December 04, 2025

Human & Clinical Microbiome

Modifiable risk factors for inflammatory bowel disease in KuwaitReem Alhasan – PLOS ONE


Host–Pathogen Interactions (Human-focused)

Pharmacokinetic profiles of Moutan Cortex after single and repeated administration in a colitis modelJin-Hwa Kim – PLOS ONE

ceRNA regulatory network and immune-neurodegenerative mechanisms of peripheral CD4+ T cells in Parkinson’s diseaseLijun Guo – PLOS ONE

Safety profile of TNF-α inhibitors in pediatric patientsYanmo Yang – PLOS ONE


Animal Microbiome

Gut bacteria induce heterologous immune priming in Rhodnius prolixusCarissa A Gilliland – PLOS Pathogens

A reliable in vitro rumen culture system for screening anti-methanogenic compoundsPhilip P Laric – PLOS ONE

High-Resolution Melting assays for discrimination of fungal pathogens causing Grapevine Trunk DiseasesFilipe Azevedo-Nogueira – PLOS ONE

Bimodal expression of Type III Secretion System 2 enables cooperative virulence in Salmonella TyphimuriumMilada Pospíšilová – PLOS Pathogens


Animal Experiments (disease models)

The female reproductive tract–gut axis in gastrointestinal parasitic infectionOlivia Shorthouse – PLOS Pathogens

Toxoplasma gondii disrupts intestinal microbiota and host metabolism in ratsJi-Xin Zhao – PLOS NTDs

Sarcopenia modelling by portal vein ligation inducing hyperammonemia in ratsMaria Nadinskaia – PLOS ONE

Evogliptin prevents ceramide-induced pyroptosis via NLRP3/GSDM-D pathwayRazia Rashid Rahil – PLOS ONE

Mechanistic insight into the antidiabetic effects of Ficus hispida fruitsNusaiba Jahan – PLOS ONE


Computational Microbiology & Modeling

Identification of dynamic models of microbial communitiesAna Paredes-Vázquez – PLOS Computational Biology

Accuracy of the Lotka–Volterra model fails in strongly coupled microbial systemsMichael P Mustri – PLOS Computational Biology


Plant, Soil & Ecological Microbiome

Distinct S-adenosylmethionine synthases link phosphatidylcholine to mitochondrial functionAthena L Munden – PLOS Biology

October 24, 2025

Gut & Human Microbiome

The microbiome and gut–lung axis in nontuberculous mycobacterial pulmonary disease – Ria N. Thompson – PLOS Pathogens

Alterations in the gut microbiota of alcoholic cirrhosis patients infected with Clonorchis sinensis in the Pearl River Delta region of China – Aijun Huang – PLOS ONE

Association between dietary B vitamins intake and age-specific blood pressure: A cross-sectional study in American adults – Xianfeng Li – PLOS ONE

Animal & Environmental Microbiomes

Cuts or carcasses? Diet form affects fecal microbial and animal fiber fractions in a large carnivore, the Asiatic lion – Mengmeng Sun – PLOS ONE

From pre-oral secretions to gut digestion: How do Lucilia sericata (Diptera: Calliphoridae) larvae handle Leishmania major? – Azam Malekian – PLOS ONE

Pathogenicity and transmission of Morganella morganii in honey bees – Yijun Chen – PLOS Pathogens

Mitogenomics of the tropical bont tick Amblyomma variegatum reveals vertical and horizontal transmission of Rickettsia africae – Elisha Chatanga – PLOS Neglected Tropical Diseases

Regulation of lipid metabolism in Spodoptera frugiperda by the symbiotic bracovirus of the gregarious parasitoid Cotesia ruficrus – Xian Li – PLOS Pathogens

The genome of Gallaecimonas pentaromativorans strain 10A, isolated from a Pacific oyster, sheds light on an environmentally widespread genus with remarkable metabolic potential – Yasmine Gouin – PLOS ONE

