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Bibliography on: Biodiversity and Metagenomics

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Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 06 Jun 2025 at 01:30 Created: 

Biodiversity and Metagenomics

If evolution is the only light in which biology makes sense, and if variation is the raw material upon which selection works, then variety is not merely the spice of life, it is the essence of life — the sine qua non without which life could not exist. To understand biology, one must understand its diversity. Historically, studies of biodiversity were directed primarily at the realm of multicellular eukaryotes, since few tools existed to allow the study of non-eukaryotes. Because metagenomics allows the study of intact microbial communities, without requiring individual cultures, it provides a tool for understanding this huge, hitherto invisible pool of biodiversity, whether it occurs in free-living communities or in commensal microbiomes associated with larger organisms.

Created with PubMed® Query: biodiversity metagenomics NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

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RevDate: 2025-06-05
CmpDate: 2025-06-05

García-Pérez P, Tomas M, Giuberti G, et al (2025)

Brassica microgreens shape gut microbiota and functional metabolite profiles in a species-related manner: A multi-omics approach following in vitro gastrointestinal digestion and large intestine fermentation.

Microbiological research, 298:128226.

Brassicaceae microgreens constitute a novel and promising source of bioactive compounds, such as polyphenols and glucosinolates. In this work, an integrative computational approach was performed to decipher the interaction between bioaccessible microgreen metabolites and human gut bacteria. To this end, in vitro gastrointestinal digestion and large intestine fermentation were performed on eight different microgreens, which were further subjected to a dual high-throughput approach that combined fecal metagenomics and untargeted metabolomics. Data reveal a significant correlation between Parabacteroides merdae and two isothiocyanates in arugula fermentates, suggesting a high bioaccessibility of these bioactive compounds. Meanwhile, two species of Roseburia were correlated with pseudooxynicotine, an anti-inflammatory catabolite of nicotine in Brassica oleracea fermentates (such as broccoli, Brussels sprouts, and red cabbage), coupled with an increase in short-chain fatty acid production. These findings confer evidence on the nutritional impact of microgreens consumption, revealing the most bioaccessible metabolites with associated health-promoting properties together with their participation in the shaping of gut microbial populations, possibly leading to prebiotic effects.

RevDate: 2025-05-31
CmpDate: 2025-05-28

Berelson MFG, Heavens D, Nicholson P, et al (2025)

From air to insight: the evolution of airborne DNA sequencing technologies.

Microbiology (Reading, England), 171(5):.

Historically, the analysis of airborne biological organisms relied on microscopy and culture-based techniques. However, technological advances such as PCR and next-generation sequencing now provide researchers with the ability to gather vast amounts of data on airborne environmental DNA (eDNA). Studies typically involve capturing airborne biological material, followed by nucleic acid extraction, library preparation, sequencing and taxonomic identification to characterize the eDNA at a given location. These methods have diverse applications, including pathogen detection in agriculture and human health, air quality monitoring, bioterrorism detection and biodiversity monitoring. A variety of methods are used for airborne eDNA analysis, as no single pipeline meets all needs. This review outlines current methods for sampling, extraction, sequencing and bioinformatic analysis, highlighting how different approaches can influence the resulting data and their suitability for specific use cases. It also explores current applications of airborne eDNA sampling and identifies research gaps in the field.

RevDate: 2025-05-30
CmpDate: 2025-05-28

von Ameln Lovison O, Zempulski Volpato FC, Weber LG, et al (2025)

Unveiling the role of the upper respiratory tract microbiome in susceptibility and severity to COVID-19.

Frontiers in cellular and infection microbiology, 15:1531084.

It is argued that commensal bacteria in the upper respiratory tract (URT) protect against pathogen colonization and infection, including respiratory viruses. Given that the microbiome can mediate immune modulation, a link between the URT microbiome (URTM) and COVID-19 susceptibility and severity is expected. This 16S metagenomics cross-sectional study assessed URTM composition, metabolic prediction, and association with laboratory biomarkers in non-COVID-19 pneumonia (NO-CoV), moderate (M-CoV), severe (S-CoV) COVID-19 patients, as well as COVID-19-negative, asymptomatic (NC) patients. The S-CoV group exhibited reduced URTM diversity, primarily due to a decreased abundance of eubiotic taxa. Some of these taxa (e.g., Haemophilus sp., Neisseria sp.) were also associated with inflammatory biomarkers. Multiple metabolic pathways (e.g., short-chain fatty acids, vitamin B12) linked to immune response, antiviral activity, and host susceptibility showed decreased abundance in S-CoV. These pathways could suggest potential alternatives for the therapeutic arsenal against COVID-19, providing reassurance about the progress in understanding and treating this disease.

RevDate: 2025-06-05
CmpDate: 2025-06-05

Merchant M, Mande SS, P Sar (2025)

Microbial community enrichment and transition in landfill for the biotransformation of unpretreated low-density polyethylene (LDPE) under aerobic and anaerobic conditions.

Chemosphere, 382:144429.

Low density polyethylene (LDPE), prevalent in single-use plastics, poses a significant environmental challenge due to its limited biodegradation. This study aims to enrich and characterize unpretreated LDPE degrading microorganisms from a nearly 50-year-old municipal landfill under aerobic and anaerobic conditions. Detailed analysis of the microbial communities through 16S rRNA gene based metataxonomy, whole genome metagenomics as well as thorough characterization of LDPE films exposed to the enriched microorganisms are done. Distinct shifts between plastisphere and bulk communities were observed. Shotgun metagenomics enabled reconstruction of thirty high-quality metagenome-assembled genomes (MAGs), revealing genes for plastic and hydrocarbon degradation, and biosurfactant production. Several plastic degradation-associated bacteria were identified, including Pseudomonas, Streptomyces, Burkholderia, Bacillus, Thermobifida, Saccharomonospora, Methylocaldum, Methylobacter, Ilumatobacter, Rubrivivax, and archaeal candidates like Methanosarcina and Nitrosarchaeum were observed. MAGs from Burkholderiales and Chlamydiales showed higher potential for LDPE degradation. Scanning electron microscopy showed biofilm formation on plastics, atomic force microscopy indicated surface topological changes, and Fourier transform infrared spectroscopy revealed increased carbonyl groups. Aerobic enrichments allowed up to 60% weight reduction of LDPE, with a degradation rate of 0.00766 mg/day and reaching half-life in nearly 90.49 days, confirming the biodegradation potential of the microbial community. From these observations, this study suggests two potential mechanisms of LDPE degradation under aerobic and anaerobic conditions by enriched communities. This study highlights role of landfill microbiomes in LDPE degradation, offering valuable insights into microbial succession of plastisphere and contributing to the development of effective plastic-degrading community. Future research could explore optimizing these for large-scale plastic waste management.

RevDate: 2025-06-05
CmpDate: 2025-06-05

Jiang JY, Fan ZX, Yang F, et al (2025)

[Composition of gut microbiota and characteristics of virulence factors genes in overweight or obese children and their relationship with liver metabolic inflammation].

Zhonghua er ke za zhi = Chinese journal of pediatrics, 63(6):642-648.

Objective: To explore the composition of gut microbiome, the characteristics of virulence factor genes and their relationship with liver metabolic inflammation in overweight or obese children. Methods: A case-control design was conducted. From the children who visited the West China Second University Hospital of Sichuan University for medical or physical examinations between August 2021 and April 2022, a total of 23 obese children (obesity group), 8 overweight children (overweight group), and 22 healthy children (control group) were recruited. The body mass index of children was calculated after anthropometric measurements; metabolic inflammation indexes such as the levels of fasting blood glucose and hepatic function and renal function etc. were detected. The composition and abundance of gut microbiota in the feces of the children were detected by metagenomic sequencing technology and the Shannon index and Simpson index were calculated to assess the α diversity of virulence factor genes. The Wilcoxon rank-sum test was used for pairwise comparison between groups. The Spearman's rank correlation test was used for correlation analysis, and the Benjamini-Hochberg method was used to correct the P-value of multiple tests. Results: The obese group included 23 children aged 8.5 (6.3, 11.8) years, of whom 9 (39%) were male. The overweight group consisted of 8 children aged 9.2 (5.5, 12.3) years, of whom 4 were male. The control group comprised 22 children aged 5.3 (5.1, 5.4) years, of whom 10 (45%) were male. The obese group exhibited higher levels of alanine aminotransferase (ALT), gamma-glutamyl transferase (γ-GT), globulin, and uric acid compared to those of the control group (all P<0.05), with ALT also higher than that of the overweight group (P<0.05). The levels of fasting blood glucose, γ-GT, globulin, and uric acid in the overweight group were all higher than those in the control group (all P<0.05). The abundance of Coprococcus A (0.76 (0.00, 3.11) vs. 0.00 (0.00, 0.00), false discovery rate (FDR)<0.05) and Parasutterella (0.89 (0.08, 1.79) vs. 0.00 (0.00, 0.08), FDR<0.05) in the gut of children in the obese group were both higher than those of the control group. The number of virulence factor genes in the obese group was higher than those of the control group (941 (886, 977) vs. 890 (807, 920), P<0.05). The Simpson index and Shannon index of gut microbial virulence factor genes in the obese group were both higher than those of the control group (0.993 (0.992, 0.993) vs. 0.991(0.990, 0.991), (5.50 (5.46, 5.56) vs. 5.37 (5.30, 5.43), both P<0.01). The abundance of gut microbiota virulence factors genes all showed positive correlations with fasting blood glucose, ALT, γ-GT, and uric acid levels in children (all r>0.3, all FDR<0.05). The abundance of 17 gut microbial virulence factor genes were all positively associated with γ-GT levels (all r>0.3, all FDR<0.05). The virulence factor genes (LpxH, LpxB, LpxK) of lipopolysaccharide were all positively correlated with plasma γ-GT and globulin levels (all r>0.3, all FDR<0.05). Conclusions: Overweight or obese children exhibited elevated liver metabolic-inflammatory markers compared to their normal-weight counterparts. Notably, obese children demonstrated gut microbiota dysbiosis accompanied by enrichment of virulence factor genes, which may promote liver metabolic inflammation through pathways such as lipopolysaccharide biosynthesis.

RevDate: 2025-06-05
CmpDate: 2025-06-05

Ren P, You C, Chen P, et al (2025)

Organic amendments derived from Chinese herb residues enhance soil ecosystem multifunctionality by enriching key microorganisms.

Microbiological research, 298:128213.

Ecosystem multifunctionality (EMF), a key metric reflecting soil health, has been proven to be positively influenced by organic amendments. Chinese herb residues (CHR), rich in bioactive compounds and with lower ecological risks, are regarded as a promising source for organic amendments. Therefore, we conducted a greenhouse experiment with four treatments: no fertilizer (CK), chemical fertilizer (CF), single application of CHR-OA (OA), and partially replacing chemical fertilizers with CHR-OA (OA-CF), aiming to explore the regulatory mechanism of CHR-OA addition to EMF. A total of 19 ecosystem functions, covering plant growth, pathogen suppression, soil physicochemical properties, and microbial diversity, were used to calculate EMF. The results showed that most of the above ecosystem functions were improved by adding CHR-OA, with the OA-CF possessing the highest EMF, followed by OA. Additionally, Lysobacter was enriched as a key genus. Further analysis revealed that Lysobacter drove EMF by influencing bacterial Simpson index, plant height, and root length, and this conclusion was confirmed in greenhouse verification experiments. Through this study, we have gained a clearer understanding of the prominent ecosystem functions provided by CHR-OA and the regulatory mechanism of EMF.

RevDate: 2025-06-05
CmpDate: 2025-06-05

Liébana-García R, López-Almela I, Olivares M, et al (2025)

Gut commensal Phascolarctobacterium faecium retunes innate immunity to mitigate obesity and metabolic disease in mice.

Nature microbiology, 10(6):1310-1322.

The gut microbiota may protect against obesity and chronic metabolic conditions by regulating the immune response to dietary triggers. Yet the specific bacteria that control the overactivation of the immune system in obesity and their mode of action remain largely unknown. Here we surveyed 7,569 human metagenomes and observed an association between the gut symbiont Phascolarctobacterium faecium and non-obese adults regardless of nationality, sex or age. In a mouse model of diet-induced obesity, we confirmed the specificity of P. faecium DSM 32890 anti-obesogenic properties compared with other species of the same genus. P. faecium reversed the inflammatory phenotype associated with obesity. Specifically, P. faecium promoted polarization of alternatively activated macrophages (M2), which reversed the obesity-induced increase in gut-resident type 1 innate lymphoid cells. This resulted in mitigation of glucose intolerance, adiposity and body weight gain irrespective of treatment with live or pasteurized bacteria. The metabolic benefits were independent of the adaptive immune system, but they were abolished by an inhibitor of M2 polarization in mice. P. faecium directly promoted M2-macrophage polarization through TLR2 signalling and these effects seemed to be independent of gut microbiota changes. Overall, we identify a previously undescribed gut commensal bacterium that could help mitigate obesity and metabolic comorbidities by retuning the innate immune response to hypercaloric diets.

RevDate: 2025-06-05
CmpDate: 2025-06-05

Wani AK, Qadir F, Elboughdiri N, et al (2025)

Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health.

Biotechnology advances, 82:108580.

Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.

RevDate: 2025-06-05
CmpDate: 2025-06-05

Saeed M, Al-Khalaifah H, Al-Nasser A, et al (2025)

Feeding the future: A new potential nutritional impact of Lactiplantibacillus plantarum and its promising interventions in future for poultry industry.

Poultry science, 104(6):105130.

The increasing demand for sustainable and efficient chicken production has intensified the interest in functional feed additives such as probiotics. Lactiplantibacillus plantarum (formerly known as Lactobacillus plantarum) is an important probiotic bacterium that has become an essential component in poultry nutrition owing to its diverse advantages. This bacterium improves gut health by regulating the intestinal microbiota, increasing food absorption, and strengthening the immune system. It also alleviates the detrimental impacts of pathogenic bacteria, thereby reducing the reliance on antibiotics and promoting antibiotic-free poultry production. Additionally, Lactobacillus plantarum enhances growth performance, feed conversion efficiency, and total flock productivity. Adding Lactobacillus plantarum to chicken feed helps the gut microbiota by encouraging good bacterial communities (e.g., Eubacterium, Faecalibacterium, Ligilactobacillus, Limosilactobacillus, Blautia and Clostridium). This leads to increased growth in chickens and helps maintain the balance of their gut flora. Lactobacillus plantarum has been extensively investigated as a potential feed additive to replace in-feed antibiotics. Published literature have revealed that a dietary additive of Lactobacillus plantarum improved the health and growth of broilers by improving the balance of bacteria and the metabolism of nutrients in the gut. This study explores the incorporation of Lactobacillus plantarum into poultry diets and its importance in sustainable and healthy poultry production. This study will encourage poultry scientists to investigate further before encapsulation. Innovations in Lactiplantibacillus plantarum, including its intestine colonization methods and novel strategies to improve its colonization, have the potential to transform the industry. Rapid development of tools and techniques (microencapsulated, nanotechnology, metagenomics, and transcriptome for L. plantarum) could help cover research and application shortages.

RevDate: 2025-06-05
CmpDate: 2025-06-05

Khan MM, Mushtaq MA, Suleman M, et al (2025)

Fecal microbiota landscape of commercial poultry farms in Faisalabad, Pakistan: A 16S rRNA gene-based metagenomics study.

Poultry science, 104(6):105089.

This study explores the microbiota of broiler and layer farms, aiming to understand how genetic breed, age, and farm type influence microbial communities in commercial settings. Fecal samples from 18 poultry farms (twelve layers and six broilers) in Faisalabad, Pakistan were analyzed using 16S rRNA gene sequencing of the V3-V4 region to evaluate bacterial composition. The dominant phylum, Firmicutes, accounted for 58.72 % of the microbial population, with Lactobacillus being the most abundant genus in both broilers and layers. The total abundance of potentially pathogenic genera was also assessed with Enterococcus and Corynebacterium being the most prevalent across all farms, regardless of bird type. Layers exhibited greater microbial richness and diversity than broilers, while the Karachi cage system (KCS) farm type showed higher richness than Floor system (FS). Although the breed significantly influenced microbial diversity, age was not a determining factor. Co-occurrence analyses revealed close interactions among phyla (Actinobacteriota, Proteobacteria, Firmicutes, Fusobacteriota, and Bacteroidota) and genera (Lactobacillus, Brevibacterium, Enterococcus), suggesting their pivotal roles within the microbial community. Additionally, functional analysis detected important metabolic pathways and traced microbial signatures of key pathogenic bacteria, enhancing our understanding of microbial contributions to poultry health. Despite limitations such as the need for broader geographic sampling and accounting for diet and medication, this study advances microbiome research in Pakistan's poultry sector, emphasizing consistent taxa and opening avenues for future investigations into microbiome manipulations for improved food safety and achieve better sustainable practices.

RevDate: 2025-06-05
CmpDate: 2025-06-05

Steinberg R, Moeller A, Gisler A, et al (2025)

Longitudinal effects of elexacaftor/tezacaftor/ivacaftor on the oropharyngeal metagenome in adolescents with cystic fibrosis.

Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society, 24(3):562-570.

BACKGROUND: Triple modulator therapy elexacaftor/tezacaftor/ivacaftor (ETI) improves lung function and impacts upon the respiratory microbiome in people with Cystic fibrosis (pwCF) with advanced lung disease. However, adolescents with cystic fibrosis (CF) are less colonized with bacterial pathogens than adult pwCF but their microbiota already differs from healthy individuals. The aim of this study was to longitudinally analyze the impact of ETI on the respiratory metagenome in adolescents with predominantly mild CF lung disease.

METHODS: In this prospective observational study, we included pwCF aged 12-20 years with at least one F508del mutation, who collected oropharyngeal swabs before and after initiation of ETI therapy twice per week to biweekly over three months. We performed whole metagenome shotgun sequencing, followed by host DNA filtering and taxonomic profiling. We used linear and additive mixed effects models adjusted for known confounders and corrected for multiple testing to study longitudinal development of the microbiome. We analyzed bacterial diversity, abundance, and strain-level phylogeny.

RESULTS: We analyzed the metagenomic data of 297 swabs of 20 pwCF. Microbiome composition changed after initiation of ETI therapy. We observed a slight diversification of the microbiome over time (Inv Simpson, Coef 0.085, 95 %CI 0.003, 0.17, p = 0.04). Strain-level analysis and clustering showed that strain retention of the most frequent bacterial species is predominant even during ETI therapy.

CONCLUSIONS: During three months of ETI therapy, commensal bacteria increased, which may help to prevent overgrowth of bacterial pathogens.

RevDate: 2025-05-31
CmpDate: 2025-05-28

Yue Y, Yang HJ, Li C, et al (2025)

Beneficial Effects of Traditional Fermented Soybean Sauce (Kanjang) on Memory Function, Body Water, and Glucose Metabolism: Roles of Gut Microbiota and Neuroinflammation.

Nutrients, 17(10):.

Background: Traditional fermented soybean foods, acting as potential synbiotics, may help mitigate cognitive impairment associated with amnesia. This study investigated the neuroprotective effects of four kanjang (Korean fermented soy sauce) varieties and their underlying mechanisms. Methods: Male Sprague Dawley rats (n = 70) were divided into seven groups: normal control, scopolamine control, positive control (1 mg/kg bw/day of donepezil), and four scopolamine-treated groups receiving different kanjang varieties (0.5% in high-fat diet). Based on their Bacillus content, the kanjang samples were categorized as traditionally made kanjang (TMK) with high Bacillus (SS-HB), TMK with medium Bacillus (SS-MB), TMK with low Bacillus (SS-LB), and factory-made kanjang (SS-FM). Results: Scopolamine administration disrupted energy, glucose, and water metabolism and impaired memory function (p < 0.05). All kanjang treatments improved insulin sensitivity, reduced inflammation, enhanced glucose tolerance, and decreased visceral fat. SS-MB, SS-HB, and SS-FM increased skeletal muscle mass. They maintained body water homeostasis by suppressing the renin-angiotensin-aldosterone system. Kanjang treatments improved memory function, with SS-FM showing the least significant effects. The treatments reduced neuronal cell death in the hippocampal CA1 region, decreased acetylcholinesterase activity, and increased brain-derived neurotrophic factor mRNA expression. Gut microbiota analysis revealed that kanjang treatments increased Lactobacillaceae and decreased Lachnospiraceae, with SS-HB and SS-LB specifically elevating Ligilactobacillus. Metagenomic analysis demonstrated enhanced glycolysis/gluconeogenesis pathways and enhanced butanoate metabolism while reducing lipopolysaccharide biosynthesis and pro-inflammatory signaling. SS-MB and SS-LB increased intestinal goblet cell counts and the serum butyrate concentration. Conclusions: These findings suggest that kanjang consumption, particularly SS-HB and SS-LB varieties, can ameliorate memory impairment in this murine model through multiple mechanisms: metabolic improvements, enhanced neurotrophic signaling, gut microbiota modulation, and reduced neuroinflammation via gut-brain axis activation. Human clinical trials are warranted to determine if these promising neuroprotective effects translate to clinical applications.

