Tag Archives: Microbiome Digest

November 28, 2025

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Human Microbiome

Awareness of human microbiome may promote healthier lifestyle and more positive environmental attitudes – Olga Rook – Nature

Viruses and Phages

Long-read metagenomics reveals phage dynamics in the human gut microbiome – Jakob Wirbel- Nature

Gut microbiome

Association Between Gut Microbiota Diversity and Body Mass Index (BMI) in Healthy Young Adults in the United States: Insights Into the Gut-Brain-Metabolic Axis Using the Curated Metagenomic Data – Nenrot S. Gopep – Cureus

Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro – Indra Roux – Nature

Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson’s disease – Rémy Villette – Microbiome

Respiratory Microbiome

Whole genome sequencing of the pulmonary microbiome in interstitial lung disease subtypes – Kristel S. Knudsen – Respiratory Research

Enrichment of Streptococcus oralis in respiratory microbiome enhance innate immunity and protects against influenza infection– Xiaohui Zou –  Signal Transduction and Targeted Therapy

Animal microbiome

Non-pasteurized milk enhances early colonization and persistence of Lactobacillus species in dairy calves promoting a stable hindgut microbiome – Shengnan Qiu – Animal Advances

The interaction of microplastics with the ruminal ecosystem in vitro – J. Eichinger – Journal of Hazardous Materials

Bacterial predation in a marine host-associated microbiome – Rory M Welsh – The ISME Journal

Water Microbiome

Spontaneous fermentation of raisin water to form wine – Mamoru Hio – Scientific Reports

Nasal Microbiome

Comparative meta-transcriptomic analysis of nasal and anal microbiota in respiratory syncytial virus mono and co-infected children – Iman Dandachi – Microbiology

Bioinformatics

SHAP-based binarization enhances metataxonomic machine learning with application to gut microbiota of inflammatory bowel disease – Youngro Lee – Scientific Reports

November 7, 2025

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General Microbiome

Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes – Ricardo Leon-Sampedro – Nature

Gut microbiome

Pushing the frontier of gut microbiome health cross-kingdom and cross-organ – Tao Zuo  (左涛) – Nature

The early-life gut microbiome in common pediatric diseases: roles and therapeutic implications – Taiwo Bankole – Frontiers in Nutrition

The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals – Christophe Boetto – Communications Biology

Respiratory Microbiome

Oral microbiome dysbiosis is associated with chronic respiratory diseases: evidence from a population-based study and a hospital cohort – Baolin Jia – Frontiers in Public Health

Distinguishing tuberculosis from non-tuberculous mycobacteria and other respiratory conditions by microbiome patterns – Jee Youn Oh –  Scientific Reports

Animal microbiome

Effects of avian Plasmodium exposure on the microbiota of Culex pipiens – Marta Garrigos – Nature

Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes – Georges P. Schmartz – Nature Communications

Animal Experiments

Fiber, microbiomes, and SCFAs: insights from companion animal models to inform personalized nutrition – Leigh A. Frame – mSystems

Water Microbiome

Microbiome of highly polluted coal mine drainage from Onyeama, Nigeria, and its potential for sequestrating toxic heavy metals – Ganiyu Oladunjoye Oyetibo – Scientific Reports

Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems – Congmin Zhu – Nature Communications

Bringing the uncultivated microbial majority of freshwater ecosystems into culture – Michaela M. Salcher – Nature Communications

Bioinformatics

Metagenomic analysis and genomic characterization of enterovirus A76 and Norovirus GI.6[P11] co-infection in a patient with acute gastroenteritis in Thailand– Watchaporn Chuchaona – Scientific Reports

Uncovering the viral aetiology of undiagnosed acute febrile illness in Uganda using metagenomic sequencing – Shirin Ashraf – Nature Communications

Metaproteomics and metagenomics reveal microbial pathways of organic matter degradation and methanogenesis in a marginally producing natural gas well – Eli K. Moore – Communications Earth & Environment 

October 13, 2025

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General Microbiome

Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research – Imane Allali – Microbiome

Gut microbiome

Gut microbiota alterations are linked to COVID-19 severity in North African and European populations – Marius Bredon – Nature

