@article {pmid38647645,
year = {2024},
author = {Zhang, M and Guo, D and Wang, H and Wu, G and Ding, N and Shi, Y and Zhou, J and Zhao, E and Li, X},
title = {Integrated characterization of filler tobacco leaves: HS-SPME-GC-MS, E-nose, and microbiome analysis across different origins.},
journal = {Bioresources and bioprocessing},
volume = {11},
number = {1},
pages = {11},
pmid = {38647645},
issn = {2197-4365},
support = {W2023JSKF0083//State-Owned Enterprises Cooperative External Program/ ; },
abstract = {This study delves into the aroma characteristics and microbial composition of filler tobacco leaves (FTLs) sourced from six distinct cigar-growing regions within Yunnan, China, following standardized fermentation. An integrated approach using gas chromatography-mass spectrometry (GC-MS), electronic nose (E-nose), and microbiome analysis was employed for comprehensive profiling. Results derived from Linear Discriminant Analysis (LDA) using E-nose data confirmed the presence of notable variability in flavor substance profiles among the FTLs from six regions. Additionally, GC-MS was used to discern disparities in volatile organic compound (VOC) distribution across FTLs from these regions, identifying 92, 81, 79, 58, 69, and 92 VOCs within each respective sample set. Significantly, 24 VOCs emerged as pivotal determinants contributing to the heterogeneity of flavor profiles among FTLs from diverse origins, as indicated by Variable Importance for the Projection (VIP) analysis. Furthermore, distinctions in free amino acid content and chemical constituents were observed across FTLs. Of noteworthy significance, solanone, isophorone, durene, (-)-alpha-terpineol, and 2,3'-bipyridine exhibited the strongest correlations with microbiome data, with fungal microorganisms exerting a more pronounced influence on metabolites, as elucidated through two-way orthogonal partial least-squares (O2PLS) modeling. These findings provide a theoretical and technical basis for accurately evaluating the synchronization of FTLs in aromas and fermentation processes, and they will enhance the quality of fermented FTLs and foster the growth of the domestic cigar tobacco industry ultimately.},
}

@article {pmid38647957,
year = {2024},
author = {Singh, V and Mahra, K and Jung, D and Shin, JH},
title = {Gut Microbes in Polycystic Ovary Syndrome and Associated Comorbidities; Type 2 Diabetes, Non-Alcoholic Fatty Liver Disease (NAFLD), Cardiovascular Disease (CVD), and the Potential of Microbial Therapeutics.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {38647957},
issn = {1867-1314},
support = {2021R1A6C101A416//Korea Basic Science Institute/ ; },
abstract = {Polycystic ovary syndrome (PCOS) is one of the most common endocrine anomalies among females of reproductive age, highlighted by hyperandrogenism. PCOS is multifactorial as it can be associated with obesity, insulin resistance, low-grade chronic inflammation, and dyslipidemia. PCOS also leads to dysbiosis by lowering microbial diversity and beneficial microbes, such as Faecalibacterium, Roseburia, Akkermenisa, and Bifidobacterium, and by causing a higher load of opportunistic pathogens, such as Escherichia/Shigella, Fusobacterium, Bilophila, and Sutterella. Wherein, butyrate producers and Akkermansia participate in the glucose uptake by inducing glucagon-like peptide-1 (GLP-1) and glucose metabolism, respectively. The abovementioned gut microbes also maintain the gut barrier function and glucose homeostasis by releasing metabolites such as short-chain fatty acids (SCFAs) and Amuc_1100 protein. In addition, PCOS-associated gut is found to be higher in gut-microbial enzyme β-glucuronidase, causing the de-glucuronidation of conjugated androgen, making it susceptible to reabsorption by entero-hepatic circulation, leading to a higher level of androgen in the circulatory system. Overall, in PCOS, such dysbiosis increases the gut permeability and LPS in the systemic circulation, trimethylamine N-oxide (TMAO) in the circulatory system, chronic inflammation in the adipose tissue and liver, and oxidative stress and lipid accumulation in the liver. Thus, in women with PCOS, dysbiosis can promote the progression and severity of type 2 diabetes, non-alcoholic fatty liver disease (NAFLD), and cardiovascular diseases (CVD). To alleviate such PCOS-associated complications, microbial therapeutics (probiotics and fecal microbiome transplantation) can be used without any side effects, unlike in the case of hormonal therapy. Therefore, this study sought to understand the mechanistic significance of gut microbes in PCOS and associated comorbidities, along with the role of microbial therapeutics that can ease the life of PCOS-affected women.},
}

@article {pmid38647290,
year = {2024},
author = {Jensen, O and Trujillo, E and Hanson, L and Ost, KS},
title = {Controlling Candida: immune regulation of commensal fungi in the gut.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0051623},
doi = {10.1128/iai.00516-23},
pmid = {38647290},
issn = {1098-5522},
abstract = {The intestinal microbiome harbors fungi that pose a significant risk to human health as opportunistic pathogens and drivers of inflammation. Inflammatory and autoimmune diseases are associated with dysbiotic fungal communities and the expansion of potentially pathogenic fungi. The gut is also the main reservoir for disseminated fungal infections. Immune interactions are critical for preventing commensal fungi from becoming pathogenic. Significant strides have been made in defining innate and adaptive immune pathways that regulate intestinal fungi, and these discoveries have coincided with advancements in our understanding of the fungal molecular pathways and effectors involved in both commensal colonization and pathogenesis within the gut. In this review, we will discuss immune interactions important for regulating commensal fungi, with a focus on how specific cell types and effectors interact with fungi to limit their colonization or pathogenic potential. This will include how innate and adaptive immune pathways target fungi and orchestrate antifungal immune responses, in addition to how secreted immune effectors, such as mucus and antimicrobial peptides, regulate fungal colonization and inhibit pathogenic potential. These immune interactions will be framed around our current understanding of the fungal effectors and pathways regulating colonization and pathogenesis within this niche. Finally, we highlight important unexplored mechanisms by which the immune system regulates commensal fungi in the gut.},
}

@article {pmid38647288,
year = {2024},
author = {Waegenaar, F and García-Timermans, C and Van Landuyt, J and De Gusseme, B and Boon, N},
title = {Impact of operational conditions on drinking water biofilm dynamics and coliform invasion potential.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0004224},
doi = {10.1128/aem.00042-24},
pmid = {38647288},
issn = {1098-5336},
abstract = {UNLABELLED: Biofilms within drinking water distribution systems serve as a habitat for drinking water microorganisms. However, biofilms can negatively impact drinking water quality by causing water discoloration and deterioration and can be a reservoir for unwanted microorganisms. In this study, we investigated whether indicator organisms for drinking water quality, such as coliforms, can settle in mature drinking water biofilms. Therefore, a biofilm monitor consisting of glass rings was used to grow and sample drinking water biofilms. Two mature drinking water biofilms were characterized by flow cytometry, ATP measurements, confocal laser scanning microscopy, and 16S rRNA sequencing. Biofilms developed under treated chlorinated surface water supply exhibited lower cell densities in comparison with biofilms resulting from treated groundwater. Overall, the phenotypic as well as the genotypic characteristics were significantly different between both biofilms. In addition, the response of the biofilm microbiome and possible biofilm detachment after minor water quality changes were investigated. Limited changes in pH and free chlorine addition, to simulate operational changes that are relevant for practice, were evaluated. It was shown that both biofilms remained resilient. Finally, mature biofilms were prone to invasion of the coliform, Serratia fonticola. After spiking low concentrations (i.e., ±100 cells/100 mL) of the coliform to the corresponding bulk water samples, the coliforms were able to attach and get established within the mature biofilms. These outcomes emphasize the need for continued research on biofilm detachment and its implications for water contamination in distribution networks.

IMPORTANCE: The revelation that even low concentrations of coliforms can infiltrate into mature drinking water biofilms highlights a potential public health concern. Nowadays, the measurement of coliform bacteria is used as an indicator for fecal contamination and to control the effectiveness of disinfection processes and the cleanliness and integrity of distribution systems. In Flanders (Belgium), 533 out of 18,840 measurements exceeded the established norm for the coliform indicator parameter in 2021; however, the source of microbial contamination is mostly unknown. Here, we showed that mature biofilms, are susceptible to invasion of Serratia fonticola. These findings emphasize the importance of understanding and managing biofilms in drinking water distribution systems, not only for their potential to influence water quality, but also for their role in harboring and potentially disseminating pathogens. Further research into biofilm detachment, long-term responses to operational changes, and pathogen persistence within biofilms is crucial to inform strategies for safeguarding drinking water quality.},
}

@article {pmid38647231,
year = {2024},
author = {Landeen, KC and DeSisto, NG and Jordan, MK and Colaianni, CA and Phillips, J},
title = {Recurrent Peritonsillar Abscess Caused by Vaginal Flora: A Common Problem From a Unique Source.},
journal = {Ear, nose, & throat journal},
volume = {},
number = {},
pages = {1455613241246486},
doi = {10.1177/01455613241246486},
pmid = {38647231},
issn = {1942-7522},
abstract = {Peritonsillar abscesses (PTAs) are typically caused by group A Streptococcus or mixed oral flora. Gardnerella vaginalis is a part of the normal vaginal microbiome, and overgrowth can cause bacterial vaginosis. We present a case of recurrent PTA with G. vaginalis superinfection, which occurred after the patient performed oral sex on a female after incision and drainage of her initial PTA. The patient continued to have recurrent PTAs until G. vaginalis was identified, and antibiotic coverage was broadened to cover both group A Streptococcus and G. vaginalis. This case highlights the importance of culturing PTA aspirate for directed antibiosis in persistent or recurrent infections. The rare superinfection also raises the question of advising abstinence from oral-genital contact after oral procedures to minimize risk of superinfection.},
}

@article {pmid38647010,
year = {2024},
author = {Sun, T and Chen, G and Jiang, W and Xu, W and You, L and Jiang, C and Chen, S and Wang, D and Zheng, X and Yuan, Y},
title = {Distinguishing bipolar depression, bipolar mania, and major depressive disorder by gut microbial characteristics.},
journal = {Bipolar disorders},
volume = {},
number = {},
pages = {},
doi = {10.1111/bdi.13439},
pmid = {38647010},
issn = {1399-5618},
support = {//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; //National Natural Science Foundation of China/ ; //"Double-first" Discipline funding of China Pharmaceutical University under the grant/ ; },
abstract = {BACKGROUND: Gut microbial disturbance has been widely confirmed in mood disorders. However, little is known about whether gut microbial characteristics can distinguish major depressive disorder (MDD), bipolar depression (BP-D), and bipolar mania (BP-M).

METHODS: This was a prospective case-control study. The composition of gut microbiota was profiled using 16S ribosomal RNA (rRNA) gene sequencing of fecal samples and compared between healthy controls (HC; n = 46), MDD (n = 51), BP-D (n = 44), and patients with BP-M (n = 45).

RESULTS: Gut microbial compositions were remarkably changed in the patients with MDD, BP-D, and BP-M. Compared to HC, distinct gut microbiome signatures were found in MDD, BP-D, and BP-M, and some gut microbial changes were overlapping between the three mood disorders. Furthermore, we identified a signature of 7 operational taxonomic units (OUT; Prevotellaceae-related OUT22, Prevotellaceae-related OUT31, Prevotellaceae-related OTU770, Ruminococcaceae-related OUT70, Bacteroidaceae-related OTU1536, Propionibacteriaceae-related OTU97, Acidaminococcaceae-related OTU34) that can distinguish patients with MDD from those with BP-D, BP-M, or HC, with area under the curve (AUC) values ranging from 0.910 to 0.996.

CONCLUSION: Our results provide the clinical rationale for the discriminative diagnosis of MDD, BP-D, and BP-M by characteristic gut microbial features.},
}

@article {pmid38646847,
year = {2024},
author = {Fontana, F and Longhi, G and Carli, E and Alessandri, G and Mancabelli, L and Lugli, GA and Tarracchini, C and Viappiani, A and Anzalone, R and Turroni, F and Milani, C and Ventura, M},
title = {Revealing the genetic traits of the foodborne microbial genus hafnia: Implications for the human gut microbiome.},
journal = {Environmental microbiology},
volume = {26},
number = {4},
pages = {e16626},
doi = {10.1111/1462-2920.16626},
pmid = {38646847},
issn = {1462-2920},
support = {//Cariparma/ ; //GenProbio Srl/ ; CUP D93C22000890001//Concession Decree No.1550 of 11 October 2022, Italian Ministry of University and Research/ ; PE00000003//Mission 4 Component 2 Investment 1.3 - Call for tender No. 341 of 15 March 2022, Italian Ministry of University and Research funded by the European Union-NextGenerationEU/ ; //the National Recovery and Resilience Plan (NRRP)/ ; //ON Foods - Research and innovation network on food and nutrition Sustainability, Safety and Security -Working ON Foods/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Animals ; Bees/microbiology ; Fatty Acids, Volatile/metabolism ; Genome, Bacterial ; Food Microbiology ; Metagenomics ; Vitamins/metabolism ; Phylogeny ; },
abstract = {The bacterial genus Hafnia has recently attracted attention due to its complex metabolic features and host-interaction capabilities, which are associated with health benefits, primarily weight loss. However, significant gaps remain in our understanding of the genomic characteristics of this emerging microbial group. In this study, we utilized all available high-quality genomes of Hafnia alvei and Hafnia paralvei to uncover the broad distribution of Hafnia in human and honeybee guts, as well as in dairy products, by analysing 1068 metagenomic datasets. We then investigated the genetic traits related to Hafnia's production of vitamins and short-chain fatty acids (SCFAs) through a comparative genomics analysis that included all dominant bacterial species in the three environments under study. Our findings underscore the extensive metabolic capabilities of Hafnia, particularly in the production of vitamins such as thiamine (B1), nicotinate (B3), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and menaquinone (K2). Additionally, Hafnia demonstrated a conserved genetic makeup associated with SCFA production, including acetate, propanoate, and butanoate. These metabolic traits were further confirmed using RNAseq analyses of a newly isolated H. paralvei strain T10. Overall, our study illuminates the ecological distribution and genetic attributes of this bacterial genus, which is of increasing scientific and industrial relevance.},
}

*Gastrointestinal Microbiome/genetics
Humans
Animals
Bees/microbiology
Fatty Acids, Volatile/metabolism
Genome, Bacterial
Food Microbiology
Metagenomics
Vitamins/metabolism
Phylogeny

@article {pmid38646773,
year = {2024},
author = {Weng, LY and Luan, DD and Zhou, DP and Guo, QG and Wang, GZ and Zhang, JL},
title = {Improving crop health by synthetic microbial communities: Progress and prospects.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {3},
pages = {847-857},
doi = {10.13287/j.1001-9332.202403.028},
pmid = {38646773},
issn = {1001-9332},
mesh = {*Crops, Agricultural/growth & development/microbiology ; *Microbiota ; *Rhizosphere ; Soil Microbiology ; Synthetic Biology/methods ; Agriculture/methods ; },
abstract = {Crop health directly affects yields and food security. At present, agrochemicals such as fertilizers and pesticides are mainly used in agricultural production to promote crop health. However, long-term excessive utilization of agrochemicals will damage the ecological environment of farmlands and increase the safety risk of agricultural products. It is urgent to explore efficient and environment-friendly agricultural products. Rhizosphere microbiome are considered as the second genome of plants, which are closely related to crop health. Understanding the key functional microbes, microbe-microbe interactions, and plant-microbe interactions are fundamental for exploring the potential of beneficial microbes in promoting crop health. However, due to the heterogeneity and complexity of the natural environment, stimulating the function of indigenous microorganisms remains uncertain. Synthetic microbial community (SynCom) is an artificial combination of two or more different strain isolates of microorganisms, with different taxonomic, genetic, or functional characteristic. Because of the advantages of maintaining species diversity and community stability, SynCom has been widely applied in the fields of human health, environmental governance and industrial production, and may also have great potential in promoting crop health. We summarized the concept and research status of SynCom, expounded the principles and methods of constructing SynCom, and analyzed the research on the promotion of crop health by exploring the mechanism of plant-microbe interactions, promoting plant growth and development, and improving stress resistance. Finally, we envisaged the future prospects to guide the using SynCom to improve crop health.},
}

*Crops, Agricultural/growth & development/microbiology
*Microbiota
*Rhizosphere
Soil Microbiology
Synthetic Biology/methods
Agriculture/methods

@article {pmid38646630,
year = {2024},
author = {Zheng, SJ and Hu, H and Li, Y and Chen, J and Li, X and Bai, T},
title = {Editorial: Microbial interaction with banana: mechanisms, symbiosis, and integrated diseases control.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1390969},
pmid = {38646630},
issn = {1664-302X},
}

@article {pmid38646629,
year = {2024},
author = {Nivetha, N and Shukla, PS and Nori, SS and Kumar, S and Suryanarayan, S},
title = {A red seaweed Kappaphycus alvarezii-based biostimulant (AgroGain[®]) improves the growth of Zea mays and impacts agricultural sustainability by beneficially priming rhizosphere soil microbial community.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1330237},
pmid = {38646629},
issn = {1664-302X},
abstract = {The overuse of chemical-based agricultural inputs has led to the degradation of soil with associated adverse effects on soil attributes and microbial population. This scenario leads to poor soil health and is reportedly on the rise globally. Additionally, chemical fertilizers pose serious risks to the ecosystem and human health. In this study, foliar sprays of biostimulant (AgroGain/LBS6) prepared from the cultivated, tropical red seaweed Kappaphycus alvarezii increased the phenotypic growth of Zea mays in terms of greater leaf area, total plant height, and shoot fresh and dry weights. In addition, LBS6 improved the accumulation of chlorophyll a and b, total carotenoids, total soluble sugars, amino acids, flavonoids, and phenolics in the treated plants. LBS6 applications also improved the total bacterial and fungal count in rhizospheric soil. The V3-V4 region of 16S rRNA gene from the soil metagenome was analyzed to study the abundance of bacterial communities which were increased in the rhizosphere of LBS6-treated plants. Treatments were found to enrich beneficial soil bacteria, i.e., Proteobacteria, especially the classes Alphaproteobacteria, Cyanobacteria, Firmicutes, Actinobacteriota, Verrucomicrobiota, Chloroflexi, and Acidobacteriota and several other phyla related to plant growth promotion. A metagenomic study of those soil samples from LBS6-sprayed plants was correlated with functional potential of soil microbiota. Enrichment of metabolisms such as nitrogen, sulfur, phosphorous, plant defense, amino acid, co-factors, and vitamins was observed in soils grown with LBS6-sprayed plants. These results were further confirmed by a significant increase in the activity of soil enzymes such as urease, acid phosphatase, FDAse, dehydrogenase, catalase, and biological index of fertility in the rhizosphere of LBS6-treated corn plant. These findings conclude that the foliar application of LBS6 on Z. mays improves and recruits beneficial microbes and alters soil ecology in a sustainable manner.},
}

@article {pmid38646625,
year = {2024},
author = {Luangphiphat, W and Prombutara, P and Muangsillapasart, V and Sukitpunyaroj, D and Eeckhout, E and Taweechotipatr, M},
title = {Exploring of gut microbiota features in dyslipidemia and chronic coronary syndrome patients undergoing coronary angiography.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1384146},
pmid = {38646625},
issn = {1664-302X},
abstract = {Chronic coronary syndrome (CCS) has a high mortality rate, and dyslipidemia is a major risk factor. Atherosclerosis, a cause of CCS, is influenced by gut microbiota dysbiosis and its metabolites. The objective of this study was to study the diversity and composition of gut microbiota and related clinical parameters among CCS patients undergoing coronary angiography and dyslipidemia patients in comparison to healthy volunteers in Thailand. CCS patients had more risk factors and higher inflammatory markers, high-sensitivity C-reactive protein (hs-CRP) than others. The alpha diversity was lower in dyslipidemia and CCS patients than in the healthy group. A significant difference in the composition of gut microbiota was observed among the three groups. The relative abundance of Proteobacteria, Fusobacteria, Enterobacteriaceae, Prevotella, and Streptococcus was significantly increased while Roseburia, Ruminococcus, and Faecalibacterium were lower in CCS patients. In CCS patients, Lachnospiraceae, Peptostreptococcaceae, and Pediococcus were positively correlated with hs-CRP. In dyslipidemia patients, Megasphaera was strongly positively correlated with triglyceride (TG) level and negatively correlated with high-density lipoprotein cholesterol (HDL-C). The modification of gut microbiota was associated with changes in clinical parameters involved in the development of coronary artery disease (CAD) in CCS patients.},
}

@article {pmid38646576,
year = {2024},
author = {Yu, Z and Yan, M and Somasundaram, S},
title = {Rumen protozoa and viruses: The predators within and their functions-A mini-review.},
journal = {JDS communications},
volume = {5},
number = {3},
pages = {236-240},
pmid = {38646576},
issn = {2666-9102},
abstract = {The rumen microbiome digests plant feedstuff that would be otherwise indigestible and provides most of the metabolizable energy and protein the host animals need. Until recently, research efforts have primarily been directed to bacteria and archaea, leaving the protozoa, fungi, and viruses much less understood. Protozoa contribute to feed digestion and fermentation, but as predators, they affect the microbiome and its function by regulating the abundance and activities of other rumen microbes both in a top-down (by directly killing the prey) and bottom-up (by affecting the metabolism of other microbes) manner. Rumen viruses (or phages, used interchangeably below) are diverse and abundant but the least understood. They are also predators (intracellular "predators") because of their lytic lifecycle, although they can co-exist peacefully with their hosts and reprogram host metabolism, buttressing host ecological fitness. In doing so, rumen viruses also affect the rumen microbiome in both a top-down and a bottom-up manner. Here we review the recent advancement in understanding both types of predators, focusing on their potential impact on the rumen microbiome and functions.},
}

@article {pmid38646566,
year = {2024},
author = {Botlagunta, N and Babu, S},
title = {Growth enhancement and changes in bacterial microbiome of cucumber plants exhibited by biopriming with some native bacteria.},
journal = {Saudi journal of biological sciences},
volume = {31},
number = {6},
pages = {103997},
pmid = {38646566},
issn = {1319-562X},
abstract = {This study investigated the impact of a mixture of six endophytic bacterial strains isolated from cucumber plants on the growth and microbiome diversity of six cucumber traditional varieties and hybrids. Six bacterial species were isolated and identified by 16 s rRNA sequencing. All the bacteria showed plant growth promoting traits. Bacillus tequilensis showed 80 % inhibition of the mycelia growth of Fusarium oxysporum f.sp. cucumarinum (Foc). Mixed culture of all the bacteria was prepared and applied back to the varieties and hybrids of cucumber plants through seed soaking. Plant growth characteristics indicated that the treated plants showed increased plant growth in terms of plant height, number of leaves, vine length, male:female flower ratio, number of fruits and fruit length. Bacteria treated plants of hybrid HiVeg Chitra recorded 19 cm increase in vine length compared to control plants. The matataxonomic analysis of leaf samples by Illumina sequencing highlighted a diverse bacterial community shift in treated plants, with significant increases in genera like Bacillus and Staphylococcus. The core microbiome analysis identified key genera such as Bacillus, Staphylococcus, Sphingomonas, Methylobacterium, etc that could be pivotal in plant growth promotion. Bacillus and Staphylococcus showed increased abundance in treated varieties, correlating with the observed in plant growth parameters thus indicating their role in growth promotion of cucumber plants. Endophytic bacterial species identified from cucumber plants when re-applied by seed soaking, they promote the plant growth by modulating the microbiome. The bacterial species identified in the study could be potential candidates as microbial bioinputs for cucumber cultivation.},
}

