Program of China/ ; 2016YFC1200500//the National Key R&amp;D Program of China/ ; 82202560//the National Natural Science Foundation of China/ ; 82161160343//the National Natural Science Foundation of China/ ; 82272361//the National Natural Science Foundation of China/ ; 2021B1212040017//the Science and Technology Planning Project of Guangdong Province/ ; 2022B1111030002//the R&amp;D Program in Key Areas of Guangdong Province/ ; 22qntd4813//the Fundamental Research Funds for the Central University/ ; B12003//the 111 Project/ ; 20201192//the 6th Nuclear Energy R&amp;D Project/ ; NPRC-2019-194-30//the National Parasitic Resource Center and Ministry of Science and Technology/ ; },
abstract = {BACKGROUND: Gastropoda, the largest class within the phylum Mollusca, houses diverse gut microbiota, and some gastropods serve as intermediate hosts for parasites. Studies have revealed that gut bacteria in gastropods are associated with various biological aspects, such as growth, immunity and host-parasite interactions. Here, we summarize our current knowledge of gastropod gut microbiomes and highlight future research priorities and perspectives.<br><br>METHODS: A literature search was undertaken using PubMed, Web of Science and CNKI for the articles on the gut microbiota of gastropods until December 31, 2022. We retrieved a total of 166 articles and identified 73 eligible articles for inclusion in this review based on the inclusion and exclusion criteria.<br><br>RESULTS: Our analysis encompassed freshwater, seawater and land snails, with a specific focus on parasite-transmitting gastropods. We found that most studies on gastropod gut microbiota have primarily utilized 16S rRNA gene sequencing to analyze microbial composition, rather than employing metagenomic, metatranscriptomic, or metabolomic approaches. This comprehensive review provided an overview of the parasites carried by snail species in the context of gut microbiota studies. We presented the gut microbial trends, a comprehensive summary of the diversity and composition, influencing factors, and potential functions of gastropod gut microbiota. Additionally, we discussed the potential applications, research gaps and future perspectives of gut microbiomes in parasite-transmitting gastropods. Furthermore, several strategies for enhancing our comprehension of gut microbiomes in snails were also discussed.<br><br>CONCLUSIONS: This review comprehensively summarizes the current knowledge on the composition, potential function, influencing factors, potential applications, limitations, and challenges of gut microbiomes in gastropods, with a specific emphasis on parasite-transmitting gastropods. These findings provide important insights for future studies aiming to understand the potential role of gastropod gut microbiota in controlling snail populations and snail-borne diseases.},
}
@article {pmid38001152,
year = {2023},
author = {Naddaf, R and Carasso, S and Reznick-Levi, G and Hasnis, E and Qarawani, A and Maza, I and Gefen, T and Half, EE and Geva-Zatorsky, N},
title = {Gut microbial signatures are associated with Lynch syndrome (LS) and cancer history in Druze communities in Israel.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20677},
pmid = {38001152},
issn = {2045-2322},
abstract = {Lynch syndrome (LS) is a hereditary cancer syndrome caused by autosomal dominant mutations, with high probability of early onset for several cancers, mainly colorectal cancer (CRC). The gut microbiome was shown to be influenced by host genetics and to be altered during cancer development. Therefore, we aimed to determine alterations in gut microbiome compositions of LS patients with and without cancer. We performed fecal microbiome analyses on samples of LS and non-LS members from the Druze ethnoreligious community in Israel, based on both their LS mutation and their cancer history. Our analysis revealed specific bacterial operational taxonomic units (OTUs) overrepresented in LS individuals as well as bacterial OTUs differentiating between the LS individuals with a history of cancer. The identified OTUs align with previous studies either correlating them to pro-inflammatory functions, which can predispose to cancer, or to the cancer itself, and as such, these bacteria can be considered as future therapeutic targets.},
}
@article {pmid38001080,
year = {2023},
author = {Choi, W and Mangal, U and Park, JY and Kim, JY and Jun, T and Jung, JW and Choi, M and Jung, S and Lee, M and Na, JY and Ryu, DY and Kim, JM and Kwon, JS and Koh, WG and Lee, S and Hwang, PTJ and Lee, KJ and Jung, UW and Cha, JK and Choi, SH and Hong, J},
title = {Occlusive membranes for guided regeneration of inflamed tissue defects.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7687},
pmid = {38001080},
issn = {2041-1723},
support = {KRIT-CT-21-034//Ministry of National Defense, Republic of Korea | Defense Acquisition Program Administration (DAPA)/ ; NRF-2022K2A9A1A0609182711//National Research Foundation of Korea (NRF)/ ; HI22C1609//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; },
abstract = {Guided bone regeneration aided by the application of occlusive membranes is a promising therapy for diverse inflammatory periodontal diseases. Symbiosis, homeostasis between the host microbiome and cells, occurs in the oral environment under normal, but not pathologic, conditions. Here, we develop a symbiotically integrating occlusive membrane by mimicking the tooth enamel growth or multiple nucleation biomineralization processes. We perform human saliva and in vivo canine experiments to confirm that the symbiotically integrating occlusive membrane induces a symbiotic healing environment. Moreover, we show that the membrane exhibits tractability and enzymatic stability, maintaining the healing space during the entire guided bone regeneration therapy period. We apply the symbiotically integrating occlusive membrane to treat inflammatory-challenged cases in vivo, namely, the open and closed healing of canine premolars with severe periodontitis. We find that the membrane promotes symbiosis, prevents negative inflammatory responses, and improves cellular integration. Finally, we show that guided bone regeneration therapy with the symbiotically integrating occlusive membrane achieves fast healing of gingival soft tissue and alveolar bone.},
}
@article {pmid38000973,
year = {2023},
author = {Armstrong, PA and Venugopal, N and Wright, TJ and Randolph, KM and Batson, RD and Yuen, KCJ and Masel, BE and Sheffield-Moore, M and Urban, RJ and Pyles, RB},
title = {Traumatic brain injury, abnormal growth hormone secretion, and gut dysbiosis.},
journal = {Best practice &amp; research. Clinical endocrinology &amp; metabolism},
volume = {},
number = {},
pages = {101841},
doi = {10.1016/j.beem.2023.101841},
pmid = {38000973},
issn = {1878-1594},
abstract = {The gut microbiome has been implicated in a variety of neuropathologies with recent data suggesting direct effects of the microbiome on host metabolism, hormonal regulation, and pathophysiology. Studies have shown that gut bacteria impact host growth, partially mediated through the growth hormone (GH)/insulin-like growth factor 1 (IGF-1) axis. However, no study to date has examined the specific role of GH on the fecal microbiome (FMB) or the changes in this relationship following a traumatic brain injury (TBI). Current literature has demonstrated that TBI can lead to either temporary or sustained abnormal GH secretion (aGHS). More recent literature has suggested that gut dysbiosis may contribute to aGHS leading to long-term sequelae now known as brain injury associated fatigue and cognition (BIAFAC). The aGHS observed in some TBI patients presents with a symptom complex including profound fatigue and cognitive dysfunction that improves significantly with exogenous recombinant human GH treatment. Notably, GH treatment is not curative as fatigue and cognitive decline typically recur upon treatment cessation, indicating the need for additional studies to address the underlying mechanistic cause.},
}
@article {pmid38000798,
year = {2023},
author = {Wadhwani, R and Williams, A},
title = {Protect the Microbiome: Be HOLISTIC.},
journal = {Neonatal network : NN},
volume = {42},
number = {6},
pages = {342-347},
doi = {10.1891/NN-2023-0001},
pmid = {38000798},
issn = {1539-2880},
abstract = {The newborn who requires intensive care hospitalization is forced into an external environment that can negatively impact the developing microbiome. The NICU nurse has a unique role that affects, and may even protect, the development of the newborn microbiome through daily nursing care. The purpose of this article is to inform neonatal nurses regarding common nursing interventions that can positively or negatively impact the developing microbiome. Evidence-based practices are presented and bundled to describe their impact the neonatal microbiome.},
}
@article {pmid38000749,
year = {2023},
author = {Lewin, S and Wende, S and Wehrhan, M and Verch, G and Ganugi, P and Sommer, M and Kolb, S},
title = {Cereals rhizosphere microbiome undergoes host selection of nitrogen cycle guilds correlated to crop productivity.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168794},
doi = {10.1016/j.scitotenv.2023.168794},
pmid = {38000749},
issn = {1879-1026},
abstract = {Sustainable transformation of agricultural plant production requires the reduction of nitrogen (N) fertilizer application. Such a reduced N fertilizer application may impede crop production due to an altered symbiosis of crops and their rhizosphere microbiome, since reduced N input may affect the competition and synergisms with the plant. The assessment of such changes in the crop microbiome functionalities at spatial scales relevant for agricultural management remains challenging. We investigated in a field plot experiment how and if the N cycling guilds of the rhizosphere of globally relevant cereal crops - winter barley, wheat and rye - are influenced by reduced N fertilization. Crop productivity was assessed by remote sensing of the shoot biomass. Microbial N cycling guilds were investigated by metagenomics targeting diazotrophs, nitrifiers, denitrifiers and the dissimilatory nitrate to ammonium reducing guild (DNRA). The functional composition of microbial N cycling guilds was explained by crop productivity parameters and soil pH, and diverged substantially between the crop species. The responses of individual microbial N cycling guild abundances to shoot dry weight and rhizosphere nitrate content was modulated by the N fertilization treatments and the crop species, which was identified based on regression analyses. Thus, characteristic shifts in the microbial N cycling guild acquisition associated with the crop host species were resolved. Particularly, the rhizosphere of rye was enriched with potentially N-preserving microbial guilds - diazotrophs and the DNRA guild - when no fertilizer was applied. We speculate that the acquisition of microbial N cycling guilds was the result of plant species-specific acquisition strategies. Thus, the investigated cereal crop holobionts have likely different symbiotic strategies that make them differently resilient against reduced N fertilizer inputs. Furthermore, we demonstrated that these belowground patterns of N cycling guilds from the rhizosphere microbiome are linked to remotely sensed aboveground plant productivity.},
}
@article {pmid38000633,
year = {2023},
author = {Hou, J and Lam, KL and Chiu, YT and Kwong, KY and Lau, HL and Marafa, LM and Tsui, SKW and Mo, IWY and Chan, PL},
title = {Urban green waste bulking agent is the major source of antimicrobial resistance genes persisted in home compost, not animal manure.},
journal = {Environmental research},
volume = {},
number = {},
pages = {117713},
doi = {10.1016/j.envres.2023.117713},
pmid = {38000633},
issn = {1096-0953},
abstract = {Urban green waste and food waste are often used as bulking agents to prepare home compost in combination with animal manure in urban horticulture and community gardening. Although it is known that antimicrobial resistance genes (ARGs) persist in home compost, their origins have not been determined. In addition, the factors contributing to ARGs persistence remain unclear. In this study, we aim to (i) characterize the changes in the microbiome and antimicrobial resistome during the composting process of home compost using metagenomics shotgun sequencing, (ii) identify the source of the ARGs persisted in home compost using SourceTracker, and (iii) elucidate the collective effect of compost microbiome and environmental factors, including the physicochemical properties and antibiotics concentration of home compost, in contributing to ARG persistence using Procrustes analysis, co-occurrence network analysis, variation partitioning analysis, and structural equation modeling. SourceTracker analysis indicated that urban green waste bulking agent was the major source of the persisting ARGs in home compost instead of animal manure. Procrustes analysis and co-occurrence network analysis revealed a strong association between microbiome and antimicrobial resistome. Variation partitioning analysis and structural equation modeling suggested that physicochemical properties shaped the antimicrobial resistome directly and indirectly by influencing the microbiome. Our results indicated that the persistence of ARGs in home compost might be due to the succession of microbial species from the urban green waste bulking agent, and the physicochemical properties might have defined the compost environment to shape the microbiome in the compost, thus, in turn, the persisting antimicrobial resistome. (248 words).},
}
@article {pmid38000281,
year = {2023},
author = {Bombaywala, S and Bajaj, A and Dafale, NA},
title = {Deterministic effect of oxygen level variation on shaping antibiotic resistome.},
journal = {Journal of hazardous materials},
volume = {465},
number = {},
pages = {133047},
doi = {10.1016/j.jhazmat.2023.133047},
pmid = {38000281},
issn = {1873-3336},
abstract = {An increase in acquisition of antibiotic resistance genes (ARGs) by pathogens under antibiotic selective pressure poses public health threats. Sub-inhibitory antibiotics induce bacteria to generate reactive oxygen species (ROS) dependent on dissolved oxygen (DO) levels, while molecular connection between ROS-mediated ARG emergence through DNA damage and metabolic changes remains elusive. Thus, the study investigates antibiotic resistome dynamics, microbiome shift, and pathogen distribution in hyperoxic (5-7 mg L[-1]), normoxic (2-4 mg L[-1]), and hypoxic (0.5-1 mg L[-1]) conditions using lab-scale bioreactor. Composite inoculums in the reactor were designed to represent comprehensive microbial community and AR profile from selected activated sludge. RT-qPCR and metagenomic analysis showed an increase in ARG count (100.98 ppm) with enrichment of multidrug efflux pumps (acrAB, mexAB) in hyperoxic condition. Conversely, total ARGs decreased (0.11 ppm) under hypoxic condition marked by a major decline in int1 abundance. Prevalence of global priority pathogens increased in hyperoxic (22.5%), compared to hypoxic (0.9%) wherein major decrease were observed in Pseudomonas, Shigella, and Borrelia. The study observed an increase in superoxide dismutase (sodA, sodB), DNA repair genes (nfo, polA, recA, recB), and ROS (10.4 µmol L[-1]) in adapted biomass with spiked antibiotics. This suggests oxidative damage that facilitates stress-induced mutagenesis providing evidence for observed hyperoxic enrichment of ARGs. Moreover, predominance of catalase (katE, katG) likely limit oxidative damage that deplete ARG breeding in hypoxic condition. The study proposes a link between oxygen levels and AR development that offers insights into mitigation and intervention of AR by controlling oxygen-related stress and strategic selection of bacterial communities.},
}
@article {pmid38000106,
year = {2023},
author = {Sidhu, D and Vasundhara, M and Dey, P},
title = {The intestinal-level metabolic benefits of green tea catechins: Mechanistic insights from pre-clinical and clinical studies.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {123},
number = {},
pages = {155207},
doi = {10.1016/j.phymed.2023.155207},
pmid = {38000106},
issn = {1618-095X},
abstract = {BACKGROUND: The intestinal-level host-microbiota interaction has been implicated in the pathogenesis of chronic diseases. The current review is intended to provide a comprehensive insight into deciphering whether intestinal-level bioactivities mediate the overall metabolic health benefits of green tea catechins.<br><br>PURPOSE: We have comprehensively discussed pre-clinical and clinical evidences of intestinal-level changes in metabolism, microbiota, and metabolome due to catechin-rich green tea treatments, ultimately limiting metabolic diseases. Exclusive emphasis has been given to purified catechins and green tea, and discussions on extraintestinal mechanisms of metabolic health benefits were avoided.<br><br>METHODS: A literature search for relevant pre-clinical and clinical studies was performed in various online databases (e.g., PubMed) using specific keywords (e.g., catechin, intestine, microbiota). Out of all the referred literature, &#x223c;15% belonged to 2021-2023, &#x223c;51% were from 2011-2020, and &#x223c;32% from 2000-2010.<br><br>RESULT: The metabolic health benefits of green tea catechins are indeed influenced by the intestinal-level bioactivities, including reduction of mucosal inflammation and oxidative stress, attenuation of gut barrier dysfunction, decrease in intestinal lipid absorption and metabolism, favorable modulation of mucosal nuclear receptor signaling, alterations of the luminal global metabolome, and mitigation of the gut dysbiosis. The results from the recent clinical studies support the pre-clinical evidences. The challenges and pitfalls of the currently available knowledge on catechin bioactivities have been discussed, and constructive directions to harness the translational benefits of green tea through future interventions have been provided.<br><br>CONCLUSION: The metabolism, metabolome, and microbiota at the intestinal epithelia play critical roles in catechin metabolism, pharmacokinetics, bioavailability, and bioactivities. Especially the reciprocal interaction between the catechins and the gut microbiota dictates the metabolic benefits of catechins.},
}
@article {pmid37999520,
year = {2023},
author = {Liu, X and Ma, Y and Wu, J and Wang, P and Wang, Y and Wang, A and Yin, Q and Ma, H and Chan, LL and Wu, B},
title = {Characterizing the Influence of a Heterotrophic Bicosoecid Flagellate Pseudobodo sp. on the Dinoflagellate Gambierdiscus balechii.},
journal = {Toxins},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/toxins15110657},
pmid = {37999520},
issn = {2072-6651},
support = {CityU 11104821//General Research Fund of the Hong Kong Research Grants Council/ ; 42176098//National Natural Science Foundation of China/ ; C7013-19GF//Collaborative Research Fund of the Hong Kong Research Grants Council/ ; 2022R52036//The Fund of Special Plan for High-Level Talents of Zhejiang/ ; SGDX20220530111204028//Shenzhen-Hong Kong-Macau Science &amp; Technology Project (Category C)/ ; },
abstract = {Microbial interactions including competition, mutualism, commensalism, parasitism, and predation, which can be triggered by nutrient acquisition and chemical communication, are universal phenomena in the marine ecosystem. The interactions may influence the microbial population density, metabolism, and even their environmental functions. Herein, we investigated the interaction between a heterotrophic bicosoecid flagellate, Pseudobodo sp. (Bicoecea), and a dinoflagellate, Gambierdiscus balechii (Dinophyceae), which is a well-known ciguatera food poisoning (CFP) culprit. The presence of Pseudobodo sp. inhibited the algal proliferation and decreased the cardiotoxicity of zebrafish in the algal extract exposure experiment. Moreover, a significant difference in microbiome abundance was observed in algal cultures with and without Pseudobodo sp. Chemical analysis targeting toxins was performed by using liquid chromatography-tandem mass spectrometry (LC-MS/MS) combined with molecular networking (MN), showing a significant alteration in the cellular production of gambierone analogs and some super-carbon chain compounds. Taken together, our results demonstrated the impact of heterotrophic flagellate on the photosynthetic dinoflagellates, revealing the complex dynamics of algal toxin production and the ecological relationships related to dinoflagellates in the marine environment.},
}
@article {pmid37999473,
year = {2023},
author = {Edmunds, CE and Welch, CB and Lourenco, JM and Callaway, TR and Pringle, TD and Dove, CR},
title = {The Effects of Dietary Manganese and Selenium on Growth and the Fecal Microbiota of Nursery Piglets.},
journal = {Veterinary sciences},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/vetsci10110650},
pmid = {37999473},
issn = {2306-7381},
abstract = {The objective of this study was to determine the impact of varying dietary manganese and selenium concentrations, antioxidant cofactors, on the growth performance and fecal microbial populations of nursery pigs. The piglets (N = 120) were blocked by weight (5.22 ± 0.7 kg) and sex. The pens (n = 5/treatment) within a block were randomly assigned to diets in a 2 × 3 factorial design to examine the effects of Se (0.1 and 0.3 mg/kg added Se) and Mn (0, 12, and 24 mg/kg added Mn) and were fed in three phases (P1 = d 1-7, P2 = d 8-21, P3 = d 22-35). The pigs and orts were weighed weekly. Fecal samples were collected d 0 and 35 for 16S rRNA bacterial gene sequencing and VFA analysis. The data were analyzed as factorial via GLM in SAS. There was a linear response (p < 0.05) in overall ADG across dietary Mn. Supplementing 24 mg/kg Mn tended to decrease (p < 0.10) the relative abundance of many bacteria possessing pathogenic traits relative to Mn controls. Meanwhile, increasing Mn concentration tended to foster the growth of bacteria correlated with gut health and improved growth (p < 0.10). The data from this study provide preliminary evidence on the positive effects of manganese on growth and gut health of nursery pigs.},
}
@article {pmid37999467,
year = {2023},
author = {Heil, BA and van Heule, M and Thompson, SK and Kearns, TA and Oberhaus, EL and King, G and Daels, P and Dini, P and Sones, JL},
title = {Effect of Sampling Method on Detection of the Equine Uterine Microbiome during Estrus.},
journal = {Veterinary sciences},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/vetsci10110644},
pmid = {37999467},
issn = {2306-7381},
support = {1/CX/CSRD VA/United States ; },
abstract = {Bacterial endometritis is among the most common causes of subfertility in mares. It has a major economic impact on the equine breeding industry. The sensitivity of detecting uterine microbes using culture-based methods, irrespective of the sample collection method, double-guarded endometrial swab, endometrial biopsy, or uterine low-volume lavage (LVL), is low. Therefore, equine bacterial endometritis often goes undiagnosed. Sixteen individual mares were enrolled, and an endometrial sample was obtained using each method from all mares. After trimming, quality control and decontamination, 3824 amplicon sequence variants were detected in the dataset. We found using 16S rRNA sequencing that the equine uterus harbors a distinct resident microbiome during estrus. All three sampling methods used yielded similar results in composition as well as relative abundance at phyla (Proteobacteria, Firmicutes, and Bacteroidota) and genus (Klebsiella, Mycoplasma, and Aeromonas) levels. A significant difference was found in alpha diversity (Chao1) between LVL and endometrial biopsy, suggesting that LVL is superior at detecting the low-abundant (rare) taxa. These new data could pave the way for innovative treatment methods for endometrial disease and subfertility in mares. This, in turn, could lead to more judicious antimicrobial use in the equine breeding industry.},
}
@article {pmid37999464,
year = {2023},
author = {Albuquerque, A and Garrido, N and Charneca, R and Egas, C and Martin, L and Ramos, A and Costa, F and Marmelo, C and Martins, JM},
title = {Influence of Sex and a High-Fiber Diet on the Gut Microbiome of Alentejano Pigs Raised to Heavy Weights.},
journal = {Veterinary sciences},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/vetsci10110641},
pmid = {37999464},
issn = {2306-7381},
abstract = {This study investigates the influence of sex and a dietary transition on the gut microbiota of a local Portuguese pig breed. Three groups of male Alentejano pigs (n = 10 each) were raised between ~40 and 160 kg LW. Group C included pigs that were surgically castrated, while the I group included intact ones; both were fed with commercial diets. The third group, IExp, included intact pigs that were fed commercial diets until ~130 kg, then replaced by an experimental diet based on legumes and agro-industrial by-products between ~130 and 160 kg. Fecal samples were collected two weeks before slaughter. The total DNA was extracted and used for 16S metabarcoding on a MiSeq[®] System. The dietary transition from a commercial diet to the experimental diet substantially increased and shifted the diversity observed. Complex carbohydrate fermenting bacteria, such as Ruminococcus spp. and Sphaerochaeta spp., were significantly more abundant in IExp (q < 0.05). On the other hand, castrated pigs presented a significantly lower abundance of the potential probiotic, Roseburia spp. and Lachnospiraceae NK4A136 group (q < 0.01), bacteria commonly associated with better gut health and lower body fat composition. Understanding the role of gut microbiota is paramount to ensure a low skatole deposition and consumers' acceptance of pork products from non-castrated male pigs.},
}
@article {pmid37999433,
year = {2023},
author = {Kalabiska, I and Annar, D and Keki, Z and Borbas, Z and Bhattoa, HP and Zsakai, A},
title = {The Oral Microbiome Profile of Water Polo Players Aged 16-20.},
journal = {Sports (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/sports11110216},
pmid = {37999433},
issn = {2075-4663},
support = {TEKA grant (EFKTA002T)//Hungarian University of Sports Science/ ; Scientific Foundations of Education Research Program 2021//Hungarian Academy of Sciences/ ; },
abstract = {OBJECTIVES: Chlorine has a strong antibacterial property and is the disinfectant most frequently used in swimming pools. Therefore, the microbiota community in the oral cavity of those who practice water sports is assumed to be special due to their regular immersion in water. Adverse changes in the composition of oral cavity microbiota may have serious health consequences. We aimed to compare the oral microbiome between water polo players and non-athletes. We hypothesized that the oral cavity microbiota community differed between water polo players and non-athletes.<br><br>MATERIALS AND METHODS: Altogether, 124 water polo players (62 males and 62 females, aged between 9 and 20 years) and 16 non-athlete youths (control group, eight males and eight females, aged between 16 and 20 years, mean age + SD = 17.1 + 1.4 years) who participated in body structure examinations voluntarily agreed to participate in the study. In a randomly selected subsample of water polo players (n: 29, aged between 16 and 20 years, mean age + SD = 17.3 + 1.0 years), saliva samples were also collected. Saliva samples were collected from all non-athlete youths (n: 16, aged between 16 and 20 years). The oral microbiome was determined from a saliva sample, and DNA was isolated using the QIAmp DNA Blood Mini Kit. The 16S rRNA gene amplicon sequencing method was used to analyze the microbiome community. PCR primers were trimmed from the sequence reads with Cutadapt. R library DADA2 was used to process reads in the abundance analysis.<br><br>RESULTS: In general, Streptococcus, Veilonella, and Prevotella genera constituted more than 50% of the oral microbiome community in the two participant groups combined (n = 45). The oral microbial profile had significant sexual dimorphism and differed between water polo players and the non-athletes. Compared to females, males had a higher (p < 0.05) relative abundance of the Atopobium (medium effect size) and Pravotella_7 (very large effect size) genera and a lower (p < 0.05) relative abundance of the Fusobacterium (large effect size), Gemella (large effect size), and Streptococcus (large effect size) genera. Compared to non-athletes, water polo players had higher (p < 0.05, medium effect size) relative abundance of the genus Veillonella and lower (p < 0.05, large effect size) relative abundance of the genus Gemella.<br><br>CONCLUSIONS: The results suggest that regular water training can unfavorably alter the composition of the oral microbial community.},
}
@article {pmid37999420,
year = {2023},
author = {Oppong-Danquah, E and Blümel, M and Tasdemir, D},
title = {Metabolomics and Microbiomics Insights into Differential Surface Fouling of Three Macroalgal Species of Fucus (Fucales, Phaeophyceae) That Co-Exist in the German Baltic Sea.},
journal = {Marine drugs},
volume = {21},
number = {11},
pages = {},
pmid = {37999420},
issn = {1660-3397},
abstract = {The brown algal genus Fucus provides essential ecosystem services crucial for marine environments. Macroalgae (seaweeds) release dissolved organic matter, hence, are under strong settlement pressure from micro- and macrofoulers. Seaweeds are able to control surface epibionts directly by releasing antimicrobial compounds onto their surfaces, and indirectly by recruiting beneficial microorganisms that produce antimicrobial/antifouling metabolites. In the Kiel Fjord, in the German Baltic Sea, three distinct Fucus species coexist: F. vesiculosus, F. serratus, and F. distichus subsp. evanescens. Despite sharing the same habitat, they show varying fouling levels; F. distichus subsp. evanescens is the least fouled, while F. vesiculosus is the most fouled. The present study explored the surface metabolomes and epiphytic microbiota of these three Fucus spp., aiming to uncover the factors that contribute to the differences in the fouling intensity on their surfaces. Towards this aim, algal surface metabolomes were analyzed using comparative untargeted LC-MS/MS-based metabolomics, to identify the marker metabolites influencing surface fouling. Their epiphytic microbial communities were also comparatively characterized using high-throughput amplicon sequencing, to pinpoint the differences in the surface microbiomes of the algae. Our results show that the surface of the least fouling species, F. distichus subsp. evanescens, is enriched with bioactive compounds, such as betaine lipids MGTA, 4-pyridoxic acid, and ulvaline, which are absent from the other species. Additionally, it exhibits a high abundance of the fungal genera Mucor and Alternaria, along with the bacterial genus Yoonia-Loktanella. These taxa are known for producing antimicrobial/antifouling compounds, suggesting their potential role in the observed fouling resistance on the surface of the F. distichus subsp. evanescens compared to F. serratus and F. vesiculosus. These findings provide valuable clues on the differential surface fouling intensity of Fucus spp., and their importance in marine chemical defense and fouling dynamics.},
}
@article {pmid37999398,
year = {2023},
author = {Jahajeeah, D and Ranghoo-Sanmukhiya, M and Schäfer, G},
title = {Metabolic Profiling, Antiviral Activity and the Microbiome of Some Mauritian Soft Corals.},
journal = {Marine drugs},
volume = {21},
number = {11},
pages = {},
pmid = {37999398},
issn = {1660-3397},
support = {WS/MUS22-01//International Centre for Genetic Engineering and Biotechnology/ ; },
abstract = {Soft corals, recognized as sessile marine invertebrates, rely mainly on chemical, rather than physical defense, by secreting intricate secondary metabolites with plausible pharmaceutical implication. Their ecological niche encompasses a diverse community of symbiotic microorganisms which potentially contribute to the biosynthesis of these bioactive metabolites. The emergence of new viruses and heightened viral resistance underscores the urgency to explore novel pharmacological reservoirs. Thus, marine organisms, notably soft corals and their symbionts, have drawn substantial attention. In this study, the chemical composition of four Mauritian soft corals: Sinularia polydactya, Cespitularia simplex, Lobophytum patulum, and Lobophytum crassum was investigated using LC-MS techniques. Concurrently, Illumina 16S metagenomic sequencing was used to identify the associated bacterial communities in the named soft corals. The presence of unique biologically important compounds and vast microbial communities found therein was further followed up to assess their antiviral effects against SARS-CoV-2 and HPV pseudovirus infection. Strikingly, among the studied soft corals, L. patulum displayed an expansive repertoire of unique metabolites alongside a heightened bacterial consort. Moreover, L. patulum extracts exerted some promising antiviral activity against SARS-CoV-2 and HPV pseudovirus infection, and our findings suggest that L. patulum may have the potential to serve as a therapeutic agent in the prevention of infectious diseases, thereby warranting further investigation.},
}
@article {pmid37999261,
year = {2023},
author = {Hou, Y and Li, J and Ying, S},
title = {Tryptophan Metabolism and Gut Microbiota: A Novel Regulatory Axis Integrating the Microbiome, Immunity, and Cancer.},
journal = {Metabolites},
volume = {13},
number = {11},
pages = {},
pmid = {37999261},
issn = {2218-1989},
support = {32170062//National Natural Science Foundation of China/ ; 2017TP1037//Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples/ ; },
abstract = {Tryptophan metabolism and gut microbiota form an integrated regulatory axis that impacts immunity, metabolism, and cancer. This review consolidated current knowledge on the bidirectional interactions between microbial tryptophan processing and the host. We focused on how the gut microbiome controls tryptophan breakdown via the indole, kynurenine, and serotonin pathways. Dysbiosis of the gut microbiota induces disruptions in tryptophan catabolism which contribute to disorders like inflammatory conditions, neuropsychiatric diseases, metabolic syndromes, and cancer. These disruptions affect immune homeostasis, neurotransmission, and gut-brain communication. Elucidating the mechanisms of microbial tryptophan modulation could enable novel therapeutic approaches like psychobiotics and microbiome-targeted dietary interventions. Overall, further research on the microbiota-tryptophan axis has the potential to revolutionize personalized diagnostics and treatments for improving human health.},
}
@article {pmid37999254,
year = {2023},
author = {Mo, Z and Wang, J and Meng, X and Li, A and Li, Z and Que, W and Wang, T and Tarnue, KF and Ma, X and Liu, Y and Yan, S and Wu, L and Zhang, R and Pei, J and Wang, X},
title = {The Dose-Response Effect of Fluoride Exposure on the Gut Microbiome and Its Functional Pathways in Rats.},
journal = {Metabolites},
volume = {13},
number = {11},
pages = {},
pmid = {37999254},
issn = {2218-1989},
support = {82273749//National Natural Science Foundation of China/ ; 81773468//National Natural Science Foundation of China/ ; LTGY23H240001//Natural Science Foundation of Zhejiang Province, China/ ; NHCKLEE20230908//the Opening Foundation of NHC Key Laboratory of Etiology and Epidemiology/ ; },
abstract = {Metabolic activities within the gut microbiome are intimately linked to human health and disease, especially within the context of environmental exposure and its potential ramifications. Perturbations within this microbiome, termed "gut microbiome perturbations", have emerged as plausible intermediaries in the onset or exacerbation of diseases following environmental chemical exposures, with fluoride being a compound of particular concern. Despite the well-documented adverse impacts of excessive fluoride on various human physiological systems-ranging from skeletal to neurological-the nuanced dynamics between fluoride exposure, the gut microbiome, and the resulting dose-response relationship remains a scientific enigma. Leveraging the precision of 16S rRNA high-throughput sequencing, this study meticulously examines the ramifications of diverse fluoride concentrations on the gut microbiome's composition and functional capabilities within Wistar rats. Our findings indicate a profound shift in the intestinal microbial composition following fluoride exposure, marked by a dose-dependent modulation in the abundance of key genera, including Pelagibacterium, Bilophila, Turicibacter, and Roseburia. Moreover, discernible alterations were observed in critical functional and metabolic pathways of the microbiome, such as D-lyxose ketol-isomerase and DNA polymerase III subunit gamma/tau, underscoring the broad-reaching implications of fluoride exposure. Intriguingly, correlation analyses elucidated strong associations between specific bacterial co-abundance groups (CAGs) and these shifted metabolic pathways. In essence, fluoride exposure not only perturbs the compositional equilibrium of the gut microbiota but also instigates profound shifts in its metabolic landscape. These intricate alterations may provide a mechanistic foundation for understanding fluoride's potential toxicological effects mediated via gut microbiome modulation.},
}
@article {pmid37999221,
year = {2023},
author = {Fineide, FA and Tashbayev, B and Elgstøen, KBP and Sandås, EM and Rootwelt, H and Hynne, H and Chen, X and Ræder, S and Vehof, J and Dartt, D and Jensen, JL and Utheim, TP},
title = {Tear and Saliva Metabolomics in Evaporative Dry Eye Disease in Females.},
journal = {Metabolites},
volume = {13},
number = {11},
pages = {},
pmid = {37999221},
issn = {2218-1989},
abstract = {Accurate diagnosis of dry eye disease (DED) is challenging, and even today there is no gold standard biomarker of DED. Hypothesis-free global metabolomic studies of tears from DED patients have great potential to discover metabolites and pathways affected in the pathophysiology of DED, and to identify possible future biomarkers. These metabolites and biomarkers could be important for diagnosing and monitoring disease as well as for new therapeutic targets and strategies. As DED is associated with dry mouth, this study aimed to perform metabolomic analyses of tears and saliva from patients with decreased tear film break-up time but normal Schirmer test, and age-matched controls with both tear production and stability within physiological range. We applied strict inclusion criteria to reduce sampling bias in the metabolomic analyses and selected only age-matched females with Schirmer test values between 10-15 mm/5 min. The tear film analysis arm included 19 patients (with tear film break-up time 0-5 s) and 12 controls (with tear film break-up time 10-30 s), while the salivary analysis arm consisted of a subset which included 18 patients and six controls. Metabolomic analyses were performed using liquid chromatography and high-resolution mass spectrometry. Analyses using a global database search detected a total of 56 metabolites in tear samples that were significantly different between the groups. Of these, several have known associations with DED. These metabolites are present in meibum and have anti-oxidative characteristics or associations with the ocular microbiome, and altered concentrations suggest that they may play a significant role in DED associated with decreased tear film stability. In saliva, hypotaurine levels were lower among patients with tear film instability. In this pilot study, we found different levels of several metabolites in patients with decreased tear film break-up time that may have associations with DED. Future studies are required to replicate our findings and clarify the exact roles of these metabolites.},
}
@article {pmid37999101,
year = {2023},
author = {Duttagupta, S and Hakozaki, T and Routy, B and Messaoudene, M},
title = {The Gut Microbiome from a Biomarker to a Novel Therapeutic Strategy for Immunotherapy Response in Patients with Lung Cancer.},
journal = {Current oncology (Toronto, Ont.)},
volume = {30},
number = {11},
pages = {9406-9427},
pmid = {37999101},
issn = {1718-7729},
abstract = {The gastrointestinal microbiome has been shown to play a key role in determining the responses to cancer immunotherapy, including immune checkpoint inhibitor (ICI) therapy and CAR-T. In patients with non-small cell lung cancer (NSCLC), increasing evidence suggests that a microbiome composition signature is associated with clinical response to ICIs as well as with the development of immune-related adverse events. In support of this, antibiotic (ATB)-related dysbiosis has been consistently linked with the deleterious impact of ICI response, shortening the overall survival (OS) among patients on ATBs prior to ICI initiation. In parallel, several preclinical experiments have unravelled various strategies using probiotics, prebiotics, diet, and fecal microbiota transplantation as new therapeutic tools to beneficially shift the microbiome and enhance ICI efficacy. These approaches are currently being evaluated in clinical trials and have achieved encouraging preliminary results. In this article, we reviewed the recent studies on the gut microbiome as a potential biomarker and an adjuvant therapy to ICIs in NSCLC patients.},
}
@article {pmid37999031,
year = {2023},
author = {Do, TH and Dao, TK and Nguyen, HD and Truong, NH},
title = {Understanding the Role of Free-Living Bacteria in the Gut of the Lower Termite Coptotermes gestroi Based on Metagenomic DNA Analysis.},
journal = {Insects},
volume = {14},
number = {11},
pages = {},
pmid = {37999031},
issn = {2075-4450},
support = {NVCC08.08/22-23//Vietnam Academy of Sicence and Technology, Vietnam/ ; },
abstract = {Termites' digestive systems, particularly in lower termites with the presence of protozoa, are unique ecological niches that shelter a diverse microbiota with a variety of functions for the host and the environment. In 2012, the metagenomic DNA (5.4 Gb) of the prokaryotes that freely live in the gut of the lower termite Coptotermes gestroi were sequenced. A total of 125,431 genes were predicted and analyzed in order to mine lignocellulolytic genes. however, the overall picture of the structure, diversity, and function of the prokaryotic gut microbiota was not investigated. In the present study, these 125,431 genes were taxonomically classified by MEGAN and functionally annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and by the Carbohydrate-Active enZYmes (CAZy) and HMMER databases. As a result, 95,751 bacterial genes were classified into 35 phyla. The structure of the bacteria, typified by a high ratio of Firmicutes to Bacterioidetes, was distinct from the structure of the entirety of the bacteria in the lower or higher termites' guts. The archaea (533 genes) were distributed into 4 phyla, 10 classes, 15 orders, 21 families, 47 genera, and 61 species. Although freely living in the guts, the prokaryotic community was formed, developed, and adapted to exhibit unique interactions in order to perform mutual roles of benefit to their hosts. Methanobacteriales, accounting for 61% of the archaea symbionts, seem to play an important role in methanogenesis. Concomitantly, bacterial methanotrophs in the gut utilize methane and combine with other bacterial groups, including potential lignocellulolytic degraders, acetogens, sulfur bacteria, and nitrogen-recycling bacteria, to efficiently convert wood with little nitrogen into acetates via certain pathway modules specified by prokaryotes that freely live in the gut. This forms an important energy source for the termites. Furthermore, bacteria carry 2223 genes involved in the biosynthesis of 17 antibiotic groups. The gut bacteria also possess genes for the degradation of 18 toxic aromatic compounds, of which four are commercial pesticides against termites commonly used for the preservation of wooden constructions. Eight of the eighteen pathways were the first to be reported from the termite gut. Overall, this study sheds light on the roles of the freely living bacteria and archaea in the C. gestroi gut, providing evidence that the gut microbiome acts as the second host genome, contributing both nutrients and immunity to support the host's existence, growth, and development.},
}
@article {pmid37998924,
year = {2023},
author = {Theologidis, I and Karamitros, T and Vichou, AE and Kizis, D},
title = {Nanopore-Sequencing Metabarcoding for Identification of Phytopathogenic and Endophytic Fungi in Olive (Olea europaea) Twigs.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {11},
pages = {},
pmid = {37998924},
issn = {2309-608X},
support = {Olive Roads//GSRI/ ; },
abstract = {Metabarcoding approaches for the identification of plant disease pathogens and characterization of plant microbial populations constitute a rapidly evolving research field. Fungal plant diseases are of major phytopathological concern; thus, the development of metabarcoding approaches for the detection of phytopathogenic fungi is becoming increasingly imperative in the context of plant disease prognosis. We developed a multiplex metabarcoding method for the identification of fungal phytopathogens and endophytes in olive young shoots, using the MinION sequencing platform (Oxford Nanopore Technologies). Selected fungal-specific primers were used to amplify three different genomic DNA loci (ITS, beta-tubulin, and 28S LSU) originating from olive twigs. A multiplex metabarcoding approach was initially evaluated using healthy olive twigs, and further assessed with naturally infected olive twig samples. Bioinformatic analysis of basecalled reads was carried out using MinKNOW, BLAST+ and R programming, and results were also evaluated using the BugSeq cloud platform. Data analysis highlighted the approaches based on ITS and their combination with beta-tubulin as the most informative ones according to diversity estimations. Subsequent implementation of the method on symptomatic samples identified major olive pathogens and endophytes including genera such as Cladosporium, Didymosphaeria, Paraconiothyrium, Penicillium, Phoma, Verticillium, and others.},