Expanding the human gut microbiome atlas of Africa -Dylan G. Maghini – Nature

Vaginal microbiome

Changes in the vaginal microbiome in female patients with condyloma acuminatum and its impact on persistent HPV infection – Zhiyu Liu – Nature

Associations among HPV persistence, the vaginal microbiome, and cervical cancer recurrence – Despina Tsementzi – Journal of Translational Medicine

Respiratory Microbiome

Impact of RNA extraction on respiratory microbiome analysis using third-generation sequencing – Alice Michel – BMC Genomics

Animal microbiome

UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog – Shuang Liu – Nature

Soil warming increases the active antibiotic resistome in the gut of invasive giant African snails – Yiyue Zhang – Microbiome

Water Microbiome

Decoding the genetic drivers of marine bacterial blooms through comparative genomics – Xavier Rey-Velasco – Microbiome

Bioinformatics

Influence of creatine pyruvate on newly received cattle: insights from metagenomics and metabolomics – Kang Mao – BMC Microbiology

Computational microbiome pharmacology analysis elucidates the anti-cancer potential of vaginal microbes and metabolites – Damilola C Lawore  – Frontiers

October 10, 2025

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Gut Microbiome & Health

Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand – Tanapon Seetaraso – PLOS ONE

Relationship between Gut microbiome and brain volumes among Japanese Men – Sabrina Ahmed – PLOS ONE

Association of serum intestinal fatty-acid binding protein, inflammatory and oxidative stress markers with colorectal cancer among Ghanaian patients – Genevieve Kwao-Zigah – PLOS ONE

Trends in incidence, mortality and disability-adjusted life years of colorectal cancer in East Asia (1990–2021): An analysis of the Global Burden of Disease study 2021 – Yuanyi Cao – PLOS ONE

Pathogens, Immunity & Host Interactions

Host- and microbial-mediated mucin degradation differentially shape Pseudomonas aeruginosa physiology and gene expression – Sabrina J. Arif – PLOS Pathogens

Blockade of mTOR ameliorates IgA nephropathy by correcting CD89 and CD71 dysfunctions in humanized mice – Alexandra Cambier – PLOS ONE

Single-cell analysis reveals an important role of CD137L+ macrophages in the host response to uropathogenic Escherichia coli infection in the bladder – Yaxiao Liu – PLOS Pathogens

Intestinal inflammation induced by heat-labile toxin-producing enterotoxigenic E. coli infection and impact on immune responses in an experimental human challenge model – Xueyan Zhang – PLOS Neglected Tropical Diseases

Vector-Borne & Parasitic Infections

The effects of mating and blood feeding on the immune defense of female Aedes aegypti mosquitoes – Brendan J. Kelly – PLOS Neglected Tropical Diseases

Temporal and spatial profiling of Aedes albopictus immune responses to chikungunya virus infection – Maria Greta Dipaola – PLOS Neglected Tropical Diseases

Distribution of schistosomes and soil-transmitted helminth infections and their association with growth and nutritional status of school-aged children in Cameroon – Estelle Mezajou Mewamba – PLOS Neglected Tropical Diseases

Risk factors influencing Coxiella burnetii seropositivity in water buffalo populations of Egypt’s Nile Delta – Abdelfattah Selim – PLOS ONE

Global genomic and antimicrobial resistance profiling of Neisseria gonorrhoeae: Insights from whole genome sequencing and minimum inhibitory concentration analysis – Elaheh Ebrahimi – PLOS Neglected Tropical Diseases

Oral & Other Microbiomes

Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients – Duangnapa Roongpiboonsopit – PLOS ONE

Bacterial communities of fungus-growing ant queens are species-specific and suggest vertical transmission – Victoria A. Sadowski – PLOS ONE

Captivity-driven microbiota reshaping: A cross-species analysis of divergent patterns in the gut microbiota of giant pandas, red pandas, and Asiatic black bears – Lin Xu – PLOS ONE

Environmental & Soil Microbiomes

Microbiome characterization of a pre-Hispanic man from Zimapán, Mexico: Insights into ancient gut microbial communities – Santiago Rosas-Plaza – PLOS ONE

The spatial distribution of salt tolerant bacteria and other soil parameters under different agricultural systems of the Indian Sundarbans – Sreemoyee Mitra – PLOS ONE