@article {pmid38646524,
year = {2024},
author = {Dey, S and Vieyra-Garcia, PA and Joshi, AA and Trajanoski, S and Wolf, P},
title = {Modulation of the skin microbiome in cutaneous T-cell lymphoma delays tumour growth and increases survival in the murine EL4 model.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1255859},
pmid = {38646524},
issn = {1664-3224},
mesh = {Animals ; *Microbiota/drug effects ; Mice ; *Skin/microbiology/pathology/immunology/drug effects ; *Skin Neoplasms/microbiology/immunology/pathology ; *Lymphoma, T-Cell, Cutaneous/microbiology/pathology/drug therapy/therapy ; *Mice, Inbred C57BL ; Disease Models, Animal ; Anti-Bacterial Agents/therapeutic use/pharmacology/administration & dosage ; Cell Line, Tumor ; Female ; Humans ; },
abstract = {Cutaneous T-cell lymphomas (CTCL) are a group of lymphoproliferative disorders of skin-homing T cells causing chronic inflammation. These disorders cause impairment of the immune environment, which leads to severe infections and/or sepsis due to dysbiosis. In this study, we elucidated the host-microbial interaction in CTCL that occurs during the phototherapeutic treatment regime and determined whether modulation of the skin microbiota could beneficially affect the course of CTCL. EL4 T-cell lymphoma cells were intradermally grafted on the back of C57BL/6 mice. Animals were treated with conventional therapeutics such as psoralen + UVA (PUVA) or UVB in the presence or absence of topical antibiotic treatment (neomycin, bacitracin, and polymyxin B sulphate) as an adjuvant. Microbial colonisation of the skin was assessed to correlate with disease severity and tumour growth. Triple antibiotic treatment significantly delayed tumour occurrence (p = 0.026), which prolonged the survival of the mice (p = 0.033). Allocation to phototherapeutic agents PUVA, UVB, or none of these, along with antibiotic intervention, reduced the tumour growth significantly (p = 0.0327, p ≤ 0.0001, p ≤ 0.0001 respectively). The beta diversity indices calculated using the Bray-Curtis model showed that the microbial population significantly differed after antibiotic treatment (p = 0.001). Upon modulating the skin microbiome by antibiotic treatment, we saw an increase in commensal Clostridium species, e.g., Lachnospiraceae sp. (p = 0.0008), Ruminococcaceae sp. (p = 0.0001)., Blautia sp. (p = 0.007) and a significant reduction in facultative pathogens Corynebacterium sp. (p = 0.0009), Pelomonas sp. (p = 0.0306), Streptococcus sp. (p ≥ 0.0001), Pseudomonas sp. (p = 0.0358), and Cutibacterium sp. (p = 0.0237). Intriguingly, we observed a significant decrease in Staphylococcus aureus frequency (p = 0.0001) but an increase in the overall detection frequency of the Staphylococcus genus, indicating that antibiotic treatment helped regain the microbial balance and increased the number of non-pathogenic Staphylococcus populations. These study findings show that modulating microbiota by topical antibiotic treatment helps to restore microbial balance by diminishing the numbers of pathogenic microbes, which, in turn, reduces chronic inflammation, delays tumour growth, and increases survival rates in our CTCL model. These findings support the rationale to modulate the microbial milieu during the disease course of CTCL and indicate its therapeutic potential.},
}

Animals
*Microbiota/drug effects
Mice
*Skin/microbiology/pathology/immunology/drug effects
*Skin Neoplasms/microbiology/immunology/pathology
*Lymphoma, T-Cell, Cutaneous/microbiology/pathology/drug therapy/therapy
*Mice, Inbred C57BL
Disease Models, Animal
Anti-Bacterial Agents/therapeutic use/pharmacology/administration & dosage
Cell Line, Tumor
Female
Humans

@article {pmid38646477,
year = {2024},
author = {Xia, Y and Feng, J and Zhang, H and Xiong, D and Kong, L and Seviour, R and Kong, Y},
title = {Effects of soil pH on the growth, soil nutrient composition, and rhizosphere microbiome of Ageratina adenophora.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17231},
pmid = {38646477},
issn = {2167-8359},
mesh = {Hydrogen-Ion Concentration ; *Rhizosphere ; *Microbiota/physiology ; *Soil/chemistry ; *Ageratina/chemistry ; *Soil Microbiology ; Plant Leaves/microbiology/chemistry ; Plant Weeds/chemistry/growth & development ; Plant Roots/microbiology ; Antioxidants/metabolism/analysis ; },
abstract = {Ageratina adenophora is an invasive weed species found in many countries. Methods to control the spread of this weed have been largely unsuccessful. Soil pH is the most important soil factor affecting the availability of nutrients for plant and impacting its growth. Understanding the mechanisms of the influence of soil pH on the growth of A. adenophora may help to develop effective control measures. In this study, we artificially changed the soil pH in pot experiments for A. adenophora. We studied the effects of acidic (pH 5.5), weakly acidic (pH 6.5), neutral (pH 7.2), and alkaline (pH 9.0) soils on the growth, availability of soil nutrients, activity of antioxidant enzymes, levels of redox markers in the leaves, and the structure and diversity of the rhizosphere microbiome. Soil with a pH 7.2 had a higher (47.8%) below-ground height versus soils of pH 5.5 at day 10; plant had a higher (11.3%) above-ground height in pH 7.2 soils than pH 9.0 soils at day 90; no differences in the fresh and dry weights of its above- and belowground parts, plant heights, and root lengths were observed in plants growing in acid, alkaline, or neutral pH soil were observed at day 180. Correspondingly, the antioxidant enzymes SOD (superoxide dismutase), POD (peroxidase), CAT (catalase) and redox markers GSH (glutathione) and MDA (malondialdehyde) were measured in the leaves. Significant differences existed in the activities of CAT and the levels of GSH between those growing in acidic and alkaline soils and those in neutral pH soil at day 90; however, only lower (36.8%) CAT activities in those grown at pH 5.5 than those grown at pH 7.2 were found at day 180. Similarly, significant differences in available P (16.89 vs 3.04 mg Kg[-1]) and total K (3.67 vs 0.96 mg Kg[-1]), total P (0.37 vs 0.25 g Kg[-1]) and total N (0.45 vs 1.09 g Kg[-1]) concentrations were found between the rhizosphere soils of A. adenophora grown at pH 9.0 and 7.2 at day 90; no such differences were seen at day 180. High throughput analyses of the 16S rRNA and ITS fragments showed that the rhizosphere microbiome diversity and composition under different soil pH conditions changed over 180 days. The rhizosphere microbiomes differed in diversity, phylum, and generic composition and population interactions under acid and alkaline conditions versus those grown in neutral soils. Soil pH had a greater impact on the diversity and composition of the prokaryotic rhizosphere communities than those of the fungal communities. A. adenophora responded successfully to pH stress by changing the diversity and composition of the rhizosphere microbiome to maintain a balanced nutrient supply to support its normal growth. The unusual pH tolerance of A. adenophora may be one crucial reason for its successful invasion. Our results suggest that attempts use soil pH to control its invasion by changing the soil pH (for example, using lime) will fail.},
}

Hydrogen-Ion Concentration
*Rhizosphere
*Microbiota/physiology
*Soil/chemistry
*Ageratina/chemistry
*Soil Microbiology
Plant Leaves/microbiology/chemistry
Plant Weeds/chemistry/growth & development
Plant Roots/microbiology
Antioxidants/metabolism/analysis

@article {pmid38646363,
year = {2024},
author = {Farahbod, K and Slouha, E and Gerts, A and Rezazadah, A and Clunes, LA and Kollias, TF},
title = {The Effects of Diet Intervention on the Gut Microbiota in Type 2 Diabetes Mellitus: A Systematic Review.},
journal = {Cureus},
volume = {16},
number = {3},
pages = {e56737},
pmid = {38646363},
issn = {2168-8184},
abstract = {The GI tract hosts a dynamic community known as the gut microbiota, which encompasses thriving bacteria that actively contribute to the physiological functions of the human body. The intricacies of its composition are profoundly influenced by dietary preferences, where the quality, quantity, and frequency of food consumption play a pivotal role in either fostering or impeding specific bacterial strains. Type 2 diabetes mellitus (T2DM) is a prevalent and deleterious condition that originates from excessive hyperglycemia. Do lifestyle interventions targeting dietary adjustments, nutritional supplements, physical activity, and weight management programs exhibit a significant relationship in altering the composition of the gut microbiome and managing T2DM? This paper aims to evaluate the effects of lifestyle interventions on patients with T2DM and the implications of these changes on disease outcomes and progression. Lifestyle interventions can significantly impact the management of T2DM, especially those targeting dietary adjustments, nutritional supplements, physical activity, and weight management programs. The adoption of a high-fiber diet and increased fruit consumption have shown positive impacts on both insulin sensitivity and the composition of the gut microbiota. Additionally, promising outcomes emerge from supplementing with Omega-3 fatty acids, Vitamin K2 (MK-7), and transglucosidase, which influence insulin levels, glycemic control, and gut microbiota composition. Personalized diet interventions and the transformative effects of the Mediterranean diet present positive outcomes in metabolic control. The intensity of exercise plays a pivotal role in shaping the composition of the gut microbiota, with moderate-intensity continuous exercise displaying positive effects on anti-inflammatory microbes. Chronic exercise showcases favorable impacts on glycemic control and systemic inflammation. Emphasizing the intricate relationship between dietary habits, gut microbiota, and the risk of T2DM underscores the potential of the gut microbiota as a universal biomarker for assessing diabetes risk. Nutritional supplements and exercise interventions provide potential avenues for the management of T2DM, emphasizing the necessity for tailored strategies. Further research is encouraged to delve into the long-term effects and intricate interplay between lifestyle factors and the gut microbiome, enhancing our understanding of T2DM pathophysiology for targeted therapeutic approaches.},
}

@article {pmid38645704,
year = {2024},
author = {Han, H and Lee, HJ and Kim, KS and Chung, J and Na, HS},
title = {Comparison of the performance of MiSeq and NovaSeq in oral microbiome study.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2344293},
pmid = {38645704},
issn = {2000-2297},
abstract = {OBJECTIVE: Next generation sequencing is commonly used to characterize the microbiome structure. MiSeq is most commonly used to analyze the microbiome due to its relatively long read length. Illumina also introduced the 250 × 2 chip for NovaSeq. The purpose of this study was to compare the performance of MiSeq and NovaSeq in the context of oral microbiome study.

METHODS: Total read count, read quality score, relative bacterial abundance, community diversity, and correlation between two platforms were analyzed. Phylogenetic trees were analyzed for Streptococcus and periodontopathogens.

RESULTS: NovaSeq produced significantly more read counts and assigned more operational taxonomic units (OTUs) compared to MiSeq. Community diversity was similar between MiSeq and NovaSeq. NovaSeq were able to detect more unique OTUs compared to MiSeq. When phylogenetic trees were constructed for Streptococcus and periodontopathogens, both platforms detected OTUs for most of the clades.

CONCLUSION: Taken together, while both MiSeq and NovaSeq platforms effectively characterize the oral microbiome, NovaSeq outperformed MiSeq in terms of read counts and detection of unique OTUs, highlighting its potential as a valuable tool for large scale oral microbiome studies.},
}

@article {pmid38645683,
year = {2024},
author = {Chen, L and Bian, L and Ma, Q and Li, Y and Wang, X and Liu, Y},
title = {Defensive alteration of root exudate composition by grafting Prunus sp. onto resistant rootstock contributes to reducing crown gall disease.},
journal = {Horticulture research},
volume = {11},
number = {4},
pages = {uhae049},
pmid = {38645683},
issn = {2662-6810},
abstract = {Grafting is a traditional and significant strategy to suppress soil-borne diseases, such as the crown gall disease caused by tumorigenic Agrobacterium and Rhizobium. Root exudates and the rhizosphere microbiome play critical roles in controlling crown gall disease, but their roles in suppressing crown gall disease in grafted plants remain unclear. Here, disease-susceptible cherry rootstock 'Gisela 6' and disease-resistant cherry rootstock 'Haiying 1' were grafted onto each other or self-grafted. The effect of their root exudates on the soil microbiome composition and the abundance of pathogenic Agrobacterium were studied. Grafting onto the disease-resistant rootstock helped to reduce the abundance of pathogenic Agrobacterium, accompanied by altering root exudation, enriching potential beneficial bacteria, and changing soil function. Then, the composition of the root exudates from grafted plants was analyzed and the potential compounds responsible for decreasing pathogenic Agrobacterium abundance were identified. Based on quantitative measurement of the concentrations of the compounds and testing the impacts of supplied pure chemicals on abundance and chemotaxis of pathogenic Agrobacterium and potential beneficial bacteria, the decreased valine in root exudates of the plant grafted onto resistant rootstock was found to contribute to decreasing Agrobacterium abundance, enriching some potential beneficial bacteria and suppressing crown gall disease. This study provides insights into the mechanism whereby grafted plants suppress soil-borne disease.},
}

@article {pmid38645395,
year = {2024},
author = {Maitra, P and Hrynkiewicz, K and Szuba, A and Jagodziński, AM and Al-Rashid, J and Mandal, D and Mucha, J},
title = {Metabolic niches in the rhizosphere microbiome: dependence on soil horizons, root traits and climate variables in forest ecosystems.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1344205},
pmid = {38645395},
issn = {1664-462X},
abstract = {Understanding belowground plant-microbial interactions is important for biodiversity maintenance, community assembly and ecosystem functioning of forest ecosystems. Consequently, a large number of studies were conducted on root and microbial interactions, especially in the context of precipitation and temperature gradients under global climate change scenarios. Forests ecosystems have high biodiversity of plants and associated microbes, and contribute to major primary productivity of terrestrial ecosystems. However, the impact of root metabolites/exudates and root traits on soil microbial functional groups along these climate gradients is poorly described in these forest ecosystems. The plant root system exhibits differentiated exudation profiles and considerable trait plasticity in terms of root morphological/phenotypic traits, which can cause shifts in microbial abundance and diversity. The root metabolites composed of primary and secondary metabolites and volatile organic compounds that have diverse roles in appealing to and preventing distinct microbial strains, thus benefit plant fitness and growth, and tolerance to abiotic stresses such as drought. Climatic factors significantly alter the quantity and quality of metabolites that forest trees secrete into the soil. Thus, the heterogeneities in the rhizosphere due to different climate drivers generate ecological niches for various microbial assemblages to foster beneficial rhizospheric interactions in the forest ecosystems. However, the root exudations and microbial diversity in forest trees vary across different soil layers due to alterations in root system architecture, soil moisture, temperature, and nutrient stoichiometry. Changes in root system architecture or traits, e.g. root tissue density (RTD), specific root length (SRL), and specific root area (SRA), impact the root exudation profile and amount released into the soil and thus influence the abundance and diversity of different functional guilds of microbes. Here, we review the current knowledge about root morphological and functional (root exudation) trait changes that affect microbial interactions along drought and temperature gradients. This review aims to clarify how forest trees adapt to challenging environments by leveraging their root traits to interact beneficially with microbes. Understanding these strategies is vital for comprehending plant adaptation under global climate change, with significant implications for future research in plant biodiversity conservation, particularly within forest ecosystems.},
}

@article {pmid38645272,
year = {2024},
author = {Xu, H and Pudlo, NA and Cantu-Jungles, TM and Tuncil, YE and Nie, X and Kaur, A and Reuhs, BL and Martens, EC and Hamaker, BR},
title = {When simplicity triumphs: niche specialization of gut bacteria exists even for simple fiber structures.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae037},
pmid = {38645272},
issn = {2730-6151},
abstract = {Structurally complex corn bran arabinoxylan (CAX) was used as a model glycan to investigate gut bacteria growth and competition on different AX-based fine structures. Nine hydrolyzate segments of the CAX polymer varying in chemical structure (sugars and linkages), CAX, five less complex non-corn arabinoxylans, and xylose and glucose were ranked from structurally complex to simple. The substrate panel promoted different overall growth and rates of growth of eight Bacteroides xylan-degrading strains. For example, Bacteroides cellulosilyticus DSM 14838 (Bacteroides cellulosilyticus) grew well on an array of complex and simple structures, while Bacteroides ovatus 3-1-23 grew well only on the simple structures. In a competition experiment, B. cellulosilyticus growth was favored over B. ovatus on the complex AX-based structure. On the other hand, on the simple structure, B. ovatus strongly outcompeted B. cellulosilyticus, which was eliminated from the competitive environment by Day 11. This adaptation to fine structure and resulting competition dynamics indicate that dietary fiber chemical structures, whether complex or simple, favor certain gut bacteria. Overall, this work supports a concept that fiber degraders diversify their competitive abilities to access substrates across the spectrum of heterogeneity of fine structural features of dietary fibers.},
}

@article {pmid38645218,
year = {2024},
author = {Moodley, S and Kroon, E and Naidoo, CC and Nyawo, GR and Wu, BG and Naidoo, S and Chiyaka, TL and Tshivhula, H and Singh, S and Li, Y and Warren, RM and Hoal, EG and Schurr, E and Clemente, J and Segal, LN and Möller, M and Theron, G},
title = {Latent tuberculosis infection is associated with an enrichment of short chain fatty acid producing bacteria in the stool of women living with HIV.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {38645218},
abstract = {Background: Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high TB burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI, including in PLHIV. Method : Within a parent study that recruited adult females with HIV from Cape Town, South Africa into predefined age categories (18-25, 35-60 years), we characterised the stool microbiota of those with [interferon- γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST-negative) LTBI (n=25 per group). 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet Multinomial Mixtures, DESeq2 and PICRUSt2. Results: No α- or β-diversity differences occurred by LTBI status; however, LTBI-positives were Faecalibacterium-, Blautia-, Gemmiger-, Bacteroides- enriched and Moryella-, Atopobium-, Corynebacterium-, Streptococcus -depleted. Inferred metagenome data showed LTBI-negative-enriched pathways included several involved in methylglyoxal degradation, L-arginine, putrescine, 4-aminobutanoate degradation and L-arginine and ornithine degradation. Stool from LTBI-positives demonstrated differential taxa abundance based on a quantitative response to antigen stimulation (Acidaminococcus- enrichment and Megamonas -, Alistipes -, and Paraprevotella -depletion associated with higher IGRA or TST responses, respectively). In LTBI-positives, older people had different β-diversities than younger people whereas, in LTBI-negatives, no differences occurred across age groups. Conclusion: Amongst female PLHIV, those with LTBI had, vs. those without LTBI, Faecalibacterium , Blautia , Gemmiger, Bacteriodes -enriched, which are producers of short chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.},
}

@article {pmid38645092,
year = {2024},
author = {Petrone, BL and Bartlett, A and Jiang, S and Korenek, A and Vintila, S and Tenekjian, C and Yancy, WS and David, LA and Kleiner, M},
title = {Metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38645092},
abstract = {Objective biomarkers of food intake are a sought-after goal in nutrition research. Most biomarker development to date has focused on metabolites detected in blood, urine, skin or hair, but detection of consumed foods in stool has also been shown to be possible via DNA sequencing. An additional food macromolecule in stool that harbors sequence information is protein. However, the use of protein as an intake biomarker has only been explored to a very limited extent. Here, we evaluate and compare measurement of residual food-derived DNA and protein in stool as potential biomarkers of intake. We performed a pilot study of DNA sequencing-based metabarcoding (FoodSeq) and mass spectrometry-based metaproteomics in five individuals' stool sampled in short, longitudinal bursts accompanied by detailed diet records (n=27 total samples). Dietary data provided by stool DNA, stool protein, and written diet record independently identified a strong within-person dietary signature, identified similar food taxa, and had significantly similar global structure in two of the three pairwise comparisons between measurement techniques (DNA-to-protein and DNA-to-diet record). Metaproteomics identified proteins including myosin, ovalbumin, and beta-lactoglobulin that differentiated food tissue types like beef from dairy and chicken from egg, distinctions that were not possible by DNA alone. Overall, our results lay the groundwork for development of targeted metaproteomic assays for dietary assessment and demonstrate that diverse molecular components of food can be leveraged to study food intake using stool samples.},
}

@article {pmid38647897,
year = {2022},
author = {Mon, ML and Marrero Díaz de Villegas, R and Campos, E and Soria, MA and Talia, PM},
title = {Characterization of a novel GH10 alkali-thermostable xylanase from a termite microbiome.},
journal = {Bioresources and bioprocessing},
volume = {9},
number = {1},
pages = {84},
pmid = {38647897},
issn = {2197-4365},
support = {PI 102//Instituto Nacional de Tecnología Agropecuaria/ ; 106//Instituto Nacional de Tecnología Agropecuaria/ ; 116//Instituto Nacional de Tecnología Agropecuaria/ ; 149//Instituto Nacional de Tecnología Agropecuaria/ ; 159//Instituto Nacional de Tecnología Agropecuaria/ ; (PICT) 2018-#4149//Agencia Nacional de Promoción Científica y Tecnológica/ ; 2020-#3570//Agencia Nacional de Promoción Científica y Tecnológica/ ; PIP-2021-2561//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; },
abstract = {The aim of the present study was to assess the biochemical and molecular structural characteristics of a novel alkali-thermostable GH10 xylanase (Xyl10B) identified in a termite gut microbiome by a shotgun metagenomic approach. This endoxylanase candidate was amplified, cloned, heterologously expressed in Escherichia coli and purified. The recombinant enzyme was active at a broad range of temperatures (37-60 ºC) and pH values (4-10), with optimal activity at 50 ºC and pH 9. Moreover, its activity remained at more than 80% of its maximum at 50 °C for 8 h. In addition, Xyl10B was found to be stable in the presence of salt and several ions and chemical reagents frequently used in the industry. These characteristics make this enzyme an interesting candidate for pulp and paper bleaching industries, since this process requires enzymes without cellulase activity and resistant to high temperatures and alkaline pH (thermo-alkaliphilic enzymes). The products of xylan hydrolysis by Xyl10B (short xylooligosaccharides, xylose and xylobiose) could be suitable for application as prebiotics and in the production of bioethanol.},
}

@article {pmid38647867,
year = {2022},
author = {Dzulkarnain, ELN and Audu, JO and Wan Dagang, WRZ and Abdul-Wahab, MF},
title = {Microbiomes of biohydrogen production from dark fermentation of industrial wastes: current trends, advanced tools and future outlook.},
journal = {Bioresources and bioprocessing},
volume = {9},
number = {1},
pages = {16},
pmid = {38647867},
issn = {2197-4365},
support = {MyBrainSC scholarship//Ministry of Higher Education, Malaysia/ ; 05G24//Universiti Teknologi Malaysia/ ; 09G86//Universiti Teknologi Malaysia/ ; },
abstract = {Biohydrogen production through dark fermentation is very attractive as a solution to help mitigate the effects of climate change, via cleaner bioenergy production. Dark fermentation is a process where organic substrates are converted into bioenergy, driven by a complex community of microorganisms of different functional guilds. Understanding of the microbiomes underpinning the fermentation of organic matter and conversion to hydrogen, and the interactions among various distinct trophic groups during the process, is critical in order to assist in the process optimisations. Research in biohydrogen production via dark fermentation is currently advancing rapidly, and various microbiology and molecular biology tools have been used to investigate the microbiomes. We reviewed here the different systems used and the production capacity, together with the diversity of the microbiomes used in the dark fermentation of industrial wastes, with a special emphasis on palm oil mill effluent (POME). The current challenges associated with biohydrogen production were also included. Then, we summarised and discussed the different molecular biology tools employed to investigate the intricacy of the microbial ecology associated with biohydrogen production. Finally, we included a section on the future outlook of how microbiome-based technologies and knowledge can be used effectively in biohydrogen production systems, in order to maximise the production output.},
}

@article {pmid38645157,
year = {2024},
author = {Goh, CE and Bohn, B and Genkinger, JM and Molinsky, R and Roy, S and Paster, BJ and Chen, CY and Yuzefpolskaya, M and Colombo, PC and Rosenbaum, M and Knight, R and Desvarieux, M and Papapanou, PN and Jacobs, DR and Demmer, RT},
title = {Dietary nitrate intake and net nitrite-generating capacity of the oral microbiome interact to enhance cardiometabolic health: Results from the Oral Infections Glucose Intolerance and Insulin Resistance Study (ORIGINS).},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.10.24305636},
pmid = {38645157},
abstract = {BACKGROUND: We investigated the association between dietary nitrate intake and early clinical cardiometabolic risk biomarkers, and explored whether the oral microbiome modifies the association between dietary nitrate intake and cardiometabolic biomarkers.