RevDate: 2025-05-31

Mirete S, Sánchez-Costa M, Díaz-Rullo J, et al (2025)

Metagenome-Assembled Genomes (MAGs): Advances, Challenges, and Ecological Insights.

Microorganisms, 13(5):.

Metagenome-assembled genomes (MAGs) have revolutionized microbial ecology by enabling the genome-resolved study of uncultured microorganisms directly from environmental samples. By leveraging high-throughput sequencing, advanced assembly algorithms, and genome binning techniques, researchers can reconstruct microbial genomes without the need for cultivation. These methodological advances have expanded the known microbial diversity, revealing novel taxa and metabolic pathways involved in key biogeochemical cycles, including carbon, nitrogen, and sulfur transformations. MAG-based studies have identified microbial lineages form Archaea and Bacteria responsible for methane oxidation, carbon sequestration in marine sediments, ammonia oxidation, and sulfur metabolism, highlighting their critical roles in ecosystem stability. From a sustainability perspective, MAGs provide essential insights for climate change mitigation, sustainable agriculture, and bioremediation. The ability to characterize microbial communities in diverse environments, including soil, aquatic ecosystems, and extreme habitats, enhances biodiversity conservation and supports the development of microbial-based environmental management strategies. Despite these advancements, challenges such as assembly biases, incomplete metabolic reconstructions, and taxonomic uncertainties persist. Continued improvements in sequencing technologies, hybrid assembly approaches, and multi-omics integration will further refine MAG-based analyses. As methodologies advance, MAGs will remain a cornerstone for understanding microbial contributions to global biogeochemical processes and developing sustainable interventions for environmental resilience.

RevDate: 2025-05-31

Jiang K, Ye L, Cao C, et al (2025)

Multi-Metagenome Analysis Unravels Community Collapse After Sampling and Hints the Cultivation Strategy of CPR Bacteria in Groundwater.

Microorganisms, 13(5):.

Groundwater harbors phylogenetically diverse Candidate Phyla Radiation (CPR) bacteria, representing an ideal ecosystem for studying this microbial dark matter. However, no CPR strains have been successfully isolated from groundwater, severely limiting further research. This study employed a multi-metagenome approach, integrating time-resolved sampling, antibiotic/nutrient interventions, and microbial correlation networks to unravel CPR ecological roles in groundwater and provide insights into their subsequent cultivation. Through 36 metagenomes from a groundwater system containing at least 68 CPR phyla, we revealed the time-sensitive collapse of CPR communities: total abundance plummeted from 7.9% to 0.15% within 48 h post-sampling, driven by competition with rapidly dividing non-CPR bacteria, such as members of Pseudomonadota. Ampicillin (100 mg/L) stabilized CPR communities by suppressing competitors, whereas low-nutrient conditions paradoxically reversed this effect. Long-term enrichment (14 months) recovered 63 CPR phyla (0.35% abundance), revealing their survival resilience despite nutrient deprivation. Correlation networks prioritized Actinomyces, a novel Acidimicrobiaceae genus, Aestuariivirga, Baekduia and Caedimonadaceae as potential CPR partners, providing actionable targets for co-culture trials. Here, we propose actionable recommendations spanning groundwater sampling, activation status, identification of CPR symbiotic partners, and optimization of culture conditions, which bypass traditional blind cultivation and are critical for future efforts to cultivate CPR bacterial strains from groundwater. Cultivating CPR bacteria will contribute to clarifying their diversity, ecological roles, evolutionary mechanisms, metabolic pathways, and genetic potential.

RevDate: 2025-05-31

Mendybayeva A, Makhambetov A, Yanin K, et al (2025)

Metagenomic Analysis of Wild Apple (Malus sieversii) Trees from Natural Habitats of Kazakhstan.

Plants (Basel, Switzerland), 14(10):.

Kazakhstan's rich biodiversity includes diverse apple populations, notably the wild apple tree (Malus sieversii) prized for traits like disease resistance and adaptability, potentially aiding breeding programs. Analyzing their microbiomes offers insights into bacterial diversity and how it influences apple tree development, making it a reliable method for understanding ecological interactions. In this research, 334 apple tree samples were collected from different mountain ranges in southeastern Kazakhstan. An analysis using nanopore-based 16S rRNA sequencing showed a distinct similarity in the microbiome compositions of samples from the Zhongar and Ile Alatau mountain ranges, with a predominance of Pseudomonadaceae, Enterobacteriaceae, and Microbacteriaceae. In contrast, samples from Ketmen ridge showed a higher prevalence of Enterobacteriaceae. Alongside the less represented Pseudomonadaceae family, in the Ketmen ridge region, bacteria of the Xanthomonadaceae, Alcaligenaceae, and Brucellaceae families were also present. Across all regions, beneficial plant-associated bacteria were identified, such as Pseudomonas veronii, Stenotrophomonas geniculata, and Kocuria rhizophila, potentially enhancing plant resilience. However, opportunistic phytopathogens were also detected, including Pseudomonas viridiflava and Serratia marcescens, particularly in the Ile Alatau region. These findings highlight the complex microbial interactions in M. sieversii, thus offering key insights into host-microbe relationships that can inform apple breeding and ecological preservation efforts.

RevDate: 2025-05-31
CmpDate: 2025-05-28

San-Martin MI, Chamizo-Ampudia A, Sanchiz Á, et al (2025)

Microbiome Markers in Gastrointestinal Disorders: Inflammatory Bowel Disease, Colorectal Cancer, and Celiac Disease.

International journal of molecular sciences, 26(10):.

Intestinal microbiota and the host's immune system form a symbiotic alliance that sustains normal development and function in the human gut. Changes such as dietary habits among societies in developed countries have led to the development of unbalanced microbial populations in the gut, likely contributing to the dramatic increase in inflammatory diseases in the last few decades. Recent advances in DNA sequencing technologies have tremendously helped to characterize the microbiome associated with disease, both in identifying global alterations and discovering specific biomarkers that potentially contribute to disease pathogenesis, as evidenced by animal studies. Beyond bacterial alterations, non-bacterial components such as fungi, viruses, and microbial metabolites have been implicated in these diseases, influencing immune responses and gut homeostasis. Multi-omics approaches integrating metagenomics, metabolomics, and transcriptomics offer a more comprehensive understanding of the microbiome's role in disease pathogenesis, paving the way for innovative diagnostic and therapeutic strategies. Unraveling the metagenomic profiles associated with disease may facilitate earlier diagnosis and intervention, as well as the development of more personalized and effective therapeutic strategies. This review synthesizes recent and relevant microbiome research studies aimed at characterizing the microbial signatures associated with inflammatory bowel disease, colorectal cancer, and celiac disease.

RevDate: 2025-05-31
CmpDate: 2025-05-28

Torraco A, Di Nicolantonio S, Cardisciani M, et al (2025)

Meta-Analysis of 16S rRNA Sequencing Reveals Altered Fecal but Not Vaginal Microbial Composition and Function in Women with Endometriosis.

Medicina (Kaunas, Lithuania), 61(5):.

Background and Objectives: Dysbiosis of the oral-gut axis is related to several extraintestinal inflammatory diseases, including endometriosis. This study aims to assess the microbial landscape and pathogenic potential of distinct biological niches during endometriosis. Materials and Methods: A microbiome meta-analysis was conducted on 182 metagenomic sequences (79 of fecal and 103 of vaginal origin) from women with and without endometriosis. Fecal and vaginal microbial diversity, differential abundance, and functional analysis based on disease status were assessed. Random forest, gradient boosting, and generalized linear modeling were used to predict endometriosis based on differentially enriched bacteria. Results: Only intestinal microbes displayed distinctive taxonomic and functional characteristics in women with endometriosis compared to control women. Taxonomic differences were quantified using the microbial endometriosis index (MEI), which effectively distinguished between individuals with and without the disease. The observed functional enrichment pointed to proinflammatory pathways previously related to endometriosis development. Conclusions: Dysbiosis in the oral-gut microbial community appears to play a prevalent role in endometriosis. Our findings pave the ground for future studies exploring the potential mechanistic involvement of the oral-gut axis in disease pathogenesis.

RevDate: 2025-05-31
CmpDate: 2025-05-28

Dimitrova L, Ilieva Y, Gouliamova D, et al (2025)

Isolation, Enrichment and Analysis of Aerobic, Anaerobic, Pathogen-Free and Non-Resistant Cellulose-Degrading Microbial Populations from Methanogenic Bioreactor.

Genes, 16(5):.

Background: Nowadays, the microbial degradation of cellulose represents a new perspective for reducing cellulose waste from industry and households and at the same time obtaining energy sources. Methods: We isolated and enriched two aerobic (at 37 °C and 50 °C) and one anaerobic microbial consortium from an anaerobic bioreactor for biogas production by continuous subculturing on peptone cellulose solution (PCS) medium supplemented with 0.3% treated or untreated Whatman filter paper under static conditions. Samples were taken every 7 days until day 21 to determine the percentage of cellulose biodegradation. We determined the antimicrobial resistance of aerobic and anaerobic consortia and some single colonies by disc diffusion method, against 42 clinically applied antibiotics. PCR analyses were performed to search for the presence of eight genes for cellulolytic activity and nine genes for antibiotic resistance. By metagenomics analysis, the bacterial and fungal genus distributions in the studied populations were determined. Results: Aerobes cultured at 50 °C degraded cellulose to the greatest extent (47%), followed by anaerobes (24-38%) and aerobes (8%) cultured at 37 °C. The bacterial sequence analysis showed that the dominant phyla are Bacillota and Bacteroidetes and genera-Paraclostridium, Defluvitalea, Anaerobacillus, Acetivibrio, Lysinibacillus, Paenibacillus, Romboutsia, Terrisporobacter, Clostridium, Sporanaerobacter, Lentimicrobium, etc. in a different ratio depending on the cultivation conditions and the stage of the process. Some of these representatives are cellulolytic and hemicellulolytic microorganisms. We performed lyophilization and proved that it is suitable for long-term storage of the most active consortium, which degrades even after the 10th re-inoculation for a period of one year. We proved the presence of ssrA, ssrA BS and blaTEM genes. Conclusions: Our findings demonstrated the potential utility of the microbial consortium of anaerobes in the degradation of waste lignocellulose biomass.

RevDate: 2025-05-31
CmpDate: 2025-05-28

Sun YF, Han ZX, Yao XK, et al (2025)

Effects of Different Stages of Training on the Intestinal Microbes of Yili Horses Analyzed Using Metagenomics.

Genes, 16(5):.

Objectives: The aim of this study was to investigate the effects of different stages of training on the intestinal microbial abundance of Yili horses. Methods: Ten Yili horses, all aged 2 years old and weighing 305 ± 20 kg, were selected and divided into a training group and an untrained group. The training group performed riding training 6 days a week, and the untrained group moved freely in the activity circle every day. Fecal samples were collected on days 30 and 60, and the intestinal microorganisms were detected and analyzed using metagenomics. Results: Compared with the 30-day untrained group, the relative abundances of Bacteroidetes were significantly increased in the 30-day training group (p < 0.01). Conversely, the abundances of Clostridiaceae, Clostridium, and Ruminococcus were significantly decreased (p < 0.01), whereas those of Prevotella, Bacteroideaceae, and Bacteroidetes were significantly increased (p < 0.05). Additionally, the relative abundances of Firmicutes and Actinomycetes were significantly decreased (p < 0.05). Compared with the 60-day untrained group, no significant differences in the phyla Bacteriaceae and Bacteriae of the 60-day training group (p > 0.05) were observed. In the linear discriminant analysis effect size analysis, seven significantly different bacteria were detected in the fecal flora of horses in the 30-day training group versus the untrained 30-day group, but only one significantly different bacterium was detected after 60 days. The Kyoto Encyclopedia of Genes and Genomes analysis showed that the differentially expressed genes were related to metabolism and the environmental information processing pathway, carbohydrate metabolism, and membrane transport pathways. Conclusions: Therefore, training seems to affect the diversity and composition of the gut microbiota of Yili horses, especially during the first 30 days of training.

RevDate: 2025-05-31
CmpDate: 2025-05-28

Guo Q, Zhang W, Xu C, et al (2025)

Comparative Analysis of Gut Microbiome Community Structures in Different Populations of Asian Elephants in China and Their Correlation with Diet.

Genes, 16(5):.

BACKGROUND: The interaction and co-evolution between the gut microbiome and the host play important roles in the host's physiology, nutrition, and health. Diet is considered an important driver of differences in the gut microbiota; however, research on the relationship between the gut microbiota and diet in Asian elephants remains limited.

METHODS: In this study, we explored the gut microbiota structure and its relationship with diet in different populations of Asian elephants through metagenomic sequencing, combined with previously published dietary data.

RESULTS: This study found that the dominant gut microbiota of Asian elephants includes the phyla Bacillota (29.85% in BP, 22.79% in RC, 21.89% in SM, 31.67% in ML, and 33.00% in NGH), Bacteroidota (25.25% in BP, 31.44% in RC, 16.44% in SM, 25.73% in ML, and 23.74% in NGH), and Spirochaetota (3.49% in BP, 6.18% in RC, 1.71% in SM, 2.69% in ML, and 3.52% in NGH), with significant differences in the gut microbiota among different populations. Correlation analysis between the gut microbiota and diet revealed that dietary diversity did not directly affect the alpha diversity of the gut microbiota. However, specific food types might play a key role in shaping the gut microbiota structure by regulating the abundance of certain microbiota.

CONCLUSIONS: This study reveals significant differences in the gut microbiota structure among different populations of Asian elephants and explores the impact of diet on the structure. The results provide foundational data for a deeper understanding of the gut microbiota structure of Asian elephants and offer important references for the scientific conservation and precise management strategies of this species.

RevDate: 2025-05-31
CmpDate: 2025-05-28

Santos AFB, Nunes M, Filipa-Silva A, et al (2025)

Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities.

International journal of environmental research and public health, 22(5):.

This study investigates viral composition in wastewater through metagenomic analysis, evaluating the performance of four bioinformatic tools-Genome Detective, CZ.ID, INSaFLU-TELEVIR and Trimmomatic + Kraken2-on samples collected from four sites in each of two wastewater treatment plants (WWTPs) in Lisbon, Portugal in April 2019. From each site, we collected and processed separately three replicates and one pool of nucleic acids extracted from the replicates. A total of 32 samples were processed using sequence-independent single-primer amplification (SISPA) and sequenced on an Illumina MiSeq platform. Across the 128 sample-tool combinations, viral read counts varied widely, from 3 to 288,464. There was a lack of consistency between replicates and their pools in terms of viral abundance and diversity, revealing the heterogeneity of the wastewater matrix and the variability in sequencing effort. There was also a difference between software tools highlighting the impact of tool selection on community profiling. A positive correlation between crAssphage and human pathogens was found, supporting crAssphage as a proxy for public health surveillance. A custom Python pipeline automated viral identification report processing, taxonomic assignments and diversity calculations, streamlining analysis and ensuring reproducibility. These findings emphasize the importance of sequencing depth, software tool selection and standardized pipelines in advancing wastewater-based epidemiology.

RevDate: 2025-06-01
CmpDate: 2025-05-28

DeSantis AH, Buss K, Coker KM, et al (2025)

Multiomics-Based Profiling of the Fecal Microbiome Reveals Potential Disease-Specific Signatures in Pediatric IBD (PIBD).

Biomolecules, 15(5):.

Inflammatory bowel disease (IBD), which includes Crohn's Disease (CD) and Ulcerative Colitis (UC), is a chronic gastrointestinal (GI) disorder affecting 1 in 100 people in the United States. Pediatric IBD (PIBD) is estimated to impact 15 per 100,000 children in North America. Factors such as the gut microbiome (GM), genetic predisposition to the disease, and certain environmental factors are thought to be involved in pathogenesis. However, the pathophysiology of IBD is incompletely understood, and diagnostic biomarkers and effective treatments, particularly for PIBD, are limited. Recent work suggests that these factors may interact to influence disease development, and multiomic approaches have emerged as promising tools to elucidate the pathophysiology. We employed metagenomics, metabolomics- and metatranscriptomics-based approaches to examine the microbiome, its genetic potential, and its activity to identify factors associated with PIBD. Metagenomics-based analyses revealed pathways such as octane oxidation and glycolysis that were differentially expressed in UC patients. Additionally, metatranscriptomics-based analyses suggested enrichment of glycan degradation and two component systems in UC samples as well as protein processing in the endoplasmic reticulum, ribosome, and protein export in CD and UC samples. In addition, metabolomics-based approaches revealed patterns of differentially abundant metabolites between healthy and PIBD individuals. Interestingly, overall microbiome community composition (as measured by alpha and beta diversity indices) did not appear to be associated with PIBD. However, we observed a small number of differentially abundant taxa in UC versus healthy controls, including members of the Classes Gammaproteobacteria and Clostridia as well as members of the Family Rikenellaceae. Accordingly, when identifying potential biomarkers for PIBD, our results suggest that multiomics-based approaches afford enhanced potential to detect putative biomarkers for PIBD compared to microbiome community composition sequence data alone.

RevDate: 2025-06-04
CmpDate: 2025-06-04

Goldman M, Zhao C, KS Pollard (2025)

Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM).

PLoS computational biology, 21(5):e1012277 pii:PCOMPBIOL-D-24-01068.

Microbiome association studies typically link host disease or other traits to summary statistics measured in metagenomics data, such as diversity or taxonomic composition. But identifying disease-associated species based on their relative abundance does not provide insight into why these microbes act as disease markers, and it overlooks cases where disease risk is related to specific strains with unique biological functions. To bridge this knowledge gap, we developed microSLAM, a mixed-effects model and an R package that performs association tests that connect host traits to the presence/absence of genes within each microbiome species, while accounting for strain genetic relatedness across hosts. Traits can be quantitative or binary (such as case/control). MicroSLAM is fit in three steps for each species. The first step estimates population structure across hosts. Step two calculates the association between population structure and the trait, enabling detection of species for which a subset of related strains confer risk. To identify specific genes whose presence/absence across diverse strains is associated with the trait, step three models the trait as a function of gene occurrence plus random effects estimated from step two. Applying microSLAM to 710 gut metagenomes from inflammatory bowel disease (IBD) samples, we discovered 56 species whose population structure correlates with IBD, meaning that different lineages are found in cases versus controls. After controlling for population structure, 20 species had genes significantly associated with IBD. Twenty-one of these genes were more common in IBD patients, while 32 genes were enriched in healthy controls, including a seven-gene operon in Faecalibacterium prausnitzii that is involved in utilization of fructoselysine from the gut environment. The vast majority of species detected by microSLAM were not significantly associated with IBD using standard relative abundance tests. These findings highlight the importance of accounting for within-species genetic variation in microbiome studies.

RevDate: 2025-06-04
CmpDate: 2025-06-04

Lei Z, Wang H, Zhang H, et al (2025)

Sultr1;2-Mediated Recruitment of Selenium-Oxidizing Bacteria Promotes Plant Selenium Uptake.

Journal of agricultural and food chemistry, 73(22):13313-13326.

Plants can shape their root microbiome to promote growth and selenium uptake. Here, we used metagenomics, 16S high-throughput sequencing, and liquid chromatography-mass spectrometry (LC-MS) metabolomics assays to investigate the role of Sultr1;2, which is the major selenium transporter gene, in recruiting microbial communities to regulate soil selenium bioavailability and plant selenium uptake. Results shows that the overexpression of Sultr1;2 in tomato significantly enriched Methylobacterium genus. The isolated strains of Methylobacterium possess multiple plant-growth-promoting functions and selenium oxidation capability and inoculation with these strains increases soil selenium availability. The upregulated metabolites of Sultr1;2-overexpressing tomato were significantly enriched in the arginine and proline metabolism pathway. The key upregulated metabolites significantly improved the growth rate and selenium-oxidizing ability of Methylobacterium strains, and the combined addition of key upregulated metabolites and synthetic microbial community significantly increased soil selenium bioavailability and plant selenium uptake. This study provides insights into leveraging plant genetic engineering to identify key functional microbial communities for sustainable selenium-rich agricultural development.

RevDate: 2025-06-04
CmpDate: 2025-06-04

Lee SH, Han C, C Shin (2025)

IUPHAR review: Microbiota-gut-brain axis and its role in neuropsychiatric disorders.

Pharmacological research, 216:107749.

The human gut microbiome, composed of a vast array of microorganisms that have co-evolved with humans, is crucial for the development and function of brain systems. Research has consistently shown bidirectional communication between the gut and the brain through neuronal, endocrine, and immunological, and chemical pathways. Recent neuroscience studies have linked changes in the microbiome and microbial metabolites to various neuropsychiatric disorders such as autism, depression, anxiety, schizophrenia, eating disorders, and neurocognitive disorders. Novel metagenome-wide association studies have confirmed these microbiome variations in large samples and expanded our understanding of the interactions between human genes and the gut microbiome. The causal relationship between gut microbiota and neuropsychiatric disorders is being elucidated through the establishment of large cohort studies incorporating microbiome data and advanced statistical techniques. Ongoing animal and human studies focused on the microbiota-gut-brain axis are promising for developing new prevention and treatment strategies for neuropsychiatric conditions. The scope of these studies has broadened from microbiome-modulating therapies including prebiotics, probiotics, synbiotics and postbiotics to more extensive approaches such as fecal microbiota transplantation. Recent systematic reviews and meta-analyses have strengthened the evidence base for these innovative treatments. Despite extensive research over the past decade, many intriguing aspects still need to be elucidated regarding the role and therapeutic interventions of the microbiota-gut-brain axis in neuropsychiatric disorders.