Pilot-scale depuration demonstrates the suitability of non-pathogenic Vibrio parahaemolyticus as a surrogate for commercial-scale validation studies – Spencer L. Lunda – PLOS ONE

Public Health & Perception

Public perceptions and support for introduced microbes to combat hospital-acquired infections and antimicrobial resistance – Christopher L. Cummings – PLOS ONE

Nutritional status and bacteremia patterns in children with diarrheal diseases: A comparative analysis of bacteremia from Salmonella Typhi versus other pathogens – Md Rezaul Hossain – PLOS ONE

Exploration of common biomarkers and pathogenesis of primary Sjögren’s syndrome and interstitial lung disease by machine learning and weighted gene co-expression networks – Jingqi Dong – PLOS ONE

September 23, 2025

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General Microbiome

Specialty grand challenge: how can we use integrative approaches to understand microbial community dynamics? – Umer Zeeshan Ijaz- Frontiers in Systems Biology

Gut microbiome

Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosis – Sunhee Jung – nature metabolism

Repopulation of the gut microbiota after a screening colonoscopy – Yezaz A Ghouri – PLOS One

Leveraging the Role of Microbiome in Endometriosis: Novel Non-Invasive Diagnostic and Therapeutic Approaches – Eleni Andria Kalopedis – Frontiers in Immunology

Vaginal microbiome

Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort – Noriaki Oguri – Nature Communications

Animal microbiome

Bacterial assemblages on eggs reflect nesting strategies in wetland-associated birds – Wouter F. D. van Dongen – PLOS One

Whole-Genome Sequencing Uncovers Chromosomal and Plasmid-Borne Multidrug Resistance and Virulence Genes in Poultry-Associated Escherichia coli from Nigeria – Chika Ejikeugwu – bioRxiv

Virome

Duck Slurry as a Matrix for Avian Influenza Virus Surveillance and Genetic Characterization in Domestic Flocks – Clément Castille – bioRxiv

Bioinformatics

Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics – Banaz Star-Shirko – BMC research notes

Bioinformatics-based stereochemical elucidation of MM 46115: an unusual antiviral spirotetronate that inhibits clathrin-mediated endocytosis – Afifah Tasnim – bioRxiv

April 22, 2025

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General microbiome

[Editorial] A blueprint for contemporary studies of microbiomes – Bindels et al. Microbiome

[Perspective] Moving from genome-scale to community-scale metabolic models for the human gut microbiome – Quinn-Bohmann et al. Nature Microbiology

[Review] Clinical translation of microbiome research – Gilbert et al. Nature Medicine

Gut microbiome

Antibiotic-induced gut microbiome perturbation alters the immune responses to the rabies vaccine – Feng et al. Cell Host & Microbe

Animal models

Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice – Zhang et al. Microbiome

Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model  – Cuisiniere et al. Microbiome

Virome

The T-series bacteriophages are reductionist models that continue to shape the field  – Barr. Nature Microbiology

Phollow reveals in situ phage transmission dynamics in the zebrafish gut microbiome at single-virion resolution  – Ortiz de ora et al. Nature Microbiology

Bioinformatics 

FGeneBERT: function-driven pre-trained gene language model for metagenomics – Duan et al. Briefings in Bioinformatics. 

TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases – Cong et al. Briefings in Bioinformatics. 

April 3, 2025

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General microbiome

[REVIEW] The regulatory framework for microbiome-based therapies: insights into European regulatory developments – Rodriguez et al. npj Biofilms and microbiomes

Early life microbiome

Bifidobacteria support optimal infant vaccine responses – Ryan et al. Nature

Gut microbiome evolution from infancy to 8 years of age – Sawhney et al. Nature Medicine

Animal experiments

Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice – Litichevskyiy et al. Nature Microbiology

Life-long microbiome rejuvenation improves intestinal barrier function and inflammaging in mice – Sommer et al. Microbiome

Faecalibacterium prausnitzii-derived outer membrane vesicles reprogram gut microbiota metabolism to alleviate Porcine Epidemic Diarrhea Virus infection – Xing et al. Microbiome

Bioinformatics

Elementary methods provide more replicable results in microbial differential abundance analysis – Pelto et al. Briefings in Bioinformatics

DMoVGPE: predicting gut microbial associated metabolites profiles with deep mixture of variational Gaussian Process experts – Weng et al. BMC Bioinformatics

March 2, 2025

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Hello, have a nice Sunday! In this Digest, we have some highlights from the literature during this week. 