METHODS: Cross-sectional data from 668 (mean [SD] age 31 [9] years, 73% women) participants was analyzed. Dietary nitrate intakes and alternative healthy eating index (AHEI) scores were calculated from food frequency questionnaire responses and a validated US food database. Subgingival 16S rRNA microbial genes (Illumina, MiSeq) were sequenced, and PICRUSt2 estimated metagenomic content. The Microbiome Induced Nitric oxide Enrichment Score (MINES) was calculated as a microbial gene abundance ratio representing enhanced net capacity for NO generation. Cardiometabolic risk biomarkers included systolic and diastolic blood pressure, HbA1c, glucose, insulin, and insulin resistance (HOMA-IR), and were regressed on nitrate intake tertiles in adjusted multivariable linear models.

RESULTS: Mean nitrate intake was 190[171] mg/day. Higher nitrate intake was associated with lower insulin, and HOMA-IR but particularly among participants with low abundance of oral nitrite enriching bacteria. For example, among participants with a low MINES, mean insulin[95%CI] levels in high vs. low dietary nitrate consumers were 5.8[5.3,6.5] vs. 6.8[6.2,7.5] (p=0.004) while respective insulin levels were 6.0[5.4,6.6] vs. 5.9[5.3,6.5] (p=0.76) among partcipants with high MINES (interaction p=0.02).

CONCLUSION: Higher dietary nitrate intake was only associated with lower insulin and insulin resistance among individuals with reduced capacity for oral microbe-induced nitrite enrichment. These findings have implications for future precision medicine-oriented approaches that might consider assessing the oral microbiome prior to enrollment into dietary interventions or making dietary recommendations.

CLINICAL PERSPECTIVE: What is new?: In this population-based study we identified an interaction between dietary nitrate intake and oral nitrite enriching bacteria on cardiometabolic outcomes. Higher dietary nitrate intake was associated with lower insulin and insulin resistance only among participants with low abundance of oral nitrite enriching bacteria. This study suggests that cardiometabolic benefits of nitrate consumption might depend on the host microbiome's capacity to metabolize nitrates.What are the clinical implications?: Among people with low microbiome capacity for nitrate metabolism, higher levels of nitrate might be necessary to realize cardiometabolic benefits.Lack of microbiome assessments in prior studies could partially explain inconsistent findings from previous nitrate supplementation trials and observational studies.Future precision-medicine oriented trials studying the effects of dietary nitrate recommendations on cardiometabolic health, should consider assessing the oral microbiome.},
}

@article {pmid38645133,
year = {2024},
author = {Zelasko, S and Swaney, MH and Sandstrom, S and Davenport, TC and Seroogy, CM and Gern, JE and Kalan, LR and Currie, CR},
title = {Upper respiratory microbial communities of healthy populations are shaped by niche and age.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.14.589416},
pmid = {38645133},
abstract = {BACKGROUND: Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and functioning across healthy 24-month-old infant (n=229) and adult (n=100) populations.

RESULTS: We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity.

CONCLUSIONS: In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functioning, with important implications for host health across the lifespan.},
}

@article {pmid38645126,
year = {2024},
author = {Schmidt, N and Ham, KVD and Bower, L and Li, S and Lorenzi, H and Doumbo, S and Doumtabe, D and Kayentao, K and Ongoiba, A and Traore, B and Crompton, P},
title = {Susceptibility to febrile malaria is associated with an inflammatory gut microbiome.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-3974068/v1},
pmid = {38645126},
abstract = {Malaria is a major public health problem, but many of the factors underlying the pathogenesis of this disease are not well understood. Here, we demonstrate in Malian children that susceptibility to febrile malaria following infection with Plasmodium falciparum is associated with the composition of the gut microbiome prior to the malaria season. Gnotobiotic mice colonized with the fecal samples of malaria-susceptible children had a significantly higher parasite burden following Plasmodium infection compared to gnotobiotic mice colonized with the fecal samples of malaria-resistant children. The fecal microbiome of the susceptible children was enriched for bacteria associated with inflammation, mucin degradation, gut permeability and inflammatory bowel disorders (e.g., Ruminococcus gauvreauii , Ruminococcus torques , Dorea formicigenerans , Dorea longicatena , Lachnoclostridium phocaeense and Lachnoclostridium sp. YL32). However, the susceptible children also had a greater abundance of bacteria known to produce anti-inflammatory short-chain fatty acids and those associated with favorable prognosis and remission following dysbiotic intestinal events (e.g., Anaerobutyricum hallii , Blautia producta and Sellimonas intestinalis). Metabolomics analysis of the human fecal samples corroborated the existence of inflammatory and recovery-associated features within the gut microbiome of the susceptible children. There was an enrichment of nitric oxide-derived DNA adducts (deoxyinosine and deoxyuridine) and long-chain fatty acids, the absorption of which has been shown to be inhibited by inflamed intestinal epithelial cells, and a decrease in the abundance of mucus phospholipids. Nevertheless, there were also increased levels of pseudouridine and hypoxanthine, which have been shown to be regulated in response to cellular stress and to promote recovery following injury or hypoxia. Overall, these results indicate that the gut microbiome may contribute malaria pathogenesis and suggest that therapies targeting intestinal inflammation could decrease malaria susceptibility.},
}

@article {pmid38645104,
year = {2024},
author = {Holcomb, M and Marshall, A and Flinn, H and Lozano, M and Soriano, S and Gomez-Pinilla, F and Treangen, TJ and Villapol, S},
title = {Probiotic treatment causes sex-specific neuroprotection after traumatic brain injury in mice.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4196801/v1},
pmid = {38645104},
abstract = {Background Recent studies have shed light on the potential role of gut dysbiosis in shaping traumatic brain injury (TBI) outcomes. Changes in the levels and types of Lactobacillus bacteria present might impact the immune system disturbances, neuroinflammatory responses, anxiety and depressive-like behaviors, and compromised neuroprotection mechanisms triggered by TBI. Objective This study aimed to investigate the effects of a daily pan-probiotic (PP) mixture in drinking water containing strains of Lactobacillus plantarum, L. reuteri, L. helveticus, L. fermentum, L. rhamnosus, L. gasseri , and L. casei , administered for either two or seven weeks before inducing TBI on both male and female mice. Methods Mice were subjected to controlled cortical impact (CCI) injury. Short-chain fatty acids (SCFAs) analysis was performed for metabolite measurements. The taxonomic profiles of murine fecal samples were evaluated using 16S rRNA V1-V3 sequencing analysis. Histological analyses were used to assess neuroinflammation and gut changes post-TBI, while behavioral tests were conducted to evaluate sensorimotor and cognitive functions. Results Our findings suggest that PP administration modulates the diversity and composition of the microbiome and increases the levels of SCFAs in a sex-dependent manner. We also observed a reduction of lesion volume, cell death, and microglial and macrophage activation after PP treatment following TBI in male mice. Furthermore, PP-treated mice show motor function improvements and decreases in anxiety and depressive-like behaviors. Conclusion Our findings suggest that PP administration can mitigate neuroinflammation and ameliorate motor and anxiety and depressive-like behavior deficits following TBI. These results underscore the potential of probiotic interventions as a viable therapeutic strategy to address TBI-induced impairments, emphasizing the need for gender-specific treatment approaches.},
}

@article {pmid38645042,
year = {2024},
author = {Scheible, K and Beblavy, R and Sohn, MB and Qui, X and Gill, AL and Narvaez-Miranda, J and Brunner, J and Miller, RK and Barrett, ES and O'Connor, TG and Gill, SR},
title = {Affective Symptoms in Pregnancy are Associated with the Vaginal Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.12.589254},
pmid = {38645042},
abstract = {UNLABELLED: Composition of the vaginal microbiome in pregnancy is associated with adverse maternal, obstetric, and child health outcomes. Identifying the sources of individual differences in the vaginal microbiome is therefore of considerable clinical and public health interest. The current study tested the hypothesis that vaginal microbiome composition during pregnancy is associated with an individual's experience of affective symptoms and stress exposure. Data were based on a prospective longitudinal study of a diverse and medically healthy community sample of 275 mother-infant pairs. Affective symptoms and stress exposure and select measures of associated biomarkers (diurnal salivary cortisol, serum measures of sex hormones) were collected at each trimester; self-report, clinical, and medical records were used to collect detailed data on socio-demographic factors and health behavior, including diet and sleep. Vaginal microbiome samples were collected in the third trimester (34-40 weeks) and characterized by 16S rRNA sequencing. Identified taxa were clustered into three community state types (CST1-3) based on dissimilarity of vaginal microbiota composition. Results indicate that depressive symptoms during pregnancy were reliably associated with individual taxa and CST3 in the third trimester. Prediction of functional potential from 16S taxonomy revealed a differential abundance of metabolic pathways in CST1-3 and individual taxa, including biosynthetic pathways for the neuroactive metabolites, serotonin and dopamine. With the exception of bioavailable testosterone, no significant associations were found between symptoms- and stress-related biomarkers and CSTs. Our results provide further evidence of how prenatal psychological distress during pregnancy alters the maternal-fetal microbiome ecosystem that may be important for understanding maternal and child health outcomes.

IMPORTANCE: Prenatal affective symptoms and stress are associated with maternal, obstetric, and child health outcomes, but the mechanisms underlying these links and their application to intervention remain unclear. The findings from this investigation extend prior microbiome-oriented research by demonstrating that the maternal vaginal microbiome composition has a biologically plausible mechanistic link with affective symptoms that also suggest additional clinical applications for assessment and intervention.},
}

@article {pmid38644496,
year = {2024},
author = {Gaston, JM and Alm, EJ and Zhang, AN},
title = {Fast and accurate variant identification tool for sequencing-based studies.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {90},
pmid = {38644496},
issn = {1741-7007},
support = {6934500//Massachusetts Institute of Technology/ ; },
mesh = {*SARS-CoV-2/genetics ; *INDEL Mutation ; Computational Biology/methods ; Humans ; Software ; COVID-19/virology ; High-Throughput Nucleotide Sequencing/methods ; Point Mutation ; Genetic Variation ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Accurate identification of genetic variants, such as point mutations and insertions/deletions (indels), is crucial for various genetic studies into epidemic tracking, population genetics, and disease diagnosis. Genetic studies into microbiomes often require processing numerous sequencing datasets, necessitating variant identifiers with high speed, accuracy, and robustness.

RESULTS: We present QuickVariants, a bioinformatics tool that effectively summarizes variant information from read alignments and identifies variants. When tested on diverse bacterial sequencing data, QuickVariants demonstrates a ninefold higher median speed than bcftools, a widely used variant identifier, with higher accuracy in identifying both point mutations and indels. This accuracy extends to variant identification in virus samples, including SARS-CoV-2, particularly with significantly fewer false negative indels than bcftools. The high accuracy of QuickVariants is further demonstrated by its detection of a greater number of Omicron-specific indels (5 versus 0) and point mutations (61 versus 48-54) than bcftools in sewage metagenomes predominated by Omicron variants. Much of the reduced accuracy of bcftools was attributable to its misinterpretation of indels, often producing false negative indels and false positive point mutations at the same locations.

CONCLUSIONS: We introduce QuickVariants, a fast, accurate, and robust bioinformatics tool designed for identifying genetic variants for microbial studies. QuickVariants is available at https://github.com/caozhichongchong/QuickVariants .},
}

*SARS-CoV-2/genetics
*INDEL Mutation
Computational Biology/methods
Humans
Software
COVID-19/virology
High-Throughput Nucleotide Sequencing/methods
Point Mutation
Genetic Variation
Sequence Analysis, DNA/methods

@article {pmid38644373,
year = {2024},
author = {Niccolai, E and Pedone, M and Martinelli, I and Nannini, G and Baldi, S and Simonini, C and Di Gloria, L and Zucchi, E and Ramazzotti, M and Spezia, PG and Maggi, F and Quaranta, G and Masucci, L and Bartolucci, G and Stingo, FC and Mandrioli, J and Amedei, A},
title = {Amyotrophic lateral sclerosis stratification: unveiling patterns with virome, inflammation, and metabolism molecules.},
journal = {Journal of neurology},
volume = {},
number = {},
pages = {},
pmid = {38644373},
issn = {1432-1459},
support = {Grant-No. RF-2016-02361616//Ministero della Salute/ ; Grant no. B008-P00634//University of Florence/ ; },
abstract = {Amyotrophic lateral sclerosis (ALS) is an untreatable and clinically heterogeneous condition primarily affecting motor neurons. The ongoing quest for reliable biomarkers that mirror the disease status and progression has led to investigations that extend beyond motor neurons' pathology, encompassing broader systemic factors such as metabolism, immunity, and the microbiome. Our study contributes to this effort by examining the potential role of microbiome-related components, including viral elements, such as torque tenovirus (TTV), and various inflammatory factors, in ALS. In our analysis of serum samples from 100 ALS patients and 34 healthy controls (HC), we evaluated 14 cytokines, TTV DNA load, and 18 free fatty acids (FFA). We found that the evaluated variables are effective in differentiating ALS patients from healthy controls. In addition, our research identifies four unique patient clusters, each characterized by distinct biological profiles. Intriguingly, no correlations were found with site of onset, sex, progression rate, phenotype, or C9ORF72 expansion. A remarkable aspect of our findings is the discovery of a gender-specific relationship between levels of 2-ethylhexanoic acid and patient survival. In addition to contributing to the growing body of evidence suggesting altered peripheral immune responses in ALS, our exploratory research underscores metabolic diversity challenging conventional clinical classifications. If our exploratory findings are validated by further research, they could significantly impact disease understanding and patient care customization. Identifying groups based on biological profiles might aid in clustering patients with varying responses to treatments.},
}

@article {pmid38644360,
year = {2024},
author = {Oh, EJ and Jang, HH and Park, S and Lim, HP and Yun, KD and Jang, W and Kim, OS and Park, C and Won, EJ},
title = {Fretibacterium Species to Fusobacterium periodonticum Ratio as a Potential Biomarker of Periodontitis Based on Salivary Microbiome Profiling.},
journal = {Annals of laboratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.3343/alm.2024.0043},
pmid = {38644360},
issn = {2234-3814},
}

@article {pmid38644048,
year = {2024},
author = {Wielkopolan, B and Szabelska-Beręsewicz, A and Gawor, J and Obrępalska-Stęplowska, A},
title = {Cereal leaf beetle-associated bacteria enhance the survival of their host upon insecticide treatments and respond differently to insecticides with different modes of action.},
journal = {Environmental microbiology reports},
volume = {16},
number = {2},
pages = {e13247},
pmid = {38644048},
issn = {1758-2229},
support = {UMO-2020/37/N/NZ9/02577//Polish National Science Centre/ ; },
mesh = {Animals ; *Insecticides/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Larva/microbiology/drug effects ; *Coleoptera/microbiology/drug effects ; RNA, Ribosomal, 16S/genetics ; Microbiota/drug effects ; Metagenomics ; Pyrethrins/pharmacology ; Chlorpyrifos ; Pantoea/genetics/drug effects ; },
abstract = {The cereal leaf beetle (CLB, Oulema melanopus) is one of the major cereal pests. The effect of insecticides belonging to different chemical classes, with different mechanisms of action and the active substances' concentrations on the CLB bacterial microbiome, was investigated. Targeted metagenomic analysis of the V3-V4 regions of the 16S ribosomal gene was used to determine the composition of the CLB bacterial microbiome. Each of the insecticides caused a decrease in the abundance of bacteria of the genus Pantoea, and an increase in the abundance of bacteria of the genus Stenotrophomonas, Acinetobacter, compared to untreated insects. After cypermethrin application, a decrease in the relative abundance of bacteria of the genus Pseudomonas was noted. The dominant bacterial genera in cypermethrin-treated larvae were Lactococcus, Pantoea, while in insects exposed to chlorpyrifos or flonicamid it was Pseudomonas. Insecticide-treated larvae were characterized, on average, by higher biodiversity and richness of bacterial genera, compared to untreated insects. The depletion of CLB-associated bacteria resulted in a decrease in larval survival, especially after cypermethrin and chlorpyrifos treatments. The use of a metagenome-based functional prediction approach revealed a higher predicted function of bacterial acetyl-CoA C-acetyltransferase in flonicamid and chlorpyrifos-treated larvae and tRNA dimethyltransferase in cypermethrin-treated insects than in untreated insects.},
}

Animals
*Insecticides/pharmacology
*Bacteria/genetics/classification/drug effects/isolation & purification
*Larva/microbiology/drug effects
*Coleoptera/microbiology/drug effects
RNA, Ribosomal, 16S/genetics
Microbiota/drug effects
Metagenomics
Pyrethrins/pharmacology
Chlorpyrifos
Pantoea/genetics/drug effects

@article {pmid38643860,
year = {2024},
author = {Xian, M and Ma, Z and Zhan, S and Shen, L and Li, T and Lin, H and Huang, M and Cai, J and Hu, T and Liang, J and Liang, S and Wang, S},
title = {Network analysis of microbiome and metabolome to explore the mechanism of raw rhubarb in the protection against ischemic stroke via microbiota-gut-brain axis.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {105969},
doi = {10.1016/j.fitote.2024.105969},
pmid = {38643860},
issn = {1873-6971},
abstract = {Ischemic stroke (IS) has attracted worldwide attention due to the high mortality and disability rate. Raw rhubarb (RR) is a traditional medicinal plant and whole-food that has been used in China for its various pharmacological activities, such as antioxidant and anti-inflammatory properties. Recent pharmacological research has shown the role of RR against IS, but its mechanism of action remains unclear, particularly in the context of the brain-gut axis. To address this gap in knowledge, the present study was conducted in the middle cerebral artery occlusion/reperfusion (MCAO/R) model with the aim of investigating the effects of RR on regulating the intestinal microbiota barrier and metabolism and thereby reducing inflammatory response so as to improve the IS. The results showed that pre-treatment of RR attenuated cerebral infarct area and inflammation response in MCAO rats. Furthermore, RR also improved intestinal barrier function, including the integrity and permeability of the intestinal barrier. Additionally, RR intervention significantly attenuated gut microbiota dysbiosis caused by ischemic stroke, especially the increased Firmicutes. Notably, the pseudo-germ-free (PGF) rats further demonstrated that the anti-stroke effect of RR might rely on intestinal microbiota. In addition, the UPLC/Q-Orbitrap-MS-Based metabolomics revealed the disrupted metabolic profiles caused by MCAO/R, and a total of 11 differential metabolites were modulated by RR administration, especially bile acids. Further correlation analysis and network pharmacology analysis also demonstrated a strong association between specific bacteria, such as Firmicutes and bile acids. In conclusion, our work demonstrated that RR could effectively ameliorate ischemic stroke by modulating the microbiota and metabolic disorders.},
}

@article {pmid38643839,
year = {2024},
author = {Chen, Z and Huang, L},
title = {Fusobacterium nucleatum carcinogenesis and drug delivery interventions.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115319},
doi = {10.1016/j.addr.2024.115319},
pmid = {38643839},
issn = {1872-8294},
abstract = {The microbiome has emerged as a significant biomarker and modulator in cancer development and treatment response. Recent research highlights the notable role of Fusobacterium nucleatum (F. nucleatum) in various tumor types, including breast, colorectal, esophageal, gastric, pancreatic, and lung cancers. Accumulating evidence suggests that the local microbial community forms an integral component of the tumor microenvironment, with bacterial communities within tumors displaying specificity to tumor types. Mechanistic investigations indicate that tumor-associated microbiota can directly influence tumor initiation, progression, and responses to chemotherapy or immunotherapy. This article presents a comprehensive review of microbial communities especially F. nucleatum in tumor tissue, exploring their roles and underlying mechanisms in tumor development, treatment, and prevention. When the tumor-associated F. nucleatum is killed, the host immune response is activated to recognize tumor cells. Bacteria epitopes restricted by the host antigens, can be identified for future anti-bacteria/tumor vaccine development.},
}

