@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.},
}

@article {pmid38635321,
year = {2024},
author = {Wang, M and Lkhagva, E and Kim, S and Zhai, C and Islam, MM and Kim, HJ and Hong, ST},
title = {The gut microbe pair of Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270 confers complete protection against SARS-CoV-2 infection by activating CD8+ T cell-mediated immunity.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2342497},
pmid = {38635321},
issn = {1949-0984},
mesh = {Animals ; Cricetinae ; Ruminococcus ; *Gastrointestinal Microbiome ; *COVID-19 ; SARS-CoV-2 ; Clostridiales ; CD8-Positive T-Lymphocytes ; Immunity, Cellular ; },
abstract = {Despite the potential protective role of the gut microbiome against COVID-19, specific microbes conferring resistance to COVID-19 have not yet been identified. In this work, we aimed to identify and validate gut microbes at the species level that provide protection against SARS-CoV-2 infection. To identify gut microbes conferring protection against COVID-19, we conducted a fecal microbiota transplantation (FMT) from an individual with no history of COVID-19 infection or immunization into a lethal COVID-19 hamster model. FMT from this COVID-19-resistant donor resulted in significant phenotypic changes related to COVID-19 sensitivity in the hamsters. Metagenomic analysis revealed distinct differences in the gut microbiome composition among the hamster groups, leading to the identification of two previously unknown bacterial species: Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270, both associated with COVID-19 resistance. Subsequently, we conducted a proof-of-concept confirmation animal experiment adhering to Koch's postulates. Oral administration of this gut microbe pair, Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270, to the hamsters provided complete protection against SARS-CoV-2 infection through the activation of CD8+ T cell mediated immunity. The prophylactic efficacy of the gut microbe pair against SARS-CoV-2 infection was comparable to, or even superior to, current mRNA vaccines. This strong prophylactic efficacy suggests that the gut microbe pair could be developed as a host-directed universal vaccine for all betacoronaviruses, including potential future emerging viruses.},
}

Animals
Cricetinae
Ruminococcus
*Gastrointestinal Microbiome
*COVID-19
SARS-CoV-2
Clostridiales
CD8-Positive T-Lymphocytes
Immunity, Cellular

@article {pmid38635106,
year = {2024},
author = {Jang, YJ and Choi, HS and Oh, I and Chung, JH and Moon, JS},
title = {Effects of Limosilactobacillus reuteri ID-D01 Probiotic Supplementation on Exercise Performance and Gut Microbiota in Sprague-Dawley Rats.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {38635106},
issn = {1867-1314},
support = {Ministry of Education (MOE)(2021RIS-001) (no.1345370811)//National Research Foundation of Korea (NRF)/ ; },
abstract = {The gut microbiota composition in animals and humans has recently been found to be influenced by exercise. Although Limosilactobacillus reuteri strains have notable probiotic properties that promote human health, understanding of its effects in combination with exercise and physical activity is limited. Therefore, this study examined the effects of L. reuteri ID-D01, a human-derived probiotic, on exercise performance and fatigue in Sprague-Dawley rats. Organ weight, maximal running distance, serum biochemistry, muscle performance, microbial community composition, and short-chain fatty acid (SCFA) levels were assessed. Results indicated that ID-D01 supplementation significantly improved endurance performance. Rats in the probiotic group demonstrated a significant increase in maximal running distance compared with that in the control group (p < 0.05). Additionally, levels of fatigue markers, such as lactate and creatine phosphokinase, were significantly reduced in the ID-D01-administered groups, suggesting its potential to alleviate exercise-induced fatigue. Microbiome analysis revealed a distinct shift in gut microbiota composition in response to ID-D01 administration. The group that received ID-D01 probiotics exhibited a significant increase in the abundance of SCFA-producing bacteria, particularly Akkermansia spp., compared with that in the control groups. Furthermore, they showed elevated production of SCFAs, such as acetate and butyrate. In conclusion, this study demonstrated that ID-D01 can enhance exercise performance and reduce fatigue. Herein, we highlighted that human-derived probiotics could improve physical performance, as observed by changes in gut microbiota composition and SCFA production.},
}

@article {pmid38635003,
year = {2024},
author = {Lee, SH and Lee, JH and Lee, SW},
title = {Application of Microbiome-Based Therapies in Chronic Respiratory Diseases.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {38635003},
issn = {1976-3794},
support = {2020R1A2C1008431//National Research Foundation of Korea/ ; 2023R1A2C2006688//National Research Foundation of Korea/ ; RS-2023-00222687//National Research Foundation of Korea/ ; 2022M3A9G8017220//National Research Foundation of Korea/ ; },
abstract = {The application of microbiome-based therapies in various areas of human disease has recently increased. In chronic respiratory disease, microbiome-based clinical applications are considered compelling options due to the limitations of current treatments. The lung microbiome is ecologically dynamic and affected by various conditions, and dysbiosis is associated with disease severity, exacerbation, and phenotype as well as with chronic respiratory disease endotype. However, it is not easy to directly modulate the lung microbiome. Additionally, studies have shown that chronic respiratory diseases can be improved by modulating gut microbiome and administrating metabolites. Although the composition, diversity, and abundance of the microbiome between the gut and lung are considerably different, modulation of the gut microbiome could improve lung dysbiosis. The gut microbiome influences that of the lung via bacterial-derived components and metabolic degradation products, including short-chain fatty acids. This phenomenon might be associated with the cross-talk between the gut microbiome and lung, called gut-lung axis. There are multiple alternatives to modulate the gut microbiome, such as prebiotics, probiotics, and postbiotics ingestion and fecal material transplantation. Several studies have shown that high-fiber diets, for example, present beneficial effects through the production of short-chain fatty acids. Additionally, genetically modified probiotics to secrete some beneficial molecules might also be utilized to treat chronic respiratory diseases. Further studies on microbial modulation to regulate immunity and potentiate conventional pharmacotherapy will improve microbiome modulation techniques, which will develop as a new therapeutic area in chronic respiratory diseases.},
}

@article {pmid38634795,
year = {2024},
author = {Siqueira, JF and Silva, WO and Romeiro, K and Gominho, LF and Alves, FRF and Rôças, IN},
title = {Apical root canal microbiome associated with primary and posttreatment apical periodontitis: A systematic review.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.14071},
pmid = {38634795},
issn = {1365-2591},
support = {//CNPq/ ; //FAPERJ/ ; },
abstract = {BACKGROUND: Microorganisms colonizing the apical root canal system are conceivably the ones directly involved with the causation and maintenance of apical periodontitis.

OBJECTIVES: This article systematically reviews the reports on the microbiome occurring exclusively at the apical root canal of teeth with primary and posttreatment apical periodontitis.

METHODS: The electronic databases PubMed, Embase, Web of Science, Science Direct, and Proquest were searched up to August 2023. Clinical studies using culture and molecular microbiology methods to identify the microbial taxa present exclusively in the apical root canal segment of infected teeth with apical periodontitis were included. Studies were critically assessed using the Joanna Briggs Institute Critical Prevalence Assessment Checklist.

RESULTS: From 2277 articles initially detected, 52 were selected for full reading and 21 were eventually included in this review. Of these, molecular methods were used in 19 and culture in 2 studies. Ten studies evaluated primary infections, 8 evaluated posttreatment infections, and 3 included both. Cryopulverization of the apical root specimens was conducted in 11 studies. All studies evaluated the prevalence and diversity of bacteria, and only one also reported on fungi. Overall, the most frequent/abundant bacterial taxa found in the apical canal of primary infections were Pseudoramibacter alactolyticus, Olsenella uli, Fusobacterium species, Streptococcus species, Porphyromonas endodontalis, Prevotella species, Actinomyces species, Parvimonas micra, Treponema denticola, Synergistetes species, and an as-yet uncharacterized taxon. In posttreatment infections, the most prevalent/abundant bacterial taxa included species of Streptococcus, Enterococcus, Fusobacterium, Actinomyces, Pseudoramibacter, Pseudomonas, and Propionibacterium. At the phylum level, Firmicutes was the most represented. The average apical bacterial load ranged from 10[5] to 10[6] in primary infections and from 10[3] to 10[4] in posttreatment infections.

DISCUSSION: Microbial diversity in the apical part of the root canal system was examined encompassing data from both primary and posttreatment infections. Heterogeneity amongst the studies, especially in sample collection and microbial identification methods, is an important limitation that prevented a meta-analysis.

CONCLUSIONS: There is a pronounced bacterial diversity in the infected apical canal, with a high interindividual variability. Different microbiome compositions at the species/genus level are observed according to the infection type.

REGISTRATION: PROSPERO CRD42021275886.},
}

@article {pmid38634770,
year = {2024},
author = {Lee, I and Jo, JW and Woo, HJ and Suk, KT and Lee, SS and Kim, BS},
title = {Proton pump inhibitors increase the risk of carbapenem-resistant Enterobacteriaceae colonization by facilitating the transfer of antibiotic resistance genes among bacteria in the gut microbiome.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2341635},
pmid = {38634770},
issn = {1949-0984},
mesh = {Humans ; Proton Pump Inhibitors ; *Gastrointestinal Microbiome ; *Carbapenem-Resistant Enterobacteriaceae ; Case-Control Studies ; Bacteria ; Anti-Bacterial Agents ; Drug Resistance, Microbial ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) pose a global health threat; however, there is still limited understanding of the risk factors and underlying mechanisms of CRE colonization in the gut microbiome. We conducted a matched case-control study involving 282 intensive care unit patients to analyze influencing covariates on CRE colonization. Subsequently, their effects on the gut microbiome were analyzed in a subset of 98 patients (47 CRE carriers and 51 non-CRE carriers) using whole metagenome sequences. The concomitant use of proton pump inhibitors (PPIs) and antibiotics was a significant risk factor for CRE colonization. The gut microbiome differed according to PPI administration, even within the CRE and non-CRE groups. Moreover, the transfer of mobile genetic elements (MGEs) harboring carbapenem resistance genes (CRGs) between bacteria was higher in the PPI-treated group than in the PPI-not-treated group among CRE carriers. The concomitant use of PPIs and antibiotics significantly alters the gut microbiome and increases the risk of CRE colonization by facilitating the transfer of CRGs among bacteria of the gut microbiome. Based on these findings, improved stewardship of PPIs as well as antibiotics can provide strategies to reduce the risk of CRE colonization, thereby potentially improving patient prognosis.},
}

Humans
Proton Pump Inhibitors
*Gastrointestinal Microbiome
*Carbapenem-Resistant Enterobacteriaceae
Case-Control Studies
Bacteria
Anti-Bacterial Agents
Drug Resistance, Microbial

@article {pmid38634692,
year = {2024},
author = {Zimmermann, J and Piecyk, A and Sieber, M and Petersen, C and Johnke, J and Moitinho-Silva, L and Künzel, S and Bluhm, L and Traulsen, A and Kaleta, C and Schulenburg, H},
title = {Gut-associated functions are favored during microbiome assembly across a major part of C. elegans life.},
journal = {mBio},
volume = {},
number = {},
pages = {e0001224},
doi = {10.1128/mbio.00012-24},
pmid = {38634692},
issn = {2150-7511},
abstract = {UNLABELLED: The microbiome expresses a variety of functions that influence host biology. The range of functions depends on the microbiome's composition, which can change during the host's lifetime due to neutral assembly processes, host-mediated selection, and environmental conditions. To date, the exact dynamics of microbiome assembly, the underlying determinants, and the effects on host-associated functions remain poorly understood. Here, we used the nematode Caenorhabditis elegans and a defined community of fully sequenced, naturally associated bacteria to study microbiome dynamics and functions across a major part of the worm's lifetime of hosts under controlled experimental conditions. Bacterial community composition initially shows strongly declining levels of stochasticity, which increases during later time points, suggesting selective effects in younger animals as opposed to more random processes in older animals. The adult microbiome is enriched in genera Ochrobactrum and Enterobacter compared to the direct substrate and a host-free control environment. Using pathway analysis, metabolic, and ecological modeling, we further find that the lifetime assembly dynamics increase competitive strategies and gut-associated functions in the host-associated microbiome, indicating that the colonizing bacteria benefit the worm. Overall, our study introduces a framework for studying microbiome assembly dynamics based on stochastic, ecological, and metabolic models, yielding new insights into the processes that determine host-associated microbiome composition and function.

IMPORTANCE: The microbiome plays a crucial role in host biology. Its functions depend on the microbiome composition that can change during a host's lifetime. To date, the dynamics of microbiome assembly and the resulting functions still need to be better understood. This study introduces a new approach to characterize the functional consequences of microbiome assembly by modeling both the relevance of stochastic processes and metabolic characteristics of microbial community changes. The approach was applied to experimental time-series data obtained for the microbiome of the nematode Caenorhabditis elegans across the major part of its lifetime. Stochastic processes played a minor role, whereas beneficial bacteria as well as gut-associated functions enriched in hosts. This indicates that the host might actively shape the composition of its microbiome. Overall, this study provides a framework for studying microbiome assembly dynamics and yields new insights into C. elegans microbiome functions.},
}

@article {pmid38634357,
year = {2024},
author = {Xu, YJ and He, Y and Chen, C and Shi, J and He, M and Liu, Y and Zhang, Y and Liu, Y and Zhang, Y},
title = {Multiomics Analysis Revealed Colorectal Cancer Pathogenesis.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.3c00894},
pmid = {38634357},
issn = {1535-3907},
abstract = {Gut microbiota-derived microbial compounds may link to the pathogenesis of colorectal cancer (CRC). However, the role of the host-microbiome in the incidence and progression of CRC remains elusive. We performed 16S rRNA sequencing, metabolomics, and proteomic studies on samples from 85 CRC patients who underwent colonoscopy examination and found two distinct changed patterns of microbiome in CRC patients. The relative abundances of Catabacter and Mogibacterium continuously increased from intramucosal carcinoma to advanced stages, whereas Clostridium, Anaerostipes, Vibrio, Flavonifractor, Holdemanella, and Hungatella were significantly altered only in intermediate lesions. Fecal metabolomics analysis exhibited consistent increases in bile acids, indoles, and urobilin as well as a decrease in heme. Serum metabolomics uncovered the highest levels of bilin, glycerides, and nucleosides together with the lowest levels of bile acids and amino acids in the stage of intermediate lesions. Three fecal and one serum dipeptides were elevated in the intermediate lesions. Proteomics analysis of colorectal tissues showed that oxidation and autophagy through the PI3K/Akt-mTOR signaling pathway contribute to the development of CRC. Diagnostic analysis showed multiomics features have good predictive capability, with AUC greater than 0.85. Our overall findings revealed new candidate biomarkers for CRC, with potentially significant diagnostic and prognostic capabilities.},
}