Human/General Microbiome

Gastrointestinal Tract

Microbiome analysis of gut microbiota in patients with colorectal polyps and healthy individuals – Dayi Deng – Scientific Reports

Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer – Ping Cai – mSystems

Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients – Yuling Qin – mSystems

Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages – Nejc Stopnisek – BMC Microbiology

Review: Helicobacter pylori, microbiota and gastric cancer – principles of microorganism-driven carcinogenesis – Jonas Wizenty – Nature Reviews. Gastroenterology & Hepatology

Skin

Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes – Diana M Proctor – Nature

Oral – Respiratory Tract

A gut Eggerthella lenta-derived metabolite impairs neutrophil function to aggravate bacterial lung infection – Le-Le Wang – Science Translational Medicine

Involvement of propionate, citrulline, homoserine, and succinate in oral microbiome metabolite-driven periodontal disease progression – Chikako Ishihara – Scientific Reports

Regulation of tryptophan-indole metabolic pathway in Porphyromonas gingivalis virulence and microbiota dysbiosis in periodontitis – Jing Ding – NPJ Biofilms and Microbiomes

Unveiling familial aggregation of nasopharyngeal carcinoma: Insights from oral microbiome dysbiosis – Ying Liao – Cell Reports. Medicine

Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types – Zizheng Wang – Microbiology Spectrum

Other Sites

Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples – Hayden N Brochu – Microbiology Spectrum

Bacteria in the brain: do they have a role in the pathogenesis of Alzheimer’s disease? – Arnav Bhattacharya – Current Opinion in Psychiatry

Beneficial Microbes and Compounds

Microbiome modulation of implant-related infection by a novel miniaturized pulsed electromagnetic field device – João Gabriel S Souza – NPJ Biofilms and Microbiomes

Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function – Benjamin S Beresford-Jones – Microbiome

Antibacterial activity and impact on keratinocyte cell growth of Cutibacterium acnes bacteriophages in a Cutibacterium acnes IA(1)- colonized keratinocyte model – Juan C Farfán-Esquivel – Current Research in Microbial Sciences

Microbiota-derived urolithin A in monoclonal gammopathies and multiple myeloma therapy – Alba Rodríguez-García – Microbiome

Environmental Microbiome / Ecology

The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns – Rodolfo A Salido – Cell

Residence Time Structures Microbial Communities Through Niche Partitioning – Emmi A Mueller – Ecology Letters

Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission – Reena Debray – Microbiome

Microbiome Analysis: Resources, Tools and Techniques

Tandem metabolic reaction-based sensors unlock in vivo metabolomics – Xuanbing Cheng – PNAS

Review: Antarctic bacterial natural products: from genomic insights to drug discovery – William Medeiros – Natural Product Reports

December 6, 2024

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Gut Microbiome

Protection against Clostridioides difficile disease by a naturally avirulent strain – Dong et al. Cell Host & Microbe

Animal experiments 

The host genotype actively shapes its microbiome across generations in laboratory mice – Benga et al. Microbiome

Prenatal antibiotics reduce breast milk IgA and induce dysbiosis in mouse offspring, increasing neonatal susceptibility to bacterial sepsis – Pietrasanta et al. Cell Host & Microbe

Oral and respiratory microbiomes

Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner – Jaber et al. npj biofilms and microbiomes

Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies – Kim et al. Communications biology

The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children – Kristensen et al. Cell Reports Medicine

Plant and environmental microbiomes

Plant microbiota feedbacks through dose-responsive expression of general non-self response genes – Keppler et al. Nature Plants

Dynamics of rice seed-borne bacteria from acquisition to seedling colonization – Chen et al. Microbiome

Bioinformatics

Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets – Bradford et al. BMC Bioinformatics

[PREPRINT] TaxSEA: an R package for rapid interpretation of differential abundance analysis output – Ryan. bioRxiv 

November 24, 2024

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Human and General Microbiome

Spatially restricted immune and microbiota-driven adaptation of the gut – Toufic Mayassi – Nature

Bacterial interactions underpin worsening lung function in cystic fibrosis-associated infections – Damian W Rivett – mBio