@article {pmid38643622,
year = {2024},
author = {Hwang, O and Emmett, B and Andersen, D and Howe, A and Ro, K and Trabue, S},
title = {Effects of swine manure dilution with lagoon effluent on microbial communities and odor formation in pit recharge systems.},
journal = {Journal of environmental management},
volume = {358},
number = {},
pages = {120884},
doi = {10.1016/j.jenvman.2024.120884},
pmid = {38643622},
issn = {1095-8630},
abstract = {Pit recharge systems (PRS) control odor by managing organic solids in swine manure. However, there needs to be more understanding of PRS's effect on the microbiome composition and its impact on odor formation. A study was conducted to understand how recharge intervals used in PRS impact manure microbiome and odor formation. Bioreactors dynamically loaded simulated recharge intervals of 14, 10, and 4 days by diluting swine manure with lagoon effluent at varying ratios. Treatment ratios tested included 10:0 (control), 7:3 (typical Korean PRS), 5:5 (enhanced PRS #1), and 2:8 (enhanced PRS #2). Manure microbial membership, chemical concentrations, and odorant concentrations were used to identify the interactions between microbiota, manure, and odor. The initial microbial community structure was controlled by dilution ratio and manure barn source material. Firmicutes and Proteobacteria were the dominant microbial phyla in manure and lagoon effluent, respectively, and significantly decreased or increased with dilution. Key microbial species were Clostridium saudiense in manure and Pseudomonas caeni in lagoon effluent. Percentages of these species declined by 8.9% or increased by 17.6%, respectively, with each unit dilution. Microbial community composition was controlled by both treatment (i.e., manure dilution ratio and barn source material) and environmental factors (i.e., solids and pH). Microbiome composition was correlated with manure odor formation profiles, but this effect was inseparable from environmental factors, which explained over 75% of the variance in odor profiles. Consequently, monitoring solids and pH in recharge waters will significantly impact odor control in PRS.},
}

@article {pmid38643472,
year = {2024},
author = {Kerekes, IK and Nagy, Á and Ősz, Á and Zalka, P},
title = {[Examination possibilities of microbial nucleic acid samples derived from the environment].},
journal = {Orvosi hetilap},
volume = {165},
number = {16},
pages = {613-619},
doi = {10.1556/650.2024.33025},
pmid = {38643472},
issn = {1788-6120},
mesh = {Humans ; *Nucleic Acids/analysis ; Environmental Microbiology ; },
}

Humans
*Nucleic Acids/analysis
Environmental Microbiology

@article {pmid38643372,
year = {2024},
author = {Hu, J and Bi, R and Luo, Y and Wu, K and Jin, S and Liu, Z and Jia, Y and Mao, CX},
title = {The gut microbiome promotes locomotion of Drosophila larvae via octopamine signaling.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.13370},
pmid = {38643372},
issn = {1744-7917},
support = {31500839//National Natural Science Foundation of China/ ; 81871121//National Natural Science Foundation of China/ ; },
abstract = {The gut microbiome is a key partner of animals, influencing various aspects of their physiology and behaviors. Among the diverse behaviors regulated by the gut microbiome, locomotion is vital for survival and reproduction, although the underlying mechanisms remain unclear. Here, we reveal that the gut microbiome modulates the locomotor behavior of Drosophila larvae via a specific neuronal type in the brain. The crawling speed of germ-free (GF) larvae was significantly reduced compared to the conventionally reared larvae, while feeding and excretion behaviors were unaffected. Recolonization with Acetobacter and Lactobacillus can fully and partially rescue the locomotor defects in GF larvae, respectively, probably due to the highest abundance of Acetobacter as a symbiotic bacterium in the larval gut, followed by Lactobacillus. Moreover, the gut microbiome promoted larval locomotion, not by nutrition, but rather by enhancing the brain levels of tyrosine decarboxylase 2 (Tdc2), which is an enzyme that synthesizes octopamine (OA). Overexpression of Tdc2 rescued locomotion ability in GF larvae. These findings together demonstrate that the gut microbiome specifically modulates larval locomotor behavior through the OA signaling pathway, revealing a new mechanism underlying larval locomotion regulated by the gut microbiome.},
}

@article {pmid38643366,
year = {2024},
author = {Lei, C and Xu, Y and Zhang, S and Huang, C and Qin, J},
title = {The role of microbiota in gastric cancer: A comprehensive review.},
journal = {Helicobacter},
volume = {29},
number = {2},
pages = {e13071},
doi = {10.1111/hel.13071},
pmid = {38643366},
issn = {1523-5378},
mesh = {Humans ; *Stomach Neoplasms ; *Helicobacter pylori ; *Helicobacter Infections ; *Microbiota ; Risk Factors ; },
abstract = {BACKGROUND: Gastric cancer (GC) continues to pose a significant global threat in terms of cancer-related fatalities. Despite notable advancements in medical research and therapies, further investigation is warranted to elucidate its underlying etiology and risk factors. Recent times have witnessed an escalated emphasis on comprehending the role of the microbiota in cancer development.

METHODS: This review briefly delves into recent developments in microbiome-related research pertaining to gastric cancer.

RESULTS: According to studies, the microbiota can influence GC growth by inciting inflammation, disrupting immunological processes, and generating harmful microbial metabolites. Furthermore, there is ongoing research into how the microbiome can impact a patient's response to chemotherapy and immunotherapy.

CONCLUSION: The utilization of the microbiome for detecting, preventing, and managing stomach cancer remains an active area of exploration.},
}

Humans
*Stomach Neoplasms
*Helicobacter pylori
*Helicobacter Infections
*Microbiota
Risk Factors

@article {pmid38643272,
year = {2024},
author = {Hauptfeld, E and Pappas, N and van Iwaarden, S and Snoek, BL and Aldas-Vargas, A and Dutilh, BE and von Meijenfeldt, FAB},
title = {Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3373},
pmid = {38643272},
issn = {2041-1723},
mesh = {*Metagenome/genetics ; Software ; Algorithms ; *Microbiota/genetics ; Metagenomics ; },
abstract = {Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.},
}

*Metagenome/genetics
Software
Algorithms
*Microbiota/genetics
Metagenomics

@article {pmid38643212,
year = {2024},
author = {Ren, M and Pan, H and Zhou, X and Yu, M and Ji, F},
title = {Alterations of the duodenal mucosal microbiome in patients with metabolic dysfunction-associated steatotic liver disease.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9124},
pmid = {38643212},
issn = {2045-2322},
support = {2019C03031//Key Research and Development Program of Zhejiang Province/ ; 82370571//National Natural Science Foundation of China/ ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Metabolic Diseases ; Duodenum ; *Microbiota ; *Non-alcoholic Fatty Liver Disease ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as nonalcoholic fatty liver disease (NAFLD), is associated with altered gut microbiota; however, there has been a focus on fecal samples, which are not representative of the entire digestive tract. Mucosal biopsies of the descending duodenum were collected. Five regions of the 16S rRNA gene were amplified and sequenced. Other assessments conducted on the study subjects included body mass index, transient elastography, liver enzymes, and lipid profile. Fifty-one subjects (36 with MASLD and 15 controls) were evaluated. There was no significant difference between the two groups regarding alpha- or beta-diversity of the duodenal mucosal microbiota. Linear discriminant analysis effect size (LEfSe) analysis showed that the genera Serratia and Aggregatibacter were more abundant in the duodenal mucosa of patients with MASLD, whereas the duodenal mucosal microbiota of the healthy controls was enriched with the genus Petrobacter. PICRUSt2 analysis revealed that genes associated with amino acid degradation and carboxylate degradation were significantly enriched in the duodenal mucosal microbiota of patients with MASLD. Our findings reveal the duodenal mucosal microbiota in patients with MASLD, which could contribute to future studies investigating the causal relationship between duodenal microbiota and MASLD.},
}

Humans
RNA, Ribosomal, 16S/genetics
*Metabolic Diseases
Duodenum
*Microbiota
*Non-alcoholic Fatty Liver Disease

@article {pmid38643180,
year = {2024},
author = {Ramaboli, MC and Ocvirk, S and Khan Mirzaei, M and Eberhart, BL and Valdivia-Garcia, M and Metwaly, A and Neuhaus, K and Barker, G and Ru, J and Nesengani, LT and Mahdi-Joest, D and Wilson, AS and Joni, SK and Layman, DC and Zheng, J and Mandal, R and Chen, Q and Perez, MR and Fortuin, S and Gaunt, B and Wishart, D and Methé, B and Haller, D and Li, JV and Deng, L and Swart, R and O'Keefe, SJD},
title = {Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3379},
pmid = {38643180},
issn = {2041-1723},
support = {R01 CA204403/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Humans ; Urbanization ; South Africa/epidemiology ; Cross-Sectional Studies ; Diet ; Metabolome ; *Gastrointestinal Microbiome ; Diet, Western ; *Colorectal Neoplasms/epidemiology/microbiology ; Feces/microbiology ; *Southern African People ; },
abstract = {Transition from traditional high-fiber to Western diets in urbanizing communities of Sub-Saharan Africa is associated with increased risk of non-communicable diseases (NCD), exemplified by colorectal cancer (CRC) risk. To investigate how urbanization gives rise to microbial patterns that may be amenable by dietary intervention, we analyzed diet intake, fecal 16 S bacteriome, virome, and metabolome in a cross-sectional study in healthy rural and urban Xhosa people (South Africa). Urban Xhosa individuals had higher intakes of energy (urban: 3,578 ± 455; rural: 2,185 ± 179 kcal/d), fat and animal protein. This was associated with lower fecal bacteriome diversity and a shift from genera favoring degradation of complex carbohydrates (e.g., Prevotella) to taxa previously shown to be associated with bile acid metabolism and CRC. Urban Xhosa individuals had higher fecal levels of deoxycholic acid, shown to be associated with higher CRC risk, but similar short-chain fatty acid concentrations compared with rural individuals. Fecal virome composition was associated with distinct gut bacterial communities across urbanization, characterized by different dominant host bacteria (urban: Bacteriodota; rural: unassigned taxa) and variable correlation with fecal metabolites and dietary nutrients. Food and skin microbiota samples showed compositional differences along the urbanization gradient. Rural-urban dietary transition in South Africa is linked to major changes in the gut microbiome and metabolome. Further studies are needed to prove cause and identify whether restoration of specific components of the traditional diet will arrest the accelerating rise in NCDs in Sub-Saharan Africa.},
}

Animals
Humans
Urbanization
South Africa/epidemiology
Cross-Sectional Studies
Diet
Metabolome
*Gastrointestinal Microbiome
Diet, Western
*Colorectal Neoplasms/epidemiology/microbiology
Feces/microbiology
*Southern African People

@article {pmid38643126,
year = {2024},
author = {Xiao, W and Chen, YL and Du, LY and Wu, J and Wang, Z and Mao, B and Wen, FQ and Gibson, PG and McDonald, VM and Yu, H and Fu, JJ},
title = {Bacterial interactome disturbance in chronic obstructive pulmonary disease clinical stability and exacerbations.},
journal = {Respiratory research},
volume = {25},
number = {1},
pages = {173},
pmid = {38643126},
issn = {1465-993X},
support = {No.82100046//National Natural Science Foundation of China/ ; No.81870014//National Natural Science Foundation of China/ ; 2023NSFSC1460//Sichuan Science and Technology Program of China/ ; 2020YFS0145//Sichuan Science and Technology Program of China/ ; },
mesh = {Humans ; *Dysbiosis ; *Pulmonary Disease, Chronic Obstructive/drug therapy ; Lung ; Haemophilus ; Sputum/microbiology ; Disease Progression ; },
abstract = {RATIONALE: Our understanding of airway dysbiosis in chronic obstructive pulmonary disease (COPD) remains incomplete, which may be improved by unraveling the complexity in microbial interactome.

OBJECTIVES: To characterize reproducible features of airway bacterial interactome in COPD at clinical stability and during exacerbation, and evaluate their associations with disease phenotypes.

METHODS: We performed weighted ensemble-based co-occurrence network analysis of 1742 sputum microbiomes from published and new microbiome datasets, comprising two case-control studies of stable COPD versus healthy control, two studies of COPD stability versus exacerbation, and one study with exacerbation-recovery time series data.

RESULTS: Patients with COPD had reproducibly lower degree of negative bacterial interactions, i.e. total number of negative interactions as a proportion of total interactions, in their airway microbiome compared with healthy controls. Evaluation of the Haemophilus interactome showed that the antagonistic interaction networks of this established pathogen rather than its abundance consistently changed in COPD. Interactome dynamic analysis revealed reproducibly reduced antagonistic interactions but not diversity loss during COPD exacerbation, which recovered after treatment. In phenotypic analysis, unsupervised network clustering showed that loss of antagonistic interactions was associated with worse clinical symptoms (dyspnea), poorer lung function, exaggerated neutrophilic inflammation, and higher exacerbation risk. Furthermore, the frequent exacerbators (≥ 2 exacerbations per year) had significantly reduced antagonistic bacterial interactions while exhibiting subtle compositional changes in their airway microbiota.

CONCLUSIONS: Bacterial interactome disturbance characterized by reduced antagonistic interactions, rather than change in pathogen abundance or diversity, is a reproducible feature of airway dysbiosis in COPD clinical stability and exacerbations, which suggests that we may target interactome rather than pathogen alone for disease treatment.},
}

Humans
*Dysbiosis
*Pulmonary Disease, Chronic Obstructive/drug therapy
Lung
Haemophilus
Sputum/microbiology
Disease Progression

@article {pmid38643115,
year = {2024},
author = {Ren, Y and Ma, Q and Zeng, X and Huang, C and Tan, S and Fu, X and Zheng, C and You, F and Li, X},
title = {Saliva‑microbiome‑derived signatures: expected to become a potential biomarker for pulmonary nodules (MCEPN-1).},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {132},
pmid = {38643115},
issn = {1471-2180},
mesh = {Humans ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Biomarkers ; *Lung Neoplasms/diagnosis/genetics ; Oxidoreductases ; },
abstract = {BACKGROUND: Oral microbiota imbalance is associated with the progression of various lung diseases, including lung cancer. Pulmonary nodules (PNs) are often considered a critical stage for the early detection of lung cancer; however, the relationship between oral microbiota and PNs remains unknown.

METHODS: We conducted a 'Microbiome with pulmonary nodule series study 1' (MCEPN-1) where we compared PN patients and healthy controls (HCs), aiming to identify differences in oral microbiota characteristics and discover potential microbiota biomarkers for non-invasive, radiation-free PNs diagnosis and warning in the future. We performed 16 S rRNA amplicon sequencing on saliva samples from 173 PN patients and 40 HCs to compare the characteristics and functional changes in oral microbiota between the two groups. The random forest algorithm was used to identify PN salivary microbial markers. Biological functions and potential mechanisms of differential genes in saliva samples were preliminarily explored using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Groups (COG) analyses.

RESULTS: The diversity of salivary microorganisms was higher in the PN group than in the HC group. Significant differences were noted in community composition and abundance of oral microorganisms between the two groups. Neisseria, Prevotella, Haemophilus and Actinomyces, Porphyromonas, Fusobacterium, 7M7x, Granulicatella and Selenomonas were the main differential genera between the PN and HC groups. Fusobacterium, Porphyromonas, Parvimonas, Peptostreptococcus and Haemophilus constituted the optimal marker sets (area under curve, AUC = 0.80), which can distinguish between patients with PNs and HCs. Further, the salivary microbiota composition was significantly correlated with age, sex, and smoking history (P < 0.001), but not with personal history of cancer (P > 0.05). Bioinformatics analysis of differential genes showed that patients with PN showed significant enrichment in protein/molecular functions related to immune deficiency and energy metabolisms, such as the cytoskeleton protein RodZ, nicotinamide adenine dinucleotide phosphate dehydrogenase (NADPH) dehydrogenase, major facilitator superfamily transporters and AraC family transcription regulators.

CONCLUSIONS: Our study provides the first evidence that the salivary microbiota can serve as potential biomarkers for identifying PN. We observed a significant association between changes in the oral microbiota and PNs, indicating the potential of salivary microbiota as a new non-invasive biomarker for PNs.

TRIAL REGISTRATION: Clinical trial registration number: ChiCTR2200062140; Date of registration: 07/25/2022.},
}

Humans
Saliva/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Biomarkers
*Lung Neoplasms/diagnosis/genetics
Oxidoreductases

@article {pmid38643067,
year = {2024},
author = {Zhu, Q and Li, MX and Yu, MC and Ma, QW and Huang, MJ and Lu, CW and Chen, CB and Chung, WH and Chang, CJ},
title = {Altered microbiome of serum exosomes in patients with acute and chronic cholecystitis.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {133},
pmid = {38643067},
issn = {1471-2180},
support = {CMRPG1E0908 and CMRPG1E0907, CMRPG1E0905//Scientific Research Project of Xiamen Chang Gung Hospital/ ; 3502Z20224ZD1135, 3502Z20224ZD113, 3502Z20224ZD1132//Xiamen Science and Technology Project Fund/ ; CMRPG1E0886, CGMH-XMCG-2022-002//CGMH-XMCG Joint Research Program/ ; GMRPG1E0221, 2020D021//Fujian Provincial Department of Science and Technology/ ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Exosomes ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Microbiota/genetics ; *Cholecystitis ; *Cholecystitis, Acute ; },
abstract = {BACKGROUND: This study aimed to investigate the differences in the microbiota composition of serum exosomes from patients with acute and chronic cholecystitis.

METHOD: Exosomes were isolated from the serum of cholecystitis patients through centrifugation and identified and characterized using transmission electron microscopy and nano-flow cytometry. Microbiota analysis was performed using 16S rRNA sequencing.

RESULTS: Compared to patients with chronic cholecystitis, those with acute cholecystitis exhibited lower richness and diversity. Beta diversity analysis revealed significant differences in the microbiota composition between patients with acute and chronic cholecystitis. The relative abundance of Proteobacteria was significantly higher in exosomes from patients with acute cholecystitis, whereas Actinobacteria, Bacteroidetes, and Firmicutes were significantly more abundant in exosomes from patients with chronic cholecystitis. Furthermore, functional predictions of microbial communities using Tax4Fun analysis revealed significant differences in metabolic pathways such as amino acid metabolism, carbohydrate metabolism, and membrane transport between the two patient groups.

CONCLUSIONS: This study confirmed the differences in the microbiota composition within serum exosomes of patients with acute and chronic cholecystitis. Serum exosomes could serve as diagnostic indicators for distinguishing acute and chronic cholecystitis.},
}

Humans
RNA, Ribosomal, 16S/genetics
*Exosomes
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Microbiota/genetics
*Cholecystitis
*Cholecystitis, Acute

@article {pmid38642914,
year = {2024},
author = {Todor, LA and Hill, DM},
title = {Retrospective analysis of pathogens for guided creation of an EMPIRic antibiotic prEscribing pathway (EMPIRE).},
journal = {Journal of burn care & research : official publication of the American Burn Association},
volume = {},
number = {},
pages = {},
doi = {10.1093/jbcr/irae069},
pmid = {38642914},
issn = {1559-0488},
abstract = {The objective of this study was to evaluate the susceptibilities of pathogens isolated from cultures within the first 7 days of admission to the burn center and in the absence of healthcare-associated infection risk factors (HAIRF) to determine if current empiric antibiotics can be narrowed for refinement of an empiric antibiotic prescribing pathway according to suspected source. A 3-year sample of patients and cultures was utilized in hopes of obtaining at least 30 isolates of the most common pathogens and their respective susceptibilities. Two-hundred and sixty-eight clinically-relevant (e.g., deemed infectious, versus colonization) pathogens were included in the final sample with sources including wounds, respiratory, blood, urine, and bone. Of the 268 pathogens included, 45% were Gram-negative and 69% of all pathogens were isolated from wound cultures. The existing empiric pathway, vancomycin plus cefepime, covered 98% and 84% of all Gram-positive and Gram-negative pathogens, respectively. In patients without HAIRF, coverage rose to 98% and 90%, respectively. Initial use of vancomycin and cefepime remains adequate for pathogens isolated within one week of admission in patients without HAIRF. For pneumonias, a narrower spectrum beta-lactam would not sufficiently cover respiratory pathogens isolated within the first week of admission. Regarding early wound infections, difficult-to-treat pathogens remain as a rare isolate of wound cultures within one week of admission.},
}

@article {pmid38642761,
year = {2024},
author = {Wu, WF and Li, XY and Chen, SC and Jin, BJ and Wu, CY and Li, G and Sun, CL and Zhu, YG and Lin, XY},
title = {Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172622},
doi = {10.1016/j.scitotenv.2024.172622},
pmid = {38642761},
issn = {1879-1026},
abstract = {The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.},
}

@article {pmid38642533,
year = {2024},
author = {Xiong, S and Xu, X and Du, T and Liu, Q and Huang, T and Ren, H and Xiong, T and Xie, M},
title = {Organic acids drove the microbiota succession and consequently altered the flavor quality of Laotan Suancai across fermentation rounds: Insights from the microbiome and metabolome.},
journal = {Food chemistry},
volume = {450},
number = {},
pages = {139335},
doi = {10.1016/j.foodchem.2024.139335},
pmid = {38642533},
issn = {1873-7072},
abstract = {Laotan Suancai, a popular traditional Chinese fermented vegetable, is manufactured in the industry via four fermentation rounds. However, the differences in flavor quality of Laotan Suancai from the four fermentation rounds and the causes of this variation remain unclear. Metabolome analysis indicated that the different content of five taste compounds and 31 aroma compounds caused the differences in flavor quality among the variated fermentation rounds of Laotan Suancai. Amplicon sequencing indicated that the microbial succession exhibited a certain pattern during four fermentation rounds and further analysis unveiled that organic acids drove the microbiota shift to more acid-resistant populations. Spearman correlation analysis highlighted that seven core microbes may be involved in the formation of differential flavor and the corresponding metabolic pathways were reconstructed by function prediction. Our findings offer a novel perspective on comprehending the deterioration of flavor quality across the fermentation rounds of Laotan Suancai.},
}

@article {pmid38642506,
year = {2024},
author = {Hao, Y and Lu, C and Xiang, Q and Sun, A and Su, JQ and Chen, QL},
title = {Unveiling the overlooked microbial niches thriving on building exteriors.},
journal = {Environment international},
volume = {187},
number = {},
pages = {108649},
doi = {10.1016/j.envint.2024.108649},
pmid = {38642506},
issn = {1873-6750},
abstract = {Rapid urbanization in the Asia-Pacific region is expected to place two-thirds of its population in concrete-dominated urban landscapes by 2050. While diverse architectural facades define the unique appearance of these urban systems. There remains a significant gap in our understanding of the composition, assembly, and ecological potential of microbial communities on building exteriors. Here, we examined bacterial and protistan communities on building surfaces along an urbanization gradient (urban, suburban and rural regions), investigating their spatial patterns and the driving factors behind their presence. A total of 55 bacterial and protist phyla were identified. The bacterial community was predominantly composed of Proteobacteria (33.7% to 67.5%). The protistan community exhibited a prevalence of Opisthokonta and Archaeplastida (17.5% to 82.1% and 1.8% to 61.2%, respectively). The composition and functionality of bacterial communities exhibited spatial patterns correlated with urbanization. In urban buildings, factors such as facade type, light exposure, and building height had comparatively less impact on bacterial composition compared to suburban and rural areas. The highest bacterial diversity and lowest Weighted Average Community Identity (WACI) were observed on suburban buildings, followed by rural buildings. In contrast, protists did not show spatial distribution characteristics related to facade type, light exposure, building height and urbanization level. The distinct spatial patterns of protists were primarily shaped by community diffusion and the bottom-up regulation exerted by bacterial communities. Together, our findings suggest that building exteriors serve as attachment points for local microbial metacommunities, offering unique habitats where bacteria and protists exhibit independent adaptive strategies closely tied to the overall ecological potential of the community.},
}

@article {pmid38642272,
year = {2024},
author = {Chen, LA and Boyle, K},
title = {The Role of the Gut Microbiome in Health and Disease in the Elderly.},
journal = {Current gastroenterology reports},
volume = {},
number = {},
pages = {},
pmid = {38642272},
issn = {1534-312X},
abstract = {PURPOSE OF REVIEW: Growing evidence supports the contribution of age in the composition and function of the gut microbiome, with specific findings associated with health in old age and longevity.