RevDate: 2025-05-31

Tóth AG, Tóth DL, Remport L, et al (2025)

A One Health Approach Metagenomic Study on Antimicrobial Resistance Traits of Canine Saliva.

Antibiotics (Basel, Switzerland), 14(5):.

Background: According to the One Health concept, the physical proximity between pets and their owners facilitates the interspecies spread of bacteria including those that may harbor numerous antimicrobial resistance genes (ARGs). Methods: A shotgun sequencing metagenomic data-based bacteriome and resistome study of 1830 canine saliva samples was conducted considering the subsets of ARGs with higher public health risk, ESKAPE pathogen relatedness (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), and survey results on the physical and behavioral characteristics of the participating dogs. Results: A total of 318 ARG types achieved sufficiently high detection rates. These ARGs can affect 31 antibiotic drug classes through various resistance mechanisms. ARGs against tetracyclines, cephalosporins, and, interestingly, peptides appeared in the highest number of samples. Other Critically Important Antimicrobials (CIAs, WHO), such as aminoglycosides, fluoroquinolones, or macrolides, were among the drug classes most frequently affected by ARGs of higher public health risk and ESKAPE pathogen-related ARGs of higher public health risk. Several characteristics, including coat color, sterilization status, size, activity, or aggressiveness, were associated with statistically significant differences in ARG occurrence rates (p < 0.0500). Conclusions: Although the oral microbiome of pet owners is unknown, the One Health and public health implications of the close human-pet bonds and the factors potentially underlying the increase in salivary ARG numbers should be considered, particularly in light of the presence of ARGs affecting critically important drugs for human medicine.

RevDate: 2025-06-03
CmpDate: 2025-06-03

Feng C, Liang Z, Liao X, et al (2025)

Microbial Dynamics on Different Microplastics in Coastal Urban Aquatic Ecosystems: The Critical Roles of Extracellular Polymeric Substances.

Environmental science & technology, 59(21):10554-10566.

Microplastics (MPs) serve as carriers for microbial community colonization, forming unique ecosystems known as plastispheres in urban aquatic ecosystems. However, interactions among microbes, extracellular polymeric substances (EPS), and MPs remain poorly understood. This study investigates microbial consortia and their EPS secretion behaviors across various plastispheres at two representative coastal urban water sites. Permutational multivariate analysis of variance revealed that MP type significantly influenced microbial community structures in reservoir environments (R[2] = 0.60, p < 0.001), highlighting the pronounced impact of MP types in high-quality urban waters. Specific microbial phyla and genera were identified as key contributors to EPS compositional variations across different plastispheres. Hierarchical partitioning results identified Acidobacteria, Nitrospirae, and Planctomycetes as influential phyla positively affecting EPS composition. Spearman correlation analysis pinpointed Robiginitialea (positive correlation) and Fimbriiglobus (negative correlation) as critical genera influencing EPS dynamics. Moreover, EPS-related gene abundance corresponded closely with observed EPS compositional differences. Dominant genes associated with protein biosynthesis included xapD in reservoirs and glnA in bays, while glmS and eno were predominant for polysaccharide biosynthesis in bays. This research advances our understanding of microbial-EPS-MP interactions in urban water systems, offering critical insights into ecological remediation and risk assessment of MP pollution.

RevDate: 2025-06-03
CmpDate: 2025-06-03

Hu T, Meng Y, Zhao C, et al (2025)

Genome-scale metabolic modeling reveals specific vaginal Lactobacillus strains and their metabolites as key inhibitors of Candida albicans.

Microbiology spectrum, 13(6):e0298424.

As the predominant constituents of the vaginal microbiome in healthy women, Lactobacillus species are considered essential in maintaining a homeostatic vaginal microbiome. Specific Lactobacillus species can produce beneficial metabolites to support their persistence within the host environment and inhibit Candida albicans colonization. Due to the extensive diversity of Lactobacillus species and their metabolites, comprehensively investigating all possible interactions remains challenging. This study employed an integrative approach combining genome-scale metabolic modeling, metagenomic sequencing, and in vitro validation to explore Lactobacillus and C. albicans interactions. Pairwise simulations of 159 Lactobacillus strains with C. albicans revealed that most strains exhibit inhibitory effects, altering fungal amino acid and carbohydrate metabolism. Key inhibitory metabolites identified included formate, L-lactate, and L-malate. Metagenomic analysis of vaginal swabs from 20 vulvovaginal candidiasis (VVC) patients and 20 healthy women showed a correlation between Lactobacillus species abundance and reduced C. albicans colonization. In vitro experiments confirmed the inhibitory effects of these metabolites and the selected Lactobacillus strains on C. albicans growth, thereby validating our computational predictions. These findings provide insights into the metabolic interactions within the vaginal microbiome and pave the way for targeted microbial or metabolite-based therapeutic strategies to manage VVC.IMPORTANCEVulvovaginal candidiasis is a prevalent fungal infection with significant implications for women's health, caused primarily by Candida albicans. Although the protective role of a Lactobacillus-dominated vaginal microbiome is well established, the metabolic mechanisms underlying the interactions between Lactobacillus species and C. albicans remain inadequately understood. Specifically, the Lactobacillus species that effectively inhibit C. albicans and the metabolic pathways involved warrant further investigation. This study offers novel insights into the metabolic mechanisms underlying Lactobacillus antagonism against C. albicans. By identifying critical metabolic pathways and inhibitory metabolites, this study enhances our understanding of vaginal microbiome dynamics and host-microbe interactions. The findings suggest that key Lactobacillus strains and their metabolites could significantly reduce harmful levels of C. albicans, paving the way for future therapeutic strategies that leverage these microbial characteristics to promote vaginal health.

RevDate: 2025-05-28
CmpDate: 2025-05-28

Wang Y, Zhou K, Zhang Y, et al (2025)

The Systemic Impact of Helicobacter pylori Infection on the Microbiome of Whole Digestive Tract Based on Mucosal, Gastric Juice, and Fecal Specimens.

Helicobacter, 30(3):e70047.

BACKGROUND: Recent studies have found that in addition to directly impacting the gastric microbiome, Helicobacter pylori (H. pylori) infection may cause intestinal microbial dysbiosis. However, most existing studies on the influence of H. pylori infection on the intestinal microbiome used fecal specimens with inconsistent conclusions. Only one limited study on 8 H. pylori-infected patients has previously assessed the impact of H. pylori infection on the microbiome of the entire gastrointestinal tract, finding no significant effect on the bacterial composition of the lower gastrointestinal tract.

METHODS: This single-center cross-sectional study collected mucosa of the esophagus, stomach, small intestine, and colon, as well as gastric juice and feces from 120 participants of the H. pylori-infected group (HIG) and 30 of the healthy control group (HCG). 16S rRNA sequencing was applied to analyze the bacterial composition and functional pathways, and metagenomics was adopted to assess the composition of viruses, eukaryotes, and archaea in the feces, as well as the antibiotic resistance gene (ARG) and virulence factors of bacteria (VF).

RESULTS: Compared with the HCG, the alpha and beta diversity of bacteria in the mucosa of the whole digestive tract and the gastric juice of the HIG showed significant changes, with increased microbial dysbiosis index and significantly different compositions at the phylum and genus levels. Functional pathway analysis revealed that the metabolic characteristics of the flora changed in the HIG, with site-specific differences. Fecal specimens demonstrated no significant differences in the above indicators between the two groups. In addition, feces-based metagenomic analysis revealed that only eukaryotes had higher diversity in the HIG, whereas viruses and archaea showed no significant changes; the Shannon index of ARG increased; and VF showed no significant change.

CONCLUSIONS: This study revealed that H. pylori infection significantly influenced the diversity, composition, and metabolic functional pathway of bacteria in different parts of the digestive tract and the gastric juice. Moreover, fecal microbial composition may not fully represent the mucosal microbial composition of the gastrointestinal tract.

TRIAL REGISTRATION: Chinese Clinical Trial Registry: ChiCTR2300073419.

RevDate: 2025-05-31
CmpDate: 2025-05-27

Li W, Cai J, Chen G, et al (2025)

Microbial community succession mediated by planting patterns in the Loess Plateau, China: Implications for ecological restoration.

PloS one, 20(5):e0324786.

Microbial community succession plays a key role in restoring fragile ecosystems and mitigating ecological degradation. However, the mechanisms by which vegetation restoration promotes ecological restoration and microbial community reconstruction in degraded soils remain unclear. This study utilized metagenomic high-throughput sequencing technology to analyze microbial community dynamics in soil samples collected from eight different planting patterns in the ecologically degraded areas of the Chinese Loess Plateau. The results indicated significant effects of terrain location and restorative cropping patterns on soil microbial abundance and function. In particular, soil C and N nutrient abundance was highest in mixed forest soils, and the total number of microorganisms was highest and more diverse. Therefore, through vegetation restoration, mixed forests significantly enhanced regional ecological functions. Notably, creating mixed forests with both trees and shrubs resulted in optimal ecological functions, providing a valuable direction for vegetation construction and structural optimization in the region.

RevDate: 2025-05-27
CmpDate: 2025-05-27

Zhang M, Zhang H, Hong A, et al (2025)

Dynamic changes of dental plaque and saliva microbiota in OSCC progression.

Clinical oral investigations, 29(6):314.

OBJECTIVES: To elucidate the changes in microbial composition and genomics in saliva and dental plaque during the progression of Oral Squamous Cell Carcinoma (OSCC), and to identify virulence factors and pathways associated with tumor differentiation in OSCC patients.

MATERIALS AND METHODS: Using metagenomic sequencing, 64 saliva and dental plaque samples from OSCC patients at different stages of differentiation were examined.

RESULTS: The results showed notable differences in the microbial composition and genomic profiles across ecological regions and differentiation degrees. Notably, the relative abundance of specific microbes, such as Porphyromonas gingivalis, Fusobacterium nucleatum, and Haemophilus parainfluenzae, increased in poorly differentiated OSCC. Microbial alpha diversity in dental plaque and saliva correlates with tumor T staging. Dental plaque microbiota shows higher specialization, especially in poorly differentiated tumors. Both microbiota types become more stable with advanced T staging. Genomic analysis reveals increased virulence factors in poorly differentiated stages.Subsequently, functional pathway analysis and tracing of pathogens reveal specific microbial mechanisms in oral cancer pathogenesis. Certain oral pathogens may promote tumorigenesis by secreting factors like GAPDH (glyceraldehyde-3-phosphate dehydrogenase), GspG (a gingipain precursor), and AllS (a lysine-specific gingipain precursor).

CONCLUSIONS: OSCC progression is associated with altered microbial composition, diversity, and genomic profiles in saliva and dental plaque. Poorly differentiated stages show higher abundance of pathogens and virulence factors, implicating them in tumorigenesis.

CLINICAL RELEVANCE: Understanding the microbial and genomic changes in saliva and dental plaque during OSCC progression could aid in developing new diagnostic biomarkers and targeted therapies, potentially enhancing early detection, treatment efficacy, and patient prognosis. Maintaining oral microbiota homeostasis may also help prevent oral cancer.

RevDate: 2025-06-02
CmpDate: 2025-06-02

Ramar M, Wiscovitch-Russo R, Yano N, et al (2025)

Live bacteria in gut microbiome dictate asthma onset triggered by environmental particles via modulation of DNA methylation in dendritic cells.

Cell reports, 44(5):115684.

Despite broad knowledge of the pathogenesis, our understanding of the origin of allergy and asthma remains poor, preventing etiotropic treatments. The gut microbiome is seen to be altered in asthmatics; however, proof of causality of the microbiome alterations is lacking. We report on gut microbiome transplantation (GMT) from mice predisposed to asthma by maternal exposure to pro-allergy environmental particles into naive recipients. This GMT confers asthma predisposition, and the effect is abrogated by gamma sterilization of the transplant material or by co-administration of antibacterials, indicating that viable bacteria are mediating the effect. Metagenomics identifies key changes in the "pro-asthma" microbiome, and metabolomics links the identified species to altered production of butyrate known to act on immune cells and epigenetic mechanisms. We further show that transplant recipients develop DNA methylation alterations in dendritic cells. Finally, dendritic cells with an altered methylome present allergen to T cells, and this effect is abrogated by an epigenetically acting drug in vitro.

RevDate: 2025-06-02
CmpDate: 2025-06-02

López-Gálvez R, Orenes-Piñero E, Rivera-Caravaca JM, et al (2025)

Microbial Insights: The Role of Diet in Modulating Gut Microbiota and Metabolites After Acute Coronary Syndrome.

Molecular nutrition & food research, 69(11):e70046.

Acute coronary syndrome (ACS) is a leading cause of global mortality, largely due to atherosclerosis influenced by lifestyle factors like diet. Gut microbiota impacts lipid metabolism, inflammation, and endothelial function, all vital in atherosclerosis. Dysbiosis increases intestinal permeability, causing inflammation and plaque instability, elevating cardiac event risk. This study investigates the impact of dietary improvements on gut microbiota and metabolite release in recent ACS patients versus healthy individuals. A cohort of 29 recent ACS patients receiving lipid-lowering therapy and dietary advice was analyzed alongside 56 healthy controls. Dietary habits, serum, and stool samples were collected at admission and after 3 months. Metagenomic analysis of stool and metabolomic analysis of serum were conducted. The results showed bacterial dysbiosis in ACS patients, characterized by a reduction in beneficial genera and an increase in potentially pro-inflammatory bacteria. After 3 months of dietary improvements, three metabolites with anti-inflammatory properties were significantly upregulated. The findings highlight the association between gut microbiota dysbiosis, fatty diets, and inflammation in ACS patients. The observed increase in anti-inflammatory metabolites following dietary changes underscore the following dietary interventions in modulating gut microbiota and improving cardiovascular and metabolic health.

RevDate: 2025-05-31
CmpDate: 2025-05-27

Clasen F, Yildirim S, Arıkan M, et al (2025)

Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson's disease and cognitive decline pathophysiology.

Gut microbes, 17(1):2506843.

The human microbiome is increasingly recognized for its crucial role in the development and progression of neurodegenerative diseases. While the gut-brain axis has been extensively studied, the contribution of the oral microbiome and gut-oral tropism in neurodegeneration has been largely overlooked. Cognitive impairment (CI) is common in neurodegenerative diseases and develops on a spectrum. In Parkinson's Disease (PD) patients, CI is one of the most common non-motor symptoms but its mechanistic development across the spectrum remains unclear, complicating early diagnosis of at-risk individuals. Here, we generated 228 shotgun metagenomics samples of the gut and oral microbiomes across PD patients with mild cognitive impairment (PD-MCI) or dementia (PDD), and a healthy cohort, to study the role of gut and oral microbiomes on CI in PD. In addition to revealing compositional and functional signatures, the role of pathobionts, and dysregulated metabolic pathways of the oral and gut microbiome in PD-MCI and PDD, we also revealed the importance of oral-gut translocation in increasing abundance of virulence factors in PD and CI. The oral-gut virulence was further integrated with saliva metaproteomics and demonstrated their potential role in dysfunction of host immunity and brain endothelial cells. Our findings highlight the significance of the oral-gut-brain axis and underscore its potential for discovering novel biomarkers for PD and CI.

RevDate: 2025-05-30
CmpDate: 2025-05-27

Shen Q, Fan X, Sun Y, et al (2025)

TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data.

BMC bioinformatics, 26(1):136.

BACKGROUND: 16S rRNA amplicon sequencing is a widely used method for microbiome composition analysis due to its cost-effectiveness and lower data requirements compared to metagenomic whole-genome sequencing (WGS). However, inherent limitations in 16S-based approach often lead to profiling discrepancies, particularly at the species level, compromising the accuracy and reliability of findings.

RESULTS: To address this issue, we present TaxaCal (Taxonomic Calibrator), a machine learning algorithm designed to calibrate species-level taxonomy profiles in 16S amplicon data using a two-tier correction strategy. Validation on in-house produced and public datasets shows that TaxaCal effectively reduces biases in amplicon sequencing, mitigating discrepancies between microbial profiles derived from 16S and WGS. Moreover, TaxaCal enables seamless cross-platform comparisons between these two sequencing approaches, significantly improving disease detection in 16S-based microbiome data.

CONCLUSIONS: Therefore, TaxaCal offers a cost-effective solution for generating high-resolution microbiome species profiles that closely align with WGS results, enhancing the utility of 16S-based profiling in microbiome research. As microbiome-based diagnostics continue to evolve, TaxaCal has the potential to be a crucial tool in advancing the utility of 16S sequencing in clinical and research settings.

RevDate: 2025-05-30
CmpDate: 2025-05-26

Wang D, Duan Y, He L, et al (2025)

Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics.

Communications biology, 8(1):804.

The interaction between gut and oropharyngeal microbiota plays a significant role in the viral infections like SARS-CoV-2, but role of the lower respiratory tract microbiota remains unclear. Our study utilized metatranscriptomics and metagenomics to analyze the microbial composition of bronchoalveolar lavage fluid and sputum samples from 116 COVID-19 patients, categorized into mild, severe, and critical groups. Our analysis revealed significant differences in viral genotypes across disease stages. As disease severity increased, the Chao index also rose. The mild group was predominantly dominated by Firmicutes, while the severe group showed an increase in Bacteroidetes. The critical group was characterized by a higher abundance of Actinobacteria and Proteobacteria. Notably, the abundance of Streptococcus and Rothia decreased as the disease progressed. Additionally, the Shannon index correlated with mortality risk, while the Chao index was associated with ICU admission, mechanical ventilation, and patient survival. These findings highlight the strong link between microbial composition and COVID-19 severity, providing valuable insights for assessing disease progression.

RevDate: 2025-06-01
CmpDate: 2025-06-01

Yin CY, Sadiq H, Liao WH, et al (2025)

Identification and functional characterization of two novel hyaluronate lyases BxHly33 and BiHly33, from the human gut microbiome.

International journal of biological macromolecules, 313:144153.

Hyaluronic acid (HA) is a key glycosaminoglycan in the extracellular matrix, essential for cellular signaling, hydration, and tissue homeostasis. This study identified two novel polysaccharide lyase family 33 (PL33) hyaluronate lyases, BxHly33 and BiHly33, from the human gut microbiome using metagenomic screening. These enzymes demonstrated high specificity and stability in degrading HA, with optimal activity at pH 6.6-7.6 and temperatures of 35-40 °C. Furthermore, structural and biochemical analyses revealed their catalytic mechanisms, highlighting key residues responsible for their function. Notably, specific alanine substitutions significantly enhanced their enzymatic activity. BxHly33 and BiHly33 present promising alternatives to conventional hyaluronidases, which are often costly and immunogenic, for drug delivery and tissue engineering applications. This study will provide novel insights into exploring their therapeutic potential in HA degradation therapies.

RevDate: 2025-06-01
CmpDate: 2025-06-01

Mo S, Wu X, Kashif M, et al (2025)

Effects of Spartina alterniflora invasion on carbon fixation and sulfate reduction in a subtropical marine mangrove ecosystem.

Marine pollution bulletin, 217:118128.

Mangrove sediments host diverse microbial communities that are crucial for carbon fixation, but their functions and pathways in subtropical ecosystems-particularly under Spartina alterniflora invasion and across varying sediment depths-remain unclear. This study employed metagenomic and qPCR analyses to explore microbial carbon fixation in Rhizophora stylosa, S. alterniflora, and bare beach habitats. Environmental factors like Cd, sulfide, pH, and salinity significantly influenced carbon fixation and sulfate reduction. Specifically, the invasion increased the abundance of key carbon fixation genes, including aclA/B, cbbL, and korA, which are involved in the Calvin-Benson-Bassham (CBB) and Arnon-Buchanan (rTCA) cycles, respectively. This shift in gene abundance was accompanied by elevated Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) activity (0.47-21.82 nmol CO2 g[-1] soil min[-1]), suggesting a potential increase in microbial CO2 fixation rates in S. alterniflora-invaded sediments. Sediment depth also affected the distribution of carbon fixation genes and carbon-metabolizing microbes. Desulfobacterota were identified as major contributors to carbon fixation via both the rTCA and CBB cycles. Moreover, a strong correlation was observed between carbon fixation and sulfate reduction. These findings reveal how S. alterniflora invasion impacts carbon fixation and enhance our understanding of the mangrove ecosystems' role in climate change regulation.

RevDate: 2025-06-01
CmpDate: 2025-06-01

Chen Y, Liu Q, XW Xu (2025)

Spatio-temporal variability of nitrogen-cycling potentials in particle-attached and free-living microbial communities in the Yangtze River estuary and adjacent regions.