@article {pmid38634147,
year = {2024},
author = {Qian, J and Zhao, X and Yuan, S and Su, S and Chen, C and Gao, J and Tang, X and Men, S and Wen, B},
title = {Metabolome-microbiome insights into therapeutic impact of 8-O-acetylharpagide against breast cancer in a murine model.},
journal = {Biomedical chromatography : BMC},
volume = {},
number = {},
pages = {e5880},
doi = {10.1002/bmc.5880},
pmid = {38634147},
issn = {1099-0801},
support = {JJ-2020-39//Beijing Science and Technology Development Fund Project of Traditional Chinese Medicine/ ; },
abstract = {Iridoid glycosides extract, which is the main active extract of Ajuga decumbens Thunb, has been proved to have anti-breast cancer activity in previous studies. However, it is still unknown whether 8-O-acetylharpagide, a main active compound in the extract, has anti-breast cancer activity. In this study, 4 T1 breast cancer mice model was first successfully established. Then the anti-breast cancer effect of 8-O-acetylharpagide was systematically investigated. Feces were collected for metabolomics and 16S rRNA analysis to assess the potential mechanism. The results showed that 8-O-acetylharpagide was effective in reducing 4 T1 mouse tumor volume and weight compared with the model group. Metabolome analysis revealed 12 potential metabolite biomarkers in feces, mainly involved in primary bile acid biosynthesis and arachidonic acid metabolism. The 16S rRNA sequencing results demonstrated that 8-O-acetylharpagide modulated the abundance of the intestinal flora in 4 T1 mice. Spearman correlation analysis showed that calcitriol and prostaglandin G2 strongly correlated with Akkermansia, Firmicutes and Muribaculum. Overall, the active compound 8-O-acetylharpagide could inhibit significantly breast cancer growth in 4 T1 breast cancer model mice. The mechanism of the anti-breast cancer effect of 8-O-acetylharpagide may be related to the regulation of primary bile acid biosynthesis and arachidonic acid metabolism and modulation of the abundance of Akkermansia and Firmicutes.},
}

@article {pmid38634136,
year = {2024},
author = {Moore, BN and Medcalf, AD and Muir, RQ and Xu, C and Marques, FZ and Pluznick, JL},
title = {Commensal Microbiota Regulate Aldosterone.},
journal = {American journal of physiology. Renal physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajprenal.00051.2024},
pmid = {38634136},
issn = {1522-1466},
support = {R01DK137762/NH/NIH HHS/United States ; },
abstract = {The gut microbiome regulates many important host physiological processes associated with cardiovascular health and disease; however, the impact of the gut microbiome on aldosterone is unclear. Investigating whether gut microbiota regulate aldosterone can offer novel insights into how the microbiome affects blood pressure. In this study, we aimed to determine whether gut microbiota regulate host aldosterone. We employed enzyme-linked immunosorbent assays (ELISAs) to assess plasma aldosterone and plasma renin activity (PRA) in female and male mice in which gut microbiota are intact, suppressed, or absent. In addition, we examined urinary aldosterone. Our findings demonstrated that when the gut microbiota is suppressed following antibiotic treatment, there is an increase in plasma and urinary aldosterone in both female and male mice. In contrast, an increase in PRA is seen only in males. We also found that when gut microbiota are absent (germ-free mice), plasma aldosterone is significantly increased compared to conventional animals (in both females and males), but PRA is not. Understanding how gut microbiota influence aldosterone levels could provide valuable insights into the development and treatment of hypertension and/or primary aldosteronism. This knowledge may open new avenues for therapeutic interventions, such as probiotics or dietary modifications to help regulate blood pressure via microbiota-based changes to aldosterone.},
}

@article {pmid38634007,
year = {2024},
author = {Wen, C and Chen, D and Zhong, R and Peng, X},
title = {Animal models of inflammatory bowel disease: category and evaluation indexes.},
journal = {Gastroenterology report},
volume = {12},
number = {},
pages = {goae021},
pmid = {38634007},
issn = {2052-0034},
abstract = {Inflammatory bowel disease (IBD) research often relies on animal models to study the etiology, pathophysiology, and management of IBD. Among these models, rats and mice are frequently employed due to their practicality and genetic manipulability. However, for studies aiming to closely mimic human pathology, non-human primates such as monkeys and dogs offer valuable physiological parallels. Guinea pigs, while less commonly used, present unique advantages for investigating the intricate interplay between neurological and immunological factors in IBD. Additionally, New Zealand rabbits excel in endoscopic biopsy techniques, providing insights into mucosal inflammation and healing processes. Pigs, with their physiological similarities to humans, serve as ideal models for exploring the complex relationships between nutrition, metabolism, and immunity in IBD. Beyond mammals, non-mammalian organisms including zebrafish, Drosophila melanogaster, and nematodes offer specialized insights into specific aspects of IBD pathology, highlighting the diverse array of model systems available for advancing our understanding of this multifaceted disease. In this review, we conduct a thorough analysis of various animal models employed in IBD research, detailing their applications and essential experimental parameters. These include clinical observation, Disease Activity Index score, pathological assessment, intestinal barrier integrity, fibrosis, inflammatory markers, intestinal microbiome, and other critical parameters that are crucial for evaluating modeling success and drug efficacy in experimental mammalian studies. Overall, this review will serve as a valuable resource for researchers in the field of IBD, offering insights into the diverse array of animal models available and their respective applications in studying IBD.},
}

@article {pmid38633890,
year = {2024},
author = {Amponsah, AS and Ankar-Brewoo, GM and Lutterodt, HE and Ofosu, IW},
title = {Assessing the microbial diversity and proximate composition of smoked-fermented bushmeat from four different bushmeat samples.},
journal = {Biotechnologia},
volume = {105},
number = {1},
pages = {5-17},
pmid = {38633890},
issn = {2353-9461},
abstract = {The ever-increasing demand for wildlife-derived raw or processed meat commonly known as bushmeat, has been identified as one of the critical factors driving the emergence of infectious diseases. This study focused on examining the bacterial community composition of smoked and fermented bushmeats, specifically grasscutter, rat, rabbit, and mona monkey. The analysis involved exploring 16Sr RNA amplicon sequences isolated from bushmeat using QIIME2. Microbiome profiles and their correlation with proximate components (PLS regression) were computed in STAMP and XLSTAT, respectively. Results indicate the predominance of Firmicutes (70.9%), Actinobacteria (18.58%), and Proteobacteria (9.12%) in bushmeat samples at the phylum level. Staphylococcus, Arthrobacter, Macrococcus, and Proteus constituted the core microbiomes in bushmeat samples, ranked in descending order. Notably, significant differences were observed between the bacterial communities of bushmeat obtained from omnivores and herbivores (rat and mona monkey, and grasscutter and mona monkey), as well as those with similar feeding habits (rat and monkey, and grasscutter and rabbit) at the family and genus levels. Each type of bushmeat possessed unique microbial diversity, with some proximate components such as fat in rat samples correlating with Staphylococcus, while proteins in Mona monkey correlated with Arthrobacter and Brevibacterium, respectively. The study underscores public health concerns and highlights probiotic benefits, as bushmeat samples contained both pathogenic and beneficial bacteria. Therefore, future research efforts could focus on improving bushmeat quality.},
}

@article {pmid38633809,
year = {2024},
author = {Dedon, LR and Yuan, H and Chi, J and Gu, H and Arias, AJ and Covault, JM and Zhou, Y},
title = {Baseline gut microbiome and metabolites are correlated with alcohol consumption in a zonisamide clinical trial of heavy drinking alcoholic civilians.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.02.24305199},
pmid = {38633809},
abstract = {Development and severity of alcohol use disorder (AUD) has been linked to variations in gut microbiota and their associated metabolites in both animal and human studies. However, the involvement of the gut microbiome in alcohol consumption of individuals with AUD undergoing treatment remains unclear. To address this, stool samples (n=48) were collected at screening (baseline) and trial completion from a single site of a multi-site double-blind, placebo-controlled trial of Zonisamide in individuals with AUD. Alcohol consumption, gamma-glutamyl transferase (GGT), and phosphatidylethanol (PEth)levels were measured both at baseline and endpoint of 16-week trial period. Fecal microbiome was analyzed via 16S rRNA sequencing and metabolome via untargeted LC-MS. Both sex (p = 0.003) and psychotropic medication usage (p = 0.025) are associated with baseline microbiome composition. The relative abundance of 12 genera at baseline was correlated with percent drinking reduction, baseline and endpoint alcohol consumption, and changes in GGT and PeTH over the course of treatment (p.adj < 0.05). Overall microbiome community structure at baseline differed between high and low responders (67-100% and 0-33% drinking reduction, respectively; p = 0.03). A positive relationship between baseline fecal GABA levels and percent drinking reduction (R=0.43, p < 0.05) was identified by microbiome function prediction and confirmed by ELISA and metabolomics. Predicted microbiome function and metabolomics analysis have found that tryptophan metabolic pathways are over-represented in low responders. These findings highlight importance of baseline microbiome and metabolites in alcohol consumption in AUD patients undergoing zonisamide treatment.},
}

@article {pmid38633744,
year = {2024},
author = {Shao, Z and Gao, H and Wang, B and Zhang, S},
title = {Exploring the impact of pathogenic microbiome in orthopedic diseases: machine learning and deep learning approaches.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1380136},
pmid = {38633744},
issn = {2235-2988},
mesh = {Humans ; *Deep Learning ; Quality of Life ; *Musculoskeletal Diseases ; Machine Learning ; *Microbiota ; },
abstract = {Osteoporosis, arthritis, and fractures are examples of orthopedic illnesses that not only significantly impair patients' quality of life but also complicate and raise the expense of therapy. It has been discovered in recent years that the pathophysiology of orthopedic disorders is significantly influenced by the microbiota. By employing machine learning and deep learning techniques to conduct a thorough analysis of the disease-causing microbiome, we can enhance our comprehension of the pathophysiology of many illnesses and expedite the creation of novel treatment approaches. Today's science is undergoing a revolution because to the introduction of machine learning and deep learning technologies, and the field of biomedical research is no exception. The genesis, course, and management of orthopedic disorders are significantly influenced by pathogenic microbes. Orthopedic infection diagnosis and treatment are made more difficult by the lengthy and imprecise nature of traditional microbial detection and characterization techniques. These cutting-edge analytical techniques are offering previously unheard-of insights into the intricate relationships between orthopedic health and pathogenic microbes, opening up previously unimaginable possibilities for illness diagnosis, treatment, and prevention. The goal of biomedical research has always been to improve diagnostic and treatment methods while also gaining a deeper knowledge of the processes behind the onset and development of disease. Although traditional biomedical research methodologies have demonstrated certain limits throughout time, they nevertheless rely heavily on experimental data and expertise. This is the area in which deep learning and machine learning approaches excel. The advancements in machine learning (ML) and deep learning (DL) methodologies have enabled us to examine vast quantities of data and unveil intricate connections between microorganisms and orthopedic disorders. The importance of ML and DL in detecting, categorizing, and forecasting harmful microorganisms in orthopedic infectious illnesses is reviewed in this work.},
}

Humans
*Deep Learning
Quality of Life
*Musculoskeletal Diseases
Machine Learning
*Microbiota

@article {pmid38633690,
year = {2024},
author = {Zhao, M and Zhang, Y and Li, Y and Liu, K and Bao, K and Li, G},
title = {Impact of Pediococcus acidilactici GLP06 supplementation on gut microbes and metabolites in adult beagles: a comparative analysis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1369402},
pmid = {38633690},
issn = {1664-302X},
abstract = {There is growing interest in the potential health benefits of probiotics for both humans and animals. The study aimed to investigate the effects of feeding the canine-derived probiotic Pediococcus acidilactici GLP06 to adult beagles by analysing the microbiome and metabolome. Twenty-four healthy adult beagles were randomly assigned to four groups. The CK group received a standard diet, while the three probiotic groups, the LG group (2 × 10[8] CFU/day/dog), MG group (2 × 10[9] CFU/day/dog), and HG group (2 × 10[10] CFU/day/dog), received the standard diet supplemented with varying amounts of probiotics. The results show that, compared to the CK group, total antioxidant capacity was significantly increased in the MG and HG groups (p < 0.05), and superoxide dismutase and catalase were significantly increased in the HG group (p < 0.05). Compared to the CK group, malondialdehyde and blood urea nitrogen content were significantly decreased in the MG and HG groups (p < 0.05). Additionally, secretory immunoglobulin A activity was significantly increased in the HG group compared to the CK and LG groups (p < 0.05), and immunoglobulin G activity was significantly increased in the HG group compared to the CK, LG, and MG groups (p < 0.05). In addition, compared with the CK group, the abundance of Faecalitalea and Collinsella increased in the LG group, and the relative abundance of Tyzzerella and Parasutterella increased in the MG group. The α diversity and the relative abundances of beneficial bacteria (Faecalibacterium, Lachnospiraceae_NK4A1316, and Ruminococcaceae_UCG-005) were higher in the HG group than in the CK group. Furthermore, acetic acid content was significantly increased in the HG group compared to the CK, LG, and MG groups (p < 0.05). Butyric acid, isobutyric acid, and the total SCFA content were significantly increased in the HG group compared to the CK group (p < 0.05). Moreover, metabolome analysis revealed 111 upregulated and 171 downregulated metabolites in the HG group. In conclusion, this study presents evidence that supplementing with P. acidilactici GLP06 can have a positive impact on antioxidant activity, immunoproteins, SCFAs, and gut microbiota in adult beagles. These findings highlight the potential of probiotics as a dietary intervention to enhance gut health and overall wellbeing in companion animals.},
}

@article {pmid38633603,
year = {2024},
author = {Bacha, AA and Suhail, M and Awwad, FA and Ismail, EAA and Ahmad, H},
title = {Role of dietary fiber and lifestyle modification in gut health and sleep quality.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1324793},
pmid = {38633603},
issn = {2296-861X},
abstract = {Dietary fiber has an immense role in the gut microbiome by modulating juvenile growth, immune system maturation, glucose, and lipid metabolism. Lifestyle changes might disrupt gut microbiota symbiosis, leading to various chronic diseases with underlying inflammatory conditions, obesity, and its associated pathologies. An interventional study of 16 weeks examined the impact of psyllium husk fiber with and without lifestyle modification on gut health and sleep quality in people with central obesity (men = 60 and women = 60), those aged from 40 to 60 years, those having WC ≥ 90 cm (men) and WC ≥ 80 cm (women), and no history of any chronic disease or regular medication. The participants were subgrouped into three intervention groups, namely, the psyllium husk fiber (PSH) group, the lifestyle modification (LSM) group, and the LSM&PSH group and control group with equal gender bifurcation (men = 15 and women = 15). A 24-h dietary recall, gastrointestinal tract (GIT) symptoms, and sleep quality analysis data were collected on validated questionnaires. The analyses of variance and covariance were used for baseline and post-intervention, respectively. Student's t-test was applied for pre- and post-intervention changes on the variable of interest. The intervention effect on GIT health was highly significant (P < 0.001). The mean GIT scores of the LSM, PSH, and LSM&PSH groups were 2.99 ± 0.14, 2.49 ± 0.14, and 2.71 ± 0.14, respectively, compared to the mean GIT scores of the control group. No significant (P = 0.205) effect of either intervention was observed on sleep quality. The study concluded that psyllium husk fiber significantly improved the GIT symptoms, while no significant effect of the intervention was observed on sleep quality analysis.},
}