RECENT FINDINGS: Current studies have associated certain microbiota, such as Butyricimonas, Akkermansia, and Odoribacter, with healthy aging and the ability to survive into extreme old age. Furthermore, emerging clinical and pre-clinical research have shown promising mechanisms for restoring a healthy microbiome in elderly populations through various interventions such as fecal microbiota transplant (FMT), dietary interventions, and exercise programs. Despite several conceptually exciting interventional studies, the field of microbiome research in the elderly remains limited. Specifically, large longitudinal studies are needed to better understand causative relationships between the microbiome and healthy aging. Additionally, individualized approaches to microbiome interventions based on patients' co-morbidities and the underlying functional capacity of their microbiomes are needed to achieve optimal results.},
}

@article {pmid38642195,
year = {2024},
author = {Tampanna, N and Chansuwan, W and Wichienchot, S},
title = {Effect of Plant-Based Mung Bean Products on Digestibility and Gut Microbiome Profiling Using In Vitro Fecal Fermentation.},
journal = {Plant foods for human nutrition (Dordrecht, Netherlands)},
volume = {},
number = {},
pages = {},
pmid = {38642195},
issn = {1573-9104},
support = {AGR6505031M//the National Science, Research and Innovation Fund (NSRF) and the Prince of Songkla University/ ; },
abstract = {The concept of plant-based protein consumption has been increasing recently because of the growing health consciousness among people. Mung bean is one of the most consumed legumes with a dense nutrient profile. Hence, current research is aimed to study the effect of mung bean protein-based products including mung bean snack (MBS) and textured vegetable protein (TVP) for treatment groups against the control groups, commercial ingredients group consisting of mung bean powder (MBP) and pea powder (PP) and commercial products group include commercial pea texture (cPT) and commercial textured vegetable protein (cTVP) for their proximate composition, digestibility, gut microbial profile and fatty acid metabolite profiling. The MBS and TVP samples had significantly higher digestibility of 74.43% and 73.24% than the commercial products. The protein content of TVP was 0.8 times higher than its commercial control. Gut microbiome profiling showed that all the samples shared around 162 similar genera. Post-fermentation analysis provided promising results by reflecting the growth of beneficial bacteria (Parabacteroides, Bifidobacterium and Lactobacillus) and the suppression of pathogens (Escherichia-Shigella, Dorea and Klebsiella). The dual relationship between gut microbiota and nutrient interaction proved the production of abundant short- and branched-chain fatty acids. The MBS sample was able to produce SCFAs (41.27 mM) significantly and BCFAs (2.02 mM) than the TVP sample (27.58 mM and 2.14 mM, respectively). Hence, our research outcomes proved that the mung bean protein-based products might infer numerous health benefits to the host due to enriched probiotics in the gut and the production of their corresponding metabolites.},
}

@article {pmid38642188,
year = {2024},
author = {Liu, Y and Lin, H and Zhong, W and Zeng, Y and Zhou, G and Chen, Z and Huang, S and Zhang, L and Liu, X},
title = {Multi-omics analysis of immune-related microbiome and prognostic model in head and neck squamous cell carcinoma.},
journal = {Clinical oral investigations},
volume = {28},
number = {5},
pages = {263},
pmid = {38642188},
issn = {1436-3771},
support = {8217102092//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Prognosis ; Squamous Cell Carcinoma of Head and Neck ; Multiomics ; *Microbiota ; *Head and Neck Neoplasms ; },
abstract = {OBJECTIVES: The aim of our study is to explore the transcriptional and microbial characteristics of head and neck cancer's immune phenotypes using a multi-omics approach.

MATERIALS AND METHODS: Employing TCGA data, we analyzed head and neck squamous cell carcinoma (HNSCC) immune cells with CIBERSORT and identified differentially expressed genes using DESeq2. Microbial profiles, obtained from the TCMA database, were analyzed using LEfSe algorithm to identify differential microbes in immune cell infiltration (ICI) subgroups. Random Forest algorithm and deep neural network (DNN) were employed to select microbial features and developed a prognosis model.

RESULTS: We categorized HNSCC into three immune subtypes, finding ICI-2 with the worst prognosis and distinct microbial diversity. Our immune-related microbiome (IRM) model outperformed the TNM staging model in predicting survival, linking higher IRM model scores with poorer prognosis, and demonstrating clinical utility over TNM staging. Patients categorized as low-risk by the IRM model showed higher sensitivity to cisplatin and sorafenib treatments.

CONCLUSIONS: This study offers a comprehensive exploration of the ICI landscape in HNSCC. We provide a detailed scenario of immune regulation in HNSCC and report a correlation between differing ICI patterns, intratumor microbiome, and prognosis. This research aids in identifying prime candidates for optimizing treatment strategies in HNSCC.

CLINICAL RELEVANCE: This study revealed the microbial signatures associated with immunophenotyping of HNSCC and further found the microbial signatures associated with prognosis. The prognostic model based on IRM microbes is helpful for early prediction of patient prognosis and assisting clinical decision-making.},
}

Humans
Prognosis
Squamous Cell Carcinoma of Head and Neck
Multiomics
*Microbiota
*Head and Neck Neoplasms

@article {pmid38642171,
year = {2024},
author = {Araujo, TT and Dionizio, A and Carvalho, TS and Boas Feitosa, CMV and Vertuan, M and Câmara, JVF and Henrique-Silva, F and Marchetto, R and Chiaratti, MR and Santos, AC and Alves, LO and Ferro, M and Buzalaf, MAR},
title = {Acquired enamel pellicle and biofilm engineering with a combination of acid-resistant proteins (CaneCPI-5, StN15, and Hemoglobin) for enhanced protection against dental caries - in vivo and in vitro investigations.},
journal = {Clinical oral investigations},
volume = {28},
number = {5},
pages = {261},
pmid = {38642171},
issn = {1436-3771},
support = {2019/08032-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/26070-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 302371/2018-4 ; 304554/2023-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Humans ; Dental Pellicle/chemistry/microbiology ; *Dental Caries/prevention & control ; Proteomics ; Biofilms ; Hemoglobins/analysis ; *Tooth Demineralization/prevention & control ; },
abstract = {OBJECTIVE: This study was designed in two-legs. In the in vivo, we explored the potential of a rinse solution containing a combination (Comb) of 0.1 mg/mL CaneCPI-5 (sugarcane-derive cystatin), 1.88 × 10[- 5]M StN15 (statherin-derived peptide) and 1.0 mg/mL hemoglobin (Hb) to change the protein profile of the acquired enamel pellicle(AEP) and the microbiome of the enamel biofilm. The in vitro, was designed to reveal the effects of Comb on the viability and bacterial composition of the microcosm biofilm, as well as on enamel demineralization.

MATERIALS AND METHODS: In vivo study, 10 participants rinsed (10mL,1 min) with either deionized water (H2O-control) or Comb. AEP and biofilm were collected after 2 and 3 h, respectively, after rinsing. AEP samples underwent proteomics analysis, while biofilm microbiome was assessed via 16 S-rRNA Next Generation Sequencing(NGS). In vitro study, a microcosm biofilm protocol was employed. Ninety-six enamel specimens were treated with: 1)Phosphate-Buffered Solution-PBS(negative-control), 2)0.12%Chlorhexidine, 3)500ppmNaF and 4)Comb. Resazurin, colony-forming-units(CFU) and Transversal Microradiography(TMR) were performed.

RESULTS: The proteomic results revealed higher quantity of proteins in the Comb compared to control associated with immune system response and oral microbial adhesion. Microbiome showed a significant increase in bacteria linked to a healthy microbiota, in the Comb group. In the in vitro study, Comb group was only efficient in reducing mineral-loss and lesion-depth compared to the PBS.

CONCLUSIONS: The AEP modification altered the subsequent layers, affecting the initial process of bacterial adhesion of pathogenic and commensal bacteria, as well as enamel demineralization.

CLINICAL RELEVANCE: Comb group shows promise in shaping oral health by potentially introducing innovative approaches to prevent enamel demineralization and deter tooth decay.},
}

Humans
Dental Pellicle/chemistry/microbiology
*Dental Caries/prevention & control
Proteomics
Biofilms
Hemoglobins/analysis
*Tooth Demineralization/prevention & control

@article {pmid38641855,
year = {2024},
author = {Coskun, M and Babayeva, A and Barlas, T and Yalcin, MM and Akturk, M and Toruner, F and Karakoc, MA and Karakan, T and Cindoruk, M and Yetkin, İ and Altinova, A},
title = {EXPRESS: Relationship between Gut Microbiome and Bone Deficits in Primary Hyperparathyroidism: A Proof of Concept Pilot Study.},
journal = {Journal of investigative medicine : the official publication of the American Federation for Clinical Research},
volume = {},
number = {},
pages = {10815589241251695},
doi = {10.1177/10815589241251695},
pmid = {38641855},
issn = {1708-8267},
abstract = {Parathyroid hormone (PTH) interacts with components of the gut microbiota to exert its bone-regulating effects. This study aimed to investigate the gut microbial composition in patients with primary hyperparathyroidism (PHPT). Nine patients with PHPT and nine age-sex and body mass index-matched healthy controls were included. Gut microbial composition was assessed using 16S rRNA gene amplicon sequencing in both groups at baseline and one month after parathyroidectomy in the PHPT group. Data were imported into QIIME-2 and both QIIME-2 and R packages were used for microbiome analysis. Alpha and beta diversity were similar between the groups and remained unchanged after parathyroidectomy. The relative abundance of Subdoligranulum was significantly higher, whereas Ruminococcus, Alloprevotella, Phascolarctobacterium and Clostridium sensu stricto_1 were significantly lower in PHPT than in controls (p<0.001). After parathyroidectomy, the relative abundance of Subdoligranulum decreased, Ruminococcus and Alloprevotella increased (p<0.001). The PHPT group had lower total femoral and lumbar bone mineral density (BMD) than the controls (p<0.05). At baseline, Alloprevotella abundance was positively correlated with serum phosphorus and Subdoligranulum was positively correlated with total lumbar BMD. Clostridium sensu stricto_1 was negatively correlated with serum calcium and positively correlated with femoral neck BMD. Postoperatively, Alloprevotella was positively correlated with baseline serum phosphorus, and Phascolarctobacterium was positively correlated with distal radius BMD. This study demonstrated that the diversity of the gut microbiome was altered, possibly in response to electrolyte changes in PHPT, both before and after parathyroidectomy.},
}

@article {pmid38641815,
year = {2024},
author = {Liu, Z and Zhang, D and Chen, S},
title = {Unveiling the gastric microbiota: implications for gastric carcinogenesis, immune responses, and clinical prospects.},
journal = {Journal of experimental & clinical cancer research : CR},
volume = {43},
number = {1},
pages = {118},
pmid = {38641815},
issn = {1756-9966},
support = {82074074//National Natural Science Foundation of China/ ; 82104447//National Natural Science Foundation of China/ ; 81874353//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota ; *Stomach Neoplasms/pathology ; Carcinogenesis ; *Helicobacter pylori ; Immunity ; },
abstract = {High-throughput sequencing has ushered in a paradigm shift in gastric microbiota, breaking the stereotype that the stomach is hostile to microorganisms beyond H. pylori. Recent attention directed toward the composition and functionality of this 'community' has shed light on its potential relevance in cancer. The microbial composition in the stomach of health displays host specificity which changes throughout a person's lifespan and is subject to both external and internal factors. Distinctive alterations in gastric microbiome signature are discernible at different stages of gastric precancerous lesions and malignancy. The robust microbes that dominate in gastric malignant tissue are intricately implicated in gastric cancer susceptibility, carcinogenesis, and the modulation of immunosurveillance and immune escape. These revelations offer fresh avenues for utilizing gastric microbiota as predictive biomarkers in clinical settings. Furthermore, inter-individual microbiota variations partially account for differential responses to cancer immunotherapy. In this review, we summarize current literature on the influence of the gastric microbiota on gastric carcinogenesis, anti-tumor immunity and immunotherapy, providing insights into potential clinical applications.},
}

Humans
*Microbiota
*Stomach Neoplasms/pathology
Carcinogenesis
*Helicobacter pylori
Immunity

@article {pmid38641475,
year = {2024},
author = {Addison, SL and Rúa, MA and Smaill, SJ and Singh, BK and Wakelin, SA},
title = {Partner or perish: tree microbiomes and climate change.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2024.03.008},
pmid = {38641475},
issn = {1878-4372},
abstract = {Understanding the complex relationships between plants, their microbiomes, and environmental changes is crucial for improving growth and survival, especially for long-lived tree species. Trees, like other plants, maintain close associations with a multitude of microorganisms on and within their tissues, forming a 'holobiont'. However, a comprehensive framework for detailed tree-microbiome dynamics, and the implications for climate adaptation, is currently lacking. This review identifies gaps in the existing literature, emphasizing the need for more research to explore the coevolution of the holobiont and the full extent of climate change impact on tree growth and survival. Advancing our knowledge of plant-microbial interactions presents opportunities to enhance tree adaptability and mitigate adverse impacts of climate changes on trees.},
}

@article {pmid38641252,
year = {2024},
author = {Liu, B and Mashimo, C and Nambu, T and Maruyama, H and Okinaga, T},
title = {Transposon insertion in Rothia dentocariosa.},
journal = {Journal of oral biosciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.job.2024.04.006},
pmid = {38641252},
issn = {1880-3865},
abstract = {OBJECTIVES: Rothia spp. are emerging as significant bacteria associated with oral health, with Rothia dentocariosa being one of the most prevalent species. However, there is a lack of studies examining these properties at the genetic level. This study aimed to establish a genetic modification platform for R. dentocariosa.

METHODS: Rothia spp. were isolated from saliva samples collected from healthy volunteers. Subsequently, R. dentocariosa strains were identified through colony morphology, species-specific polymerase chain reaction (PCR), and 16S ribosomal RNA gene sequencing. The identified strains were then transformed with plasmid pJRD215, and the most efficient strain was selected. Transposon insertion mutagenesis was performed to investigate the possibility of genetic modifications.

RESULTS: A strain demonstrating high transforming ability, designated as R. dentocariosa LX16, was identified. This strain underwent transposon insertion mutagenesis and was screened for 5-fluoroorotic acid-resistant transposants. The insertion sites were confirmed using arbitrary primed PCR, gene-specific PCR, and Sanger sequencing.

CONCLUSION: This study marks the first successful genetic modification of R. dentocariosa. Investigating R. dentocariosa at the genetic level can provide insights into its role within the oral microbiome.},
}

@article {pmid38641145,
year = {2024},
author = {Saeid, AB and De Rubis, G and Williams, KA and Yeung, S and Chellappan, DK and Singh, SK and Gupta, G and Hansbro, PM and Shahbazi, MA and Gulati, M and Kaur, IP and Santos, HA and Paudel, KR and Dua, K},
title = {Revolutionising Lung Health: Exploring the Latest Breakthroughs and Future Prospects of Synbiotic Nanostructures in Lung Diseases.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {111009},
doi = {10.1016/j.cbi.2024.111009},
pmid = {38641145},
issn = {1872-7786},
abstract = {The escalating prevalence of lung diseases underscores the need for innovative therapies. Dysbiosis in human body microbiome has emerged as a significant factor in these diseases, indicating a potential role for synbiotics in restoring microbial equilibrium. However, effective delivery of synbiotics to the target site remains challenging. Here, we aim to explore suitable nanoparticles for encapsulating synbiotics tailored for applications in lung diseases. Nanoencapsulation has emerged as a prominent strategy to address the delivery challenges of synbiotics in this context. Through a comprehensive review, we assess the potential of nanoparticles in facilitating synbiotic delivery and their structural adaptability for this purpose. Our review reveals that nanoparticles such as nanocellulose, starch, and chitosan exhibit high potential for synbiotic encapsulation. These offer flexibility in structure design and synthesis, making them promising candidates for addressing delivery challenges in lung diseases. Furthermore, our analysis highlights that synbiotics, when compared to probiotics alone, demonstrate superior anti-inflammatory, antioxidant, antibacterial and anticancer activities. This review underscores the promising role of nanoparticle-encapsulated synbiotics as a targeted and effective therapeutic approach for lung diseases, contributing valuable insights into the potential of nanomedicine in revolutionizing treatment strategies for respiratory conditions, ultimately paving the way for future advancements in this field.},
}

@article {pmid38641112,
year = {2024},
author = {Meng, J and Xu, F and Yang, H and Li, X and Zhao, P},
title = {Exploring microbiome and plankton responses and interactions in the mangrove ecosystem through eDNA and network analysis.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172581},
doi = {10.1016/j.scitotenv.2024.172581},
pmid = {38641112},
issn = {1879-1026},
abstract = {The comprehensive analysis of multiple biological communities is essential for assessing diversities within mangrove ecosystems, yet such studies are infrequent. Environmental DNA (eDNA) facilitates the simultaneous exploration of organisms across various levels within a single ecosystem. In this investigation, 16S rRNA, cytochrome C oxidase I (COI), and Mito-fish primers were employed to characterize the microbiome, eukaryotic plankton, and fish communities, along with their intricate interactions, across 24 samples from three Chinese mangrove reservoirs. The resulting dataset encompasses 3779 taxonomic groups (genus level), spanning from the microbiome to vertebrates. Diversity analysis unveiled a higher level of stability in the microbiome community compared to plankton, underscoring the superior site-specificity of plankton. The association analysis revealed that biodiversity was primarily affected by temperature, turbidity, and fluorescent dissolved organic matter (fDOM). Notably, the physicochemical factors, turbidity, and fDOM had a more pronounced impact on the microbiome than on plankton, explaining their distinct sensitivities to site-specific conditions. Network analysis constructed 15 biological interaction subnetworks representing various community connections. The most connected genera in each subnetwork, highly responsive to different environmental factors, could serve as potential indicators of distinct ecosystem states. In summary, our findings represent the first comparison of the response sensitivities of different communities and the construction of their interaction networks in mangrove environments. These results contribute valuable insights into marine ecosystem dynamics and the role of environmental factors in shaping biodiversity.},
}

@article {pmid38641088,
year = {2024},
author = {Jain, N},
title = {The molecular interplay between human and bacterial amyloids: Implications in neurodegenerative diseases.},
journal = {Biochimica et biophysica acta. Proteins and proteomics},
volume = {1872},
number = {4},
pages = {141018},
doi = {10.1016/j.bbapap.2024.141018},
pmid = {38641088},
issn = {1878-1454},
abstract = {Neurodegenerative disorders such as Parkinson's (PD) and Alzheimer's diseases (AD) are linked with the assembly and accumulation of proteins into structured scaffold called amyloids. These diseases pose significant challenges due to their complex and multifaceted nature. While the primary focus has been on endogenous amyloids, recent evidence suggests that bacterial amyloids may contribute to the development and exacerbation of such disorders. The gut-brain axis is emerging as a communication pathway between bacterial and human amyloids. This review delves into the novel role and potential mechanism of bacterial amyloids in modulating human amyloid formation and the progression of AD and PD.},
}

@article {pmid38641025,
year = {2024},
author = {Chakraborty, P and Gamage, HKAH and Laird, AS},
title = {Butyrate as a potential therapeutic agent for neurodegenerative disorders.},
journal = {Neurochemistry international},
volume = {},
number = {},
pages = {105745},
doi = {10.1016/j.neuint.2024.105745},
pmid = {38641025},
issn = {1872-9754},
abstract = {Maintaining an optimum microbial community within the gastrointestinal tract is intricately linked to human metabolic, immune and brain health. Disturbance to these microbial populations perturbs the production of vital bioactive compounds synthesised by the gut microbiome, such as short-chain fatty acids (SCFAs). Of the SCFAs, butyrate is known to be a major source of energy for colonocytes and has valuable effects on the maintenance of intestinal epithelium and blood brain barrier integrity, gut motility and transit, anti-inflammatory effects, and autophagy induction. Inducing endogenous butyrate production is likely to be beneficial for gut-brain homeostasis and for optimal neuronal function. For these reasons, butyrate has gained interest as a potential therapy for not only metabolic and immunological disorders, but also conditions related to the brain, including neurodegenerative diseases. While direct and indirect sources of butyrate, including prebiotics, probiotics, butyrate pro-drugs and glucosidase inhibitors, offer a promising therapeutic avenue, their efficacy and dosage in neurodegenerative conditions remain largely unknown. Here, we review current literature on effects of butyrate relevant to neuronal function, the impact of butyrate in a range of neurodegenerative diseases and related treatments that may have potential for the treatment of neurodegenerative diseases.},
}