}
@article {pmid37998910,
year = {2023},
author = {Carlson, SL and Mathew, L and Savage, M and Kok, K and Lindsay, JO and Munro, CA and McCarthy, NE},
title = {Mucosal Immunity to Gut Fungi in Health and Inflammatory Bowel Disease.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {11},
pages = {},
pmid = {37998910},
issn = {2309-608X},
abstract = {The gut microbiome is a diverse microbial community composed of bacteria, viruses, and fungi that plays a major role in human health and disease. Dysregulation of these gut organisms in a genetically susceptible host is fundamental to the pathogenesis of inflammatory bowel disease (IBD). While bacterial dysbiosis has been a predominant focus of research for many years, there is growing recognition that fungal interactions with the host immune system are an important driver of gut inflammation. Candida albicans is likely the most studied fungus in the context of IBD, being a near universal gut commensal in humans and also a major barrier-invasive pathogen. There is emerging evidence that intra-strain variation in C. albicans virulence factors exerts a critical influence on IBD pathophysiology. In this review, we describe the immunological impacts of variations in C. lbicans colonisation, morphology, genetics, and proteomics in IBD, as well as the clinical and therapeutic implications.},
}
@article {pmid37998819,
year = {2023},
author = {DuPont, HL and Salge, MMH},
title = {The Importance of a Healthy Microbiome in Pregnancy and Infancy and Microbiota Treatment to Reverse Dysbiosis for Improved Health.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
pmid = {37998819},
issn = {2079-6382},
abstract = {BACKGROUND: The microbiome of newborn infants during the first 1000 days, influenced early on by their mothers' microbiome health, mode of delivery and breast feeding, orchestrates the education and programming of the infant's immune system and determines in large part the general health of the infant for years.<br><br>METHODS: PubMed was reviewed for maternal infant microbiome health and microbiota therapy in this setting with prebiotics, probiotics, vaginal seeding and fecal microbiota transplantation (FMT).<br><br>RESULTS: A healthy nonobese mother, vaginal delivery and strict breast feeding contribute to microbiome health in a newborn and young infant. With reduced microbiome diversity (dysbiosis) during pregnancy, cesarean delivery, prematurity, and formula feeding contribute to dysbiosis in the newborn. Microbiota therapy is an important approach to repair dysbiosis in pregnant women and their infants. Currently available probiotics can have favorable metabolic effects on mothers and infants, but these effects are variable. In research settings, reversal of infant dysbiosis can be achieved via vaginal seeding or FMT. Next generation probiotics in development should replace current probiotics and FMT.<br><br>CONCLUSIONS: The most critical phase of human microbiome development is in the first 2-3 years of life. Preventing and treating dysbiosis during pregnancy and early life can have a profound effect on an infant's later health.},
}
@article {pmid37998812,
year = {2023},
author = {Chun Giok, K and Menon, RK},
title = {The Microbiome of Peri-Implantitis: A Systematic Review of Next-Generation Sequencing Studies.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
pmid = {37998812},
issn = {2079-6382},
support = {//Ajman University/ ; },
abstract = {(1) Introduction: Current evidence shows that mechanical debridement augmented with systemic and topical antibiotics may be beneficial for the treatment of peri-implantitis. The microbial profile of peri-implantitis plays a key role in identifying the most suitable antibiotics to be used for the treatment and prevention of peri-implantitis. This systematic review aimed to summarize and critically analyze the methodology and findings of studies which have utilized sequencing techniques to elucidate the microbial profiles of peri-implantitis. (2) Results: Fusobacterium, Treponema, and Porphyromonas sp. are associated with peri-implantitis. Veillonella sp. are associated with healthy implant sites and exhibit a reduced prevalence in deeper pockets and with greater severity of disease progression. Streptococcus sp. have been identified both in diseased and healthy sites. Neisseria sp. have been associated with healthy implants and negatively correlate with the probing depth. Methanogens and AAGPRs were also detected in peri-implantitis sites. (3) Methods: The study was registered with the International Prospective Register of Systematic Reviews (PROSPERO) (CRD42023459266). The PRISMA criteria were used to select articles retrieved from a systematic search of the Scopus, Cochrane, and Medline databases until 1 August 2023. Title and abstract screening was followed by a full-text review of the included articles. Thirty-two articles were included in the final qualitative analysis. (4) Conclusions: A distinct microbial profile could not be identified from studies employing sequencing techniques to identify the microbiome. Further studies are needed with more standardization to allow a comparison of findings. A universal clinical parameter for the diagnosis of peri-implantitis should be implemented in all future studies to minimize confounding factors. The subject pool should also be more diverse and larger to compensate for individual differences, and perhaps a distinct microbial profile can be seen with a larger sample size.},
}
@article {pmid37998808,
year = {2023},
author = {Thavamani, A and Sankararaman, S and Al-Shakhshir, H and Retuerto, M and Velayuthan, S and Sferra, TJ and Ghannoum, M},
title = {Impact of Erythromycin as a Prokinetic on the Gut Microbiome in Children with Feeding Intolerance-A Pilot Study.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
pmid = {37998808},
issn = {2079-6382},
support = {Rainbow Children's Foundation, Cleveland//Rainbow Children's Foundation, Cleveland/ ; AI145289//National Institutes of Health grant to Mahmoud Ghannoum./ ; },
abstract = {BACKGROUND: Studies have demonstrated that the gut microbiome changes upon exposure to systemic antibiotics. There is a paucity of literature regarding impact on the gut microbiome by long-term usage of erythromycin ethyl succinate (EES) when utilized as a prokinetic.<br><br>METHODS: Stool samples from pediatric patients with feeding intolerance who received EES (N = 8) as a prokinetic were analyzed for both bacteriome and mycobiome. Age-matched children with similar clinical characteristics but without EES therapy were included as controls (N = 20).<br><br>RESULTS: In both groups, Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant bacterial phyla. Ascomycota was the most abundant fungal phyla, followed by Basidiomycota. There were no significant differences in richness between the groups for both bacterial and fungal microbiome. Alpha diversity (at genus and species levels) and beta diversity (at the genus level) were not significantly different between the groups for both bacterial and fungal microbiome. At the species level, there was a significant difference between the groups for fungal microbiota, with a p-value of 0.029. We also noted that many fungal microorganisms had significantly higher p-values in the EES group than controls at both genera and species levels.<br><br>CONCLUSIONS: In this observational case-control study, the prokinetic use of EES was associated with changes in beta diversity between the groups for mycobiome at the species level. Many fungal microorganisms were significantly higher in the EES group when compared to the controls. Confirmation of these results in larger trials will provide further evidence regarding the impact of EES on gut microbiota when utilized as a prokinetic agent.},
}
@article {pmid37998794,
year = {2023},
author = {Akomoneh, EA and Gestels, Z and Abdellati, S and Vereecken, K and Bartholomeeusen, K and Van den Bossche, D and Kenyon, C and Manoharan-Basil, SS},
title = {Genome Mining Uncovers NRPS and PKS Clusters in Rothia dentocariosa with Inhibitory Activity against Neisseria Species.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
pmid = {37998794},
issn = {2079-6382},
support = {2021//SOFI 2021 grant/ ; },
abstract = {The growing global threat of antimicrobial resistance is reaching a crisis point as common bacterial infections, including those caused by pathogenic Neisseria species, are becoming increasingly untreatable. This is compelling the scientific community to search for new antimicrobial agents, taking advantage of computational mining and using whole genome sequences to discover natural products from the human microbiome with antibiotic effects. In this study, we investigated the crude extract from a Rothia dentocariosa strain with demonstrated antimicrobial activity against pathogenic Neisseria spp. by spot-on-lawn assay. The genomic DNA of the R. dentocariosa strain was sequenced, and bioinformatic evaluation was performed using antiSMASH and PRISM to search for biosynthetic gene clusters (BGCs). The crude extract with potential antimicrobial activity was run on Tricine-SDS-PAGE, and the putative peptides were characterised using liquid chromatography-tandem mass spectrometry (LC-MS). The crude extract inhibited the growth of the pathogenic Neisseria spp. Six BGCs were identified corresponding to non-ribosomal peptide synthases (NRPSs), polyketide synthases (PKSs), and ribosomally synthesised and post-translationally modified peptides. Three peptides were also identified corresponding to Actinorhodin polyketide putative beta-ketoacyl synthase 1. These findings serve as a useful reference to facilitate the research and development of NRPS and PKS as antimicrobial products against multidrug-resistant N. gonorrhoeae.},
}
@article {pmid37998359,
year = {2023},
author = {Bosveld, CJ and Guth, C and Limjunyawong, N and Pundir, P},
title = {Emerging Role of the Mast Cell-Microbiota Crosstalk in Cutaneous Homeostasis and Immunity.},
journal = {Cells},
volume = {12},
number = {22},
pages = {},
pmid = {37998359},
issn = {2073-4409},
support = {NSERC RGPIN-2022-03453//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {The skin presents a multifaceted microbiome, a balanced coexistence of bacteria, fungi, and viruses. These resident microorganisms are fundamental in upholding skin health by both countering detrimental pathogens and working in tandem with the skin's immunity. Disruptions in this balance, known as dysbiosis, can lead to disorders like psoriasis and atopic dermatitis. Central to the skin's defense system are mast cells. These are strategically positioned within the skin layers, primed for rapid response to any potential foreign threats. Recent investigations have started to unravel the complex interplay between these mast cells and the diverse entities within the skin's microbiome. This relationship, especially during times of both balance and imbalance, is proving to be more integral to skin health than previously recognized. In this review, we illuminate the latest findings on the ties between mast cells and commensal skin microorganisms, shedding light on their combined effects on skin health and maladies.},
}
@article {pmid37998334,
year = {2023},
author = {Newman, TM and Wilson, AS and Clear, KYJ and Tallant, EA and Gallagher, PE and Cook, KL},
title = {Probiotic and Muscadine Grape Extract Interventions Shift the Gut Microbiome and Improve Metabolic Parameters in Female C57BL/6 Mice.},
journal = {Cells},
volume = {12},
number = {22},
pages = {},
pmid = {37998334},
issn = {2073-4409},
support = {T32CA247819/CA/NCI NIH HHS/United States ; P30CA012197/CA/NCI NIH HHS/United States ; },
abstract = {Obesity and Western-like diet consumption leads to gut microbiome dysbiosis, which is associated with the development of cardio-metabolic diseases and poor health outcomes. The objective of this study was to reduce Western diet-mediated gut microbial dysbiosis, metabolic dysfunction, and systemic inflammation through the administration of a novel combined intervention strategy (oral probiotic bacteria supplements and muscadine grape extract (MGE)). To do so, adult female C57BL/6 mice were fed a low-fat control or Western-style diet and sub-grouped into diet alone, probiotic intervention, antibiotic treatments, MGE supplementation, a combination of MGE and probiotics, or MGE and antibiotics for 13 weeks. Mouse body weight, visceral adipose tissue (VAT), liver, and mammary glands (MG) were weighed at the end of the study. Fecal 16S rRNA sequencing was performed to determine gut bacterial microbiome populations. Collagen, macrophage, and monocyte chemoattractant protein-1 (MCP-1) in the VAT and MG tissue were examined by immunohistochemistry. Adipocyte diameter was measured in VAT. Immunohistochemistry of intestinal segments was used to examine villi length, muscularis thickness, and goblet cell numbers. We show that dietary interventions in Western diet-fed mice modulated % body weight gain, visceral adiposity, MG weight, gut microbial populations, and inflammation. Intervention strategies in both diets effectively reduced VAT and MG fibrosis, VAT and MG macrophages, adipocyte diameter, and VAT and MG MCP-1. Interventions also improved intestinal health parameters. In conclusion, dietary intervention with MGE and probiotics modulates several microbial, inflammatory, and metabolic factors reducing poor health outcomes associated with Western diet intake.},
}
@article {pmid37998032,
year = {2023},
author = {Li, X and Yang, L and Jiang, S and Zhou, F and Jiang, S and Li, Y and Chen, X and Yang, Q and Duan, Y and Huang, J},
title = {Effect of Fly Maggot Protein as Dietary on Growth and Intestinal Microbial Community of Pacific White Shrimp Litopenaeus vannamei.},
journal = {Biology},
volume = {12},
number = {11},
pages = {},
pmid = {37998032},
issn = {2079-7737},
support = {2022YFD2400104, 2022SPY02001&#xff0c;2022SPY00002&#xff0c;2022SJS02001, CARS-48, CAFS (NO.2023TD34)//National Key R &amp; D Program of China (2022YFD2400104), Rural Revitalization Strategy Special Fund Seed Industry Revitalization Project of Guangdong Province (2022SPY02001&#xff0c;2022SPY00002&#xff0c;2022SJS02001), China Agriculture Research System of MOF and MARA(CARS-48/ ; },
abstract = {As the intensive development of aquaculture persists, the demand for fishmeal continues to grow; however, since fishery resources are limited, the price of fishmeal remains high. Therefore, there is an urgent need to develop new sources of protein. They are rich in proteins, fatty acids, amino acids, chitin, vitamins, minerals, and antibacterial substances. Maggot meal-based diet is an ideal source of high-quality animal protein and a new type of protein-based immune enhancer with good application prospects in animal husbandry and aquaculture. In the present study, we investigated the effects of three different diets containing maggot protein on the growth and intestinal microflora of Litopenaeus vannamei. The shrimp were fed either a control feed (no fly maggot protein added), FM feed (compound feed with 30% fresh fly maggot protein added), FF feed (fermented fly maggot protein), or HT feed (high-temperature pelleted fly maggot protein) for eight weeks. The results showed that fresh fly maggot protein in the feed was detrimental to shrimp growth, whereas fermented and high-temperature-pelleted fly maggot protein improved shrimp growth and survival. The effects of different fly maggot protein treatments on the intestinal microbiota of L. vannamei also varied. Fermented fly maggot protein feed and high-temperature-pelleted fly maggot protein feed increased the relative abundance of Ruegeria and Pseudomonas, which increased the abundance of beneficial bacteria and thus inhibited the growth of harmful bacteria. In contrast, fresh fly maggot proteins alter the intestinal microbiome, disrupting symbiotic relationships between bacteria, and causing invasion by Vibrio and antibiotic-resistant bacteria. These results suggest that fresh fly maggot proteins affect the composition of intestinal microorganisms, which is detrimental to the intestinal tract of L. vannamei, whereas fermented fly maggot protein feed affected the growth of L. vannamei positively by improving the composition of intestinal microorganisms.},
}
@article {pmid37998019,
year = {2023},
author = {Goraj, W and Pytlak, A and Grządziel, J and Gałązka, A and Stępniewska, Z and Szafranek-Nakonieczna, A},
title = {Dynamics of Methane-Consuming Biomes from Wieliczka Formation: Environmental and Enrichment Studies.},
journal = {Biology},
volume = {12},
number = {11},
pages = {},
pmid = {37998019},
issn = {2079-7737},
support = {DEC-2014/15/N/NZ8/00315//National Science Center/ ; },
abstract = {The rocks surrounding Wieliczka salt deposits are an extreme, deep subsurface ecosystem that as we studied previously harbors many microorganisms, including methanotrophs. In the presented research bacterial community structure of the Wieliczka Salt Mine was determined as well as the methanotrophic activity of the natural microbiome. Finally, an enrichment culture of methane-consuming methanotrophs was obtained. The research material used in this study consisted of rocks surrounding salt deposits in the Wieliczka Salt Mine. DNA was extracted directly from the pristine rock material, as well as from rocks incubated in an atmosphere containing methane and mineral medium, and from a methanotrophic enrichment culture from this ecosystem. As a result, the study describes the composition of the microbiome in the rocks surrounding the salt deposits, while also explaining how biodiversity changes during the enrichment culture of the methanotrophic bacterial community. The contribution of methanotrophic bacteria ranged from 2.614% in the environmental sample to 64.696% in the bacterial culture. The methanotrophic enrichment culture was predominantly composed of methanotrophs from the genera Methylomonas (48.848%) and Methylomicrobium (15.636%) with methane oxidation rates from 3.353 ± 0.105 to 4.200 ± 0.505 µmol CH4 mL[-1] day[-1].},
}
@article {pmid37997962,
year = {2023},
author = {Yang, L and Wan, X and Zhou, R and Yuan, Y},
title = {The Composition and Function of the Rhizosphere Bacterial Community of Paeonia lactiflora Varies with the Cultivar.},
journal = {Biology},
volume = {12},
number = {11},
pages = {},
pmid = {37997962},
issn = {2079-7737},
abstract = {The composition and diversity of the rhizosphere microbial community maintain the stability of the root microclimate, and several studies have focused on this aspect of rhizosphere microorganisms. However, how these communities vary with cultivars of a species is not completely understood. Paeonia lactiflora-a perennial herb species of the family Paeoniaceae-includes a wide variety of cultivars, with rich rhizosphere microbial resources. Hence, we studied the differences in rhizosphere bacterial communities associated with eight P. lactiflora cultivars. We noted that Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Planctomycetes and Chloroflexi were the dominant phyla associated with the cultivars. The composition of rhizosphere bacterial community of different cultivars was highly similar at taxonomic levels, but there were slightly differences in the relative abundance. LEfSe analysis showed that the cultivars "Sheng Tao Hua" and "Zi Lou Xian Jin" exhibited the most biomarkers. Differential ASV analysis revealed the maximum difference in ASV abundance between "Lian Tai" and "Zi Hong Zheng Hui", as well as between "Sheng Tao Hua" and "Tao Hua Fei Xue", and the maximum similarity between "Duo Ye Zi" and "Xue Feng". Co-occurrence network analysis revealed that rhizosphere bacteria in most cultivars maintain homeostasis by cooperation, wherein Actinobacteria and Proteobacteria played a vital role. In addition, microbial resources related to cultivars like bioremediation, organic degradation and resistance to diseases are found. This study revealed the structures of the rhizosphere bacterial communities associated with different cultivars of P. lactiflora and explored their stress resistance potential, which can be used to guide future agricultural practices.},
}
@article {pmid37997887,
year = {2023},
author = {Png, LH and Ng, DHL and Teo, NWY},
title = {Infectious disease for the rhinologist.},
journal = {Current opinion in otolaryngology &amp; head and neck surgery},
volume = {},
number = {},
pages = {},
pmid = {37997887},
issn = {1531-6998},
abstract = {PURPOSE OF REVIEW: The purpose of this review is to summarize the recent literature relating to viral, fungal and bacterial infections and their interactions within the sinonasal tract in the past 18 months.<br><br>RECENT FINDINGS: Coronavirus disease 2019 (COVID-19)-associated olfactory dysfunction (OD) is variant dependent. Magnetic resonance imaging studies have found greater olfactory cleft opacification and higher olfactory bulb volume in post-COVID-19 OD. Olfactory training remains the mainstay of treatment, while platelet-rich plasma injections and ultramicronized palmitoylethanolamide and luteolin combination oral supplementation have shown early promise.Consensus statements on paranasal sinus fungal balls and acute invasive fungal sinusitis have been released.Studies on the nasal microbiome have reported Staphylococcus and Corynebacterium as the most abundant genera, with higher levels of Staphylococcus and Corynebacterium being found in patients with chronic rhinosinusitis (CRS) and healthy individuals respectively. However, there is conflicting evidence on the significance of biodiversity of the nasal microbiome found in CRS versus healthy patients.<br><br>SUMMARY: While the peak of the COVID-19 pandemic is behind us, its sequelae continue to pose treatment challenges. Further studies in OD have implications in managing the condition, beyond those afflicted post-COVID-19 infection. Similarly, more research is needed in studying the nasal microbiome and its implications in the development and treatment of CRS.},
}
@article {pmid37997859,
year = {2023},
author = {Cox, A and Bomstein, Z and Jayaraman, A and Allred, C},
title = {The intestinal microbiota as mediators between dietary contaminants and host health.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {},
number = {},
pages = {15353702231208486},
doi = {10.1177/15353702231208486},
pmid = {37997859},
issn = {1535-3699},
abstract = {The gut microbiota sit at an important interface between the host and the environment, and are exposed to a multitude of nutritive and non-nutritive substances. These microbiota are critical to maintaining host health, but their supportive roles may be compromised in response to endogenous compounds. Numerous non-nutritive substances are introduced through contaminated foods, with three common groups of contaminants being bisphenols, phthalates, and mycotoxins. The former contaminants are commonly introduced through food and/or beverages packaged in plastic, while mycotoxins contaminate various crops used to feed livestock and humans alike. Each group of contaminants have been shown to shift microbial communities following exposure; however, specific patterns in microbial responses have yet to be identified, and little is known about the capacity of the microbiota to metabolize these contaminants. This review characterizes the state of existing research related to gut microbial responses to and biotransformation of bisphenols, phthalates, and mycotoxins. Collectively, we highlight the need to identify consistent, contaminant-specific responses in microbial shifts, whether these community alterations are a result of contaminant effects on the host or microbiota directly, and to identify the extent of contaminant biotransformation by microbiota, including if these transformations occur in physiologically relevant contexts.},
}
@article {pmid37997816,
year = {2024},
author = {Kumavath, R and Pavithran, H and Paul, S and Anju, VT and Busi, S and Dyavaiah, M},
title = {Effects of gut microbiome and obesity on the development, progression and prevention of cancer (Review).},
journal = {International journal of oncology},
volume = {64},
number = {1},
pages = {},
doi = {10.3892/ijo.2023.5592},
pmid = {37997816},
issn = {1791-2423},
abstract = {Cancer is one of the leading causes of death worldwide and it is estimated that the mortality rate of cancer will increase in the coming years. The etiology of the development and progression of cancer is multifactorial. Insights have been gained on the association between the human microbiome and tumor cell malignancy. A number of commensal microbe species are present in the human gut. They serve pivotal roles in maintaining several health and disease conditions, such as inflammatory bowel disease, irritable bowel syndrome, obesity and diabetes. Known major factors involved in cancer development include age, hormone levels, alcohol consumption, diet, being overweight, obesity, and infections, regardless of the type of cancer. Therefore, the present review aims to discuss the relationship between the gut microbiome and obesity‑associated malignancies, including colorectal, gastric and liver cancer. Obesity has been reported to contribute to the development of numerous types of cancer primarily caused by high fatty food intake. In addition, obesity‑associated microbiome alterations can lead to cancer and its progression. Dysbiosis of the gut microbiota can alter the metabolite profile, whilst increasing the levels of toxins, such as Bacteroides fragilis toxin and colibactin and cytolethal distending toxin, which are responsible for oncogenesis. The present review provides insights into the impact of gut microbiome dysbiosis on the progression of different types of cancers associated with obesity. It also discusses possible strategies for preserving a healthy gut microbiome. Different pre‑clinical and clinical models are available for studying cancer development downstream of gut microbiome dysbiosis. Furthermore, the role of metabolites or drugs employed in colorectal, gastric and liver cancer therapy would be discussed.},
}
@article {pmid37997753,
year = {2023},
author = {Oldereid, TS and Jiang, X and Øgaard, J and Schrumpf, E and Bjørnholt, JV and Rasmussen, H and Melum, E},
title = {Microbial exposure during early life regulates development of bile duct inflammation.},
journal = {Scandinavian journal of gastroenterology},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/00365521.2023.2278423},
pmid = {37997753},
issn = {1502-7708},
abstract = {OBJECTIVES: The early life microbiome has been linked to inflammatory diseases in adulthood and a role for the microbiome in bile duct inflammation is supported by both human and murine studies. We utilized the NOD.c3c4 mouse model that develops a spontaneous immune-driven biliary disease with a known contribution of the microbiome to evaluate the temporal effects of the early life microbiome.<br><br>MATERIALS AND METHODS: Germ-free (GF) NOD.c3c4 mice were conventionalized into a specific pathogen free environment at birth (conventionally raised, CONV-R) or at weaning (germ-free raised, GF-R) and compared with age and gender-matched GF and conventional (CONV) NOD.c3c4 mice. At 9&#x2009;weeks of age, liver pathology was assessed by conventional histology and flow cytometry immunophenotyping.<br><br>RESULTS: Neonatal exposure to microbes (CONV-R) increased biliary inflammation to similar levels as regular conventional NOD.c3c4 mice, while delayed exposure to microbes (GF-R) restrained the biliary inflammation. Neutrophil infiltration was increased in all conventionalized mice compared to GF. An immunophenotype in the liver similar to CONV was restored in both CONV-R and GF-R compared to GF mice displaying a proportional increase of B cells and reduction of T cells in the liver.<br><br>CONCLUSIONS: Microbial exposure during early life has a temporal impact on biliary tract inflammation in the NOD.c3c4 mouse model suggesting that age-sensitive interaction with commensal microbes have long-lasting effects on biliary immunity that can be of importance for human cholangiopathies.},
}
@article {pmid37997472,
year = {2023},
author = {Akbari, E and Milani, A and Seyedinkhorasani, M and Bolhassani, A},
title = {HPV co-infections with other pathogens in cancer development: A comprehensive review.},
journal = {Journal of medical virology},
volume = {95},
number = {11},
pages = {e29236},
doi = {10.1002/jmv.29236},
pmid = {37997472},
issn = {1096-9071},
abstract = {High-risk human papillomaviruses (HR-HPVs) cause various malignancies in the anogenital and oropharyngeal regions. About 70% of cervical and oropharyngeal cancers are caused by HPV types 16 and 18. Notably, some viruses including herpes simplex virus, Epstein-Barr virus, and human immunodeficiency virus along with various bacteria often interact with HPV, potentially impacting its replication, persistence, and cancer progression. Thus, HPV infection can be significantly influenced by co-infecting agents that influence infection dynamics and disease progression. Bacterial co-infections (e.g., Chlamydia trachomatis) along with bacterial vaginosis-related species also interact with HPV in genital tract leading to viral persistence and disease outcomes. Co-infections involving HPV and diverse infectious agents have significant implications for disease transmission and clinical progression. This review explores multiple facets of HPV infection encompassing the co-infection dynamics with other pathogens, interaction with the human microbiome, and its role in disease development.},
}
@article {pmid37996960,
year = {2023},
author = {Gafen, HB and Liu, CC and Ineck, NE and Scully, CM and Mironovich, MA and Taylor, CM and Luo, M and Leis, ML and Scott, EM and Carter, RT and Hernke, DM and Paul, NC and Lewin, AC},
title = {Alterations to the bovine bacterial ocular surface microbiome in the context of infectious bovine keratoconjunctivitis.},
journal = {Animal microbiome},
volume = {5},
number = {1},
pages = {60},
pmid = {37996960},
issn = {2524-4671},
support = {12897461//USDA AFRI/ ; },
abstract = {BACKGROUND: Infectious bovine keratoconjunctivitis (IBK) is a common cause of morbidity in cattle, resulting in significant economic losses. This study aimed to characterize the bovine bacterial ocular surface microbiome (OSM) through conjunctival swab samples from Normal eyes and eyes with naturally acquired, active IBK across populations of cattle using a three-part approach, including bacterial culture, relative abundance (RA, 16 S rRNA gene sequencing), and semi-quantitative random forest modeling (real-time polymerase chain reaction (RT-PCR)).<br><br>RESULTS: Conjunctival swab samples were obtained from eyes individually classified as Normal (n&#x2009;=&#x2009;376) or IBK (n&#x2009;=&#x2009;228) based on clinical signs. Cattle unaffected by IBK and the unaffected eye in cattle with contralateral IBK were used to obtain Normal eye samples. Moraxella bovis was cultured from similar proportions of IBK (7/228, 3.07%) and Normal eyes (1/159, 0.63%) (p&#x2009;=&#x2009;0.1481). Moraxella bovoculi was cultured more frequently (p&#x2009;<&#x2009;0.0001) in IBK (59/228, 25.88%) than Normal (7/159, 4.40%) eyes. RA (via 16&#xa0;S rRNA gene sequencing) of Actinobacteriota was significantly higher in Normal eyes (p&#x2009;=&#x2009;0.0045). Corynebacterium variabile and Corynebacterium stationis (Actinobacteriota) were detected at significantly higher RA (p&#x2009;=&#x2009;0.0008, p&#x2009;=&#x2009;0.0025 respectively) in Normal eyes. Rothia nasimurium (Actinobacteriota) was detected at significantly higher RA in IBK eyes (p&#x2009;<&#x2009;0.0001). Alpha-diversity index was not significantly different between IBK and Normal eyes (p&#x2009;>&#x2009;0.05). Alpha-diversity indices for geographic location (p&#x2009;<&#x2009;0.001), age (p&#x2009;<&#x2009;0.0001), sex (p&#x2009;<&#x2009;0.05) and breed (p&#x2009;<&#x2009;0.01) and beta-diversity indices for geographic location (p&#x2009;<&#x2009;0.001), disease status (p&#x2009;<&#x2009;0.01), age (p&#x2009;<&#x2009;0.001), sex (p&#x2009;<&#x2009;0.001) and breed (p&#x2009;<&#x2009;0.001) were significantly different between groups. Modeling of RT-PCR values reliably categorized the microbiome of IBK and Normal eyes; primers for Moraxella bovoculi, Moraxella bovis, and Staphylococcus spp. were consistently the most significant canonical variables in these models.<br><br>CONCLUSIONS: The results provide further evidence that multiple elements of the bovine bacterial OSM are altered in the context of IBK, indicating the involvement of a variety of bacteria in addition to Moraxella bovis, including Moraxella bovoculi and R. nasimurium, among others. Actinobacteriota RA is altered in IBK, providing possible opportunities for novel therapeutic interventions. While RT-PCR modeling provided limited further support for the involvement of Moraxella bovis in IBK, this was not overtly reflected in culture or RA results. Results also highlight the influence of geographic location and breed type (dairy or beef) on the bovine bacterial OSM. RT-PCR modeling reliably categorized samples as IBK or Normal.},
}
@article {pmid37996910,
year = {2023},
author = {Li, J and Zou, Y and Li, Q and Zhang, J and Bourne, DG and Lyu, Y and Liu, C and Zhang, S},
title = {A coral-associated actinobacterium mitigates coral bleaching under heat stress.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {83},
pmid = {37996910},
issn = {2524-6372},
support = {42122045//National Natural Science Foundation of China/ ; 41890853//National Natural Science Foundation of China/ ; GJTD-2020-12//K. C. Wong Education Foundation/ ; },
abstract = {BACKGROUND: The positive effects of exposing corals to microorganisms have been reported though how the benefits are conferred are poorly understood. Here, we isolated an actinobacterial strain (SCSIO 13291) from Pocillopora damicornis with capabilities to synthesize antioxidants, vitamins, and antibacterial and antiviral compounds supported with phenotypic and/or genomic evidence. Strain SCSIO 13291 was labeled with 5 (and - 6)-carboxytetramethylrhodamine, succinimidyl ester and the labeled cell suspension directly inoculated onto the coral polyp tissues when nubbins were under thermal stress in a mesocosm experiment. We then visualized the labelled bacterial cells and analyzed the coral physiological, transcriptome and microbiome to elucidate the effect this strain conferred on the coral holobiont under thermal stress.<br><br>RESULTS: Subsequent microscopic observations confirmed the presence of the bacterium attached to the coral polyps. Addition of the SCSIO 13291 strain reduced signs of bleaching in the corals subjected to heat stress. At the same time, alterations in gene expression, which were involved in reactive oxygen species and light damage mitigation, attenuated apoptosis and exocytosis in addition to metabolite utilization, were observed in the coral host and Symbiodiniaceae populations. In addition, the coral associated bacterial community altered with a more stable ecological network for samples inoculated with the bacterial strain.<br><br>CONCLUSIONS: Our results provide insights into the benefits of a putative actinobacterial probiotic strain that mitigate coral bleaching signs. This study suggests that the inoculation of bacteria can potentially directly benefit the coral holobiont through conferring metabolic activities or through indirect mechanisms of suppling additional nutrient sources.},
}
@article {pmid37996903,
year = {2023},
author = {Swift, JF and Migicovsky, Z and Trello, GE and Miller, AJ},
title = {Grapevine bacterial communities display compartment-specific dynamics over space and time within the Central Valley of California.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {84},
pmid = {37996903},
issn = {2524-6372},
support = {1546869//National Science Foundation Plant Genome Research Program/ ; 1758713//National Science Foundation Graduate Research Fellowship/ ; },
abstract = {BACKGROUND: Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose 'terroir', the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity via genome-to-genome interactions.<br><br>RESULTS: To understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA amplicon sequencing to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflected rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time.<br><br>CONCLUSIONS: These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local soil microbiome in the Central Valley of California.},
}
@article {pmid37996810,
year = {2023},
author = {Hülpüsch, C and Rauer, L and Nussbaumer, T and Schwierzeck, V and Bhattacharyya, M and Erhart, V and Traidl-Hoffmann, C and Reiger, M and Neumann, AU},
title = {Benchmarking MicrobIEM - a user-friendly tool for decontamination of microbiome sequencing data.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {269},
pmid = {37996810},
issn = {1741-7007},
abstract = {BACKGROUND: Microbiome analysis is becoming a standard component in many scientific studies, but also requires extensive quality control of the 16S rRNA gene sequencing data prior to analysis. In particular, when investigating low-biomass microbial environments such as human skin, contaminants distort the true microbiome sample composition and need to be removed bioinformatically. We introduce MicrobIEM, a novel tool to bioinformatically remove contaminants using negative controls.<br><br>RESULTS: We benchmarked MicrobIEM against five established decontamination approaches in four 16S rRNA amplicon sequencing datasets: three serially diluted mock communities (10[8]-10[3] cells, 0.4-80% contamination) with even or staggered taxon compositions and a skin microbiome dataset. Results depended strongly on user-selected algorithm parameters. Overall, sample-based algorithms separated mock and contaminant sequences best in the even mock, whereas control-based algorithms performed better in the two staggered mocks, particularly in low-biomass samples (&#x2264;&#x2009;10[6] cells). We show that a correct decontamination benchmarking requires realistic staggered mock communities and unbiased evaluation measures such as Youden's index. In the skin dataset, the Decontam prevalence filter and MicrobIEM's ratio filter effectively reduced common contaminants while keeping skin-associated genera.<br><br>CONCLUSIONS: MicrobIEM's ratio filter for decontamination performs better or as good as established bioinformatic decontamination tools. In contrast to established tools, MicrobIEM additionally provides interactive plots and supports selecting appropriate filtering parameters via a user-friendly graphical user interface. Therefore, MicrobIEM is the first quality control tool for microbiome experts without coding experience.},
}
@article {pmid37996708,
year = {2023},
author = {Kost, C and Patil, KR and Friedman, J and Garcia, SL and Ralser, M},
title = {Metabolic exchanges are ubiquitous in natural microbial communities.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {37996708},
issn = {2058-5276},
support = {KO 3909/9-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KO 3909/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KO 3909/4-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KO 3909/6-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 9B831//Volkswagen Foundation (VolkswagenStiftung)/ ; 866028//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ERC-SyG-2020 951475//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 883/22//Israel Science Foundation (ISF)/ ; 2022-03077//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; IA 200829/Z/16/Z//Wellcome Trust (Wellcome)/ ; },
abstract = {Microbial communities drive global biogeochemical cycles and shape the health of plants and animals-including humans. Their structure and function are determined by ecological and environmental interactions that govern the assembly, stability and evolution of microbial communities. A widely held view is that antagonistic interactions such as competition predominate in microbial communities and are ecologically more important than synergistic interactions-for example, mutualism or commensalism. Over the past decade, however, a more nuanced picture has emerged, wherein bacteria, archaea and fungi exist within interactive networks in which they exchange essential and non-essential metabolites. These metabolic interactions profoundly impact not only the physiology, ecology and evolution of the strains involved, but are also central to the functioning of many, if not all, microbiomes. Therefore, we advocate for a balanced view of microbiome ecology that encompasses both synergistic and antagonistic interactions as key forces driving the structure and dynamics within microbial communities.},
}
@article {pmid37996661,
year = {2023},
author = {Romanowicz, KJ and Crump, BC and Kling, GW},
title = {Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {124},
pmid = {37996661},
issn = {2730-6151},
support = {DEB-1637459//National Science Foundation (NSF)/ ; DEB-1754835//National Science Foundation (NSF)/ ; DEB-22-24743//National Science Foundation (NSF)/ ; OPP-1936769//National Science Foundation (NSF)/ ; },
abstract = {Microorganisms drive many aspects of organic carbon cycling in thawing permafrost soils, but the compositional trajectory of the post-thaw microbiome and its metabolic activity remain uncertain, which limits our ability to predict permafrost-climate feedbacks in a warming world. Using quantitative metabarcoding and metagenomic sequencing, we determined relative and absolute changes in microbiome composition and functional gene abundance during thaw incubations of wet sedge tundra collected from northern Alaska, USA. Organic soils from the tundra active-layer (0-50 cm), transition-zone (50-70 cm), and permafrost (70+ cm) depths were incubated under reducing conditions at 4 °C for 30 days to mimic an extended thaw duration. Following extended thaw, we found that iron (Fe)-cycling Gammaproteobacteria, specifically the heterotrophic Fe(III)-reducing Rhodoferax sp. and chemoautotrophic Fe(II)-oxidizing Gallionella sp., increased by 3-5 orders of magnitude in absolute abundance within the transition-zone and permafrost microbiomes, accounting for 65% of community abundance. We also found that the abundance of genes for Fe(III) reduction (e.g., MtrE) and Fe(II) oxidation (e.g., Cyc1) increased concurrently with genes for benzoate degradation and pyruvate metabolism, in which pyruvate is used to generate acetate that can be oxidized, along with benzoate, to CO2 when coupled with Fe(III) reduction. Gene abundance for CH4 metabolism decreased following extended thaw, suggesting dissimilatory Fe(III) reduction suppresses acetoclastic methanogenesis under reducing conditions. Our genomic evidence indicates that microbial carbon degradation is dominated by iron redox metabolism via an increase in gene abundance associated with Fe(III) reduction and Fe(II) oxidation during initial permafrost thaw, likely increasing microbial respiration while suppressing methanogenesis in wet sedge tundra.},
}
@article {pmid37996511,
year = {2023},
author = {Vänni, P and Tejesvi, MV and Ainonen, S and Renko, M and Korpela, K and Salo, J and Paalanne, N and Tapiainen, T},
title = {Author Correction: Delivery mode and perinatal antibiotics influence the predicted metabolic pathways of the gut microbiome.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20598},
doi = {10.1038/s41598-023-47520-y},
pmid = {37996511},
issn = {2045-2322},
}
@article {pmid37996480,
year = {2023},
author = {Abdollahiyan, S and Nabavi-Rad, A and Keshavarz Azizi Raftar, S and Monnoye, M and Salarieh, N and Farahanie, A and Asadzadeh Aghdaei, H and Zali, MR and Hatami, B and Gérard, P and Yadegar, A},
title = {Characterization of gut microbiome composition in Iranian patients with nonalcoholic fatty liver disease and nonalcoholic steatohepatitis.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20584},
pmid = {37996480},
issn = {2045-2322},
support = {no. RIGLD 1088//Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran/ ; },
abstract = {Gut microbiota dysbiosis is intimately associated with development of non-alcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH). Nevertheless, the gut microbial community during the course of NAFLD and NASH is yet to be comprehensively profiled. This study evaluated alterations in fecal microbiota composition in Iranian patients with NAFLD and NASH compared with healthy individuals. This cross-sectional study enrolled 15 NAFLD, 15 NASH patients, and 20 healthy controls, and their clinical parameters were examined. The taxonomic composition of the fecal microbiota was determined by sequencing the V3-V4 region of 16S rRNA genes of stool samples. Compared to the healthy controls, NAFLD and NASH patients presented reduced bacterial diversity and richness. We noticed a reduction in the relative abundance of Bacteroidota and a promotion in the relative abundance of Proteobacteria in NAFLD and NASH patients. L-histidine degradation I pathway, pyridoxal 5'-phosphate biosynthesis I pathway, and superpathway of pyridoxal 5'-phosphate biosynthesis and salvage were more abundant in NAFLD patients than in healthy individuals. This study examined fecal microbiota dysbiosis in NAFLD and NASH patients and presented consistent results to European countries. These condition- and ethnicity-specific data could provide different diagnostic signatures and therapeutic targets.},
}
@article {pmid37996396,
year = {2023},