@article {pmid38633411,
year = {2024},
author = {Han, M and Wang, N and Han, W and Liu, X and Sun, T and Xu, J},
title = {Highly specific vaginal microbiome signature for gynecological cancers.},
journal = {Open life sciences},
volume = {19},
number = {1},
pages = {20220850},
doi = {10.1515/biol-2022-0850},
pmid = {38633411},
issn = {2391-5412},
abstract = {To investigate the vaginal microbiota signature of patients with gynecologic cancer and evaluate its diagnostic biomarker potential. We incorporated vaginal 16S rRNA-seq data from 529 women and utilized VSEARCH to analyze the raw data. α-Diversity was evaluated utilizing the Chao1, Shannon, and Simpson indices, and β-diversity was evaluated through principal component analysis using Bray-Curtis distances. Linear discriminant analysis effect size (LEfSe) was utilized to determine species differences between groups. A bacterial co-abundance network was constructed utilizing Spearman correlation analysis. A random forest model of gynecologic tumor risk based on genus was constructed and validated to test its diagnostic efficacy. In gynecologic cancer patients, vaginal α-diversity was significantly greater than in controls, and vaginal β-diversity was significantly separated from that of controls; there was no correlation between these characteristics and menopause status among the subject women. Women diagnosed with gynecological cancer exhibited a reduction in the abundance of vaginal Firmicutes and Lactobacillus, while an increase was observed in the proportions of Bacteroidetes, Proteobacteria, Prevotella, Streptococcus, and Anaerococcus. A random forest model constructed based on 56 genus achieved high accuracy (area under the curve = 84.96%) in gynecological cancer risk prediction. Furthermore, there were discrepancies observed in the community complexity of co-abundance networks between gynecologic cancer patients and the control group. Our study provides evidence that women with gynecologic cancer have a unique vaginal flora structure and microorganisms may be involved in the gynecologic carcinogenesis process. A gynecological cancer risk prediction model based on characteristic genera has good diagnostic value.},
}

@article {pmid38633385,
year = {2024},
author = {Rooney, J and Rivera-de-Torre, E and Li, R and Mclean, K and Price, DRG and Nisbet, AJ and Laustsen, AH and Jenkins, TP and Hofmann, A and Bakshi, S and Zarkan, A and Cantacessi, C},
title = {Structural and functional analyses of nematode-derived antimicrobial peptides support the occurrence of direct mechanisms of worm-microbiota interactions.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {1522-1533},
pmid = {38633385},
issn = {2001-0370},
abstract = {The complex relationships between gastrointestinal (GI) nematodes and the host gut microbiota have been implicated in key aspects of helminth disease and infection outcomes. Nevertheless, the direct and indirect mechanisms governing these interactions are, thus far, largely unknown. In this proof-of-concept study, we demonstrate that the excretory-secretory products (ESPs) and extracellular vesicles (EVs) of key GI nematodes contain peptides that, when recombinantly expressed, exert antimicrobial activity in vitro against Bacillus subtilis. In particular, using time-lapse microfluidics microscopy, we demonstrate that exposure of B. subtilis to a recombinant saposin-domain containing peptide from the 'brown stomach worm', Teladorsagia circumcincta, and a metridin-like ShK toxin from the 'barber's pole worm', Haemonchus contortus, results in cell lysis and significantly reduced growth rates. Data from this study support the hypothesis that GI nematodes may modulate the composition of the vertebrate gut microbiota directly via the secretion of antimicrobial peptides, and pave the way for future investigations aimed at deciphering the impact of such changes on the pathophysiology of GI helminth infection and disease.},
}

@article {pmid38633306,
year = {2024},
author = {Zhang, L and Liu, X and Fan, B and Chen, J and Chen, J and Li, Q and Wu, X},
title = {Microbiome features in bronchoalveolar lavage fluid of patients with idiopathic inflammatory myopathy-related interstitial lung disease.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1338947},
pmid = {38633306},
issn = {2296-858X},
abstract = {BACKGROUND: Interstitial lung disease (ILD) is a common complication of idiopathic inflammatory myopathy (IIM), which is one of the connective tissue diseases (CTD). It can lead to poor prognosis and increased mortality. However, the distribution and role of the lower respiratory tract (LRT) microbiome in patients with IIM-ILD remains unclear. This study aimed to investigate the microbial diversity and community differences in bronchoalveolar lavage fluid (BALF) in patients with IIM-ILD.

METHODS: From 28 June 2021 to 26 December 2023, 51 individual BALF samples were enrolled, consisting of 20 patients with IIM-ILD, 16 patients with other CTD-ILD (including 8 patients with SLE and 8 with RA) and 15 patients with CAP. The structure and function of microbiota in BALF were identified by metagenomic next-generation sequencing (mNGS).

RESULTS: The community evenness of LRT microbiota within the IIM-ILD group was marginally lower compared to the other CTD-ILD and CAP groups. Nonetheless, there were no noticeable differences. The species community structure was similar among the three groups, based on the Bray-Curtis distance between the samples. At the level of genus, the IIM-ILD group displayed a considerably higher abundance of Pseudomonas and Corynebacterium in comparison to the CAP group (p < 0.01, p < 0.05). At the species level, we found that the relative abundance of Pseudomonas aeruginosa increased significantly in the IIM-ILD group compared to the CAP group (p < 0.05). Additionally, the relative abundance of Prevotella pallens was significantly higher in other CTD-ILD groups compared to that in the IIM-ILD group (p < 0.05). Of all the clinical indicators examined in the correlation analysis, ferritin level demonstrated the strongest association with LRT flora, followed by Serum interleukin-6 level (p < 0.05).

CONCLUSION: Our research has identified particular LRT microorganisms that were found to be altered in the IIM-ILD group and were significantly associated with immune function and inflammatory markers in patients. The lower respiratory tract microbiota has potential in the diagnosis and treatment of IIM-ILD.},
}

@article {pmid38632606,
year = {2024},
author = {Liu, X and Zeng, X and Li, X and Xin, S and Zhang, F and Liu, F and Zeng, Y and Wu, J and Zou, Y and Xiong, X},
title = {Landscapes of gut bacterial and fecal metabolic signatures and their relationship in severe preeclampsia.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {360},
pmid = {38632606},
issn = {1479-5876},
support = {82160298//National Natural Science Foundation of China/ ; },
mesh = {Female ; Pregnancy ; Humans ; *Gastrointestinal Microbiome/genetics ; *Pre-Eclampsia ; *Agmatine ; Reproducibility of Results ; Feces/microbiology ; Metabolome ; Inflammation ; *Pregnancy Complications ; Bacteria ; *Hypertension ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: Preeclampsia is a pregnancy-specific disease leading to maternal and perinatal morbidity. Hypertension and inflammation are the main characteristics of preeclampsia. Many factors can lead to hypertension and inflammation, including gut microbiota which plays an important role in hypertension and inflammation in humans. However, alterations to the gut microbiome and fecal metabolome, and their relationships in severe preeclampsia are not well known. This study aims to identify biomarkers significantly associated with severe preeclampsia and provide a knowledge base for treatments regulating the gut microbiome.

METHODS: In this study, fecal samples were collected from individuals with severe preeclampsia and healthy controls for shotgun metagenomic sequencing to evaluate changes in gut microbiota composition. Quantitative polymerase chain reaction analysis was used to validate the reliability of our shotgun metagenomic sequencing results. Additionally, untargeted metabolomics analysis was performed to measure fecal metabolome concentrations.

RESULTS: We identified several Lactobacillaceae that were significantly enriched in the gut of healthy controls, including Limosilactobacillus fermentum, the key biomarker distinguishing severe preeclampsia from healthy controls. Limosilactobacillus fermentum was significantly associated with shifts in KEGG Orthology (KO) genes and KEGG pathways of the gut microbiome in severe preeclampsia, such as flagellar assembly. Untargeted fecal metabolome analysis found that severe preeclampsia had higher concentrations of Phenylpropanoate and Agmatine. Increased concentrations of Phenylpropanoate and Agmatine were associated with the abundance of Limosilactobacillus fermentum. Furthermore, all metabolites with higher abundances in healthy controls were enriched in the arginine and proline metabolism pathway.

CONCLUSION: Our research indicates that changes in metabolites, possibly due to the gut microbe Limosilactobacillus fermentum, can contribute to the development of severe preeclampsia. This study provides insights into the interaction between gut microbiome and fecal metabolites and offers a basis for improving severe preeclampsia by modulating the gut microbiome.},
}

Female
Pregnancy
Humans
*Gastrointestinal Microbiome/genetics
*Pre-Eclampsia
*Agmatine
Reproducibility of Results
Feces/microbiology
Metabolome
Inflammation
*Pregnancy Complications
Bacteria
*Hypertension
RNA, Ribosomal, 16S

@article {pmid38632579,
year = {2024},
author = {Yin, X and Duan, C and Zhang, L and Zhu, Y and Qiu, Y and Shi, K and Wang, S and Zhang, X and Zhang, H and Hao, Y and Yuan, F and Tian, Y},
title = {Microbiota-derived acetate attenuates neuroinflammation in rostral ventrolateral medulla of spontaneously hypertensive rats.},
journal = {Journal of neuroinflammation},
volume = {21},
number = {1},
pages = {101},
pmid = {38632579},
issn = {1742-2094},
support = {QN2021103//Science and Technology Project of Higher Education of Hebei Province/ ; H2021206203//Natural Science Foundation of Hebei Province for Innovative Research Group Project/ ; 82000401//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Rats ; Animals ; Rats, Inbred SHR ; Neuroinflammatory Diseases ; *Hypertension/metabolism ; Blood Pressure ; Medulla Oblongata/metabolism ; *Microbiota ; Acetates/pharmacology ; },
abstract = {BACKGROUND: Increased neuroinflammation in brain regions regulating sympathetic nerves is associated with hypertension. Emerging evidence from both human and animal studies suggests a link between hypertension and gut microbiota, as well as microbiota-derived metabolites short-chain fatty acids (SCFAs). However, the precise mechanisms underlying this gut-brain axis remain unclear.

METHODS: The levels of microbiota-derived SCFAs in spontaneously hypertensive rats (SHRs) were determined by gas chromatography-mass spectrometry. To observe the effect of acetate on arterial blood pressure (ABP) in rats, sodium acetate was supplemented via drinking water for continuous 7 days. ABP was recorded by radio telemetry. The inflammatory factors, morphology of microglia and astrocytes in rostral ventrolateral medulla (RVLM) were detected. In addition, blood-brain barrier (BBB) permeability, composition and metabolomics of the gut microbiome, and intestinal pathological manifestations were also measured.

RESULTS: The serum acetate levels in SHRs are lower than in normotensive control rats. Supplementation with acetate reduces ABP, inhibits sympathetic nerve activity in SHRs. Furthermore, acetate suppresses RVLM neuroinflammation in SHRs, increases microglia and astrocyte morphologic complexity, decreases BBB permeability, modulates intestinal flora, increases fecal flora metabolites, and inhibits intestinal fibrosis.

CONCLUSIONS: Microbiota-derived acetate exerts antihypertensive effects by modulating microglia and astrocytes and inhibiting neuroinflammation and sympathetic output.},
}

Humans
Rats
Animals
Rats, Inbred SHR
Neuroinflammatory Diseases
*Hypertension/metabolism
Blood Pressure
Medulla Oblongata/metabolism
*Microbiota
Acetates/pharmacology

@article {pmid38632506,
year = {2024},
author = {Alkathiry, HA and Alghamdi, SQ and Sinha, A and Margos, G and Stekolnikov, AA and Alagaili, AN and Darby, AC and Makepeace, BL and Khoo, JJ},
title = {Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {380},
pmid = {38632506},
issn = {1471-2164},
mesh = {Animals ; *Scrub Typhus/epidemiology/microbiology ; *Trombiculidae/genetics/microbiology ; *Wolbachia/genetics ; Phylogeny ; *Borrelia/genetics ; Multilocus Sequence Typing ; RNA, Ribosomal, 16S/genetics ; Saudi Arabia ; *Orientia tsutsugamushi/genetics ; Rodentia/genetics ; DNA ; *Microbiota ; Orientia ; },
abstract = {BACKGROUND: Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear.

RESULTS: Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin.

CONCLUSIONS: P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites.},
}

Animals
*Scrub Typhus/epidemiology/microbiology
*Trombiculidae/genetics/microbiology
*Wolbachia/genetics
Phylogeny
*Borrelia/genetics
Multilocus Sequence Typing
RNA, Ribosomal, 16S/genetics
Saudi Arabia
*Orientia tsutsugamushi/genetics
Rodentia/genetics
DNA
*Microbiota
Orientia

@article {pmid38632488,
year = {2024},
author = {Pais, N and Ravishanker, N and Rajasekaran, S and Weinstock, G and Tran, DB},
title = {Randomized feature selection based semi-supervised latent Dirichlet allocation for microbiome analysis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8855},
pmid = {38632488},
issn = {2045-2322},
mesh = {Humans ; Algorithms ; *Microbiota ; *Gastrointestinal Microbiome ; },
abstract = {Health and disease are fundamentally influenced by microbial communities and their genes (the microbiome). An in-depth analysis of microbiome structure that enables the classification of individuals based on their health can be crucial in enhancing diagnostics and treatment strategies to improve the overall well-being of an individual. In this paper, we present a novel semi-supervised methodology known as Randomized Feature Selection based Latent Dirichlet Allocation (RFSLDA) to study the impact of the gut microbiome on a subject's health status. Since the data in our study consists of fuzzy health labels, which are self-reported, traditional supervised learning approaches may not be suitable. As a first step, based on the similarity between documents in text analysis and gut-microbiome data, we employ Latent Dirichlet Allocation (LDA), a topic modeling approach which uses microbiome counts as features to group subjects into relatively homogeneous clusters, without invoking any knowledge of observed health status (labels) of subjects. We then leverage information from the observed health status of subjects to associate these clusters with the most similar health status making it a semi-supervised approach. Finally, a feature selection technique is incorporated into the model to improve the overall classification performance. The proposed method provides a semi-supervised topic modelling approach that can help handle the high dimensionality of the microbiome data in association studies. Our experiments reveal that our semi-supervised classification algorithm is effective and efficient in terms of high classification accuracy compared to popular supervised learning approaches like SVM and multinomial logistic model. The RFSLDA framework is attractive because it (i) enhances clustering accuracy by identifying key bacteria types as indicators of health status, (ii) identifies key bacteria types within each group based on estimates of the proportion of bacteria types within the groups, and (iii) computes a measure of within-group similarity to identify highly similar subjects in terms of their health status.},
}