Marine pollution bulletin, 217:118121.

Particle-attached (PA) and free-living (FL) microorganisms regulate coastal biogeochemical cycles, yet their roles in nitrogen transformation remain unclear. To address this knowledge gap, we seasonally sampled PA and FL from seawater along salinity gradients in the Yangtze River estuary (YRE) and adjacent regions to investigate the spatio-temporal variability of microbial communities, abundances of nitrogen-cycling genes, and key microbial groups affiliated with the nitrogen cycle in PA and FL. Compared to FL, the composition, structure and diversity of PA exhibited more pronounced variations in response to salinity and [NO3[-]]. Metagenomic analyses indicated a predominant role of denitrification in both PA and FL, with greater abundances of genes involved in most nitrogen transformation processes observed in the estuarine region. The potential for the nitrogen cycle in PA was relatively lower in May, while greater in FL, potentially due to competition for nitrogen substrates between PA and phytoplankton during spring. PERMANOVA and Mantel tests showed that gene abundances exhibited spatio-temporal dynamics and were associated with species and environmental factors. Gene-affiliated taxa identification and the Weighted Correlation Network Analysis revealed that the differences in environmental factors and taxa responsible for the nitrogen transformation drove spatio-temporal variations of the nitrogen cycle between PA and FL, and implied the significance of their interaction in nitrogen fates in coastal ecosystem. Gammaproteobacteria and Betaproteobacteria were highly affiliated with nitrogen-cycling genes, while Nitrososphaeria played an important role in nitrification and denitrification. This study offered practical insights for mitigating eutrophication through targeted regulation of microbial-mediated nitrogen fluxes.

RevDate: 2025-06-01
CmpDate: 2025-06-01

Ma G, Yang P, Lu T, et al (2025)

Comparative analysis of oral, placental, and gut microbiota characteristics, functional features and microbial networks in healthy pregnant women.

Journal of reproductive immunology, 169:104535.

AIM: Most studies on pregnant women focus on analyzing individual microbial species at specific body sites. This study aims to explore the characteristics, functions, and microbial networks of the oral, placental, and gut microbiota in healthy pregnant women.

METHODS: A total of 23 healthy pregnant women were enrolled in this study. We analyzed the microbial composition, functional profiles, and microbial networks of the oral, placental, and gut microbiota using 16S rRNA gene sequencing.

RESULTS: Our findings revealed significant differences in microbial composition across these three sites. The placental microbiota contained a relatively high proportion of low-abundance microorganisms, which were more diverse and evenly distributed compared to the gut and oral microbiota. The microbial composition at each site displayed distinct characteristics, likely influenced by environmental, physiological, and biological factors. The placental microbiota exhibited a complex network of tightly interconnected genera, whereas the gut microbiota showed sparser connections, with fewer closely related genera compared to the placental and oral microbiota. Functional differences were also observed among the three microbiota, with each playing a unique role in maintaining host health and metabolic balance. While the oral and gut microbiota shared functional similarities, the placental microbiota exhibited distinct functional characteristics.

CONCLUSIONS: This study provides valuable insights into the microbial communities of healthy pregnant women, offering important data for microbiological research during pregnancy and laying the foundation for future investigations into the roles of these microbial communities in maternal health.

RevDate: 2025-05-30
CmpDate: 2025-05-26

Lu W, Hua J, Zhang M, et al (2025)

Metagenomic sequencing reveals the taxonomic and functional characteristics of rumen microorganisms in Dongliu buffalo.

Scientific reports, 15(1):18398.

In this study, the composition of the rumen microbiota and its functional characteristics were investigated using a metagenomic approach in Dongliu buffalo. This study compared the rumen microbial communities of six female and four male Dongliu buffaloes of similar age, weight and lifestyle. Taxonomic analysis identified 964 genera across 52 phyla, dominated by Bacteroidota (47.54%) and Bacillota (28.20%). While alpha and beta diversity showed no sex differences (PERMANOVA P = 0.82), males exhibited higher Fibrobacter at the genus level (P = 0.02). Functional profiling revealed 429 KEGG pathways, with carbohydrate metabolism (11.17%) and amino acid metabolism (9.74%) as dominant processes. Males showed enrichment in cellulose-degrading enzymes (EC2.4.1.20, EC1.2.1.90, EC2.7.1.58) and CAZymes (GH94, GT35), while females had higher Bacteroides abundance (P = 0.01) and CAZymes like CBM47. Core cellulolytic genera (Prevotella, Ruminococcus) demonstrated male-biased GH/CBM activity, linked to enhanced fiber degradation. COG annotation highlighted carbohydrate metabolism as central, with sex-specific functional partitioning in replication (female-enriched) and secondary metabolism (male-enriched). Network analysis revealed Prevotella's dominance in CAZymeme contributions and functional specialization in lignocellulose degradation pathways, suggesting sex-driven microbial adaptation to dietary fiber utilization.

RevDate: 2025-05-27
CmpDate: 2025-05-26

Guo Y, Lin L, Zhang M, et al (2025)

Salivary mycobiome alterations in HIV-infected MSM: dominance of Pseudogymnoascus and functional shifts across disease stages.

Frontiers in cellular and infection microbiology, 15:1564891.

BACKGROUND: Oral health is increasingly recognized as a crucial determinant of overall health in people living with HIV/AIDS (PLWHA). Specifically, the oral mycobiome may play a pivotal role in HIV-associated oral complications. However, the fungal species involved and their potential as biomarkers for HIV-related oral conditions remain poorly understood. This study investigates salivary fungal profiles in PLWHA who have sex with men (MSM), focusing on diversity, functional shifts, and correlations with disease progression.

METHODS: A cross-sectional study included 25 MSM participants divided into five groups: HIV-negative controls (n = 5) and four HIV-positive groups stratified by CD4 count: Stage 0 (HIV RNA-positive/antibody-negative; n = 5), Stage 1 (CD4 ≥500 cells/μL; n = 5), Stage 2 (CD4 200-499 cells/μL; n = 5), and Stage 3 (CD4 <200 cells/μL or opportunistic infections; n = 5). Saliva samples were collected and analyzed using metagenomic sequencing (Illumina NovaSeq platform). Bioinformatic analyses included genome assembly (MEGAHIT), gene clustering (CD-HIT), gene abundance calculation (SOAPaligner), species annotation (BLASTP), and KEGG pathway annotation (KOBAS 2.0). Statistical analyses (Kruskal-Wallis tests, Spearman's correlation) assessed associations between fungal profiles, CD4 count, and viral loads.

RESULTS: A total of 51 fungal genera were identified, with Pseudogymnoascus being the most abundant. Functional analysis revealed 113 shared KEGG pathways, of which 69 were unique to Stage 3, primarily related to metabolic and disease-related processes. Notably, Auricularia exhibited a positive correlation with CD4 count (P ≤ 0.01), while Mucor showed a negative correlation (P = 0.0299).

CONCLUSIONS: Salivary mycobiome composition and function shift significantly across HIV stages, reflecting immune decline. Pseudogymnoascus dominance challenges conventional views of oral fungal ecology in immunocompromised hosts. These findings highlight the mycobiome's diagnostic potential for monitoring HIV-related oral health. Longitudinal studies are needed to validate clinical relevance.

RevDate: 2025-05-30
CmpDate: 2025-05-25

Rashid MH, Pascottini OB, Xie L, et al (2025)

Shotgun metagenomic composition, microbial interactions and functional insights into the uterine microbiome of postpartum dairy cows with clinical and subclinical endometritis.

Scientific reports, 15(1):18274.

Clinical endometritis (CE) is associated with bacterial pathogens while the same has not been proved about subclinical endometritis (SCE). We aimed to use shotgun metagenomic sequencing to investigate the associations between potentially unidentified pathogens and SCE. Uterine cytobrush samples from multiparous Holstein cows (n = 23) were taken at 21 days in milk (DIM) and sequenced via the Illumina shotgun platform. At 36 DIM, the cows were diagnosed as CE (n = 7), SCE (n = 7), or healthy (n = 9). We did not find differences in the alpha and beta diversity of bacteria and eukaryotes among the health groups. Relative abundance of typical pathogens i.e. Fusobacterium, Peptoniphilus, Peptostreptococcus, and Trueperella was greater in CE than healthy controls. We did not find evidence of eukaryotic or viral association in infection, yet, distinct patterns of bacterial co-occurrence were observed among pathogenic and non-pathogenic bacteria. In CE cows, Wnt/catenin pathway had lower abundance than SCE or healthy cows. Our findings support that CE is characterized by domination of pathogenic bacteria that intercorrelate, whereas SCE is not associated with bacterial colonization.

RevDate: 2025-05-30
CmpDate: 2025-05-25

Thompson TP, Rice CJ, Athanasakis E, et al (2025)

The effect of sample type and location on industrial workplace sink and hand dryer microbiomes.

BMC microbiology, 25(1):325.

One major issue in tackling antimicrobial resistance (AMR) is the ability to effectively track resistance spread in environments where surveillance is limited. Such environments include those experiencing high volumes of hand washing and drying from multiple users. This study characterised the microbial populations and antimicrobial resistomes of two different sample types from a pharmaceutical industrial site as part of an AMR environmental surveillance programme. Paired samples were collected from hand dryers and adjacent sinks in distinct sampling locations: from toilets adjacent to 'wet' labs, and locations associated with 'dry' activities. Microbial populations in hand dryers were significantly different to those of sinks, whereas there was no significant difference based on sample location. The opposite effect was observed for resistomes, where profiles differed significantly based on sample location, but not sample type. When both sample type and location were considered together, differences in microbiomes were driven primarily by hand dryer profiles from different locations. Analysis of metagenomically-assembled genomes revealed the presence of many poorly characterised organisms, and suggested no specific families predominated in terms of ARG carriage. This study emphasises the impact of human activities in determining the resistome of commonly used appliances, and the need for continued AMR surveillance programmes.

RevDate: 2025-05-30
CmpDate: 2025-05-25

Kousgaard SJ, Dall SM, Albertsen M, et al (2025)

Fecal microbiota transplantation from a healthy pouch donor for chronic pouchitis: a proof-of-concept study.

Gut microbes, 17(1):2510464.

Chronic pouchitis is a common complication after ileal pouch-anal anastomosis (IPAA) with limited treatment options. In this case series, we aimed to investigate clinical and microbiome changes, as well as adverse events, associated with using fecal microbiota transplantation (FMT) from a donor with a normal functioning IPAA to induce remission in patients with chronic pouchitis. Methods The study was a case-series including a 4-week intervention period and 12-month follow-up. Patients with chronic pouchitis who met the inclusion criteria were recruited from the Department of Gastrointestinal Surgery at Aalborg University Hospital, Denmark. Participants received FMT derived from a donor with a normal functioning IPAA. Treatment was administered by enema daily for two weeks, then every other day for two more weeks. Disease severity and quality of life (QoL) were accessed at baseline and 30-day follow-up. Clinical remission was defined as Pouchitis Disease Activity Index (PDAI) <7. Fecal samples from participants, healthy donors, and the IPAA donor were analyzed using shotgun metagenomic sequencing. Results Three patients with chronic pouchitis were included and completed the treatment protocol and follow-up visits. At the 30-day follow-up, all participants achieved clinical remission with reduced endoscopic inflammation. The median total PDAI score decreased from 8 (range 10-8) at baseline to 6 (range 6-5) at 30 days. Two participants reported improved QoL, while one reported no change. Few mild, self-limited adverse events were reported by all participants during treatment, with no serious events. Principal component analysis of fecal samples distinguished two clusters: healthy donors and the IPAA donor, with participant samples forming a separate cluster Conclusion We observed that all participants achieved clinical remission with reduced endoscopic inflammation following a 4-week FMT intervention. Adverse events were mild and self-limited. Metagenomic analysis revealed distinct microbiome clusters between IPAA donor and recipients, both of which differed from those of healthy donors.

RevDate: 2025-05-30
CmpDate: 2025-05-30

Ma JY, Liu JH, Chen CZ, et al (2025)

Characteristics of microbial carbon pump in the sediment of kelp aquaculture zone and its contribution to recalcitrant dissolved organic carbon turnover: insights into metabolic patterns and ecological functions.

Environmental research, 277:121559.

The study delves into the microbial carbon pump (MCP) within the sediments of kelp aquaculture zones, focusing on its influence on the turnover of recalcitrant dissolved organic carbon (RDOC). Following kelp harvest, significant alterations in the microbial community structure were noted, with a decrease in complexity and heterogeneity within co-occurrence networks potentially impacting RDOC production efficiency. Metabolic models constructed identified four key microbial lineages crucial for RDOC turnover, with their abundance observed to decrease post-harvest. Analysis of metabolic complementarity revealed that RDOC-degrading microorganisms exhibit broad substrate diversity and are engaged in specific resource exchange patterns, with cross-feeding interactions possibly enhancing the ecological efficiency of the MCP. Notably, the degradation of RDOC was found not to deplete the RDOC pool; as aromatic compounds break down, new ones are released into the environment, thus supporting the renewal of the RDOC pool. The research highlights the pivotal role of microbial communities in RDOC turnover and offers fresh insights into their cross-feeding behavior related to RDOC cycling, providing valuable data to support the future development and application of MCP theory.

RevDate: 2025-05-30
CmpDate: 2025-05-30

Yang X, Yu X, Ming Y, et al (2025)

The vertical distribution and metabolic versatility of complete ammonia oxidizing communities in mangrove sediments.

Environmental research, 277:121602.

Recently discovered complete ammonia-oxidizing (comammox) microorganisms can completely oxidize ammonia to nitrate and play an important role in the nitrogen (N) cycle across various ecosystems. However, little is known about the vertical distribution and metabolic versatility of comammox communities in mangrove ecosystems. Here we profiled comammox communities from deep sediments (up to 5 m) in a mangrove wetland by combining metagenome sequencing and physicochemical properties analysis. Our results showed that the relative abundance of comammox bacteria (23.2 %) was higher than ammonia-oxidizing bacteria (AOB, 12.0 %), but lower than ammonia-oxidizing archaea (AOA, 64.8 %). The abundance of comammox communities significantly (p < 0.01) decreased with the sediment depth, and dissolved organic carbon and total sulfur appeared to be major environmental factors influencing the nitrifying microbial community structure. We also recovered a high-quality metagenome-assembled genome (MAG) of comammox bacteria (Nitrospira sp. bin2030) affiliated with comammox clade A. Nitrospira sp. bin2030 possessed diverse metabolic processes, not only the key genes for ammonia oxidation and urea utilization in the N cycle, but also key genes involved in carbon and energy metabolisms, sulfur metabolism, and environmental adaptation (e.g., oxidative stress, salinity, temperature, heavy metal tolerance). The findings advance our understanding of vertical distribution and metabolic versatility of comammox communities in mangrove sediments, having important implications for quantifying their contribution to nitrification processes in mangrove ecosystems.

RevDate: 2025-05-30
CmpDate: 2025-05-30

Genitsaris S, Stefanidou N, Kourkoutmani P, et al (2025)

Do coastal bacterioplankton communities hold the molecular key to the rapid biodegradation of Polycyclic Aromatic Hydrocarbons (PAHs) from shipping scrubber effluent?.

Environmental research, 277:121563.

Shipping scrubber effluents, containing a cocktail of Polycyclic Aromatic Hydrocarbons (PAHs), show undisputed effects at single-species experiments while PAHs fate in the marine environment after effluent discharge is still investigated. Bacterioplankton, composed of abundant diverse taxa with xenobiotic-degrading capabilities, are the first responders to scrubber emissions and can affect PAHs impacts on marine life. This work aims to examine the fate of scrubber effluent PAHs and alkyl-PAHs in mesocosms of coastal bacterioplankton communities from a pristine (phytoplankton carbon biomass was 8.16 μg C L[-1]) and a eutrophic (105.35 μg C L[-1]) coastal site. High-throughput 16S rRNA metabarcoding revealed differential responses of the bacterioplankton linked to their initial community structure and population abundances. Taxa known for their PAHs-degrading capacity were retrieved, including the genera Roseobacter, Porticoccus, Marinomonas, Arcobacter, Lentibacter, Lacinutrix, Pseudospirillum, Glaciecola, Vibrio, Marivita, and Mycobacterium, and were found to have increased roles in shifted communities by increasing their relative abundances at least 5-fold in treatments with high scrubber effluent additions. Additionally, metagenomic analysis of shotgun sequencing, indicated an increase on the number of Clusters of Orthologous Genes (COGs) associated with pathways involved in PAHs degradation. Up to 198 more COGs involved in signal transduction were retrieved in scrubber effluent enriched mesocosms compared to controls, while 15, 86, and 136 more COGs associated with naphthalene, aromatic compound, and benzoate degradation, respectively, were detected in the pristine mesocosms after effluent additions. In both experiments, bacterioplankton responses towards xenobiotic degradation under increased PAHs and alkyl-PAHs were coupled with a drop in their concentrations, below the limit of detection by Day 3 of the experiment in the eutrophic community, and by half in Day 6 in the pristine environment's community. Our findings indicate that PAHs and alkyl-PAHs impacts can be rapidly reduced in natural systems of high bacterial activity.

RevDate: 2025-05-25
CmpDate: 2025-05-25

Zhang DY, Li D, Chen SJ, et al (2025)

Bacteroides uniformis-generated hexadecanedioic acid ameliorates metabolic-associated fatty liver disease.

Gut microbes, 17(1):2508433.

Gut microbiota exerts a pivotal influence on the development of Metabolic Associated Fatty Liver Disease (MAFLD), although the specific contributions of individual bacterial strains and their metabolites remain poorly defined. We conducted stool shotgun metagenomic sequencing and plasma untargeted metabolomics in a large prospective cohort comprising 120 MAFLD patients and 120 matched healthy controls. The mechanisms and microbial-derived metabolites involved in MAFLD were further investigated through multi-omics analyses in vitro and in vivo. Distinct differences were identified in both the microbial community structure and metabolomic profiles between MAFLD patients and healthy controls. Bacteroides uniformis (B. uniformis) was the most significantly depleted species in MAFLD and negatively correlated with hepatic steatosis and BMI. MAFLD was characterized by marked disruptions in fatty acid and amino acid metabolism. Combined analysis of metabolomic and metagenomic data achieved high diagnostic accuracy for MAFLD and hepatic steatosis severity (AUC = 0.93). Transplantation of fecal microbiota from MAFLD subjects into ABX mice led to the onset of MAFLD-like symptoms, whereas B. uniformis administration alleviate disease progression by inhibiting intestinal fat absorption, FFA from eWAT influx into liver via the gut-liver axis, and IRE1α-XBP1s-mediated flipogenesis and ferroptosis, as confirmed by hepatic transcriptomic and proteomic analyses. Hexadecanedioic acid (HDA), potentially identified as a key metabolite produced by B. uniformis, ameliorated MAFLD symptoms. Mechanistically, B. uniformis-derived HDA also inhibited fat absorption and transported, and entered the liver via the portal vein to suppress IRE1α-XBP1s-mediated flipogenesis and ferroptosis. B. uniformis and its potential putative metabolite HDA may contribute to MAFLD progression modulation, through regulation of the IRE1α-XBP1s axis. This study provides new insights into the gut-liver axis in MAFLD and offers promising therapeutic targets based on specific microbes and their metabolites.

RevDate: 2025-05-27
CmpDate: 2025-05-25

Ju J, He J, Ye B, et al (2025)

Microbial metabolism mediates the deteriorative effects of sedentary behaviour on insulin resistance.

Clinical and translational medicine, 15(5):e70348.

BACKGROUND: Prolonged sedentary time is a strong risk factor for insulin resistance. Recent evidence indicates that gut microbiota may influence the regulation of insulin sensitivity and demonstrates a distinct profile between sedentary and physically active individuals. However, whether and how microbial metabolism mediates the progression of insulin resistance induced by prolonged sedentary time remains unclear.

METHODS: 560 male participants without hypoglycaemic therapy were included, and insulin resistance was evaluated using the Homeostatic Model Assessment of Insulin Resistance (HOMA-IR). The gut microbiota was identified through metagenomics, host genetic data were obtained using a genotyping array, and plasma metabolites were quantified by liquid chromatography mass spectrometry.

RESULTS: A panel of 15 sedentary-related species and 38 sedentary-associated metabolic capacities accounted for 31.68% and 21.48% of the sedentary time-related variation in HOMA-IR, respectively. Specifically, decreased Roseburia sp. CAG:471, Intestinibacter bartlettii, and Firmicutes bacterium CAG:83, but increased Bacteroides xylanisolvens related to longer sedentary time, were causally linked to the development of insulin resistance. Furthermore, integrative analysis with metabolomics identified reduced L-citrulline and L-serine, resulting from a suppression of arginine biosynthesis as key microbial effectors linking longer sedentary time to enhanced insulin resistance.

CONCLUSIONS: In summary, our findings provide insights into the mediating role of gut microbiota on the progression of insulin resistance induced by excessive sedentary time, and highlight the possibility of counteracting the detrimental effect of prolonged sedentary time on insulin resistance by microbiota-modifying interventions.