author = {Duperron, S and Foucault, P and Duval, C and Goto, M and Gallet, A and Colas, S and Marie, B},
title = {Multi-omics analyses from a single sample: prior metabolite extraction does not alter the 16S rRNA-based characterization of prokaryotic community in a diversity of sample types.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnad125},
pmid = {37996396},
issn = {1574-6968},
abstract = {Massive sequencing of the 16S rRNA gene has become a standard first step to describe and compare microbial communities from various samples. Parallel analysis of high numbers of samples makes it relevant to the statistical testing of the influence of natural or experimental factors and variables. However, these descriptions fail to document changes in community or ecosystem functioning. Non-targeted metabolomics are a suitable tool to bridge this gap, yet extractions protocols are different. In this study, prokaryotic community compositions are documented by 16S rRNA gene sequencing after direct DNA extraction, or after metabolites extraction followed by DNA extraction. Results obtained using the V3-V4 region on non-axenic cultures of cyanobacteria, lake water column, biofilm, gut of wild and lab-reared fish, indicate that prior extraction of metabolites does not influence the obtained image of prokaryotic communities. This validates sequential extraction of metabolites followed by DNA as a way to combine 16S rRNA sequencing with metabolome characterization from a single sample. This approach has the potential to complement community structure characterization with a proxy of their functioning, without the uncertainties associated with the use of separate samples.},
}
@article {pmid37996257,
year = {2023},
author = {Venugopal, N and Armstrong, PA and Wright, TJ and Randolph, KM and Batson, RD and Yuen, KCJ and Masel, B and Sheffield-Moore, M and Pyles, RB and Urban, RJ},
title = {Is there a role for growth hormone replacement in adults to control acute and post-acute COVID-19?.},
journal = {Best practice &amp; research. Clinical endocrinology &amp; metabolism},
volume = {},
number = {},
pages = {101842},
doi = {10.1016/j.beem.2023.101842},
pmid = {37996257},
issn = {1878-1594},
abstract = {The SARS-CoV-2 pandemic created a multitude of medical crossroads requiring real time adaptations of best practice covering preventative and interventional aspects of care. Among the many discoveries borne from efforts to address the myriad clinical presentations across multiple organ systems was a common impact on tissues with cells that express the ACE-2 receptor. The vast majority of acute infections began and often ended in the respiratory tract, but more recent evaluations have confirmed significant extrapulmonary manifestations including symptom clusters that extend beyond the acute phase of infection collectively referred to as "post-acute sequelae SARS-CoV-2 infection" (PASC) or more commonly as "long (-haul) COVID". Both acute SARS-CoV-2 infection and PASC are associated with gut microbiome dysbiosis and alterations in the gut-brain and HPA-axis in a subset of the infected. Mounting evidence suggests these extrapulmonary manifestations may ultimately lead to reduced growth hormone (GH) secretion as demonstrated following stimulation tests. Disrupted GH secretion could cause or exacerbate long lasting neuropsychological symptoms as seen in other similar manifesting conditions. Ongoing clinical research has shown promising improvement in PASC patients with fatigue and cognition complaints can be achieved via GH replacement therapy. GH stimulation testing should be considered in PASC workups and future research should delve deeper into the mechanistic effects of GH on acute COVID and PASC.},
}
@article {pmid37996087,
year = {2023},
author = {Chen, YF and Li, SC and Huang, EY},
title = {Role of microbiota in radiation-induced small-bowel damage.},
journal = {Journal of radiation research},
volume = {},
number = {},
pages = {},
doi = {10.1093/jrr/rrad084},
pmid = {37996087},
issn = {1349-9157},
support = {CORPG8K0161//Kaohsiung Chang Gung Medical Research Project/ ; },
abstract = {Radiation-induced gastrointestinal damage is a common acute radiation syndrome. Previous studies have highlighted that Galectin-1 and Interleukin-6 (IL-6) are associated with flaking of small intestinal villi and intestinal radioresistance. Therefore, our goal is to study whether gut bacteria regulated by galectin-1 or IL-6 can mitigate radiation-induced small intestine damage. In this study, differences between galectin-1, sgp130-regulated and wild-type (WT) mice were analyzed by microbiome array. The effects of the Firmicutes/Bacteroidetes (F/B) ratio and the proportion of bacterial distribution at the phylum level were observed after 18 Gy whole abdomen radiation. Fecal microbiota transplantation was used to implant radioresistant gut flora into WT mice, and the number of viable small intestinal crypt foci was observed by immunohistochemistry. Fecal transplantation from galectin-1 knockout and sgp130 transgenic mice, with higher radiation resistance, into WT mice significantly increased the number of surviving small intestinal crypts. This radiation resistance, generated through gene regulation, was not affected by the F/B ratio. We initially found that the small intestinal villi of WT mice receiving radioresistant mouse fecal bacteria demonstrated better repair outcomes after radiation exposure. These results indicate the need for a focus on the identification and application of superior radioresistant bacterial strains. In our laboratory, we will further investigate specific radioresistant bacterial strains to alleviate acute side effects of radiation therapy to improve the patients' immune ability and postoperative quality of life.},
}
@article {pmid37996062,
year = {2023},
author = {Aggarwal, H and Gautam, J and Kumari, D and Gupta, SK and Bajpai, S and Chaturvedi, K and Kumar, Y and Dikshit, M},
title = {Comparative profiling of gut microbiota and metabolome in diet-induced obese and insulin-resistant C57BL/6J mice.},
journal = {Biochimica et biophysica acta. Molecular cell research},
volume = {},
number = {},
pages = {119643},
doi = {10.1016/j.bbamcr.2023.119643},
pmid = {37996062},
issn = {1879-2596},
abstract = {Diet-based models are commonly used to investigate obesity and related disorders. We conducted a comparative profiling of three obesogenic diets HFD, high fat diet; HFHF, high fat high fructose diet; and HFCD, high fat choline deficient diet to assess their impact on the gut microbiome and metabolome. After 20 weeks, we analyzed the gut microbiota and metabolomes of liver, plasma, cecal, and fecal samples. Fecal and plasma bile acids (BAs) and fecal short-chain fatty acids (SCFAs) were also examined. Significant changes were observed in fecal and cecal metabolites, with increased Firmicutes and decreased Bacteroidetes in the HFD, HFHF, and HFCD-fed mice compared to chow and LFD (low fat diet)-fed mice. Most BAs were reduced in plasma and fecal samples of obese groups, except taurocholic acid, which increased in HFCD mice's plasma. SCFAs like acetate and butyrate significantly decreased in obesogenic diet groups, while propionic acid specifically decreased in the HFCD group. Pathway analysis revealed significant alterations in amino acid, carbohydrate metabolism, and nucleic acid biosynthesis pathways in obese mice. Surprisingly, even LFD-fed mice showed distinct changes in microbiome and metabolite profiles compared to the chow group. This study provides insights into gut microbiome dysbiosis and metabolite alterations induced by obesogenic and LFD diets in various tissues. These findings aid in selecting suitable diet models to study the role of the gut microbiome and metabolites in obesity and associated disorders, with potential implications for understanding similar pathologies in humans.},
}
@article {pmid37995886,
year = {2023},
author = {Wang, P and Wang, J and Wang, L and Lv, J and Shao, Y and He, D},
title = {High throughput sequencing technology reveals alteration of lower respiratory tract microbiome in severe aspiration pneumonia and its association with inflammation.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105533},
doi = {10.1016/j.meegid.2023.105533},
pmid = {37995886},
issn = {1567-7257},
abstract = {BACKGROUND: Aspiration pneumonia is a common and severe clinical condition. The microbiome present in the lower respiratory tract plays a crucial role in regulating human inflammatory response. However, the relationship between the altered lower respiratory tract microbiome and inflammation in aspiration pneumonia remains inadequately explored.<br><br>PURPOSE: To investigate the alteration of the lower respiratory tract microbiome in severe aspiration pneumonia patients and explore the potential correlation between microbiome components and inflammatory response.<br><br>METHOD: Patients in the severe aspiration pneumonia group and control group were enrolled from the intensive care unit of Jinshan Hospital, Fudan University between December 31,2020 and, August 19,2021. Sputum specimens were collected from all participants and subsequently subjected to 16S rDNA high throughput sequencing technology. The concentration of inflammatory cytokines in serum was measured using enzyme-linked immunosorbent assay (ELISA) kits, and collected data including patients' demographic information, clinical data, and laboratory examination results were recorded for further analysis.<br><br>RESULTS: Alteration in the lower respiratory tract microbiome was observed in severe aspiration pneumonia. Compared to the control group, a significant decrease in the relative abundance of Firmicutes was found at the phylum level (P&#x202f;<&#x202f;0.01). At the family level, the relative abundance of Corynebacteriaceae, Enterobacteriaceae and Enterococcaceae increased significantly (P&#x202f;<&#x202f;0.001, P&#x202f;<&#x202f;0.05, P&#x202f;<&#x202f;0.01). There were no significant differences in community diversity of the lower respiratory tract between the two groups. Patients in the severe aspiration pneumonia group exhibited significantly higher levels of inflammation compared to those in the control group. Correlation analysis showed that the relative abundance of Corynebacteriaceae was positively correlated with the expression level of IL-1&#x3b2; and IL-18 (P&#x202f;=&#x202f;0.002, P&#x202f;=&#x202f;0.02); the relative abundance of Enterobacteriaceae was negatively correlated with IL-4 (P&#x202f;=&#x202f;0.011); no other significant correlations have been identified between microbiota and inflammatory indicators thus far (P&#x202f;>&#x202f;0.05).<br><br>CONCLUSIONS: Alteration of the lower respiratory tract microbiome is critically involved in inflammation and disease progression in severe cases of aspiration pneumonia. The potential inflammation regulation properties of the microbiome hold promising value for developing novel therapeutic approaches aimed at mitigating the severity of the disease.},
}
@article {pmid37995844,
year = {2023},
author = {Bonnici, V and Mengoni, C and Mangoni, M and Franco, G and Giugno, R},
title = {PanDelos-frags: A methodology for discovering pangenomic content of incomplete microbial assemblies.},
journal = {Journal of biomedical informatics},
volume = {},
number = {},
pages = {104552},
doi = {10.1016/j.jbi.2023.104552},
pmid = {37995844},
issn = {1532-0480},
abstract = {Pangenomics was originally defined as the problem of comparing the composition of genes into gene families within a set of bacterial isolates belonging to the same species. The problem requires the calculation of sequence homology among such genes. When combined with metagenomics, namely for human microbiome composition analysis, gene-oriented pangenome detection becomes a promising method to decipher ecosystem functions and population-level evolution. Established computational tools are able to investigate the genetic content of isolates for which a complete genomic sequence is available. However, there is a plethora of incomplete genomes that are available on public resources, which only a few tools may analyze. Incomplete means that the process for reconstructing their genomic sequence is not complete, and only fragments of their sequence are currently available. However, the information contained in these fragments may play an essential role in the analyses. Here, we present PanDelos-frags, a computational tool which exploits and extends previous results in analysing complete genomes. It provides a new methodology for inferring missing genetic information and thus for managing incomplete genomes. PanDelos-frags outperforms state-of-the-art approaches in reconstructing gene families in synthetic benchmarks and in a real use case of metagenomics. PanDelos-frags is publicly available at https://github.com/InfOmics/PanDelos-frags.},
}
@article {pmid37995697,
year = {2023},
author = {Giez, C and Pinkle, D and Giencke, Y and Wittlieb, J and Herbst, E and Spratte, T and Lachnit, T and Klimovich, A and Selhuber-Unkel, C and Bosch, TCG},
title = {Multiple neuronal populations control the eating behavior in Hydra and are responsive to microbial signals.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.10.038},
pmid = {37995697},
issn = {1879-0445},
abstract = {Although recent studies indicate the impact of microbes on the central nervous systems and behavior, it remains unclear how the relationship between the functionality of the nervous system, behavior, and the microbiota evolved. In this work, we analyzed the eating behavior of Hydra, a host that has a simple nervous system and a low-complexity microbiota. To identify the neuronal subpopulations involved, we used a subpopulation-specific cell ablation system and calcium imaging. The role of the microbiota was uncovered by manipulating the diversity of the natural microbiota. We show that different neuronal subpopulations are functioning together to control eating behavior. Animals with a drastically reduced microbiome had severe difficulties in mouth opening due to a significantly increased level of glutamate. This could be reversed by adding a full complement of the microbiota. In summary, we provide a mechanistic explanation of how Hydra's nervous system controls eating behavior and what role microbes play in this.},
}
@article {pmid37995518,
year = {2023},
author = {Liu, Z and Liu, J and Geng, J and Wu, E and Zhu, J and Cong, B and Wu, R and Sun, H},
title = {Metatranscriptomic characterization of six types of forensic samples and its potential application to body fluid/tissue identification: A pilot study.},
journal = {Forensic science international. Genetics},
volume = {68},
number = {},
pages = {102978},
doi = {10.1016/j.fsigen.2023.102978},
pmid = {37995518},
issn = {1878-0326},
abstract = {Microorganisms are potential markers for identifying body fluids (venous and menstrual blood, semen, saliva, and vaginal secretion) and skin tissue in forensic genetics. Existing published studies have mainly focused on investigating microbial DNA by 16 S rRNA gene sequencing or metagenome shotgun sequencing. We rarely find microbial RNA level investigations on common forensic body fluid/tissue. Therefore, the use of metatranscriptomics to characterize common forensic body fluids/tissue has not been explored in detail, and the potential application of metatranscriptomics in forensic science remains unknown. Here, we performed 30 metatranscriptome analyses on six types of common forensic sample from healthy volunteers by massively parallel sequencing. After quality control and host RNA filtering, a total of 345,300 unigenes were assembled from clean reads. Four kingdoms, 137 phyla, 267 classes, 488 orders, 985 families, 2052 genera, and 4690 species were annotated across all samples. Alpha- and beta-diversity and differential analysis were also performed. As a result, the saliva and skin groups demonstrated high alpha diversity (Simpson index), while the venous blood group exhibited the lowest diversity despite a high Chao1 index. Specifically, we discussed potential microorganism contamination and the "core microbiome," which may be of special interest to forensic researchers. In addition, we implemented and evaluated artificial neural network (ANN), random forest (RF), and support vector machine (SVM) models for forensic body fluid/tissue identification (BFID) using genus- and species-level metatranscriptome profiles. The ANN and RF prediction models discriminated six forensic body fluids/tissue, demonstrating that the microbial RNA-based method could be applied to BFID. Unlike metagenomic research, metatranscriptomic analysis can provide information about active microbial communities; thus, it may have greater potential to become a powerful tool in forensic science for microbial-based individual identification. This study represents the first attempt to explore the application potential of metatranscriptome profiles in forensic science. Our findings help deepen our understanding of the microorganism community structure at the RNA level and are beneficial for other forensic applications of metatranscriptomics.},
}
@article {pmid37995468,
year = {2023},
author = {Huh, E and Choi, JG and Choi, Y and Ju, IG and Kim, B and Shin, YJ and An, JM and Park, MG and Yim, SV and Chung, SJ and Seo, SU and Kim, D and Kim, CH and Kim, DH and Oh, MS},
title = {P. mirabilis-derived pore-forming haemolysin, HpmA drives intestinal alpha-synuclein aggregation in a mouse model of neurodegeneration.},
journal = {EBioMedicine},
volume = {98},
number = {},
pages = {104887},
doi = {10.1016/j.ebiom.2023.104887},
pmid = {37995468},
issn = {2352-3964},
abstract = {BACKGROUND: Recent studies suggesting the importance of the gut-microbiome in intestinal aggregated alpha synuclein (α-syn) have led to the exploration of the possible role of the gut-brain axis in central nervous system degeneration. Proteus mirabilis (P. mirabilis), a gram-negative facultative anaerobic bacterium, has been linked to brain neurodegeneration in animal studies. We hypothesised that P. mirabilis-derived virulence factors aggregate intestinal α-synuclein and could prompt the pathogenesis of dopaminergic neurodegeneration in the brain.<br><br>METHODS: We used vagotomised- and antibiotic-treated male murine models to determine the pathogenesis of P.&#xa0;mirabilis during brain neurodegeneration. The neurodegenerative factor that is driven by P.&#xa0;mirabilis was determined using genetically mutated P.&#xa0;mirabilis. The pathological functions and interactions of the virulence factors were determined in&#xa0;vitro.<br><br>FINDINGS: The results showed that P.&#xa0;mirabilis-induced motor dysfunction and neurodegeneration are regulated by intestinal &#x3b1;-syn aggregation in vagotomised- or antibiotic-treated murine models. We deduced that the specific virulence factor, haemolysin A (HpmA), plays a role in the pathogenesis of P.&#xa0;mirabilis. HpmA is involved in &#x3b1;-synuclein oligomerisation and membrane pore formation, resulting in the activation of mTOR-mediated autophagy signalling in intestinal neuroendocrine cells.<br><br>INTERPRETATION: Taken together, the results of the present study suggest that HpmA can interact with &#x3b1;-syn and act as a possible indicator of brain neurodegenerative diseases that are induced by P.&#xa0;mirabilis.<br><br>FUNDING: This study was supported by a grant from the National Research Foundation of Korea.},
}
@article {pmid37995431,
year = {2023},
author = {Liao, L and Sun, Y and Huang, L and Ye, L and Chen, L and Shen, M},
title = {A novel approach for exploring the regional features of vaginal fluids based on microbial relative abundance and alpha diversity.},
journal = {Journal of forensic and legal medicine},
volume = {100},
number = {},
pages = {102615},
doi = {10.1016/j.jflm.2023.102615},
pmid = {37995431},
issn = {1878-7487},
abstract = {Vaginal fluids are one of the most common biological samples in forensic sexual assault cases, and their characterization is vital to narrow the scope of investigation. Presently, approaches for identifying vaginal fluids in different regions are not only rare but also have certain limitations. However, the microbiome has shown the potential to identify the source of body fluids and reveal the characteristics of individuals. In this study, 16S rRNA gene high-throughput sequencing was used to characterize the vaginal microbial community from three regions, Sichuan, Hainan and Hunan. In addition, data on relative abundance and alpha diversity were used to construct a random forest model. The results revealed that the dominant genera in the three regions were Lactobacillus, followed by Gardnerella. In addition, Ureaplasma, Nitrospira, Nocardiodes, Veillonella and g-norank-f-Vicinamibacteraceae were significantly enriched genera in Sichuan, llumatobacter was enriched in Hainan, and Pseudomonas was enriched in Hunan. The random forest classifier based on combined data on relative abundance and alpha diversity had a good ability to distinguish vaginal fluids with similar dominant microbial compositions in the three regions. The study suggests that combining high-throughput sequencing data with machine learning models has good potential for application in the biogeographic inference of vaginal fluids.},
}
@article {pmid37995430,
year = {2023},
author = {Rubin-Blum, M and Yudkovsky, Y and Marmen, S and Raveh, O and Amrani, A and Kutuzov, I and Guy-Haim, T and Rahav, E},
title = {Tar patties are hotspots of hydrocarbon turnover and nitrogen fixation during a nearshore pollution event in the oligotrophic southeastern Mediterranean Sea.},
journal = {Marine pollution bulletin},
volume = {197},
number = {},
pages = {115747},
doi = {10.1016/j.marpolbul.2023.115747},
pmid = {37995430},
issn = {1879-3363},
abstract = {Weathered oil, that is, tar, forms hotspots of hydrocarbon degradation by complex biota in marine environment. Here, we used marker gene sequencing and metagenomics to characterize the communities of bacteria, archaea and eukaryotes that colonized tar patties and control samples (wood, plastic), collected in the littoral following an offshore spill in the warm, oligotrophic southeastern Mediterranean Sea (SEMS). We show potential aerobic and anaerobic hydrocarbon catabolism niches on tar interior and exterior, linking carbon, sulfur and nitrogen cycles. Alongside aromatics and larger alkanes, short-chain alkanes appear to fuel dominant populations, both the aerobic clade UBA5335 (Macondimonas), anaerobic Syntropharchaeales, and facultative Mycobacteriales. Most key organisms, including the hydrocarbon degraders and cyanobacteria, have the potential to fix dinitrogen, potentially alleviating the nitrogen limitation of hydrocarbon degradation in the SEMS. We highlight the complexity of these tar-associated communities, where bacteria, archaea and eukaryotes co-exist, likely exchanging metabolites and competing for resources and space.},
}
@article {pmid37995097,
year = {2023},
author = {Niu, X and Meng, Y and Cui, J and Li, R and Ding, X and Niu, B and Chang, G and Xu, N and Li, G and Wang, Y and Wang, L},
title = {Hepatic Stellate Cell- and Liver Microbiome-Specific Delivery System for Dihydrotanshinone I to Ameliorate Liver Fibrosis.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.3c06626},
pmid = {37995097},
issn = {1936-086X},
abstract = {Liver fibrosis is a major contributor to the morbidity and mortality associated with liver diseases, yet effective treatment options remain limited. Hepatic stellate cells (HSCs) are a promising target for hepatic fibrogenesis due to their pivotal role in disease progression. Our previous research has demonstrated the potential of Dihydrotanshinone I (DHI), a lipophilic component derived from the natural herb Salvia miltiorrhiza Bunge, in treating liver fibrosis by inhibiting the YAP/TEAD2 interaction in HSCs. However, the clinical application of DHI faces challenges due to its poor aqueous solubility and lack of specificity for HSCs. Additionally, recent studies have implicated the impact of liver microbiota, distinct from gut microbiota, on the pathogenesis of liver diseases. In this study, we have developed an HSC- and microbiome-specific delivery system for DHI by conjugating prebiotic-like cyclodextrin (CD) with vitamin A, utilizing PEG2000 as a linker (VAP2000@CD). Our results demonstrate that VAP2000@CD markedly enhances the cellular uptake in human HSC line LX-2 and enhances the deposition of DHI in the fibrotic liver in vivo. Subsequently, intervention with DHI-VAP2000@CD has shown a notable reduction in bile duct-like structure proliferation, collagen accumulation, and the expression of fibrogenesis-associated genes in rats subjected to bile duct ligation. These effects may be attributed to the regulation of the YAP/TEAD2 interaction. Importantly, the DHI-VAP2000@CD intervention has also restored microbial homeostasis in the liver, promoting the amelioration of liver inflammation. Overall, our findings indicate that DHI-VAP2000@CD represents a promising therapeutic approach for liver fibrosis by specifically targeting HSCs and restoring the liver microbial balance.},
}
@article {pmid37995075,
year = {2023},
author = {Yu, L and Chen, X and Bai, X and Fang, J and Sui, M},
title = {Microbiota Alters and Its Correlation with Molecular Regulation Underlying Depression in PCOS Patients.},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {37995075},
issn = {1559-1182},
support = {2022J01279//Natural Science Foundation of Fujian Province/ ; BS202203//doctoral research project of the Second Affiliated Hospital of Fujian Medical University/ ; 2019-1-48//Fujian Provincial Health Research Talents Training Project/ ; },
abstract = {Depression is one of the complications in patients with polycystic ovary syndrome (PCOS) that leads to considerable mental health. Accumulating evidence suggests that human gut microbiomes are associated with the progression of PCOS and depression. However, whether microbiota influences depression development in PCOS patients is still uncharacterized. In this study, we employed metagenomic sequencing and transcriptome sequencing (RNA-seq) to profile the composition of the fecal microbiota and gene expression of peripheral blood mononuclear cells in depressed women with PCOS (PCOS-DP, n = 27) in comparison to mentally healthy women with PCOS (PCOS, n = 18) and compared with healthy control (HC, n = 27) and patients with major depressive disorder (MDD, n = 29). Gut microbiota assessment revealed distinct patterns in the relative abundance in the PCOS-DP compared to HC, MDD, and PCOS groups. Several gut microbes exhibited uniquely and significantly higher abundance in the PCOS-DP compared to PCOS patients, inducing EC Ruminococcus torques, Coprococcus comes, Megasphaera elsdenii, Acidaminococcus intestini, and Barnesiella viscericola. Bacteroides eggerthii was a potential gut microbial biomarker for the PCOS-DP. RNA-seq profiling identified that 35 and 37 genes were significantly elevated and downregulated in the PCOS-DP, respectively. The enhanced differential expressed genes (DEGs) in the PCOS-DP were enriched in pathways involved in signal transduction and endocrine and metabolic diseases, whereas several lipid metabolism pathways were downregulated. Intriguingly, genes correlated with the gut microbiota were found to be significantly enriched in pathways of neurodegenerative diseases and the immune system, suggesting that changes in the microbiota may have a systemic impact on the expression of neurodegenerative diseases and immune genes. Gut microbe-related DEGs of CREB3L3 and CCDC173 were possible molecular biomarkers and therapeutic targets of women with PCOS-DP. Our multi-omics data indicate shifts in the gut microbiome and host gene regulation in PCOS patients with depression, which is of possible etiological and diagnostic importance.},
}
@article {pmid37994761,
year = {2023},
author = {Micheletti, C and Medori, MC and Bonetti, G and Iaconelli, A and Aquilanti, B and Matera, G and Bertelli, M},
title = {Effects of Carob Extract on the Intestinal Microbiome and Glucose Metabolism: A Systematic Review and Meta-Analysis.},
journal = {La Clinica terapeutica},
volume = {174},
number = {Suppl 2(6)},
pages = {169-172},
doi = {10.7417/CT.2023.2484},
pmid = {37994761},
issn = {1972-6007},
mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; Polyphenols/pharmacology ; Glucose ; *Fabaceae ; Pectins ; },
abstract = {The legume tree known as carob (Ceratonia siliqua L.) is indigenous to the Mediterranean area and over the centuries its pods had been traditionally used mostly as animal feed. However, it has gained great attention in human nutrition due to the molecular compounds it contains, which could offer many potential health benefits: for example, carob is renowned for its high content of fiber, vitamins, and minerals. Moreover, in traditional medicine it is credited with the ability to control glucose metabolism and gut microbiome. Modern science has also extensively acknowledged the numerous health ad-vantages deriving from its consumption, including its anti-diabetic, anti-inflammatory, and antioxidant properties. Due to its abundant contents of pectin, gums, and polyphenols (such as pinitol), carob has garnered significant attention as a well-researched plant with remarkable therapeutic properties. Notably, carob is extensively used in the production of semi-finished pastry products, particularly in ice cream and other creams (especially as a substitute for cocoa/chocolate): these applications indeed facilitate the exploration of its positive effects on glucose metabolism. Our study aimed at examining the effects of carob extract on intestinal microbiota and glucose metabolism. In this review, we conducted a thorough examination, comprising in vitro, in vivo, and clinical trials to appraise the consequences on human health of polyphenols and pectin from different carob species, including recently discovered ones with high polyphenol contents. Our goal was to learn more about the mechanisms through which carob extract can support a balanced gut flora and improve one's glucose metabolism. These results could influence the creation of novel functional foods and dietary supplements, to help with the management and prevention of chronic illnesses like diabetes and obesity.},
}
@article {pmid37994755,
year = {2023},
author = {Donato, K and Donato, K and Bonetti, G and Cristoni, S and Connelly, ST and Bertelli, M},
title = {Exploring the Impact of Tobacco Usage on Microbiome Dysbiosis and Associated Health Risks: A Comprehensive Review of Recent Advancements and Future Directions.},
journal = {La Clinica terapeutica},
volume = {174},
number = {Suppl 2(6)},
pages = {119-125},
doi = {10.7417/CT.2023.2478},
pmid = {37994755},
issn = {1972-6007},
mesh = {Humans ; Tobacco ; Dysbiosis/microbiology ; *Microbiota ; *Colitis, Ulcerative ; *Crohn Disease ; },
abstract = {All over the world, tobacco usage is quickly expanding. Though it presents a major health risk and is anticipated to have long-lasting impacts on the public and economic health of the country, its consumers are increasing with every passing day. Tobacco is being used in a variety of ways, with cigarettes being the most popular. Smoking affects the healthy oral, intestinal, and pulmonary microbiomes, often altering the dynamic equilibrium of the diverse bacteria that make up the human microbiome, or "dysbiosis". Smoking-induced dysbiosis can lead to developing conditions like asthma, chronic obstructive pul-monary disease, Crohn's disease, ulcerative colitis, and periodontitis. The purpose of the following article is to provide a better and more comprehensive overview of the key areas that the tobacco industry needs to investigate, such as microbiome manipulation, to provide a complete picture of recent advancements in tobacco research while also keeping public safety in mind, and the various diseases linked to tobacco use.},
}
@article {pmid37994721,
year = {2023},
author = {Ameratunga, D and Yazdani, A and Kroon, B},
title = {Antibiotics prior to or at the time of embryo transfer in ART.},
journal = {The Cochrane database of systematic reviews},
volume = {11},
number = {},
pages = {CD008995},
pmid = {37994721},
issn = {1469-493X},
abstract = {BACKGROUND: After an assisted reproductive technology (ART) cycle, embryo transfer (ET) involves the placement of one or more embryos into the uterine cavity, usually by passing a catheter through the cervical os. Despite the transfer of high-quality embryos, many ETs do not result in a pregnancy. There are many factors that may affect the success of ET. There is some evidence to suggest that increased endocervical microbial colonization at the time of ET results in lower pregnancy rates. The association between the cervico-vaginal microbiome and reduced pregnancy rates after ET may indicate either pre-existing dysbiosis in this patient population, or that the passage of the ET catheter itself may be introducing microbes that alter the microbiome of the endometrial cavity or lead to infection. Such an upper genital tract infection, contamination or alteration may have a negative impact on implantation and in vitro fertilization (IVF) success rates by both endometrial and embryonic mechanisms. The administration of antibiotics at the time of ET has been suggested as an intervention to reduce levels of microbial colonization and hence improve pregnancy rates.<br><br>OBJECTIVES: To evaluate the benefits and harms of antibiotic administration prior to or at the time of embryo transfer (ET) during assisted reproductive technology (ART) cycles.<br><br>SEARCH METHODS: We searched the Cochrane Gynaecology and Fertility (CGF) Group trials register, CENTRAL (now containing output from two trial registers and CINAHL), MEDLINE, Embase and PsycINFO, together with reference checking and contact with study authors and experts in the field to identify additional studies. The search date was November 2022.<br><br>SELECTION CRITERIA: We included two randomized controlled trials (RCT) that compared antibiotics administered by any route versus no antibiotics prior to ET.<br><br>DATA COLLECTION AND ANALYSIS: We used standard methodological procedures recommended by Cochrane, including assessing risk of bias of the included studies using the RoB 2 tool. The primary review outcome was live birth rate (LBR) or ongoing pregnancy, and secondary outcomes were clinical pregnancy rate (CPR), genital tract colonization rate, miscarriage rate, ectopic pregnancy rate, multiple pregnancy rate, fetal abnormalities, adverse events and pelvic infection.<br><br>MAIN RESULTS: We included two RCTs with 377 women in the review. Using the GRADE method, we assessed the certainty of the evidence as very low to low across measured outcomes. We are uncertain whether antibiotics given prior to or at the time of ET improved LBR (odds ratio (OR) 0.48, 95% confidence interval (CI) 0.10 to 2.23; 1 study, 27 women; low-certainty evidence). The evidence suggests that if LBR without antibiotics was 60%, the rate with antibiotics would be between 13% and 77%. We are uncertain whether antibiotics given prior to or at the time of ET improve CPR (OR 1.01, 95% CI 0.67 to 1.55; I&#xb2; = 0%; 2 studies, 377 women; low-certainty evidence). If the CPR without antibiotics was 37%, the rate with antibiotics would be between 29% and 48%. The administration of antibiotics prior to or at the time of ET may reduce genital tract colonization slightly (OR 0.59, 95% CI 0.37 to 0.95; 1 study, 130 women; very low-certainty evidence). If the genital tract colonization rate without antibiotics was 29%, the rate with antibiotics would be between 13% and 28%. However, this did not correspond to an effect on the pregnancy outcome. Only one study with low numbers of women reported on miscarriage rate, with one miscarriage reported in the group not receiving antibiotics (OR 4.04, 0.15 to 108.57; 1 study, 27 women; low-certainty evidence). There was insufficient evidence to reach a conclusion regarding adverse effects and other outcomes as no studies reported data suitable for analysis.<br><br>AUTHORS' CONCLUSIONS: We are uncertain if administration of antibiotics prior to or at the time of ET improves LBR in women undergoing ART based on a single study of 27 women with low-certainty evidence. We are uncertain whether there was a difference in CPR. There was evidence for a reduction in genital tract colonization rates, but the evidence was very low certainty. Data were lacking on other secondary outcomes. The pooled results should be interpreted with caution, due to the small number of women included in the analysis.},
}
@article {pmid37994699,
year = {2023},
author = {Hirsch, P and Tagirdzhanov, A and Kushnareva, A and Olkhovskii, I and Graf, S and Schmartz, GP and Hegemann, JD and Bozhüyük, KAJ and Müller, R and Keller, A and Gurevich, A},
title = {ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkad1086},
pmid = {37994699},
issn = {1362-4962},
support = {//Saarland University/ ; 466168626//DFG/ ; },
abstract = {The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.},
}
@article {pmid37994666,
year = {2023},
author = {Imai, K and Niwa, R and Fujioka, M and Ito, K},
title = {Understanding the quality and safety of food production through the lens of The Microbiome of The Built Environment.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbad164},
pmid = {37994666},
issn = {1347-6947},
abstract = {The Microbiome of the Built Environment (MoBE) is profoundly implicated in various sectors, including food science. The balance between beneficial and pathogenic microbes in these facilities directly influences product quality and public health. Maintaining a careful check on MoBE and external microbes is vital to the food industry to ensure quality control. There is also a risk of contamination in meat processing facility as well. However, over-sanitization can increase drug-resistant microbes, highlighting the importance of balanced microbial management. Additionally, facility design, influenced by understanding MoBE, can optimize the growth of beneficial microbes and inhibit pathogenic microbes. Microbial mapping, an emerging practice, offers insights into microbial hotspots within facilities, resulting in targeted interventions. As the food industry evolves, the intricate understanding and management of MoBE will be pivotal to ensuring optimal food quality, safety, and innovation.},
}
@article {pmid37994646,
year = {2023},
author = {Johannesson, L and Testa, G and Petrillo, N and Gregg, AR},
title = {Unique risk factors for unplanned preterm delivery in the uterus transplant recipient.},
journal = {Human reproduction (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/humrep/dead240},
pmid = {37994646},
issn = {1460-2350},
abstract = {STUDY QUESTION: Do characteristics of the lower uterine segment and cervix modify the risk of preterm delivery in uterus transplant (UTx) recipients?<br><br>SUMMARY ANSWER: The cervical length showed little association with preterm delivery, however, cervical inflammation deserves further exploration as a cause of preterm delivery.<br><br>WHAT IS KNOWN ALREADY: UTx recipients do not have the risk factors normally used to stratify pregnancies that would benefit from cervical length assessment. In addition, unique factors related to absent tissues, a different blood supply, inflammatory processes of rejection, cervical biopsies, and a different microbiome challenge the normal progressive remodeling of the cervix and thus cervical competence.<br><br>STUDY DESIGN, SIZE, DURATION: This is a subanalysis of a clinical trial of 20 women undergoing uterus transplantation at Baylor University Medical Center from 2016 to 2020, in addition to two women who received transplantation outside of a research protocol at our institution through September 2022. In this report, the first 16 UTx recipients that achieved live birth are included.<br><br>The focus of this study was 20 pregnancies that reached the second trimester in 16 women following UTx. We analyzed recipient, transplant, and donor factors to determine if characteristics were associated with delivery outcome. We compared obstetrical outcomes, including planned versus unplanned delivery, by factors such as number of superior venous anastomoses, warm ischemia and cold ischemia times, donor factors including cesarean sections, cervical biopsy results, and cervical ultrasound results.<br><br>Planned term deliveries occurred in 44% (8/18) of live births. Of the preterm births, 30% (3/10) were planned and 70% (7/10) were unplanned. Unplanned deliveries occurred in women with spontaneous preterm labor, severe rejection, subchorionic hematoma, and placenta previa. Cervical length in UTx recipients averaged 33.5&#x2009;mm at 24&#x2009;weeks and 31.5&#x2009;mm at 28&#x2009;weeks, comparable to values from the general population. No relationship was seen between delivery outcome and number of veins used, ischemic time, or number of previous cesarean sections.<br><br>The study's small size allows limited conclusions. The obstetric history of all donors was limited to mode of delivery.<br><br>Cervical length measurements in the UTx population are not expected to deviate from those with a native uterus. While cervical length surveillance remains important, attention must be paid to the results of cervical biopsies which are obtained to monitor rejection. Inflammatory processes seem most predictive of preterm delivery.<br><br>No funding was provided for this study. The authors report no conflicts of interest.<br><br>TRIAL REGISTRATION NUMBER: NCT02656550.},
}
@article {pmid37994199,
year = {2023},
author = {Wijewardene, L and Schwenker, JA and Friedrichsen, M and Jensen, A and Löbel, F and Austen, T and Ulrich, U and Fohrer, N and Bang, C and Waschina, S and Hölzel, CS},
title = {Selection of aquatic microbiota exposed to the herbicides flufenacet and metazachlor.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16535},
pmid = {37994199},
issn = {1462-2920},
abstract = {Herbicides are important, ubiquitous environmental contaminants, but little is known about their interaction with bacterial aquatic communities. Here, we sampled a protected natural freshwater habitat and characterised its microbiome in interaction with herbicides. We evolved the freshwater microbiomes in a microcosm assay of exposure (28 days) to flufenacet and metazachlor at environmental concentrations of 0.5, 5 and 50 μg L[-1] . Inhibitory effects of herbicides were exemplarily assessed in cultured bacteria from the same pond (Pseudomonas alcaligenes, Paenibacillus amylolyticus and Microbacterium hominis). Findings were compared to long-term concentrations as provided by local authorities. Here, environmental concentrations reached up to 11 μg L[-1] (flufenacet) and 76 μg L[-1] (metazachlor). Bacteria were inhibited at minimum inhibitory concentrations far above these values; however, concentrations of 50 μg L[-1] of flufenacet resulted in measurable growth impairment. While most herbicide-exposed microcosm assays did not differ from controls, Acidobacteria were selected at high environmental concentrations of herbicides. Alpha-diversity (e.g., taxonomic richness on phylum level) was reduced when aquatic microbiomes were exposed to 50 μg metazachlor or flufenacet. One environmental strain of P. alcaligenes showed resistance to high concentrations of flufenacet (50 g L[-1]). In total, this study reveals that ecologic imbalance due to herbicide use significantly impacts aquatic microbiomes.},
}
@article {pmid37993728,
year = {2023},
author = {Sun, D and Herath, J and Zhou, S and Ellepola, G and Meegaskumbura, M},
title = {Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {123},
pmid = {37993728},
issn = {2730-6151},
abstract = {Amphibian skin harbors microorganisms that are associated with the fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes chytridiomycosis, one of the most significant wildlife diseases known. This pathogen originated in Asia, where diverse Bd lineages exist; hence, native amphibian hosts have co-existed with Bd over long time periods. Determining the nuances of this co-existence is crucial for understanding the prevalence and spread of Bd from a microbial context. However, associations of Bd with the natural skin microbiome remain poorly understood for Asian hosts, especially in relation to skin-associated fungi. We used 16 S rRNA and fungal internal transcribed spacer (ITS) gene sequencing to characterize the skin microbiome of four native Asian amphibian species and examined the relationships between Bd infection and their skin bacterial and fungal communities; we also analyzed the correlates of the putative anti-Bd bacteria. We show that both skin bacterial and fungal community structure and composition had significant associations with infection status (Bd presence/absence) and infection intensity (frequency of Bd sequence reads). We also found that the putative anti-Bd bacterial richness was correlated with Bd infection status and infection intensity, and observed that the relative abundance of anti-Bd bacteria roughly correspond with changes in both Bd prevalence and mean infection intensity in populations. Additionally, the microbial co-occurrence network of infected frogs was significantly different from that of uninfected frogs that were characterized by more keystone nodes (connectors) and larger proportions in correlations between bacteria, suggesting stronger inter-module bacterial interactions. These results indicate that the mutual effects between Bd and skin-associated microbiome, including the interplay between bacteria and fungi, might vary with Bd infection in susceptible amphibian species. This knowledge will help in understanding the dynamics of Bd from a microbial perspective, potentially contributing to mitigate chytridiomycosis in other regions of the world.},
}
@article {pmid37993724,
year = {2023},