@article {pmid38640799,
year = {2024},
author = {Jin, X and Pan, J and Zhang, C and Cao, X and Wang, C and Yue, L and Li, X and Liu, Y and Wang, Z},
title = {Toxic mechanism in Daphnia magna due to phthalic acid esters and CuO nanoparticles co-exposure: The insight of physiological, microbiomic and metabolomic profiles.},
journal = {Ecotoxicology and environmental safety},
volume = {277},
number = {},
pages = {116338},
doi = {10.1016/j.ecoenv.2024.116338},
pmid = {38640799},
issn = {1090-2414},
abstract = {Various phthalic acid esters (PAEs) such as dibutyl phthalate (DBP) and butyl benzyl phthalate (BBP) co-exist with nanopollutants in aquatic environment. In this study, Daphnia magna was exposed to nano-CuO and DBP or BBP at environmental relevant concentrations for 21-days to investigate these combined toxic effects. Acute EC50 values (48 h) of nano-CuO, DBP, and BBP were 12.572 mg/L, 8.978 mg/L, and 4.785 mg/L, respectively. Results showed that co-exposure with nano-CuO (500 μg/L) for 21 days significantly enhanced the toxicity of DBP (100 μg/L) and BBP (100 μg/L) to Daphnia magna by 18.37% and 18.11%, respectively. The activities of superoxide dismutase, catalase, and glutathione S-transferase were enhanced by 10.95% and 14.07%, 25.63% and 25.91%, and 39.93% and 35.01% in nano-CuO+DBP and nano-CuO+BBP treatments as compared to the individual exposure groups, verifying that antioxidative defense responses were activated. Furthermore, the co-exposure of nano-CuO and PAEs decreased the population richness and diversity microbiota, and changed the microbial community composition in Daphnia magna. Metabolomic analysis elucidated that nano-CuO + PAEs exposure induced stronger disturbance on metabolic network and molecular function, including amino acid, nucleotides, and lipid metabolism-related metabolic pathways, as comparison to PAEs single exposure treatments. In summary, the integration of physiological, microflora, and untargeted metabolomics analysis offers a fresh perspective into the potential ecological risk associated with nanopollutants and phthalate pollution in aquatic ecosystems.},
}

@article {pmid38640559,
year = {2024},
author = {Muttaleb Asfoor, H and Saied Hamied, A},
title = {Immune response to colonization of Candida albicans in mice treated with Cefoperazone.},
journal = {Cytokine},
volume = {179},
number = {},
pages = {156611},
doi = {10.1016/j.cyto.2024.156611},
pmid = {38640559},
issn = {1096-0023},
abstract = {Candida species are a normal human flora in humans' digestive and reproductive systems, oral cavity, skin, and mucosal surfaces. This study aimed to detect the immunological role of Candida infection by using some immunological markers. The results of levels in serum showed high concentrations of IgA (56.20 ± 12 pg/ml,29.55 ± 4.5 pg/ml respectively) and IgG (12.05 ± 3.218 pg/ml, 3.836 ± 1.23 pg/ml respectively) in mice infected with C. albicans and mice treated with Cefoperazone and infected with Candida with significant differences (P value < 0.05). The results showed high serum levels of IL-17(191.5 ± 42.81 pg/ml) and TLR2(7.651 ± 1.5 pg/ml) in group mice infected with C. albicans compared with negative control and group mice treated with Cefoperazone. Also, high levels of IL-17 (91.33 ± 4.816 pg/ml) and TLR2 (2.630 ± 0.5 pg/ml) in group mice treated with Cefoperazone and infected with Candida compared with negative control and group mice treated with Cefoperazone (P value < 0.05). The results of antibodies and immunological markers in the intestine showed high levels of IgA and IgG in mice infected with C.albicans (55.7 ± 4.9 pg/ml, 18.19 ± 0.63 pg/ml respectively).Also,IgA and IgG in mice treated with Cefoperazone and infected with Candida were high level (43.04 ± 2.1 pg/ml, 2.927 ± 0.2 pg/ml respectively) in mice infected with C. albicans with significant differences (P value < 0.05). The results levels of IL-17 and TLR2 were increased in mice infected with C. albicans (191.5 ± 42.81 pg/ml, 7.651 ± 1.5 pg/ml respectively) and mice treated with Cefoperazone and infected with Candida (91.33 ± 4.816 pg/ml,2.630 ± 0.5 pg/ml respectively) with significant differences (P < 0.05). In conclusion, this study demonstrated that cefoperazone treatment and infection by Candida albicans changed the microbiome components in the gut and finally can change host immune responses. It was observed that elevated levels of the antibodies production (IgA and IgG) and immunological markers (IL-17, and TLR2) in serum and the gut.},
}

@article {pmid38640440,
year = {2024},
author = {Bosch, J and Dobbler, PT and Větrovský, T and Tláskal, V and Baldrian, P and Brabcová, V},
title = {Decomposition of Fomes fomentatius fruiting bodies - transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {5},
pages = {},
pmid = {38640440},
issn = {1574-6941},
support = {21-09334 J//Czech Science Foundation/ ; },
mesh = {Animals ; *Arthropods ; *Coriolaceae ; *Microbiota/genetics ; *Ascomycota ; Fruiting Bodies, Fungal ; Bacteria/genetics ; },
abstract = {Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbial community associated with healthy living and decomposing F. fomentarius fruiting bodies to assess the functional potential of the fruiting body-associated microbiome and to determine the main players involved in fruiting body decomposition. F. fomentarius sequences in the metagenomes were replaced by bacterial sequences as the fruiting body decomposed. Most CAZymes expressed in decomposing fruiting bodies targeted components of the fungal cell wall with almost all chitin-targeting sequences, plus a high proportion of beta-glucan-targeting sequences, belonging to Arthropoda. We suggest that decomposing fruiting bodies of F. fomentarius represent a habitat rich in bacteria, while its decomposition is primarily driven by Arthropoda. Decomposing fruiting bodies thus represent a specific habitat supporting both microorganisms and microfauna.},
}

Animals
*Arthropods
*Coriolaceae
*Microbiota/genetics
*Ascomycota
Fruiting Bodies, Fungal
Bacteria/genetics

@article {pmid38640403,
year = {2024},
author = {Ekpruke, CD and Alford, R and Parker, E and Silveyra, P},
title = {Gonadal sex and chromosome complement influence the gut microbiome in a mouse model of allergic airway inflammation.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00003.2024},
pmid = {38640403},
issn = {1531-2267},
support = {R01HL159764//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R03HL141618//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; },
abstract = {Evidence abounds that gut microbiome components are associated with sex disparities in the immune system. However, it remains unclear whether the observed sex disparity in asthma incidence is associated with sex-dependent differences in immune-modulating gut microbiota, and/or its influence on allergic airway inflammatory processes. Using a mouse model of house dust mite (HDM)-induced allergic inflammation and the four core genotypes (FCG) model, we have previously reported sex differences in lung inflammatory phenotypes. Here, we investigated associations of gut microbiomes to these phenotypes by challenging FCG mice (XXM, XXF, XYM, XYF, n=7/group) withHDM (25 μg) or PBS intranasally for 5 weeks and collecting fecal samples. We extracted fecal DNA and analyzed the 16S microbiome via Targeted Metagenomic Sequencing. We compared alpha and beta diversity across genotypes and assessed the Firmicutes/Bacteroidetes ratio (F/B). When comparing baseline and after exposure for the FCG, we found that the gut F/B was only increased in the XXM genotype. We also found that alpha diversity was significantly increased in all FCG mice upon HDM challenge, with the highest increase in the XXF, and the lowest in the XXM genotypes. Similarly, beta diversity of the microbial community was also affected by challenge in a gonad- and chromosome-dependent manner. In summary, our results indicated that HDM treatment, gonads, and sex chromosomes significantly influence the gut microbial community composition. We concluded that allergic lung inflammation may be affected by the gut microbiome in a sex-dependent manner involving both hormonal and genetic influences.},
}

@article {pmid38639049,
year = {2024},
author = {Peng, Z and Zhang, J and Zhang, M and Yin, L and Zhou, Z and Lv, C and Wang, Z and Tang, J},
title = {Tryptophan metabolites relieve intestinal Candida albicans infection by altering the gut microbiota to reduce IL-22 release from group 3 innate lymphoid cells of the colon lamina propria.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo00432a},
pmid = {38639049},
issn = {2042-650X},
abstract = {Invasive candidiasis may be caused by Candida albicans (C. albicans) colonization of the intestinal tract. Preventing intestinal damage caused by Candida albicans infection and protecting intestinal barrier function have become a critical issue. Integrated analyses of the microbiome with metabolome revealed a remarkable shift of the gut microbiota and tryptophan metabolites, kynurenic acid (KynA), and indolacrylic acid (IA) in mice infected with C. albicans. The transcriptome sequencing indicated that differentially expressed genes were significantly associated with innate immune responses and inflammatory responses. The results of this study suggest that KynA and IA (KI) can alleviate intestinal damage caused by Candida albicans infection in mice by reducing intestinal permeability, increasing intestinal firmness, alleviating intestinal inflammation, and reducing the secretion of interleukin-22 (IL-22) in the 3 groups of colon innate lymphoid cells (ILC3). We performed a fecal microbiota transplantation (FMT) experiment and found that the intestinal barrier function, inflammation, and IL-22 secretion of ILC3 in the colon lamina propria of the recipient mice subjected to C. albicans infection and KI treatment were consistent with the trends of the donor mice. Our results suggest that tryptophan metabolites may directly regulate colon lamina ILC3 to promote intestinal resistance to C. albicans invasion, or indirectly regulate the ILC3 secretion of IL-22 to play a protective role in the intestinal barrier by affecting intestinal microorganisms, which may become a potential target for alleviating intestine borne C. albicans infection.},
}

@article {pmid38638911,
year = {2024},
author = {Wan, S and You, P and Shi, Q and Hu, H and Zhang, L and Chen, L and Wu, Z and Lin, S and Song, X and Luo, Y and Wang, Y and Ju, F and Jin, D and Chen, Y},
title = {Gut microbiome changes in mouse, Mongolian gerbil, and hamster models following Clostridioides difficile challenge.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1368194},
pmid = {38638911},
issn = {1664-302X},
abstract = {INTRODUCTION: Clostridioides difficile infection (CDI), as well as its etiology and pathogenesis, have been extensively investigated. However, the absence of suitable CDI animal models that reflect CDI symptoms and the associated gut microbiome changes in humans has limited research progress in this field. Thus, we aimed to investigate whether Mongolian gerbils, which present a range of human pathological conditions, can been used in studies on CDI. Methods: In this study, we infected Mongolian gerbils and two existing CDI model animals, mice and hamsters, with the hypervirulent ribotype 027 C. difficile strain, and comparatively analyzed changes in their gut microbiome composition via 16S rRNA gene sequencing.

METHODS: In this study, we infected Mongolian gerbils and two existing CDI model animals, mice and hamsters, with the hypervirulent ribotype 027 C. difficile strain, and comparatively analyzed changes in their gut microbiome composition via 16S rRNA gene sequencing.

RESULTS: The results obtained showed that C. difficile colonized the gastrointestinal tracts of the three rodents, and after the C. difficile challenge, C57BL/6J mice did not manifest CDI symptoms and their intestines showed no significant pathological changes. However, the hamsters showed explosive intestinal bleeding and inflammation and the Mongolian gerbils presented diarrhea as well as increased infiltration of inflammatory cells, mucus secretion, and epithelial cell shedding in their intestinal tissue. Further, intestinal microbiome analysis revealed significant differences with respect to intestinal flora abundance and diversity. Specifically, after C. difficile challenge, the Firmicutes/Bacteroidetes ratio decreased for C57BL/6J mice, but increased significantly for Mongolian gerbils and hamsters. Furthermore, the abundance of Proteobacteria increased in all three models, especially in hamsters, while that of Verrucomicrobia only increased significantly in C57BL/6J mice and Mongolian gerbils. Our results also indicated that differences in the relative abundances of Lactobacillaceae and Akkermansia were primarily responsible for the observed differences in response to C. difficile challenge.

CONCLUSION: Based on the observed responses to C. difficile challenge, we concluded for the first time that the Mongolian gerbil could be used as an animal model for CDI. Additionally, the taxa identified in this study may be used as biomarkers for further studies on CDI and to improve understanding regarding changes in gut microbiome in CDI-related diseases.},
}

@article {pmid38638909,
year = {2024},
author = {Santangelo, BE and Apgar, M and Colorado, ASB and Martin, CG and Sterrett, J and Wall, E and Joachimiak, MP and Hunter, LE and Lozupone, CA},
title = {Integrating biological knowledge for mechanistic inference in the host-associated microbiome.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1351678},
pmid = {38638909},
issn = {1664-302X},
abstract = {Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.},
}

@article {pmid38638907,
year = {2024},
author = {Huang, F and Lyu, B and Xie, F and Li, F and Xing, Y and Han, Z and Lai, J and Ma, J and Zou, Y and Zeng, H and Xu, Z and Gao, P and Luo, Y and Bolund, L and Tong, G and Fengping, X},
title = {From gut to liver: unveiling the differences of intestinal microbiota in NAFL and NASH patients.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1366744},
pmid = {38638907},
issn = {1664-302X},
abstract = {Non-alcoholic fatty liver disease (NAFLD) is increasingly recognized for its global prevalence and potential progression to more severe liver diseases such as non-alcoholic steatohepatitis (NASH). The gut microbiota plays a pivotal role in the pathogenesis of NAFLD, yet the detailed characteristics and ecological alterations of gut microbial communities during the progression from non-alcoholic fatty liver (NAFL) to NASH remain poorly understood. Methods: In this study, we conducted a comparative analysis of gut microbiota composition in individuals with NAFL and NASH to elucidate differences and characteristics. We utilized 16S rRNA sequencing to compare the intestinal gut microbiota among a healthy control group (65 cases), NAFL group (64 cases), and NASH group (53 cases). Random forest machine learning and database validation methods were employed to analyze the data. Results: Our findings indicate a significant decrease in the diversity of intestinal flora during the progression of NAFLD (p < 0.05). At the phylum level, high abundances of Bacteroidetes and Fusobacteria were observed in both NAFL and NASH patients, whereas Firmicutes were less abundant. At the genus level, a significant decrease in Prevotella expression was seen in the NAFL group (AUC 0.738), whereas an increase in the combination of Megamonas and Fusobacterium was noted in the NASH group (AUC 0.769). Furthermore, KEGG pathway analysis highlighted significant disturbances in various types of glucose metabolism pathways in the NASH group compared to the NAFL group, as well as notably compromised flavonoid and flavonol biosynthesis functions. The study uncovers distinct microbiota characteristics and microecological changes within the gut during the transition from NAFL to NASH, providing insights that could facilitate the discovery of novel biomarkers and therapeutic targets for NAFLD.},
}

@article {pmid38638900,
year = {2024},
author = {Yang, W and Li, X and Yan, H and Sun, Y and Wu, D and Du, Y and Luo, Y},
title = {Recruitment of beneficial cucumber rhizosphere microbes mediated by amino acid secretion induced by biocontrol Bacillus subtilis isolate 1JN2.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1379566},
pmid = {38638900},
issn = {1664-302X},
abstract = {INTRODUCTION: At present, the use of beneficial microorganisms to control cucumber Fusarium wilt is a widely used method, and the rhizosphere microecological reset is one of the mechanisms involved. However, how biocontrol strains reshape cucumber rhizosphere microecology remains to be further studied.

METHODS: The composition changes of cucumber root exudates induced by biocontrol strain 1JN2, the microbial ecology of cucumber rhizosphere and the colonization ability of biocontrol strain 1JN2 in cucumber rhizosphere were analyzed through UHPLC-MS/MS analysis, Illumina high-throughput sequencing and SEM, respectively.

RESULTS: First, cucumber plants treated with biocontrol Bacillus 1JN2 reduced the disease severity of Fusarium wilt by 60%. Significant changes in cucumber root exudates were found after 1JN2 inoculation and the contents of four amino acids including glutamine, tryptophan, glycine and glutamic acid were significantly increased. Second, It was found that the bacterial diversity in the rhizosphere of cucumber was significantly increased in both the strain treatment group and the amino acid mixture treatment group, The number of Bacillus was the largest in all dominant populations, exceeded 20% in all treatment groups. The bacteria of Hydrogenispora and Vicinamibacteria were significantly increased after treatment.

DISCUSSION: Overall, the results demonstrated that amino acid substances in cucumber root exudates induced by biocontrol strain 1JN2 can shift the cucumber root microenvironment and prevent the occurrence of Fusarium wilt disease.},
}

@article {pmid38638898,
year = {2024},
author = {Hua, H and Yongtong, W and Xufeng, D and Fang, L and Jing, G and Fumao, Z and Jie, J and Lijiang, J},
title = {Hemp seeds attenuate loperamide-induced constipation in mice.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1353015},
pmid = {38638898},
issn = {1664-302X},
abstract = {Constipation is a common gastrointestinal disease that seriously affects human physical and mental health. Studies have reported that hemp seeds can improve constipation, however the specific mechanism is still unclear. This study investigates that hemp seed (HS) and its water-ethanol extract (HSE) attenuates loperamide-induced constipation in mice. The research results show that: the fecal water content and small intestinal transit rate of mice in the hemp seed group and hemp seed hydroalcoholic extract group were significantly increased compared with MC group, and the first red feces defecation time was significantly shortened; HS and HSE significantly influence serum levels of Gastrin (Gas), motilin (MTL), substance P (SP), and endothelin (ET), potentially mediating their effects on gastrointestinal motility. HS and HSE can improve colon inflammation in constipated mice with H&E staining. Compared with the model of constipation group, the content of short-chain fatty acids in the HS group and HSE group increased significantly. Gut microbiome studies have shown that the structure and abundance of intestinal flora are altered. HS and HSE changed the abundance of Odoribacter, Bacteroide, Lactobacillus and Prevotella. Together, these results suggest that HS have the potential to stimulate the proliferation of beneficial gut microbes and promote intestinal motility, thereby improving gut health and relieving symptoms of constipation.},
}

@article {pmid38638832,
year = {2024},
author = {Filardo, S and Di Pietro, M and Sessa, R},
title = {Current progresses and challenges for microbiome research in human health: a perspective.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1377012},
pmid = {38638832},
issn = {2235-2988},
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; Metagenomics ; },
abstract = {It is becoming increasingly clear that the human microbiota, also known as "the hidden organ", possesses a pivotal role in numerous processes involved in maintaining the physiological functions of the host, such as nutrient extraction, biosynthesis of bioactive molecules, interplay with the immune, endocrine, and nervous systems, as well as resistance to the colonization of potential invading pathogens. In the last decade, the development of metagenomic approaches based on the sequencing of the bacterial 16s rRNA gene via Next Generation Sequencing, followed by whole genome sequencing via third generation sequencing technologies, has been one of the great advances in molecular biology, allowing a better profiling of the human microbiota composition and, hence, a deeper understanding of the importance of microbiota in the etiopathogenesis of different pathologies. In this scenario, it is of the utmost importance to comprehensively characterize the human microbiota in relation to disease pathogenesis, in order to develop novel potential treatment or preventive strategies by manipulating the microbiota. Therefore, this perspective will focus on the progress, challenges, and promises of the current and future technological approaches for microbiome profiling and analysis.},
}

Humans
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Metagenome
Metagenomics

@article {pmid38638830,
year = {2024},
author = {Narrowe, AB and Lemons, JMS and Mahalak, KK and Firrman, J and den Abbeele, PV and Baudot, A and Deyaert, S and Li, Y and Yu, LL and Liu, L},
title = {Targeted remodeling of the human gut microbiome using Juemingzi (Senna seed extracts).},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1296619},
pmid = {38638830},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; Senna Extract/analysis/pharmacology ; *Microbiota ; Bacteria ; Feces/microbiology ; Seeds ; Sennosides/analysis/pharmacology ; *Anti-Infective Agents/pharmacology ; *Drugs, Chinese Herbal ; },
abstract = {The genus Senna contains globally distributed plant species of which the leaves, roots, and seeds have multiple traditional medicinal and nutritional uses. Notable chemical compounds derived from Senna spp. include sennosides and emodin which have been tested for antimicrobial effects in addition to their known laxative functions. However, studies of the effects of the combined chemical components on intact human gut microbiome communities are lacking. This study evaluated the effects of Juemingzi (Senna sp.) extract on the human gut microbiome using SIFR[®] (Systemic Intestinal Fermentation Research) technology. After a 48-hour human fecal incubation, we measured total bacterial cell density and fermentation products including pH, gas production and concentrations of short chain fatty acids (SCFAs). The initial and post-incubation microbial community structure and functional potential were characterized using shotgun metagenomic sequencing. Juemingzi (Senna seed) extracts displayed strong, taxon-specific anti-microbial effects as indicated by significant reductions in cell density (40%) and intra-sample community diversity. Members of the Bacteroidota were nearly eliminated over the 48-hour incubation. While generally part of a healthy gut microbiome, specific species of Bacteroides can be pathogenic. The active persistence of the members of the Enterobacteriaceae and selected Actinomycetota despite the reduction in overall cell numbers was demonstrated by increased fermentative outputs including high concentrations of gas and acetate with correspondingly reduced pH. These large-scale shifts in microbial community structure indicate the need for further evaluation of dosages and potential administration with prebiotic or synbiotic supplements. Overall, the very specific effects of these extracts may offer the potential for targeted antimicrobial uses or as a tool in the targeted remodeling of the gut microbiome.},
}

Humans
*Gastrointestinal Microbiome
Senna Extract/analysis/pharmacology
*Microbiota
Bacteria
Feces/microbiology
Seeds
Sennosides/analysis/pharmacology
*Anti-Infective Agents/pharmacology
*Drugs, Chinese Herbal

@article {pmid38638561,
year = {2024},
author = {Ma, X and Lazarowski, L and Zhang, Y and Krichbaum, S and Smith, JG and Zheng, J and Cao, W and Haney, PS and Wilborn, RR and Price, SB and Singletary, M and Waggoner, P and Wang, X},
title = {Associations between memory performance and Bifidobacterium pseudolongum abundance in the canine gut microbiome.},
journal = {iScience},
volume = {27},
number = {5},
pages = {109611},
pmid = {38638561},
issn = {2589-0042},
abstract = {Memory has been identified as the least heritable cognitive trait in canines, suggesting a significant influence of non-genetic factors. We observed a trend that overall memory scores (OMS) improve with age in a cohort of 27 young dogs, but considerable plasticity exists. Employing linear discriminant analysis of gut microbiome data from dogs exhibiting low and high OMS, a single bacterial species, Bifidobacterium pseudolongum, was identified and confirmed to be correlated with elevated OMS. Subsequent analysis using a random forest regression model revealed that sex, litter, and breed identity had minimal predictive importance. Age had some predictive value but failed to achieve statistical significance in this dataset. In sharp contrast, the abundance of 17 bacterial taxa in the microbiome showed a stronger predictive capacity for memory performance. Our findings provide insights into microbiome underpinnings of mammalian cognitive functions and suggest avenues for developing psychobiotics to enhance canine memory and learning.},
}