Humans
Algorithms
*Microbiota
*Gastrointestinal Microbiome

@article {pmid38632454,
year = {2024},
author = {},
title = {Video game unleashes millions of citizen scientists on microbiome research.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {38632454},
issn = {1546-1696},
}

@article {pmid38632445,
year = {2024},
author = {Marchal, I},
title = {Mapping the landscape of host-microbiome interactions.},
journal = {Nature biotechnology},
volume = {42},
number = {4},
pages = {571},
doi = {10.1038/s41587-024-02219-x},
pmid = {38632445},
issn = {1546-1696},
}

@article {pmid38632423,
year = {2024},
author = {King, A},
title = {Exploring the lung microbiome's role in disease.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38632423},
issn = {1476-4687},
}

@article {pmid38632312,
year = {2024},
author = {Chen, S and Hu, Z and Tang, J and Zhu, H and Zheng, Y and Xiao, J and Xu, Y and Wang, Y and Luo, Y and Mo, X and Wu, Y and Guo, J and Zhang, Y and Luo, H},
title = {High temperature and humidity in the environment disrupt bile acid metabolism, the gut microbiome, and GLP-1 secretion in mice.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {465},
pmid = {38632312},
issn = {2399-3642},
support = {82174244//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2021xk40//Guangzhou University of Chinese Medicine (GUCM)/ ; },
mesh = {Animals ; Mice ; *Glucagon-Like Peptide 1/genetics/metabolism ; *Gastrointestinal Microbiome ; Humidity ; Proteomics ; RNA, Ribosomal, 16S ; Temperature ; Transcription Factors ; Bile Acids and Salts ; Lithocholic Acid ; },
abstract = {High temperature and humidity in the environment are known to be associated with discomfort and disease, yet the underlying mechanisms remain unclear. We observed a decrease in plasma glucagon-like peptide-1 levels in response to high-temperature and humidity conditions. Through 16S rRNA gene sequencing, alterations in the gut microbiota composition were identified following exposure to high temperature and humidity conditions. Notably, changes in the gut microbiota have been implicated in bile acid synthesis. Further analysis revealed a decrease in lithocholic acid levels in high-temperature and humidity conditions. Subsequent in vitro experiments demonstrated that lithocholic acid increases glucagon-like peptide-1 secretion in NCI-H716 cells. Proteomic analysis indicated upregulation of farnesoid X receptor expression in the ileum. In vitro experiments revealed that the combination of lithocholic acid with farnesoid X receptor inhibitors resulted in a significant increase in GLP-1 levels compared to lithocholic acid alone. In this study, we elucidate the mechanism by which reduced lithocholic acid suppresses glucagon-like peptide 1 via farnesoid X receptor activation under high-temperature and humidity condition.},
}

Animals
Mice
*Glucagon-Like Peptide 1/genetics/metabolism
*Gastrointestinal Microbiome
Humidity
Proteomics
RNA, Ribosomal, 16S
Temperature
Transcription Factors
Bile Acids and Salts
Lithocholic Acid

@article {pmid38632045,
year = {2024},
author = {Alwali, AY and Santos, D and Aguilar, C and Birch, A and Rodriguez-Orduña, L and Roberts, CB and Modi, R and Licona-Cassani, C and Parkinson, EI},
title = {Discovery of Streptomyces species CS-62, a novel producer of the Acinetobacter baumannii selective antibiotic factumycin.},
journal = {Journal of industrial microbiology & biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jimb/kuae014},
pmid = {38632045},
issn = {1476-5535},
abstract = {Narrow spectrum antibiotics are of great interest given their ability to spare the microbiome and decrease widespread antibiotic resistance compared to broad spectrum antibiotics. Herein we screened an in-house library of Actinobacteria strains for selective activity against Acinetobacter baumannii and successfully identified Streptomyces sp. CS-62 as a producer of a natural product with this valuable activity. Analysis of the cultures via high resolution mass spectrometry and tandem mass spectrometry followed by comparison with molecules in the Natural Product Atlas (NP Atlas) and the Global Natural Products Social Molecular Networking (GNPS) platform suggested a novel natural product. Genome mining analysis initially supported the production of a novel kirromycin derivative. Isolation and structure elucidation via mass spectrometry and NMR analyses revealed that the active natural product was the known natural product factumycin, exposing omissions and errors in the consulted databases. While public databases are generally very useful for avoiding rediscovery of known molecules, rediscovery remains a problem due to public databases either being incomplete or having errors that result in failed dereplication. Overall, the work describes the ongoing problem of dereplication and the continued need for public database curation.},
}

@article {pmid38631877,
year = {2024},
author = {Browning, BD and Kirkland, AE and Green, R and Liu, H and Glover, JS and Ticer, TD and Engevik, MA and Alekseyenko, AV and Ferguson, PL and Tomko, RL and Squeglia, LM},
title = {Adolescent alcohol use is associated with differences in the diversity and composition of the oral microbiome.},
journal = {Alcohol, clinical & experimental research},
volume = {},
number = {},
pages = {},
doi = {10.1111/acer.15331},
pmid = {38631877},
issn = {2993-7175},
support = {F31AA030920/AA/NIAAA NIH HHS/United States ; K24AA031052/AA/NIAAA NIH HHS/United States ; K23AA025399/AA/NIAAA NIH HHS/United States ; K12DA031794/AA/NIAAA NIH HHS/United States ; F32AA029930/AA/NIAAA NIH HHS/United States ; T32GM132055/AA/NIAAA NIH HHS/United States ; T32DK124191/AA/NIAAA NIH HHS/United States ; K01DK123195/AA/NIAAA NIH HHS/United States ; U54DA016511/NH/NIH HHS/United States ; UL1 TR001450/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Adolescence is a sensitive stage of oral microbial development that often coincides with the initiation and escalation of alcohol use. Thus, adolescents may be particularly susceptible to alcohol-induced alterations in the oral microbiome, though minimal research has been done in this area. Understanding the connection between the oral microbiome and alcohol use during adolescence is important to understand fully the biological consequences of alcohol use to mitigate potential adverse outcomes.

METHODS: Saliva samples were collected from adolescents aged 17-19 who used alcohol heavily (n = 21, 52.4% female) and those who did not use alcohol or any other substances (n = 18, 44.4% female). We utilized 16S rRNA sequencing to examine differences in microbial diversity and composition between the groups.

RESULTS: For alpha diversity, evenness was significantly lower in the drinking group than the control group as indicated by Pielou's evenness, Shannon, and Simpson indices. There were no statistically significant findings for beta diversity. Differential abundance analyses revealed higher abundances of Rothia and Corynebacterium in the alcohol-using group using both centered-log-ratio and relative abundance normalization. These genera are known for their high capacity to convert alcohol into acetaldehyde, a toxic metabolite reported to play a role in the neurobiological effects of alcohol. An unclassified Clostridia UCG-014, Streptobacillus, Comamonas, unclassified Lachnospiraceae, and Parvimonas were also identified as significantly different between groups when using only one of the normalization techniques.

CONCLUSIONS: This is the first study designed specifically to compare the oral microbiome of adolescents who use alcohol with that of control participants. Our findings reveal distinct alcohol-related differences in microbial composition and taxon abundance, emphasizing the importance of understanding the impact on the oral microbiome of alcohol use during adolescence. Because the oral microbiome is malleable, this study provides foundational work for future prevention and intervention studies.},
}

@article {pmid38631839,
year = {2024},
author = {Wyatt, NJ and Watson, H and Anderson, CA and Kennedy, NA and Raine, T and Ahmad, T and Allerton, D and Bardgett, M and Clark, E and Clewes, D and Cotobal Martin, C and Doona, M and Doyle, JA and Frith, K and Hancock, HC and Hart, AL and Hildreth, V and Irving, PM and Iqbal, S and Kennedy, C and King, A and Lawrence, S and Lees, CW and Lees, R and Letchford, L and Liddle, T and Lindsay, JO and Maier, RH and Mansfield, JC and Marchesi, JR and McGregor, N and McIntyre, RE and Ostermayer, J and Osunnuyi, T and Powell, N and Prescott, NJ and Satsangi, J and Sharma, S and Shrestha, T and Speight, A and Strickland, M and Wason, JM and Whelan, K and Wood, R and Young, GR and Zhang, X and Parkes, M and Stewart, CJ and Jostins-Dean, L and Lamb, CA},
title = {Defining predictors of responsiveness to advanced therapies in Crohn's disease and ulcerative colitis: protocol for the IBD-RESPONSE and nested CD-metaRESPONSE prospective, multicentre, observational cohort study in precision medicine.},
journal = {BMJ open},
volume = {14},
number = {4},
pages = {e073639},
doi = {10.1136/bmjopen-2023-073639},
pmid = {38631839},
issn = {2044-6055},
mesh = {Humans ; *Crohn Disease/drug therapy ; *Colitis, Ulcerative/therapy ; Precision Medicine ; Prospective Studies ; Quality of Life ; *Inflammatory Bowel Diseases/drug therapy ; Observational Studies as Topic ; Multicenter Studies as Topic ; },
abstract = {INTRODUCTION: Characterised by chronic inflammation of the gastrointestinal tract, inflammatory bowel disease (IBD) symptoms including diarrhoea, abdominal pain and fatigue can significantly impact patient's quality of life. Therapeutic developments in the last 20 years have revolutionised treatment. However, clinical trials and real-world data show primary non-response rates up to 40%. A significant challenge is an inability to predict which treatment will benefit individual patients.Current understanding of IBD pathogenesis implicates complex interactions between host genetics and the gut microbiome. Most cohorts studying the gut microbiota to date have been underpowered, examined single treatments and produced heterogeneous results. Lack of cross-treatment comparisons and well-powered independent replication cohorts hampers the ability to infer real-world utility of predictive signatures.IBD-RESPONSE will use multi-omic data to create a predictive tool for treatment response. Future patient benefit may include development of biomarker-based treatment stratification or manipulation of intestinal microbial targets. IBD-RESPONSE and downstream studies have the potential to improve quality of life, reduce patient risk and reduce expenditure on ineffective treatments.

METHODS AND ANALYSIS: This prospective, multicentre, observational study will identify and validate a predictive model for response to advanced IBD therapies, incorporating gut microbiome, metabolome, single-cell transcriptome, human genome, dietary and clinical data. 1325 participants commencing advanced therapies will be recruited from ~40 UK sites. Data will be collected at baseline, week 14 and week 54. The primary outcome is week 14 clinical response. Secondary outcomes include clinical remission, loss of response in week 14 responders, corticosteroid-free response/remission, time to treatment escalation and change in patient-reported outcome measures.

ETHICS AND DISSEMINATION: Ethical approval was obtained from the Wales Research Ethics Committee 5 (ref: 21/WA/0228). Recruitment is ongoing. Following study completion, results will be submitted for publication in peer-reviewed journals and presented at scientific meetings. Publications will be summarised at www.ibd-response.co.uk.

TRIAL REGISTRATION NUMBER: ISRCTN96296121.},
}

Humans
*Crohn Disease/drug therapy
*Colitis, Ulcerative/therapy
Precision Medicine
Prospective Studies
Quality of Life
*Inflammatory Bowel Diseases/drug therapy
Observational Studies as Topic
Multicenter Studies as Topic

@article {pmid38631472,
year = {2024},
author = {Wong, MH and Minkina, T and Vasilchenko, N and Sushkova, S and Delegan, Y and Ranjan, A and Saxena, P and Tarigholizadeh, S and Dudnikova, T and Barbashev, A and Maksimov, A and Faenson, A and Kızılkaya, R},
title = {Assessment of Antibiotic Resistance Genes in Soils Polluted by Chemical and Technogenic Ways with Poly-Aromatic Hydrocarbons and Heavy Metals.},
journal = {Environmental research},
volume = {},
number = {},
pages = {118949},
doi = {10.1016/j.envres.2024.118949},
pmid = {38631472},
issn = {1096-0953},
abstract = {Anthropogenic activities are leaving lots of chemical footprints on the soil. It alters the physiochemical characteristics of the soil thereby modifying the natural soil microbiome. The prevalence of antimicrobial-resistance microbes in polluted soil has gained attention due to its obvious public health risks. This study focused on assessing the prevalence and distribution of antibiotic-resistance genes in polluted soil ecosystems impacted by industrial enterprises in southern Russia. Metagenomic analysis was conducted on soil samples collected from polluted sites using various approaches, and the prevalence of antibiotic-resistance genes was investigated. The results revealed that efflux-encoding pump sequences were the most widely represented group of genes, while genes whose products replaced antibiotic targets were less represented. The level of soil contamination increased, and there was an increase in the total number of antibiotic-resistance genes in proteobacteria, but a decrease in actinobacteria. The study proposed an optimal mechanism for processing metagenomic data in polluted soil ecosystems, which involves mapping raw reads by the KMA method, followed by a detailed study of specific genes. The study's conclusions provide valuable insights into the prevalence and distribution of antibiotic-resistance genes in polluted soils and have been illustrated in heat maps.},
}

@article {pmid38631287,
year = {2024},
author = {Wargo, JA and Ajami, NJ and Daniel-MacDougall, CR},
title = {Jennifer A. Wargo, Nadim J. Ajami, and Carrie R. Daniel-MacDougall.},
journal = {Cell reports. Medicine},
volume = {5},
number = {4},
pages = {101509},
doi = {10.1016/j.xcrm.2024.101509},
pmid = {38631287},
issn = {2666-3791},
abstract = {Dr. Jennifer A. Wargo, Dr. Nadim J. Ajami, and Dr. Carrie R. Daniel-MacDougall describe their academic and clinical work on the role of the microbiome to determine response to immunotherapies and discuss current challenges and potential needs to integrate their findings into clinical practice.},
}

@article {pmid38631286,
year = {2024},
author = {Chen, H and Zitvogel, L and Peng, Z and Yin, X and McAllister, F},
title = {Microbiome and cancer immunotherapies.},
journal = {Cell reports. Medicine},
volume = {5},
number = {4},
pages = {101514},
doi = {10.1016/j.xcrm.2024.101514},
pmid = {38631286},
issn = {2666-3791},
mesh = {Humans ; *Microbiota ; Immunotherapy ; *Stomach Neoplasms ; },
abstract = {Here, we present 3 different perspectives on how the microbiome has impacted cancer patients, treatment, and clinical studies. We hear about the challenges of implementing microbiome analyses into the clinics, the impact these analyses might have on patients' care, and treatment in the future, specifically for gastric cancer treatment. These are a few of the many voices that are highlighting the role of the microbiome in cancer development, treatment, and clinical outcomes.},
}