author = {Gutiérrez-García, K and Whitaker, MRL and Bustos-Díaz, ED and Salzman, S and Ramos-Aboites, HE and Reitz, ZL and Pierce, NE and Cibrián-Jaramillo, A and Barona-Gómez, F},
title = {Gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA) are rich in siderophore biosynthesis.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {122},
pmid = {37993724},
issn = {2730-6151},
support = {1541560, 1309425, 1906333//National Science Foundation (NSF)/ ; NAF/R2/180631//Newton Fund/ ; 169701, 179290, 177568, FON.INST./265/2016 285746,//Consejo Nacional de Ciencia y Tecnolog&#xed;a (National Council of Science and Technology, Mexico)/ ; },
abstract = {Ingestion of the cycad toxins β-methylamino-L-alanine (BMAA) and azoxyglycosides is harmful to diverse organisms. However, some insects are specialized to feed on toxin-rich cycads with apparent immunity. Some cycad-feeding insects possess a common set of gut bacteria, which might play a role in detoxifying cycad toxins. Here, we investigated the composition of gut microbiota from a worldwide sample of cycadivorous insects and characterized the biosynthetic potential of selected bacteria. Cycadivorous insects shared a core gut microbiome consisting of six bacterial taxa, mainly belonging to the Proteobacteria, which we were able to isolate. To further investigate selected taxa from diverging lineages, we performed shotgun metagenomic sequencing of co-cultured bacterial sub-communities. We characterized the biosynthetic potential of four bacteria from Serratia, Pantoea, and two different Stenotrophomonas lineages, and discovered a suite of biosynthetic gene clusters notably rich in siderophores. Siderophore semi-untargeted metabolomics revealed a broad range of chemically related yet diverse iron-chelating metabolites, including desferrioxamine B, suggesting the occurrence of an unprecedented desferrioxamine-like biosynthetic pathway that remains to be identified. These results provide a foundation for future investigations into how cycadivorous insects tolerate diets rich in azoxyglycosides, BMAA, and other cycad toxins, including a possible role for bacterial siderophores.},
}
@article {pmid37993702,
year = {2023},
author = {Kassem, NM and Abdelmegid, YA and El-Sayed, MK and Sayed, RS and Abdel-Aalla, MH and Kassem, HA},
title = {Nutrigenomics and microbiome shaping the future of personalized medicine: a review article.},
journal = {Journal, genetic engineering &amp; biotechnology},
volume = {21},
number = {1},
pages = {134},
pmid = {37993702},
issn = {2090-5920},
abstract = {The relationship between nutrition and genes has long been hinted at and sometimes plainly associated with certain diseases. Now, after many years of research and coincidental findings, it is believed that this relationship, termed "Nutrigenomics," is certainly a factor of major importance in various conditions. In this review article, we discuss nutrigenomics, starting with basics definitions and enzymatic functions and ending with its palpable association with cancer. Now, diet is basically what we eat on a daily basis. Everything that enters through our alimentary tract ends up broken down to minute molecules and amino acids. These molecules interact with our microbiome and genome in discreet ways. For instance, we demonstrate how proper intake of probiotics enhances beneficial bacteria and may alleviate IBS and prevent colorectal cancer on the long term. We also show how a diet rich in folic acid is essential for methylenetetrahydrofolate reductase (MTHFR) function, which lowers risk of colorectal cancer. Also, we discuss how certain diets were associated with development of certain cancers. For example, red and processed meat are highly associated with colorectal and prostate cancer, salty diets with stomach cancer, and obesity with breast cancer. The modification of these diets significantly lowered the risk and improved prognosis of these cancers among many others. We also examined how micronutrients had a role in cancer prevention, as vitamin A and C exert anti-carcinogenic effects through their function as antioxidants. In addition, we show how folic acid prevent DNA mutations by enhancing protein methylation processes. Finally, after a systematic review of myriad articles on the etiology and prevention of cancer, we think that diet should be a crucial feature in cancer prevention and treatment programs. In the future, healthy diets and micronutrients may even be able to successively alter the liability to genetic mutations that result in cancer. It also will play a role in boosting treatment and improving prognosis of diagnosed cancers.},
}
@article {pmid37993692,
year = {2023},
author = {Sagerfors, S and Edslev, S and Lindblad, BE and Lilje, B and Stegger, M and Söderquist, B},
title = {In the eye of the ophthalmologist: the corneal microbiome in microbial keratitis.},
journal = {Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie},
volume = {},
number = {},
pages = {},
pmid = {37993692},
issn = {1435-702X},
abstract = {PURPOSE: To describe the bacterial findings by a targeted sequencing approach from corneal samples of patients with microbial keratitis and factors influencing culture outcome of indirectly inoculated corneal specimen.<br><br>METHODS: Prospective inclusion of patients fulfilling predefined criteria of microbial keratitis. Samples from the corneal lesion were collected and dispensed in liquid transport medium, from which both culture and targeted amplification and sequencing of the V3-V4 region of the 16S rRNA gene were carried out. Additional standard corneal culture from the corneal lesions was also performed. Factors influencing culture outcome of indirectly inoculated corneal samples were identified by a multivariate regression model incorporating quantitative data from sequencing.<br><br>RESULTS: Among the 94 included patients with microbial keratitis, contact lens wear (n&#x2009;=&#x2009;69; 73%) was the most common risk factor. Contact lens wearers displayed significant differences in the bacterial community composition of the corneal lesion compared to no lens wearers, with higher abundance of Staphylococcus spp., Corynebacterium spp., and Stenotrophomonas maltophilia. Targeted sequencing detected a potential corneal pathogen in the highest proportional abundance among 9 of the 24 (38%) culture-negative patients with microbial keratitis. Age, bacterial density in the sample, and prior antibiotic treatment significantly influenced culture outcome of indirectly inoculated corneal samples.<br><br>CONCLUSION: Targeted sequencing may provide insights on pathogens in both culture negative episodes of microbial keratitis and among subgroups of patients with microbial keratitis as well as factors influencing culture outcome of indirectly inoculated corneal samples.},
}
@article {pmid37993687,
year = {2023},
author = {Coll, Y and Geddes, A},
title = {Is there a significant difference in the oral microbiome in vapers vs non-vapers?.},
journal = {Evidence-based dentistry},
volume = {},
number = {},
pages = {},
pmid = {37993687},
issn = {1476-5446},
abstract = {DATA SOURCES: This study was a secondary data analysis of a parent study that was initially designed to assess saliva and exhaled breath for passive e-cigarette vapour exposure in children. The initial study collected patients using convenience sampling of the local community between July 2018 and February 2019 and ethical approval was obtained prior to commencing.<br><br>DATA EXTRACTION AND SYNTHESIS: Eligibility criteria for the parent vapers in the original study included self-reported daily use of e-cigarettes in the presence of children via the use of a questionnaire. Microbiome data for a total of 36 adults were collected and analysed in this study (18 vapers and 18 non-vapers).<br><br>RESULTS: Vapers have a distinct oral microbiome compared with non-vapers. They tend to have a higher relative abundance of Veilonella, an opportunistic pathogen that can stimulate the growth of other opportunistic pathogens. This species has also been found in carious lesions compared with healthy tooth surface.},
}
@article {pmid37993375,
year = {2023},
author = {Mouzan, ME and Hussaini, AA and Sarkhy, AA and Assiri, A},
title = {Intestinal fungal profile in healthy Saudi children.},
journal = {Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajg.2023.11.001},
pmid = {37993375},
issn = {2090-2387},
abstract = {BACKGROUND AND STUDY AIM: Fungi have a well-established role in medicine. Herein, we describe the fungal profile and abundance in the gut of healthy Saudi children.<br><br>PATIENTS AND METHODS: Fecal samples from a random sample of 20 school-age Saudi children were collected, stored at -80&#xa0;&#xb0;C, and dispatched to the laboratory in the USA where fungal DNAs were isolated and shotgun metagenomic sequencing was performed. Abundance was presented as average percentage of fungal taxa.<br><br>RESULTS: The median age of the participants was 12.5&#xa0;years (range: 7-16&#xa0;years), and 35&#xa0;% were male. Ascomycota were the most abundant phyla and Eurotiomycetes, Saccharomycetes, were the most abundant class. The average abundance of fungal genera were Histoplasma (36&#xa0;%) and Saccharomyces (31&#xa0;%). The most abundant species were Histoplasma capsulatum (36&#xa0;%) and Saccharomyces pastorianus (23&#xa0;%). Other less abundant but may be functionally important genera and species included Candida (2.6&#xa0;%) and Saccharomycescerevisiae (8&#xa0;%).<br><br>CONCLUSION: The profile and abundance of the gut fungi in healthy Saudi children reveals important differences compared to Western literature. Accordingly, this report represents a more appropriate reference than Western data to use as controls for regional studies aiming to identify fungi associated with disease.},
}
@article {pmid37993021,
year = {2023},
author = {Giatti, S and Diviccaro, S and Cioffi, L and Cosimo Melcangi, R},
title = {POST-FINASTERIDE SYNDROME AND POST-SSRI SEXUAL DYSFUNCTION: TWO CLINICAL CONDITIONS APPARENTLY DISTANT, BUT VERY CLOSE.},
journal = {Frontiers in neuroendocrinology},
volume = {},
number = {},
pages = {101114},
doi = {10.1016/j.yfrne.2023.101114},
pmid = {37993021},
issn = {1095-6808},
abstract = {Post-finasteride syndrome and post-SSRI sexual dysfunction, are two poorly explored clinical conditions in which men treated for androgenetic alopecia with finasteride or for depression with SSRI antidepressants show persistent side effects despite drug suspension (e.g., sexual dysfunction, psychological complaints, sleep disorders). Because of some similarities in the symptoms, common pathological mechanisms are proposed here. Indeed, as discussed, clinical studies and preclinical data obtained so far suggest an important role for brain modulators (i.e., neuroactive steroids), neurotransmitters (i.e., serotonin, and cathecolamines), and gut microbiota in the context of the gut-brain axis. In particular, the observed interconnections of these signals in these two clinical conditions may suggest similar etiopathogenetic mechanisms, such as the involvement of the enzyme converting norepinephrine into epinephrine (i.e., phenylethanolamine N-methyltransferase). However, despite the current efforts, more work is still needed to advance the understanding of these clinical conditions in terms of diagnostic markers and therapeutic strategies.},
}
@article {pmid37992902,
year = {2023},
author = {Liu, C and Pan, K and Xu, H and Song, Y and Qi, X and Lu, Y and Jiang, X and Liu, H},
title = {The effects of enrofloxacin exposure on responses to oxidative stress, intestinal structure and intestinal microbiome community of largemouth bass (Micropterus salmoides).},
journal = {Chemosphere},
volume = {},
number = {},
pages = {140751},
doi = {10.1016/j.chemosphere.2023.140751},
pmid = {37992902},
issn = {1879-1298},
abstract = {Antibiotic residues in the aquaculture environments may lead to antibiotic resistance, and potentially exert adverse effects on health of the non-target organisms and humans. In order to evaluate the effect of enrofloxacin of environmental concentrations on largemouth bass (Micropterus salmoides). Two hundred and seventy largemouth basses (with an average weight of 7.88 ± 0.60 g) were randomly divided into three groups, and separately exposed to 0, 1, 100 μg/L enrofloxacin (Control, ENR1, ENR100) for 30 days to detect the effect of enrofloxacin on the growth performance, oxidative stress, intestinal microbiota structure, inflammatory response and structure of the intestine. The results showed that ENR significantly reduced the final body weight (FBW) and weight gain rate (WGR), and increased feed conversion ratio (FCR) (P < 0.05). The histopathological analysis revealed that the villus width and muscular thickness of anterior intestine were significantly decreased with the increasing of enrofloxacin concentration. The activity of SOD was significantly increased at enrofloxacin stress, while CAT and POD activity were significantly decreased compared to control group (P < 0.05). The activities of lysozyme (LZM), alkaline phosphatase (AKP) and peroxidase (POD) in ENR1 was higher than that of control and ENR100 groups. Enrofloxacin treatment up-regulated the expression IL-1β and TNF-α, and down-regulated IL-10, and decreasing the expression level ZO-1, claudin-1, and occludin. Furthermore, the enrofloxacin treatment significantly decreased the intestinal bacterial diversity (P < 0.05). Exposure to 100 μg/L enrofloxacin obviously increased the relative abundance of Bacteroidota, Myxococcota, and Zixibacteria of fish gut, and reduced Firmicutes; 1 μg/L enrofloxacin considerably increased Bacteroidota, Myxococcota, and Actinobacteria, and reduced Firmicutes. The relative abundance of DTB120 and Elusimicrobiota was positively correlated with the occludin and claudin-1 gene. Taken together, exposure to enrofloxacin inhibited the growth of largemouth bass, influenced intestinal health, and induced dysbiosis of the intestinal microbiota.},
}
@article {pmid37992830,
year = {2023},
author = {Pan, Z and Wang, W and Chen, J and Chen, Z and Avellán-Llaguno, RD and Xu, W and Duan, Y and Liu, B and Huang, Q},
title = {Temporal dynamics of microbial composition and antibiotic resistome in fermentation bed culture pig farms across various ages.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168728},
doi = {10.1016/j.scitotenv.2023.168728},
pmid = {37992830},
issn = {1879-1026},
abstract = {The discharge from pig farms presents significant challenges to the environment and human health, specifically regarding the dissemination of antimicrobial resistance (AMR). Fermentation bed culture has emerged as an increasingly popular and environmentally friendly pig farming model in China, as it minimizes the release of harmful substances into the environment. However, there remains a limited understanding of the occurrence and dynamics of microbiome and antibiotic resistome in fermentation bed culture. Herein, we collected fermentation bed materials (FBM) from four fermentation bed culture pig farms with varying service ages and investigated their bacterial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metal resistance genes (MRGs) and potential antibiotic-resistant bacterial hosts through metagenomics. Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota were identified as the dominant phyla present in the FBM. In total, we detected 258 unique ARGs in the FBM samples, with 79 core ARGs shared by all FBM samples, accounting for 95 % of the total ARG abundance. Our results revealed significant variations in microbial communities and ARG profiles across varying service ages of FBM. Compared to long-term FBW, short-term FBM exhibited higher numbers and abundances of ARGs, MRGs and MGEs, along with higher levels of potential bacterial pathogens and high-risk ARGs. Further analysis of metagenome-assembled genome (MAG) indicated that the putative hosts of ARGs primarily belonged to Pseudomonadota, Actinomycetota and Bacillota. Alarmingly, among the 80 recovered ARG-carrying MAGs, 23 MAGs encoded multi-resistance, including clinically significant species that require urgent attention. Overall, this study provided valuable insights into the temporal patterns of antibiotic resistome and bacterial communities within FBM, enhancing our understanding of FBM in pig farming. The findings could potentially contribute to the development of effective strategies for evaluating and regulating fermentation bed culture practices in pig farming.},
}
@article {pmid37992816,
year = {2023},
author = {Wang, Q and Mackay, CR},
title = {High Metabolite Concentrations in Portal Venous Blood as a Possible Mechanism for Microbiota Effects on the Immune System, and Western Diseases.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2023.10.029},
pmid = {37992816},
issn = {1097-6825},
abstract = {We show that the gut bacterial metabolites, short chain fatty acids (SCFAs), are present at exceptionally high concentrations in the portal venous circulation, particularly small blood vessels that emanate from colonic mucosa. Likely, many other metabolites will be present at high concentrations. Herein we propose a model for immune conditioning, whereby metabolites such as butyrate affect immune cells as they pass through the portal venous system. Deficiency of SCFA would lead to pro-inflammatory immune cell skewing through insufficient G-protein coupled receptor (GPCR) signalling, or lack of histone deacetylase (HDAC) inhibition. Such pro-inflammatory immune cells may travel to tissues such as the brain, the lung, the kidney etc and promote disease. This model helps explain how the gut microbiome may be affecting peripheral immune cells, and consequently Western lifestyle diseases, most of which are immune based, in tissues remote from the gut.},
}
@article {pmid37992712,
year = {2023},
author = {Zhang, C and Yu, L and Ma, C and Jiang, S and Zhang, Y and Wang, S and Tian, F and Xue, Y and Zhao, J and Zhang, H and Liu, L and Chen, W and Huang, S and Zhang, J and Zhai, Q},
title = {A key genetic factor governing arabinan utilization in the gut microbiome alleviates constipation.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2023.10.011},
pmid = {37992712},
issn = {1934-6069},
abstract = {Impaired gastrointestinal motility is associated with gut dysbiosis. Probiotics, such as Bifidobacteria, can improve this bowel disorder; however, efficacy is strain-dependent. We determine that a genetic factor, the abfA cluster governing arabinan utilization, in Bifidobacterium longum impacts treatment efficacy against functional constipation (FC). In mice with FC, B. longum, but not an abfA mutant, improved gastrointestinal transit time, an affect that was dependent upon dietary arabinan. abfA genes were identified in other commensal bacteria, whose effects in ameliorating murine FC were similarly abfA-dependent. In a double-blind, randomized, placebo-controlled clinical trial, supplementation with abfA-cluster-carrying B. longum, but not an abfA-deficient strain, enriched arabinan-utilization residents, increased beneficial metabolites, and improved FC symptoms. Across human cohorts, abfA-cluster abundance can predict FC, and transplantation of abfA cluster-enriched human microbiota to FC-induced germ-free mice improved gut motility. Collectively, these findings demonstrate a role for microbial abfA cluster in ameliorating FC, establishing principles for genomics-directed probiotic therapies.},
}
@article {pmid37992649,
year = {2023},
author = {Romualdo, GR and Valente, LC and de Souza, JLH and Rodrigues, J and Barbisan, LF},
title = {Modifying effects of 2,4-D and Glyphosate exposures on gut-liver-adipose tissue axis of diet-induced non-alcoholic fatty liver disease in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {268},
number = {},
pages = {115688},
doi = {10.1016/j.ecoenv.2023.115688},
pmid = {37992649},
issn = {1090-2414},
abstract = {Nonalcoholic fatty liver disease (NAFLD), which is linked to western diet (WD) intake, affects 30% of the world's population and involves the crosstalk of liver steatosis, hypertrophy/inflammation of adipose tissue and deregulation of gut microbiome. Glyphosate and 2,4-D are some of the most applied herbicides worldwide, and their roles in NAFLD have not been investigated. Thus, the present study evaluated whether glyphosate and 2,4-D, in single or mixed exposure, alter WD-induced NAFLD in a mouse model. Male C57Bl/6 mice (n = 10/group) received a fat (30% lard, 0.02% cholesterol), and sucrose-rich diet (20%) and high sugar solution (23.1 and 18.9 g/L of fructose and glucose) for 6 months. Simultaneously, animals received glyphosate (0.05 or 5 mg/kg/day), 2,4-D (0.02 or 2 mg/kg/day), or their combination (0.05 +0.02 or 5 +2 mg/kg/day) by intragastrical administration (5 ×/week). Doses were based on the Acceptable Daily Intake (ADIs) or No Observed Adverse Effect Level (NOAEL) levels. Herbicide exposures featured differential responses. WD-induced obesity, hypercholesterolemia, and hyperglycemia remained unaltered. Compared to the group receiving only WD, only the concomitant exposure to WD and 2,4-D (2 mg) enhanced the percentage of mice with moderate/severe hepatic inflammation, CD68 macrophage infiltration, and malondialdehyde levels in the liver. In line, this herbicide modulated immune response- (including Cd4, C8b, Cd28, Cxcr3, Cxcr6) and oxidative stress-related (such as Gsta1, Gsta2, Gsta4, Gstm1, Gstm2, Gstm3, Gstm4, Nqo1, Gpx2) genes in the hepatic transcriptome analysis. This exposure also enriched pro-inflammatory Deferribacteres phylum in fecal microbiome. In general, the herbicide mixtures did not feature the same effects attributed to 2,4-D isolated exposure. Our findings indicate that 2,4-D, at a dose within the toxicological limits, was able to induce disturbances in mainly at the liver and gut axes involved in NAFLD development in male mice.},
}
@article {pmid37992468,
year = {2023},
author = {Nanfack, AD and Nguefack, J and Musonerimana, S and La China, S and Giovanardi, D and Stefani, E},
title = {Exploiting the microbiome associated with normal and abnormal sprouting rice (Oryza sativa L.) seed phenotypes through a metabarcoding approach.},
journal = {Microbiological research},
volume = {279},
number = {},
pages = {127546},
doi = {10.1016/j.micres.2023.127546},
pmid = {37992468},
issn = {1618-0623},
abstract = {Rice germination and seedlings' growth are crucial stages that influence crop establishment and productivity. These performances depend on several factors, including the abundance and diversity of seed microbial endophytes. Two popular rainfed rice varieties cultivated in Cameroon, NERICA 3 and NERICA 8, were used for investigating the seed-associated microbiome using the Illumina-based 16 S rRNA gene. Significant differences were observed in terms of richness index between normal and abnormal seedlings developed from sprouting seeds, although no significant species evenness index was assessed within either phenotype. Two hundred ninety-two bacterial amplicon sequence variants were identified in seed microbiome of the rice varieties, and principal coordinate analysis revealed that microbial communities formed two distinct clusters in normal and abnormal seedling phenotypes. Overall, 38 bacteria genera were identified, belonging to 6 main phyla. Furthermore, the core microbiome was defined, and the differential abundance of 28 bacteria genera was assessed. Based on the collected results, putative bacterial genera were directly correlated with the development of normal seedlings. For most genera that are recognised to include beneficial species, such as Brevundimonas, Sphingomonas, Exiguobacterium, Luteibacter, Microbacterium and Streptomyces, a significant increase of their relative abundance was found in normal seedlings. Additionally, in abnormal seedlings, we also observed an increased abundance of the genera Kosakonia and Paenibacillus, which might have controversial aspects (beneficial or pathogenic), together with the presence of some genera (Clostridium sensu stricto) that are commonly correlated to sick plants. The putative functional gene annotation revealed the higher abundance of genes related to the metabolic biosynthesis of soluble carbohydrates and starch, tryptophan, nucleotides and ABC transporters in normal seedlings. Data presented in this study may help in further understanding the importance of the seed endophyte microbiome for driving a correct development of rice plants at the early stages and to identify possible beneficial bacteria for technological applications aimed to increase seed quality and crop productivity.},
}
@article {pmid37992406,
year = {2023},
author = {Jesser, KJ and Trueba, G and Konstantinidis, KT and Levy, K},
title = {Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2281010},
doi = {10.1080/19490976.2023.2281010},
pmid = {37992406},
issn = {1949-0984},
mesh = {Humans ; Escherichia coli ; *Escherichia coli Infections/microbiology ; *Gastrointestinal Microbiome/genetics ; Ecuador ; Case-Control Studies ; Diarrhea/microbiology ; },
abstract = {A high proportion of enteric infections, including those caused by diarrheagenic Escherichia coli (DEC), are asymptomatic for diarrhea. The factors responsible for the development of diarrhea symptoms, or lack thereof, remain unclear. Here, we used DEC isolate genome and whole stool microbiome data from a case-control study of diarrhea in Ecuador to examine factors associated with diarrhea symptoms accompanying DEC carriage. We investigated i) pathogen abundance, ii) gut microbiome characteristics, and iii) strain-level pathogen characteristics from DEC infections with diarrhea symptoms (symptomatic infections) and without diarrhea symptoms (asymptomatic infections). We also included data from individuals with and without diarrhea who were not infected with DEC (uninfected cases and controls). i) E. coli relative abundance in the gut microbiome was highly variable, but higher on-average in individuals with symptomatic compared to asymptomatic DEC infections. Similarly, the number and relative abundances of virulence genes in the gut were higher in symptomatic than asymptomatic DEC infections. ii) Measures of microbiome diversity were similar regardless of diarrhea symptoms or DEC carriage. Proteobacterial families that have been described as pathobionts were enriched in symptomatic infections and uninfected cases, whereas potentially beneficial taxa, including the Bacteroidaceae and Bifidobacteriaceae, were more abundant in individuals without diarrhea. An analysis of high-level gene functions recovered in metagenomes revealed that genes that were differentially abundant by diarrhea and DEC infection status were more abundant in symptomatic than asymptomatic DEC infections. iii) DEC isolates from symptomatic versus asymptomatic individuals showed no significant differences in virulence or accessory gene content, and there was no phylogenetic signal associated with diarrhea symptoms. Together, these data suggest signals that distinguish symptomatic from asymptomatic DEC infections. In particular, the abundance of E. coli, the virulence gene content of the gut microbiome, and the taxa present in the gut microbiome have an apparent role.},
}
@article {pmid37992398,
year = {2023},
author = {Bornholdt, J and Müller, CV and Nielsen, MJ and Strickertsson, J and Rago, D and Chen, Y and Maciag, G and Skov, J and Wellejus, A and Schweiger, PJ and Hansen, SL and Broholm, C and Gögenur, I and Maimets, M and Sloth, S and Hendel, J and Baker, A and Sandelin, A and Jensen, KB},
title = {Detecting host responses to microbial stimulation using primary epithelial organoids.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2281012},
doi = {10.1080/19490976.2023.2281012},
pmid = {37992398},
issn = {1949-0984},
abstract = {The intestinal epithelium is constantly exposed to microbes residing in the lumen. Traditionally, the response to microbial interactions has been studied in cell lines derived from cancerous tissues, e.g. Caco-2. It is, however, unclear how the responses in these cancer cell lines reflect the responses of a normal epithelium and whether there might be microbial strain-specific effects. To address these questions, we derived organoids from the small intestine from a cohort of healthy individuals. Culturing intestinal epithelium on a flat laminin matrix induced their differentiation, facilitating analysis of microbial responses via the apical membrane normally exposed to the luminal content. Here, it was evident that the healthy epithelium across multiple individuals (n = 9) demonstrates robust acute both common and strain-specific responses to a range of probiotic bacterial strains (BB-12[Ⓡ], LGG[Ⓡ], DSM33361, and Bif195). Importantly, parallel experiments using the Caco-2 cell line provide no acute response. Collectively, we demonstrate that primary epithelial cells maintained as organoids represent a valuable resource for assessing interactions between the epithelium and luminal microbes across individuals, and that these models are likely to contribute to a better understanding of host microbe interactions.},
}
@article {pmid37921362,
year = {2023},
author = {Cottrell, EC},
title = {Should the non-canonical pathway of nitric oxide generation be targeted in hypertensive pregnancies?.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.16276},
pmid = {37921362},
issn = {1476-5381},
support = {FS/15/31/31418/BHF_/British Heart Foundation/United Kingdom ; },
abstract = {Hypertension in pregnancy is prevalent, affecting around 10% of pregnancies worldwide, and significantly increases the risk of adverse outcomes for both mothers and their babies. Current treatment strategies for pregnant women with hypertension are limited, and new approaches for the management of hypertension in pregnancy are urgently needed. Substantial evidence from non-pregnant subjects has demonstrated the potential for dietary nitrate supplementation to increase nitric oxide (NO) bioavailability and lower blood pressure, following bioactivation via the non-canonical NO pathway. Emerging data suggest this approach may also be of benefit in pregnant women, although studies are limited. This review aims to summarise the current evidence from preclinical and clinical studies of nitrate supplementation in pregnancy, drawing on data from non-pregnant populations where appropriate and highlighting key gaps in knowledge that remain to be addressed in future trials.},
}
@article {pmid37877360,
year = {2023},
author = {Davies, IG},
title = {Exploring high-protein diets in the context of cardiac rehabilitation.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-12},
doi = {10.1017/S0029665123004779},
pmid = {37877360},
issn = {1475-2719},
abstract = {The review aims to explore the potential benefit and risk of high-protein diets (HPD) regarding the comorbidity of sarcopoenia and CVD in the setting of cardiac rehabilitation (CR). CR is standard care for individuals who have experienced a cardiac event, but the current practice of predominantly aerobic exercise, a lower-fat diet and weight loss poorly addresses the issue of sarcopoenia. HPD, especially when combined with resistance exercise (RE), may be valuable adjuncts to current CR practice and benefit both muscle and cardiovascular health. Meta-analyses and randomised controlled trials of HPD and CVD risk show beneficial but variable effects regarding weight loss, the lipid profile, insulin resistance and lean body mass in those living with or high risk of CVD. Meta-analyses of prospective cohort studies on hard CVD endpoints favour lower- and plant-protein diets over higher animal protein, but the evidence is inconsistent. HPD augment the strength and muscle gaining benefits of RE in older populations, but there are no published data in those living with CVD providing promising opportunities for CR research. HPD raise concern regarding renal and bone health, the microbiome, branched chain amino acids and environmental sustainability and findings suggest that plant-based HPD may confer ecological and overall health advantages compared to animal-based HPD. However, incorporating RE with HPD might alleviate certain health risks. In conclusion, a largely plant-based HPD is deemed favourable for CR when combined with RE, but further research regarding efficacy and safety in CR populations is needed.},
}
@article {pmid37992186,
year = {2023},
author = {Aslamy, A and Wood, AC and Jensen, ET and Bertoni, AG and Sheridan, PA and Wong, KE and Ramesh, G and Rotter, JI and Chen, YI and Goodarzi, MO},
title = {Increased plasma branched short-chain fatty acids and improved glucose homeostasis: The Microbiome and Insulin Longitudinal Evaluation Study (MILES).},
journal = {Diabetes},
volume = {},
number = {},
pages = {},
doi = {10.2337/db23-0401},
pmid = {37992186},
issn = {1939-327X},
abstract = {Short chain fatty acids (SCFA) have been extensively studied for potential beneficial roles in glucose homeostasis and risk of diabetes; however, most of this research has focused on butyrate, acetate, and propionate. The effect on metabolism of branched short chain fatty acids (BSCFA), isobutyrate, isovalerate, and methylbutyrate, is largely unknown. In a cohort of 219 non-Hispanic Whites and 126 African Americans, we examined the association of BSCFA with dysglycemia (prediabetes and diabetes) and oral glucose tolerance test-based measures of glucose and insulin homeostasis, as well as with demographic, anthropometric, lifestyle, lipid traits, and other SCFA. We observed a bimodal distribution of BSCFA, with 25 individuals having high levels (HBSCFA group) and 320 individuals having lower levels (L-BSCFA group). The prevalence of dysglycemia was lower in the H-BSCFA group compared to the L-BSCFA group (16% versus 49%, P=0.0014). This association remained significant after adjustment for age, sex, race, BMI, and levels of other SCFA. Consistent with the lower rate of dysglycemia, fasting and postprandial glucose were lower and disposition index was higher in the H-BSCFA group. Additional findings in H-BSCFA versus L-BSCFA included lower fasting and postprandial Cpeptide levels and lower insulin clearance without differences in insulin levels, insulin sensitivity, insulin secretion, or other variables examined, including diet and physical activity. As one of the first human studies associating higher BSCFA levels with lower odds of dysglycemia and improved glucose homeostasis, this study sets the stage for further investigation of BSCFA as a novel target for prevention or treatment of diabetes.},
}
@article {pmid37992156,
year = {2023},
author = {de Wit, DF and Hanssen, NMJ and Wortelboer, K and Herrema, H and Rampanelli, E and Nieuwdorp, M},
title = {Evidence for the contribution of the gut microbiome to obesity and its reversal.},
journal = {Science translational medicine},
volume = {15},
number = {723},
pages = {eadg2773},
doi = {10.1126/scitranslmed.adg2773},
pmid = {37992156},
issn = {1946-6242},
abstract = {Obesity has become a worldwide pandemic affecting more than 650 million people and is associated with a high burden of morbidity. Alongside traditional risk factors for obesity, the gut microbiome has been identified as a potential factor in weight regulation. Although rodent studies suggest a link between the gut microbiome and body weight, human evidence for causality remains scarce. In this Review, we postulate that existing evidence remains to establish a contribution of the gut microbiome to the development of obesity in humans but that modified probiotic strains and supraphysiological dosages of microbial metabolites may be beneficial in combatting obesity.},
}
@article {pmid37992054,
year = {2023},
author = {Zhang, M and Yang, T and Li, R and Ren, K and Li, J and He, M and Chen, J and Yi, SQ},
title = {Gut microbiota of Suncus murinus, a naturally obesity-resistant animal, improves the ecological diversity of the gut microbiota in high-fat-diet-induced obese mice.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0293213},
pmid = {37992054},
issn = {1932-6203},
abstract = {BACKGROUND: The global population of obese individuals is increasing, affecting human health. High-fat diets are a leading cause of this epidemic, and animal models, such as mice, are often used in related research. Obese individuals have a different gut microbiota composition from non-obese ones, characterized by a sizeable population of certain bacteria associated with fat storage. The gut microbiome plays a significant role in regulating human physiological and metabolic functions. Links between obesity, high-fat diets and gut microbiota have become hot topics of discussion. Recently, research on the modulation of the gut microbiota has focused on fecal microbiota transplantation (FMT), which has been recognized as an effective method of studying the function of gut microbiota.<br><br>OBJECTIVES: The purpose of this study was to investigate how the gut microbiota of Suncus murinus, a naturally obesity-resistant animal, through FMT, affected the ecology of the gut microbiota of high-fat diet induced obese mice.<br><br>METHODS: In this study, Suncus murinus was used as a donor for FMT. High-fat diet induced C57BL/6NCrSIc mice were used as recipients, the body weight changes were measured and changes in their gut flora were analyzed using a 16S rRNA gene analysis.<br><br>RESULTS: The study found that, after the FMT procedure, the FMT group tended to have a lower body weight than the control group. At the phylum level, the most predominant phyla in all groups were Firmicutes and Proteobacteria, while Deferribacteres was not detected in the FMT or antibiotic administration groups, and Bacteroidetes was not present in the antibiotic administration group. At the genus level, the FMT group had significantly lower OTU richness than the control group but greater diversity than the control group.<br><br>CONCLUSIONS: These results indicate that FMT from Suncus murinus can help reorganize and improve the gut microbiota of mice in a balanced and diverse ecosystem.},
}
@article {pmid37992050,
year = {2023},
author = {Aiman, S and Ahmad, A and Khan, A and Ali, Y and Malik, A and Alkholief, M and Akhtar, S and Khan, RS and Li, C and Jalil, F and Ali, Y},
title = {Vaccinomics-aided next-generation novel multi-epitope-based vaccine engineering against multidrug resistant Shigella Sonnei: Immunoinformatics and chemoinformatics approaches.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0289773},
pmid = {37992050},
issn = {1932-6203},
abstract = {Shigella sonnei is a gram-negative bacterium and is the primary cause of shigellosis in advanced countries. An exceptional rise in the prevalence of the disease has been reported in Asia, the Middle East, and Latin America. To date, no preventive vaccine is available against S. sonnei infections. This pathogen has shown resistances towards both first- and second-line antibiotics. Therefore, an effective broad spectrum vaccine development against shigellosis is indispensable. In the present study, vaccinomics-aided immunoinformatics strategies were pursued to identify potential vaccine candidates from the S. sonnei whole proteome data. Pathogen essential proteins that are non-homologous to human and human gut microbiome proteome set, are feasible candidates for this purpose. Three antigenic outer membrane proteins were prioritized to predict lead epitopes based on reverse vaccinology approach. Multi-epitope-based chimeric vaccines was designed using lead B- and T-cell epitopes combined with suitable linker and adjuvant peptide sequences to enhance immune responses against the designed vaccine. The SS-MEVC construct was prioritized based on multiple physicochemical, immunological properties, and immune-receptors docking scores. Immune simulation analysis predicted strong immunogenic response capability of the designed vaccine construct. The Molecular dynamic simulations analysis ensured stable molecular interactions of lead vaccine construct with the host receptors. In silico restriction and cloning analysis predicted feasible cloning capability of the SS-MEVC construct within the E. coli expression system. The proposed vaccine construct is predicted to be more safe, effective and capable of inducing robust immune responses against S. sonnei infections and may be worthy of examination via in vitro/in vivo assays.},
}
@article {pmid37991947,
year = {2023},
author = {Arya, S and George, AB and O'Dwyer, JP},
title = {Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {48},
pages = {e2307313120},
doi = {10.1073/pnas.2307313120},
pmid = {37991947},
issn = {1091-6490},
support = {376199//Simons Foundation (SF)/ ; },
abstract = {Microbiome engineering offers the potential to leverage microbial communities to improve outcomes in human health, agriculture, and climate. To translate this potential into reality, it is crucial to reliably predict community composition and function. But a brute force approach to cataloging community function is hindered by the combinatorial explosion in the number of ways we can combine microbial species. An alternative is to parameterize microbial community outcomes using simplified, mechanistic models, and then extrapolate these models beyond where we have sampled. But these approaches remain data-hungry, as well as requiring an a priori specification of what kinds of mechanisms are included and which are omitted. Here, we resolve both issues by introducing a mechanism-agnostic approach to predicting microbial community compositions and functions using limited data. The critical step is the identification of a sparse representation of the community landscape. We then leverage this sparsity to predict community compositions and functions, drawing from techniques in compressive sensing. We validate this approach on in silico community data, generated from a theoretical model. By sampling just [Formula: see text]1% of all possible communities, we accurately predict community compositions out of sample. We then demonstrate the real-world application of our approach by applying it to four experimental datasets and showing that we can recover interpretable, accurate predictions on composition and community function from highly limited data.},
}
@article {pmid37991629,
year = {2023},
author = {Zhang, G and Zhao, L and Li, W and Yao, H and Lu, C and Zhao, G and Wu, Y and Li, Y and Kong, G},
title = {Changes in physicochemical properties and microbial community succession during leaf stacking fermentation.},
journal = {AMB Express},
volume = {13},
number = {1},
pages = {132},
pmid = {37991629},
issn = {2191-0855},
support = {110202101012(XJ-04)/2021530000241002//China Tobacco Monopoly Bureau Grants/ ; 2020530000241001/2021530000241004//China Tobacco Monopoly Bureau Grants/ ; },
abstract = {Leaf stacking fermentation involves enzymatic actions of many microorganisms and is an efficient and environmentally benign process for degrading macromolecular organic compounds. We investigated the dynamics of metabolite profiles, bacterial and fungal communities and their interactions during fermentation using cigar leaves from three geographic regions. The results showed that the contents of total sugar, reducing sugar, starch, cellulose, lignin, pectin, polyphenol and protein in cigar tobacco leaves was significantly decreased during fermentation. Notably, the furfural, neophytadiene, pyridine, benzyl alcohol, geranylacetone, 3-hydroxy-2-butanone, N-hexanal, 3-Methyl-1-butanol and 2,3-pentanedione were important features volatile aroma compounds during fermentation. The α-diversity of fungi and bacteria initially increased and then decreased during fermentation. An analysis of variance showed that microbial diversity was influenced by fermentation stages and growing locations, in which the all stages had greater impacts on α- and β-diversity than all regions. Microbiome profiling had identified several core bacteria including Sphingomonas, Bacillus, Staphylococcus, Pseudomonas, Ralstonia, Massilia and Fibrobacter. Fungal biomarkers included Aspergillus, Penicillium, Fusarium, Cladosporium and Trichomonascus. Interestingly, the molecular ecological networks showed that the core taxa had significant correlations with metabolic enzymes and physicochemical properties; bacteria and fungi jointly participated in the carbohydrate and nitrogen compound degrading and volatile aroma compound chemosynthesis processes during fermentation. These studies provide insights into the coupling of material conversion and microbial community succession during leaf fermentation.},
}
@article {pmid37991578,
year = {2023},
author = {Liu, HH and Chen, L and Shao, HB and Gao, S and Hong, XY and Bing, XL},
title = {Environmental Factors and the Symbiont Cardinium Influence the Bacterial Microbiome of Spider Mites Across the Landscape.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {1},
pmid = {37991578},
issn = {1432-184X},
support = {32001905 and 32020103011//National Natural Science Foundation of China/ ; 32001905 and 32020103011//National Natural Science Foundation of China/ ; 2022YFC2601000//National Key Research and Development Program of China/ ; BK20211213//Natural Science Foundation of Jiangsu Province/ ; KJQN202110//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Humans ; Animals ; *Tetranychidae ; RNA, Ribosomal, 16S/genetics ; Bacteroidetes/genetics ; *Arthropods ; *Microbiota ; },