@article {pmid38638560,
year = {2024},
author = {Yan, Y and Zheng, X and Liu, G and Shi, G and Li, C and Chen, H and He, X and Lin, K and Deng, Z and Zhang, H and Li, WG and Chen, H and Tong, X and Zhu, Z},
title = {Gut microbiota-derived cholic acid mediates neonatal brain immaturity and white matter injury under chronic hypoxia.},
journal = {iScience},
volume = {27},
number = {5},
pages = {109633},
pmid = {38638560},
issn = {2589-0042},
abstract = {Chronic hypoxia, common in neonates, disrupts gut microbiota balance, which is crucial for brain development. This study utilized cyanotic congenital heart disease (CCHD) patients and a neonatal hypoxic rat model to explore the association. Both hypoxic rats and CCHD infants exhibited brain immaturity, white matter injury (WMI), brain inflammation, and motor/learning deficits. Through 16s rRNA sequencing and metabolomic analysis, a reduction in B. thetaiotaomicron and P. distasonis was identified, leading to cholic acid accumulation. This accumulation triggered M1 microglial activation and inflammation-induced WMI. Administration of these bacteria rescued cholic acid-induced WMI in hypoxic rats. These findings suggest that gut microbiota-derived cholic acid mediates neonatal WMI and brain inflammation, contributing to brain immaturity under chronic hypoxia. Therapeutic targeting of these bacteria provides a non-invasive intervention for chronic hypoxia patients.},
}

@article {pmid38638559,
year = {2024},
author = {Paraschiv, AC and Vacaras, V and Nistor, C and Vacaras, C and Strilciuc, S and Muresanu, DF},
title = {The effect of multiple sclerosis therapy on gut microbiota dysbiosis: a longitudinal prospective study.},
journal = {Microbial cell (Graz, Austria)},
volume = {11},
number = {},
pages = {106-115},
pmid = {38638559},
issn = {2311-2638},
abstract = {Gut microbiota has complex immune functions, related to different pathologies, including multiple sclerosis (MS).This study evaluated the influence of treatments on gut microbiota in people with MS (PwMS). The research comprised 60 participants, including 39 PwMS and 21 healthy controls (HC). Among the PwMS, 20 were prescribed a disease-modifying therapy (DMT), either interferon beta1a or teriflunomide, while 19 received a combination of classical DMT and an immunoglobulin Y (IgY) supplement. For each participant, two sets of gut samples were collected: one at the study's outset and another after two months. Alpha and beta diversity analyses revealed no significant differences between groups. In comparison to the HC, the MS group exhibited an increase in Prevotella stercorea and a decrease in Faecalibacterium prausnitzii. Following treatment, individuals with MS showed enrichment in Lachnospiraceae and Streptococcus. The second sample, compared to the first one, demonstrated an increase in Bifidobacterium angulatum and a decrease in Oscillospira for individuals with MS. Gut microbiota diversity in PwMS is not significantly different to HC.However, specific taxonomic changes indicate the presence of a dysbiosis state. The use of DMTs and immunoglobulin Y supplements may contribute to alterations in microbial composition, potentially leading to the restoration of a healthier microbiome.},
}

@article {pmid38638485,
year = {2024},
author = {Atchade, AM and Williams, JL and Mermelstein, L and Nemesure, B},
title = {Unraveling the complexities of early-onset colorectal cancer: a perspective on dietary and microbial influences.},
journal = {Frontiers in public health},
volume = {12},
number = {},
pages = {1370108},
pmid = {38638485},
issn = {2296-2565},
mesh = {Adult ; Humans ; *Colorectal Neoplasms/epidemiology/diagnosis/pathology ; Diet ; Obesity/epidemiology ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents ; },
abstract = {While advances in screening have resulted in declining rates of colorectal cancer (CRC) among adults ≥50 years of age since the mid-2000s, the incidence of early-onset CRC (EOCRC) has steadily increased over the last decade. This increase is not fully accounted for by hereditary factors, and the hypothesis that a sedentary lifestyle and obesity are the primary culprits is not fully supported by recent reports indicating that many affected individuals lead active lifestyles, maintain normal weight, and are otherwise healthy. Attention has shifted toward dietary patterns, notably the consumption of processed and ultra-processed foods found in Western diets, which are suspected of disrupting the gut microbiome balance that potentially leads to EOCRC. The impact of antibiotic use on the gut microbiome is also posited as a contributing factor, given its rising prevalence in medical and agricultural practices. We propose that a paradigm shift is necessary for EOCRC research, moving beyond metabolic factors to a broader exploration of dietary and microbial influences. Future research must prioritize understanding the relationship between dietary habits, particularly processed food intake, antibiotic exposure, and gut microbiome dynamics, to unravel the complex etiology of EOCRC. This will be crucial in developing comprehensive preventive strategies to address the increasing incidence of this malignancy in younger populations.},
}

Adult
Humans
*Colorectal Neoplasms/epidemiology/diagnosis/pathology
Diet
Obesity/epidemiology
*Gastrointestinal Microbiome
Anti-Bacterial Agents

@article {pmid38638378,
year = {2024},
author = {Yang, K and Zeng, J and Wu, H and Liu, H and Ding, Z and Liang, W and Wu, L and Lin, Z and Huang, W and Xu, J and Dong, F},
title = {Nonalcoholic Fatty Liver Disease: Changes in Gut Microbiota and Blood Lipids.},
journal = {Journal of clinical and translational hepatology},
volume = {12},
number = {4},
pages = {333-345},
pmid = {38638378},
issn = {2310-8819},
abstract = {BACKGROUND AND AIMS: The global prevalence of nonalcoholic fatty liver disease (NAFLD) is 25%. This study aimed to explore differences in the gut microbial community and blood lipids between normal livers and those affected by NAFLD using 16S ribosomal deoxyribonucleic acid sequencing.

METHODS: Gut microbiome profiles of 40 NAFLD and 20 non-NAFLD controls were analyzed. Information about four blood lipids and 13 other clinical features was collected. Patients were divided into three groups by ultrasound and FibroScan, those with a normal liver, mild FL (FL1), and moderate-to-severe FL (FL2). FL1 and FL2 patients were divided into two groups, those with either hyperlipidemia or non-hyperlipidemia based on their blood lipids. Potential keystone species within the groups were identified using univariate analysis and a specificity-occupancy plot. Significant difference in biochemical parameters ion NAFLD patients and healthy individuals were identified by detrended correspondence analysis and canonical correspondence analysis.

RESULTS: Decreased gut bacterial diversity was found in patients with NAFLD. Firmicutes/Bacteroidetes decreased as NAFLD progressed. Faecalibacterium and Ruminococcus 2 were the most representative fatty-related bacteria. Glutamate pyruvic transaminase, aspartate aminotransferase, and white blood cell count were selected as the most significant biochemical indexes. Calculation of areas under the curve identified two microbiomes combined with the three biochemical indexes that identified normal liver and FL2 very well but performed poorly in diagnosing FL1.

CONCLUSIONS: Faecalibacterium and Ruminococcus 2, combined with glutamate pyruvic transaminase, aspartate aminotransferase, and white blood cell count distinguished NAFLD. We speculate that regulating the health of gut microbiota may release NAFLD, in addition to providing new targets for clinicians to treat NAFLD.},
}

@article {pmid38638154,
year = {2024},
author = {Huang, F and Lei, M and Li, W},
title = {The rhizosphere and root selections intensify fungi-bacteria interaction in abiotic stress-resistant plants.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17225},
pmid = {38638154},
issn = {2167-8359},
mesh = {*Fungi/genetics ; *Rhizosphere ; Plant Roots/microbiology ; Soil Microbiology ; Soil ; Plants ; Bacteria ; Stress, Physiological ; },
abstract = {The microbial communities, inhabiting around and in plant roots, are largely influenced by the compartment effect, and in turn, promote the growth and stress resistance of the plant. However, how soil microbes are selected to the rhizosphere, and further into the roots is still not well understood. Here, we profiled the fungal, bacterial communities and their interactions in the bulk soils, rhizosphere soils and roots of eleven stress-resistant plant species after six months of growth. The results showed that the root selection (from the rhizosphere soils to the roots) was stronger than the rhizosphere selection (from the bulk soils to the rhizosphere soils) in: (1) filtering stricter on the fungal (28.5% to 40.1%) and bacterial (48.9% to 68.1%) amplicon sequence variants (ASVs), (2) depleting more shared fungal (290 to 56) and bacterial (691 to 2) ASVs measured by relative abundance, and (3) increasing the significant fungi-bacteria crosskingdom correlations (142 to 110). In addition, the root selection, but not the rhizosphere selection, significantly increased the fungi to bacteria ratios (f:b) of the observed species and shannon diversity index, indicating unbalanced effects to the fungal and bacteria communities exerted by the root selection. Based on the results of network analysis, the unbalanced root selection effects were associated with increased numbers of negative interaction (140 to 99) and crosskingdom interaction (123 to 92), suggesting the root selection intensifies the negative fungi-bacteria interactions in the roots. Our findings provide insights into the complexity of crosskingdom interactions and improve the understanding of microbiome assembly in the rhizosphere and roots.},
}

*Fungi/genetics
*Rhizosphere
Plant Roots/microbiology
Soil Microbiology
Soil
Plants
Bacteria
Stress, Physiological

@article {pmid38638142,
year = {2024},
author = {Megow, A and Bouras, G and Alsuliman, Y and Cooksley, C and Vyskocil, E and Murphy, W and Vreugde, S and Wormald, PJ},
title = {Chitogel with deferiprone following endoscopic sinus surgery: improved wound healing and microbiome.},
journal = {Frontiers in surgery},
volume = {11},
number = {},
pages = {1338209},
pmid = {38638142},
issn = {2296-875X},
abstract = {BACKGROUND: Adhesion formation, sinus ostial narrowing, and presence of pathogenic bacteria are associated with poor outcomes following endoscopic sinus surgery (ESS) for chronic rhinosinusitis. Chitogel has been shown to improve wound healing, restore a healthier microbiome, and reduce post-operative infections post ESS. Deferiprone has antibacterial properties and has been shown to reduce adhesion formation. The aim of the study was to assess whether the addition of low concentration deferiprone to Chitogel further improves surgical outcomes following ESS compared with Chitogel alone.

METHODS: In this double-blinded trial, 45 patients undergoing ESS were prospectively recruited. At the end of the surgery, patients were randomised to receive Chitogel alone, Chitogel with 1 mM of deferiprone, or Chitogel with 5 mM of deferiprone to one side of the sinuses (allowing the other side to serve as control). Patients underwent routine follow-ups with symptom questionnaires and nasoendoscopies performed at 2, 6, and 12 weeks post-operatively. Sinus ostial measurements, microbiology, and microbiome swabs from bilateral middle meatuses were collected intraoperatively and at 12 weeks post-operatively.

RESULTS: A significant improvement in the endoscopic appearance of the sinuses and frontal ostial patency was noted at 12 weeks post-operatively (p < 0.05) in all three treatment groups compared with the control. There was no significant difference noted between patients who received Chitogel alone and those who received Chitogel with 1 or 5 mM deferiprone.

CONCLUSION: Chitogel alone, Chitogel with 1 mM deferiprone, and Chitogel with 5 mM deferiprone used following ESS led to a significant improvement in endoscopic appearance of the sinuses and frontal ostial preservation at 12 weeks post-operatively. No significant difference was found with the addition of deferiprone to Chitogel.},
}

@article {pmid38638127,
year = {2023},
author = {Zeng, Z and Jiang, M and Li, X and Yuan, J and Zhang, H},
title = {Precision medicine in inflammatory bowel disease.},
journal = {Precision clinical medicine},
volume = {6},
number = {4},
pages = {pbad033},
pmid = {38638127},
issn = {2516-1571},
abstract = {Inflammatory bowel disease (IBD) is an incurable disease characterized by remission-relapse cycles throughout its course. Both Crohn's disease (CD) and ulcerative colitis (UC), the two main forms of IBD, exhibit tendency to develop complications and substantial heterogeneity in terms of frequency and severity of relapse, thus posing great challenges to the clinical management for IBD. Current treatment strategies are effective in different ways in induction and maintenance therapies for IBD. Recent advances in studies of genetics, pharmacogenetics, proteomics and microbiome provide a strong driving force for identifying molecular markers of prognosis and treatment response, which should help clinicians manage IBD patients more effectively, and then, improve clinical outcomes and reduce treatment costs of patients. In this review, we summarize and discuss precision medicine in IBD, focusing on predictive markers of disease course and treatment response, and monitoring indices during therapeutic drug monitoring.},
}

@article {pmid38637894,
year = {2024},
author = {Wainwright, BJ and Leon, J and Vilela, E and Hickman, KJE and Caldwell, J and Aimone, B and Bischoff, P and Ohran, M and Morelli, MW and Arlyza, IS and Marwayana, ON and Zahn, G},
title = {Wallace's line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {23},
pmid = {38637894},
issn = {2524-6372},
abstract = {BACKGROUND: The processes that shape microbial biogeography are not well understood, and concepts that apply to macroorganisms, like dispersal barriers, may not affect microorganisms in the same predictable ways. To better understand how known macro-scale biogeographic processes can be applied at micro-scales, we examined seagrass associated microbiota on either side of Wallace's line to determine the influence of this cryptic dispersal boundary on the community structure of microorganisms. Communities were examined from twelve locations throughout Indonesia on either side of this theoretical line.

RESULTS: We found significant differences in microbial community structure on either side of this boundary (R[2] = 0.09; P = 0.001), and identified seven microbial genera as differentially abundant on either side of the line, six of these were more abundant in the West, with the other more strongly associated with the East. Genera found to be differentially abundant had significantly smaller minimum cell dimensions (GLM: t923 = 59.50, P < 0.001) than the overall community.

CONCLUSION: Despite the assumed excellent dispersal ability of microbes, we were able to detect significant differences in community structure on either side of this cryptic biogeographic boundary. Samples from the two closest islands on opposite sides of the line, Bali and Komodo, were more different from each other than either was to its most distant island on the same side. We suggest that limited dispersal across this barrier coupled with habitat differences are primarily responsible for the patterns observed. The cryptic processes that drive macroorganism community divergence across this region may also play a role in the bigeographic patterns of microbiota.},
}

@article {pmid38637854,
year = {2024},
author = {Arponen, H and Vakkilainen, S and Tomnikov, N and Kallonen, T and Silling, S and Mäkitie, O and Rautava, J},
title = {Altered oral microbiome, but normal human papilloma virus prevalence in cartilage-hair hypoplasia patients.},
journal = {Orphanet journal of rare diseases},
volume = {19},
number = {1},
pages = {169},
pmid = {38637854},
issn = {1750-1172},
mesh = {Humans ; Human Papillomavirus Viruses ; *Papillomavirus Infections/epidemiology ; Prevalence ; Cross-Sectional Studies ; *Osteochondrodysplasias/genetics/*congenital ; *Microbiota ; *Primary Immunodeficiency Diseases ; Hair/*abnormalities ; *Hirschsprung Disease ; },
abstract = {BACKGROUND: Cartilage-hair hypoplasia (CHH) is a rare syndromic immunodeficiency with metaphyseal chondrodysplasia and increased risk of malignancy. In this cross-sectional observational study, we examined HPV status and oral microbiome in individuals with CHH. Oral brush samples were collected from 20 individuals with CHH (aged 5-59 years) and 41 controls (1-69 years). Alpha HPVs (43 types) were tested by nested PCR followed by bead-based probe hybridization. Separately, beta-, gamma-, mu- and nu- HPV types were investigated, and a genome-based bacterial microbiome sequencing was performed.

RESULTS: We found a similar alpha HPV prevalence in individuals with CHH (45%) and controls (36%). The HPV types of individuals with CHH were HPV-16 (25%), 27, 28, and 78, and of controls HPV-3, 16 (21%), 27, and 61. Beta HPV positivity and combined beta/gamma/mu/nu prevalence was detected in 11% and 11% of individuals with CHH and in 5% and 3% of the controls, respectively. Individuals with CHH differed from the controls in bacterial microbiota diversity, richness, and in microbial composition. Individuals with CHH had lower abundance of species Mitsuokella sp000469545, Parascardovia denticolens, Propionibacterium acidifaciens, UMGS1907 sp004151455, Salinicola halophilus, Haemophilus_A paraphrohaemolyticus, Fusobacterium massiliense, and Veillonella parvula, and higher abundance of Slackia exigua.

CONCLUSIONS: Individuals with CHH exhibit similar prevalence of HPV DNA but different bacterial microbiota on their oral mucosa compared to healthy controls. This may partly explain the previously observed high prevalence of oral diseases in CHH, and regular oral examination is warranted.},
}

Humans
Human Papillomavirus Viruses
*Papillomavirus Infections/epidemiology
Prevalence
Cross-Sectional Studies
*Osteochondrodysplasias/genetics/*congenital
*Microbiota
*Primary Immunodeficiency Diseases
Hair/*abnormalities
*Hirschsprung Disease

@article {pmid38637580,
year = {2024},
author = {Wan, S and Wang, K and Huang, P and Guo, X and Liu, W and Li, Y and Zhang, J and Li, Z and Song, J and Yang, W and Zhang, X and Ding, X and Leong, DT and Wang, L},
title = {Mechanoelectronic stimulation of autologous extracellular vesicle biosynthesis implant for gut microbiota modulation.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3343},
pmid = {38637580},
issn = {2041-1723},
support = {52203170, 22207056 and 62288102//National Natural Science Foundation of China (National Science Foundation of China)/ ; BK20220384 and BK20210580//Natural Science Foundation of Jiangsu Province (Jiangsu Provincial Natural Science Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Microbiota ; *Colitis ; *Extracellular Vesicles ; Hydrogels/pharmacology ; Dysbiosis ; },
abstract = {Pathogenic gut microbiota is responsible for a few debilitating gastrointestinal diseases. While the host immune cells do produce extracellular vesicles to counteract some deleterious effects of the microbiota, the extracellular vesicles are of insufficient doses and at unreliable exposure times. Here we use mechanical stimulation of hydrogel-embedded macrophage in a bioelectronic controller that on demand boost production of up to 20 times of therapeutic extracellular vesicles to ameliorate the microbes' deleterious effects in vivo. Our miniaturized wireless bioelectronic system termed inducible mechanical activation for in-situ and sustainable generating extracellular vesicles (iMASSAGE), leverages on wireless electronics and responsive hydrogel to impose mechanical forces on macrophages to produce extracellular vesicles that rectify gut microbiome dysbiosis and ameliorate colitis. This in vivo controllable extracellular vesicles-produced system holds promise as platform to treat various other diseases.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Microbiota
*Colitis
*Extracellular Vesicles
Hydrogels/pharmacology
Dysbiosis

@article {pmid38637223,
year = {2024},
author = {Wortelboer, K and Herrema, H},
title = {Opportunities and challenges in phage therapy for cardiometabolic diseases.},
journal = {Trends in endocrinology and metabolism: TEM},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tem.2024.03.007},
pmid = {38637223},
issn = {1879-3061},
abstract = {The worldwide prevalence of cardiometabolic diseases (CMD) is increasing, and emerging evidence implicates the gut microbiota in this multifactorial disease development. Bacteriophages (phages) are viruses that selectively target a bacterial host; thus, phage therapy offers a precise means of modulating the gut microbiota, limiting collateral damage on the ecosystem. Several studies demonstrate the potential of phages in human disease, including alcoholic and steatotic liver disease. In this opinion article we discuss the potential of phage therapy as a predefined medicinal product for CMD and discuss its current challenges, including the generation of effective phage combinations, product formulation, and strict manufacturing requirements.},
}

@article {pmid38637108,
year = {2024},
author = {Tarracchini, C and Milani, C and Lugli, GA and Mancabelli, L and Turroni, F and van Sinderen, D and Ventura, M},
title = {The infant gut microbiota as the cornerstone for future gastrointestinal health.},
journal = {Advances in applied microbiology},
volume = {126},
number = {},
pages = {93-119},
doi = {10.1016/bs.aambs.2024.02.001},
pmid = {38637108},
issn = {0065-2164},
mesh = {Infant ; Female ; Humans ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; *Microbiota ; Mothers ; Diet ; },
abstract = {The early postnatal period represents a critical window of time for the establishment and maturation of the human gut microbiota. The gut microbiota undergoes dramatic developmental changes during the first year of life, being influenced by a variety of external factors, with diet being a major player. Indeed, the introduction of complementary feeding provides novel nutritive substrates and triggers a shift from milk-adapted gut microbiota toward an adult-like bacterial composition, which is characterized by an enhancement in diversity and proportions of fiber-degrading bacterial genera like Ruminococcus, Prevotella, Eubacterium, and Bacteroides genera. Inadequate gut microbiota development in early life is frequently associated with concomitant and future adverse health conditions. Thus, understanding the processes that govern initial colonization and establishment of microbes in the gastrointestinal tract is of great importance. This review summarizes the actual understanding of the assembly and development of the microbial community associated with the infant gut, emphasizing the importance of mother-to-infant vertical transmission events as a fundamental arrival route for the first colonizers.},
}

Infant
Female
Humans
*Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology
*Microbiota
Mothers
Diet

@article {pmid38637082,
year = {2024},
author = {Sonets, IV and Solovyev, MA and Ivanova, VA and Vasiluev, PA and Kachalkin, AV and Ochkalova, SD and Korobeynikov, AI and Razin, SV and Ulianov, SV and Tyakht, AV},
title = {Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider.},
journal = {Food microbiology},
volume = {121},
number = {},
pages = {104520},
doi = {10.1016/j.fm.2024.104520},
pmid = {38637082},
issn = {1095-9998},
mesh = {*Saccharomyces cerevisiae/genetics ; Beer/microbiology ; Bacteria/genetics ; Plasmids ; *Saccharomyces/genetics ; Metagenome ; Metagenomics ; Enterobacteriaceae/genetics ; },
abstract = {Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.},
}

*Saccharomyces cerevisiae/genetics
Beer/microbiology
Bacteria/genetics
Plasmids
*Saccharomyces/genetics
Metagenome
Metagenomics
Enterobacteriaceae/genetics