Humans
*Microbiota
Immunotherapy
*Stomach Neoplasms

@article {pmid38631285,
year = {2024},
author = {Kang, X and Lau, HC and Yu, J},
title = {Modulating gut microbiome in cancer immunotherapy: Harnessing microbes to enhance treatment efficacy.},
journal = {Cell reports. Medicine},
volume = {5},
number = {4},
pages = {101478},
doi = {10.1016/j.xcrm.2024.101478},
pmid = {38631285},
issn = {2666-3791},
mesh = {Humans ; *Gastrointestinal Microbiome ; Immunotherapy ; Treatment Outcome ; *Microbiota ; Fecal Microbiota Transplantation ; *Neoplasms ; },
abstract = {Immunotherapy has emerged as a robust approach against cancer, yet its efficacy has varied among individuals, accompanied by the occurrence of immune-related adverse events. As a result, the efficacy of immunotherapy is far from satisfactory, and enormous efforts have been invested to develop strategies to improve patient outcomes. The gut microbiome is now well acknowledged for its critical role in immunotherapy, with better understanding on host-microbes interaction in the context of cancer treatment. Also, an increasing number of trials have been conducted to evaluate the potential and feasibility of microbiome-targeting approaches to enhance efficacy of cancer treatment in patients. Here, the role of the gut microbiome and metabolites (e.g., short-chain fatty acids, tryptophan metabolites) in immunotherapy and the underlying mechanisms are explored. The application of microbiome-targeting approaches that aim to improve immunotherapy efficacy (e.g., fecal microbiota transplantation, probiotics, dietary intervention) is also elaborated, with further discussion on current challenges and suggestions for future research.},
}

Humans
*Gastrointestinal Microbiome
Immunotherapy
Treatment Outcome
*Microbiota
Fecal Microbiota Transplantation
*Neoplasms

@article {pmid38630889,
year = {2024},
author = {Li, Z and Liu, Y and Wang, Y and Cai, Q and Wang, Y and Bai, Y and Liu, H and Xu, C and Zhang, F},
title = {Sodium oligomannate's amelioration of reproductive and metabolic phenotypes in a letrozole-induced PCOS-like mouse model depends on the gut microbiome.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioae058},
pmid = {38630889},
issn = {1529-7268},
support = {22ZR1409100//Shanghai Natural Science Foundation/ ; },
abstract = {It has been well-established that there is a connection between polycystic ovary syndrome (PCOS) pathology and gut microbiome dysbiosis. A marine-derived oligosaccharide, GV-971, has been reported to alter gut microbiota and alleviate Aβ amyloidosis. In this study, the effects of GV-971 on PCOS-like mice were explored. Mice were randomly assigned into four groups: control, letrozole, letrozole + GV-971, control + GV-971. Glucose metabolism in PCOS-like mice was ameliorated by GV-971, while the reproductive endocrine disorder of PCOS-like mice was partially reversed. The messenger ribonucleic acid levels of steroidogenic enzymes in ovaries of PCOS-like mice were improved. GV-971 restored the fertility of PCOS-like mice and significantly increase the number of litters. Furthermore, GV-971 treatment effectively mitigated abnormal bile acid metabolism. Notably, after GV-971 intervention, gut microbiota alpha-diversity was considerably raised and the relative abundance of Firmicutes was reduced. In conclusion, the hyperinsulinemia and hyperandrogenemia of PCOS-like mice were alleviated by GV-971 intervention, which was associated with mitigating bile acid metabolism and modulating gut microbiota.},
}

@article {pmid38630846,
year = {2024},
author = {Phan, HV and Tsitsiklis, A and Maguire, CP and Haddad, EK and Becker, PM and Kim-Schulze, S and Lee, B and Chen, J and Hoch, A and Pickering, H and van Zalm, P and Altman, MC and Augustine, AD and Calfee, CS and Bosinger, S and Cairns, CB and Eckalbar, W and Guan, L and Jayavelu, ND and Kleinstein, SH and Krammer, F and Maecker, HT and Ozonoff, A and Peters, B and Rouphael, N and , and Montgomery, RR and Reed, E and Schaenman, J and Steen, H and Levy, O and Diray-Arce, J and Langelier, CR},
title = {Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology.},
journal = {Science translational medicine},
volume = {16},
number = {743},
pages = {eadj5154},
doi = {10.1126/scitranslmed.adj5154},
pmid = {38630846},
issn = {1946-6242},
mesh = {Humans ; Aged ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged, 80 and over ; *COVID-19 ; SARS-CoV-2 ; Prospective Studies ; Multiomics ; Chemokines ; },
abstract = {Age is a major risk factor for severe coronavirus disease 2019 (COVID-19), yet the mechanisms behind this relationship have remained incompletely understood. To address this, we evaluated the impact of aging on host immune response in the blood and the upper airway, as well as the nasal microbiome in a prospective, multicenter cohort of 1031 vaccine-naïve patients hospitalized for COVID-19 between 18 and 96 years old. We performed mass cytometry, serum protein profiling, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody assays, and blood and nasal transcriptomics. We found that older age correlated with increased SARS-CoV-2 viral abundance upon hospital admission, delayed viral clearance, and increased type I interferon gene expression in both the blood and upper airway. We also observed age-dependent up-regulation of innate immune signaling pathways and down-regulation of adaptive immune signaling pathways. Older adults had lower naïve T and B cell populations and higher monocyte populations. Over time, older adults demonstrated a sustained induction of pro-inflammatory genes and serum chemokines compared with younger individuals, suggesting an age-dependent impairment in inflammation resolution. Transcriptional and protein biomarkers of disease severity differed with age, with the oldest adults exhibiting greater expression of pro-inflammatory genes and proteins in severe disease. Together, our study finds that aging is associated with impaired viral clearance, dysregulated immune signaling, and persistent and potentially pathologic activation of pro-inflammatory genes and proteins.},
}

Humans
Aged
Adolescent
Young Adult
Adult
Middle Aged
Aged, 80 and over
*COVID-19
SARS-CoV-2
Prospective Studies
Multiomics
Chemokines

@article {pmid38630611,
year = {2024},
author = {Roy, G and Prifti, E and Belda, E and Zucker, JD},
title = {Deep learning methods in metagenomics: a review.},
journal = {Microbial genomics},
volume = {10},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001231},
pmid = {38630611},
issn = {2057-5858},
mesh = {Humans ; *Deep Learning ; *Microbiota ; Metagenome ; *Gastrointestinal Microbiome ; Metagenomics/methods ; },
abstract = {The ever-decreasing cost of sequencing and the growing potential applications of metagenomics have led to an unprecedented surge in data generation. One of the most prevalent applications of metagenomics is the study of microbial environments, such as the human gut. The gut microbiome plays a crucial role in human health, providing vital information for patient diagnosis and prognosis. However, analysing metagenomic data remains challenging due to several factors, including reference catalogues, sparsity and compositionality. Deep learning (DL) enables novel and promising approaches that complement state-of-the-art microbiome pipelines. DL-based methods can address almost all aspects of microbiome analysis, including novel pathogen detection, sequence classification, patient stratification and disease prediction. Beyond generating predictive models, a key aspect of these methods is also their interpretability. This article reviews DL approaches in metagenomics, including convolutional networks, autoencoders and attention-based models. These methods aggregate contextualized data and pave the way for improved patient care and a better understanding of the microbiome's key role in our health.},
}

Humans
*Deep Learning
*Microbiota
Metagenome
*Gastrointestinal Microbiome
Metagenomics/methods

@article {pmid38630422,
year = {2024},
author = {Sonu, I and Oh, SJ and Rao, SSC},
title = {Capsules for the Diagnosis and Treatment of Gastrointestinal Motility Disorders- A Game Changer.},
journal = {Current gastroenterology reports},
volume = {},
number = {},
pages = {},
pmid = {38630422},
issn = {1534-312X},
support = {DK115572-02/GF/NIH HHS/United States ; },
abstract = {PURPOSE OF REVIEW: Over the last few decades, there have been remarkable strides in endoscopy and radiological imaging that have advanced gastroenterology. However, the management of neurogastroenterological disorders has lagged behind, in part handicapped by the use of catheter-based manometry that is both non-physiological and uncomfortable. The advent of capsule technology has been a game changer for both diagnostic and therapeutic applications.

RECENT FINDINGS: Here, we discuss several capsule devices that are available or under investigation. There are three technologies that are FDA approved. Wireless motility capsule measures pH and pressure and provides clinically impactful information regarding gastric, small intestine and colonic transit, without radiation that has been demonstrated to guide management of gastroparesis, dyspepsia and constipation. Wireless ambulatory pH monitoring capsule is currently the gold standard for assessing gastroesophageal acid reflux. In the therapeutics arena, an orally ingested vibrating capsule has been recently FDA approved for the treatment of chronic constipation, supported by a robust phase 3 clinical trial which showed significant improvement in constipation symptoms and quality of life. There are several capsules currently under investigation. Smart capsule bacterial detection system and Capscan® are capsules that can sample fluid in the small or large bowel and provide microbiome analysis for detection of small intestinal bacterial (SIBO) or fungal overgrowth (SIFO). Another investigational gas sensing capsule analyzing hydrogen, CO2, volatile fatty acids and capsule orientation, can measure regional gut transit time and luminal gas concentrations and assess gastroparesis, constipation or SIBO. Therapeutically, other vibrating capsules are in development. Innovations in capsule technology are poised to transform our ability to investigate gut function physiologically, and non-invasively deliver targeted treatment(s), thereby providing both accurate diagnostic information and luminally-directed, safe therapy.},
}

@article {pmid38630350,
year = {2024},
author = {Saadh, MJ and Ahmed, HM and Alani, ZK and Al Zuhairi, RAH and Almarhoon, ZM and Ahmad, H and Ubaid, M and Alwan, NH},
title = {The Role of Gut-derived Short-Chain Fatty Acids in Multiple Sclerosis.},
journal = {Neuromolecular medicine},
volume = {26},
number = {1},
pages = {14},
pmid = {38630350},
issn = {1559-1174},
mesh = {Humans ; *Multiple Sclerosis ; Central Nervous System ; *Gastrointestinal Microbiome ; Colon ; Fatty Acids, Volatile ; Inflammation ; },
abstract = {Multiple sclerosis (MS) is a chronic condition affecting the central nervous system (CNS), where the interplay of genetic and environmental factors influences its pathophysiology, triggering immune responses and instigating inflammation. Contemporary research has been notably dedicated to investigating the contributions of gut microbiota and their metabolites in modulating inflammatory reactions within the CNS. Recent recognition of the gut microbiome and dietary patterns as environmental elements impacting MS development emphasizes the potential influence of small, ubiquitous molecules from microbiota, such as short-chain fatty acids (SCFAs). These molecules may serve as vital molecular signals or metabolic substances regulating host cellular metabolism in the intricate interplay between microbiota and the host. A current emphasis lies on optimizing the health-promoting attributes of colonic bacteria to mitigate urinary tract issues through dietary management. This review aims to spotlight recent investigations on the impact of SCFAs on immune cells pivotal in MS, the involvement of gut microbiota and SCFAs in MS development, and the considerable influence of probiotics on gastrointestinal disruptions in MS. Comprehending the gut-CNS connection holds promise for the development of innovative therapeutic approaches, particularly probiotic-based supplements, for managing MS.},
}

Humans
*Multiple Sclerosis
Central Nervous System
*Gastrointestinal Microbiome
Colon
Fatty Acids, Volatile
Inflammation

@article {pmid38630349,
year = {2024},
author = {Ra, YE and Bang, YJ},
title = {Balancing Act of the Intestinal Antimicrobial Proteins on Gut Microbiota and Health.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {38630349},
issn = {1976-3794},
support = {Creative-Pioneering Researchers Program//Seoul National University/ ; RS-2023-00217157//National Research Foundation/ ; RS-2022-00165890//National Research Foundation of Korea/ ; },
abstract = {The human gut houses a diverse and dynamic microbiome critical for digestion, metabolism, and immune development, exerting profound effects on human health. However, these microorganisms pose a potential threat by breaching the gut barrier, entering host tissues, and triggering infections, uncontrolled inflammation, and even sepsis. The intestinal epithelial cells form the primary defense, acting as a frontline barrier against microbial invasion. Antimicrobial proteins (AMPs), produced by these cells, serve as innate immune effectors that regulate the gut microbiome by directly killing or inhibiting microbes. Abnormal AMP production, whether insufficient or excessive, can disturb the microbiome equilibrium, contributing to various intestinal diseases. This review delves into the complex interactions between AMPs and the gut microbiota and sheds light on the role of AMPs in governing host-microbiota interactions. We discuss the function and mechanisms of action of AMPs, their regulation by the gut microbiota, microbial evasion strategies, and the consequences of AMP dysregulation in disease. Understanding these complex interactions between AMPs and the gut microbiota is crucial for developing strategies to enhance immune responses and combat infections within the gut microbiota. Ongoing research continues to uncover novel aspects of this intricate relationship, deepening our understanding of the factors shaping gut health. This knowledge has the potential to revolutionize therapeutic interventions, offering enhanced treatments for a wide range of gut-related diseases.},
}

@article {pmid38630187,
year = {2024},
author = {Reddy, GKK and Kavibharathi, K and Singh, A and Nancharaiah, YV},
title = {Growth-dependent cr(VI) reduction by Alteromonas sp. ORB2 under haloalkaline conditions: toxicity, removal mechanism and effect of heavy metals.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {6},
pages = {165},
pmid = {38630187},
issn = {1573-0972},
support = {CG VISION PROJECT//Department of Atomic Energy, Government of India/ ; CG VISION PROJECT//Department of Atomic Energy, Government of India/ ; CG VISION PROJECT//Department of Atomic Energy, Government of India/ ; CG VISION PROJECT//Department of Atomic Energy, Government of India/ ; },
mesh = {*Alteromonas ; Sodium Chloride/pharmacology ; Cadmium ; Lead/toxicity ; Wastewater ; *Metals, Heavy/toxicity ; *Chromium ; },
abstract = {Bacterial reduction of hexavalent chromium (VI) to chromium (III) is a sustainable bioremediation approach. However, the Cr(VI) containing wastewaters are often characterized with complex conditions such as high salt, alkaline pH and heavy metals which severely impact the growth and Cr(VI) reduction potential of microorganisms. This study investigated Cr(VI) reduction under complex haloalkaline conditions by an Alteromonas sp. ORB2 isolated from aerobic granular sludge cultivated from the seawater-microbiome. Optimum growth of Alteromonas sp. ORB2 was observed under haloalkaline conditions at 3.5-9.5% NaCl and pH 7-11. The bacterial growth in normal culture conditions (3.5% NaCl; pH 7.6) was not inhibited by 100 mg/l Cr(VI)/ As(V)/ Pb(II), 50 mg/l Cu(II) or 5 mg/l Cd(II). Near complete reduction of 100 mg/l Cr(VI) was achieved within 24 h at 3.5-7.5% NaCl and pH 8-11. Cr(VI) reduction by Alteromonas sp. ORB2 was not inhibited by 100 mg/L As(V), 100 mg/L Pb(II), 50 mg/L Cu(II) or 5 mg/L Cd(II). The bacterial cells grew in the medium with 100 mg/l Cr(VI) contained lower esterase activity and higher reactive oxygen species levels indicating toxicity and oxidative stress. In-spite of toxicity, the cells grew and reduced 100 mg/l Cr(VI) completely within 24 h. Cr(VI) removal from the medium was driven by bacterial reduction to Cr(III) which remained in the complex medium. Cr(VI) reduction was strongly linked to aerobic growth of Alteromonas sp. The Cr(VI) reductase activity of cytosolic protein fraction was pronounced by supplementing with NADPH in vitro assays. This study demonstrated a growth-dependent aerobic Cr(VI) reduction by Alteromonas sp. ORB2 under complex haloalkaline conditions akin to wastewaters.},
}