abstract = {Microbes play a key role in the biology, ecology, and evolution of arthropods. Despite accumulating data on microbial communities in arthropods that feed on plants using piercing-sucking mouthparts, we still lack a comprehensive understanding of the composition and assembly factors of the microbiota, particularly in field-collected spider mites. Here, we applied 16S rRNA amplicon sequencing to investigate the characters of the bacterial community in 140 samples representing 420 mite individuals, belonging to eight Tetranychus species (Acari: Tetranychidae) collected from 26 sites in China. The results showed that the bacterial composition of spider mites varied significantly among different species, locations, and plants. The environment showed a significant influence on the bacterial community of spider mites, with different relative contributions. Latitude and precipitation were found to be the main factors influencing the bacterial community composition. The dissimilarity of bacterial community and geographical distance between mite locations were significantly correlated. The assembly of spider mite bacterial communities seemed to be mainly influenced by stochastic processes. Furthermore, the symbiont Cardinium was found to be important in shaping the microbiota of many Tetranychus species. The relative abundance of Cardinium was > 50% in T. viennensis, T. urticae G, T. urticae R, and T. turkestani. Removing Cardinium reads from our analysis significantly changed Shannon diversity index and weighted beta diversity in these species. Altogether, this study provides novel insights into bacterial diversity patterns that contribute to our knowledge of the symbiotic relationships between arthropods and their bacterial communities.},
}
@article {pmid37991377,
year = {2023},
author = {Šigutová, H and Pyszko, P and Šigut, M and Czajová, K and Kostovčík, M and Kolařík, M and Hařovská, D and Drozd, P},
title = {Concentration-dependent effect of plant secondary metabolites on bacterial and fungal microbiomes in caterpillar guts.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0299423},
doi = {10.1128/spectrum.02994-23},
pmid = {37991377},
issn = {2165-0497},
abstract = {The caterpillar gut is an excellent model system for studying host-microbiome interactions, as it represents an extreme environment for microbial life that usually has low diversity and considerable variability in community composition. Our study design combines feeding caterpillars on a natural and artificial diet with controlled levels of plant secondary metabolites and uses metabarcoding and quantitative PCR to simultaneously profile bacterial and fungal assemblages, which has never been performed. Moreover, we focus on multiple caterpillar species and consider diet breadth. Contrary to many previous studies, our study suggested the functional importance of certain microbial taxa, especially bacteria, and confirmed the previously proposed lower importance of fungi for caterpillar holobiont. Our study revealed the lack of differences between monophagous and polyphagous species in the responses of microbial assemblages to plant secondary metabolites, suggesting the limited role of the microbiome in the plasticity of the herbivore diet.},
}
@article {pmid37991375,
year = {2023},
author = {Tamés, H and Sabater, C and Royo, F and Margolles, A and Falcón, JM and Ruas-Madiedo, P and Ruiz, L},
title = {Mouse intestinal microbiome modulation by oral administration of a GABA-producing Bifidobacterium adolescentis strain.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0258023},
doi = {10.1128/spectrum.02580-23},
pmid = {37991375},
issn = {2165-0497},
abstract = {The gut microbiome-brain communication signaling has emerged in recent years as a novel target for intervention with the potential to ameliorate some conditions associated with the central nervous system. Hence, probiotics with capacity to produce neurotransmitters, for instance, have come up as appealing alternatives to treat disorders associated with disbalanced neurotransmitters. Herein, we further deep into the effects of administering a gamma-aminobutyric acid (GABA)-producing Bifidobacterium strain, previously demonstrated to contribute to reduce serum glutamate levels, in the gut microbiome composition and metabolic activity in a mouse model. Our results demonstrate that the GABA-producing strain administration results in a specific pattern of gut microbiota modulation, different from the one observed in animals receiving non-GABA-producing strains. This opens new avenues to delineate the specific mechanisms by which IPLA60004 administration contributes to reducing serum glutamate levels and to ascertain whether this effect could exert health benefits in patients of diseases associated with high-glutamate serum concentrations.},
}
@article {pmid37991154,
year = {2023},
author = {Jaeger, ACH and Hartmann, M and Conz, RF and Six, J and Solly, EF},
title = {Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.13211},
pmid = {37991154},
issn = {1758-2229},
support = {PZ00P2_180030//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
abstract = {Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.},
}
@article {pmid37990937,
year = {2023},
author = {Wei, J and Guo, X and Yang, X and Liu, J and Duan, Q and Tan, Y and Zhang, Q and Sun, T and Qi, C and Li, X and Ji, G},
title = {Sintilimab plus fluorouracil, leucovorin, oxaliplatin and docetaxel regimen as neoadjuvant therapy for resectable gastric cancer and biomarker exploration.},
journal = {Future oncology (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.2217/fon-2022-0929},
pmid = {37990937},
issn = {1744-8301},
abstract = {At present, preoperative chemotherapy is the standard of care for the neoadjuvant treatment of potentially resectable gastric cancer (GC). However, because the efficacy and prognosis are not ideal, curative effects for this population are unsatisfactory. With the development of immune checkpoint inhibitors, the results of a few encouraging early trials of immunotherapeutic agents as neoadjuvant therapies for resectable GC have been reported. However, markers of the efficacy of immune checkpoint inhibitors remain unclear. This prospective single-center, single-arm observational study was designed to evaluate the efficacy of sintilimab plus the fluorouracil, leucovorin, oxaliplatin and docetaxel regimen as a neoadjuvant treatment for localized GC. More importantly, this work assesses multiple dimensions and include ctDNA, the immune microenvironment and intestinal microbiome to explore correlations between biomarkers and neoadjuvant therapeutic efficacy. Clinical trial registration: ChiCTR2200061629 (www.chictr.org.cn/index.aspx).},
}
@article {pmid37990779,
year = {2023},
author = {Leem, S and Keum, HL and Song, HJ and Gu, KN and Kim, Y and Seo, JY and Shin, JG and Lee, SG and Lee, SM and Sul, WJ and Kang, NG},
title = {Skin aging-related microbial types separated by Cutibacterium and α-diversity.},
journal = {Journal of cosmetic dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jocd.16070},
pmid = {37990779},
issn = {1473-2165},
support = {//LG Household &amp; Health Care (LG H&amp;H), Ltd/ ; },
abstract = {BACKGROUND: Studies on the skin microbiome have been conducted to uncover the relationship between skin microbes and the host. However, most of these studies have primarily focused on analyzing individual microbial compositions, which has resulted in a limited understanding of the overall relationship.<br><br>METHODS: We analyzed the facial skin characteristics and microbial profiles of 100 healthy Korean female volunteers using the V1-V2 region of the 16S ribosomal RNA gene.<br><br>RESULTS: The two most prominent features of the facial skin microbiome, the proportion of Cutibacterium and &#x3b1;-diversity, were associated with most of the skin characteristics. Based on clustering results, we proposed four types of facial skin microbiome: type C for Cutibacterium, type B for balanced, type CB for those between types&#xa0;C and B, and type O for others. Type C, which has a high proportion of Cutibacterium, showed high levels of pigmentation, wrinkles, pores, and sagging pores, indicating a tendency for severe skin aging. Type B, which has no dominant species and high microbial diversity, had lower values for pigmentation and wrinkles indicating less severe skin aging. Type CB was an intermediate type between type C and type B in terms of microbial composition and the level of skin aging. Type O dominated by microorganisms other than Cutibacterium, had high levels of sebum and pores but low levels of wrinkles.<br><br>CONCLUSION: We proposed a criterion for classifying facial skin microbial types, each of which showed distinct facial skin aging features. Our simplified microbial types will contribute to a better understanding of facial skin microbial studies.},
}
@article {pmid37990616,
year = {2023},
author = {Zhao, H and Yu, F and Wang, C and Han, Z and Liu, S and Chen, D and Liu, D and Meng, X and He, X and Huang, Z},
title = {The impacts of sodium lauroyl sarcosinate in facial cleanser on facial skin microbiome and lipidome.},
journal = {Journal of cosmetic dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jocd.16092},
pmid = {37990616},
issn = {1473-2165},
support = {2019120024002608//Tianjin University of Science and Technology/ ; },
abstract = {BACKGROUND: The human skin microbiome and lipidome are essential for skin homeostasis and barrier function, and have become a focus in both dermatological and cosmetic fields. However, the influence of surfactants commonly used in cosmetic products on the skin resident microbiome and lipidome remains poorly characterized.<br><br>METHODS: We conducted self-control experiments to systematically study the effects of surfactant (sodium lauroyl sarcosinate [SLS]) on facial skin. Wrinkles, pores, porphyrins, and superficial lipids were examined to evaluate the biophysical state of skin. Quantitative real-time PCR was used to detect the numbers of bacteria and fungi. The diversity and structure of prokaryotic and eukaryotic microbiomes were assessed using 16S rDNA and ITS amplicon sequencing, respectively. Moreover, 22 lipids were identified to evaluate lipidome variations. SPSS software was used for statistical analysis.<br><br>RESULTS: SLS in facial cleanser did not extensively influence skin biophysical parameters, but caused a decrease in porphyrin. After using the SLS-added facial cleanser for 3&#x2009;weeks, the alpha diversity of the prokaryotic microbial community decreased significantly, while the eukaryotic microbial community showed a continuous downward trend but no statistically significant. A shift in the structure of prokaryotic microbiome was observed as a result of SLS exposure, mainly reflected by the increase in Acinetobacter, Escherichia-Shigella, Streptococcus, and Ralstonia, while the SLS had little effect on the structure of the eukaryotic microbiome. Furthermore, SLS exposure had a great impact on skin lipidome, mainly manifested by the increase of phosphatidylglycerol (PG) and phosphatidylcholine (PC), and the decrease of ceramides. Spearman's correlations analysis showed that Escherichia-Shigella, Pseudomonas, and Acinetobacter are positively correlated with PG and PC; however, the correlation is not statistically significant.<br><br>CONCLUSION: In this study, we found the SLS in facial cleanser primarily affected lipidome and the prokaryotic microbiome of facial skin. These findings are useful for reminding us to be vigilant about the ingredients in personal care products, even the common ingredients, and designing effective formulations for repairing ecological balance of skin.},
}
@article {pmid37990608,
year = {2023},
author = {Santoro, D and Saridomichelakis, M and Eisenschenk, M and Tamamoto-Mochizuki, C and Hensel, P and Pucheu-Haston, C and , },
title = {Update on the skin barrier, cutaneous microbiome and host defence peptides in canine atopic dermatitis.},
journal = {Veterinary dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/vde.13215},
pmid = {37990608},
issn = {1365-3164},
abstract = {BACKGROUND: Canine atopic dermatitis (AD) is a complex inflammatory skin disease associated with cutaneous microbiome, immunological and skin barrier alterations. This review summarises the current evidence on skin barrier defects and on cutaneous microbiome dysfunction in canine AD.<br><br>OBJECTIVE: To this aim, online citation databases, abstracts and proceedings from international meetings on skin barrier and cutaneous microbiome published between 2015 and 2023 were reviewed.<br><br>RESULTS: Since the last update on the pathogenesis of canine AD, published by the International Committee on Allergic Diseases of Animals in 2015, 49 articles have been published on skin barrier function, cutaneous/aural innate immunity and the cutaneous/aural microbiome in atopic dogs. Skin barrier dysfunction and cutaneous microbial dysbiosis are essential players in the pathogenesis of canine AD. It is still unclear if such alterations are primary or secondary to cutaneous inflammation, although some evidence supports their primary involvement in the pathogenesis of canine AD.<br><br>Although many studies have been published since 2015, the understanding of the cutaneous host-microbe interaction is still unclear, as is the role that cutaneous dysbiosis plays in the development and/or worsening of canine AD. More studies are needed aiming to design new therapeutic approaches to restore the skin barrier, to increase and optimise the cutaneous natural defences, and to rebalance the cutaneous microbiome.},
}
@article {pmid37990603,
year = {2023},
author = {Athulya, PA and Chandrasekaran, N and Thomas, J},
title = {Polystyrene microplastics interaction and influence on the growth kinetics and metabolism of tilapia gut probiotic Bacillus tropicus ACS1.},
journal = {Environmental science. Processes &amp; impacts},
volume = {},
number = {},
pages = {},
doi = {10.1039/d3em00369h},
pmid = {37990603},
issn = {2050-7895},
abstract = {Gut probiotic bacteria play a significant role in the host health, immunity, and survival. In aquaculture, changes in the gut microbiome of fishes affect the overall productivity and product quality. In the scenario of growing plastic pollution and associated microplastic prevalence, the current study was designed to investigate the interactions and impact of prepared polystyrene microplastics (PS-MPs) of irregular surface morphology on a probiotic bacteria Bacillus tropicus ACS1, isolated from the gut of Oreochromis mossambicus (commonly called as Tilapia). The cell viability was significantly increased along with changes in bacterial growth kinetics upon exposure to varying concentrations of PS-MPs. The microplastic exposure also increased the production of exopolysaccharides (EPS) and induced slight changes in the IR spectra of the EPS. A peak representing a carbonyl linkage that could be attributed to the glycosidic linkages between sugars disappeared following exposure to higher concentrations of PS-MPs. The interaction between the bacteria and the microplastics was visualized using scanning electron microscopy (SEM) and the colonization of the bacteria with active biofilm formation was observed. The investigation of PS-MP induced oxidative stress in the bacteria revealed the generation of reactive oxygen species (ROS) and increase in anti-oxidant enzyme concentrations, superoxide dismutase (SOD), and catalase. The study provides new insights into the effect of microplastics on gut probiotics of an economically significant aquaculture species.},
}
@article {pmid37990415,
year = {2023},
author = {Cui, G and Li, S and Ye, H and Yang, Y and Jia, X and Lin, M and Chu, Y and Feng, Y and Wang, Z and Shi, Z and Zhang, X},
title = {Gut microbiome and frailty: insight from genetic correlation and mendelian randomization.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2282795},
doi = {10.1080/19490976.2023.2282795},
pmid = {37990415},
issn = {1949-0984},
abstract = {Observational studies have shown that the gut microbiome is associated with frailty. However, whether these associations underlie causal effects remains unknown. Thus, this study aimed to assess the genetic correlation and causal relationships between the genetically predicted gut microbiome and frailty using linkage disequilibrium score regression (LDSC) and Mendelian Randomization (MR). Summary statistics for the gut microbiome were obtained from a genome-wide association study (GWAS) meta-analysis of the MiBioGen consortium (N = 18,340). Summary statistics for frailty were obtained from a GWAS meta-analysis, including the UK Biobank and TwinGene (N = 175,226). We used LDSC and MR analyses to estimate the genetic correlation and causality between the genetically predicted gut microbiome and frailty. Our findings indicate a suggestive genetic correlation between Christensenellaceae R-7 and frailty. Moreover, we found evidence for suggestive causal effects of twelve genus-level gut microbes on frailty using at least two MR methods. There was no evidence of horizontal pleiotropy or heterogeneity in the MR analysis. This study provides suggestive evidence for a potential genetic correlation and causal association between several genetically predicted gut microbes and frailty. More population-based observational studies and animal experiments are required to clarify this association and the underlying mechanisms.},
}
@article {pmid37990191,
year = {2023},
author = {Lu, Y and Ge, S and Zhang, H and Lu, W and Bao, X and Pan, S and Pang, Q},
title = {Metabolomic and microbiome analysis of the protective effects of Puerarin against Salmonella Enteritidis Infection in chicks.},
journal = {BMC veterinary research},
volume = {19},
number = {1},
pages = {242},
pmid = {37990191},
issn = {1746-6148},
support = {32273089,31872532 and 31272628//National Natural Science Foundation of China/ ; 32273089,31872532 and 31272628//National Natural Science Foundation of China/ ; 32273089,31872532 and 31272628//National Natural Science Foundation of China/ ; PT2021-1-1,PT2021-1-2//Science and technology Project of Research Fund of Heze University/ ; PT2021-1-1,PT2021-1-2//Science and technology Project of Research Fund of Heze University/ ; PT2021-1-1,PT2021-1-2//Science and technology Project of Research Fund of Heze University/ ; PT2021-1-1,PT2021-1-2//Science and technology Project of Research Fund of Heze University/ ; PT2021-1-1,PT2021-1-2//Science and technology Project of Research Fund of Heze University/ ; },
abstract = {BACKGROUND: Salmonella Enteritidis is a zoonotic pathogen and poses a substantial risk to human health, as well as significant financial losses to the livestock and poultry industries. It is currently urgent to identify alternatives to antibiotic treatment.<br><br>RESULTS: In this study, we explored the influence of Puerarin on the immunological response, intestinal flora, serum metabolome, and growth performance of chicks infected with Salmonella Enteritidis. Chicks were weighed at specific time points and the average daily gain (ADG) was calculated. Serum, intestinal, and cecal content samples were collected on days 10 and 17. The results showed that 100&#xa0;mg/kg of Puerarin significantly suppressed inflammation and enhanced immune function. Metabolomic analysis showed significant differences in serum metabolites after Puerarin treatment and suggested that Puerarin may regulate abnormal amino acid and lipid metabolism after Salmonella Enteritidis infection through the autophagic and ABC transporter pathways. In addition, Puerarin suppressed Salmonella Enteritidis-induced intestinal flora dysbiosis through modulation of the microbial community structures (increased Lactobacillus, Faecalibacterium, and Subdoligranulum), as demonstrated by 16S rRNA analysis.<br><br>CONCLUSIONS: In conclusion, Puerarin can improve growth performance in chicks, suppress the inflammatory response in vivo, enhance immunity, and regulate lipid and amino acid metabolism and the intestinal flora.},
}
@article {pmid37989666,
year = {2023},
author = {Chua, C and Sethi, R and Ong, J and Low, JH and Yew, YW and Tay, A and Howland, SW and Ginhoux, F and Chen, J and Common, JEA and Andiappan, AK},
title = {Late inflammatory monocytes define circulatory immune dysregulation observed in skin microbiome-stratified atopic dermatitis.},
journal = {Journal of dermatological science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jdermsci.2023.10.006},
pmid = {37989666},
issn = {1873-569X},
}
@article {pmid37989575,
year = {2023},
author = {Llera-Romero, AS and Adobes-Martín, M and Iranzo-Cortés, JE and Montiel-Company, JM and Garcovich, D},
title = {Periodontal health status, oral microbiome, white-spot lesions and oral health related to quality of life-clear aligners versus fixed appliances: A systematic review, meta-analysis and meta-regression.},
journal = {Korean journal of orthodontics},
volume = {53},
number = {6},
pages = {374-392},
pmid = {37989575},
issn = {2234-7518},
abstract = {OBJECTIVE: : Assess and evaluate the different indicators of oral health-related quality of life (OHRQoL) among patients treated with clear aligners (CAs) versus those treated with conventional fixed orthodontics (FAs).<br><br>METHODS: : An electronic search was performed on the database is Web of Science, Scopus, and Embase databases. Randomized and non-randomized control trials, cross-sectional, prospective cohort and retrospective trials were included. Quality was assessed with risk of bias tool and risk of bias in non-randomised studies. Meta-analyses were performed with random effects models, estimating the standardized and non-standardized mean differences, odds ratio and risk ratio as the measure of effect. The effect on time was determined using a meta-regression model.<br><br>RESULTS: : Thirty one articles were included in the qualitative synthesis and 17 in the meta-analysis. CAs had a significantly lower negative impact on QoL, with an "important" effect size, while the influence of time was not significant. Periodontal indicators plaque index (PI), gingival index (GI), probing depth (PD), and bleeding on probing show significantly better values in patients treated with CAs, with moderate to large effect sizes. PI and GI have a significant tendency to improve over time. In microbiological indicators, CAs present a lower biofilm mass without differences in the percentage of patients with high counts of Streptococcus mutans and Lactobacilli bacteria. The risk of white spot lesion onset is ten times lower in carriers of CAs.<br><br>CONCLUSIONS: : Patients wearing CAs show better periodontal indicators, less risk of white spot development, less biofilm mass and a better QoL than patients with FAs.},
}
@article {pmid37989149,
year = {2023},
author = {Chen, YC and Wang, WS and Lewis, SJG and Wu, SL},
title = {Fighting Against the Clock: Circadian Disruption and Parkinson's Disease.},
journal = {Journal of movement disorders},
volume = {},
number = {},
pages = {},
doi = {10.14802/jmd.23216},
pmid = {37989149},
issn = {2005-940X},
abstract = {Circadian disruption is being increasingly recognized as a critical factor in the development and progression of Parkinson's disease (PD). This review aims to provide an in-depth overview of the relationship between circadian disruption and PD, exploring the molecular, cellular, and behavioral aspects of this interaction. This will include a comprehensive understanding of how the clock gene system and transcription-translation feedback loops (TTFLs) function and how they go away in PD. The article also discusses the role of clock genes in the regulation of circadian rhythms, the impact of clock gene dysregulation on mitochondrial function, oxidative stress, and neuroinflammation, including the microbiota-gut-brain axis, which have all been proposed as crucial mechanisms in the pathophysiology of PD. Finally, this review highlights potential therapeutic strategies targeting the clock gene system and circadian rhythm for the treatment of PD.},
}
@article {pmid37988808,
year = {2023},
author = {Siponen, S and Jayaprakash, B and Hokajärvi, AM and Gomez-Alvarez, V and Inkinen, J and Ryzhikov, I and Räsänen, P and Ikonen, J and Pursiainen, A and Kauppinen, A and Kolehmainen, M and Paananen, J and Torvinen, E and Miettinen, IT and Pitkänen, T},
title = {Composition of active bacterial communities and presence of opportunistic pathogens in disinfected and non-disinfected drinking water distribution systems in Finland.},
journal = {Water research},
volume = {248},
number = {},
pages = {120858},
doi = {10.1016/j.watres.2023.120858},
pmid = {37988808},
issn = {1879-2448},
abstract = {Many factors, including microbiome structure and activity in the drinking water distribution system (DWDS), affect the colonization potential of opportunistic pathogens. The present study aims to describe the dynamics of active bacterial communities in DWDS and identify the factors that shape the community structures and activity in the selected DWDSs. Large-volume drinking water and hot water, biofilm, and water meter deposit samples were collected from five DWDSs. Total nucleic acids were extracted, and RNA was further purified and transcribed into its cDNA from a total of 181 water and biofilm samples originating from the DWDS of two surface water supplies (disinfected with UV and chlorine), two artificially recharged groundwater supplies (non-disinfected), and a groundwater supply (disinfected with UV and chlorine). In chlorinated DWDSs, concentrations of <0.02-0.97 mg/l free chlorine were measured. Bacterial communities in the RNA and DNA fractions were analysed using Illumina MiSeq sequencing with primer pair 341F-785R targeted to the 16S rRNA gene. The sequence libraries were analysed using QIIME pipeline, Program R, and MicrobiomeAnalyst. Not all bacterial cells were active based on their 16S rRNA content, and species richness was lower in the RNA fraction (Chao1 mean value 490) than in the DNA fraction (710). Species richness was higher in the two DWDSs distributing non-disinfected artificial groundwater (Chao1 mean values of 990 and 1 000) as compared to the two disinfected DWDSs using surface water (Chao1 mean values 190 and 460) and disinfected DWDS using ground water as source water (170). The difference in community structures between non-disinfected and disinfected water was clear in the beta-diversity analysis. Distance from the waterworks also affected the beta diversity of community structures, especially in disinfected distribution systems. The two most abundant bacteria in the active part of the community (RNA) and total bacterial community (DNA) belonged to the classes Alphaproteobacteria (RNA 28 %, DNA 44 %) and Gammaproteobacteria (RNA 32 %, DNA 30 %). The third most abundant and active bacteria class was Vampirovibrionia (RNA 15 %), whereas in the total community it was Paceibacteria (DNA 11 %). Class Nitrospiria was more abundant and active in both cold and hot water in DWDS that used chloramine disinfection compared to non-chlorinated or chlorine-using DWDSs. Thirty-eight operational taxonomic units (OTU) of Legionella, 30 of Mycobacterium, and 10 of Pseudomonas were detected among the sequences. The (RT)-qPCR confirmed the presence of opportunistic pathogens in the DWDSs studied as Legionella spp. was detected in 85 % (mean value 4.5 × 10[4] gene copies/100 ml), Mycobacterium spp. in 95 % (mean value 8.3 × 10[6] gene copies/100 ml), and Pseudomonas spp. in 78 % (mean value 1.6 × 10[5] gene copies/100 ml) of the water and biofilm samples. Sampling point inside the system (distance from the waterworks and cold/hot system) affected the active bacterial community composition. Chloramine as a chlorination method resulted in a recognizable community composition, with high abundance of bacteria that benefit from the excess presence of nitrogen. The results presented here confirm that each DWDS is unique and that opportunistic pathogens are present even in conditions when water quality is considered excellent.},
}
@article {pmid37988614,
year = {2023},
author = {Holzhausen, EA and Peppard, PE and Sethi, AK and Safdar, N and Malecki, KC and Schultz, AA and Deblois, CL and Hagen, EW},
title = {Associations of gut microbiome richness and diversity with objective and subjective sleep measures in a population sample.},
journal = {Sleep},
volume = {},
number = {},
pages = {},
doi = {10.1093/sleep/zsad300},
pmid = {37988614},
issn = {1550-9109},
abstract = {STUDY OBJECTIVES: Alterations in gut microbiota composition have been associated with several conditions, and there is emerging evidence that sleep quantity and quality are associated with the composition of the gut microbiome. Therefore, this study aimed to assess the associations between several measures of sleep and the gut microbiome in a large, population based sample.<br><br>METHODS: Data were collected from participants in the Survey of the Health of Wisconsin from 2016-2017 (N=720). Alpha-diversity was estimated using Chao1 richness, Shannon's diversity, and Inverse Simpson's diversity. Beta-diversity was estimated using Bray-Curtis dissimilarity. Models for each of the alpha-diversity outcomes were calculated using linear mixed effects models. Permutational multivariate analysis of variance tests were performed to test whether gut microbiome composition differed by sleep measures. Negative binomial models were used to assess whether sleep measures were associated with individual taxa relative abundance.<br><br>RESULTS: Participants were a mean (SD) age of 55 (16) years and 58% were female. The sample was 83% non-Hispanic White, 10.6% non-Hispanic Black, and 3.5% Hispanic. Greater actigraphy-measured night-to-night sleep duration variability, wake after sleep onset (WASO), lower sleep efficiency, and worse self-reported sleep quality were associated with lower microbiome richness and diversity. Sleep variables were associated with beta-diversity, including actigraphy-measured night-to-night sleep duration variability, sleep latency and efficiency, and self-reported sleep quality, sleep apnea, and napping. Relative abundance of several taxa was associated with night-to-night sleep duration variability, average sleep latency and sleep efficiency, and sleep quality.<br><br>CONCLUSION: This study suggests that sleep may be associated with the composition of the gut microbiome. These results contribute to the body of evidence that modifiable health habits can influence the human gut microbiome.},
}
@article {pmid37988132,
year = {2023},
author = {Eom, JA and Jeong, JJ and Han, SH and Kwon, GH and Lee, KJ and Gupta, H and Sharma, SP and Won, SM and Oh, KK and Yoon, SJ and Joung, HC and Kim, KH and Kim, DJ and Suk, KT},
title = {Gut-microbiota prompt activation of natural killer cell on alcoholic liver disease.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2281014},
doi = {10.1080/19490976.2023.2281014},
pmid = {37988132},
issn = {1949-0984},
mesh = {Humans ; Animals ; Mice ; Mice, Inbred C57BL ; Liver Cirrhosis, Alcoholic ; *Hepatitis, Alcoholic ; *Gastrointestinal Microbiome ; *Liver Diseases, Alcoholic ; Killer Cells, Natural ; Ethanol ; },
abstract = {The liver is rich in innate immune cells, such as natural killer (NK) cells, natural killer T cells, and Kupffer cells associated with the gut microbiome. These immune cells are dysfunctional owing to alcohol consumption. However, there is insufficient data on the association between immune cells and gut microbiome in alcoholic liver disease (ALD). Therefore, the purpose of this study was to evaluate the effects of probiotic strains on NK cells in ALD patients. In total, 125 human blood samples [control (n = 22), alcoholic hepatitis (n = 43), and alcoholic cirrhosis (n = 60]) were collected for flow cytometric analysis. C57BL/6J mice were divided into four groups (normal, EtOH-fed, and 2 EtOH+strain groups [Phocaeicola dorei and Lactobacillus helveticus]). Lymphocytes isolated from mouse livers were analyzed using flow cytometry. The frequency of NK cells increased in patients with alcoholic hepatitis and decreased in patients with alcoholic cirrhosis. The expression of NKp46, an NK cell-activating receptor, was decreased in patients with alcoholic hepatitis and increased in patients with alcoholic cirrhosis compared to that in the control group. The number of cytotoxic CD56dimCD16[+] NK cells was significantly reduced in patients with alcoholic cirrhosis. We tested the effect of oral administration P. dorei and L. helveticus in EtOH-fed mice. P. dorei and L. helveticus improved liver inflammation and intestinal barrier damage caused by EtOH supply and increased NK cell activity. Therefore, these observations suggest that the gut microbiome may ameliorate ALD by regulating immune cells.},
}
@article {pmid37987847,
year = {2023},
author = {Caprara, GL and von Ameln Lovison, O and Martins, AF and Bernardi, JR and Goldani, MZ},
title = {Gut microbiota transfer evidence from mother to newborn.},
journal = {European journal of pediatrics},
volume = {},
number = {},
pages = {},
pmid = {37987847},
issn = {1432-1076},
abstract = {Early life microbiota is a risk factor for future diseases. The main purpose of this study was to investigate the transfer of gut microbiota from mother to newborn. A biological sample was collected from the anal mucosa of the pregnant women before delivery and from the newborns between 24 and 48 h after delivery, as it was not possible to collect a meconium sample at that time. The microbiome of the samples was analyzed by sequencing the hypervariable regions V3-V4 of the 16S gene. To determine the likelihood of microbiota transfer from mother to newborn and examine the relationship with the mode of delivery, we utilized Fisher's exact test and odds ratio. A weighted transfer ratio was employed as a comprehensive measure of transfer. A total of 5767 ASVs were identified in newborn samples (n = 30) and 7253 in maternal samples (n = 30). In the analysis of transfer correlated with the mode of delivery, we observed significant ASVs (p < 0.05). Vaginal delivery showed a positive probability of transfer (OR = 2.184 and WTR = 1.852). We found a negative correlation (OR < 1) between the abundance of maternal ASVs and the likelihood of microbiota transfer to the newborn in both delivery modes. The relationship was inversely proportional for both cesarean section (log10 = - 0.2229) and vaginal delivery (log10 = - 0.1083), with statistical significance observed only for cesarean section (p = 0.0083). Conclusion: In our sample, the maternal gut microbiome was found to be associated with the infant gut microbiome, indicating evidence of ASV-specific transfer from the maternal microbiome to newborns. What is Known: • There is a relationship of early-life microbiota composition with future health outcomes. What is New: • This was the first study to evaluate maternal gut microbiota transfer to newborns in Brazil.},
}
@article {pmid37987621,
year = {2023},
author = {Liu, X and Sun, M and Pu, F and Ren, J and Qu, X},
title = {Transforming Intratumor Bacteria into Immunopotentiators to Reverse Cold Tumors for Enhanced Immuno-chemodynamic Therapy of Triple-Negative Breast Cancer.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.3c09472},
pmid = {37987621},
issn = {1520-5126},
abstract = {Immunotherapy of triple-negative breast cancer (TNBC) has an unsatisfactory therapeutic outcome due to an immunologically "cold" microenvironment. Fusobacterium nucleatum (F. nucleatum) was found to be colonized in triple-negative breast tumors and was responsible for the immunosuppressive tumor microenvironment and tumor metastasis. Herein, we constructed a bacteria-derived outer membrane vesicle (OMV)-coated nanoplatform that precisely targeted tumor tissues for dual killing of F. nucleatum and cancer cells, thus transforming intratumor bacteria into immunopotentiators in immunotherapy of TNBC. The as-prepared nanoparticles efficiently induced immunogenic cell death through a Fenton-like reaction, resulting in enhanced immunogenicity. Meanwhile, intratumoral F. nucleatum was killed by metronidazole, resulting in the release of pathogen-associated molecular patterns (PAMPs). PAMPs cooperated with OMVs further facilitated the maturation of dendritic cells and subsequent T-cell infiltration. As a result, the "kill two birds with one stone" strategy warmed up the cold tumor environment, maximized the antitumor immune response, and achieved efficient therapy of TNBC as well as metastasis prevention. Overall, this strategy based on a microecology distinction in tumor and normal tissue as well as microbiome-induced reversal of cold tumors provides new insight into the precise and efficient immune therapy of TNBC.},
}
@article {pmid37990721,
year = {2022},
author = {Kheirvari, M and Lacy, VA and Goudarzi, H and RabieNezhad Ganji, N and Kamali Ardekani, M and Anbara, T},
title = {The changes in cognitive function following bariatric surgery considering the function of gut microbiome.},
journal = {Obesity Pillars (Online)},
volume = {3},
number = {},
pages = {100020},
pmid = {37990721},
issn = {2667-3681},
abstract = {BACKGROUND: There is a correlation between gut microbiota and cognitive function. The mechanisms and pathways explain why the incidence of Alzheimer's disease in subjects undergoing bariatric surgery is lower than in other people with obesity.<br><br>METHODS: In this review article, we aim to discuss the association of obesity, cognitive impairment, and physiological changes after bariatric surgery.<br><br>RESULTS: Bariatric surgery has a series of physiological benefits which may lead to an improvement in cognitive functions in individuals who are prone to later developing Alzheimer's disease. Also, taxonomical change in the gut microbiome profile provides a healthy condition for living with better levels of cognition without neuropathological damages in older ages.<br><br>CONCLUSION: It can be concluded that there is a possible correlation between cognitive dysfunction and increased risk of cognitive dysfunction in people with a BMI higher than 40&#xa0;kg/m[2]. Bariatric surgery may increase neurotransmitters and improve the gut bacteria, leading to a significant reduction in the risk of Alzheimer's disease.},
}
@article {pmid37990718,
year = {2022},
author = {Shetye, B and Hamilton, FR and Bays, HE},
title = {Bariatric surgery, gastrointestinal hormones, and the microbiome: An Obesity Medicine Association (OMA) Clinical Practice Statement (CPS) 2022.},
journal = {Obesity Pillars (Online)},
volume = {2},
number = {},
pages = {100015},
pmid = {37990718},
issn = {2667-3681},
abstract = {BACKGROUND: This Obesity Medicine Association (OMA) Clinical Practice Statement (CPS) is intended to provide clinicians an overview of bariatric surgery (i.e., bariatric procedures that improve metabolic disease are often termed "metabolic and bariatric surgery"), gastrointestinal hormones, and the microbiome as they relate to patients with obesity.<br><br>METHODS: The scientific information for this CPS is based upon published scientific citations, clinical perspectives of OMA authors, and peer review by the Obesity Medicine Association leadership.<br><br>RESULTS: This CPS includes the pros and cons of the most common types of bariatric procedures; the roles of gastrointestinal (GI) hormones in regulating hunger, digestion, and postabsorptive nutrient metabolism; and the microbiome's function and relationship with body weight. This CPS also describes patient screening for bariatric surgery, patient care after bariatric surgery, and treatment of potential nutrient deficiencies before and after bariatric surgery. Finally, this CPS explores the interactions between bariatric surgery, GI hormones, and the microbiome.<br><br>CONCLUSIONS: This Obesity Medicine Association (OMA) Clinical Practice Statement (CPS) regarding bariatric surgery, gastrointestinal hormones, and the microbiome is one of a series of OMA CPSs designed to assist clinicians in the care of patients with the disease of obesity. Implementation of appropriate care before and after bariatric surgery, as well as an awareness of GI hormones and the microbiome, may improve the health of patients with obesity, especially patients with adverse fat mass and adiposopathic metabolic consequences.},
}
@article {pmid37987478,
year = {2023},
author = {Lushington, GH and Linde, A and Melgarejo, T},
title = {Bacterial Proteases as Potentially Exploitable Modulators of SARS-CoV-2 Infection: Logic from the Literature, Informatics, and Inspiration from the Dog.},
journal = {Biotech (Basel (Switzerland))},
volume = {12},
number = {4},
pages = {},
pmid = {37987478},
issn = {2673-6284},
support = {N/A//The study was made possible with funding from the WesternU Office for Research and Biotechnology, the College of Veterinary Medicine Office for Research, and the True One Medicine Initiative./ ; },
abstract = {(1) Background: The COVID-19 pandemic left many intriguing mysteries. Retrospective vulnerability trends tie as strongly to odd demographics as to exposure profiles, genetics, health, or prior medical history. This article documents the importance of nasal microbiome profiles in distinguishing infection rate trends among differentially affected subgroups. (2) Hypothesis: From a detailed literature survey, microbiome profiling experiments, bioinformatics, and molecular simulations, we propose that specific commensal bacterial species in the Pseudomonadales genus confer protection against SARS-CoV-2 infections by expressing proteases that may interfere with the proteolytic priming of the Spike protein. (3) Evidence: Various reports have found elevated Moraxella fractions in the nasal microbiomes of subpopulations with higher resistance to COVID-19 (e.g., adolescents, COVID-19-resistant children, people with strong dietary diversity, and omnivorous canines) and less abundant ones in vulnerable subsets (the elderly, people with narrower diets, carnivorous cats and foxes), along with bioinformatic evidence that Moraxella bacteria express proteases with notable homology to human TMPRSS2. Simulations suggest that these proteases may proteolyze the SARS-CoV-2 spike protein in a manner that interferes with TMPRSS2 priming.},
}
@article {pmid37987328,
year = {2023},
author = {Radwan, K and Wu, G and Banks-Word, K and Rosenberger, R},
title = {An Open-Label Case Series of Glutathione Use for Symptomatic Management in Children with Autism Spectrum Disorder.},
journal = {Medical sciences (Basel, Switzerland)},
volume = {11},
number = {4},
pages = {},
pmid = {37987328},
issn = {2076-3271},
support = {691694//University of Chicago Medical Center/ ; },
mesh = {Child ; Humans ; Antioxidants/therapeutic use/metabolism ; *Autism Spectrum Disorder/drug therapy/diagnosis/metabolism ; Glutathione/therapeutic use/metabolism ; Oxidative Stress ; Pilot Projects ; },
abstract = {Autism spectrum disorder (ASD) is a type of neurodevelopmental disorder that has been diagnosed in an increasing number of children around the world. The existing data suggest that early diagnosis and intervention can improve ASD outcomes. The causes of ASD remain complex and unclear, and there are currently no clinical biomarkers for autism spectrum disorder. There is an increasing recognition that ASD might be associated with oxidative stress through several mechanisms including abnormal metabolism (lipid peroxidation) and the toxic buildup of reactive oxygen species (ROS). Glutathione acts as an antioxidant, a free radical scavenger and a detoxifying agent. This open-label pilot study investigates the tolerability and effectiveness of oral supplementation with Opitac[TM] gluthathione as a treatment for patients with ASD. The various aspects of glutathione Opitac[TM] glutathione bioavailability were examined when administered by oral routes. The absorption of glutathione from the gastrointestinal tract has been recently investigated. The results of this case series suggest that oral glutathione supplementation may improve oxidative markers, but this does not necessarily translate to the observed clinical improvement of subjects with ASD. The study reports a good safety profile of glutathione use, with stomach upset reported in four out of six subjects. This article discusses the role of the gut microbiome and redox balance in ASD and notes that a high baseline oxidative burden may make some patients poor responders to glutathione supplementation. In conclusion, an imbalance in redox reactions is only one of the many factors contributing to ASD, and further studies are necessary to investigate other factors, such as impaired neurotransmission, immune dysregulation in the brain, and mitochondrial dysfunction.},
}
@article {pmid37986834,
year = {2023},
author = {Wang, SH and Zheng, T and Fawzi, NL},
title = {Structure and position-specific interactions of prion-like domains in transcription factor Efg1 phase separation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.09.566450},
pmid = {37986834},
abstract = {UNLABELLED: Candida albicans , a prominent member of the human microbiome, can make an opportunistic switch from commensal coexistence to pathogenicity accompanied by an epigenetic shift between the white and opaque cell states. This transcriptional switch is under precise regulation by a set of transcription factors (TFs), with Enhanced Filamentous Growth Protein 1 (Efg1) playing a central role. Previous research has emphasized the importance of Egf1's prion-like domain (PrLD) and the protein's ability to undergo phase separation for the white-to-opaque transition of C. albicans . However, the underlying molecular mechanisms of Efg1 phase separation have remained underexplored. In this study, we delved into the biophysical basis of Efg1 phase separation, revealing the significant contribution of both N-terminal (N) and C-terminal (C) PrLDs. Through NMR structural analysis, we found that Efg1 N-PrLD and C-PrLD are mostly disordered though have prominent partial α-helical secondary structures in both domains. NMR titration experiments suggest that the partially helical structures in N-PrLD act as hubs for self-interaction as well as Efg1 interaction with RNA. Using condensed-phase NMR spectroscopy, we uncovered diverse amino acid interactions underlying Efg1 phase separation. Particularly, we highlight the indispensable role of tyrosine residues within the transient α-helical structures of PrLDs particularly in the N-PrLD compared to the C-PrLD in stabilizing phase separation. Our study provides evidence that the transient α-helical structure is present in the phase separated state and highlights the particular importance of aromatic residues within these structures for phase separation. Together, these results enhance the understanding of C. albicans TF interactions that lead to virulence and provide a crucial foundation for potential antifungal therapies targeting the transcriptional switch.<br><br>STATEMENT OF SIGNIFICANCE: Phase separated condensates have been found across the domains of life and many types of cells. To understand their varied functions, seeing the residue-by-residue details of the structure and interactions of component protein constituents is essential. A set of transcription factors that phase-separate controls cell fate of the pathogenic yeast Candida albicans. Here, we examine the structural and interaction details of a main regulator of this process, Efg1, using NMR spectroscopy and biochemical assays. We find Efg1's phase-separating domains are not entirely disordered as often assumed but in fact contain helical regions that persist upon phase separation. We also reveal the balance of contacts formed in the condensed phase and the importance of specific residues and regions in phase separation.},