Plant, Soil & Microbial Ecology

Starve or share? Phosphate availability shapes plant–microbe interactions – Maja Schmidt – PLOS Pathogens

PMA-qPCA: Accelerating the market release of high-quality Bradyrhizobium diazoefficiens inoculant – Mariana Cap – PLOS ONE

Ancient & Evolutionary Microbiomes

Targeted pathogen profiling of ancient feces reveals common enteric infections in the Rio Zape Valley, 725–920 CE – Drew Capone – PLOS ONE

Health, Disease & Microbial Interactions

Differential regulation of the eicosanoid biosynthesis pathway in response to Enterocytozoon hepatopenaei infection in Litopenaeus vannamei – Wananit Wimuttisuk – PLOS ONE

Microplastic exposure and allergic rhinitis: Network toxicology and molecular docking insights – Yaojun Wang – PLOS ONE

Comparative evaluation of the antimicrobial, antioxidant, and cytotoxic properties of essential oils from vetiver, lemongrass, and clove buds with implications for topical application – Acharawan Thongmee – PLOS ONE

October 10, 2025

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

March 2, 2025

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

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

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

November 17, 2024

Human and General Microbiome

F. prausnitzii potentially modulates the association between citrus intake and depression – Chatpol Samuthpongtorn – Microbiome

Perturbations in the airway microbiome are associated with type 2 asthma phenotype and severity – Wei Zhang – Annals of Allergy, Asthma & Immunology

Altered intestinal microbiota and fecal metabolites in patients with latent and active pulmonary tuberculosis – Hua Zhang – Tuberculosis

Mendelian randomization analyses support causal relationships between gut microbiome and longevity – Shu Chen – Journal of Translational Medicine

Natal factors influencing newborn’s oral microbiome diversity – Yoon-Hee Kim – Scientific Reports

Age-related loss of intestinal barrier integrity plays an integral role in thymic involution and T cell ageing – Jessica Conway – Aging Cell

Early-life Upper Airway Microbiota are Associated with Decreased Lower Respiratory Tract Infections – Susan Zelasko – The Journal of Allergy and Clinical Immunology

Human Milk Microbiome Is Associated With Allergic Diseases in Early Childhood – Jie Ma – Allergy

Faecal microbiota composition and impulsivity in a cohort of older adults with metabolic syndrome – Prokopis Konstanti – Scientific Reports

Microbiota-induced alteration of kynurenine metabolism in macrophages drives formation of creeping fat in Crohn’s disease – Jinjie Wu – Cell Host & Microbe

Review: Estimates of microbiome heritability across hosts – Andrew H Morris – Nature Microbiology

Beneficial Microbes and Compounds

High barley intake in non-obese individuals is associated with high natto consumption and abundance of butyrate-producing bacteria in the gut: a cross-sectional study – Satoko Maruyama – Frontiers in Nutrition

Review: Prebiotics in food and dietary supplements: a roadmap to EU health claims – Kieran Tuohy – Gut Microbes

Animal Models

The Microbiome Modifies Manifestations of Hemophagocytic Lymphohistiocytosis in Perforin-Deficient Mice – Jasmin Mann – European Journal of Immunology

Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut – Guillaume Urtecho – Cell Systems

Non-Model Animal Microbiome

Multi-omics investigation into long-distance road transportation effects on respiratory health and immunometabolic responses in calves – Jiancheng Qi – Microbiome

Plant and Soil Microbiome

Wild again: recovery of a beneficial Cannabis seed endophyte from low domestication genotypes – Carolina Lobato – Microbiome

Trade-offs and adaptation to metalliferous soils: The role of soil microbiome in metal tolerance and uptake in Arabidopsis halleri ecotypes from a reciprocal transplant experiment – Priyanka Kushwaha – The Science of the Total Environment

Effect of plant-derived microbial soil legacy in a grafting system-a turn for the better – Tingting Wang – Microbiome

Environmental Microbiome

Microbiome shifts elicited by ornamental lighting of granite facades identified by MinION sequencing – Anxo Méndez – Journal of Photochemistry and Photobiology (B, Biology)