*Alteromonas
Sodium Chloride/pharmacology
Cadmium
Lead/toxicity
Wastewater
*Metals, Heavy/toxicity
*Chromium

@article {pmid38630015,
year = {2024},
author = {Srivastava, S and Basak, U and Naghibi, M and Vijayakumar, V and Parihar, R and Patel, J and Jadon, PS and Pandit, A and Dargad, RR and Khanna, S and Kumar, S and Day, R},
title = {A randomized double-blind, placebo-controlled trial to evaluate the safety and efficacy of live Bifidobacterium longum CECT 7347 (ES1) and heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) in participants with diarrhea-predominant irritable bowel syndrome.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2338322},
doi = {10.1080/19490976.2024.2338322},
pmid = {38630015},
issn = {1949-0984},
mesh = {Adult ; Humans ; *Irritable Bowel Syndrome/therapy ; Quality of Life ; Hot Temperature ; *Gastrointestinal Microbiome ; *Bifidobacterium longum ; Diarrhea ; *Peptides, Cyclic ; },
abstract = {To determine the efficacy of the probiotic Bifidobacterium longum CECT 7347 (ES1) and postbiotic heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) in improving symptom severity in adults with diarrhea-predominant irritable bowel syndrome (IBS-D), a randomised, double-blind, placebo-controlled trial with 200 participants split into three groups was carried out. Two capsules of either ES1, HT-ES1 or placebo were administered orally, once daily, for 84 days (12 weeks). The primary outcome was change in total IBS-Symptom Severity Scale (IBS-SSS) score from baseline, compared to placebo. Secondary outcome measures were stool consistency, quality of life, abdominal pain severity and anxiety scores. Safety parameters and adverse events were also monitored. The change in IBS-SSS scores from baseline compared to placebo, reached significance in the ES1 and HT-ES1 group, on Days 28, 56 and 84. The decrease in mean IBS-SSS score from baseline to Day 84 was: ES1 (-173.70 [±75.60]) vs placebo (-60.44 [±65.5]) (p < .0001) and HT-ES1 (-177.60 [±79.32]) vs placebo (-60.44 [±65.5]) (p < .0001). Secondary outcomes included changes in IBS-QoL, APS-NRS, stool consistency and STAI-S and STAI-T scores, with changes from baseline to Day 84 being significant in ES1 and HT-ES1 groups, compared to the placebo group. Both ES1 and HT-ES1 were effective in reducing IBS-D symptom severity, as evaluated by measures such as IBS-SSS, IBS-QoL, APS-NRS, stool consistency, and STAI, in comparison to the placebo. These results are both statistically significant and clinically meaningful, representing, to the best of the authors' knowledge, the first positive results observed for either a probiotic or postbiotic from the same strain, in this particular population.},
}

Adult
Humans
*Irritable Bowel Syndrome/therapy
Quality of Life
Hot Temperature
*Gastrointestinal Microbiome
*Bifidobacterium longum
Diarrhea
*Peptides, Cyclic

@article {pmid38629838,
year = {2024},
author = {Fernandez, M and Thompson, J and Calle, A},
title = {Novel feed additive delivers antimicrobial copper and influences fecal microbiota in pigs.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0428023},
doi = {10.1128/spectrum.04280-23},
pmid = {38629838},
issn = {2165-0497},
abstract = {Dehydrated alginate beads formulated with copper were synthesized and tested as a feed additive to influence the microbiota in finishing pigs and potentially use them as a preharvest intervention to reduce fecal pathogen shedding. The efficacy of the copper beads was tested in vitro and in vivo. In vitro, Salmonella was significantly (P < 0.05) reduced when in contact with the copper beads solution for up to 6 h, with a 5.4 log CFU/mL reduction over the first hour. Chemical analysis of the soak solutions demonstrated the beads delivered their copper payload gradually over the same period the bactericidal effect was observed. For the in vivo experiments, pigs (n = 48) supplemented with the copper beads experienced significant shifts in their microbiota. Enterobacteriaceae (EB) increased by 1.07 log CFU/g (P < 0.05), while lactic acid bacteria (LAB) decreased by 1.22 log CFU/g (P < 0.05) during the treatment period. When beads were removed from the feed, EB and LAB concentrations returned to baseline, indicating copper beads led to measurable and significant changes in microbial loads. Fecal microbiome analysis conducted to explore additional changes by copper bead supplementation demonstrated that, at the phylum level, there was an increase in Firmicutes, Euryarchaeota, and Acidobacteriota, while at the genus level, an increase in Methanosphaera and Pseudomonas was observed. Measures of copper in swine feces showed values ~20 times higher in the treatment group than in the control group during the treatment period, suggesting that dehydrated alginate copper beads were effective in delivering antimicrobial copper to the animal hindgut.IMPORTANCECopper has long been known to have antimicrobial properties. However, when water-soluble salts are fed to livestock, the copper may rapidly dissolve in gastric contents and fail to reach the gut. Here, specially formulated copper beads are seamlessly incorporated into feed and allow copper to remain longer in the gastrointestinal tract of animals, reach deep into both the foregut and hindgut, and shift microbial populations. The technology delivers antimicrobial copper to the animal hindgut and potentially reduces pathogenic microorganisms before animal slaughter.},
}

@article {pmid38629663,
year = {2024},
author = {He, Y and Nong, Y and Qin, J and Feng, L and Qin, J and Wang, Q and Deng, L and Tang, S and Zhang, M and Fan, X and Dong, M and Wei, J and Pan, S and Su, Z},
title = {Protective effects of oyster polypeptide from oyster (Crassostrea ariakensis) on cyclophosphamide induced immunosuppression rats based on [1]H NMR metabolomics and 16S rRNA gene sequencing.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.13537},
pmid = {38629663},
issn = {1097-0010},
abstract = {BACKGROUND: Oyster polypeptide (OP) is a mixture of oligopeptides extracted from oysters through enzyme lysis, separation and purification. OP is associated with immunomodulatory effects, but the underlying mechanisms are not known. Therefore, this study combined [1]H-NMR urinary metabolomics and 16S rRNA gene sequencing of the gut microbiome to determine the immunoprotective mechanisms of OP in rats subjected to cyclophosphamide-induced immunosuppression.

RESULTS: OP can restored the body weight and the structure of spleen and thymus in cyclophosphamide-induced immunosuppression rats. OP upregulated the levels of white blood cells (WBCs), hemoglobin (HGB), platelets (PLT), red blood cells (RBCs), immunoglobulin G (IgG), immunoglobulin M (IgM), cytokines such as IL-6 and TNF-α, and the numbers of CD3[+] and CD4[+] T cells in the immunosuppression rats. The [1]H-NMR metabolomics results showed that OP significantly reversed the levels of ten metabolites in urinary, including 2-oxoglutarate, citrate, dimethylamine, taurine, N-phenylacetylglycine, alanine, betaine, creatinine, uracil, and benzoate. The 16S rRNA gene sequencing results showed that OP restored the gut microbiome homeostasis by increasing the abundance of beneficial bacteria and reducing the abundance of pathogenic bacteria. Finally combining metabolomics and microbiomics found that taurine an hypotaurine metabolism, also alanine, aspartate and glutamate metabolish were disturbed, but these metabolic pathways were restored by OP.

CONCLUSION: This study demonstrated that OP had immunoprotective effects in cyclophosphamide-induced immunosuppression rats by restoring key metabolic pathways and the gut microbiome homeostasis. Our findings provides a framework for further research into the immunoregulatory mechanisms of OP and its potential use in drugs and nutritional supplements. This article is protected by copyright. All rights reserved.},
}

@article {pmid38629051,
year = {2024},
author = {Weber, KT and Varian, BJ and Erdman, SE},
title = {The gut microbiome and sociability.},
journal = {Frontiers in neuroscience},
volume = {18},
number = {},
pages = {1372274},
pmid = {38629051},
issn = {1662-4548},
abstract = {The human gut microbiome plays an important role in the maturation of the neural, immune, and endocrine systems. Research data from animal models shows that gut microbiota communicate with the host's brain in an elaborate network of signaling pathways, including the vagus nerve. Part of the microbiome's influence extends to the behavioral and social development of its host. As a social species, a human's ability to communicate with others is imperative to their survival and quality of life. Current research explores the gut microbiota's developmental influence as well as how these gut-brain pathways can be leveraged to alleviate the social symptoms associated with various neurodevelopmental and psychiatric diseases. One intriguing vein of research in animal models centers on probiotic treatment, which leads to downstream increased circulation of endogenous oxytocin, a neuropeptide hormone relevant to sociability. Further research may lead to therapeutic applications in humans, particularly in the early stages of their lives.},
}

@article {pmid38628559,
year = {2024},
author = {Zhang, J and Dong, C and Lin, Y and Shang, L and Ma, J and Hu, R and Wang, H},
title = {Causal relationship between gut microbiota and gastric cancer: A two‑sample Mendelian randomization analysis.},
journal = {Molecular and clinical oncology},
volume = {20},
number = {5},
pages = {38},
pmid = {38628559},
issn = {2049-9469},
abstract = {The gut microbiota is associated with GC; however, the causal association between the gut microbiota and GC remains to be determined. The aim of the present study was to investigate the causal association between gut microbiota and gastric cancer (GC) from the perspective of Mendelian randomization (MR). The present study performed MR analysis using summary statistics from a genome-wide association study of the gut microbiome and GC. Inverse-variance weighted, MR-Egger and weighted median methods were used to investigate the causal relationship between gut microbiota and GC. Heterogeneity tests were performed using Cochrane's Q statistic. Horizontal polytropy was detected using Mendelian Randomization Pleiotropy RESidual Sum and Outlier were eliminated. Estimates from MR indicated that nine gut microorganism remained stable with regard to acceptance of heterogeneity and sensitivity methods. Among them, the genera Prevotella 7, Roseburia and Ruminococcaceae UCG014 were associated with an increased risk of GC; by contrast, the family Enterobacteriaceae, the genera Allisonella, Lachnospiraceae FCS020, Ruminococcaceae UCG004 and Ruminococcaceae UCG009, and the order Enterobacteriales decreased the risk of GC development. The present study demonstrated the potential importance of modulating the abundance of gut microbiota for the prevention and treatment of GC.},
}

@article {pmid38628369,
year = {2024},
author = {Darriaut, R and Marzari, T and Lailheugue, V and Tran, J and Martins, G and Marguerit, E and Masneuf-Pomarède, I and Lauvergeat, V},
title = {Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1358213},
pmid = {38628369},
issn = {1664-462X},
abstract = {When grapevine decline, characterized by a premature decrease in vigor and yield and sometimes plant death, cannot be explained by pathological or physiological diseases, one may inquire whether the microbiological status of the soil is responsible. Previous studies have shown that the composition and structure of bacterial and fungal microbial communities in inter-row soil are affected in areas displaying vine decline, compared to areas with non-declining vines within the same plot. A more comprehensive analysis was conducted in one such plot. Although soil chemical parameters could not directly explain these differences, the declining vines presented lower vigor, yield, berry quality, and petiole mineral content than those in non-declining vines. The bacterial and fungal microbiome of the root endosphere, rhizosphere, and different horizons of the bulk soil were explored through enzymatic, metabolic diversity, and metabarcoding analysis in both areas. Despite the lower microbial diversity and richness in symptomatic roots and soil, higher microbial activity and enrichment of potentially both beneficial bacteria and pathogenic fungi were found in the declining area. Path modeling analysis linked the root microbial activity to berry quality, suggesting a determinant role of root microbiome in the berry mineral content. Furthermore, certain fungal and bacterial taxa were correlated with predicted metabolic pathways and metabolic processes assessed with Eco-Plates. These results unexpectedly revealed active microbial profiles in the belowground compartments associated with stressed vines, highlighting the interest of exploring the functional microbiota of plants, and more specifically roots and rhizosphere, under stressed conditions.},
}

@article {pmid38628220,
year = {2024},
author = {Nehmi-Filho, V and de Freitas, JA and Franco, LA and Martins, RC and Turri, JAO and Santamarina, AB and Fonseca, JVDS and Sabino, EC and Moraes, BC and Souza, E and Murata, GM and Costa, SF and Alcântara, PS and Otoch, JP and Pessoa, AFM},
title = {Modulation of the gut microbiome and Firmicutes phylum reduction by a nutraceutical blend in the obesity mouse model and overweight humans: A double-blind clinical trial.},
journal = {Food science & nutrition},
volume = {12},
number = {4},
pages = {2436-2454},
pmid = {38628220},
issn = {2048-7177},
abstract = {Overweight and obesity are closely linked to gut dysbiosis/dysmetabolism and disrupted De-Ritis ratio [aspartate aminotransferase (AST)/alanine aminotransferase (ALT) ratio], which may contribute to chronic noncommunicable diseases onset. Concurrently, extensive research explores nutraceuticals, and health-enhancing supplements, for disease prevention or treatment. Thus, sedentary overweight volunteers were double-blind randomized into two groups: Novel Nutraceutical_(S) (without silymarin) and Novel Nutraceutical (with silymarin). Experimental formulations were orally administered twice daily over 180 consecutive days. We evaluated fecal gut microbiota, based on partial 16S rRNA sequences, biochemistry and endocrine markers, steatosis biomarker (AST/ALT ratio), and anthropometric parameters. Post-supplementation, only the Novel Nutraceutical group reduced Clostridium clostridioforme (Firmicutes), Firmicutes/Bacteroidetes ratio (F/B ratio), and De-Ritis ratio, while elevating Bacteroides caccae and Bacteroides uniformis (Bacteroidetes) in Brazilian sedentary overweight volunteers after 180 days. In summary, the results presented here allow us to suggest the gut microbiota as the action mechanism of the Novel Nutraceutical promoting metabolic hepatic recovery in obesity/overweight non-drug interventions.},
}