}
@article {pmid37986824,
year = {2023},
author = {Berryhill, BA and Burke, KB and Fontaine, J and Brink, CE and Harvill, MG and Goldberg, DA and Konstantinidis, KT and Levin, BR and Woodworth, MH},
title = {Enteric Populations of Escherichia coli are Likely to be Resistant to Phages Due to O Antigen Production.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.08.566299},
pmid = {37986824},
abstract = {UNLABELLED: Bioinformatic and experimental data show that bacteriophages are ubiquitous in human enteric microbiomes. However, there are gaps in understanding the contribution of these viruses in shaping the bacterial strain and species composition of the gut microbiome and how these phages are maintained over time. To address these questions, we adapted and analyzed the properties of a mathematical model of the population and evolutionary dynamics of bacteria and phage and performed experiments with Escherichia coli and phages isolated from four fecal microbiota transplantation (FMT) doses as representative samples of non-dysbiotic enteric microbiota. Our models predict and experiments confirm that due to production of the O antigen, E. coli in the enteric microbiome are likely to be resistant to infection with co-occurring phages. However, phages can be maintained in these populations in high densities due to high rates of transition between resistant and sensitive states, which we call leaky resistance. Based on these models and observations, we postulate that the phages found in the human gut are likely to play little role in shaping the composition of E. coli in the enteric microbiome in healthy individuals. How general this is for other species of bacteria in enteric microbiota is not yet clear, although O antigen production is broadly conserved across many taxa.<br><br>SIGNIFICANCE STATEMENT: Little is known about the role that bacteriophages play in shaping the bacterial species and strain composition in the human gut microbiome or how they are maintained over time in this dynamic environment. Here we show that Escherichia coli isolated from fecal samples are likely to be resistant to their co-existing phages due to production of the O antigen. However, phages can be maintained in populations of mostly resistant bacteria if there is a rapid transition between resistant and sensitive states, a state called leaky resistance. Based on these results, we postulate that bacteriophages are likely playing little role of shaping the abundance and diversity of bacteria in the human gut microbiome in healthy individuals.},
}
@article {pmid37986792,
year = {2023},
author = {Bring Horvath, ER and Brazelton, WJ and Kim, MC and Cullum, R and Mulvey, MA and Fenical, W and Winter, JM},
title = {Bacterial Diversity and Chemical Ecology of Natural Product-Producing Bacteria from Great Salt Lake Sediment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.07.565188},
pmid = {37986792},
abstract = {Great Salt Lake (GSL), located northwest of Salt Lake City, UT, is the largest terminal lake in the United States. While the average salinity of seawater is ∼3.3%, the salinity in GSL ranges between 5-28%. In addition to being a hypersaline environment, GSL also contains toxic concentrations of heavy metals, such as arsenic, mercury, and lead. The extreme environment of GSL makes it an intriguing subject of study, both for its unique microbiome and its potential to harbor novel natural product-producing bacteria, which could be used as resources for the discovery of biologically active compounds. Though work has been done to survey and catalogue bacteria found in GSL, the Lake's microbiome is largely unexplored, and little-to-no work has been done to characterize the natural product potential of GSL microbes. Here, we investigate the bacterial diversity of two important regions within GSL, describe the first genomic characterization of Actinomycetota isolated from GSL sediment, including the identification of a new Saccharomonospora species, and provide the first survey of the natural product potential of GSL bacteria.},
}
@article {pmid37986770,
year = {2023},
author = {Liu, Y and Cheng, YY and Zhou, Z and Vivas, EI and Warren, MF and Rey, FE and Anantharaman, K and Venturelli, OS},
title = {Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.01.10.523442},
pmid = {37986770},
abstract = {The arginine dihydrolase pathway (arc operon) is present in a minority of diverse human gut species and enables arginine catabolism. We lack a quantitative understanding of the role of this specialized metabolic pathway in the human gut microbiome. We investigate the role of the arc operon in probiotic E. coli Nissle 1917 on community assembly and health-relevant metabolite production in vitro and in murine gut. The arc operon shapes community assembly and can enhance butyrate production at physiologically relevant environmental pH levels in vitro . In the presence of the arc operon, human gut communities display reduced variability in composition in response to variations in initial pH. Dynamic computational modeling of community assembly reveals the extent of pH-mediated inter-species interactions. Overall, we demonstrate that a specialized metabolic pathway can serve as the control knob of community assembly and beneficial metabolite production.},
}
@article {pmid37986759,
year = {2023},
author = {Fei, N and Xie, B and Long, TJ and StGeorge, M and Tan, A and Manzoor, S and Sidebottom, AM and Spedale, M and Theriault, BR and Sulakhe, D and Chang, EB},
title = {The Host-specific Microbiota is Required for Diet-Specific Metabolic Homeostasis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.05.565654},
pmid = {37986759},
abstract = {UNLABELLED: In complex mammals, the importance and host-specificity of microbial communities have been demonstrated through their positive effects on host immune fitness or performance. However, whether host metabolic physiology homeostasis depends on a specific bacterial community exclusive to the host remains unclear. Here, we show that the coevolved host-specific microbiota is required to maintain diet-specific flexible and sufficient metabolic homeostasis through a high colonization rate, modulating gut metabolites, and related targets. Using germ-free (GF) mice, we tested whether the fitness benefiting the host metabolic phenotype of microbiota was host-specific. We demonstrated that GF mice associated with exogenous microbiota (human microbiota (HM)), which exhibited different and reduced gut microbial species diversity, significantly elevated metabolic rate, and exhibited metabolic insufficiency, all characteristics of GF mice. Strikingly, the absence of the host-specific microbiome attenuated high-fat diet-specific metabolism features. Different diets caused different metabolic changes in only host-specific microbiota-associated mice, not the host-microbiota mismatched mice. While RNA sequencing revealed subtle changes in the expression of genes in the liver, GF mice and HM mice showed considerably altered expression of genes associated with metabolic physiology compared to GF mice associated with host-specific microbiota. The effect of diet outweighed microbiota in the liver transcriptome. These changes occurred in the setting of decreased luminal short-chain fatty acids (SCFAs) and the secondary bile acid (BAs) pool and downstream gut signaling targets in HM and GF mice, which affects whole-body metabolism. These data indicate that a foreign microbial community provides little metabolic benefit to the host when compared to a host-specific microbiome, due to the colonization selection pressure and microbiota-derived metabolites dysfunction. Overall, microbiome fitness effects on the host metabolic phenotype were host-specific. Understanding the impact of the host-specificity of the microbiome on metabolic homeostasis may provide important insights for building a better probiotic.<br><br>HIGHLIGHTS: Microbiome fitness effects on the host metabolic phenotype were host-specific in mammals.Human microbiota-associated mice exhibited lower host metabolic fitness or performance, and similar functional costs in GF mice.Different diets cause different metabolic changes only in host-specific microbiota-associated mice, not the host-microbiota mismatched mice.The defective gut microbiota in host-specific microbiota, microbial metabolites and related targets likely drive the metabolic homeostasis.},
}
@article {pmid37986509,
year = {2023},
author = {Bacil, GP and Romualdo, GR and Rodrigues, J and Barbisan, LF},
title = {Indole-3-carbinol and chlorogenic acid combination modulates gut microbiome and attenuates nonalcoholic steatohepatitis in a murine model.},
journal = {Food research international (Ottawa, Ont.)},
volume = {174},
number = {Pt 1},
pages = {113513},
doi = {10.1016/j.foodres.2023.113513},
pmid = {37986509},
issn = {1873-7145},
mesh = {Mice ; Humans ; Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy/prevention &amp; control ; Chlorogenic Acid/pharmacology ; Disease Models, Animal ; *Gastrointestinal Microbiome ; },
abstract = {Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease worldwide, affecting almost 32% of the population and ranging from simple steatosis to nonalcoholic steatohepatitis (NASH). Recent findings indicate that the fast-growing prevalence of NAFLD might be linked to adherence to a Westernized diet (WD), mostly composed of fat/sugar-enriched foods. The WD has been reportedly targeted as a potential driver of gut-liver axis unbalance, suggesting a major role in NASH. On the other hand, bioactive food compounds feature as a potential chemopreventive strategy against NASH, due to their beneficial effects (i.e, anti-inflammatory/oxidant activity and modulation of gut microbiome). Brassicaceae vegetables are known for their high amount of isothiocyanates and polyphenols, as indole-3-carbinol (I3C) and chlorogenic acid (CGA). Thus, we sought to assess the effects of human relevant doses of I3C and CGA isolated or in combination (5/125 mg/Kg of body weight, respectively) on a diet/chemical-induced murine model of NASH. I3C + CGA oral treatment diminished NAFLD activity score (NAS) (p < 0.0001), as well as alleviated the hepatic lipid (p = 0.0011) accumulation, prevented hepatic stellate cell (HSC) activation (p < 0.0001), and subsequent fibrosis (p < 0.0001). The combination also reduced the number of both hepatic CD68-positive macrophages (p < 0.0001) and cleaved caspase-3 hepatocytes (p < 0.0001) and diminished the malondialdehyde levels (p = 0.0155). Additionally, the combination of I3C + CGA restored the relative abundance of Alistipes (p = 0.0299), Allobaculum (p = 0.0014), Bacteroides (p = 0.0046), and Odoribacter (p = 0.0030) bacteria genera on the gut microbiome. Taken together, these findings show that the combination of I3C + CGA at populational-relevant ingestion, rather than the I3C or CGA alone, was able to modulate gut microbiome and attenuate NASH in this hybrid model mouse.},
}
@article {pmid37986481,
year = {2023},
author = {Rocha, HA and Borém, FM and Alves, APC and Santos, CMD and Schwan, RF and Haeberlin, L and Nakajima, M and Sugino, R},
title = {Natural fermentation with delayed inoculation of the yeast Torulaspora delbrueckii: Impact on the chemical composition and sensory profile of natural coffee.},
journal = {Food research international (Ottawa, Ont.)},
volume = {174},
number = {Pt 1},
pages = {113632},
doi = {10.1016/j.foodres.2023.113632},
pmid = {37986481},
issn = {1873-7145},
mesh = {*Torulaspora ; Fermentation ; *Yeast, Dried ; Fungi/metabolism ; Fatty Acids/metabolism ; },
abstract = {All coffee production stages occur in a microbiome, which is generally composed of bacteria, yeasts, and filamentous fungi. The use of starter cultures in post-harvest processing stages is an interesting alternative, since they promote faster removal of mucilage and incorporation of compounds that improve sensory quality, which can result in diverse sensory attributes for the beverage. This study was therefore developed with the objective of evaluating the effect of the following processing procedures on the chemical and sensory characteristics of the coffee beverage: first, fermentation of coffee fruit of the yellow Catucaí variety of Coffea arabica with indigenous microorganisms, followed by inoculation of the starter culture Torulaspora delbrueckii CCMA 0684 during the drying stage. The fruit was divided into two lots, which were differentiated by a natural fermentation process before drying began. The starter culture was inoculated on the coffee at different times during the drying process: at 0 h, 24 h, 48 h, or 72 h after drying began. The sensory attributes, the volatile compound composition of the roasted beans, the organic acid profile, the bioactive compounds, and the fatty acid profile of the green coffee beans were analyzed. The fatty acid and bioactive compound content showed little variation among treatments. Analysis of volatile compounds and organic acids and evaluation of sensory attributes made it possible to distinguish the two treatments. We conclude that natural fermentation of coffee fruit improve the chemical and sensory quality of the coffee beverage. The effect of natural fermentation may be before inoculation of the starter cultures or even during drying.},
}
@article {pmid37986094,
year = {2023},
author = {Pinnell, LJ and Young, JD and Thompson, TW and Wolfe, CA and Bryant, TC and Nair, MN and Richeson, JT and Morley, PS},
title = {Establishing the link between microbial communities in bovine liver abscesses and the gastrointestinal tract.},
journal = {Animal microbiome},
volume = {5},
number = {1},
pages = {58},
pmid = {37986094},
issn = {2524-4671},
abstract = {BACKGROUND: Liver abscesses (LAs) are one of the most common and important problems faced by the beef industry. The most efficacious method for the prevention of LAs in North America is through dietary inclusion of low doses of antimicrobial drugs such as tylosin, but the mechanisms by which this treatment prevents LAs are not fully understood. LAs are believed to result from mucosal barrier dysfunction in the gastrointestinal tract (GIT) allowing bacterial translocation to the liver via the portal vein, yet differences in the GIT microbiome of cattle with and without LAs have not been explored. Here, we characterized microbial communities from LAs, rumen, ileum, and colon from the same cattle for the first time.<br><br>RESULTS: Results demonstrate that tylosin supplementation was associated with differences in microbial community structure in the rumen and small intestine, largely because of differences in the predominance of Clostridia. Importantly, we show for the first time that microbial communities from multiple LAs in one animal's liver are highly similar, suggesting that abscesses found at different locations in the liver may originate from a localized source in the GIT (rather than disparate locations). A large portion of abscesses were dominated by microbial taxa that were most abundant in the hindgut. Further, we identified taxa throughout the GIT that were differentially abundant between animals with and without liver abscesses. Bifidobacterium spp.-a bacteria commonly associated with a healthy GIT in several species-were more abundant in the rumen and ileum of animals without LAs compared to those with LAs.<br><br>CONCLUSIONS: Together these results provide the first direct comparison of GIT and LA microbial communities within the same animal, add considerable evidence to the hypothesis that some LA microbial communities arise from the hindgut, and suggest that barrier dysfunction throughout the GIT may be the underlying cause of LA formation in cattle.},
}
@article {pmid37986012,
year = {2023},
author = {Basbas, C and Garzon, A and Schlesener, C and van Heule, M and Profeta, R and Weimer, BC and Silva-Del-Rio, N and Byrne, BA and Karle, B and Aly, SS and Lima, FS and Pereira, RV},
title = {Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome.},
journal = {Animal microbiome},
volume = {5},
number = {1},
pages = {59},
pmid = {37986012},
issn = {2524-4671},
abstract = {BACKGROUND: The goal of this study was to assess the microbial ecology and diversity present in the uterus of post-partum dairy cows with and without metritis from 24 commercial California dairy farms using shotgun metagenomics. A set subset of 95 intrauterine swab samples, taken from a larger selection of 307 individual cow samples previously collected, were examined for α and β diversity and differential abundance associated with metritis. Cows within 21 days post-partum were categorized into one of three clinical groups during sample collection: control (CT, n = 32), defined as cows with either no vaginal discharge or a clear, non-purulent mucus vaginal discharge; metritis (MET, n = 33), defined as a cow with watery, red or brown colored, and fetid vaginal discharge; and purulent discharge cows (PUS, n = 31), defined as a non-fetid purulent or mucopurulent vaginal discharge.<br><br>RESULTS: All three clinical groups (CT, MET, and PUS) were highly diverse, with the top 12 most abundant genera accounting for 10.3%, 8.8%, and 10.1% of mean relative abundance, respectively. The &#x3b1; diversity indices revealed a lower diversity from samples collected from MET and PUS when compared to CT cows. PERMANOVA statistical testing revealed a significant difference (P adjusted&#x2009;<&#x2009;0.01) in the diversity of genera between CT and MET samples (R2&#x2009;=&#x2009;0.112, P&#x2009;=&#x2009;0.003) and a non-significant difference between MET and PUS samples (R2&#x2009;=&#x2009;0.036, P&#x2009;=&#x2009;0.046). ANCOM-BC analysis revealed that from the top 12 most abundant genera, seven genera were increased in the natural log fold change (LFC) of abundance in MET when compared to CT samples: Bacteroides, Clostridium, Fusobacterium, Phocaeicola, Porphyromonas, Prevotella, and Streptococcus. Two genera, Dietzia and Microbacterium, were decreased in natural LFC of abundance when comparing MET (regardless of treatment) and CT, while no changes in natural LFC of abundance were observed for Escherichia, Histophilus, and Trueperella.<br><br>CONCLUSIONS: The results presented here, are the current deepest shotgun metagenomic analyses conducted on the bovine uterine microbiome to date (mean of 256,425 genus-level reads per sample). Our findings support that uterine samples from cows without metritis (CT) had increased &#x3b1;-diversity but decreased &#x3b2;-diversity when compared to metritis or PUS cows, characteristic of dysbiosis. In summary, our findings highlight that MET cows have an increased abundance of Bacteroides, Porphyromonas, and Fusobacterium when compared to CT and PUS, and support the need for further studies to better understand their potential causal role in metritis pathogenesis.},
}
@article {pmid37986003,
year = {2023},
author = {Cheng, L and Tao, J and Qu, Z and Lu, P and Liang, T and Meng, L and Zhang, W and Liu, N and Zhang, J and Cao, P and Jin, J},
title = {Carbon nanosol-induced assemblage of a plant-beneficial microbiome consortium.},
journal = {Journal of nanobiotechnology},
volume = {21},
number = {1},
pages = {436},
pmid = {37986003},
issn = {1477-3155},
abstract = {Carbon nanosol (CNS) is a carbon-based nanomaterial that promotes plant growth; however, its functional mechanisms and effects on the microbiome are not fully understood. Here, we explored the effects of CNS on the relationship between the soil, endophytic microbiomes and plant productivity. CNS treatment increased the fresh biomass of tobacco (Nicotiana tabacum L.) plants by 27.4% ± 9.9%. Amplicon sequencing analysis showed that the CNS treatment significantly affected the composition and diversity of the microbial communities in multiple ecological niches associated with tobacco, especially the bulk soil and stem endophytic microbiome. Furthermore, the application of CNS resulted in enhanced network connectivity and stability of the microbial communities in different niches, particularly in the soil, implying a strengthening of certain microbial interactions. Certain potentially growth-promoting root endophytic bacteria were more abundant under the CNS treatment. In addition, CNS increased the abundance of some endophytic microbial functional genes known to enhance plant growth, such as those associated with nutrient metabolism and the plant hormone biosynthesis pathways. We isolated two bacterial strains (Sphingopyxis sp. and Novosphingobium sp.) that were enriched under CNS treatment, and they were confirmed to promote tobacco plant growth in vitro. These results suggested that CNS might, at least in part, promote plant growth by enriching beneficial bacteria in the microbiome.},
}
@article {pmid37985956,
year = {2023},
author = {Zhang, L and Zhang, X and Yi, N},
title = {Bayesian compositional generalized linear models for analyzing microbiome data.},
journal = {Statistics in medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/sim.9946},
pmid = {37985956},
issn = {1097-0258},
abstract = {The crucial impact of the microbiome on human health and disease has gained significant scientific attention. Researchers seek to connect microbiome features with health conditions, aiming to predict diseases and develop personalized medicine strategies. However, the practicality of conventional models is restricted due to important aspects of microbiome data. Specifically, the data observed is compositional, as the counts within each sample are bound by a fixed-sum constraint. Moreover, microbiome data often exhibits high dimensionality, wherein the number of variables surpasses the available samples. In addition, microbiome features exhibiting phenotypical similarity usually have similar influence on the response variable. To address the challenges posed by these aspects of the data structure, we proposed Bayesian compositional generalized linear models for analyzing microbiome data (BCGLM) with a structured regularized horseshoe prior for the compositional coefficients and a soft sum-to-zero restriction on coefficients through the prior distribution. We fitted the proposed models using Markov Chain Monte Carlo (MCMC) algorithms with R package rstan. The performance of the proposed method was assessed by extensive simulation studies. The simulation results show that our approach outperforms existing methods with higher accuracy of coefficient estimates and lower prediction error. We also applied the proposed method to microbiome study to find microorganisms linked to inflammatory bowel disease (IBD). To make this work reproducible, the code and data used in this article are available at https://github.com/Li-Zhang28/BCGLM.},
}
@article {pmid37985877,
year = {2023},
author = {Ntekas, I and De Vlaminck, I},
title = {Spatial methods for microbiome-host interactions.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {37985877},
issn = {1546-1696},
}
@article {pmid37985876,
year = {2023},
author = {Lötstedt, B and Stražar, M and Xavier, R and Regev, A and Vickovic, S},
title = {Spatial host-microbiome sequencing reveals niches in the mouse gut.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {37985876},
issn = {1546-1696},
support = {HG011014-01//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; },
abstract = {Mucosal and barrier tissues, such as the gut, lung or skin, are composed of a complex network of cells and microbes forming a tight niche that prevents pathogen colonization and supports host-microbiome symbiosis. Characterizing these networks at high molecular and cellular resolution is crucial for understanding homeostasis and disease. Here we present spatial host-microbiome sequencing (SHM-seq), an all-sequencing-based approach that captures tissue histology, polyadenylated RNAs and bacterial 16S sequences directly from a tissue by modifying spatially barcoded glass surfaces to enable simultaneous capture of host transcripts and hypervariable regions of the 16S bacterial ribosomal RNA. We applied our approach to the mouse gut as a model system, used a deep learning approach for data mapping and detected spatial niches defined by cellular composition and microbial geography. We show that subpopulations of gut cells express specific gene programs in different microenvironments characteristic of regional commensal bacteria and impact host-bacteria interactions. SHM-seq should enhance the study of native host-microbe interactions in health and disease.},
}
@article {pmid37985875,
year = {2023},
author = {Saarenpää, S and Shalev, O and Ashkenazy, H and Carlos, V and Lundberg, DS and Weigel, D and Giacomello, S},
title = {Spatial metatranscriptomics resolves host-bacteria-fungi interactomes.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {37985875},
issn = {1546-1696},
support = {2017-01066//Svenska Forskningsr&#xe5;det Formas (Swedish Research Council Formas)/ ; 2020-04864//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; },
abstract = {The interactions of microorganisms among themselves and with their multicellular host take place at the microscale, forming complex networks and spatial patterns. Existing technology does not allow the simultaneous investigation of spatial interactions between a host and the multitude of its colonizing microorganisms, which limits our understanding of host-microorganism interactions within a plant or animal tissue. Here we present spatial metatranscriptomics (SmT), a sequencing-based approach that leverages 16S/18S/ITS/poly-d(T) multimodal arrays for simultaneous host transcriptome- and microbiome-wide characterization of tissues at 55-µm resolution. We showcase SmT in outdoor-grown Arabidopsis thaliana leaves as a model system, and find tissue-scale bacterial and fungal hotspots. By network analysis, we study inter- and intrakingdom spatial interactions among microorganisms, as well as the host response to microbial hotspots. SmT provides an approach for answering fundamental questions on host-microbiome interplay.},
}
@article {pmid37985845,
year = {2023},
author = {Ye, Q and Sun, S and Deng, J and Chen, X and Zhang, J and Lin, S and Du, H and Gao, J and Zou, X and Lin, X and Cai, Y and Lu, Z},
title = {Using 16S rDNA and metagenomic sequencing technology to analyze the fecal microbiome of children with avoidant/restrictive food intake disorder.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20253},
pmid = {37985845},
issn = {2045-2322},
mesh = {Humans ; Child ; Anti-Bacterial Agents ; *Avoidant Restrictive Food Intake Disorder ; Drug Resistance, Bacterial ; Macrolides ; *Microbiota ; Bacteria/genetics ; *Actinobacteria/genetics ; Eating ; RNA, Ribosomal, 16S/genetics ; },
abstract = {To investigate the gut microbiota distribution and its functions in children with avoidant/restrictive food intake disorder (ARFID). A total of 135 children were enrolled in the study, including 102 children with ARFID and 33 healthy children. Fecal samples were analyzed to explore differences in gut microbiota composition and diversity and functional differences between the ARFID and healthy control (HC) groups via 16S rDNA and metagenomic sequencing. The gut microbiota composition and diversity in children with ARFID were different from those in heathy children, but there is no difference in the composition and diversity of gut microbiota between children at the age of 3-6 and 7-12 with ARFID. At the phylum level, the most abundant microbes in the two groups identified by 16S rDNA and metagenomic sequencing were the same. At the genus level, the abundance of Bacteroides was higher in the ARFID group (P > 0.05); however, different from the result of 16SrDNA sequencing, metagenomic sequencing showed that the abundance of Bacteroides in the ARFID group was significantly higher than that in the HC group (P = 0.041). At the species level, Escherichia coli, Streptococcus thermophilus and Lachnospira eligens were the most abundant taxa in the ARFID group, and Prevotella copri, Bifidobacterium pseudocatenulatum, and Ruminococcus gnavus were the top three microbial taxa in the HC group; there were no statistically significant differences between the abundance of these microbial taxa in the two groups. LefSe analysis indicated a greater abundance of the order Enterobacterales and its corresponding family Enterobacteriaceae, the family Bacteroidaceae and corresponding genus Bacteroides, the species Bacteroides vulgatus in ARFID group, while the abundance of the phylum Actinobacteriota and its corresponding class Actinobacteria , the order Bifidobacteriales and corresponding family Bifidobacteriaceae, the genus Bifidobacterium were enriched in the HC group. There were no statistically significant differences in the Chao1, Shannon and Simpson indices between the Y1 and Y2 groups (P = 0.1, P = 0.06, P = 0.06). At the phylum level, Bacillota, Bacteroidota, Proteobacteria and Actinobacteriota were the most abundant taxa in both groups, but there were no statistically significant differences among the abundance of these bacteria (P = 0.958, P = 0.456, P = 0.473, P = 0.065). At the genus level, Faecalibacterium was more abundant in the Y2 group than in the Y1 group, and the difference was statistically significant (P = 0.037). The KEGG annotation results showed no significant difference in gut microbiota function between children with ARFID and healthy children; however, GT26 was significantly enriched in children with ARFID based on the CAZy database. The most abundant antibiotic resistance genes in the ARFID group were the vanT, tetQ, adeF, ermF genes, and the abundance of macrolide resistance genes in the ARFID group was significantly higher than that in the HC group (P = 0.041). Compared with healthy children, children with ARFID have a different distribution of the gut microbiota and functional genes. This indicates that the gut microbiome might play an important role in the pathogenesis of ARFID.Clinical trial registration: ChiCTR2300074759.},
}
@article {pmid37985702,
year = {2023},
author = {Shanmugham, M and Devasia, AG and Chin, YL and Cheong, KH and Ong, ES and Bellanger, S and Ramasamy, A and Leo, CH},
title = {Time-dependent specific molecular signatures of inflammation and remodelling are associated with trimethylamine-N-oxide (TMAO)-induced endothelial cell dysfunction.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20303},
pmid = {37985702},
issn = {2045-2322},
support = {SRG-SMT-2020-156//SUTD Start-up Research Grant/ ; ZJUVP2000102//SUTD-ZJU Grant/ ; SKI_2021_02_05//SUTD Kickstarter Initiative/ ; },
mesh = {Humans ; *Endothelial Cells/metabolism ; Methylamines/metabolism ; Inflammation/chemically induced/genetics/metabolism ; *Vascular Diseases ; Oxides ; },
abstract = {Endothelial dysfunction is a critical initiating factor contributing to cardiovascular diseases, involving the gut microbiome-derived metabolite trimethylamine N-oxide (TMAO). This study aims to clarify the time-dependent molecular pathways by which TMAO mediates endothelial dysfunction through transcriptomics and metabolomics analyses in human microvascular endothelial cells (HMEC-1). Cell viability and reactive oxygen species (ROS) generation were also evaluated. TMAO treatment for either 24H or 48H induces reduced cell viability and enhanced oxidative stress. Interestingly, the molecular signatures were distinct between the two time-points. Specifically, few Gene Ontology biological processes (BPs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were modulated after a short (24H) compared to a long (48H) treatment. However, the KEGG signalling pathways namely "tumour necrosis factor (TNF)" and "cytokine-cytokine receptor interaction" were downregulated at 24H but activated at 48H. In addition, at 48H, BPs linked to inflammatory phenotypes were activated (confirming KEGG results), while BPs linked to extracellular matrix (ECM) structural organisation, endothelial cell proliferation, and collagen metabolism were repressed. Lastly, metabolic profiling showed that arachidonic acid, prostaglandins, and palmitic acid were enriched at 48H. This study demonstrates that TMAO induces distinct time-dependent molecular signatures involving inflammation and remodelling pathways, while pathways such as oxidative stress are also modulated, but in a non-time-dependent manner.},
}
@article {pmid37985659,
year = {2023},
author = {Mejia, ME and Mercado-Evans, V and Zulk, JJ and Ottinger, S and Ruiz, K and Ballard, MB and Fowler, SW and Britton, RA and Patras, KA},
title = {Vaginal microbial dynamics and pathogen colonization in a humanized microbiota mouse model.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {87},
pmid = {37985659},
issn = {2055-5008},
support = {DK128053//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; AI157981//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; F31AI167538//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; F31AI167547//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI157981//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; NGP10103//Burroughs Wellcome Fund (BWF)/ ; T32GM136554//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32GM136554//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; F31HD111236//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; },
mesh = {Humans ; Female ; Animals ; Mice ; RNA, Ribosomal, 16S/genetics ; *Escherichia coli/genetics ; Mice, Inbred C57BL ; Vagina ; *Microbiota ; Disease Models, Animal ; Streptococcus agalactiae/genetics ; },
abstract = {Vaginal microbial composition is associated with differential risk of urogenital infection. Although Lactobacillus spp. are thought to confer protection against infection, the lack of in vivo models resembling the human vaginal microbiota remains a prominent barrier to mechanistic discovery. Using 16S rRNA amplicon sequencing of C57BL/6J female mice, we found that vaginal microbial composition varies within and between colonies across three vivaria. Noting vaginal microbial plasticity in conventional mice, we assessed the vaginal microbiome of humanized microbiota mice ([HMb]mice). Like the community structure in conventional mice, [HMb]mice vaginal microbiota clustered into community state types but, uniquely, [HMb]mice communities were frequently dominated by Lactobacillus or Enterobacteriaceae. Compared to conventional mice, [HMb]mice were less susceptible to uterine ascension by urogenital pathobionts group B Streptococcus (GBS) and Prevotella bivia. Although Escherichia and Lactobacillus both correlated with the absence of uterine GBS, vaginal pre-inoculation with exogenous [HMb]mouse-derived E. coli, but not Ligilactobacillus murinus, reduced vaginal GBS burden. Overall, [HMb]mice serve as a useful model to elucidate the role of endogenous microbes in conferring protection against urogenital pathogens.},
}
@article {pmid37985447,
year = {2023},
author = {Wang, M and Chen, J and Wang, Z and Wang, Y and Zhang, Y and Feng, Q and Wei, F},
title = {Salivary microbiomes vary among orthodontic appliances and associate with clinical periodontal parameters.},
journal = {Orthodontics &amp; craniofacial research},
volume = {},
number = {},
pages = {},
doi = {10.1111/ocr.12733},
pmid = {37985447},
issn = {1601-6343},
support = {//Construction Engineering Special Fund "Taishan Scholars" with grant No. tsqn201611068/ ; //National Natural Science Foundation of China through Project No. 82071080/ ; },
abstract = {OBJECTIVE: To investigate the salivary bacterial communities during the first 6-month orthodontic treatment with Clear Aligners (CA) and Fixed Appliances (FA), and its correlation with clinical periodontal parameters.<br><br>MATERIALS AND METHODS: Saliva and periodontal parameters were sampled from individuals wearing CA or FA before treatment (T0), and after 3- (T3) and 6-month (T6) treatments. Salivary bacterial communities characterized based on the 16S rRNA V3-V4 region were compared between FA and CA and correlated with clinical periodontal parameters.<br><br>RESULTS: Probing Depth (PD) significantly increased at T6 in the FA group versus T0, whereas it remained stable in the CA group. The Shannon and Pielou indices were significantly higher in the FA group and significantly positively correlated with periodontal inflammation parameters. &#x3b2;-diversity analysis revealed distinct communities between the FA group and CA group at T6. The relative abundances of 3 genera and 15 species were significantly higher in the FA group. Among the above appliance-type related taxa, bacterial genera Selenomonas, Stomatobaculum, Olsenella and Faecalicoccus and bacterial species Selenomonas_sputigena, Dialister_invisus, Olsenella_profus, Prevotella_buccae, Cryptobacterium_curtum and Clostridium_spiroforme were significantly positively associated with periodontal parameters.<br><br>CONCLUSIONS: Orthodontic treatments trigger appliance-related salivary bacterial communities, highlighting the importance of developing appliance-orientated periodontal strategies during orthodontic treatments. Salivary bacterial communities harboured by patients wearing FA possess higher bacterial parameters which were associated with increasing PD, PI and Gingival Index.},
}
@article {pmid37985032,
year = {2024},
author = {Yang, Y and Ren, Q and Zhou, Z and Li, X and Ren, D and Ji, Z and Mao, J},
title = {Structural elucidation of a highly branched α-D-glucan from Huangjiu and its hepatoprotective activity via gut microbiome regulation and intestinal barrier repairment.},
journal = {Carbohydrate polymers},
volume = {324},
number = {},
pages = {121423},
doi = {10.1016/j.carbpol.2023.121423},
pmid = {37985032},
issn = {1879-1344},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Glucans/pharmacology ; *Liver Diseases, Alcoholic/drug therapy/prevention &amp; control ; Liver ; Ethanol ; Mice, Inbred C57BL ; },
abstract = {Polysaccharides in Huangjiu, a traditional fermented food, are expected to be potentially effective ingredients in protecting against alcoholic liver disease (ALD). Elucidating their precise structural and functional characteristics is essential for in-depth understanding of structure-activity relationships of hepatoprotective polysaccharides. Herein, a major polysaccharide component HJPS1-2 was purified from Huangjiu with an average molecular weight of 3.49 kDa. Structural analyses inferred that HJPS1-2 backbone was composed of (1 → 4)-linked α-D-Glcp and a single α(1 → 6)-D-Glcp-α(1 → 6)-D-Glcp branched unit for every three α(1 → 4)-D-Glcp. An ALD mouse model was further established to clarify the underlying effect of HJPS1-2 on ALD alleviation. Biochemical detection and histopathological assessment revealed that HJPS1-2 intervention remarkably improved ethanol-induced hepatic dysfunction and steatosis. HJPS1-2 treatment ameliorated gut microbiota dysbiosis of ALD mice in a dose-dependent manner, mainly manifested as restoration of microbial diversities, community structure and bacterial interaction patterns. Compared with ethanol group, the strikingly elevated intestinal short-chain fatty acids' levels and enhanced intestinal barrier function after HJPS1-2 intake might contribute to reduced serum and liver lipopolysaccharide levels and subsequently suppressed release of hepatic inflammatory cytokines, thus mitigating ALD. Collectively, this research supports the potential of food-derived polysaccharides to hinder the early formation and progression of ALD through maintaining intestinal homeostasis.},
}
@article {pmid37984746,
year = {2023},
author = {Li, O and Xu, H and Kim, D and Yang, F and Bao, Z},
title = {Roles of human gut microbiota in liver cirrhosis risk: a two-sample mendelian randomization study.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2023.11.011},
pmid = {37984746},
issn = {1541-6100},
abstract = {BACKGROUND: Accumulating evidence suggests that alterations in gut microbiota composition and diversity are associated with liver cirrhosis. But whether gut microbiota promotes or hampers the genesis and development of liver cirrhosis remains vague.<br><br>OBJECTIVES: The primary objective of this study was to establish a causal relationship between gut microbiota and the development of liver fibrosis and cirrhosis. To achieve this, we employed a two-sample Mendelian Randomization (MR) analysis utilizing genome-wide association study (GWAS) summary statistics. This approach enabled us to assess the potential impact of gut microbiota on liver cirrhosis.<br><br>METHODS: The independent genetic instruments of gut microbiota were obtained from the MiBioGen (up to 18,340 participants), which is a large-scale genome-wide genotype and 16S fecal microbiome dataset. Cirrhosis data were derived from the FinnGen biobank analysis, which included 214,403 individuals of European ancestry (811 patients and 213,592 controls). To assess the causal relationship between gut microbiota and cirrhosis, we applied four different methods of Mendelian Randomization (MR) analysis: the inverse variance weighted method (IVW), the MR-Egger regression, the weighted median analysis (WME), and the weighted mode. Furthermore, sensitivity analyses were conducted to evaluate heterogeneity and horizontal pleiotropy.<br><br>RESULTS: Results of MR analyses provided evidence of a causal association between 4 microbiota features and cirrhosis, including 2 family [Lachnosiraceae: odds ratio (OR): 1.82626178; 95% confidence interval (CI): 1.05208209, 3.17012532; P = 0.0323194; Lactobacillaceae : OR: 0.62897502; 95% CI: 0.42513162, 0.93055788; P=0.02033345] and 2 genus [Butyricicoccus: OR: 0.41432215; 95% CI: 0.22716865, 0.75566257; P = 0.0040564; Lactobacillus: OR: 0.6663767; 95% CI: 0.45679511, 0.97211616; P=0.03513627].<br><br>CONCLUSIONS: Our findings offered compelling evidence of a causal association between gut microbiota and cirrhosis in European population and identified specific bacteria taxa that may regulate the genesis and progression of liver fibrosis and cirrhosis, may offer a new direction for the treatment of cirrhosis.},
}
@article {pmid37984648,
year = {2023},
author = {Bhattarai, B and Bhattacharjee, AS and Coutinho, FH and Goel, R},
title = {Investigating the viral ecology and contribution to the microbial ecology in full-scale mesophilic anaerobic digesters.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {140743},
doi = {10.1016/j.chemosphere.2023.140743},
pmid = {37984648},
issn = {1879-1298},
abstract = {In an attempt to assess the diversity of viruses and their potential to modulate the metabolism of functional microorganisms in anaerobic digesters, we collected digestate from three mesophilic anaerobic digesters in full-scale wastewater treatment plants treating real municipal wastewater. The reads were analyzed using bioinformatics algorithms to elucidate viral diversity, identify their potential role in modulating the metabolism of functional microorganisms, and provide essential genomic information for the potential use of virus-mediated treatment in controlling the anaerobic digester microbiome. We found that Siphoviridae was the dominant family in mesophilic anaerobic digesters, followed by Myoviridae and Podoviridae. Lysogeny was prevalent in mesophilic anaerobic digesters as the majority of metagenome-assembled genomes contained at least one viral genome within them. One virus within the genome of an acetoclastic methanogen (Methanothrix soehngenii) was observed with a gene (fwdE) acquired via lateral transfer from hydrogenotrophic methanogens. The virus-mediated acquisition of fwdE gene enables possibility of mixotrophic methanogenesis in Methanothrix soehngenii. This evidence highlighted that lysogeny provides fitness advantage to methanogens in anaerobic digesters by adding flexibility to changing substrates. Similarly, we found auxiliary metabolic genes, such as cellulase and alpha glucosidase, of bacterial origin responsible for sludge hydrolysis in viruses. Additionally, we discovered novel viral genomes and provided genomic information on viruses infecting acidogenic, acetogenic, and pathogenic bacteria that can potentially be used for virus-mediated treatment to deal with the souring problem in anaerobic digesters and remove pathogens from biosolids before land application. Collectively, our study provides a genome-level understanding of virome in conjunction with the microbiome in anaerobic digesters that can be used to optimize the anaerobic digestion process for efficient biogas generation.},
}
@article {pmid37984489,
year = {2023},
author = {Montoya-Hernández, D and Dufoo-Hurtado, E and Cruz-Hernández, A and Campos-Vega, R},
title = {Spent coffee grounds and its antioxidant dietary fiber promote different colonic microbiome signatures: Benefits for subjects with chronodisruption.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {106431},