Aerobic bacterial group as an early-stage biomarker from faecal samples of patients with colorectal cancer without distant metastasis – D Lee – Beneficial Microbes

The Parkinson’s disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration – Fátima C Pereira – Nature Microbiology

Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts – Paolo Manghi – Nature Microbiology

Enteric bacterial infection stimulates remodelling of bile metabolites to promote intestinal homeostasis – Ting Zhang – Nature Microbiology

Microbiome-Based Colon Cancer Patient Stratification and Survival Analysis – Joshua Smyth – Cancer Medicine

Why HPV16? Why, now, HPV42? How the discovery of HPV42 in rare cancers provides an opportunity to challenge our understanding about the transition between health and disease for common members of the healthy microbiota – Ignacio G Bravo – FEMS Microbiology Reviews

Acarbose impairs gut Bacteroides growth by targeting intracellular glucosidases – Haley A Brown – mBio

Review: More than just a number: the gut microbiota and brain function across the extremes of life – Nathan D Nuzum – Gut Microbes

Review: Microbiota-derived small molecule genotoxins: host interactions and ecological impact in the gut ecosystem – Ellen L Zechner – Gut Microbes

Review: Citizen science as an instrument for women’s health research – Sarah Ahannach – Nature Medicine

Review: Normal Gut Microbiomes in Diverse Populations: Clinical Implications – Omprakash Shete – Annual Review of Medicine

Review: Synthetic Ecosystems: From the Test Tube to the Biosphere – Ricard Solé – ACS Synthetic Biology

Animal Model Microbiome

Limosilactobacillus reuteri ameliorates maternal separation stress in newborn mice and alters subsequent adult behaviour – Z M Saleh – Beneficial Microbes

Sodium oligomannate disrupts the adherence of Rib(high) bacteria to gut epithelia to block SAA-triggered Th1 inflammation in 5XFAD transgenic mice – Xinyi Wang – Cell Discovery

B. vulgatus ameliorates high-fat diet-induced obesity through modulating intestinal serotonin synthesis and lipid absorption in mice – Xinxin Wen – Gut Microbes

Animal Microbiome

Multiomics of yaks reveals significant contribution of microbiome into host metabolism – Shuli Yang – NPJ Biofilms and Microbiomes

Single-strain probiotics enhance growth, anti-pathogen immunity, and resistance to Nocardia seriolae in grey mullet (Mugil cephalus) via gut microbiota modulation – Ching-Hung Chan – Animal Microbiome

The gut microbiota of three avian species living in sympatry – Hugo Pereira – BMC Ecology and Evolution

Butyrate reduces epithelial barrier dysfunction induced by the foodborne mycotoxin deoxynivalenol in cell monolayers derived from pig jejunum organoids – Julie Alberge – Gut Microbes

Plant Microbiome

Trophic modulation of endophytes by rhizosphere protists – Rasit Asiloglu – The ISME Journal

Metagenome-based diversity and functional analysis of culturable microbes in sugarcane – Haidong Lin – Microbiology Spectrum

Root hair developmental regulators orchestrate drought triggered microbiome changes and the interaction with beneficial Rhizobiaceae – Zhenghong Wang – Nature Communications

Functional diversity of the above-ground fungal community under long-term integrated, organic and biodynamic Vineyard Management – Katharina Steng – Environmental Microbiome

Environmental Microbiome

A functional microbiome catalogue crowdsourced from North American rivers – Mikayla A Borton – Nature

Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains – María Dolores Ramos-Barbero – The ISME Journal

Selenium alters the gene content but not the taxonomic composition of the soil microbiome – Alison E Bennett – Environmental Microbiome

Evaluation of microbial community dynamics and chlorinated solvent biodegradation in methane-amended microcosms from an acidic aquifer – Myung Hwangbo – Biodegradation

Viruses

Rotavirus rewires host cell metabolic pathways toward glutamine catabolism for effective virus infection – Suvrotoa Mitra – Gut Microbes

Microbiome Analysis

SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects – Baptiste Ruiz – PLoS Computational Biology

Micro-DeMix: a mixture beta-multinomial model for investigating the heterogeneity of the stool microbiome compositions – Ruoqian Liu – Bioinformatics