@article {pmid38626403,
year = {2024},
author = {McKay, DM and Defaye, M and Rajeev, S and MacNaughton, WK and Nasser, Y and Sharkey, KA},
title = {Neuroimmunophysiology of the Gastrointestinal Tract.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00075.2024},
pmid = {38626403},
issn = {1522-1547},
abstract = {Gut physiology is the epicentre of a web of internal communication systems (i.e., neural, immune, hormonal) mediated by cell-cell contacts, soluble factors, and external influences, such as the microbiome, diet, and the physical environment. Together these provide the signals that shape enteric homeostasis and, when they go awry, lead to disease. Faced with the seemingly paradoxical tasks of nutrient uptake (digestion) and retarding pathogen invasion (host defense), the gut integrates interactions between a variety of cells and signaling molecules to keep the host nourished and protected from pathogens. When the system fails, the outcome can be acute or chronic disease, often labelled as "idiopathic" in nature (e.g., irritable bowel syndrome, inflammatory bowel disease). Here we underscore the importance of a holistic approach to gut physiology, placing an emphasis on inter-cellular connectedness, using enteric neuroimmunophysiology as the paradigm. The goal of this opinion piece is to acknowledge the pace of change brought to our field via single-cell and -omic methodologies, and other techniques such as cell lineage tracing, transgenic animal models, methods for culturing patient tissue, and advanced imaging. We identify gaps in the field and hope to inspire and challenge colleagues to take up the mantle and advance awareness of the subtleties, intricacies, and nuances of intestinal physiology in health and disease by defining communication pathways between gut resident cells, those recruited from the circulation and 'external' influences such as the central nervous system and the gut microbiota.},
}

@article {pmid38630064,
year = {2021},
author = {Wang, C and Zhou, X and Wang, M and Chen, X},
title = {The Impact of SARS-CoV-2 on the Human Immune System and Microbiome.},
journal = {Infectious microbes & diseases},
volume = {3},
number = {1},
pages = {14-21},
pmid = {38630064},
issn = {2641-5917},
abstract = {A recent outbreak of coronavirus disease 2019 (COVID-19) caused by the single-stranded enveloped RNA virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has developed into a global pandemic, after it was first reported in Wuhan in December 2019. SARS-CoV-2 is an emerging virus, and little is known about the basic characteristics of this pathogen, the underlying mechanism of infection, and the potential treatments. The immune system has been known to be actively involved in viral infections. To facilitate the development of COVID-19 treatments, the understanding of immune regulation by this viral infection is urgently needed. This review describes the mechanisms of immune system involvement in viral infections and provides an overview of the dysregulation of immune responses in COVID-19 patients in recent studies. Furthermore, we emphasize the role of gut microbiota in regulating immunity and summarized the impact of SARS-CoV-2 infection on the composition of the microbiome. Overall, this review provides insights for understanding and developing preventive and therapeutic strategies by regulating the immune system and microbiota.},
}

@article {pmid38630083,
year = {2020},
author = {Chen, L and Li, S and Ai, L and Zhou, J and Huang, J and Xu, F and Zeng, X and Han, J and Yin, F and Zhu, Y and Xie, Y},
title = {The Correlation Between Heart Failure and Gut Microbiome Metabolites.},
journal = {Infectious microbes & diseases},
volume = {2},
number = {4},
pages = {136-143},
pmid = {38630083},
issn = {2641-5917},
abstract = {Heart failure (HF) is a global public health problem, with morbidity and mortality increasing year by year. The gut microbiome actively affects the physiological and pathological activities of the human body in a variety of ways. More and more studies have suggested a strong correlation between HF and gut microbiome metabolites. Our review summarizes the specific alteration of these metabolites and their connection to the progression of HF, aiming at considering new approaches toward regulating the gut microbiome and using its metabolic pathways to treat HF, potentially decreasing the morbidity and mortality of HF as well as improving prognosis.},
}

@article {pmid38628202,
year = {2024},
author = {Khalil, NA and ALFaris, NA and ALTamimi, JZ and Mohamed Ahmed, IA},
title = {Anti-inflammatory effects of bay laurel (Laurus nobilis L.) towards the gut microbiome in dextran sodium sulfate induced colitis animal models.},
journal = {Food science & nutrition},
volume = {12},
number = {4},
pages = {2650-2660},
pmid = {38628202},
issn = {2048-7177},
abstract = {Bay laurel (Laurus nobilis L.) contains active antioxidative phenolic components that are beneficial to human health. However, none was examined and reported utilizing health effects related to inflammatory bowel diseases (IBD) mainly ulcerative colitis (UC) in correlation to gut microbiota (GM). Thus, the current study aimed to investigate the impacts of bay leaves on UC albino rats targeting on the GM composition and their metabolites production (i.e., short-chain fatty acids; SCFAs) for improving the gut barrier functions. UC models were induced by supplementing 5% DSS into their drinking water. The models were then divided randomly for the diet with 1%, 2%, and 3% of bay leaves, as well as two control studies (positive and negative). Colon-to-body weight ratio was used as an indicator for the presence of edema tissue. From the collected fecal samples at 0, 24 h, and final day, the population changes of gut microbiota (Lactobacillus, Bifidobacteria, Clostridium, and sulfate-reducing bacteria) and SCFAs production were evaluated using fluorescence in situ hybridization (FISH) and gas-liquid chromatography (GC). The colon-to-body weight ratio of the rat models consuming 2% and 3% bay leaves was found to be significantly lower with better recovery of colonic function. Models consuming 3% bay leaves showed the best treatment effects on GM compositions; promoting the growth of Bifidobacteria and Lactobacillus in addition to producing high butyric acid levels. Meanwhile, the number of Clostridium and SRB was significantly reduced. Conclusively, consuming bay leaves brought significant colon health benefits other than stimulating appetite for a better taste.},
}

@article {pmid38628125,
year = {2024},
author = {Baiz, MD and Wood, AW and Toews, DPL},
title = {Association between the gut microbiome and carotenoid plumage phenotype in an avian hybrid zone.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2021},
pages = {20240238},
pmid = {38628125},
issn = {1471-2954},
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome ; Phenotype ; Vertebrates ; *Passeriformes ; Carotenoids ; },
abstract = {Vertebrates host complex microbiomes that impact their physiology. In many taxa, including colourful wood-warblers, gut microbiome similarity decreases with evolutionary distance. This may suggest that as host populations diverge, so do their microbiomes, because of either tight coevolutionary dynamics, or differential environmental influences, or both. Hybridization is common in wood-warblers, but the effects of evolutionary divergence on the microbiome during secondary contact are unclear. Here, we analyse gut microbiomes in two geographically disjunct hybrid zones between blue-winged warblers (Vermivora cyanoptera) and golden-winged warblers (Vermivora chrysoptera). We performed 16S faecal metabarcoding to identify species-specific bacteria and test the hypothesis that host admixture is associated with gut microbiome disruption. Species identity explained a small amount of variation between microbiomes in only one hybrid zone. Co-occurrence of species-specific bacteria was rare for admixed individuals, yet microbiome richness was similar among admixed and parental individuals. Unexpectedly, we found several bacteria that were more abundant among admixed individuals with a broader deposition of carotenoid-based plumage pigments. These bacteria are predicted to encode carotenoid biosynthesis genes, suggesting birds may take advantage of pigments produced by their gut microbiomes. Thus, host admixture may facilitate beneficial symbiotic interactions which contribute to plumage ornaments that function in sexual selection.},
}

Humans
Animals
*Gastrointestinal Microbiome
Phenotype
Vertebrates
*Passeriformes
Carotenoids

@article {pmid38628120,
year = {2024},
author = {Rohner, PT and Moczek, AP},
title = {Vertically inherited microbiota and environment modifying behaviours conceal genetic variation in dung beetle life history.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2021},
pages = {20240122},
pmid = {38628120},
issn = {1471-2954},
mesh = {Animals ; *Coleoptera/genetics ; *Microbiota/genetics ; Larva/genetics ; Biological Evolution ; Genetic Variation ; },
abstract = {Diverse organisms actively manipulate their (sym)biotic and physical environment in ways that feed back on their own development. However, the degree to which these processes affect microevolution remains poorly understood. The gazelle dung beetle both physically modifies its ontogenetic environment and structures its biotic interactions through vertical symbiont transmission. By experimentally eliminating (i) physical environmental modifications and (ii) the vertical inheritance of microbes, we assess how environment modifying behaviour and microbiome transmission shape heritable variation and evolutionary potential. We found that depriving larvae of symbionts and environment modifying behaviours increased additive genetic variance and heritability for development time but not body size. This suggests that larvae's ability to manipulate their environment has the potential to modify heritable variation and to facilitate the accumulation of cryptic genetic variation. This cryptic variation may become released and selectable when organisms encounter environments that are less amenable to organismal manipulation or restructuring. Our findings also suggest that intact microbiomes, which are commonly thought to increase genetic variation of their hosts, may instead reduce and conceal heritable variation. More broadly, our findings highlight that the ability of organisms to actively manipulate their environment may affect the potential of populations to evolve when encountering novel, stressful conditions.},
}

Animals
*Coleoptera/genetics
*Microbiota/genetics
Larva/genetics
Biological Evolution
Genetic Variation

@article {pmid38627868,
year = {2024},
author = {Ho, M and Nguyen, HN and Van Hoang, M and Bui, TTT and Vu, BQ and Dinh, THT and Vo, HTM and Blaydon, DC and Eldirany, SA and Bunick, CG and Bui, CB},
title = {Altered skin microbiome, inflammation, and JAK/STAT signaling in Southeast Asian ichthyosis patients.},
journal = {Human genomics},
volume = {18},
number = {1},
pages = {38},
pmid = {38627868},
issn = {1479-7364},
support = {K08AR070290/AR/NIAMS NIH HHS/United States ; },
mesh = {Humans ; Case-Control Studies ; Leukocytes, Mononuclear ; Southeast Asian People ; Inflammation/genetics ; *Microbiota/genetics ; *Ichthyosis/genetics ; },
abstract = {BACKGROUND: Congenital ichthyosis (CI) is a collective group of rare hereditary skin disorders. Patients present with epidermal scaling, fissuring, chronic inflammation, and increased susceptibility to infections. Recently, there is increased interest in the skin microbiome; therefore, we hypothesized that CI patients likely exhibit an abnormal profile of epidermal microbes because of their various underlying skin barrier defects. Among recruited individuals of Southeast Asian ethnicity, we performed skin meta-genomics (i.e., whole-exome sequencing to capture the entire multi-kingdom profile, including fungi, protists, archaea, bacteria, and viruses), comparing 36 CI patients (representing seven subtypes) with that of 15 CI age-and gender-matched controls who had no family history of CI.

RESULTS: This case-control study revealed 20 novel and 31 recurrent pathogenic variants. Microbiome meta-analysis showed distinct microbial populations, decreases in commensal microbiota, and higher colonization by pathogenic species associated with CI; these were correlated with increased production of inflammatory cytokines and Th17- and JAK/STAT-signaling pathways in peripheral blood mononuclear cells. In the wounds of CI patients, we identified specific changes in microbiota and alterations in inflammatory pathways, which are likely responsible for impaired wound healing.

CONCLUSIONS: Together, this research enhances our understanding of the microbiological, immunological, and molecular properties of CI and should provide critical information for improving therapeutic management of CI patients.},
}

Humans
Case-Control Studies
Leukocytes, Mononuclear
Southeast Asian People
Inflammation/genetics
*Microbiota/genetics
*Ichthyosis/genetics

@article {pmid38627822,
year = {2024},
author = {Williams, J and Pettorelli, N and Hartmann, AC and Quinn, RA and Plaisance, L and O'Mahoney, M and Meyer, CP and Fabricius, KE and Knowlton, N and Ransome, E},
title = {Decline of a distinct coral reef holobiont community under ocean acidification.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {75},
pmid = {38627822},
issn = {2049-2618},
support = {NE/R012229/1//Natural Environment Research Council/ ; 2022717//National Science Foundation/ ; 1558868//National Science Foundation/ ; 1558868//National Science Foundation/ ; },
mesh = {Animals ; Coral Reefs ; Ecosystem ; Hydrogen-Ion Concentration ; Ocean Acidification ; Seawater ; *Anthozoa/physiology ; *Microbiota ; },
abstract = {BACKGROUND: Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH - an important global coral reef stressor - can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome.

RESULTS: We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO2 seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation.

CONCLUSIONS: We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem changed. Video Abstract.},
}

Animals
Coral Reefs
Ecosystem
Hydrogen-Ion Concentration
Ocean Acidification
Seawater
*Anthozoa/physiology
*Microbiota

@article {pmid38627726,
year = {2024},
author = {Su, C and Wan, S and Ding, J and Ni, G and Ding, H},
title = {Blood lipids mediate the effects of gut microbiome on endometriosis: a mendelian randomization study.},
journal = {Lipids in health and disease},
volume = {23},
number = {1},
pages = {110},
pmid = {38627726},
issn = {1476-511X},
support = {82201820//National Natural Science Foundation of China/ ; 82201820//National Natural Science Foundation of China/ ; 82201820//National Natural Science Foundation of China/ ; 82201820//National Natural Science Foundation of China/ ; },
mesh = {Female ; Humans ; *Gastrointestinal Microbiome/genetics ; *Endometriosis/genetics ; Bayes Theorem ; Genome-Wide Association Study ; Mendelian Randomization Analysis ; Lipids ; Triglycerides ; },
abstract = {BACKGROUND: There is evidence for an association between the gut microbiome and endometriosis. However, their causal relationship and the mediating role of lipid metabolism remain unclear.

METHODS: Using genome-wide association study (GWAS) data, we conducted a bidirectional Mendelian randomization (MR) analysis to investigate the causal relationships between gut microbiome and endometriosis. The inverse variance weighted (IVW) method was used as the primary model, with other MR models used for comparison. Sensitivity analysis based on different statistical assumptions was used to evaluate whether the results were robust. A two-step MR analysis was further conducted to explore the mediating effects of lipids, by integrating univariable MR and the multivariate MR method based on the Bayesian model averaging method (MR-BMA).

RESULTS: We identified four possible intestinal bacteria genera associated with the risk of endometriosis through the IVW method, including Eubacterium ruminantium group (odds ratio [OR] = 0.881, 95% CI: 0.795-0.976, P = 0.015), Anaerotruncus (OR = 1.252, 95% CI: 1.028-1.525, P = 0.025), Olsenella (OR = 1.110, 95% CI: 1.007-1.223, P = 0.036), and Oscillospira (OR = 1.215, 95% CI: 1.014-1.456, P = 0.035). The further two-step MR analysis identified that the effect of Olsenella on endometriosis was mediated by triglycerides (proportion mediated: 3.3%; 95% CI = 1.5-5.1%).