doi = {10.1016/j.micpath.2023.106431},
pmid = {37984489},
issn = {1096-1208},
abstract = {Chronodisruption, commonly displayed by people living with obesity (PLO), is linked to colonic microbiota dysbiosis, and may increase the risk of many chronic non-communicable diseases, whereas dietary interventions-called chrononutrition may mitigate it. We evaluated the in vitro effects of spent coffee grounds (SCG), and their antioxidant dietary fiber (SCG-DF) on the colonic microbiota of an obese donor displaying dysbiosis and chronodisruption. Basal microbiota pattern was associated with an increased risk of non-communicable chronic diseases. Both samples decrease species richness and increase microbiota diversity (p < 0.05; Chao and Shannon index, respectively), positively enhancing Firmicutes/Bacteroidetes index (SCG, p < 0.04; SCG-DF, p < 0.02). SCG and SCG-DF modulated the microbiota, but SCG-DF induced greater changes, significantly increasing. p_Actonobacterias (SCG p < 0.04; SCG-DF, p < 0.02), and reducing g_Alistipes; s_putredinis, g_Prevotella;s_copri. The highest increase was displayed by p_Proteobacteria (f_Desulfovibrionaceae and f_Alcanigenaceae, p < 0.05), while g_Haemophilus; s_parainfluenzae decreased (p < 0.05). However, neither SCG nor SCG-DF modulated g_Alistipes (evening-type colonic microbial marker) beneficially. SCG and SCG-DF reduced (p < 0.05) g_Lachnospira, a microbial evening-type marker, among other microbial populations, of an obese donor displaying chronodisruption and dysbiosis. SCG and SCG-DF displayed a prebiotic effect with the potential to mitigate diseases linked to chronodisruption.},
}
@article {pmid37984277,
year = {2023},
author = {Monga, N and Sharma, S and Bhatia, R and Bishnoi, M and Kiran Kondepudi, K and Naura, AS},
title = {Immunomodulatory action of synbiotic comprising of newly isolated lactic acid producing bacterial strains against allergic asthma in mice.},
journal = {Cellular immunology},
volume = {393-394},
number = {},
pages = {104786},
doi = {10.1016/j.cellimm.2023.104786},
pmid = {37984277},
issn = {1090-2163},
abstract = {Given the reported role of gut-microbiota in asthma pathogenesis, the present work was carried to evaluate immunomodulatory action of newly isolated lactic acid producing bacterial strains Bifidobacterium breve Bif11 and Lactiplantibacillus plantarum LAB31 against asthma using ovalbumin (OVA) based mouse model. Our results show that both strains modulate Th2 immune response potentially through production of short chain fatty acids (SCFAs), resulting in suppression of OVA-induced airway inflammation. Furthermore, synbiotic comprising of both strains and prebiotic, Isomaltooligosaccharide exhibited superior potential in amelioration of OVA-induced airway inflammation through improved modulation of Th2 immune response. Further, synbiotic protects against OVA-induced mucus hyper-production and airway-hyperresponsiveness. Such protection was associated with normalization of gut microbiome and enhanced production of SCFAs in cecum which correlates closely with population of T-regulatory cells in spleen. Overall, our novel synbiotic possesses the ability to fine-tune the immune response for providing protection against allergic asthma.},
}
@article {pmid37984213,
year = {2023},
author = {Wei, G and Liang, Y and Zhang, G and Zhang, Z and Zhang, Y and Chen, S and Dong, L},
title = {Influence of sampling location and processing on the assembly and network of Polygoni Multiflori Radix surface microbiome.},
journal = {International journal of food microbiology},
volume = {410},
number = {},
pages = {110442},
doi = {10.1016/j.ijfoodmicro.2023.110442},
pmid = {37984213},
issn = {1879-3460},
abstract = {The raw and processed roots of Polygonum multiflorum Thunb is a popular traditional Chinese medicine. However, Polygoni Multiflori Radix is easily contaminated by toxigenic fungi and mycotoxins during harvesting, processing, and transportation, thereby posing a health risk for consumers. This study aims to investigate the presence of fungi on the surface of raw and processed Polygoni Multiflori Radix collected from four producing areas using high-throughput sequencing. Results showed that the phyla Ascomycota and Basidiomycota, the genera Xeromyces, Cystofilobasidium, Eurotium, and Aspergillus were the dominant fungus, and significant differences are presented in four areas and two processed products. Three potential mycotoxin-producing fungi were detected, namely Trichosporon cutaneum, Aspergillus restrictus, and Fusarium oxysporum. The α-diversity and network complexity showed significant differences in four areas. Chao 1 and Shannon were highest in Yunnan (YN), then incrementally decreased from SC (Sichuan) to AH (Anhui) and GD (Guangdong) areas. Meanwhile, α-diversity was also strongly influenced by processing. Chao 1 and Shannon indices were higher in the raw group, however, the network complexity and connectivity were higher in the processed group. In conclusion, the assembly and network of the surface microbiome on Polygoni Multiflori Radix were influenced by sampling location and processing. This work provides details on the surface microbiome of Polygoni Multiflori Radix samples, which could ensure the drug and consumers' safety.},
}
@article {pmid37983635,
year = {2023},
author = {Park, KH and Ordinola-Zapata, R and Noblett, WC and Lima, BP and Staley, C},
title = {The effect of ultrasonic and multisonic irrigation on root canal microbial communities: An ex vivo study.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.13996},
pmid = {37983635},
issn = {1365-2591},
support = {UL1-TR002494/TR/NCATS NIH HHS/United States ; },
abstract = {AIM: To analyse the effect of ultrasonic irrigant activation (UIA) and the GentleWave (GW) multisonic irrigation (GW) with minimal instrumentation on the root canal microbial diversity in an ex vivo model that used extracted molars with a history of pulp necrosis.<br><br>METHODOLOGY: Twenty-three mandibular molars were prepared ex&#xa0;vivo for collection of superficial (surface control), pre-treatment and post-treatment samples 24&#x2009;h after extraction. Samples were divided into two groups: UIA using 6% NaOCl (n&#x2009;=&#x2009;11) and GW group (n&#x2009;=&#x2009;12). All samples were processed using quantitative real-time polymerase chain reaction (qPCR) and 16S rRNA next-generation sequencing to measure microbial diversity before and after the antimicrobial treatment. For qPCR, a t-test (&#x3b1;&#x2009;=&#x2009;.05) was used to compare the log10 reduction. The Chao1 and Shannon indices evaluated alpha diversity. Differences in community composition (beta diversity) were evaluated by analysis of similarity (ANOSIM). Kruskal-Wallis test with Bonferroni corrections was performed to evaluate the differences in abundances genera in the samples.<br><br>RESULTS: Quantitative real-time polymerase chain reaction revealed an estimated 1.6 and 2.6 log10 reduction for UIA and GW groups respectively (p&#x2009;=&#x2009;.048). An average of 5&#x2009;&#xb1;&#x2009;4 and 3&#x2009;&#xb1;&#x2009;5 operational taxonomic units (OTUs) were found in surface's samples in the UIA and GW group respectively. These values were significantly lower (p&#x2009;<&#x2009;.001) compared to the number of preoperative OTUs in those groups (155&#x2009;&#xb1;&#x2009;79 and 187&#x2009;&#xb1;&#x2009;121). In assessing beta diversity, there were no significant differences found in pre-treatment samples (R&#x2009;=&#x2009;.090, p&#x2009;=&#x2009;.070 ANOSIM with Bonferroni corrections). Also, no significant differences in community composition were observed in post-treatment samples (R&#x2009;=&#x2009;-.05, p&#x2009;=&#x2009;.829). After treatment, there was a significant reduction of Eubacterium using conventional treatment with UIA and a significant reduction of Prevotella using minimal instrumentation with GW irrigation (p&#x2009;=&#x2009;.007 and p&#x2009;=&#x2009;.002 respectively).<br><br>CONCLUSION: Quantitative PCR analysis revealed a significant reduction in microbial load for GW group. Overall, diversity changes were similar between UIA and GW irrigation in this ex&#xa0;vivo model that used extracted teeth with a history of pulp necrosis. OTUs obtained from the surface sample were negligible and did not affect the statistical outcome of the study.},
}
@article {pmid37983567,
year = {2023},
author = {Wang, QW and Jia, DJ and He, JM and Sun, Y and Qian, Y and Ge, QW and Qi, YD and Wang, QY and Hu, YY and Wang, L and Fang, YF and He, HQ and Luo, M and Feng, LJ and Si, JM and Song, ZF and Wang, LJ and Chen, SJ},
title = {Lactobacillus Intestinalis Primes Epithelial Cells to Suppress Colitis-Related Th17 Response by Host-Microbe Retinoic Acid Biosynthesis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2303457},
doi = {10.1002/advs.202303457},
pmid = {37983567},
issn = {2198-3844},
support = {82270573//National Natural Science Foundation of China/ ; 82370556//National Natural Science Foundation of China/ ; LQ19H030006//Natural Science Foundation of Zhejiang Province/ ; 2021KY732//Medicine and Health Research Project of Zhejiang/ ; JCYJ20190808115003699//Natural Science Foundation of Shenzhen City/ ; },
abstract = {Gut microbiome is integral to the pathogenesis of ulcerative colitis. A novel probiotic Lactobacillus intestinalis (L. intestinalis) exerts a protective effect against dextran sodium sulfate-induced colitis in mice. Based on flow cytometry, colitis-associated Th17 cells are the target of L. intestinalis, which is supported by the lack of protective effects of L. intestinalis in T cell-null Rag1[-/-] mice or upon anti-IL-17-A antibody-treated mice. Although L. intestinalis exerts no direct effect on T cell differentiation, it decreases C/EBPA-driven gut epithelial SAA1 and SAA2 production, which in turn impairs Th17 cell differentiation. Cometabolism of L. intestinalis ALDH and host ALDH1A2 contributed to elevated biosynthesis of retinoic acid (RA), which accounts for the anti-colitis effect in RAR-α -mediated way. In a cohort of ulcerative colitis patients, it is observed that fecal abundance of L. intestinalis is negatively associated with the C/EBPA-SAA1/2-Th17 axis. Finally, L. intestinalis has a synergistic effect with mesalazine in alleviating murine colitis. In conclusion, L. intestinalis and associated metabolites, RA, have potential therapeutic effects for suppressing colonic inflammation by modulating the crosstalk between intestinal epithelia and immunity.},
}
@article {pmid37982894,
year = {2023},
author = {Roxo, I and Amaral, A and Portugal, A and Trovão, J},
title = {A preliminary metabarcoding analysis of Portuguese raw honeys.},
journal = {Archives of microbiology},
volume = {205},
number = {12},
pages = {386},
pmid = {37982894},
issn = {1432-072X},
abstract = {The microbial diversity in Portuguese raw honeys remains largely uncharacterized, constituting a serious knowledge gap in one of the country's most important resources. This work provides an initial investigation with amplicon metabarcoding analysis of two Lavandula spp. from different geographical regions of Portugal and one Eucalyptus spp. honey. The results obtained allowed to identify that each honey harbors diverse microbiomes with taxa that can potentially affect bee and human health, cause spoilage, and highlight bad bee-hive management practices. We verified that prokaryotes had a tendency towards a more marked core bacterial and a relative homogenous taxa distribution, and that the botanical origin of honey is likely to have a stronger impact on the fungal community. Thus, the results obtained in this work provide important information that can be helpful to improve this critical Portuguese product and industry.},
}
@article {pmid37982445,
year = {2023},
author = {Lee, SH and Choe, DH and Rust, MK and Lee, CY},
title = {Oral toxicity of an artificial sweetener sucralose on the German cockroach (Blattodea: Ectobiidae) and its impact on water balance and gut microbiome.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toad206},
pmid = {37982445},
issn = {1938-291X},
support = {//UCR Urban Entomology Endowed Chair Research Fund/ ; },
abstract = {Artificial or non-nutritive sweeteners are indigestible by most animals. Some sweeteners are orally toxic to insects and have received recent interest as potential safe insecticides due to their low mammalian toxicity. In this study, we investigated the oral toxicity of sucralose on insecticide-susceptible and resistant German cockroaches, Blattella germanica (L.). In a nonchoice test, we evaluated 5, 10, and 20% sucralose solutions. Depending on the cockroach strains, mean mortality ranged from 62.5 to 92.5%, 15 to 55%, and 2.5 to 27.5% for 20, 10, and 5% sucralose, respectively. Next, we measured the impact of a 20% sucralose treatment on water loss rates in the cockroach strains. All strains lost 23.0-30.29% of body water by 6 d. Dehydrated cockroaches were more prone to be killed by sucralose than nondehydrated ones. Lastly, we evaluated the effect of 20% sucralose treatment on gut bacterial composition and found the diversity of gut bacteria in treated cockroaches was significantly reduced after 3 days, implicating a rapid change in the alimentary environment.},
}
@article {pmid37982439,
year = {2023},
author = {Shaw, VR and Byun, J and Pettit, RW and Hou, JK and Walsh, KM and Han, Y and Amos, CI},
title = {An Atlas Characterizing the Shared Genetic Architecture of Inflammatory Bowel Disease with Clinical and Behavioral Traits.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izad269},
pmid = {37982439},
issn = {1536-4844},
support = {ES030285/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) development is a complex, multifactorial process that involves extrinsic and intrinsic factors such as host genetics, the immune system, the gut microbiome, and environmental risks. To help understand the genetic contribution of clinical, behavioral, psychiatric, and diet-related traits, we aim to provide a deep and comprehensive characterization of the shared genetic architecture between IBD and hundreds of potentially related traits.<br><br>METHODS: Utilizing publicly available summary statistics from a previously published IBD genome-wide association study and hundreds of traits from the United Kingdom BioBank (UKBB), we performed linkage disequilibrium score regression (LDSR) analysis to estimate cross-trait genetic correlations between Crohn's disease (CD), ulcerative colitis (UC), and IBD summary statistics with the UKBB traits of interest.<br><br>RESULTS: Nominally significant (P&#x2005;<&#x2005;.05) genetic correlations were observed for 181 traits in overall IBD, 239 traits in CD, and 94 traits in UC. We replicate the known association between smoking behavior and CD/UC, namely that current tobacco smoking has a positive genetic correlation with CD (rg&#x2005;=&#x2005;0.12, P&#x2005;=&#x2005;4.2&#x2005;&#xd7;&#x2005;10-4), while "ever smoking" has a negative genetic correlation with UC (rg&#x2005;=&#x2005;-0.07, P&#x2005;=&#x2005;.042). Globally, all 3 strata (IBD, CD, and UC) demonstrated increased genetic correlations for psychiatric-related traits related to anxiety and depression.<br><br>CONCLUSION: The present analysis reveals the shared genetic architecture between multiple traits and IBD, CD, and UC. Understanding the relevance of joint occurrences of IBD with psychiatric diseases may moderate management of these diseases for individuals jointly affected by them.},
}
@article {pmid37981872,
year = {2023},
author = {Oliva-Hemker, M and Kahn, SA and Steinbach, WJ and , and , },
title = {Fecal Microbiota Transplantation: Information for the Pediatrician.},
journal = {Pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1542/peds.2023-062922},
pmid = {37981872},
issn = {1098-4275},
abstract = {Fecal microbiota transplantation (FMT) involves the delivery of an entire microbial community from a healthy donor to a recipient with the intention of ameliorating or curing a specific disease. Current evidence strongly supports a role for FMT in the treatment of Clostridiodes difficile infection, with cure rates of approximately 80% to 90%. This success has led to increasing attention for FMT as a potential therapeutic intervention for other conditions associated with disturbances of the intestinal microbiome, including inflammatory bowel diseases, autism spectrum disorder, and obesity. This clinical report endorses the joint society statement by the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition, and the European Society for Pediatric Gastroenterology, Hepatology and Nutrition and is meant to provide the general pediatrician with a broad overview to enable appropriate guidance to families seeking FMT as treatment of a child's condition.},
}
@article {pmid37981746,
year = {2023},
author = {Arora, U and Kedia, S and Ahuja, V},
title = {The practice of fecal microbiota transplantation in inflammatory bowel disease.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2023.00085},
pmid = {37981746},
issn = {1598-9100},
abstract = {Current evidence posits a central role for gut microbiota and the metabolome in the pathogenesis and progression of inflammatory bowel disease (IBD). Fecal microbiota transplantation (FMT) has been established as a means to manipulate this microbiome safely and sustainably. Several aspects of the technical improvement including pretreatment with antibiotics, use of frozen stool samples as well as short donor-to-recipient time are proposed to improve its response rates. Its efficacy in ulcerative colitis has been proven in clinical trials while data is emerging for Crohn's disease. This review describes briefly the biology behind FMT, the available evidence for its use in IBD, and the host, recipient and procedural factors which determine the clinical outcomes.},
}
@article {pmid37982076,
year = {2021},
author = {Yim, SS and Wang, HH},
title = {Exploiting interbacterial antagonism for microbiome engineering.},
journal = {Current opinion in biomedical engineering},
volume = {19},
number = {},
pages = {},
pmid = {37982076},
issn = {2468-4511},
support = {R01 AI132403/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R21 AI146817/AI/NIAID NIH HHS/United States ; },
abstract = {Interbacterial antagonism can significantly impact microbiome assembly and stability and can potentially be exploited to modulate microbes and microbial communities in diverse environments, ranging from natural habitats to industrial bioreactors. Here we highlight key mechanisms of interspecies antagonism that rely on direct cell-to-cell contact or diffusion of secreted biomolecules, and discuss recent advances to provide altered function and specificities for microbiome engineering. We further outline the use of ecological design principles based on antagonistic interactions for bottom-up assembly of synthetic microbial communities. Manipulating microbial communities through these negative interactions will be critical for understanding complex microbiome processes and properties and developing new applications of microbiome engineering.},
}
@article {pmid37981701,
year = {2023},
author = {Sadeghi, J and Chaganti, SR and Johnson, TB and Heath, DD},
title = {Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {258},
pmid = {37981701},
issn = {2049-2618},
support = {819047//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; Phylogeny ; *Microbiota/genetics ; Fishes ; *Gastrointestinal Microbiome/genetics ; Water ; },
abstract = {BACKGROUND: While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed bacterial community composition using 16S metabarcoding and tested for community variation.<br><br>RESULTS: We found that the water microbiota was distinct from the fish microbiota, although the skin microbiota more closely resembled the water microbiota. We also found that environmental (sample location), habitat, fish diet, and host species factors shape and promote divergence or convergence of the fish microbiota. Since host species significantly affected both gut and skin microbiota (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus bacterial community dissimilarity. We found significant phylogenetic effects on bacterial community dissimilarity, consistent with phylosymbiosis for both the fish skin and gut microbiota, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes.<br><br>CONCLUSIONS: Analyzing the gut and skin mucus microbiota across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host. Video Abstract.},
}
@article {pmid37981364,
year = {2023},
author = {Li, S and Wang, S and Wang, L and Liu, X and Wang, X and Cai, R and Yuan, Y and Yue, T and Wang, Z},
title = {Unraveling symbiotic microbial communities, metabolomics and volatilomics profiles of kombucha from diverse regions in China.},
journal = {Food research international (Ottawa, Ont.)},
volume = {174},
number = {Pt 2},
pages = {113652},
doi = {10.1016/j.foodres.2023.113652},
pmid = {37981364},
issn = {1873-7145},
mesh = {Metabolomics ; *Microbiota ; Lactones ; China ; *Saccharomycetales ; *Acetobacteraceae ; },
abstract = {Kombucha is a natural fermented beverage (mixed system). This study aimed to unravel the signatures of kombucha in China to achieve tailor-made microbial consortium. Here, biochemical parameters, microbiome, metabolite production and volatile profile were comprehensively compared and characterized across four regions (AH, HN, SD, SX), both commonalities and distinctions were highlighted. The findings revealed that yeast species yeast Starmerella, Zygosaccharomyces, Dekkera, Pichia and bacterium Komagataeibacter, Gluconobacter were the most common microbes. Additionally, the composition, distribution and stability of microbial composition in liquid phase were superior to those in biofilm. The species diversity, differences, marker and association were analyzed across four areas. Metabolite profiles revealed a total of 163 bioactive compounds (23 flavonoids, 13 phenols), and 68 differential metabolites were screened and identified. Moreover, the metabolic pathways of phenylpropanoids biosynthesis were closely linked with the highest number of metabolites, followed by flavonoid biosynthesis. Sixty-five volatile compounds (23 esters) were identified. Finally, the correlation analysis among the microbial composition and volatile and functional metabolites showed that Komagataeibacter, Gluconolactone, Zygosacchaaromycess, Starmerella and Dekkera seemed closely related to bioactive compounds, especially Komagataeibacter displayed positive correlations with 1-hexadecanol, 5-keto-D-gluconate, L-malic acid, 6-aminohexanoate, Starmerella contributed greatly to gluconolactone, thymidine, anabasine, 2-isopropylmalic acid. Additionally, Candida was related to β-damascenone and α-terpineol, and Arachnomyces and Butyricicoccus showed the consistency of associations with specific esters and alcohols. These findings provided crucial information for creating a stable synthetic microbial community structure, shedding light on fostering stable kombucha and related functional beverages.},
}
@article {pmid37981189,
year = {2023},
author = {Heinken, A and El Kouche, S and Rodriguez-Guéant, RM and Guéant, JL},
title = {Towards personalized genome-scale modeling of inborn errors of metabolism for systems medicine applications.},
journal = {Metabolism: clinical and experimental},
volume = {},
number = {},
pages = {155738},
doi = {10.1016/j.metabol.2023.155738},
pmid = {37981189},
issn = {1532-8600},
abstract = {Inborn errors of metabolism (IEMs) are a group of more than 1000 inherited diseases that are individually rare but have a cumulative global prevalence of 50 per 100,000 births. Recently, it has been recognized that like common diseases, patients with rare diseases can greatly vary in the manifestation and severity of symptoms. Here, we review omics-driven approaches that enable an integrated, holistic view of metabolic phenotypes in IEM patients. We focus on applications of Constraint-based Reconstruction and Analysis (COBRA), a widely used mechanistic systems biology approach, to model the effects of inherited diseases. Moreover, we review evidence that the gut microbiome is also altered in rare diseases. Finally, we outline an approach using personalized metabolic models of IEM patients for the prediction of biomarkers and tailored therapeutic or dietary interventions. Such applications could pave the way towards personalized medicine not just for common, but also for rare diseases.},
}
@article {pmid37981184,
year = {2023},
author = {Lin, W and Qin, Y and Ren, Y},
title = {Flunitrazepam and its metabolites compromise zebrafish nervous system functionality: An integrated microbiome, metabolome, and genomic analysis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {122949},
doi = {10.1016/j.envpol.2023.122949},
pmid = {37981184},
issn = {1873-6424},
abstract = {The psychotropic drug flunitrazepam (FLZ) is frequently detected in aquatic environments, yet its neurotoxicity to aquatic organisms has not received sufficient attention. In this study, microbiome, metabolome, and genome analyses were conducted to study the effects of FLZ and its metabolite 7-aminoflunitrazepam (7-FLZ) on the zebrafish nervous system and understand their toxic mechanisms. The results demonstrated that drug exposure induced gut dysbiosis, decreased short-chain fatty acids and promoted the production of lipopolysaccharides (LPS). LPS entered the brain and interacted with Toll-like receptors to cause neuroinflammation by upregulating the expression of proinflammatory cytokines TNFα and NF-κB. The increased ratio of S-adenosylmethionine to S-adenosylhomocysteine in brain tissues indicated abnormal expression of Dnmt1 gene. Whole-genome bisulfite sequencing displayed an increase in differentially methylated regions (DMRs) associated-genes and pertinent biological pathways encompassed the MAPK signaling pathway, calcium signaling pathway, and Wnt signaling pathway. Correlation analysis confirmed connections between gut microbiota, their metabolites, inflammatory factors, and DNA methylation-related markers in brain tissue. These findings indicate that while the toxicity is somewhat reduced in metabolized products, both FLZ and 7-FLZ can induce DNA methylation in brain tissue and ultimately affect the biological function of the nervous system by disrupting gut microbiota and their metabolites.},
}
@article {pmid37980979,
year = {2023},
author = {Pay, R and Sharrock, AV and Elder, R and Maré, A and Bracegirdle, J and Torres, D and Malone, N and Vorster, J and Kelly, L and Ryan, A and Josephy, PD and Allen-Vercoe, E and Ackerley, DF and Keyzers, RA and Harvey, JE},
title = {Preparation, analysis and toxicity characterisation of the redox metabolites of the azo food dye tartrazine.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {114193},
doi = {10.1016/j.fct.2023.114193},
pmid = {37980979},
issn = {1873-6351},
abstract = {Tartrazine (E102, FD&amp;C Yellow 5) is a vibrant yellow azo dye added to many processed foods. The safety of this ubiquitous chemical has not been fully elucidated, and it has been linked to allergic reactions and ADHD in some individuals. In our study, bacterial species isolated from human stool decolourised tartrazine and, upon exposure to air, a purple compound formed. Tartrazine is known to undergo reduction in the gut to sulfanilic acid and 4-amino-3-carboxy-5-hydroxy-1-(4-sulfophenyl)pyrazole (SCAP). These metabolites and their derivatives are relevant to the toxicology of tartrazine. The toxicity of sulfanilic acid has been studied before, but the oxidative instability of SCAP has previously prevented full characterisation. We have verified the chemical identity of SCAP and confirmed that the purple-coloured oxidation derivative is 4-(3-carboxy-5-hydroxy-1-(4-sulfophenyl)-1H-pyrazol-4-yl)imino-5-oxo-1-(4-sulfophenyl)-4,5-dihydro-1H-pyrazole-3-carboxylic acid (purpurazoic acid, PPA), as proposed by Westöö in 1965. A yellow derivative of SCAP is proposed to be the hydrolysed oxidation product, 4,5-dioxo-1-(4-sulfophenyl)-4,5-dihydro-1H-pyrazole-3-carboxylic acid. Both SCAP and PPA are moderately toxic to human cells (IC50 89 and 78 μM against HEK-293, respectively), but had no apparent effect on Escherichia coli and Bacillus subtilis bacteria. These results prompt further analyses of the toxicology of tartrazine and its derivatives.},
}
@article {pmid37980944,
year = {2023},
author = {Liu, W and Xu, J and Pi, Z and Chen, Y and Jiang, G and Wan, Y and Mao, W},
title = {Untangling the web of intratumor microbiota in lung cancer.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {},
number = {},
pages = {189025},
doi = {10.1016/j.bbcan.2023.189025},
pmid = {37980944},
issn = {1879-2561},
abstract = {Microbes are pivotal in contemporary cancer research, influencing various biological behaviors in cancer. The previous notion that the lung was sterile has been destabilized by the discovery of microbiota in the lower airway and lung, even within tumor tissues. Advances of biotechnology enable the association between intratumor microbiota and lung cancer to be revealed. Nonetheless, the origin and tumorigenicity of intratumor microbiota in lung cancer still remain implicit. Additionally, accumulating evidence indicates that intratumor microbiota might serve as an emerging biomarker for cancer diagnosis, prognosis, and even a therapeutic target across multiple cancer types, including lung cancer. However, research on intratumor microbiota's role in lung cancer is still nascent and warrants more profound exploration. Herein, this paper provides an extensive review of recent advancements in the following fields, including 1) established and emerging biotechnologies utilized to study intratumor microbiota in lung cancer, 2) causation between intratumor microbiota and lung cancer from the perspectives of translocation, cancerogenesis and metastasis, 3) potential application of intratumor microbiota as a novel biomarker for lung cancer diagnosis and prognosis, and 4) promising lung cancer therapies via regulating intratumor microbiota. Moreover, this review addresses the limitations, challenges, and future prospects of studies focused on intratumor microbiota in lung cancer.},
}
@article {pmid37980564,
year = {2023},
author = {Hayes, JA and Lunger, AW and Sharma, AS and Fernez, MT and Carrier, RL and Koppes, AN and Koppes, R and Woolston, BM},
title = {Engineered bacteria titrate hydrogen sulfide and induce concentration-dependent effects on the host in a gut microphysiological system.},
journal = {Cell reports},
volume = {42},
number = {12},
pages = {113481},
doi = {10.1016/j.celrep.2023.113481},
pmid = {37980564},
issn = {2211-1247},
abstract = {Hydrogen sulfide (H2S) is a gaseous microbial metabolite whose role in gut diseases is debated, with contradictory results stemming from experimental difficulties associated with accurate dosing and measuring H2S and the use of model systems that do not accurately represent the human gut environment. Here, we engineer Escherichia coli to titrate H2S across the physiological range in a gut microphysiological system (chip) supportive of the co-culture of microbes and host cells. The chip is engineered to maintain H2S gas tension and enables visualization of co-culture in real time with confocal microscopy. Engineered strains colonize the chip and are metabolically active for 2 days, during which they produce H2S across a 16-fold range and induce changes in host gene expression and metabolism in an H2S-concentration-dependent manner. These results validate a platform for studying the mechanisms underlying microbe-host interactions by enabling experiments that are infeasible with current animal and in vitro models.},
}
@article {pmid37980506,
year = {2023},
author = {Jin, M and Cui, J and Ning, H and Wang, M and Liu, W and Yao, K and Yuan, J and Zhong, X},
title = {Alterations in gut microbiota and metabolite profiles in patients with infantile cholestasis.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {357},
pmid = {37980506},
issn = {1471-2180},
support = {QN-2020-06//Youth Foundation of the Capital Institute of Pediatrics/ ; },
mesh = {Infant ; Child ; Humans ; *Gastrointestinal Microbiome ; *Cholestasis/metabolism ; Liver/metabolism ; Streptococcus ; Bilirubin/metabolism ; Bile Acids and Salts/metabolism ; },
abstract = {BACKGROUND: Infantile cholestasis (IC) is the most common hepatobiliary disease in infants, resulting in elevated direct bilirubin levels. Indeed, hepatointestinal circulation impacts bile acid and bilirubin metabolism. This study evaluates changes in the gut microbiota composition in children with IC and identifies abnormal metabolite profiles associated with microbial alterations.<br><br>RESULTS: The gut microbiota in the IC group exhibits the higher abundance of Veillonella, Streptococcus and Clostridium spp. (P&#x2009;<&#x2009;0.05), compared to healthy infants (CON) group. Moreover, the abundance of Ruminococcus, Vibrio butyricum, Eubacterium coprostanogenes group, Intestinibacter, and Faecalibacterium were lower (P&#x2009;<&#x2009;0.05). In terms of microbiota-derived metabolites, the levels of fatty acids (palmitoleic, &#x3b1;-linolenic, arachidonic, and linoleic) (P&#x2009;<&#x2009;0.05) increased and the levels of amino acids decreased in IC group. Furthermore, the abundances of Ruminococcus, Eubacterium coprostanoligenes group, Intestinibacter and Butyrivibrio are positively correlated with proline, asparagine and aspartic acid, but negatively correlated with the &#x3b1;-linolenic acid, linoleic acid, palmitoleic acid and arachidonic acid. For analysis of the relationship between the microbiota and clinical index, it was found that the abundance of Veillonella and Streptococcus was positively correlated with serum bile acid content (P&#x2009;<&#x2009;0.05), while APTT, PT and INR were negatively correlated with Faecalibalum and Ruminococcus (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: Microbiota dysbiosis happened in IC children, which also can lead to the abnormal metabolism, thus obstructing the absorption of enteral nutrition and aggravating liver cell damage. Veillonella, Ruminococcus and Butyrivibrio may be important microbiome related with IC and need further research.},
}
@article {pmid37980461,
year = {2023},
author = {Cunningham-Oakes, E and Bronowski, C and Chinyama, E and Jere, KC and Sindhu, KNC and Kang, G and Iturriza-Gómara, M and Darby, AC and Parker, EPK},
title = {Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {354},
pmid = {37980461},
issn = {1471-2180},
mesh = {Humans ; Infant ; *Rotavirus/genetics ; *Rotavirus Vaccines ; Malawi ; Prospective Studies ; Immunogenicity, Vaccine ; *Rotavirus Infections/prevention &amp; control ; India ; Vaccines, Attenuated ; Antibodies, Viral ; },
abstract = {The immunogenicity and effectiveness of oral rotavirus vaccines (ORVs) against severe rotavirus-associated gastroenteritis are impaired in low- and middle-income countries (LMICs) where the burden of disease is highest. Determining risk factors for impaired ORV response may help identify strategies to enhance vaccine effectiveness. In this study, we use metagenomic sequencing to provide a high-resolution taxonomic analysis of stool samples collected at 6 weeks of age (coinciding with the first ORV dose) during a prospective study of ORV immunogenicity in India and Malawi. We then analyse the functional capacity of the developing microbiome in these cohorts. Microbiome composition differed significantly between countries, although functional capacity was more similar than taxonomic composition. Our results confirm previously reported findings that the developing microbiome is more diverse in taxonomic composition in ORV non-seroconverters compared with seroconverters, and we additionally demonstrate a similar pattern in functional capacity. Although taxonomic or functional feature abundances are poor predictors of ORV response, we show that skews in the direction of associations within these microbiome data can be used to identify consistent markers of ORV response across LMIC infant cohorts. We also highlight the systemic under-representation of reference genes from LMICs that limit functional annotation in our study (7% and 13% annotation at pathway and enzyme commission level, respectively). Overall, higher microbiome diversity in early life may act as marker for impaired ORV response in India and Malawi, whilst a holistic perspective of functional capacity may be hidden in the "dark matter" of the microbiome.},
}
@article {pmid37980457,
year = {2023},
author = {He, S and Sun, Y and Sun, W and Tang, M and Meng, B and Liu, Y and Kong, Q and Li, Y and Yu, J and Li, J},
title = {Oral microbiota disorder in GC patients revealed by 2b-RAD-M.},
journal = {Journal of translational medicine},
volume = {21},
number = {1},
pages = {831},
pmid = {37980457},
issn = {1479-5876},
support = {81973983//National Natural Science Foundation of China/ ; 82270015//National Natural Science Foundation of China/ ; 82100017//National Natural Science Foundation of China/ ; 2021lcxk006//the joint construction project of clinical medicine university and hospital/ ; 2208085MH264//the Natural Science Foundation in Anhui Province/ ; MTP2022A015//China Primary Health Care Foundation/ ; 2021xkj138//the Project Supported by Anhui Medical University/ ; 2021xkj067//the Project Supported by Anhui Medical University/ ; },
abstract = {BACKGROUND: Microbiota alterations are linked with gastric cancer (GC). However, the relationship between the oral microbiota (especially oral fungi) and GC is not known. In this study, we aimed to apply 2b-RAD sequencing for Microbiome (2b-RAD-M) to characterize the oral microbiota in patients with GC.<br><br>METHODS: We performed 2b-RAD-M analysis on the saliva and tongue coating of GC patients and healthy controls. We carried out diversity, relative abundance, and composition analyses of saliva and tongue coating bacteria and fungi in the two groups. In addition, indicator analysis, the Gini index, and the mean decrease accuracy were used to identify oral fungal indicators of GC.<br><br>RESULTS: In this study, fungal imbalance in the saliva and tongue coating was observed in the GC group. At the species level, enriched Malassezia globosa (M. globosa) and decreased Saccharomyces cerevisiae (S. cerevisiae) were observed in saliva and tongue coating samples of the GC group. Random forest analysis indicated that M. globosa in saliva and tongue coating samples could serve as biomarkers to diagnose GC. The Gini index and mean decreases in accuracy for M. globosa in saliva and tongue coating samples were the largest. In addition, M. globosa in saliva and tongue coating samples classified GC from the control with areas under the receiver operating curve (AUCs) of 0.976 and 0.846, respectively. Further ecological analysis revealed correlations between oral bacteria and fungi.<br><br>CONCLUSION: For the first time, our data suggested that changes in oral fungi between GC patients and controls may help deepen our understanding of the complex spectrum of the different microbiotas involved in GC development. Although the cohort size was small, this study is the first to use 2b-RAD-M to reveal that oral M. globosa can be a fungal biomarker for detecting GC.},
}
@article {pmid37980332,
year = {2023},
author = {Zeamer, AL and Salive, MC and An, X and Beaudoin, FL and House, SL and Stevens, JS and Zeng, D and Neylan, TC and Clifford, GD and Linnstaedt, SD and Rauch, SL and Storrow, AB and Lewandowski, C and Musey, PI and Hendry, PL and Sheikh, S and Jones, CW and Punches, BE and Swor, RA and Hudak, LA and Pascual, JL and Seamon, MJ and Harris, E and Pearson, C and Peak, DA and Merchant, RC and Domeier, RM and Rathlev, NK and O'Neil, BJ and Sergot, P and Sanchez, LD and Bruce, SE and Kessler, RC and Koenen, KC and McLean, SA and Bucci, V and Haran, JP},
title = {Association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure.},
journal = {Translational psychiatry},
volume = {13},
number = {1},
pages = {354},
pmid = {37980332},
issn = {2158-3188},
mesh = {Adult ; Humans ; *Microbiota ; *Stress Disorders, Post-Traumatic/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology ; Biological Availability ; },
abstract = {Patients exposed to trauma often experience high rates of adverse post-traumatic neuropsychiatric sequelae (APNS). The biological mechanisms promoting APNS are currently unknown, but the microbiota-gut-brain axis offers an avenue to understanding mechanisms as well as possibilities for intervention. Microbiome composition after trauma exposure has been poorly examined regarding neuropsychiatric outcomes. We aimed to determine whether the gut microbiomes of trauma-exposed emergency department patients who develop APNS have dysfunctional gut microbiome profiles and discover potential associated mechanisms. We performed metagenomic analysis on stool samples (n = 51) from a subset of adults enrolled in the Advancing Understanding of RecOvery afteR traumA (AURORA) study. Two-, eight- and twelve-week post-trauma outcomes for post-traumatic stress disorder (PTSD) (PTSD checklist for DSM-5), normalized depression scores (PROMIS Depression Short Form 8b) and somatic symptom counts were collected. Generalized linear models were created for each outcome using microbial abundances and relevant demographics. Mixed-effect random forest machine learning models were used to identify associations between APNS outcomes and microbial features and encoded metabolic pathways from stool metagenomics. Microbial species, including Flavonifractor plautii, Ruminococcus gnavus and, Bifidobacterium species, which are prevalent commensal gut microbes, were found to be important in predicting worse APNS outcomes from microbial abundance data. Notably, through APNS outcome modeling using microbial metabolic pathways, worse APNS outcomes were highly predicted by decreased L-arginine related pathway genes and increased citrulline and ornithine pathways. Common commensal microbial species are enriched in individuals who develop APNS. More notably, we identified a biological mechanism through which the gut microbiome reduces global arginine bioavailability, a metabolic change that has also been demonstrated in the plasma of patients with PTSD.},
}
@article {pmid37980258,
year = {2023},
author = {Leonardi, SS and Tan, KS},
title = {Blastocystis: view from atop the gut-brain iceberg.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2023.10.002},
pmid = {37980258},
issn = {1471-5007},
abstract = {Blastocystis is a common intestinal parasite that has been linked to gut pathology in humans. In this article, we highlight recent publications that offer insight into how these organisms can influence human cognition and the gut microbiome. We also suggest a potential mechanism of action by which this might occur.},
}
@article {pmid37980123,
year = {2024},
author = {Jank, L and Bhargava, P},
title = {Relationship Between Multiple Sclerosis, Gut Dysbiosis, and Inflammation: Considerations for Treatment.},
journal = {Neurologic clinics},
volume = {42},
number = {1},
pages = {55-76},
doi = {10.1016/j.ncl.2023.07.005},
pmid = {37980123},
issn = {1557-9875},
mesh = {Humans ; *Multiple Sclerosis/therapy ; Dysbiosis/complications/therapy/metabolism ; Inflammation/therapy/metabolism ; },
abstract = {Multiple sclerosis is associated with gut dysbiosis, marked by changes in the relative abundances of specific microbes, circulating gut-derived metabolites, and altered gut permeability. This gut dysbiosis promotes disease pathology by increasing circulating proinflammatory bacterial factors, reducing tolerogenic factors, inducing molecular mimicry, and changing microbial nutrient metabolism. Beneficial antiinflammatory effects of the microbiome can be harnessed in therapeutic interventions. In the future, it is essential to assess the efficacy of these therapies in randomized controlled clinical trials to help make dietary and gut dysbiosis management an integral part of multiple sclerosis care.},
}
@article {pmid37980043,
year = {2024},
author = {Wu, D and Lu, X and Dong, LX and Tian, J and Deng, J and Wei, L and Wen, H and Zhong, S and Jiang, M},
title = {Nano polystyrene microplastics could accumulate in Nile tilapia (Oreochromis niloticus): Negatively impacts on the intestinal and liver health through water exposure.},
journal = {Journal of environmental sciences (China)},
volume = {137},
number = {},
pages = {604-614},
doi = {10.1016/j.jes.2023.02.018},
pmid = {37980043},
issn = {1001-0742},
mesh = {Animals ; Polystyrenes/toxicity/metabolism ; Microplastics/toxicity ; Plastics ; *Cichlids/metabolism ; Water ; Liver/metabolism ; *Water Pollutants, Chemical/toxicity/metabolism ; },
abstract = {Microplastics (MPs) have become a significant concern for their potential toxicity. However, the correlation between the size of plastic particles and their toxicity remains inconclusive. Here, we investigate the toxic effects of different sizes (80 nm, 800 nm, 8 µm and 80 µm) polystyrene MPs (PS-MPs) on the model organism Nile tilapia (Oreochromis niloticus). The results of bioluminescent imaging indicate that the 80 nm PS-MPs are more likely to invade the body. H&amp;E staining shows severe damage on the intestinal villi and distinct hepatic steatosis in the 80 nm group. EdU labeling shows that the proliferation activity of intestinal and liver cells reduces significantly in the 80 nm group. The gut microbiome analysis shows a severe imbalance of gut microbiota homeostasis in the 80 nm group. The analysis of liver transcriptomics and metabolomics shows that the liver lipid metabolism is disordered in the 80 nm group. In conclusion, this study confirms that the 80 nm PS-MPs are more likely to induce intestinal and liver toxicity. All the above lay the foundation for further study on the pathological damage of MPs to other organisms.},
}
@article {pmid37979958,
year = {2023},