KEY POINTS: Prolonged sedentary time leads to a depletion of Roseburia sp. CAG:471 and Firmicutes bacterium CAG:83, and suppresses arginine biosynthesis. Decreased L-citrulline and L-serine function as key microbial effectors mediating the adverse effect of sedentary time on insulin sensitivity. Targeting gut microbiota holds promise to combat insulin resistance induced by excessive sedentary time.

RevDate: 2025-05-27
CmpDate: 2025-05-24

Brandão Gontijo J, Huang L, Levintal E, et al (2025)

Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge.

Scientific data, 12(1):858.

Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.

RevDate: 2025-05-24
CmpDate: 2025-05-24

Wang C, Tian Z, Luan X, et al (2025)

Distribution of antibiotic resistance genes on chromosomes, plasmids and phages in aerobic biofilm microbiota under antibiotic pressure.

Journal of environmental sciences (China), 156:647-659.

The objective of this study is to quantitatively reveal the main genetic carrier of antibiotic resistance genes (ARGs) for blocking their environmental dissemination. The distribution of ARGs in chromosomes, plasmids, and phages for understanding their respective contributions to the development of antimicrobial resistance in aerobic biofilm consortium under increasing stresses of oxytetracycline, streptomycin, and tigecycline were revealed based on metagenomics analysis. Results showed that the plasmids harbored 49.2 %-83.9 % of resistomes, which was higher (p < 0.001) than chromosomes (2.0 %-35.6 %), and no ARGs were detected in phage contigs under the strict alignment standard of over 80 % identity used in this study. Plasmids and chromosomes tended to encode different types of ARGs, whose abundances all increased with the hike of antibiotic concentrations, and the variety of ARGs encoded by plasmids (14 types and 64 subtypes) was higher than that (11 types and 27 subtypes) of chromosomes. The dosing of the three antibiotics facilitated the transposition and recombination of ARGs on plasmids, mediated by transposable and integrable transfer elements, which increased the co-occurrence of associated and unassociated ARGs. The results quantitatively proved that plasmids dominate the proliferation of ARGs in aerobic biofilm driven by antibiotic selection, which should be a key target for blocking ARG dissemination.

RevDate: 2025-05-29
CmpDate: 2025-05-29

An X, Zhao R, Wang L, et al (2025)

Thiocyanate degradation by mixed bacterial consortia: Adaptive mechanism in response to thiocyanate stress and metabolic pathway.

Environmental research, 278:121688.

Thiocyanate, frequently detected in various industrial wastewater, poses significant risks to organisms. The activated sludge isolate thiocyanate-degrading bacterial consortia (TDBC) efficiently metabolizes thiocyanate. However, the adaptive mechanism in response to thiocyanate stress and metabolic pathway by TDBC have not been elucidated. Metagenomic analysis showed that Thiobacillus (77.73 %) were the primary degraders for the efficient degradation of thiocyanate. A total of 27 genes related to thiocyanate biodegradation were identified, including SCNase, COSase, sulfur oxidation, denitrification and carbon fixation. Metaproteomic revealed the high expression of chemotaxis protein and thioredoxin enhances cellular oxidative stress and maintains normal physiological metabolism. Additionally, the differentially expressed proteins were primarily involved in metabolic pathways including sphingolipid metabolism, energy metabolism, oxidative phosphorylation, two-component system and amino acid metabolism. Then the lipid, organic acid and amino acid metabolism were up-regulated by metabolomic analysis, thereby achieving the degradation of thiocyanate. Using a combination of qRT-PCR and parallel reaction monitoring (PRM), 27 key genes involved in thiocyanate biodegradation have been identified, providing a theoretical basis for developing microbial strategies to mitigate thiocyanate pollution. Molecular docking deepens the understanding of the interaction between degrading enzyme and thiocyanate. This study provides a theoretical basis for the microbial remediation of thiocyanate-containing wastewater.

RevDate: 2025-05-29
CmpDate: 2025-05-29

Chang FM, Chen YH, Hsu PS, et al (2025)

RNA metagenomics revealed insights into the viromes of honey bees (Apis mellifera) and Varroa mites (Varroa destructor) in Taiwan.

Journal of invertebrate pathology, 211:108341.

The honey bee (Apis mellifera) is a vital pollinator for crops. However, they are infested by an ecto-parasite that has spread worldwide, Varroa mite (Varroa destructor). The Varroa mite is a vector of various western honey bee viruses. In this study, the prevalence of seven honey bee viruses (Deformed wing virus, Lake Sinai virus, Acute bee paralysis virus, Sacbrood virus, Kashmir bee virus, Black queen cell virus, Israeli acute paralysis virus), was screened with the honey bees, which were collected from fourteen apiaries from March 2023 to January 2024, and the Varroa mites, which were collected from two apiaries from July to October 2023 by using RT-PCR. Subsequently, metagenomic analyses were conducted on seven honey bee samples and two Varroa mite samples using next-generation sequencing with poly-A capture and rRNA depletion library construction methods. The results showed that 50% to 85.7% of honey bee viruses in each sample were detected by both methods, with up to three additional viruses identified when combining the two approaches. These findings underscore the importance of integrating both methods for comprehensive virome analysis. According to the virome analysis, 28 honey bee viruses were identified in honey bees and 11 in Varroa mites. Among these, 23 viruses were newly recorded in Taiwanese honey bee populations. Notably, three of the newly recorded viruses, Acute bee paralysis virus, Israeli acute paralysis virus, and Apis mellifera filamentous virus, are known to cause symptoms in honey bees, posing potential risks to their health. Six of these viruses were also detected in Varroa mites, highlighting their role in viral transmission. This study represents the first virome analysis of honey bees and Varroa mites in Taiwan, providing critical insights into honey bee health and establishing a foundation for future health assessment indices and mitigation strategies.

RevDate: 2025-05-29
CmpDate: 2025-05-29

Silva CJFD, Silva CVFD, Cardoso AM, et al (2025)

Exploring clinical parameters and salivary microbiome profiles associated with metabolic syndrome in a population of Rio de Janeiro, Brazil.

Archives of oral biology, 175:106251.

OBJECTIVES: This study investigates for the first time the association between metabolic syndrome and oral microbial profiles in a population-based sample from Rio de Janeiro, Brazil.

DESIGN: We assessed 66 volunteers, collecting detailed sociodemographic, anthropometric, and clinical data alongside salivary samples for metagenomic analysis.

RESULTS: Our findings reveal significant differences in anthropometric parameters, including waist circumference, glycemia, High-Density Lipoprotein (HDL), and triglycerides between the metabolic syndrome and control groups. Increased abundance of Bacteroidetes and Bacteroidia was observed in the metabolic syndrome group, suggesting a potential link between these phyla and metabolic dysregulation. While no significant differences in alpha diversity were found between the overall groups, stratification by body mass index (BMI) indicated that the normal weight subgroup without Metabolic Syndrome exhibited notable variations compared to overweight and obese individuals.

CONCLUSIONS: This study identifies specific shifts in oral microbiota composition that are associated with metabolic syndrome, highlighting their potential as microbial biomarkers for this condition. These findings suggest a link between oral dysbiosis and metabolic dysregulation, providing new insights into the pathophysiology of metabolic syndrome. Additionally, the results pave the way for the development of non-invasive diagnostics tools and targeted therapies that leverage the oral microbiome's role in systemic health.

RevDate: 2025-05-25
CmpDate: 2025-05-24

Chu B, Ge S, He W, et al (2025)

Gut symbiotic bacteria enhance reproduction in Spodoptera frugiperda (J.E. Smith) by regulating juvenile hormone III and 20-hydroxyecdysone pathways.

Microbiome, 13(1):132.

BACKGROUND: The insect gut microbiota forms a complex, multifunctional system that significantly affects phenotypic traits linked to environmental adaptation. Strong reproductive potential underpins the migratory success, population growth and destructive impact of the fall armyworm, Spodoptera frugiperda (J.E. Smith). However, the precise role of gut bacteria in S. frugiperda reproductive processes, distribution and transmission dynamics remains unclear.

RESULTS: We examined the gut microbiota of S. frugiperda a major invasive agricultural pest, identifying Enterococcus, Enterobacter, and Klebsiella as core microorganisms present throughout its life cycle. These microbes showed heightened activity during the egg stage, early larval stages and pre-oviposition period in females. Using an axenic insect re-infection system, Enterococcus quebecensis FAW181, Klebsiella michiganensis FAW071 and Enterobacter hormaechei FAW049 were found to significantly enhance host fecundity, increasing egg production by 62.73%, 59.95%, and 56.71%, respectively. Metagenomic and haemolymph metabolomic analyses revealed a positive correlation between gut symbiotic bacteria and hormone metabolism in female S. frugiperda. Further analysis of metabolites in the insect hormone biosynthesis pathway, along with exogenous injection of juvenile hormone III and 20-hydroxyecdysone, revealed that gut microbes regulate these hormones, maintaining levels equivalent to those in control insects. This regulation supports improved fecundity in S. frugiperda, aiding rapid colonization and population expansion.

CONCLUSIONS: These findings emphasize the pivotal role of gut bacteria E. quebecensis FAW181, E. hormaechei FAW049, and K. michiganensis FAW071 in enhancing S. frugiperda reproduction by modulating JH III levels through JHAMT regulation and concurrently modulating the levels of 20E and its precursors via PHM. Our results provide novel insights into microbe-host symbiosis and pest management strategies for alien invasive species. Video Abstract.

RevDate: 2025-05-26
CmpDate: 2025-05-23

Chen AS, Kim H, Nzabarushimana E, et al (2025)

Association of distinct microbial and metabolic signatures with microscopic colitis.

Nature communications, 16(1):4644.

Microscopic colitis (MC) is a chronic inflammatory disease of the large intestine that primarily affects older adults and presents with chronic diarrhea. The etiology is unknown and there are currently no FDA approved medications or biomarkers for treatment or monitoring of the disease. Emerging evidence have implicated the gut microbiome and metabolome disturbances in MC pathogenesis. We conduct a comprehensive analysis of gut microbial and metabolic changes in a cohort of 683 participants, including 131 patients with active MC, 159 with chronic diarrhea, and 393 age- and sex-matched controls without diarrhea. Stool microbiome and metabolome are profiled using whole-genome shotgun metagenomic sequencing and ultra-high performance liquid chromatography-mass spectrometry, respectively. Compared to controls, eight microbial species including pro-inflammatory oral-typical Veillonella dispar and Haemophilus parainfluenzae, and 11 species, including anti-inflammatory Blautia glucerasea and Bacteroides stercoris are enriched and depleted in MC, respectively. Pro-inflammatory metabolites, including lactosylceramides, ceramides, lysophospholipids, and lysoplasmalogens, are enriched in active MC. Multi-omics analyses reveal robust associations between microbial species, metabolic pathways, and metabolites, suggesting concordant disruptions in MC. Here, we show distinct shifts in gut microbiome and metabolome in MC that can inform the development of non-invasive biomarkers and novel therapeutics.

RevDate: 2025-05-23

Su C, Zhou H, Wang Y, et al (2025)

Contrasting Effects of Atmospheric Particulate Matter Deposition on Free-Living and Particle-Associated Bacteria in the South China Sea.

Environmental science & technology [Epub ahead of print].

Atmospheric particulate matter (PM) deposition has become an important nutrient source in marine ecosystems, increasing particulate organic carbon and resource heterogeneity. However, their effects on marine bacterial communities remain unclear. In this study, by conducting on-board microcosm experiments with anthropogenic East Asian PM in the oligotrophic South China Sea, the response of particle-associated (PA) bacteria was investigated and compared with its free-living (FL) counterparts. Results showed that PM input increased nutrient heterogeneity, shifting bacterial community composition and lifestyle. Copiotrophic PA bacteria became more abundant and contributed a disproportionately higher percentage to total bacterial production despite a decline in total bacterial abundance. FL bacteria showed increased diversity, shifting from oligotrophs to copiotrophs, while PA bacteria displayed reduced diversity and nondirectional compositional changes, suggesting their distinct assembly mechanisms in response to external nutrient inputs. Metagenomic analysis further revealed that PM drives a shift toward a copiotrophic, particle-attached lifestyle with upregulated pathways for chemotaxis, motility, and biofilm formation. Notably, PM addition also increased the relative abundance of oil-degrading taxa. These findings reveal the complexity of microbial responses to environmental perturbations and underscore the need to consider unique ecological niches and bacterial lifestyles.

RevDate: 2025-05-23
CmpDate: 2025-05-23

Zhou S, Wang K, Huang J, et al (2025)

Indole-3-lactic acid suppresses colorectal cancer via metabolic reprogramming.

Gut microbes, 17(1):2508949.

Research indicates that abnormal gut microbiota metabolism is linked to colorectal cancer (CRC) progression, but the role of microbiota-related tryptophan metabolism disruption remains unclear. Using metagenomic sequencing and targeted Trp metabolomics, our research identified that CRC patients had abnormal indole-3-lactic acid (ILA) levels, which were related to tumor malignancy. Exogenous ILA administration suppressed CRC development in AOM/DSS induced and xenograft mice models. Furthermore, in vitro experiments demonstrated that ILA inhibits tumor cell proliferation, migration, and anti-apoptotic capabilities. Mechanistically, ILA appears to directly occupy the phosphorylation sites of STAT3, leading to a reduction in intracellular phosphorylated STAT3 (p-STAT3) levels and the inhibition of the HK2 pathway, thereby downregulating glucose metabolism in cancer cells. Notably, this inhibition is independent of the aryl hydrocarbon receptor (AHR). In conclusion, our research findings demonstrate that alterations in tryptophan metabolism among CRC patients can influence tumor progression and reveal a novel mechanism through which ILA exerts its inhibitory effects on CRC. These findings offer new insights into the role of gut microbiota in CRC and identify potential clinical therapeutic targets.

RevDate: 2025-05-23
CmpDate: 2025-05-23

Creskey M, Silva Angulo F, Wu Q, et al (2025)

Metaproteomics reveals age-specific alterations of gut microbiome in hamsters with SARS-CoV-2 infection.

Gut microbes, 17(1):2505117.

The gut microbiome's pivotal role in health and disease is well established. SARS-CoV-2 infection often causes gastrointestinal symptoms and is associated with changes of the microbiome in both human and animal studies. While hamsters serve as important animal models for coronavirus research, there exists a notable void in the functional characterization of their microbiomes with metaproteomics. In this study, we present a workflow for analyzing the hamster gut microbiome, including a metagenomics-derived hamster gut microbial protein database and a data-independent acquisition metaproteomics method. Using this workflow, we identified 32,419 protein groups from the fecal microbiomes of young and old hamsters infected with SARS-CoV-2. We showed age-specific changes in the expressions of microbiome functions and host proteins associated with microbiomes, providing further functional insight into the interactions between the microbiome and host in SARS-CoV-2 infection. Altogether, this study established and demonstrated the capability of metaproteomics for the study of hamster microbiomes.

RevDate: 2025-05-25
CmpDate: 2025-05-23

Song T, Yin L, Zhou X, et al (2025)

Microbiota profiling from biopsied tissues in complex infections: a diagnostic and prognostic analysis through metagenomic next-generation sequencing.

Frontiers in cellular and infection microbiology, 15:1567981.

BACKGROUND: Infectious diseases that require tissue biopsy are usually more difficult to diagnose through conventional microbiological tests (CMT), and knowledge of the infection microbiota pattern from biopsied tissues remains incomplete. Our study aimed to investigate the diagnostic and prognostic value of metagenomic next-generation sequencing (mNGS), characterize the microbiota profile from biopsied tissues, and examine its relationship with clinical outcomes.

METHODS: This retrospective cohort study included 110 patients who underwent tissue biopsy and sent both mNGS and CMT due to suspected complex infection. Microbiota patterns were illustrated via unsupervised hierarchical clustering analysis. Multivariate regression analysis was used to investigate the effect measures.

RESULTS: The sensitivity of mNGS was significantly higher than that of CMT regarding bacteria (87.23% vs 40.43%, P=0.01), viruses (100% vs 5.56%, P<0.001), and fungi (87.5% vs 28.6%, P=0.04). Polymicrobial infection accounted for 45.2% (33/73) of the infection samples. In skeletal articular biopsied tissues, Staphylococcus presented the highest mean abundance among different species of bacteria (21.2% of all bacterial reads, standard deviation (SD) 38.9). Anaerobic bacteria (24.0%, SD 25.9) represented the most common bacteria in biopsied tissue from the lung or mediastinum. The presence of gram-negative bacteria (adjusted OR 5.21, 95% CI 1.39-19.43, P=0.01), Enterobacteriaceae (adjusted OR 5.71, 95% CI 1.17-28.03, P=0.03) and Staphylococcus (adjusted OR 8.64, 95% CI 1.95-38.34, P=0.005) was associated with an increased risk of treatment failure. Early mNGS sampling within 7 days after admission was associated with a significantly decreased risk of all-cause mortality (HR 0.18, 95% CI 0.04-0.94; P=0.04), treatment failure (OR 0.17, 95% CI 0.05-0.66; P=0.01), and increased probability of clinical resolution (OR 3.03, 95% CI 1.24-7.40; P=0.01).

CONCLUSION: mNGS demonstrates significant diagnostic and prognostic efficacy in patients undergoing tissue biopsy for suspected complex infections. The presence of Gram-negative bacteria, Enterobacteriaceae, and Staphylococcus is associated with a higher probability of treatment failure, which underscores the advantage of using mNGS to guide more aggressive antibiotic strategies.

RevDate: 2025-05-25
CmpDate: 2025-05-23

Yasmin A, Rahman MS, Kador SM, et al (2025)

Metagenomic insights into microbial diversity and potential pathogenic transmission in poultry farm environments of Bangladesh.

BMC microbiology, 25(1):318.

The microbiome plays a critical role in poultry health and productivity, influencing growth, immunity, and the overall farm ecosystem. This study investigated microbial diversity, antibiotic resistance pathways, and functional potential across various components of poultry ecosystems-cloacal swabs, droppings, feed, hand swabs, soil, and water-in different districts of Bangladesh. Using 16S rRNA gene amplicon sequencing, we identified 2,745 Operational Taxonomic Units (OTUs) and analyzed microbial richness, community structure, and functional pathways. Alpha diversity metrics revealed that droppings exhibited the highest microbial richness (726 OTUs in Noakhali), while feed samples showed the lowest diversity (211 OTUs). Beta diversity analysis indicated significant differences in microbial composition across sample sources, with PERMANOVA confirming that sample origin accounted for 51.45% of the variability (p < 0.001). Proteobacteria dominated the microbial communities (48.36%), followed by Firmicutes (19.83%) and Cyanobacteria (12.02%). Key genera of concern, such as Enterobacter (26.62% in hand swabs), Acinetobacter (30.87% in cloacal swabs), and Shigella (22.89% in cloacal swabs), were identified, highlighting potential contamination and zoonotic risks. Conversely, beneficial genera like Lactobacillus (36.89% in feed) and Enterococcus (10.78% in droppings) were prevalent, suggesting roles in gut health and nutrient cycling. Functional pathway analysis (KEGG) revealed that carbohydrate and amino acid metabolism were highly active in droppings and feed, reflecting nutrient utilization. Antimicrobial resistance (AMR) pathways, such as 23S rRNA-methyltransferase and multidrug efflux pumps, were widespread, with pathogenic genera (Enterobacter, Acinetobacter, Shigella, Pseudomonas) showing strong positive correlations with AMR pathways. These findings underscore the influence of environmental factors on microbial diversity and functional potential in poultry farming. The study highlights the need for improved management practices and biosecurity measures to mitigate risks associated with microbial pathogens and antimicrobial resistance, ultimately supporting healthier and more sustainable poultry production in Bangladesh.

RevDate: 2025-05-25
CmpDate: 2025-05-22

Li J, Chen Z, Yan X, et al (2025)

Effects of USP25 knockout on the gut microbial diversity and composition in mice.

BMC microbiology, 25(1):315.

BACKGROUND: The gut microbiota plays a crucial role in host health. Recent study revealed that ubiquitin-specific protease 25 (USP25) deficiency affected colonic immune responses and resistance to certain bacterial infection. This study aimed to investigate the impact of USP25 gene deletion on the gut microbiota of mice, utilizing 16 S rRNA amplicon sequencing and metagenomic sequencing to provide a comprehensive analysis of microbial diversity, composition and functional characteristics.

METHODS: We collected fecal samples from 10 wild type (WT) C57BL/6J mice and 10 USP25[-/-] mice (C57BL/6J-Usp25[em1]cyagen) for 16 S rRNA amplicon sequencing. Subsequently, the 6 of the 20 samples underwent further analysis using metagenomic sequencing.