Synthetic communities derived from the core endophytic microbiome of hyperaccumulators and their role in cadmium phytoremediation – Lukuan Huang – Microbiome

Other Microbes

Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays – Victoria de la Sovera – Applied Microbiology and Biotechnology

Microbiome Analysis: Tools, Procedures and Resources

Faecal sample storage without ethanol for up to 24 h followed by freezing performs better than storage with ethanol for shotgun metagenomic microbiome analysis in patients with inflammatory and non-inflammatory intestinal diseases and healthy controls – Ida Marie Bruun Grønbæk – BMC Research Notes

HMicroDB: A Comprehensive Database of Herpetofaunal Microbiota With a Focus on Host Phylogeny, Physiological Traits, and Environment Factors – Jiaying Li – Molecular Ecology Resources

Comparison of commonly used software pipelines for analyzing fungal metabarcoding data – Theresa Rzehak – BMC Genomics

MosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies – Aidan Foo – PLoS Biology

November 14, 2024

General human microbiome

Mapping the gut microbial structural variations in healthy aging within the Chinese population – Shen et al. Cell Reports

Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: results from two observational, population-based microbiome studies – Killberg et al. The Lancet Microbe

[Correspondence related to the above article] Reassessing the role of butyrate-producing bacteria in infection risk – Parsanathan. The Lancet Microbe

Microbiome science of human excrement composting – Meilander & Caporaso. ISME

Microbiota-derived lysophosphatidylcholine alleviates Alzheimer’s disease pathology via suppressing ferroptosis – Zha et al. Cell Metabolism

Probiotics

Probiotics and their metabolite spermidine enhance IFN-γ+CD4+ T cell immunity to inhibit hepatitis B virus – Wang et al. Cell Reports Medicine

Virome

The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission – Majzoub et al. Nature Communications

Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus–host interactions – Du et al. ISME

Bioinformatics & metagenomics

mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data – Tan et al. Briefings in Bioinformatics. 

AMRColab – a user-friendly antimicrobial resistance detection and visualization tool – Lam et al. Microbial Genomics

Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections – Benoit et al. Nature Medicine

November 13, 2024

Today we are highlighting a recent call to action by leading scientists and scientific organizations around the globe aimed at drawing attention to the increasingly urgent climate catastrophe. The authors argue for the use of microbe-based solutions that could be promising in addressing the crisis, and yet are not used effectively at scale. Here we’ve included links to the press release and the journals which have jointly published the paper:

[PRESS RELEASE] Scientists issue call to action underlining importance of microbial solutions to tackle climate crisis – Linda Stewart – The Microbiologist by Applied Microbiology International

Microbial solutions must be deployed against climate catastrophe – Raquel Peixoto, Christian R Voolstra, Lisa Y Stein, Philip Hugenholtz, Joana Falcao Salles, Shady A Amin, Max Häggblom, Ann Gregory, Thulani P Makhalanyane, Fengping Wang, Nadège Adoukè Agbodjato, Yinzhao Wang, Nianzhi Jiao, Jay T Lennon, Antonio Ventosa, Patrik M Bavoil, Virginia Miller, Jack A Gilbert – Sustainable Microbiology

The paper can also be found in journals published by FEMS, ISME, ASM, and Nature.

Human gut microbiome

Predictable regulation of gut microbiome in immunotherapeutic efficacy of gastric cancer – Wei Gao et al – Genes & Immunity

Multimodal analysis identifies microbiome changes linked to stem cell transplantation-associated diseases – Alejandro Artacho et al – BMC Microbiome

Human oral microbiome

Large-scale metagenomic analysis of oral microbiomes reveals markers for autismspectrum disorders – Paolo Manghi et al – Nature Communications

[REVIEW] Viral infection and antiviral immunity in the oral cavity – Heather D. Hickman & Niki M. Moutsopoulos – Nature Reviews Immunology

Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized – Eria P. Ryu et al – BMC Microbiome