author = {Prinz, E and Schlupp, L and Dyson, G and Barrett, M and Szymczak, A and Velasco, C and Izda, V and Dunn, CM and Jeffries, MA},
title = {OA susceptibility in mice is partially mediated by the gut microbiome, is transferrable via microbiome transplantation and is associated with immunophenotype changes.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1136/ard-2023-224907},
pmid = {37979958},
issn = {1468-2060},
abstract = {OBJECTIVES: The Murphy Roths Large (MRL)/MpJ 'superhealer' mouse strain is protected from post-traumatic osteoarthritis (OA), although no studies have evaluated the microbiome in the context of this protection. This study characterised microbiome differences between MRL and wild-type mice, evaluated microbiome transplantation and OA and investigated microbiome-associated immunophenotypes.<br><br>METHODS: Cecal material from mixed sex C57BL6/J (B6) or female MRL/MpJ (MRL) was transplanted into B6 and MRL mice, then OA was induced by disruption of the medial meniscus surgery (DMM). In other experiments, transplantation was performed after DMM and transplantation was performed into germ-free mice. Transplanted mice were bred through F2. OARSI, synovitis and osteophyte scores were determined blindly 8 weeks after DMM. 16S microbiome sequencing was performed and metagenomic function was imputed. Immunophenotypes were determined using mass cytometry.<br><br>RESULTS: MRL-into-B6 transplant prior to DMM showed reduced OA histopathology (OARSI score 70% lower transplant vs B6 control), synovitis (60% reduction) and osteophyte scores (30% reduction) 8 weeks after DMM. When performed 48&#x2009;hours after DMM, MRL-into-B6 transplant improved OA outcomes but not when performed 1-2 weeks after DMM. Protection was seen in F1 (60% reduction) and F2 progeny (30% reduction). Several cecal microbiome clades were correlated with either better (eg, Lactobacillus, R=-0.32, p=0.02) or worse (eg, Rikenellaceae, R=0.43, p=0.001) OA outcomes. Baseline immunophenotypes associated with MRL-into-B6 transplants and MRL included reduced double-negative T cells and increased CD25+CD4+ T cells.<br><br>CONCLUSION: The gut microbiome is responsible in part for OA protection in MRL mice and is transferrable by microbiome transplantation. Transplantation induces resting systemic immunophenotyping changes that correlate with OA protection.},
}
@article {pmid37979881,
year = {2023},
author = {Liang, Y and Liu, D and Li, Y and Hou, H and Li, P and Ma, X and Li, P and Zhan, J and Wang, P},
title = {Maternal polysorbate 80 intake promotes offspring metabolic syndrome through vertical microbial transmission in mice.},
journal = {The Science of the total environment},
volume = {909},
number = {},
pages = {168624},
doi = {10.1016/j.scitotenv.2023.168624},
pmid = {37979881},
issn = {1879-1026},
abstract = {Polysorbate 80 (P80) is an emulsifier extensively produced, consumed and discharged into the environment, consequently making human exposure inevitable. Despite evidence suggesting that P80 intake causes metabolic syndrome (MS) in mammals via microbial perturbation, limited data exist on its transgenerational impacts on offspring. In this study, we found that maternal P80 treatment impaired intestinal barrier integrity, leading to metabolic endotoxemia, low-grade inflammation and MS-related symptoms in C57BL/6J female offspring. Further analysis of the gut microbiome revealed MS-related changes in the offspring of P80-treated dams. Fecal microbiota transplantation experiment confirmed the crucial role of the altered microbiome in offspring in the transgenerational impacts of P80. Furthermore, we found that the P80-induced microbial alterations were directly transmitted from P80-treated mothers to their offspring and that interrupting vertical microbial transmission through cesarean section and foster nursing blocked the transgenerational impacts of P80 on the offspring microbiome and metabolic health. Moreover, maternal pectin supplementation also effectively mitigated P80-induced microbial alterations and MS-associated phenotypes in offspring. Together, our results indicated that maternal P80 intake could impair offspring metabolic health through the mother-to-offspring transmission of the microbiome, and maternal pectin supplementation might be a promising strategy for reducing the adverse effects of P80.},
}
@article {pmid37979870,
year = {2023},
author = {Xiao, Z and Lu, C and Wu, Z and Li, X and Ding, K and Zhu, Z and Han, R and Zhao, J and Ge, T and Li, G and Zhu, YG},
title = {Continuous cropping disorders of eggplants (Solanum melongena L.) and tomatoes (Solanum lycopersicum L.) in suburban agriculture: Microbial structure and assembly processes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168558},
doi = {10.1016/j.scitotenv.2023.168558},
pmid = {37979870},
issn = {1879-1026},
abstract = {Deciphering the intricate relationships between microorganisms and plants remains a formidable challenge in plant microbial ecology, an area that holds promise for optimizing microbial interventions to enhance stress resilience and agricultural yields. In our investigation, we procured samples during 2019 and 2022 from a suburban agricultural greenhouse. Our study delineated the composition of bacterial and fungal communities across various ecological niches-namely, the rhizosphere soil, bulk soil, and phyllosphere of healthy, Ralstonia solanacearum-infected, and dead eggplants and tomatoes. The structure and composition of both fungal and bacterial communities change significantly under the influence of the host genotype across all samples. In the tomato or eggplant groups, bacterial wilt exerts a more pronounced impact on the bacterial community than on the fungal community. We speculate that the rhizosphere of healthy eggplants and tomatoes harbored more antibiotic-producing (e.g., Amycolatopsis and Penicillium) and biocontrol (e.g., Bacillus) strains, which can lead to have lower absolute abundance of R. solanacearum. In the context of R. solanacearum invasion, deterministic processes were responsible for shaping 70.67 % and 80.63 % of the bacterial community assembly in the rhizosphere of eggplants and tomatoes, respectively. Deterministic processes dominated the assembly of fungal communities in the rhizosphere of R. solanacearum-infected eggplants, whereas the opposite was true in the tomatoes. Homogeneous selection emerged as the predominant force governing the bacterial community assembly in the rhizospheres of R. solanacearum-infected eggplants and tomatoes. The bacterial co-occurrence networks in healthy rhizosphere soil were characterized by reduced vulnerability and enhanced stability (i.e., robustness index) and complexity (i.e., cohesion index), compared to their infected counterparts. In summary, complex microbial networks in rhizosphere soils are more resistant to invasion by soil-borne pathogens. The dynamics of bacterial interactions and community assembly processes are pivotal for effective microbiome management and offer predictive insights into the ecological ramifications of R. solanacearum invasions.},
}
@article {pmid37979832,
year = {2023},
author = {Wang, Y and Shen, Y and Lu, S and Wu, J},
title = {EVOO supplement prevents type 1 diabetes by modulating gut microbiota and serum metabolites in NOD mice.},
journal = {Life sciences},
volume = {335},
number = {},
pages = {122274},
doi = {10.1016/j.lfs.2023.122274},
pmid = {37979832},
issn = {1879-0631},
abstract = {AIMS: Extra virgin olive oil (EVOO) is the highest quality olive oil available and has been shown to regulate postprandial blood glucose in patients with type 1 diabetes (T1D). However, it remains uncertain whether EVOO can prevent the onset of T1D. In this study, we investigated the potential preventive effect of orally administered EVOO on T1D in non-obese diabetic (NOD) mice.<br><br>MAIN METHODS: We analyzed changes in fecal microbes using 16&#xa0;s rDNA sequencing and serum metabolites using Ultra High-Performance Liquid Chromatography and Quadrupole Time-of-Flight Mass Spectrometry (Q-TOF-MS).<br><br>KEY FINDINGS: Our findings showed that EVOO supplementation in NOD mice slowed gastric emptying, reduced insulitis, and delayed T1D onset. Moreover, EVOO altered the composition of fecal microbes, increasing the Bacteroidetes/Firmicutes ratio, and promoting the growth of short-chain fatty acids (SCFAs)-producing bacteria, such as Lachnoclostridium and Ruminococcaceae_UCG-005. Moreover, it also increased beneficial serum metabolites, including unsaturated fatty acid and triterpenoid, which positively correlated with the increased SCFA-producing bacteria and negatively correlated with the disease indicators. Conversely, most decreased serum lipid metabolites, such as Oleamide, showed the opposite trend.<br><br>SIGNIFICANCE: Our study demonstrates that EVOO may ameliorate pancreas inflammation and prevent T1D onset in NOD mice by modulating gut microbiota and serum metabolites.},
}
@article {pmid37979767,
year = {2023},
author = {Li, H and Yang, W and Wu, X and Tian, L and Zhang, W and Tian, H and Liang, X and Huang, L and Guo, L and Li, X and Gao, W},
title = {Cationic fructan-based pH and intestinal flora dual stimulation nanoparticle with berberine for targeted therapy of IBD.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {127987},
doi = {10.1016/j.ijbiomac.2023.127987},
pmid = {37979767},
issn = {1879-0003},
abstract = {Inflammatory bowel disease (IBD) can cause intestinal microbial imbalance and aggravate intestinal inflammation. Mixed fructan is more easily fermented by colonic microorganisms and can be used as colonic drug delivery materials. Here, we constructed a mixed fructan based nanoparticle with dual targeted stimulation of pH and intestinal flora to effectively deliver berberine for the treatment of ulcerative colitis (UC). The complex of fructan based nanoparticle and berberine (BBRNPs) significantly ameliorated the inflammatory response of sodium dextran sulfate (DSS)-induced colitis in mice by inhibiting the activation of NF-κB/STAT-3 pathway and increasing tight junction protein expression in vivo. Importantly, BBRNPs improved the responsiveness of colitis microbiome and effectively regulated the relative homeostasis of harmful flora Enterobacteriaceae and Escherichia-shigolla, and beneficial flora Ruminococcaceae and Akkermansiaceae. This study provides a promising strategy for the effective treatment of UC and expands the application of branched fructan in pharmaceutics.},
}
@article {pmid37979632,
year = {2023},
author = {Subramaniam, S and Elz, A and Wignall, A and Kamath, S and Ariaee, A and Hunter, A and Newblack, T and Wardill, HR and Prestidge, CA and Joyce, P},
title = {Self-emulsifying drug delivery systems (SEDDS) disrupt the gut microbiota and trigger an intestinal inflammatory response in rats.},
journal = {International journal of pharmaceutics},
volume = {648},
number = {},
pages = {123614},
doi = {10.1016/j.ijpharm.2023.123614},
pmid = {37979632},
issn = {1873-3476},
abstract = {Self-emulsifying drug delivery systems (i.e. SEDDS, SMEDDS and SNEDDS) are widely employed as solubility and bioavailability enhancing formulation strategies for poorly water-soluble drugs. Despite the capacity for SEDDS to effectively facilitate oral drug absorption, tolerability concerns exist due to the capacity for high concentrations of surfactants (typically present within SEDDS) to induce gastrointestinal toxicity and mucosal irritation. With new knowledge surrounding the role of the gut microbiota in modulating intestinal inflammation and mucosal injury, there is a clear need to determine the impact of SEDDS on the gut microbiota. The current study is the first of its kind to demonstrate the detrimental impact of SEDDS on the gut microbiota of Sprague-Dawley rats, following daily oral administration (100 mg/kg) for 21 days. SEDDS comprising a lipid phase (i.e. Type I, II and III formulations according to the Lipid Formulation Classification Scheme) induced significant changes to the composition and diversity of the gut microbiota, evidenced through a reduction in operational taxonomic units (OTUs) and alpha diversity (Shannon's index), along with statistically significant shifts in beta diversity (according to PERMANOVA of multi-dimensional Bray-Curtis plots). Key signatures of gut microbiota dysbiosis correlated with the increased expression of pro-inflammatory cytokines within the jejunum, while mucosal injury was characterised by significant reductions in plasma citrulline levels, a validated biomarker of enterocyte mass and mucosal barrier integrity. These findings have potential clinical ramifications for chronically administered drugs that are formulated with SEDDS and stresses the need for further studies that investigate dose-dependent effects of SEDDS on the gastrointestinal microenvironment in a clinical setting.},
}
@article {pmid37979452,
year = {2023},
author = {Xi, D and Liu, P and Feng, Y and Teng, Y and Liang, Y and Zhou, J and Deng, H and Zeng, G and Zong, S},
title = {Fecal microbiota transplantation regulates the microbiota-gut-spinal cord axis to promote recovery after spinal cord injury.},
journal = {International immunopharmacology},
volume = {126},
number = {},
pages = {111212},
doi = {10.1016/j.intimp.2023.111212},
pmid = {37979452},
issn = {1878-1705},
abstract = {Spinal cord injury (SCI) is devastating for patients, and currently lacks effective treatments. Dysbiosis commonly occurs after SCI and has significant immunomodulatory effects, but its impact on recovery remains unclear. The current study investigated the effects and mechanisms of fecal microbiota transplantation (FMT) in SCI. FMT was administered in a rat model of SCI and spinal pathology, inflammatory cytokines, and gut microbiome composition were assessed. Flow cytometry identified a source of interleukin (IL)-17 in spinal cord tissues, and carboxyfluorescein succimidyl ester labeling tracked γδ T cell migration. In vitro coculture was used to analyze the regulatory mechanisms of γδ T cells. Seahorse analysis was used to profile dendritic cell (DC) metabolism. Here we show that FMT improved spinal pathology and dampened post-injury inflammation. It also corrected post-SCI dysbiosis, increasing levels of the beneficial bacterium Akkermansia. The therapeutic effects of FMT were mediated by IL-17 produced by γδ T cells. FMT regulated γδ T cells via DC-T regulatory cell interaction, and induced metabolic reprogramming in DCs. These findings suggest that FMT represents a promising therapeutic approach for SCI, with potential to target IL-17[+] γδ T cells. Elucidating the interconnected pathways between microbiota, immunity, and the spinal cord may facilitate novel treatment strategies.},
}
@article {pmid37979302,
year = {2023},
author = {Chai, G and Li, J and Li, Z},
title = {The interactive effects of ocean acidification and warming on bioeroding sponge Spheciospongia vesparium microbiome indicated by metatranscriptomics.},
journal = {Microbiological research},
volume = {278},
number = {},
pages = {127542},
doi = {10.1016/j.micres.2023.127542},
pmid = {37979302},
issn = {1618-0623},
abstract = {Global climate change will cause coral reefs decline and is expected to increase the reef erosion potential of bioeroding sponges. Microbial symbionts are essential for the overall fitness and survival of sponge holobionts in changing ocean environments. However, we rarely know about the impacts of ocean warming and acidification on bioeroding sponge microbiome. Here, the structural and functional changes of the bioeroding sponge Spheciospongia vesparium microbiome, as well as its recovery potential, were investigated at the RNA level in a laboratory system simulating 32 °C and pH 7.7. Based on metatranscriptome analysis, acidification showed no significant impact, while warming or simultaneous warming and acidification disrupted the sponge microbiome. Warming caused microbial dysbiosis and recruited potentially opportunistic and pathogenic members of Nesiotobacter, Oceanospirillaceae, Deltaproteobacteria, Epsilonproteobacteria, Bacteroidetes and Firmicutes. Moreover, warming disrupted nutrient exchange and molecular interactions in the sponge holobiont, accompanied by stimulation of virulence activity and anaerobic metabolism including denitrification and dissimilatory reduction of nitrate and sulfate to promote sponge necrosis. Particularly, the interaction between acidification and warming alleviated the negative effects of warming and enhanced the Rhodobacteraceae-driven ethylmalonyl-CoA pathway and sulfur-oxidizing multienzyme system. The microbiome could not recover during the experiment period after warming or combined stress was removed. This study suggests that warming or combined warming and acidification will irreversibly destabilize the S. vesparium microbial community structure and function, and provides insight into the molecular mechanisms of the interactive effects of acidification and warming on the sponge microbiome.},
}
@article {pmid37979154,
year = {2023},
author = {Kujawa, D and Laczmanski, L and Budrewicz, S and Pokryszko-Dragan, A and Podbielska, M},
title = {Targeting gut microbiota: new therapeutic opportunities in multiple sclerosis.},
journal = {Gut microbes},
volume = {15},
number = {2},
pages = {2274126},
doi = {10.1080/19490976.2023.2274126},
pmid = {37979154},
issn = {1949-0984},
abstract = {Multiple sclerosis (MS) causes long-lasting, multifocal damage to the central nervous system. The complex background of MS is associated with autoimmune inflammation and neurodegeneration processes, and is potentially affected by many contributing factors, including altered composition and function of the gut microbiota. In this review, current experimental and clinical evidence is presented for the characteristics of gut dysbiosis found in MS, as well as for its relevant links with the course of the disease and the dysregulated immune response and metabolic pathways involved in MS pathology. Furthermore, therapeutic implications of these investigations are discussed, with a range of pharmacological, dietary and other interventions targeted at the gut microbiome and thus intended to have beneficial effects on the course of MS.},
}
@article {pmid37978895,
year = {2023},
author = {Sigall Boneh, R and Westoby, C and Oseran, I and Sarbagili-Shabat, C and Albenberg, LG and Lionetti, P and Manuel Navas-López, V and Martín-de-Carpi, J and Yanai, H and Maharshak, N and Van Limbergen, J and Wine, E},
title = {The Crohn's Disease Exclusion Diet: A Comprehensive Review of Evidence, Implementation Strategies, Practical Guidance, and Future Directions.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izad255},
pmid = {37978895},
issn = {1536-4844},
support = {//Nestle Health Sciences/ ; },
abstract = {Dietary therapy is increasingly recognized for the management of Crohn's disease (CD) over recent years, including the use of exclusive enteral nutrition (EEN) as first-line therapy for pediatric CD according to current guidelines. The Crohn's disease exclusion diet (CDED) is a whole-food diet designed to reduce exposure to dietary components that are potentially pro-inflammatory, mediated by negative effects on the gut microbiota, immune response, and the intestinal barrier. The CDED has emerged as a valid alternative to EEN with cumulative evidence, including randomized controlled trials, supporting use for induction of remission and possibly maintenance in children and adults. We gathered a group of multidisciplinary experts, including pediatric and adult gastroenterologists, inflammatory bowel diseases (IBD) expert dietitians, and a psychologist to discuss the evidence, identify gaps, and provide insights into improving the use of CDED based on a comprehensive review of CDED literature and professional experience. This article reviews the management of CDED in both children and adults, long-term aspects of CDED, indications and contraindications, selecting the best candidates, identifying challenges with CDED, globalization, the role of the multidisciplinary team, especially of dietitian, and future directions. We concluded that CDED is an established dietary therapy that could serve as an alternative to EEN in many pediatric and adult cases, especially with mild to moderate disease. In severe disease, complicated phenotypes, or with extraintestinal involvement, CDED should be considered on a case-by-case basis, according to physician and dietitians' discretion. More studies are warranted to assess the efficacy of CDED in different scenarios.},
}
@article {pmid37978888,
year = {2023},
author = {Cohen, DG and Wingert, RA},
title = {Forever young by Alpha(diversity)ville: restricting intestinal microbiome maturation stunts immune system development and increases susceptibility to infection.},
journal = {Tissue barriers},
volume = {},
number = {},
pages = {2281209},
doi = {10.1080/21688370.2023.2281209},
pmid = {37978888},
issn = {2168-8370},
abstract = {The microbiome is a keystone of adult gastrointestinal (GI) tract health, where it facilitates digestion, wards off pathogen colonization, and exerts a powerful influence on the physiological health of organs ranging from the brain to the kidneys. From its establishment at birth and through the initial years of childhood, the human microbiome is particularly dynamic, shifting in its composition and alpha (species) diversity to an adult profile as dietary sustenance transitions from milk-based sources to others such as solid food. An innovative study has now demonstrated how microbiome maturation is requisite both for the progression of immune system development and for long-term gut barrier function. These insights have significant ramifications for designing pediatric approaches to cultivate immune cell ontogeny in the formative stages of human infancy.},
}
@article {pmid37978561,
year = {2023},
author = {Song, D and Li, A and Chen, B and Feng, J and Duan, T and Cheng, J and Chen, L and Wang, W and Min, Y},
title = {Multi-omics analysis reveals the molecular regulatory network underlying the prevention of Lactiplantibacillus plantarum against LPS-induced salpingitis in laying hens.},
journal = {Journal of animal science and biotechnology},
volume = {14},
number = {1},
pages = {147},
pmid = {37978561},
issn = {1674-9782},
support = {No. 32002192//The National Natural Sciences Foundation of China/ ; JY2016//Research Fund for National Non-profit Research Institution/ ; CARS-40-S20//China Agriculture Research System of MOF and MARA/ ; },
abstract = {BACKGROUND: Salpingitis is one of the common diseases in laying hen production, which greatly decreases the economic outcome of laying hen farming. Lactiplantibacillus plantarum was effective in preventing local or systemic inflammation, however rare studies were reported on its prevention against salpingitis. This study aimed to investigate the preventive molecular regulatory network of microencapsulated Lactiplantibacillus plantarum (MLP) against salpingitis through multi-omics analysis, including microbiome, transcriptome and metabolome analyses.<br><br>RESULTS: The results revealed that supplementation of MLP in diet significantly alleviated the inflammation and atrophy of uterus caused by lipopolysaccharide (LPS) in hens (P&#x2009;<&#x2009;0.05). The concentrations of plasma IL-2 and IL-10 in hens of MLP-LPS group were higher than those in hens of LPS-stimulation group (CN-LPS group) (P&#x2009;<&#x2009;0.05). The expression levels of TLR2, MYD88, NF-&#x3ba;B, COX2, and TNF-&#x3b1; were significantly decreased in the hens fed diet supplemented with MLP and suffered with LPS stimulation (MLP-LPS group) compared with those in the hens of CN-LPS group (P&#x2009;<&#x2009;0.05). Differentially expressed genes (DEGs) induced by&#x2009; MLP were involved in inflammation, reproduction, and calcium ion transport. At the genus level, the MLP supplementation significantly increased&#x2009; the abundance of Phascolarctobacterium, whereas decreased the abundance of Candidatus_Saccharimonas in LPS challenged hens (P&#x2009;<&#x2009;0.05). The metabolites altered by dietary supplementation with MLP were mainly involved in galactose, uronic acid, histidine, pyruvate and primary bile acid metabolism. Dietary supplementation with MLP inversely regulates LPS-induced differential metabolites such as LysoPA (24:0/0:0) (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: In summary, dietary supplementation with microencapsulated Lactiplantibacillus plantarum prevented salpingitis by modulating the abundances of Candidatus_Saccharimonas, Phascolarctobacterium, Ruminococcus_torques_group and Eubacterium_hallii_group while downregulating the levels of plasma metabolites, p-tolyl sulfate, o-cresol and N-acetylhistamine and upregulating S-lactoylglutathione, simultaneously increasing the expressions of CPNE4, CNTN3 and ACAN genes in the uterus, and ultimately inhibiting oviducal inflammation.},
}
@article {pmid37978477,
year = {2023},
author = {Shi, L and Ju, P and Meng, X and Wang, Z and Yao, L and Zheng, M and Cheng, X and Li, J and Yu, T and Xia, Q and Yan, J and Zhu, C and Zhang, X},
title = {Intricate role of intestinal microbe and metabolite in schizophrenia.},
journal = {BMC psychiatry},
volume = {23},
number = {1},
pages = {856},
pmid = {37978477},
issn = {1471-244X},
mesh = {Humans ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; *Schizophrenia ; Dysbiosis/complications/microbiology ; Metabolomics ; },
abstract = {BACKGROUND: The brain-gut axis has gained increasing attention due to its contribution to the etiology of various central nervous system disorders. This study aims to elucidate the hypothesis that schizophrenia is associated with disturbances in intestinal microflora and imbalance in intestinal metabolites. By exploring the intricate relationship between the gut and the brain, with the goal of offering fresh perspectives and valuable insights into the potential contribution of intestinal microbial and metabolites dysbiosis to the etiology of schizophrenia.<br><br>METHODS: In this study, we used a 16S ribosomal RNA (16S rRNA) gene sequence-based approach and an untargeted liquid chromatography-mass spectrometry-based metabolic profiling approach to measure the gut microbiome and microbial metabolites from 44 healthy controls, 41 acute patients, and 39 remission patients, to evaluate whether microbial dysbiosis and microbial metabolite biomarkers were linked with the severity of schizophrenic symptoms.<br><br>RESULTS: Here, we identified 20 dominant disturbances in the gut microbial composition of patients compared with healthy controls, with 3 orders, 4 families, 9 genera, and 4 species. Several unique bacterial taxa associated with schizophrenia severity. Compared with healthy controls, 145 unusual microflora metabolites were detected in the acute and remission groups, which were mainly involved in environmental information processing, metabolism, organismal systems, and human diseases in the Kyoto encyclopedia of genes and genomes pathway. The Sankey diagram showed that 4 abnormal intestinal and 4 anomalous intestinal microbial metabolites were associated with psychiatric clinical symptoms.<br><br>CONCLUSIONS: These findings suggest a possible interactive influence of the gut microbiota and their metabolites on the pathophysiology of schizophrenia.},
}
@article {pmid37978427,
year = {2023},
author = {Huang, Q and Wu, X and Zhou, X and Sun, Z and Shen, J and Kong, M and Chen, N and Qiu, JG and Jiang, BH and Yuan, C and Zheng, Y},
title = {Association of cigarette smoking with oral bacterial microbiota and cardiometabolic health in Chinese adults.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {346},
pmid = {37978427},
issn = {1471-2180},
support = {2021YFA1301000//National Key Research and Development Program of China/ ; 81973032//National Natural Science Foundation of China/ ; },
abstract = {The interplay among cigarette smoking status, oral microbiota, and cardiometabolic health is poorly understood. We aimed to examine the association of cigarette smoking status with oral microbiota and to assess the association of the identified microbial features with cardiometabolic risk factors in a Chinese population. This study included 587 participants within the Central China Cohort, including 111 smokers and 476 non-smokers, and their oral microbiota was profiled by 16S rRNA sequencing. Both oral microbial alpha- and beta-diversity were distinct between smokers and non-smokers (p < 0.05). With adjustment for sociodemographics, alcohol and tea drinking, tooth brushing frequency, and body mass index, the relative abundance of nine genera and 26 pathways, including the genus Megasphaera and two pathways involved in inositol degradation which have potentially adverse effects on cardiometabolic health, was significantly different between two groups (FDR q < 0.20). Multiple microbial features related to cigarette smoking were found to partly mediate the associations of cigarette smoking with serum triglycerides and C-reactive protein levels (p-mediation < 0.05). In conclusion, cigarette smoking status may have impacts on the oral microbial features, which may partially mediate the associations of cigarette smoking and cardiometabolic health.},
}
@article {pmid37978422,
year = {2023},
author = {Li, H and Zhang, H and Geng, L and Huang, H and Nie, C and Zhu, Y},
title = {Association between vaginal microbiome alteration and povidone iodine use during delivery.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {348},
pmid = {37978422},
issn = {1471-2180},
support = {82101811//National Natural Science Foundation of China/ ; 2023A1515010674//Guangdong Basic and Applied Basic Research Foundation/ ; },
mesh = {Female ; Humans ; Pregnancy ; *Povidone-Iodine/pharmacology ; Vagina/microbiology ; *Microbiota/genetics ; Bacteria/genetics ; Menstrual Cycle ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The vaginal microbiome is a dynamic community of microorganisms in the vagina. Its alteration may be influenced by multiple factors, including gestational status, menstrual cycle, sexual intercourse, hormone levels, hormonal contraceptives, and vaginal drug administration. Povidone iodine has been used before delivery to reduce infection that may be caused by the ascendance of pathogenic and opportunistic bacteria from the vagina to the uterus. This study aimed to elucidate the impact of povidone iodine use during delivery on the vaginal microbiome.<br><br>METHODS: This study enrolled a total of 67 women from maternity services in three hospitals. During the delivery process, we have applied povidone iodine in three doses such as low dose, medium dose, and high dose based on the amount of povidone iodine administered, thus, we studied the three groups of women based on the doses applied. Vaginal swab samples were collected both before and immediately after delivery, and the microbial communities were characterized using 16&#xa0;S rRNA sequencing. The identification of differentially abundant microbial taxa was performed using ZicoSeq software.<br><br>RESULTS: Before delivery, the vaginal microbiome was dominated by the genus Lactobacillus, with different percentage observed (86.06%, 85.24%, and 73.42% for the low, medium, and high dose groups, respectively). After delivery, the vaginal microbial community was restructured, with a significant decrease in the relative abundance of Lactobacillus in all three groups (68.06%, 50.08%, and 25.89%), and a significant increase in alpha diversity across all 3 groups (P&#x2009;<&#x2009;0.01). Furthermore, as the dose of povidone iodine used during delivery increased, there was a corresponding decrease in the relative abundance of Lactobacillus (P&#x2009;<&#x2009;0.01). Contrary, there was an increase in microbial diversity and the relative abundances of Pseudomonas (0.13%, 0.26%, and 13.04%, P&#x2009;<&#x2009;0.01) and Ralstonia (0.01%, 0.02%, and 16.07%, P&#x2009;<&#x2009;0.01) across the groups. Notably, some functional metabolic pathways related to sugar degradation were observed to have significant change with increasing use of povidone iodine.<br><br>CONCLUSION: Povidone iodine was associated with the vaginal microbiome alterations after parturition, and its significant change was associated to the dosage of povidone iodine administered. The escalation in iodine dosage was linked to a decrease in Lactobacilli abundance, and elevated prevalence of Pseudomonas and Ralstonia. There is a need for longitudinal studies to clearly understanding the effect of povidone iodine use on maternal and infant microbiome.},
}
@article {pmid37978413,
year = {2023},
author = {Pascar, J and Middleton, H and Dorus, S},
title = {Aedes aegypti microbiome composition covaries with the density of Wolbachia infection.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {255},
pmid = {37978413},
issn = {2049-2618},
mesh = {Humans ; Animals ; Female ; *Dengue Virus ; *Aedes ; *Wolbachia/genetics ; Mosquito Vectors/microbiology ; Drosophila melanogaster/microbiology ; *Microbiota ; },
abstract = {BACKGROUND: Wolbachia is a widespread bacterial endosymbiont that can inhibit vector competency when stably transinfected into the mosquito, Aedes aegypti, a primary vector of the dengue virus (DENV) and other arboviruses. Although a complete mechanistic understanding of pathogen blocking is lacking, it is likely to involve host immunity induction and resource competition between Wolbachia and DENV, both of which may be impacted by microbiome composition. The potential impact of Wolbachia transinfection on host fitness is also of importance given the widespread release of mosquitos infected with the Drosophila melanogaster strain of Wolbachia (wMel) in wild populations. Here, population-level genomic data from Ae. aegypti was surveyed to establish the relationship between the density of wMel infection and the composition of the host microbiome.<br><br>RESULTS: Analysis of genomic data from 172 Ae. aegypti females across six populations resulted in an expanded and quantitatively refined, species-level characterization of the bacterial, archaeal, and fungal microbiome. This included 844 species of bacteria across 23 phyla, of which 54 species were found to be ubiquitous microbiome members across these populations. The density of wMel infection was highly variable between individuals and negatively correlated with microbiome diversity. Network analyses revealed wMel as a hub comprised solely of negative interactions with other bacterial species. This contrasted with the large and highly interconnected network of other microbiome species that may represent members of the midgut microbiome community in this population.<br><br>CONCLUSION: Our bioinformatic survey provided a species-level characterization of Ae. aegypti microbiome composition and variation. wMel load varied substantially across populations and individuals and, importantly, wMel was a major hub of a negative interactions across the microbiome. These interactions may be an inherent consequence of heightened pathogen blocking in densely infected individuals or, alternatively, may result from antagonistic Wolbachia-incompatible bacteria that could impede the efficacy of wMel as a biological control agent in future applications. The relationship between wMel infection variation and the microbiome warrants further investigation in the context of developing wMel as a multivalent control agent against other arboviruses. Video Abstract.},
}
@article {pmid37978412,
year = {2023},
author = {Domin, H and Zimmermann, J and Taubenheim, J and Fuentes Reyes, G and Saueressig, L and Prasse, D and Höppner, M and Schmitz, RA and Hentschel, U and Kaleta, C and Fraune, S},
title = {Sequential host-bacteria and bacteria-bacteria interactions determine the microbiome establishment of Nematostella vectensis.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {257},
pmid = {37978412},
issn = {2049-2618},
support = {CRC1182 (Project B1, A1, Z2, Z3, INF)//Deutsche Forschungsgemeinschaft/ ; CRC1182 (Project B1, A1, Z2, Z3, INF)//Deutsche Forschungsgemeinschaft/ ; CRC1182 (Project B1, A1, Z2, Z3, INF)//Deutsche Forschungsgemeinschaft/ ; CRC1182 (Project B1, A1, Z2, Z3, INF)//Deutsche Forschungsgemeinschaft/ ; CRC1182 (Project B1, A1, Z2, Z3, INF)//Deutsche Forschungsgemeinschaft/ ; CRC1182 (Project B1, A1, Z2, Z3, INF)//Deutsche Forschungsgemeinschaft/ ; CRC1182 (Project B1, A1, Z2, Z3, INF)//Deutsche Forschungsgemeinschaft/ ; CRC1182 (Project B1, A1, Z2, Z3, INF)//Deutsche Forschungsgemeinschaft/ ; CRC1182 (Project B1, A1, Z2, Z3, INF)//Deutsche Forschungsgemeinschaft/ ; CRC1182 (Project B1, A1, Z2, Z3, INF)//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Microbiota/genetics ; Bacteria/genetics ; *Sea Anemones ; Chitin ; Silicones ; },
abstract = {BACKGROUND: The microbiota of multicellular organisms undergoes considerable changes during host ontogeny but the general mechanisms that control community assembly and succession are poorly understood. Here, we use bacterial recolonization experiments in Nematostella vectensis as a model to understand general mechanisms determining bacterial establishment and succession. We compared the dynamic establishment of the microbiome on the germfree host and on inert silicone tubes.<br><br>RESULTS: Following the dynamic reconstruction of microbial communities on both substrates, we show that the initial colonization events are strongly influenced by the host but not by the silicone tube, while the subsequent bacteria-bacteria interactions are the main driver of bacterial succession. Interestingly, the recolonization pattern on adult hosts resembles the ontogenetic colonization succession. This process occurs independently of the bacterial composition of the inoculum and can be followed at the level of individual bacteria. To identify potential metabolic traits associated with initial colonization success and potential metabolic interactions among bacteria associated with bacterial succession, we reconstructed the metabolic networks of bacterial colonizers based on their genomes. These analyses revealed that bacterial metabolic capabilities reflect the recolonization pattern, and the degradation of chitin might be a selection factor during early recolonization of the animal. Concurrently, transcriptomic analyses revealed that Nematostella possesses two chitin synthase genes, one of which is upregulated during early recolonization.<br><br>CONCLUSIONS: Our results show that early recolonization events are strongly controlled by the host while subsequent colonization depends on metabolic bacteria-bacteria interactions largely independent of host ontogeny. Video Abstract.},
}
@article {pmid37977879,
year = {2023},
author = {Batool, M and Carvalhais, LC and Fu, B and Schenk, PM},
title = {Customized plant microbiome engineering for food security.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2023.10.012},
pmid = {37977879},
issn = {1878-4372},
abstract = {Plant microbiomes play a vital role in promoting plant growth and resilience to cope with environmental stresses. Plant microbiome engineering holds significant promise to increase crop yields, but there is uncertainty about how this can best be achieved. We propose a step-by-step approach involving customized direct and indirect methods to condition soils and to match plants and microbiomes. Although three approaches, namely the development of (i) 'plant- and microbe-friendly' soils, (ii) 'microbe-friendly' plants, and (iii) 'plant-friendly' microbiomes, have been successfully tested in isolation, we propose that the combination of all three may lead to a step-change towards higher and more stable crop yields. This review aims to provide knowledge, future directions, and practical guidance to achieve this goal via customized plant microbiome engineering.},
}
@article {pmid37977855,
year = {2023},
author = {Touchette, D and Gostinčar, C and Whyte, LG and Altshuler, I},
title = {Lichen-associated microbial members are prevalent in the snow microbiome of a sub-arctic alpine tundra.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiad151},
pmid = {37977855},
issn = {1574-6941},
abstract = {Snow is the largest component of the cryosphere, with its cover and distribution rapidly decreasing over the last decade due to climate warming. It is imperative to characterize the snow (nival) microbial communities to better understand the role of microorganisms inhabiting these rapidly changing environments. Here, we investigated the core nival microbiome, the cultivable microbial members, and the microbial functional diversity of the remote Uapishka mountain range, a massif of alpine sub-arctic tundra and boreal forest. Snow samples were taken over a two-month interval along an altitude gradient with varying degree of anthropogenic traffic and vegetation cover. The core snow alpine tundra/boreal microbiome, which was present across all samples, constituted of Acetobacterales, Rhizobiales and Acidobacteriales bacterial orders, and of Mycosphaerellales and Lecanorales fungal orders, with the dominant fungal taxa being associated with lichens. The snow samples had low active functional diversity, with Richness values ranging from 0 to 19.5. The culture-based viable microbial enumeration ranged from 0 to 8.05 × 103 CFUs/mL. We isolated and whole-genome sequenced five microorganisms which included three fungi, one alga, and one potentially novel bacterium of the Lichenihabitans genus; all of which appear to be part of lichen-associated taxonomic clades.},
}
@article {pmid37977446,
year = {2023},
author = {Ali, AH and Li, S and Liu, SQ and Gan, RY and Li, HB and Kamal-Eldin, A and Ayyash, M},
title = {INVITED REVIEW: Camel Milk and Gut Health: Understanding Digestibility and the Impact on Gut Microbiota.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2023-23995},
pmid = {37977446},
issn = {1525-3198},
abstract = {Camel milk (CM), known for its immune-regulatory, anti-inflammatory, antiapoptotic, and antidiabetic properties, is a natural healthy food. It is easily digestible due to the high levels of β-casein and diverse secreted antibodies, exhibiting superior antibacterial and antiviral activities compared with bovine milk. β-casein is less allergic and more digestible since it is more susceptible to the digestive hydrolysis in gut, and therefore, higher levels of β-casein make CM advantageous for human health. Furthermore, antibodies help the digestive system by destroying the antigens, which are then overwhelmed and digested by macrophages. Gut microbiota in human health has gained a substantial research attention, as it offers potential benefits and supports disease treatment. It has a vital role in regulating the host health, since it helps in several biological functions, such as protection against pathogens, immune functions regulation, energy harvesting from digested foods, and reinforcement digestive track biochemical barriers. These functions could be affected by the changes in gut microbiota profile, and the differences of gut microbiota are associated with several diseases, such as inflammatory bowel disease, colon cancer, irritable bowel disorder, mental illness, allergy, and obesity. This review focuses on the digestibility of CM components, particularly protein and fat, and their influences on gut microbiota modulation. Notably, CM's hypoallergenic properties and small fat globules contribute to enhanced digestibility. Considering the rapid digestion of its proteins under conditions simulating infant gastrointestinal digestion, CM exhibits promise as a potential alternative for infant formula preparation due to the high β-/αs-casein ratio and protective proteins, in addition to the absence of β-lactoglobulin.},
}
@article {pmid37977078,
year = {2023},
author = {Saelens, G and Houf, K},
title = {The involvement of Pseudoterranova decipiens fish infestation on the shelf-life of fresh Atlantic cod (Gadus morhua) fillet.},
journal = {International journal of food microbiology},
volume = {410},
number = {},
pages = {110426},
doi = {10.1016/j.ijfoodmicro.2023.110426},
pmid = {37977078},
issn = {1879-3460},
abstract = {Zoonotic nematodes of the family Anisakidae are highly common in many marine fish species, which act as paratenic hosts for the third larval stage. In the fish, these parasites may migrate from the fish's gastro-intestinal tract (GI-tract) further to the coelomic cavity and muscles, making them a possible contamination source of bacteria they carry on their cuticle and in their GI-tract. A previous study revealed no apparent effect of Anisakis simplex on spoilage of fish, but the equally common anisakid species Pseudoterranova decipiens has a larger body surface potentially increasing the bacterial load brought into the fish muscle upon migration. As the presence of shelf-life reducing spoilage bacteria in the microbiome of this anisakid species has been demonstrated, the objective of the present study was to assess the potential shelf-life reducing effect of P. decipiens in fresh fish fillets stored in a domestic refrigerator. Atlantic cod was used as a model since members of the cod family are the third most consumed marine fish globally and it has the highest prevalence of P. decipiens infections. Infected and non-infected codfish fillet portions were collected and microbiologically analyzed at day 0 and day 4 of storage in a domestic fridge. Three isolation media were used to enhance maximum bacterial recovery and isolates were identified using MALDI-TOF MS and 16S rRNA gene sequencing. In parallel to the microbiological examination, sensory analysis was performed daily on the cod fillets to evaluate the freshness of the fish. Results revealed the presence of typical spoilage bacteria (e.g., Pseudomonas sp., Photobacterium sp.) in all fish, but based on the total viable counts, total H2S-producing bacteria, and sensory analysis, there were no objective indications to assume an increased fish spoilage rate by the presence