RESULTS: Our results revealed significant differences in the gut microbiota between USP25 knockout (KO) mice and wild-type (WT) controls, with KO mice exhibiting 1,858 unique amplicon sequence variants (ASVs) compared to 1,723 in WT mice. Notably, the KO group displayed a higher tendency for biofilm formation and a greater proportion of gram-negative bacteria, while the WT group demonstrated enhanced stress tolerance and a higher presence of gram-positive bacteria. Functional prediction analyses indicated an increase in antibiotic resistance genes in the KO mice, particularly for tetracycline, cephalosporin, and sulfonamides, suggesting a potential risk for clinical antibiotic treatment efficacy. Moreover, KEGG pathway enrichment analysis revealed significant enrichment for fructose and mannose metabolism, streptomycin biosynthesis in the KO group. Furthermore, an increase in protective microbes alongside a decrease in potential pathogens in the KO microbiota hinted at altered immune responses due to USP25 deletion.

CONCLUSION: Our findings elucidate the essential role of USP25 in modulating gut microbiota composition and function, providing insights for future therapeutic strategies targeting gut microbiota in disease contexts.

CLINICAL TRAIL NUMBER: Not applicable.

RevDate: 2025-05-25
CmpDate: 2025-05-22

Terbtothakun P, Visedthorn S, Klomkliew P, et al (2025)

Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing.

Scientific reports, 15(1):17772.

Tuberculosis (TB) remains a significant global health challenge, demanding rapid and comprehensive diagnostics for effective treatment. Secondary infections further complicate TB infection, worsening outcomes. Conventional diagnostics are hindered by prolonged turnaround times, high costs, and inability to detect co-infections. This study utilizes full-length 16S rDNA and internal transcribed spacer (ITS) amplicon sequencing based on Oxford Nanopore Technologies (ONT) to analyze clinical metagenomics of sputum microbiota from patients suspected with TB Infection. Our findings highlight the potential of ONT for profiling microbial communities associated with TB infection. The MTB group exhibited a significant abundance of Mycobacterium tuberculosis (M. tuberculosis) and Stenotrophomonas maltophilia. In contrast, Prevotella melaninogenica, Veillonella parvula, Corynebacterium striatum and Pseudomonas aeruginosa were more abundant in the negative samples. Fungal analysis revealed Candida orthopsilosis was enriched in MTB samples, while Aureobasidium leucospermi and Wallemia muriae predominated in negative samples. Correlation network analysis revealed M. tuberculosis exhibits positive and negative correlations with other microbial species, suggesting cooperative and competitive interactions that may influence microbial community dynamics and disease progression in TB patients. This study demonstrates the promise of ONT-based clinical metagenomics for rapid, comprehensive detection of bacterial and fungal co-infections, addressing limitations of conventional diagnostics and improving outcomes.

RevDate: 2025-05-25
CmpDate: 2025-05-22

Dillard LR, Glass EM, Kolling GL, et al (2025)

Genome-scale metabolic network reconstruction analysis identifies bacterial vaginosis-associated metabolic interactions.

Nature communications, 16(1):4768.

Bacterial vaginosis (BV) is the most prevalent vaginal condition among reproductive-age women presenting with vaginal complaints. Despite its significant impact on women's health, limited knowledge exists regarding the microbial community composition and metabolic interactions associated with BV. In this study, we analyze metagenomic data obtained from human vaginal swabs to generate in silico predictions of BV-associated bacterial metabolic interactions via genome-scale metabolic network reconstructions (GENREs). While most efforts to characterize symptomatic BV (and thus guide therapeutic intervention by identifying responders and non-responders to treatment) are based on genomic profiling, our in silico simulations reveal functional metabolic relatedness between species as quite distinct from genetic relatedness. We grow several of the most common co-occurring bacteria (Prevotella amnii, Prevotella buccalis, Hoylesella timonensis, Lactobacillus iners, Fannyhessea vaginae, and Aerrococcus christenssii) on the spent media of Gardnerella species and perform metabolomics to identify potential mechanisms of metabolic interaction. Through these analyses, we identify BV-associated bacteria that produce caffeate, a compound implicated in estrogen receptor binding, when grown in the spent media of other BV-associated bacteria. These findings underscore the complex and diverse nature of BV-associated bacterial community structures and several of these mechanisms are of potential significance in understanding host-microbiome relationships.

RevDate: 2025-05-22

Callens M, Le Berre G, Van den Bulcke L, et al (2025)

An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples.

Molecular ecology resources [Epub ahead of print].

DNA-based techniques are a popular approach for assessing biodiversity in ecological research, especially for organisms which are difficult to detect or identify morphologically. Metabarcoding, the most established method for determining species composition and relative abundance in bulk samples, can be more sensitive and time- and cost-effective than traditional morphological approaches. However, one drawback of this method is PCR bias caused by between-species variation in the amplification efficiency of a marker gene. Metagenomics, bypassing PCR amplification, has been proposed as an alternative to overcome this bias. Several studies have already shown the promising potential of metagenomics, but they all indicate the unavailability of reference genomes for most species in any ecosystem as one of the primary bottlenecks preventing its wider implementation. In this study, we present a strategy that combines unassembled reads of low-coverage whole genome sequencing and publicly available reference genomes to construct a genomic reference database, thus circumventing high sequencing costs and intensive bioinformatic processing. We show that this approach is superior to metabarcoding for approximating relative biomass of macrobenthos species from bulk samples. Furthermore, these results can be obtained with a sequencing effort comparable to metabarcoding. The strategy presented here can thus accelerate the implementation of metagenomics in biodiversity assessments, as it should be relatively easy to adopt by laboratories familiar with metabarcoding and can be used as an accessible alternative.

RevDate: 2025-05-24
CmpDate: 2025-05-21

Jarmukhanov Z, Vinogradova E, Mukhanbetzhanov N, et al (2025)

Parity influences postpartum adaptations in the maternal gut microbiota.

Scientific reports, 15(1):17636.

The gut microbiome undergoes substantial modifications during pregnancy, yet its postpartum adaptations remain poorly understood, particularly with respect to the influence of parity. Here, we investigated the impact of childbirth history on maternal gut microbiome composition and function one month postpartum. By conducting metagenomic sequencing analysis on 60 participants (34 postpartum mothers and 26 controls), we demonstrated significant differences in microbial diversity and community structure between postpartum mothers and control, as well as subtle differences between first-time mothers and multiple-birth mothers. We identified parity-specific signatures, with first-time mothers showing enrichment in Dysosmobacter welbionis, Candidatus Saccharibacteria, and Anaerotruncus species. Functional analysis revealed distinct metabolic reprogramming patterns, including increased amino acid biosynthesis and modified fermentation pathways supporting postpartum recovery. We observed significant correlations between specific bacterial taxa and metabolic pathways, particularly in energy metabolism and immune modulation. Notably, the enhanced capacity for short-chain fatty acid production in primiparous mothers, mediated by Anaerotruncus and Dysosmobacter welbionis, suggests a potential role in shaping breast milk composition, which may influence neonatal development. These findings establish the concept of parity-dependent microbiome programming and provide insights into the biological mechanisms underlying maternal adaptation to pregnancy and childbirth.

RevDate: 2025-05-23
CmpDate: 2025-05-21

Abdillah A, Ravaux I, Mokhtari S, et al (2025)

Do Malassezia yeasts colonize the guts of people living with HIV?.

PloS one, 20(5):e0322982.

Malassezia yeasts are commensals of human skin. In contrast to culture-based studies, metagenomic studies have detected abundant Malassezia reads in the gut, especially in patients living with HIV. Whether Malassezia colonizes and persists in the gut remains an open question. This study aimed to describe the influence of HIV-associated immunodeficiency on gut colonization by Malassezia and to assess whether Malassezia are alive. Stool samples were prospectively collected over one-five visits from ten controls and 23 patients living with HIV (10 had CD4 < 200/mm3 and 13 had CD4 > 500/mm3). Each sample was cultured and subjected to Malassezia viability PCR and both fungal and bacterial metabarcoding. Abundant M. furfur colonies were cultured from an HIV-immunocompromised patient. M. furfur and M. globosa were isolated in very low quantities from healthy volunteers. Viability Malassezia-specific qPCR was positive in three HIV-immunocompromised patients. Metagenomic analyses showed that Malassezia reads were significantly more abundant in immunocompromised patients living with HIV and erratic over time in all participants. Our findings emphasise that Malassezia are rarely cultured from human stool samples, despite the use of specific culture media. Although HIV-related immunosuppression appears to be associated with the presence of Malassezia, these yeasts do not persist and colonise the gut, even in immunocompromised patients.

RevDate: 2025-05-21

Zhang T, Han Y, Peng Y, et al (2025)

The risk of pathogenicity and antibiotic resistance in deep-sea cold seep microorganisms.

mSystems [Epub ahead of print].

UNLABELLED: Deep-sea cold seeps host high microbial biomass and biodiversity that thrive on hydrocarbon and inorganic compound seepage, exhibiting diverse ecological functions and unique genetic resources. However, potential health risks from pathogenic or antibiotic-resistant microorganisms in these environments remain largely overlooked, especially during resource exploitation and laboratory research. Here, we analyzed 165 metagenomes and 33 metatranscriptomes from 16 global cold seep sites to investigate the diversity and distribution of virulence factors (VFs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A total of 2,353 VFs are retrieved in 689 metagenome-assembled genomes (MAGs), primarily associated with indirect pathogenesis like adherence. In addition, cold seeps harbor nearly 100,000 ARGs, as important reservoirs, with high-risk ARGs (11.22%) presenting at low abundance. Compared to other environments, microorganisms in cold seeps exhibit substantial differences in VF and ARG counts, with potential horizontal gene transfer facilitating their spread. These virulome and resistome profiles provide valuable insights into the evolutionary and ecological implications of pathogenicity and antibiotic resistance in extreme deep-sea ecosystems. Collectively, these results indicate that cold seep sediments pose minimal public health risks, shedding light on environmental safety in deep-sea resource exploitation and research.

IMPORTANCE: In the "One Health" era, understanding pathogenicity and antibiotic resistance in vast and largely unexplored regions like deep-sea cold seeps is critical for assessing public health risks. These environments serve as critical reservoirs where resistant and virulent bacteria can persist, adapt, and undergo genetic evolution. The increasing scope of human activities, such as deep-sea mining, is disrupting these previously isolated ecosystems, heightening the potential for microbial exchange between deep-sea communities and human or animal populations. This interaction poses a significant risk for the dissemination of resistance and virulence genes, with potential consequences for global public health and ecosystem stability. This study offers the first comprehensive analysis of virulome, resistome, and mobilome profiles in cold seep microbial communities. While cold seeps act as reservoirs for diverse ARGs, high-risk ARGs are rare, and most VFs were low risk that contribute to ecological functions. These results provide a reference for monitoring the spread of pathogenicity and resistance in extreme ecosystems, informing environmental safety assessments during deep-sea resource exploitation.

RevDate: 2025-05-21

Xin T, Ye Q, D Hu (2025)

A relationship between body size and the gut microbiome suggests a conservation strategy.

Microbiology spectrum [Epub ahead of print].

A key goal of conservation is to protect the biodiversity of wild species to support their continued evolution and survival. Conservation practice has long been guided by genetic, ecological, and demographic indicators of risk. Cope's rule suggests that species tend to evolve larger body sizes over time. Here, we provide strong evidence to support the inclusion of body size when formulating wildlife conservation strategies. The gut microbiome can mirror the physiological and environmental adaptation status of the host. This study established a connection between body size and the gut microbiome in the Felidae family using 70 fecal samples collected from 18 individuals through metagenomic data analysis and mining metagenome-assembled genomes (MAGs). Two enterotypes were identified in the Felidae gut: Bacteroides and Clostridium. Medium-sized felids predominantly harbored Clostridium, associated with pathogenicity, whereas large and small felids harbored both beneficial Bacteroides and pathogenic Clostridium. Species that evolved larger body sizes over time exhibited distinct changes in gut microbial communities, such as enhanced nutrient extraction and metabolic capabilities. Larger felids exhibited a more diverse, stable gut microbiome engaged in metabolic processes and extensive host interactions, indicating an evolved functional role in various biological processes. Conversely, that of smaller felids is less diverse, with more viruses and pathogenic elements primarily involved in chemical synthesis. These findings provide essential insights for developing conservation strategies that consider the nutritional needs of different-sized feline species, control the transmission of pathogens, and allocate resources based on their unique gut microbiome characteristics.IMPORTANCEBody size is a fundamental trait that varies greatly among taxa and has important implications for life history and ecology. Cope's rule suggests that species tend to evolve larger body sizes over time. However, its correlation to body size evolution remains unclear. This study aimed to establish a connection between body size and the gut microbiome in the Felidae family through metagenomic data analysis. Our results support Cope's rule, illustrating that increased body size correlates with shifts in the gut microbiome, enhancing survival and adaptability.

RevDate: 2025-05-25
CmpDate: 2025-05-21

Zöggeler T, Kavallar AM, Pollio AR, et al (2025)

Meta-analysis of shotgun sequencing of gut microbiota in obese children with MASLD or MASH.

Gut microbes, 17(1):2508951.

Alterations in the gut microbiome affect the development and severity of metabolic dysfunction-associated steatotic liver disease (MASLD) or metabolic dysfunction-associated steatohepatitis (MASH). We analyzed microbiomes of obese children with and without MASLD, MASH, and healthy controls. Electronic databases were searched for studies on the gut microbiome in children with obesity with/without MASLD or MASH, providing shotgun-metagenomic-sequencing data. Nine studies and an additionally recruited cohort were included. Fecal microbiomes of children with MASLD (n = 153) and MASH (n = 70) were significantly different in alpha- and beta-diversity (p < 0.001) compared to obese (n = 58) and healthy (n = 132). Species Faecalibacterium_prausnitzii and Prevotella_copri are differentially abundant between obese, MASLD and MASH groups. XGBoost and random forest-models accurately predict MASLD over obesity with an AUROC of 87% and MASH over MASLD with 89%. Pathway-abundance-based models accurately predict MASLD over obesity with an AUROC of 81% and MASH over MASLD with 88%. The composition of the gut microbiome is altered with increasing hepatic fibrosis and concomitant species-abundance increase of Prevotella_copri (p = 0.0082). Machine-learning models discriminate pediatric from adult MASH with an AUROC of 97%. The gut microbial composition is increasingly altered in children with the progression of MASLD toward MASH. This can be utilized as a fecal biomarker and highlights the impact of diet on the gut microbiome for disease intervention.

RevDate: 2025-05-20
CmpDate: 2025-05-20

You Q, Wang K, Zhao Z, et al (2025)

Reduction of Bacteroides fragilis in Gut Microbiome of Chronic Hepatitis B Patients Promotes Liver Injury.

Journal of medical virology, 97(5):e70395.

In chronic hepatitis B (CHB) patients under antiviral treatment, liver injury, as evidenced by elevated alanine transaminase (ALT), is associated with unfavorable outcomes and needs effective treatment. The interaction between gut microbiota and liver injury in CHB patients remains unclear. Using a case-control design, 28 cases with elevated ALT and 28 matched controls with normal ALT were randomly selected from CHB patients with viral control. Clinical characteristics were comparable between groups. Metagenomic sequencing revealed that Bacteroides fragilis was decreased in cases and exhibited the greatest disparity between cases and controls. Mice colonized by gut microbiota from cases exhibited more severe liver damage in both LPS-induced and MCD diet-induced liver injury models, and had a lower abundance of B. fragilis compared to mice colonized by gut microbiota from controls. Oral gavage of B. fragilis improved both LPS-induced and MCD diet-induced liver injury. Metabolomics analysis revealed that the levels of 7-Ketolithocholic acid (7-Keto-LCA) were positively correlated with B. fragilis and significantly increased in the cultural supernatant of B. fragilis. Consistently, 7-Keto-LCA exerted protective effects against both LPS-induced and MCD diet-induced liver damage. Targeting gut microbiota might be a promising therapeutic treatment for alleviation residual liver inflammation in CHB patients with viral control.

RevDate: 2025-05-23
CmpDate: 2025-05-20

Yatera K, Wang Z, Shibata Y, et al (2025)

Sputum Microbiome, Potentially Pathogenic Organisms, and Clinical Outcomes in Japanese Patients with COPD and Moderate Airflow Limitation: The Prospective AERIS-J Study.

International journal of chronic obstructive pulmonary disease, 20:1477-1492.

BACKGROUND: In Western studies, lung microbiome changes are reported in patients with chronic obstructive pulmonary disease (COPD) and are associated with poorer outcomes, but similar studies in Asian patients or those with less severe COPD are limited.

METHODS: The Acute Exacerbation and Respiratory InfectionS in COPD Japan (AERIS-J; jRCT1080224632/NCT03957577) was a prospective, non-interventional study to evaluate sputum microbiome diversity at baseline and after 12 months (V2; exploratory analysis), in patients aged 40-80 years with stable COPD (June 2019-June 2022). Baseline sputum potentially pathogenic organisms (PPOs) were identified. Blood cell counts and COPD Assessment Test (CAT) scores were collected at baseline and COPD symptoms measured over 12 months using the Evaluating Respiratory Symptoms in COPD and EXAcerbations of Chronic pulmonary disease Tool, collected by eDiary.

RESULTS: Patients (N=63) had a mean age of 72.8 years, and percent predicted post-bronchodilator forced expiratory volume in 1 second was 58.3%; 92% were male. Across 62 baseline sputum samples, microbiome composition was similar between 16S rRNA/metagenomic datasets. Patients graded Global Initiative for Chronic Obstructive Lung Disease (GOLD) III versus GOLD I/II had minimal differences in their microbial taxonomic profile and no differences in microbial diversity (Wilcoxon P=0.71). Alpha diversity (Shannon index) positively correlated with blood basophils (rho=0.41; P=0.0019) and negatively correlated with CAT score (rho=0.36; P=0.0069). Alpha diversity and sputum (rho: -0.0637; P=0.7836) or blood (rho: 0.1739; P=0.2043) eosinophils were not correlated. No difference in alpha (P=0.5) or beta (P=0.3) diversity or Operational Taxonomic Unit (Anosim R=-0.024; P=0.892) was observed between PPO-positive or -negative sputum.

CONCLUSION: A less diverse microbiome correlated with poorer health status and lower blood basophils in patients with COPD and moderate airflow limitation. There was no relationship between PPO presence and microbiome diversity.

RevDate: 2025-05-28
CmpDate: 2025-05-28

El-Son MAM, Elbahnaswy S, Khormi MA, et al (2025)

Harnessing the fish gut microbiome and immune system to enhance disease resistance in aquaculture.

Fish & shellfish immunology, 163:110394.

The increasing global reliance on aquaculture is challenged by disease outbreaks, exacerbated by antibiotic resistance, and environmental stressors. Traditional strategies, such as antibiotic treatments and chemical interventions, are becoming less effective, necessitating a shift toward microbiota-based disease control. The fish gut microbiome is a key determinant of immune homeostasis and pathogen resistance. However, previous reviews lack integration of microbiome engineering, machine learning, and next-generation sequencing in fish health strategies. This review encompasses recent advancements in microbiome research, including dietary strategies such as prebiotics, probiotics, synbiotics, and phytogenic feed additives. It synthesizes the latest metagenomic insights, microbiota modulation techniques, and AI-driven disease prediction models. It presents a novel conceptual framework for disease control using microbiome-based approaches in aquaculture. Additionally, we explore emerging methodologies, including microbiota transplantation and synthetic probiotics, to develop precision microbiome interventions. By bridging existing knowledge gaps, this review provides actionable insights into sustainable aquaculture practices through microbiome-driven disease resistance.

RevDate: 2025-05-28
CmpDate: 2025-05-28

Tanaka M, Toyonaga T, Nakagawa F, et al (2025)

Dietary 3-aminobenzoic acid enhances intestinal barrier integrity and attenuates experimental colitis.

American journal of physiology. Gastrointestinal and liver physiology, 328(6):G801-G810.

Disruption of intestinal epithelial integrity and increased permeability is central to the pathogenesis of ulcerative colitis (UC). In this study, we identified 3-aminobenzoic acid (3-ABA), a dietary component abundant in azuki beans, soybeans, and chickpeas as a regulator of epithelial permeability and inflammation in the colon. Screening 119 gut microbial metabolites revealed the ability of 4-ABA, a structural isomer of 3-ABA, to enhance barrier function in Caco2 cells. Further analysis of structural isomers identified 3-ABA as the most effective, significantly increasing transepithelial electrical resistance and reducing epithelial permeability. Using liquid chromatography-mass spectrometry, 3-ABA was detected in dietary beans and human fecal samples. Fecal 3-ABA levels were significantly lower in patients with UC compared with healthy individuals. Metagenomic and functional prediction analyses revealed dysbiosis in patients with UC, characterized by an enrichment of bacterial genes involved in ABA degradation. Gene expression analysis of 3-ABA-stimulated Caco2 cells demonstrated upregulation of tight junction molecules, such as CLDN1 and TJP1, enhancing epithelial barrier integrity. In a dextran sodium sulfate-induced colitis mouse model, rectal 3-ABA administration ameliorated colitis by enhancing epithelial barrier function and reducing inflammation. These findings highlight 3-ABA's potential as a dietary therapeutic agent for UC, offering a novel strategy to enhance intestinal integrity and mitigate inflammation.NEW & NOTEWORTHY Increased intestinal epithelial permeability is central to the pathogenesis of ulcerative colitis (UC). 3-Aminobenzoic acid (3-ABA), a dietary component abundant in beans, decreased epithelial permeability and attenuated colonic inflammation in a mouse experimental colitis model. Reduced fecal 3-ABA levels in patients with UC were associated with dysbiosis-driven accelerated degradation. These findings highlight the therapeutic potential of 3-ABA in UC by targeting colonic epithelium.