Human respiratory microbiome

Major alteration of lung microbiome and the host responses in critically ill COVID-19 patients with high viral load – Ingrid G. Bustos et al – Scientific Reports

Human skin microbiome

The healing process of diabetic ulcers correlates with changes in the cutaneous microbiota – Emanuele Bruni et al – Scientific Reports

Soil microbiome

Microplastic diversity increases the abundance of antibiotic resistance genes in soil – Yi-Fei Wang et al – Nature Communications

Built environment microbiome

Moving beyond species: fungal function in house dust provides novel targets for potential indicators of mold growth in homes – Neeraja Balasubrahmaniam et al – BMC Microbiome

Animal microbiome

Reef site and habitat influence effectiveness of Acropora palmata restoration and its microbiome in the Florida Keys – Stephanie M. Rosales et al – Nature Communications Earth & Environment

Melatonin alleviates heat stress-induced spermatogenesis dysfunction in male dairy goats by regulating arachidonic acid metabolism mediated by remodeling the gut microbiota – Xinrui Guo et al – BMC Microbiome

Pathobiont and symbiont contribute to microbiota homeostasis through Malpighian tubules-gut countercurrent flow in Bactrocera dorsalis – Yanning Liu et al – ISME Journal

Medium-chain fatty acid triglycerides improve feed intake and oxidative stress of finishing bulls by regulating ghrelin concentration and gastrointestinal tract microorganisms and rumen metabolites – Jiaming Luan et al – BMC Microbiome

Intestinal commensal bacteria promote Bactrocera dorsalis larval development through the vitamin B6 synthesis pathway – Jian Gu et al – BMC Microbiome

Water & extremophile microbiome

Latitudinal gradients and ocean fronts strongly influence protist communities in the southern Pacific Ocean – Daniela Sturm et al – FEMS Microbial Ecology

Urea assimilation and oxidation support activity of phylogenetically diverse microbial communities of the dark ocean – Nestor Arandia-Gorostidi et al – ISME Journal

Bioinformatics & tools

MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes – Annabel Cansdale & James P.J. Chong – BMC Microbiome

November 10, 2024

Human and General Microbiome

Novel biomarkers for hepatocellular carcinoma detection and treatment – Hongyuan Yi – Hepatobiliary Surgery and Nutrition

Animal Model Experiments

Gut microbiota modulates depressive-like behaviors induced by chronic ethanol exposure through short-chain fatty acids – Hui Shen – Journal of Neuroinflammation

Host genetics and gut microbiota influence lipid metabolism and inflammation: potential implications for ALS pathophysiology in SOD1(G93A) mice – Elena Niccolai – Acta Neuropathologica Communications

Lactobacillus rhamnosus modulates murine neonatal gut microbiota and inflammation caused by pathogenic Escherichia coli – Hao Xuan – BMC Microbiology

Animal Microbiome

Introduction into natural environments shifts the gut microbiome of captivity-raised filter-feeding bivalves – Stephanie N Vaughn – ISME Communications

A metagenomic catalogue of the ruminant gut archaeome – Jiandui Mi – Nature Communications

Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates – Bo Xu – NPJ Biofilms and Microbiomes

Diet affects reproductive development and microbiota composition in honey bees – Anjali Zumkhawala-Cook – Animal Microbiome

Plant Microbiome

Biological and experimental factors that define the effectiveness of microbial inoculation on plant traits: a meta-analysis – Hamed Azarbad – ISME Communications

Can microbiome adaptations protect crops from pests and climate change? – Carolyn Beans – PNAS

Environmental Microbiome

Ecological roles of nano-picoplankton in stratified waters of an embayment in the southern Benguela – Nicole R Dames – FEMS Microbiology Letters

Metagenomic insights into inhibition of soil microbial carbon metabolism by phosphorus limitation during vegetation succession – Haocai Wang – ISME Communications

Microbiome Analysis

Cross-comparison of gut metagenomic profiling strategies – Gábor Gulyás – Communications Biology