@article {pmid38637066,
year = {2024},
author = {Lee, AW and Ng, IC and Wong, EY and Wong, IT and Sze, RP and Chan, KY and So, TY and Zhang, Z and Ka-Yee Fung, S and Choi-Ying Wong, S and Tam, WY and Lao, HY and Lee, LK and Leung, JS and Chan, CT and Ng, TT and Zhang, J and Chow, FW and Leung, PH and Siu, GK},
title = {Comprehensive identification of pathogenic microbes and antimicrobial resistance genes in food products using nanopore sequencing-based metagenomics.},
journal = {Food microbiology},
volume = {121},
number = {},
pages = {104493},
doi = {10.1016/j.fm.2024.104493},
pmid = {38637066},
issn = {1095-9998},
mesh = {Food Microbiology ; Anti-Bacterial Agents/pharmacology ; *Nanopore Sequencing ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents ; Bacteria/genetics ; Metagenomics ; },
abstract = {Foodborne pathogens, particularly antimicrobial-resistant (AMR) bacteria, remain a significant threat to global health. Given the limitations of conventional culture-based approaches, which are limited in scope and time-consuming, metagenomic sequencing of food products emerges as a promising solution. This method provides a fast and comprehensive way to detect the presence of pathogenic microbes and antimicrobial resistance genes (ARGs). Notably, nanopore long-read sequencing provides more accurate bacterial taxonomic classification in comparison to short-read sequencing. Here, we revealed the impact of food types and attributes (origin, retail place, and food processing methods) on microbial communities and the AMR profile using nanopore metagenomic sequencing. We analyzed a total of 260 food products, including raw meat, sashimi, and ready-to-eat (RTE) vegetables. Clostridium botulinum, Acinetobacter baumannii, and Vibrio parahaemolyticus were identified as the top three foodborne pathogens in raw meat and sashimi. Importantly, even with low pathogen abundance, higher percentages of samples containing carbapenem and cephalosporin resistance genes were identified in chicken and RTE vegetables, respectively. In parallel, our results demonstrated that fresh, peeled, and minced foods exhibited higher levels of pathogenic bacteria. In conclusion, this comprehensive study offers invaluable data that can contribute to food safety assessments and serve as a basis for quality indicators.},
}

Food Microbiology
Anti-Bacterial Agents/pharmacology
*Nanopore Sequencing
Drug Resistance, Bacterial/genetics
*Anti-Infective Agents
Bacteria/genetics
Metagenomics

@article {pmid38636860,
year = {2024},
author = {Zhou, ZZ and Zhu, J and Yin, Y and Ding, LJ},
title = {Seasonal variations of profiles of antibiotic resistance genes and virulence factor genes in household dust from Beijing, China revealed by the metagenomics.},
journal = {The Science of the total environment},
volume = {928},
number = {},
pages = {172542},
doi = {10.1016/j.scitotenv.2024.172542},
pmid = {38636860},
issn = {1879-1026},
abstract = {Household-related microbiome is closely related with human health. However, the knowledge about profiles of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) which are carried by microbes inside homes and their temporal dynamics are rather limited. Here we monitored the seasonal changes of bacterial community (especially pathogenic bacteria), ARGs, and VFGs in household dust samples during two years. Based on metagenomic sequencing, the dust-related bacterial pathogenic community, ARGs, and VFGs all harbored the lowest richness in spring among four seasons. Their structure (except that of VFGs) also exhibited remarkable differences among the seasons. The structural variations of ARGs and VFGs were almost explained by mobile genetic elements (MGEs), bacterial pathogens, and particulate matter-related factors, with MGEs explaining the most. Moreover, the total normalized abundance of ARGs or VFGs showed no significant change across the seasons. Results of metagenomic binning and microbial network both showed that several pathogenic taxa (e.g., Ralstonia pickettii) were strongly linked with numerous ARGs (mainly resistant to multidrug) and VFGs (mainly encoding motility) simultaneously. Overall, these findings underline the significance of MGEs in structuring ARGs and VFGs inside homes along with seasonal variations, suggesting that household dust is a neglected reservoir for ARGs and VFGs.},
}

@article {pmid38636822,
year = {2024},
author = {Nannini, G and Di Gloria, L and Russo, E and Sterrantino, G and Kiros, ST and Coppi, M and Niccolai, E and Baldi, S and Ramazzotti, M and Di Pilato, V and Lagi, F and Bartolucci, G and Rossolini, GM and Bartoloni, A and Amedei, A},
title = {Oral microbiota signatures associated with viremia and CD4 recovery in treatment-naïve HIV-1-infected patients.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105339},
doi = {10.1016/j.micinf.2024.105339},
pmid = {38636822},
issn = {1769-714X},
abstract = {PURPOSE: Few reports focused on the role of oral microbiome diversity in HIV infection. We characterized the microbiota-immunity axis in a cohort of treatment-naïve HIV-1-infected patients undergoing antiretroviral therapy (ART) focusing on the oral microbiome (OM) and immunological responsivity.

METHODS: The sequencing of 16S rRNA V3-V4 hypervariable region was performed on salivary samples of 15 healthy control (HC) and 12 HIV+ patients before starting ART and after reaching virological suppression. Then, we correlated the OM composition with serum cytokines and the Short Chain Fatty acids (SCFAs).

RESULTS: The comparison between HIV patients and HC oral microbiota showed differences in the bacterial α-diversity and richness. We documented a negative correlation between oral Prevotella and intestinal valeric acid at before starting ART and a positive correlation between oral Veillonella and gut acetic acid after reaching virological suppression. Finally, an increase in the phylum Proteobacteria was observed comparing saliva samples of immunological responders (IRs) patients against immunological non-responders (INRs).

CONCLUSIONS: For the first time, we described an increase in the oral pro-inflammatory Proteobacteria phylum in INRs compared to IRs. We provided more evidence that saliva could be a non-invasive and less expensive approach for research involving the oral cavity microbiome in HIV patients.},
}

@article {pmid38636749,
year = {2024},
author = {Xu, Y and Niu, C and Liang, S and Guo, J and Li, K and Zhang, J and Li, J and Jin, Y and Bai, J and Dai, J and Lu, C},
title = {An inulin-based glycovesicle for pathogen-targeted drug delivery to ameliorate salmonellosis.},
journal = {International journal of biological macromolecules},
volume = {267},
number = {Pt 2},
pages = {131656},
doi = {10.1016/j.ijbiomac.2024.131656},
pmid = {38636749},
issn = {1879-0003},
abstract = {The gut microbiota plays a significant role in the pathogenesis and remission of inflammatory bowel disease. However, conventional antibiotic therapies may alter microbial ecology and lead to dysbiosis of the gut microbiome, which greatly limits therapeutic efficacy. To address this challenge, novel nanomicelles that couple inulin with levofloxacin via disulfide bonds for the treatment of salmonellosis were developed in this study. Owing to their H2S-responsiveness, the nanomicelles can target the inflamed colon and rapidly release levofloxacin to selectively fight against enteric pathogens. Moreover, the embedded inulin can serve as prebiotic fiber to increase the amount of Bifidobacteria and Lactobacilli in mice with salmonellosis, thus maintaining the intestinal mechanical barrier and regulating the balance of the intestinal flora. Therefore, multifunctional nanomicelles had a better curative effect than pure levofloxacin on ameliorating inflammation in vivo. The pathogen-targeted glycovesicle represents a promising drug delivery platform to maximize the efficacy of antibacterial drugs for the treatment of inflammatory bowel disease.},
}

@article {pmid38636612,
year = {2024},
author = {Biessy, L and Pearman, JK and Mertens, KN and Réveillon, D and Savar, V and Hess, P and Hampton, H and Thompson, L and Lebrun, L and Terre-Terrillon, A and Smith, KF},
title = {Sudden peak in tetrodotoxin in French oysters during the summer of 2021: Source investigation using microscopy, metabarcoding and droplet digital PCR.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {243},
number = {},
pages = {107721},
doi = {10.1016/j.toxicon.2024.107721},
pmid = {38636612},
issn = {1879-3150},
abstract = {Tetrodotoxin (TTX) is a potent neurotoxin causing human intoxications from contaminated seafood worldwide and is of emerging concern in Europe. Shellfish have been shown to contain varying TTX concentrations globally, with concentrations typically higher in Pacific oysters Crassostrea gigas in Europe. Despite many decades of research, the source of TTX remains unknown, with bacterial or algal origins having been suggested. The aim of this study was to identify potential source organisms causing TTX contamination in Pacific oysters in French coastal waters, using three different techniques. Oysters were deployed in cages from April to September 2021 in an estuary where TTX was previously detected. Microscopic analyses of water samples were used to investigate potential microalgal blooms present prior or during the peak in TTX. Differences in the bacterial communities from oyster digestive glands (DG) and remaining flesh were explored using metabarcoding, and lastly, droplet digital PCR assays were developed to investigate the presence of Cephalothrix sp., one European TTX-bearing species in the DG of toxic C. gigas. Oysters analysed by liquid chromatography-tandem mass spectrometry contained quantifiable levels of TTX over a three-week period (24 June-15 July 2021), with concentrations decreasing in the DG from 424 μg/kg for the first detection to 101 μg/kg (equivalent to 74 to 17 μg/kg of total flesh), and trace levels being detected until August 13, 2021. These concentrations are the first report of the European TTX guidance levels being exceeded in French shellfish. Microscopy revealed that some microalgae bloomed during the TTX peak, (e.g., Chaetoceros spp., reaching 40,000 cells/L). Prokaryotic metabarcoding showed increases in abundance of Rubritaleaceae (genus Persicirhabdus) and Neolyngbya, before and during the TTX peak. Both phyla have previously been described as possible TTX-producers and should be investigated further. Droplet digital PCR analyses were negative for the targeted TTX-bearing genus Cephalothrix.},
}

@article {pmid38636461,
year = {2024},
author = {Zafar, H and Saier, MH},
title = {An insider's perspective about the pathogenic relevance of gut bacterial transportomes.},
journal = {Microbial physiology},
volume = {},
number = {},
pages = {},
doi = {10.1159/000538779},
pmid = {38636461},
issn = {2673-1673},
abstract = {BACKGROUND: The gut microbiome is integral to host health, hosting complex interactions between the host and numerous microbial species in the gastrointestinal tract. Key among the molecular mechanisms employed by gut bacteria are transportomes, consisting of diverse transport proteins crucial for bacterial adaptation to the dynamic, nutrient-rich environment of the mammalian gut. These transportomes facilitate the movement of a wide array of molecules, impacting both the host and the microbial community.

SUMMARY: This communication explores the significance of transportomes in gut bacteria, focusing on their role in nutrient acquisition, competitive interactions among microbes, and potential pathogenicity. It delves into the transportomes of key gut bacterial species like E. coli, Salmonella, Bacteroides, Lactobacillus, Clostridia, and Bifidobacterium, examining the functions of predicted transport proteins. The overview synthesizes recent research efforts, highlighting how these transportomes influence host-microbe interactions and contribute to the microbial ecology of the gut.

KEY MESSAGES: Transportomes are vital for the survival and adaptation of bacteria in the gut, enabling the import and export of various nutrients and molecules. The complex interplay of transport proteins not only supports bacterial growth and competition but also has implications for host health, potentially contributing to pathogenic processes. Understanding the pathogenic potential of transportomes in major gut bacterial species provides insights into gut health and disease, offering avenues for future research and therapeutic strategies.},
}

@article {pmid38636269,
year = {2024},
author = {Chen, H and Xu, Z and Zhou, Y and Jiang, YH and Chen, J and Xiong, Y and Zhou, M and Wu, X and Hong, D},
title = {Rituximab-induced gut microbiota changes in Chinese neuromyelitis optica spectrum disorders.},
journal = {Multiple sclerosis and related disorders},
volume = {86},
number = {},
pages = {105606},
doi = {10.1016/j.msard.2024.105606},
pmid = {38636269},
issn = {2211-0356},
abstract = {BACKGROUND: Recent evidence shows that immunosuppressive agents can affect the gut microbiota in autoimmune diseases. However, the relationship between the gut microbiome and B-cell depletion immunotherapy in neuromyelitis optica spectrum disorder (NMOSD) remains poorly understood.

OBJECTIVES: To evaluate the distinct intestinal microbial patterns and serum cytokine levels after short-term rituximab treatment (three months) in patients with NMOSD.

METHODS: Firstly, we conducted a cross-sectional study involving 46 treatment-naïve NMOSD patients and 48 matched healthy controls. We collected fecal specimens, which were then analyzed using next-generation sequencing, and quantified serum cytokines. Subsequently, fecal and serum samples were re-collected and re-evaluated in 31 of the 46 treatment-naïve NMOSD patients after RTX treatment.

RESULTS: Comparing the gut microbiome of treatment-naïve NMOSD patients to that of healthy controls revealed low α-diversity and distinct microbial compositions in the former. The microbial composition in NMOSD patients underwent changes following three months of RTX treatment. Specifically, the levels of IL-17F and IL-6 decreased, while those of IL-10 and TNFα increased after RTX treatment. LEfSe analysis identified 27 KEGG categories with significantly differential abundances between NMOSD patients and RTX treatment group.

CONCLUSIONS: Our study provides a comprehensive understanding of the gut microbiota landscape in the context of B-cell depletion immunotherapy. We observed dysbiosis in the gut microbiome of NMOSD patients, which was partially alleviated by three months of RTX treatment. This suggests that B-cell depletion may play a crucial role in driving changes in the gastrointestinal environment.},
}

@article {pmid38636203,
year = {2024},
author = {Chang, Y and Guo, R and Gu, T and Zong, Y and Sun, H and Xu, W and Chen, L and Tian, Y and Li, G and Lu, L and Zeng, T},
title = {Integrated transcriptome and microbiome analyses of residual feed intake in ducks during high production period.},
journal = {Poultry science},
volume = {103},
number = {6},
pages = {103726},
pmid = {38636203},
issn = {1525-3171},
abstract = {Residual feed intake (RFI) is a crucial parameter for assessing the feeding efficiency of poultry. Minimizing RFI can enhance feed utilization and reduce costs. In this study, 315 healthy female ducks were individually housed in cages. Growth performance was monitored during the high laying period, from 290 to 325 d of age. The cecal transcriptome and microbiome of 12 ducks with high RFI and 12 with low residual feed intake (LRFI) were analyzed. Regarding growth performance, the LRFI group exhibited significantly lower RFI, feed conversion ratio (FCR), and feed intake (Fi) compared to the HRFI group (p < 0.01). However, there were no significant differences observed in body weight (BW), body weight gain (BWG), and egg mass (EML) between the groups (p > 0.05). Microbiome analysis demonstrated that RFI impacted gut microbial abundance, particularly affecting metabolism and disease-related microorganisms such as Romboutsia, Enterococcus, and Megamonas funiformis. Transcriptome analysis revealed that varying RFI changed the expression of genes related to glucose metabolism and lipid metabolism, including APOA1, G6PC1, PCK1, and PLIN1. The integrated analysis indicated that host genes were closely linked to the microbiota and primarily function in lipid metabolism, which may enhance feeding efficiency by influencing metabolism and maintaining gut homeostasis.},
}

@article {pmid38636083,
year = {2024},
author = {Nakao, T and Shimada, M and Yoshikawa, K and Tokunaga, T and Nishi, M and Kashihara, H and Takasu, C and Wada, Y and Yoshimoto, T},
title = {Number of Healthy Teeth Can Predict the Response of Rectal Cancer to Chemoradiotherapy: A Retrospective Study.},
journal = {The American surgeon},
volume = {},
number = {},
pages = {31348241244628},
doi = {10.1177/00031348241244628},
pmid = {38636083},
issn = {1555-9823},
abstract = {BACKGROUND: It has been reported that the oral and gut microbiomes are associated with the prognosis in patients who undergo surgery, chemotherapy, and radiation for colorectal cancer. This study is the first to identify a correlation between the number of healthy teeth, which is an oral health indicator, and the efficacy of preoperative chemotherapy for rectal cancer.

METHODS: This retrospective single-center study included 30 patients who underwent radical surgery after preoperative chemoradiotherapy (CRT) between December 2013 and June 2021. The relationship between number of teeth before CRT and the efficacy of CRT, CRT-related adverse events, postoperative complications, and long-term postoperative outcomes was examined.

RESULTS: The number of healthy teeth was significantly greater in patients with downstaging of their disease than in those without downstaging (P = .027) and in patients with a complete response according to the Response Evaluation Criteria in Solid Tumors than in those who did not have a complete response (P = .014). Patients were divided into two groups according to whether they had ≥15 teeth or ≤14 teeth. There was no significant between-group difference in CRT-related adverse events. The incidence of all postoperative complications and grade II postoperative complications tended to be higher in patients with ≥15 teeth (P = .071 and P = .092, respectively), as did the 5-year overall survival rate (P = .083) and the 5-year disease-free rate (P = .007).

DISCUSSION: The number of healthy teeth predicted the response to preoperative CRT, postoperative complications, and the outcome of subsequent surgery in patients with rectal cancer.},
}

@article {pmid38635882,
year = {2024},
author = {Al Radi, ZMA and Prins, FM and Collij, V and Vich Vila, A and Festen, EAM and Dijkstra, G and Weersma, RK and Klaassen, MAY and Gacesa, R},
title = {Exploring the Predictive Value of Gut Microbiome Signatures for Therapy Intensification in Patients With Inflammatory Bowel Disease: A 10-Year Follow-up Study.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izae064},
pmid = {38635882},
issn = {1536-4844},
support = {//Netherlands Organization for Scientific Research/ ; MLDS D16-14//Dutch Digestive Foundation/ ; },
abstract = {BACKGROUND: Inflammatory bowel diseases (IBDs) pose a significant challenge due to their diverse, often debilitating, and unpredictable clinical manifestations. The absence of prognostic tools to anticipate the future complications that require therapy intensification presents a substantial burden to patient private life and health. We aimed to explore whether the gut microbiome is a potential biomarker for future therapy intensification in a cohort of 90 IBD patients.

METHODS: We conducted whole-genome metagenomics sequencing on fecal samples from these patients, allowing us to profile the taxonomic and functional composition of their gut microbiomes. Additionally, we conducted a retrospective analysis of patients' electronic records over a period of 10 years following the sample collection and classified patients into (1) those requiring and (2) not requiring therapy intensification. Therapy intensification included medication escalation, intestinal resections, or a loss of response to a biological treatment. We applied gut microbiome diversity analysis, dissimilarity assessment, differential abundance analysis, and random forest modeling to establish associations between baseline microbiome profiles and future therapy intensification.

RESULTS: We identified 12 microbial species (eg, Roseburia hominis and Dialister invisus) and 16 functional pathways (eg, biosynthesis of L-citrulline and L-threonine) with significant correlations to future therapy intensifications. Random forest models using microbial species and pathways achieved areas under the curve of 0.75 and 0.72 for predicting therapy intensification.

CONCLUSIONS: The gut microbiome is a potential biomarker for therapy intensification in IBD patients and personalized management strategies. Further research should validate our findings in other cohorts to enhance the generalizability of these results.},
}

@article {pmid38635872,
year = {2024},
author = {Zhong, Z and Zhang, Y and Wei, Y and Li, X and Ren, L and Li, Y and Zhang, X and Chen, C and Yin, X and Liu, R and Wang, Q},
title = {Fucoidan Improves Early Stage Diabetic Nephropathy via the Gut Microbiota-Mitochondria Axis in High-Fat Diet-Induced Diabetic Mice.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.3c08503},
pmid = {38635872},
issn = {1520-5118},
abstract = {Diabetic nephropathy (DN) is a common microvascular complication of diabetes. Fucoidan, a polysaccharide containing fucose and sulfate group, ameliorates DN. However, the underlying mechanism has not been fully understood. This study aimed to explore the effects and mechanism of fucoidan on DN in high-fat diet-induced diabetic mice. A total of 90 C57BL/6J mice were randomly assigned to six groups (n = 15) as follows: normal control (NC), diabetes mellitus (DM), metformin (MTF), low-dose fucoidan (LFC), medium-dose fucoidan (MFC), and high-dose fucoidan (HFC). A technique based on fluorescein isothiocyanate (FITC-sinistin) elimination kinetics measured percutaneously was applied to determine the glomerular filtration rate (GFR). After 24 weeks, the mice were sacrificed and an early stage DN model was confirmed by GFR hyperfiltration, elevated urinary creatinine, normal urinary albumin, tubulointerstitial fibrosis, and glomerular hypertrophy. Fucoidan significantly improved the GFR hyperfiltration and renal fibrosis. An enriched SCFAs-producing bacteria and increased acetic concentration in cecum contents were found in fucoidan groups, as well as increased renal ATP levels and improved mitochondrial dysfunction. The renal inflammation and fibrosis were ameliorated through inhibiting the MAPKs pathway. In conclusion, fucoidan improved early stage DN targeting the microbiota-mitochondria axis by ameliorating mitochondrial oxidative stress and inhibiting the MAPKs pathway.},
}

@article {pmid38635629,
year = {2024},
author = {Wang, T and Weiss, A and You, L},
title = {A generic approach to infer community-level fitness of microbial genes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {17},
pages = {e2318380121},
doi = {10.1073/pnas.2318380121},
pmid = {38635629},
issn = {1091-6490},
support = {R01AI125604//HHS | National Institutes of Health (NIH)/ ; R01GM098642//HHS | National Institutes of Health (NIH)/ ; R01EB031869//HHS | National Institutes of Health (NIH)/ ; MCB-1937259//National Science Foundation (NSF)/ ; },
abstract = {The gene content in a metagenomic pool defines the function potential of a microbial community. Natural selection, operating on the level of genomes or genes, shapes the evolution of community functions by enriching some genes while depriving the others. Despite the importance of microbiomes in the environment and health, a general metric to evaluate the community-wide fitness of microbial genes remains lacking. In this work, we adapt the classic neutral model of species and use it to predict how the abundances of different genes will be shaped by selection, regardless of at which level the selection acts. We establish a simple metric that quantitatively infers the average survival capability of each gene in a microbiome. We then experimentally validate the predictions using synthetic communities of barcoded Escherichia coli strains undergoing neutral assembly and competition. We further show that this approach can be applied to publicly available metagenomic datasets to gain insights into the environment-function interplay of natural microbiomes.},
}

@article {pmid38635587,
year = {2024},
author = {Ohdera, AH and Mansbridge, M and Wang, M and Naydenkov, P and Kamel, B and Goentoro, L},
title = {The microbiome of a Pacific moon jellyfish Aurelia coerulea.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0298002},
pmid = {38635587},
issn = {1932-6203},
abstract = {The impact of microbiome in animal physiology is well appreciated, but characterization of animal-microbe symbiosis in marine environments remains a growing need. This study characterizes the microbial communities associated with the moon jellyfish Aurelia coerulea, first isolated from the East Pacific Ocean and has since been utilized as an experimental system. We find that the microbiome of this Pacific Aurelia culture is dominated by two taxa, a Mollicutes and Rickettsiales. The microbiome is stable across life stages, although composition varies. Mining the host sequencing data, we assembled the bacterial metagenome-assembled genomes (MAGs). The bacterial MAGs are highly reduced, and predict a high metabolic dependence on the host. Analysis using multiple metrics suggest that both bacteria are likely new species. We therefore propose the names Ca. Mariplasma lunae (Mollicutes) and Ca. Marinirickettsia aquamalans (Rickettsiales). Finally, comparison with studies of Aurelia from other geographical populations suggests the association with Ca. Mariplasma lunae occurs in Aurelia from multiple geographical locations. The low-diversity microbiome of Aurelia provides a relatively simple system to study host-microbe interactions.},
}