RevDate: 2025-05-20
CmpDate: 2025-05-20

Ren Z, Wang M, Yu J, et al (2025)

Unearthing Vertical Stratified Archaeal Community and Associated Methane Metabolism in Thermokarst Sediments.

Environmental microbiology, 27(5):e70110.

Thermokarst lakes are hotspots for greenhouse gas emissions across the Arctic and Qinghai-Tibet Plateau. Investigating the vertical stratification of archaeal communities in thermokarst lake sediments is essential for understanding their ecological roles and contributions to methane production. Here, we analysed archaeal communities along a depth gradient in thermokarst lake sediments. Alpha diversity (richness and Shannon index) generally decreased with depth. Euryarchaeota was the most abundant phylum, though its relative abundance declined with depth, while Thaumarchaeota increased. At the order level, Methanosarcinales and Nitrosopumilales showed increased relative abundance with depth, indicating adaptation to deeper anoxic layers, whereas Methanomicrobiales and Methanotrichales decreased. Beta diversity increased with depth, shifting from stochastic to deterministic processes. Network topology revealed reduced species connectivity but heightened modularity at depth, signalling niche specialisation. Functionally, genes associated with the initial steps of methane metabolism (Fwd, Mtd, Mer) increased with depth, while those involved in later steps (Mtr, Mcr) decreased, suggesting reduced energy conservation efficiency and lower overall methanogenesis rates in deeper sediments. These findings highlight the significant impact of vertical stratification on archaeal community structure, interaction networks, and functional capabilities.

RevDate: 2025-05-21
CmpDate: 2025-05-20

Liao H, Wen C, Huang D, et al (2025)

Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces.

Microbiome, 13(1):127.

BACKGROUND: Antimicrobial resistance poses a substantial and growing threat to global health. While antibiotic resistance genes (ARGs) are tracked most closely in clinical settings, their spread remains poorly understood in non-clinical environments. Mitigating the spread of ARGs in non-clinical contexts such as soil could limit their enrichment in food webs.

RESULTS: Multi-omics (involving metagenomics, metatranscriptomics, viromics, and metabolomics) and direct experimentation show that targeting keystone bacterial taxa by phages can limit ARG maintenance and dissemination in natural soil environments. Based on the metagenomic analysis, we first show that phages from activated sludge can regulate soil microbiome composition and function in terms of reducing ARG abundances and changing the bacterial community composition. This effect was mainly driven by a reduction in the abundance and activity of Streptomyces genus, which is well known for encoding both antibiotic resistance and synthesis genes. To validate the significance of this keystone species for the loss of ARGs, we enriched phage consortia specific to Streptomyces and tested their effect on ARG abundances on 48 soil samples collected across China. We observed a consistent reduction in ARG abundances across all soils, confirming that Streptomyces-enriched phages could predictably change the soil microbiome resistome and mitigate the prevalence of ARGs. This study highlights that phages can be used as ecosystem engineers to control the spread of antibiotic resistance in the environment.

CONCLUSION: Our study demonstrates that some bacterial keystone taxa are critical for ARG maintenance and dissemination in soil microbiomes, and opens new ecological avenues for microbiome modification and resistome control. This study advances our understanding of how metagenomics-informed phage consortia can be used to predictably regulate soil microbiome composition and functioning by targeting keystone bacterial taxa. Video Abstract.

RevDate: 2025-05-21
CmpDate: 2025-05-20

Teng T, Huang F, Xu M, et al (2025)

Microbiota alterations leading to amino acid deficiency contribute to depression in children and adolescents.

Microbiome, 13(1):128.

BACKGROUND: Major depressive disorder (MDD) in children and adolescents is a growing global public health concern. Metabolic alterations in the microbiota-gut-brain (MGB) axis have been implicated in MDD pathophysiology, but their specific role in pediatric populations remains unclear.

RESULTS: We conducted a multi-omics study on 256 MDD patients and 307 healthy controls in children and adolescents, integrating plasma metabolomics, fecal metagenomics, and resting-state functional magnetic resonance imaging (rs-fMRI) of the brain. KEGG enrichment analysis of 360 differential expressed metabolites (DEMs) indicated significant plasma amino acid (AA) metabolism deficiencies (p-value < 0.0001). We identified 58 MDD-enriched and 46 MDD-depleted strains, as well as 6 altered modules in amino acid metabolism in fecal metagenomics. Procrustes analysis revealed the association between the altered gut microbiome and circulating AA metabolism (p-value = 0.001, M[2] = 0.932). Causal analyses suggested that plasma AAs might mediate the impact of altered gut microbiota on depressive and anxious symptoms. Additionally, rs-fMRI revealed that connectivity deficits in the frontal lobe are associated with depression and 22 DEMs in AA metabolism. Furthermore, transplantation of fecal microbiota from MDD patients to adolescent rats induced depressive-like behaviors and 14 amino acids deficiency in the prefrontal cortex (PFC). Moreover, the dietary lysine restriction increased depression susceptibility in adolescent rats by reducing the expression of excitatory amino acid transporters in the PFC.

CONCLUSIONS: Our findings highlight that gut microbiota alterations contribute to AAs deficiency, particularly lysine, which plays a crucial role in MDD pathogenesis in children and adolescents. Targeting AA metabolism may offer novel therapeutic strategies for pediatric depression. Video Abstract.

RevDate: 2025-05-22
CmpDate: 2025-05-19

Yang M, Qi Y, Gao P, et al (2025)

Changes in the assembly and functional adaptation of endophytic microbial communities in Amorphophallus species with different levels of resistance to necrotrophic bacterial pathogen stress.

Communications biology, 8(1):766.

Pcc is one of the key pathogenic factors responsible for destructive soft rot in konjac. To date, the assembly and functional adaptation of the plant endophytic microbiome under Pcc stress remain poorly understood. Here, we found that Pcc stress leads to rapid reorganization of the endogenous microbiome in multiple organs of both susceptible and resistant konjac plants. Under Pcc stress, the negative interactions within the bacterial-fungal interdomain network intensified, suggesting an increase in ecological competition between bacterial and fungal taxa. We further discovered that the relative abundance dynamics of the classes Dothideomycetes and Sordariomycetes, as core fungal taxa, changed in response to Pcc stress. By isolating culturable microorganisms, we demonstrated that 46 fungal strains strongly inhibited the growth of Pcc. This implies that endophytic fungal taxa in konjac may protect the host plant through ecological competition or by inhibiting the growth of pathogenic bacteria. Metagenomic analysis demonstrated that microbial communities associated with resistant Amorphophallus muelleri exhibited unique advantages over susceptible Amorphophallus konjac in enhancing environmental adaptability, regulating plant immune signaling, strengthening cell walls, and inducing defense responses. Our work provides important evidence that endophytic fungal taxa play a key role in the host plant's defense against necrotizing bacterial pathogens.

RevDate: 2025-05-27
CmpDate: 2025-05-27

Majernik SN, Beaver L, PH Bradley (2025)

Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.

mSphere, 10(5):e0085724.

Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which, in turn, are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the Lachnospiraceae and then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as Veillonella and Haemophilus, unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the Lachnospira eligens pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses.IMPORTANCEMetagenome-assembled genomes, or MAGs, can be constructed without pure cultures of microbes. Large-scale efforts to build MAGs have yielded more complete pangenomes (i.e., sets of all genes found in one species). Pangenomes allow us to measure strain variation in gene content, which can strongly affect phenotype. However, because MAGs come from mixed communities, they can contaminate pangenomes with unrelated DNA; how much this impacts downstream analyses has not been studied. Using a metagenomic study of gut microbes in cirrhosis as our test case, we investigate how contamination affects analyses of microbial gene content. Surprisingly, even small, typical amounts of MAG contamination (<5%) result in disproportionately high levels of false positive associations (38%). Fortunately, we show that most contaminants can be automatically flagged and provide a simple method for doing so. Furthermore, applying this method reveals a new association between cirrhosis and gut microbial motility.

RevDate: 2025-05-27
CmpDate: 2025-05-27

Doing G, Shanbhag P, Bell I, et al (2025)

TEAL-Seq: targeted expression analysis sequencing.

mSphere, 10(5):e0098424.

Metagenome sequencing enables the genetic characterization of complex microbial communities. However, determining the activity of isolates within a community presents several challenges, including the wide range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many sites. To address these limitations, we developed "targeted expression analysis sequencing" or TEAL-seq, enabling sensitive species-specific analyses of gene expression using highly multiplexed custom probe pools. For proof of concept, we targeted about 1,700 core and accessory genes of Staphylococcus aureus and S. epidermidis, two key species of the skin microbiome. Two targeting methods were applied to laboratory cultures and human nasal swab specimens. Both methods showed a high degree of specificity, with >90% reads on target, even in the presence of complex microbial or human background DNA/RNA. Targeting using molecular inversion probes demonstrated excellent correlation in inferred expression levels with bulk RNA-seq. Furthermore, we show that a linear pre-amplification step to increase the number of nucleic acids for analysis yielded consistent and predictable results when applied to complex samples and enabled profiling of expression from as little as 1 ng of total RNA. TEAL-seq is much less expensive than bulk metatranscriptomic profiling, enables detection across a greater dynamic range, and uses a strategy that is readily configurable for determining the transcriptional status of organisms in any microbial community.IMPORTANCEThe gene expression patterns of bacteria in microbial communities reflect their activity and interactions with other community members. Measuring gene expression in complex microbiome contexts is challenging, however, due to the large dynamic range of microbial abundances and transcript levels. Here we describe an approach to assessing gene expression for specific species of interest using highly multiplexed pools of targeting probes. We show that an isothermal amplification step enables the profiling of low biomass samples. TEAL-seq should be widely adaptable to the study of microbial activity in natural environments.

RevDate: 2025-05-27
CmpDate: 2025-05-27

Yuan J, Yang J, Sun Y, et al (2025)

An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP).

Science China. Life sciences, 68(6):1541-1554.

China's progressing space program, as evidenced by the formal operation of the China Space Station (CSS), has provided great opportunities for various space missions. Since microbes can present potential risks to human health and the normal operation of spacecraft, the study on space-microorganisms in the CSS is always a matter of urgency. In addition, the knowledge on the interactions between microorganisms, astronauts, and spacecraft equipment will shed light on our understanding of life activities in space and a closed environment. Here, we present the first comprehensive report on the microbial communities aboard the CSS based on the results of the first two survey missions of the CSS Habitation Area Microbiome Program (CHAMP). By combining metagenomic and cultivation methods, we have discovered that, in the early stage of the CSS, microbial communities are dominated by human-associated microbes, with strikingly large differences in both composition and functional diversity compared to those found on the International Space Station (ISS). While the samples from two missions of CHAMP possessed substantial differences in microbial composition, no significant difference in functional diversity was found, although signs of accumulating antibiotic resistance were evident. Meanwhile, strong bacteria co-occurrence was noted within the station's microbiota. At the strain level, environmental isolates from the CSS exhibited numerous genomic mutations compared to those from the Assembly, Integration, and Test (AIT) center, potentially linked to the adaptation to the unique conditions of space. Besides, the intraspecies variation within four high-abundance species suggests possible propagation and residency effects between sampling sites. In summary, this study offers critical insights that not only advance our understanding of space microbiology but also lay the groundwork for effective microbial management in future long-term human space missions.

RevDate: 2025-05-22
CmpDate: 2025-05-19

Salehi M, Laitinen V, Bhanushali S, et al (2025)

Gender differences in global antimicrobial resistance.

NPJ biofilms and microbiomes, 11(1):79.

Antimicrobial resistance is one of the leading causes of mortality globally. However, little is known about the distribution of antibiotic resistance genes (ARGs) in human gut metagenomes, collectively referred to as the resistome, across socio-demographic gradients. In particular, limited evidence exists on gender-based differences. We investigated how the resistomes differ between women and men in a global dataset of 14,641 publicly available human gut metagenomes encompassing countries with widely variable economic statuses. We observed a 9% higher total ARG load in women than in men in high-income countries. However, in low- and middle-income countries, the difference between genders was reversed in univariate models, but not significant after adjusting for covariates. Interestingly, the differences in ARG load between genders emerged in adulthood, suggesting resistomes differentiate between genders after childhood. Collectively, our data-driven analyses shed light on global, gendered antibiotic resistance patterns, which may help guide further research and targeted interventions.

RevDate: 2025-05-22
CmpDate: 2025-05-19

Kohnert E, C Kreutz (2025)

Benchmarking Differential Abundance Tests for 16S microbiome sequencing data using simulated data based on experimental templates.

PloS one, 20(5):e0321452.

Differential abundance (DA) analysis of metagenomic microbiome data is essential for understanding microbial community dynamics across various environments and hosts. Identifying microorganisms that differ significantly in abundance between conditions (e.g., health vs. disease) is crucial for insights into environmental adaptations, disease development, and host health. However, the statistical interpretation of microbiome data is challenged by inherent sparsity and compositional nature, necessitating tailored DA methods. This benchmarking study aims to simulate synthetic 16S microbiome data using metaSPARSim (Patuzzi I, Baruzzo G, Losasso C, Ricci A, Di Camillo B. MetaSPARSim: a 16S rRNA gene sequencing count data simulator. BMC Bioinformatics. 2019;20:416. https://doi.org/10.1186/s12859-019-2882-6 PMID: 31757204) MIDASim (He M, Zhao N, Satten GA. MIDASim: a fast and simple simulator for realistic microbiome data. Available from: https://doi.org/10.1101/2023.03.23.533996), and sparseDOSSA2 (Ma S, Ren B, Mallick H, Moon YS, Schwager E, Maharjan S, et al. A statistical model for describing and simulating microbial community profiles. PLOS Comput Biol. 2021;17(9):e1008913. https://doi.org/10.1371/journal.pcbi.1008913 PMID: 34516542) , leveraging 38 real-world experimental templates (S3 Table) previously utilized in a benchmark study comparing DA tools. These datasets, drawn from diverse environments such as human gut, soil, and marine habitats, serve as the foundation for our simulation efforts. We employ the same 14 DA tests that were previously used with the same experimental data in benchmark studies alongside 8 DA tests that were developed subsequently. Initially, we will generate synthetic data closely mirroring the experimental datasets, incorporating a known truth to cover a broad range of real-world data characteristics. This approach allows us to assess the ability of DA methods to recover known true differential abundances. We will further simulate datasets by altering sparsity, effect size, and sample size, thus creating a comprehensive collection for applying the 22 DA tests. The outcomes, focusing on sensitivities and specificities, will provide insights into the performance of DA tests and their dependencies on sparsity, effect size, and sample size. Additionally, we will calculate data characteristics (S1 and S2 Table) for each simulated dataset and use a multiple regression to identify informative data characteristics influencing test performance. Our prior study, where we used simulated data without incorporating a known truth, demonstrated the feasibility of using synthetic data to validate experimental findings. This current study aims to enhance our understanding by systematically evaluating the impact of known truth incorporation on DA test performance, thereby providing further information for the selection and application of DA methods in microbiome research.

RevDate: 2025-05-21
CmpDate: 2025-05-19

Wang S, Kong F, Dai D, et al (2025)

Deterministic succession patterns in the rumen and fecal microbiome associate with host metabolic shifts in peripartum dairy cattle.

GigaScience, 14:.

BACKGROUND: Metabolic disorders in peripartum ruminants affect health and productivity, with gut microbiota playing a key role in host metabolism. Therefore, our study aimed to characterize the gut microbiota of peripartum dairy cows to better understand the relationship between metabolic phenotypes and the rumen and fecal microbiomes during the peripartum period.

RESULTS: In a longitudinal study of 91 peripartum cows, we analyzed rumen and fecal microbiomes via 16S rRNA and metagenomic sequencing across six time points. By using enterotype classification, ecological model, and random forest analysis, we identified distinct deterministic succession patterns in the rumen and fecal microbiomes (rumen: rapid transition-transition-stable; hindgut: stable-transition-stable). Key microbes, such as Succiniclasticum and Bifidobacterium, were found to drive microbial succession by balancing stochastic and deterministic processes. Notably, we observed that changes in gut microbiota succession patterns significantly influenced metabolic phenotypes (e.g., serum non-esterified fatty acid, glucose, and insulin levels). Mediation analysis suggested that specific gut microbes (e.g., Prevotella sp900315525 in the rumen and Alistipes sp015059845 in the hindgut) and metabolic pathways (e.g., glucose-related pathway) were associated with host metabolic phenotypes.

CONCLUSIONS: Overall, utilizing a large gut microbiome dataset and enterotype- and ecological model-based microbiome analyses, we comprehensively elucidated the succession and assembly of the gut microbiota in peripartum dairy cows. We further confirmed that changes in gut microbiota succession patterns were significantly related to the metabolic phenotypes of peripartum dairy cows. These findings provide valuable insights for developing health management strategies for peripartum ruminants.

RevDate: 2025-05-26
CmpDate: 2025-05-26

Liu H, Gan Y, He B, et al (2025)

mNGS technique was used to analyze the microbiome structure of intervertebral disc tissue in 99 patients with degenerative disc disease.

European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society, 34(5):1709-1721.

OBJECTIVE: Whether bacterial hypotoxic infection in the intervertebral disc is the cause of disc degenerative disease (DDD) is controversial. The mNGS technique can provide valuable insights by obtaining more comprehensive evidence of the presence of bacteria in the intervertebral disc. This study was designed to analyze the characteristics of intervertebral microbiome structure in patients with lumbar disc degenerative disease and its correlation with clinical indicators.

METHODS: A total of 104 patients with lumbar disc degenerative diseases were included in this study. The surgically removed lumbar intervertebral disc tissues were collected for clinical culture and metagenomic second-generation sequencing (mNGS), and the consistency of the two microbial detection methods was compared.According to the collected clinical information, patients were grouped according to the modified Pfirrmann grading, Modic typing and age, and the differences of microbial communities detected by mNGS among different groups were compared, including α diversity analysis, β diversity analysis, species abundance difference analysis, etc. Spearman correlation between clinical features and generic relative abundance was calculated.

RESULTS: The effective culture results of 104 intervertebral disc tissue samples were only 19 cases positive, with a positive rate of 18.3% (19/104), and the mNGS detection results were positive in 99 cases, with a positive rate of 95.2% (99/104). According to the 19 samples with positive culture, nearly half 47.4% (9/19) of staphylococcus species were positive, and all the positive species were basically epidermal common colonization species or environmental common bacteria. At the same time, we conducted two times of mNGS sequencing for these 19 samples, and the consistency rate between the two sequencing results and the culture results was 84.2% (16/19). According to the results of mNGS detection, 250 species from 110 genera were detected in 99 positive samples. The results of group analysis showed that patients with lower degree of disc degeneration (modified Pfirrmann ≤ 4) and young patients (age < 45 years) had more abundant microbial communities in disc tissue (P < 0.05). Correlation analysis showed that there was a positive correlation between Arcobacter skirrowii and improved Pfirrmann classification at the species level (P < 0.01). There was a negative correlation between pseudomonas thermotolerans and modified Pfirrmann classification (P < 0.05). There was a positive correlation between Staphylococcus hominis and Modic typing scores (P < 0.05). Staphylococcus arlettae was negatively correlated with age (P < 0.05). At the genus level, Arcobacter had a significant positive correlation with the modified Pfirrmann grade and Modic classification (P < 0.05), Corynebacterium had a significant negative correlation with the modified Pfirrmann grade (P < 0.05), and Pseudomonas had a significant negative correlation with age (P < 0.05). After our follow-up of six months to one year, two of the patients included in this study eventually developed severe lumbar disc infection, and the rest did not develop infection.

CONCLUSIONS: This study proves that hypotoxic infection may be involved in the degeneration of intervertebral disc, and the bacterial species that cause this occult infection may be more abundant than previously thought. In addition, there was a significant correlation between the biome structure of these bacteria and clinical indicators. The hypothesis of the cause of this insidious infection has the potential to change the way the disease is treated.

RevDate: 2025-05-26
CmpDate: 2025-05-26

Torshizi Esfahani A, Zafarjafarzadeh N, Vakili F, et al (2025)

Gut microbiome in colorectal cancer: metagenomics from bench to bedside.

JNCI cancer spectrum, 9(3):.