CONCLUSION: This MR study found evidence for specific gut microbiomes associated with the risk of endometriosis, which might partially be mediated by triglycerides.},
}

Female
Humans
*Gastrointestinal Microbiome/genetics
*Endometriosis/genetics
Bayes Theorem
Genome-Wide Association Study
Mendelian Randomization Analysis
Lipids
Triglycerides

@article {pmid38627687,
year = {2024},
author = {Zhang, K and Paul, K and Jacobs, JP and Cockburn, MG and Bronstein, JM and Del Rosario, I and Ritz, B},
title = {Ambient long-term exposure to organophosphorus pesticides and the human gut microbiome: an observational study.},
journal = {Environmental health : a global access science source},
volume = {23},
number = {1},
pages = {41},
pmid = {38627687},
issn = {1476-069X},
support = {K01AG07204401/AG/NIA NIH HHS/United States ; R01ES031106/ES/NIEHS NIH HHS/United States ; },
mesh = {Animals ; Humans ; Aged ; *Pesticides/adverse effects ; *Gastrointestinal Microbiome ; Organophosphorus Compounds ; *Parkinson Disease ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria ; },
abstract = {BACKGROUND: Organophosphorus pesticides (OP) have been associated with various human health conditions. Animal experiments and in-vitro models suggested that OP may also affect the gut microbiota. We examined associations between ambient chronic exposure to OP and gut microbial changes in humans.

METHODS: We recruited 190 participants from a community-based epidemiologic study of Parkinson's disease living in a region known for heavy agricultural pesticide use in California. Of these, 61% of participants had Parkinson's disease and their mean age was 72 years. Microbiome and predicted metagenome data were generated by 16S rRNA gene sequencing of fecal samples. Ambient long-term OP exposures were assessed using pesticide application records combined with residential addresses in a geographic information system. We examined gut microbiome differences due to OP exposures, specifically differences in microbial diversity based on the Shannon index and Bray-Curtis dissimilarities, and differential taxa abundance and predicted Metacyc pathway expression relying on regression models and adjusting for potential confounders.

RESULTS: OP exposure was not associated with alpha or beta diversity of the gut microbiome. However, the predicted metagenome was sparser and less evenly expressed among those highly exposed to OP (p = 0.04). Additionally, we found that the abundance of two bacterial families, 22 genera, and the predicted expression of 34 Metacyc pathways were associated with long-term OP exposure. These pathways included perturbed processes related to cellular respiration, increased biosynthesis and degradation of compounds related to bacterial wall structure, increased biosynthesis of RNA/DNA precursors, and decreased synthesis of Vitamin B1 and B6.

CONCLUSION: In support of previous animal studies and in-vitro findings, our results suggest that ambient chronic OP pesticide exposure alters gut microbiome composition and its predicted metabolism in humans.},
}

Animals
Humans
Aged
*Pesticides/adverse effects
*Gastrointestinal Microbiome
Organophosphorus Compounds
*Parkinson Disease
RNA, Ribosomal, 16S/genetics
*Microbiota
Bacteria

@article {pmid38627617,
year = {2024},
author = {Chen, M and Feng, S and Lv, H and Wang, Z and Zeng, Y and Shao, C and Lin, W and Zhang, Z},
title = {OsCIPK2 mediated rice root microorganisms and metabolites to improve plant nitrogen uptake.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {285},
pmid = {38627617},
issn = {1471-2229},
support = {2021J01093//National Natural Science Foundation of Fujian/ ; },
mesh = {*Oryza ; Plant Roots/metabolism ; Nitrogen/metabolism ; *Nitrogen-Fixing Bacteria/metabolism ; Soil ; Rhizosphere ; Citric Acid ; Soil Microbiology ; },
abstract = {Crop roots are colonized by large numbers of microorganisms, collectively known as the root-microbiome, which modulate plant growth, development and contribute to elemental nutrient uptake. In conditions of nitrogen limitation, the over-expressed Calcineurin B-like interacting protein kinase 2 (OsCIPK2) gene with root-specific promoter (RC) has been shown to enhance growth and nitrogen uptake in rice. Analysis of root-associated bacteria through high-throughput sequencing revealed that OsCIPK2 has a significant impact on the diversity of the root microbial community under low nitrogen stress. The quantification of nifH gene expression demonstrated a significant enhancement in nitrogen-fixing capabilities in the roots of RC transgenetic rice. Synthetic microbial communities (SynCom) consisting of six nitrogen-fixing bacterial strains were observed to be enriched in the roots of RC, leading to a substantial improvement in rice growth and nitrogen uptake in nitrogen-deficient soils. Forty and twenty-three metabolites exhibiting differential abundance were identified in the roots and rhizosphere soils of RC transgenic rice compared to wild-type (WT) rice. These findings suggest that OSCIPK2 plays a role in restructuring the microbial community in the roots through the regulation of metabolite synthesis and secretion. Further experiments involving the exogenous addition of citric acid revealed that an optimal concentration of this compound facilitated the growth of nitrogen-fixing bacteria and substantially augmented their population in the soil, highlighting the importance of citric acid in promoting nitrogen fixation under conditions of low nitrogen availability. These findings suggest that OsCIPK2 plays a role in enhancing nitrogen uptake by rice plants from the soil by influencing the assembly of root microbial communities, thereby offering valuable insights for enhancing nitrogen utilization in rice cultivation.},
}

*Oryza
Plant Roots/metabolism
Nitrogen/metabolism
*Nitrogen-Fixing Bacteria/metabolism
Soil
Rhizosphere
Citric Acid
Soil Microbiology

@article {pmid38626906,
year = {2024},
author = {Bongers, KS and Massett, A and O'Dwyer, DN},
title = {The Oral-Lung Microbiome Axis in Connective Tissue Disease-Related Interstitial Lung Disease.},
journal = {Seminars in respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1055/s-0044-1785673},
pmid = {38626906},
issn = {1098-9048},
abstract = {Connective tissue disease-related interstitial lung disease (CTD-ILD) is a frequent and serious complication of CTD, leading to high morbidity and mortality. Unfortunately, its pathogenesis remains poorly understood; however, one intriguing contributing factor may be the microbiome of the mouth and lungs. The oral microbiome, which is a major source of the lung microbiome through recurrent microaspiration, is altered in ILD patients. Moreover, in recent years, several lines of evidence suggest that changes in the oral and lung microbiota modulate the pulmonary immune response and thus may play a role in the pathogenesis of ILDs, including CTD-ILD. Here, we review the existing data demonstrating oral and lung microbiota dysbiosis and possible contributions to the development of CTD-ILD in rheumatoid arthritis, Sjögren's syndrome, systemic sclerosis, and systemic lupus erythematosus. We identify several areas of opportunity for future investigations into the role of the oral and lung microbiota in CTD-ILD.},
}

@article {pmid38626862,
year = {2024},
author = {Peixoto, S and Morgado, RG and Prodana, M and Cardoso, DN and Malheiro, C and Neves, J and Santos, C and Khodaparast, Z and Pavlaki, MD and Rodrigues, S and Rodrigues, SM and Henriques, I and Loureiro, S},
title = {Responses of soil microbiome to copper-based materials (nano and bulk) for agricultural applications: An indoor-mesocosm experiment.},
journal = {NanoImpact},
volume = {},
number = {},
pages = {100506},
doi = {10.1016/j.impact.2024.100506},
pmid = {38626862},
issn = {2452-0748},
abstract = {The foreseen increasing application of copper-based nanomaterials (Cu-NMs), replacing or complementing existing Cu-agrochemicals, may negatively impact the soil microbiome. Thus, we studied the effects on soil microbiome function and composition of nano copper oxide (nCuO) or copper hydroxide NMs in a commercial (Kocide®3000) or a lab-synthetized formulation (nCu(OH)2) or bulk copper hydroxide (Cu(OH)2-B), at the commonly recommended Cu dose of 50 mg(Cu)kg[-1] soil. Microbial responses were studied over 28 days in a designed indoor mesocosm. On day-28, in comparison to non-treated soil (CT), all Cu-treatments led to a reduction in dehydrogenase (95% to 68%), arylsulfatase (41% to 27%), and urease (40% to 20%) activity. There was a 32% increase in the utilization of carbon substrates in the nCuO-treatment and an increased abundance of viable bacteria in the nCu(OH)2-treatment (75% of heterotrophic and 69% of P-solubilizing bacteria). The relative abundance of Acidobacteria [Kocide®3000, nCuO, and Cu(OH)2-B treatments] and Flavobacteriia [nCu(OH)2-treatment] was negatively affected by Cu exposure. The abundance of Cu-tolerant bacteria increased in soils treated with Kocide®3000 (Clostridia) and nCu(OH)2 (Gemmatimonadetes). All Cu-treated soils exhibited a reduced abundance of denitrification-related genes (0.05% of nosZ gene). The DTPA-extractable pool of ionic Cu(II) varied among treatments: Cu(OH)2-B > Kocide®3000 ~ nCuO>nCu(OH)2, which may explain changes on the soil microbiome composition, at the genera and OTU levels. Thus, our study revealed that Cu-materials (nano and bulk) influence the soil microbiome with implications on its ecological role. It highlights the importance of assessing the impact of Cu-materials under dynamic and complex exposure scenarios and emphasizes the need for specific regulatory frameworks for NMs.},
}

@article {pmid38626296,
year = {2024},
author = {Denburg, JA and O'Byrne, PM and Gauvreau, GM},
title = {Eosinophil Plasticity and Diversity: Proceedings of the 2023 International Eosinophil Society Symposium.},
journal = {Journal of leukocyte biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jleuko/qiae089},
pmid = {38626296},
issn = {1938-3673},
abstract = {This issue highlights and details the programme and scientific presentations at the International Eosinophil Society's 12th biennial Symposium, which was held in Hamilton, Ontario, Canada in July 2023. The meeting included sessions on regulation of eosinophil development; cell death, stress, and autophagy in eosinophils; local immunity interactions of eosinophils with multiple cell types; eosinophils in host defense; eosinophils and mast cells in gastrointestinal disorders; reciprocal interactions between eosinophils and the microbiome in homeostasis and dysbiosis; and, eosinophils in tissue injury and repair, in tumor biology and cancer therapy. There was a mixture of special invited lectures and cutting-edge abstracts on specific aspects of eosinophil science, as well as enlivened pro-con debates on targeting eosinophils with biologics. A major thrust and overarching theme was that eosinophils exhibit remarkable plasticity and heterogeneity in executing their functions both in homeostasis and in pathobiology; there is a new "Eo-verse" to understand. We trust that this special volume of the Journal of Leukocyte Biology will be of interest across many disciplines and medical sub-specialties in biomedical sciences and demonstrate both the complexity and versatility of the eosinophil in biology and medicine.},
}

@article {pmid38625898,
year = {2024},
author = {Goforth, M and Cooper, MA and Oliver, AS and Pinzon, J and Skots, M and Obergh, V and Suslow, TV and Flores, GE and Huynh, S and Parker, CT and Mackelprang, R and Cooper, KK},
title = {Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0297453},
pmid = {38625898},
issn = {1932-6203},
mesh = {Humans ; *Prunus persica ; Seasons ; Bacteria ; *Citrus sinensis/microbiology ; Fruit/microbiology ; },
abstract = {Assessing the microbes present on tree fruit carpospheres as the fruit enters postharvest processing could have useful applications, as these microbes could have a major influence on spoilage, food safety, verification of packing process controls, or other aspects of processing. The goal of this study was to establish a baseline profile of bacterial communities associated with apple (pome fruit), peach (stone fruit), and Navel orange (citrus fruit) at harvest. We found that commercial peaches had the greatest bacterial richness followed by oranges then apples. Time of harvest significantly changed bacterial diversity in oranges and peaches, but not apples. Shifts in diversity varied by fruit type, where 70% of the variability in beta diversity on the apple carposphere was driven by the gain and loss of species (i.e., nestedness). The peach and orange carposphere bacterial community shifts were driven by nearly an even split between turnover (species replacement) and nestedness. We identified a small core microbiome for apples across and between growing seasons that included only Methylobacteriaceae and Sphingomonadaceae among the samples, while peaches had a larger core microbiome composed of five bacterial families: Bacillaceae, Geodermtophilaceae, Nocardioidaceae, Micrococcaeceae, and Trueperaceae. There was a relatively diverse core microbiome for oranges that shared all the families present on apples and peaches, except for Trueperaceae, but also included an additional nine bacterial families not shared including Oxalobacteraceae, Cytophagaceae, and Comamonadaceae. Overall, our findings illustrate the important temporal dynamics of bacterial communities found on major commercial tree fruit, but also the core bacterial families that constantly remain with both implications being important entering postharvest packing and processing.},
}

Humans
*Prunus persica
Seasons
Bacteria
*Citrus sinensis/microbiology
Fruit/microbiology

@article {pmid38625646,
year = {2024},
author = {Han, JH and Kim, HS},
title = {Skin Deep: The Potential of Microbiome Cosmetics.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {38625646},
issn = {1976-3794},
support = {2023R1A2C1007759//The National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; HI23C086000//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI) funded by the Ministry of Health & Welfare, Republic of Korea/ ; },
abstract = {The interplay between the skin microbiome and its host is a complex facet of dermatological health and has become a critical focus in the development of microbiome cosmetics. The skin microbiome, comprising various microorganisms, is essential from birth, develops over the lifespan, and performs vital roles in protecting our body against pathogens, training the immune system, and facilitating the breakdown of organic matter. Dysbiosis, an imbalance of these microorganisms, has been implicated in a number of skin conditions such as acne, atopic dermatitis, and skin cancer. Recent scientific findings have spurred cosmetic companies to develop products that preserve and enhance the skin's microbial diversity balance. These products may incorporate elements like prebiotics, probiotics, and postbiotics, which are beneficial for the skin microbiome. Beyond topical products, there's increasing interest in ingestible beauty supplements (i.e. oral probiotics), highlighting the connection between the gut and skin. This review examines the influence of the microbiome on skin health and the emerging trends of microbiome skincare products.},
}

@article {pmid38625645,
year = {2024},
author = {Lee, C and Lee, S and Yoo, W},
title = {Metabolic Interaction Between Host and the Gut Microbiota During High-Fat Diet-Induced Colorectal Cancer.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {38625645},
issn = {1976-3794},
abstract = {Colorectal cancer (CRC) is the second-highest cause of cancer-associated mortality among both men and women worldwide. One of the risk factors for CRC is obesity, which is correlated with a high-fat diet prevalent in Western dietary habits. The association between an obesogenic high-fat diet and CRC has been established for several decades; however, the mechanisms by which a high-fat diet increases the risk of CRC remain unclear. Recent studies indicate that gut microbiota strongly influence the pathogenesis of both high-fat diet-induced obesity and CRC. The gut microbiota is composed of hundreds of bacterial species, some of which are implicated in CRC. In particular, the expansion of facultative anaerobic Enterobacteriaceae, which is considered a microbial signature of intestinal microbiota functional imbalance (dysbiosis), is associated with both high-fat diet-induced obesity and CRC. Here, we review the interaction between the gut microbiome and its metabolic byproducts in the context of colorectal cancer (CRC) during high-fat diet-induced obesity. In addition, we will cover how a high-fat diet can drive the expansion of genotoxin-producing Escherichia coli by altering intestinal epithelial cell metabolism during gut inflammation conditions.},
}