Colorectal cancer (CRC) is a major global health challenge. Emerging research highlights the pivotal role of the gut microbiota in influencing CRC risk, progression, and treatment response. Metagenomic approaches, especially high-throughput shotgun sequencing, have provided unprecedented insights into the intricate connections between the gut microbiome and CRC. By enabling comprehensive taxonomic and functional profiling, metagenomics has revealed microbial signatures, activities, and biomarkers associated with colorectal tumorigenesis. Furthermore, metagenomics has shown a potential to guide patient stratification, predict treatment outcomes, and inform microbiome-targeted interventions. Despite remaining challenges in multi-omics data integration, taxonomic gaps, and validation across diverse cohorts, metagenomics has propelled our comprehension of the intricate gut microbiome-CRC interplay. This review underscores the clinical relevance of microbial signatures as potential diagnostic and prognostic tools in CRC. Furthermore, it discusses personalized treatment strategies guided by this omics' approach.

RevDate: 2025-05-26
CmpDate: 2025-05-26

Liu X, Luo Y, Chen X, et al (2025)

Fecal microbiota transplantation against moderate-to-severe atopic dermatitis: A randomized, double-blind controlled explorer trial.

Allergy, 80(5):1377-1388.

BACKGROUND: Fecal microbiota transplantation (FMT) is a novel treatment for inflammatory diseases. Herein, we assess its safety, efficacy, and immunological impact in patients with moderate-to-severe atopic dermatitis (AD).

METHODS: In this randomized, double-blind, placebo-controlled clinical trial, we performed the efficacy and safety assessment of FMT for moderate-to-severe adult patients with AD. All patients received FMT or placebo once a week for 3 weeks, in addition to their standard background treatments. Patients underwent disease severity assessments at weeks 0, 1, 2, 4, 8, 12, and 16, and blood and fecal samples were collected for immunologic analysis and metagenomic shotgun sequencing, respectively. Safety was monitored throughout the trial.

RESULTS: Improvements in eczema area and severity index (EASI) scores and percentage of patients achieving EASI 50 (50% reduction in EASI score) were greater in patients treated with FMT than in placebo-treated patients. No serious adverse reactions occurred during the trial. FMT treatment decreased the Th2 and Th17 cell proportions among the peripheral blood mononuclear cells, and the levels of TNF-α, and total IgE in serum. By contrast, the expression levels of IL-12p70 and perforin on NK cells were increased. Moreover, FMT altered the abundance of species and functional pathways of the gut microbiota in the patients, especially the abundance of Megamonas funiformis and the pathway for 1,4-dihydroxy-6-naphthoate biosynthesis II.

CONCLUSION: FMT was a safe and effective therapy in moderate-to-severe adult patients with AD; the treatment changed the gut microbiota compositions and functions.

RevDate: 2025-05-21
CmpDate: 2025-05-19

Bonacolta AM, Krause-Massaguer J, Unuma T, et al (2025)

The Sea Cucumber-Infecting Parasite Apostichocystis gudetama gen. nov. sp. nov. Expands Marine-Host-Specific Clade of Apicomplexans.

The Journal of eukaryotic microbiology, 72(3):e70013.

Unknown ellipsoid bodies, later classified as apicomplexan cysts, are prevalent in the ovaries of Japanese sea cucumbers (Apostichopus japonicus), where they can lead to lower fecundity in infected individuals and adverse effects on wild populations as well as aquaculture efforts for this endangered species. Apicomplexans are widespread and essential to marine environments, where they can affect the health and fitness of host populations. We performed genomic sequencing of recovered cysts to gain more ecological and evolutionary information on this parasite. We recovered this apicomplexan's complete nuclear ribosomal RNA (rrn) operon, the entire mitochondrial genome, and a partial apicoplast (relic chloroplast) genome. The rrn operon phylogeny revealed this parasite as being closely related to coccidian-like parasites of marine fish (ichthyocolids) and cnidarians (corallicolids), while organelle phylogenomics hint at a closer relation to the protococcidian Eleutheroschizon. Using this new phylogenetic context and previous morphological descriptions, we describe this parasite as Apostichocystis gudetama gen. nov. sp. nov. Mining available microbiomes reveal the presence of Apostichocystis spp. beyond its host range, alluding to other potential hosts or cryptic, closely related lineages. Its phylogenetic placement has important implications concerning the evolution of parasitism within Apicomplexa and the divergence of a marine-host-specific clade of coccidian-like parasites.

RevDate: 2025-05-20
CmpDate: 2025-05-17

Yang Q, Downey R, Stark JS, et al (2025)

The Microbial Ecology of Antarctic Sponges.

Microbial ecology, 88(1):44.

Microbial communities in Antarctic marine sponges have distinct taxonomic and functional profiles due to low temperatures, seasonal days and nights, and geographic isolation. These sponge holobionts contribute to nutrient cycling, structural habitat formation, and benthic ecosystem resilience. We review Antarctic sponge holobiont knowledge, integrating culture-based and molecular data across environmental and taxonomic gradients. Although microbiome data exist for only a fraction of the region's 593 known sponge species, these hosts support diverse symbionts spanning at least 63 bacterial, 5 archaeal, and 6 fungal phyla, highlighting the complexity and ecological significance of these understudied polar microbiomes. A conserved core microbiome, dominated by Proteobacteria, Bacteroidetes, Nitrospinae, and Planctomycetes, occurs across Antarctic sponges, alongside taxa shaped by host identity, depth, and environment. Metagenomic data indicate microbial nitrogen cycling, chemoautotrophic carbon fixation, and stress tolerance. Despite these advances, major knowledge gaps remain, particularly in deep-sea and sub-Antarctic regions, along with challenges in taxonomy, methodological biases, and limited functional insights. We identify key research priorities, including developing standardised methodologies, expanded sampling across ecological and depth gradients, and integrating multi-omics with environmental and host metadata. Antarctic sponge holobionts provide a tractable model for investigating microbial symbiosis, functional adaptation, and ecosystem processes in one of Earth's most rapidly changing marine environments.

RevDate: 2025-05-20
CmpDate: 2025-05-17

Schilling M, Jagdev M, Thomas H, et al (2025)

Metagenomic analysis of mosquitoes from Kangerlussuaq, Greenland reveals a unique virome.

Scientific reports, 15(1):17141.

Climate change is dramatically affecting vector ecology in extreme environments such as the Arctic. However, little is known about the current status of viruses of arthropod vectors located in such northerly locations. As part of a field survey on the role of wildlife in international movement of zoonotic pathogens, we sampled mammalophilic mosquitoes near the settlement of Kangerlussuaq, Greenland in July 2022 and July 2023 to investigate their virome. The majority of mosquitoes were identified as either Aedes impiger or Aedes nigripes. Metagenomic analysis of RNA extracted from species pools detected a number of novel RNA viruses belonging to a range of different virus families, including Flaviviridae, Orthomyxoviridae, Bunyavirales, Totiviridae and Rhabdoviridae. However, the sequence identities when compared to previously published, were as low as 34% at the amino acid level. Furthermore, a comparison of virome diversity between Aedes species emphasises the uniqueness of both Aedes impiger and Aedes nigripes from this secluded ecosystem. It also highlights the need to better understand the viromes of potential pathogen vectors as the impacts of climate change are experienced in such northerly ecosystems.

RevDate: 2025-05-17
CmpDate: 2025-05-17

Zhang Z, Ran X, Guo Z, et al (2025)

Microbial diversity, functional properties, and flavor characteristics of high-temperature Daqu with different colors.

Food research international (Ottawa, Ont.), 212:116406.

High-temperature Daqu (HTD) plays a crucial role in the quality of sauce-flavor baijiu. Daqu of different colors serves distinct functions in the baijiu brewing process. However, indicators for distinguishing among different-colored Daqu remain insufficient. This study investigated the microbial community structures, physicochemical properties, and E-sensory characteristics of different-colored HTD from Shandong Province. The results revealed significant differences in microbial communities among the three HTD types (P < 0.05). Kroppenstedtia eburnea, three Bacillus species, and Weizmannia coagulans were significantly enriched in white Daqu; an unclassified Staphylococcus species dominated in black Daqu; and Aspergillus oryzae, Aspergillus fumigatus, and Proteus mirabilis were highly abundant in yellow Daqu. Compared to HTD from Guizhou and Hubei, Shandong HTD was characterized by microbial species such as Proteus mirabilis and Bacillus velezensis. Using metagenomic analysis, we, for the first time, identified Thermomyces lanuginosus, Lentibacillus daqui, and an unclassified Thermoascus species as potential major contributors to pyrazine synthesis in HTD. The primary differences among the three colored Shandong Daqu types lay in their aroma profiles rather than taste. Electronic nose and electronic tongue analyses demonstrated that the W6S and W3S sensors effectively distinguished black and white Daqu, respectively, marking a novel application of these technologies in Daqu analysis. Acidity was identified as a key factor influencing microbial community structure, flavor characteristics, and enzyme activities, with a nonlinear relationship observed between acidity and enzyme activities. This study highlights the microbial and sensory distinctions among different-colored HTD and provides effective indicators for distinguishing these three types of Daqu.

RevDate: 2025-05-19
CmpDate: 2025-05-17

Zhang S, Zheng N, Zhao S, et al (2025)

Allicin enhances urea-N conversion to microbial-N by inhibiting urease activity and modulating the rumen microbiome in cattle.

Microbiome, 13(1):124.

BACKGROUND: Urea serves as a vital nonprotein nitrogen source in ruminant nutrition, but its efficient utilization is often hampered due to rapid urease activity in the rumen. This study explores the potential of allicin, a garlic-derived compound, as a urease inhibitor to improve urea nitrogen utilization. Enzyme inhibition kinetics and molecular docking were used to identify allicin's interaction sites on urease. Additionally, metagenomic and [15]N-urea metabolic flux analyses were conducted to evaluate allicin's impact on microbial populations and urea-N metabolism.

RESULTS: Allicin was identified as an inhibitor of ruminal urease, with an IC50 of 126.77 ± 1.21 μM. Molecular docking studies have shown that allicin forms hydrogen bonds with key urease residues, leading to the preemption of the urease active site and thus impeding urea binding. In a simulated rumen environment, allicin significantly reduced urea hydrolysis and ammonia production. Furthermore, allicin modified the rumen microbial community by inhibiting Prevotella species while promoting the growth of Ruminobacter species and Denitrobacterium detoxificans. A [15]N-urea metabolic flux analysis revealed that allicin facilitated the incorporation of urea-derived nitrogen into microbial amino acids and nucleotides.

CONCLUSION: Allicin effectively inhibits urease activity in the rumen, enhancing the conversion of urea-N into microbial biomass. These findings suggest that allicin has significant potential to optimize urea metabolism in the rumen, offering a novel strategy for improving ruminant nitrogen nutrition. Video Abstract.

RevDate: 2025-05-16
CmpDate: 2025-05-16

Sarhan MS, Antonello G, Weissensteiner H, et al (2025)

Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat?.

Cell, 188(10):2561-2566.

Human DNA is unavoidably present in metagenomic analyses of human microbiomes. While current protocols remove human DNA before submission to public repositories, mitochondrial DNA (mtDNA) has been overlooked and frequently persists. We discuss the privacy risks and research opportunities associated with mtDNA, urging consideration by the scientific, ethics, and legal communities.

RevDate: 2025-05-19
CmpDate: 2025-05-16

Veseli I, Chen YT, Schechter MS, et al (2025)

Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.

eLife, 12:.

A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health vs IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.

RevDate: 2025-05-24
CmpDate: 2025-05-24

Ahmad W, Coffman L, Ray R, et al (2025)

Flooding episodes and seed treatment influence the microbiome diversity and function in the soybean root and rhizosphere.

The Science of the total environment, 982:179554.

Climate change-related events such as flooding have threatened crop productivity, agricultural sustainability, and global food security by causing hypoxic conditions. Such conditions impaire root development and nutrient acquisition, and alter root rhizospheric microbial communities that are vital for plant health and productivity. Seed treatment with pathogen protection have been key to maintaining early seed germination and plant productivity in field conditions. Still, their role in flooding stress and microbiome diversity and functionality in soybeans is poorly understood. Here, we performed field-based investigations to understand the impact of flooding episodes (0, 3, and 7 days after floodings; DAF) and seed treatment (Cruiser MAXX) on soybean plant growth and rhizosphere microbiome diversity and functionality. Flooding episodes significantly reduced seed yield (746 kg ha[-1]) compared to untreated control. However, the seed treatment increased plant height and pods per plant (3-DAF) and reduced flood injury by 33 % (7-DAF). The shotgun metagenomic analysis showed that seed treatment significantly enhanced the microbial community in rhizospheric soil. Flooding episodes impacted the microbial communities with higher abundance at 3-DAF than at 7-DAF. Flooding stress reduced the microbial diversity, although Proteobacteria increased as root endophytes. Seed treatment and flooding combinations decreased microbiome functionality and reduced gene counts for phytohormone biosynthesis, fermentation, nitrogen, symbiosis, and degradation pathways. Similarly, flooding stress shifted the carbohydrate synthesis to a more specialized substrate. These findings enhance understanding of soybean root and rhizosphere microbiome diversity and functionality dynamics during flooding stress and provide a platform to develop sustainable agricultural practices for enhancing soybean stress tolerance to flooding.

RevDate: 2025-05-25
CmpDate: 2025-05-25

Zhi N, Chang X, Zha L, et al (2025)

Platycodonis radix polysaccharides suppress progression of high-fat-induced obesity through modulation of intestinal microbiota and metabolites.

Phytomedicine : international journal of phytotherapy and phytopharmacology, 142:156653.

BACKGROUND: Obesity is a prevalent chronic condition worldwide, posing a significant risk to public health. Polysaccharides derived from Platycodonis Radix (PR) have been identified as the primary bioactive compounds in combating obesity, although the underlying molecular mechanisms remain inadequately understood.

PURPOSE: The purpose of the research is to analyze the potential anti-obesity influnces within PR polysaccharides (PG: PG1 and PG2) by analyzing their impact on gut microbiota (GM) composition, SCFA and BA metabolism, and the regulation of associated gene and protein expression.

STUDY DESIGN AND METHODS: In this research, 7-week-old male C57BL/6 mice were assigned to a HFD or a control chow diet for 90 days to evaluate the therapeutic effects of PG intervention. Metagenomic analysis was performed to assess GM alterations, while GC-MS and LC-MS were used to quantify SCFA and BA concentrations in cecal contents, respectively. Furthermore, the effects of PG on SCFA- and BA-associated metabolic pathways were examined through qRT-PCR and WB.

RESULTS: PG1 demonstrated superior efficacy compared to PG2 in reducing HFD-induced obesity and associated metabolic disturbances. High-dose PG1 treatment effectively inhibited weight gain, dyslipidemia, inflammation, liver damage, and fat deposition caused by the HFD. Additionally, PG1 treatment primarily promoted the abundance of SCFA-producing bacteria, enhanced the expression of GPR41 and GPR43 genes, significantly elevated levels of GLP-1 and PYY, and improved circulating leptin and adiponectin levels. The intervention with PG1 notably enhanced the relative abundances of bacteria involved in the production of secondary BAs, such as Lachnospiraceae_NK4A136 and Eubacterium coprostanoligenes. This augmentation facilitated the transformation of primary BAs into secondary forms, diminished the relative expression of intestinal FXR and FGF15, and reduced FGFR4 levels. Consequently, this led to an upregulation of hepatic CYP7A1, accelerating liver cholesterol metabolism and the synthesis of new BAs.

CONCLUSION: Supplementation with PG1 protects mice from obesity induced by an HFD. The observed protective effects of PG1 appear to be primarily mediated through the activation of the GM-SCFA-GPR pathway and the inhibition of the GM-BA-FXR-FGF15 signaling pathway.

RevDate: 2025-05-25
CmpDate: 2025-05-25

Hong Y, Cui J, Xu G, et al (2025)

Intestinal IL-17 family orchestrates microbiota-driven histone deacetylation and promotes Treg differentiation to mediate the alleviation of asthma by Ma-Xing-Shi-Gan decoction.

Phytomedicine : international journal of phytotherapy and phytopharmacology, 142:156656.

BACKGROUND: Gut microbiota imbalance is well-known as one important trigger of allergic asthma. Ma-Xing-Shi-Gan decoction (MXSG) is a traditional Chinese medicine prescription with ideal clinical efficacy on asthma. However, whether and how MXSG exerts its efficacy on asthma through gut microbiota remains unclear.

PURPOSE: To investigate the underlying mechanism of MXSG against asthma using multi-omics technologies.

METHODS: An asthma model was established using 8-week-old C57BL/6 J mice, after which they were daily administrated with high-, medium- and low-dose MXSG for 7 days. Histopathological examinations and flow cytometry were performed to evaluate the effects of MXSG on lung immune injury. Key regulatory pathways were predicted via network pharmacology and verified using 16S rRNA sequencing, metagenomics, metabolomics, and in vivo experiments including the knockout of the targeting gene.

RESULTS: MXSG alleviated asthma symptoms, elevated intestinal microbial diversities, and enriched potential beneficial microbes such as Lactococcus, Lactobacillus, and Limosilactobacillus. Network pharmacology and experimental validation highlighted the IL-17/Treg signaling as crucial for asthma treatment. IL-17 knockout experiments revealed its necessity for Treg differentiation during asthma. Moreover, IL-17-deficient asthmatic mice exhibited lower levels of Lactobacillus and significant changes in microbial genes involving histone deacetylases (HDAC) and short-chain fatty acids (SCFAs). Finally, MXSG significantly boosted SCFA production and reduced HDAC9 expression, which were correlated with Treg cell ratios.

CONCLUSION: Our study delineates a novel mechanism where MXSG synergizes with the IL-17 family to enrich intestinal beneficial microbes (e.g. Lactobacillus) and SCFAs. This inhibits the expression of SCFA-downstream HDAC9 to promote Treg differentiation, and thus potentially alleviates asthma.

RevDate: 2025-05-22
CmpDate: 2025-05-22

Orsi AS, Lemos Junior WJF, Alegbeleye OO, et al (2025)

Sodium chloride reduction in meat processing: Microbial shifts, spoilage risks, and metagenomic insights.

Meat science, 226:109848.

This review evaluated the impact of sodium chloride (NaCl) reduction or substitution on the microbial ecology of meat products, with a focus on how these changes affect shelf life and safety. Reducing NaCl in fresh meat products promotes the growth of psychrotrophic spoilage bacteria, such as Pseudomonas sp., which thrive at low temperatures, and mesophilic pathogens like Escherichia coli and Staphylococcus aureus, particularly under inadequate storage conditions. In cured and fermented meats, such as salami, lowering NaCl levels disrupts the balance of salt-tolerant microorganisms, notably lactic acid bacteria (LAB) and coagulase-negative staphylococci, potentially leading to increased spoilage and pathogen proliferation. In smoked meats, the combination of reduced NaCl and altered microbial ecology, including a shift toward LAB dominance, may weaken the inhibitory effects on spore-forming bacteria like Clostridium botulinum. Additionally, using metagenomics, we explore the shifts in microbial communities observed in studies involving meat, revealing critical insights into the composition and diversity of bacteria in meat products, as well as the gaps in research on the impact of NaCl reduction and/or substitution on the microbiota. This review provides a comprehensive understanding of these microbial shifts, highlighting the distinct responses of psychrotrophic, mesophilic, and LAB groups to NaCl modification and the need to understand the effects of these alternatives on the meat product microbiome, as well as the neglected microorganisms that can affect the quality and safety of these products.

RevDate: 2025-05-24
CmpDate: 2025-05-24

Li X, He N, Wang H, et al (2025)

Therapeutic effect of Faecalibacterium longum CM04-06 on DSS-induced ulcerative colitis in mice.

Journal of applied microbiology, 136(5):.

AIMS: This study explores the impact of Faecalibacterium longum CM04-06 on inflammatory bowel disease (IBD) by regulating gut microbiota in mice.

METHODS AND RESULTS: We reanalyzed the distribution of the CM04-06 genome in the metagenome of the IBD cohort and observed a significantly higher abundance of CM04-06 in healthy individuals compared to patients with UC or CD. The prophylactic administration of CM04-06 was evaluated for its effects on intestinal microbial diversity and community composition after a two-week trial in mice. The intestinal microbiota was characterized using metagenomic sequencing of fecal samples on the DNBSEQ platform. CM04-06 treatment resulted in a significant reduction in the Disease Activity Index (DAI) and histological scores, as well as a decrease in the levels of pro-inflammatory cytokines, including IL-1β, IL-6, and TNF-α, in both the colon and serum of DSS-induced mice. Furthermore, supplementation with CM04-06 significantly reduced the levels of pro-inflammatory cytokines in both the colon and serum. Additionally, CM04-06 enhanced the integrity of the intestinal epithelial barrier by increasing the expression of tight junction proteins and mucin. Moreover, we observed greater abundances of Faecalibaculum rodentium, Alistipes onderdonkii, Alistipes shahii, and Bifidobacterium animalis after CM04-06 treatment.

CONCLUSIONS: CM04-06 prevents and alleviates intestinal inflammation by modulating the composition of the microbiota community, increasing the abundance of beneficial probiotics, and suppressing pro-inflammatory cytokine levels.

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RJR Experience and Expertise

Researcher

Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.

Educator

Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.

Administrator

Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.

Technologist

Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.

Publisher

While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.

Speaker

Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.

Facilitator

Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.

Designer

Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

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RJR Picks from Around the Web (updated 11 MAY 2018 )