Tag Archives: Animal microbiome

December 19, 2025

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Animal microbiome

The innate immune IMD pathway is a key regulator of gut microbiome and metabolic homeostasis in the black tiger shrimp (Penaeus monodon) – Premruethai Supungul – PLOS ONE

Human gut microbiome & nutrition

The evaluation of indoxyl sulfate in the general population in Kanegasaki Iwate: A cross-sectional study (KANEGASAKI study) – Mizuki Hisano – PLOS ONE

The relationship between dietary intake of B vitamins and Helicobacter pylori seropositivity – Yuexia Lu – PLOS ONE

Plant, soil & ecological microbiome

Zinc ion increases the effectiveness of phosphorus in agricultural soils through microbial solubilization – Lanxin Tang – PLOS ONE

Optimizing soil quality and rhizosphere ecology to enhance Annona squamosa yield and quality through water–fertilizer–mulching synergy – Weihua Wang – PLOS ONE

Concentration-dependent effects of fermented spent coffee grounds and contrasting effects of earthworms on growth and phytochemicals in medicinal plant Glechoma longituba – Bing-Nan Zhao – PLOS ONE

Animal experiments (model organisms)

The Drosophila G protein-coupled receptor, GulpR, is essential for lipid mobilization in response to nutrient limitation – Daniela Barraza – PLOS Genetics

High-protein diets reduce plasma pro-inflammatory cytokines following lipopolysaccharide challenge in Swiss Albino mice – Hellen W Kinyi – PLOS ONE

Clinical research & public health

Impact of an integrated intervention package during preconception, pregnancy, and early childhood on inflammation, IGF-1, IGFBP3 during first 6 months of life: Findings from the WINGS randomized controlled trial – Ranadip Chowdhury – PLOS Global Public Health

Lack of association between loneliness, social isolation and inflammation in people living with HIV aged ≥50 years – Jose-Ramon Blanco – PLOS ONE

Effect of obesity and exercise training on circulating lipids in American Indian adolescents – Charles F Hojjat – PLOS ONE

From mental health detention to health systems reform: Co-producing policy and practice recommendations with Black men and their communities – Elaine Craig – PLOS Mental Health

Microbial genetics & bacterial physiology

Whole-genome analysis of Lysinibacillus boronitolerans MSR1: A dairy-isolated multidrug-resistant and non-pathogenic strain – Md Shahedur Rahman – PLOS ONE

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and intra-species cooperation – Ben Vezina – PLOS Biology

Clinical biomarkers & immunology

Blood RNA biomarkers and a point-of-care elastase assay for detecting host immune activation in suspected sepsis – John E Lafleur – PLOS ONE

Multi-omics analysis reveals diagnostic and therapeutic biomarkers for aging phenotypes in ulcerative colitis – Lei Guo – PLOS ONE

Oral health & microbiome

The impact of diet and oral hygiene on dental caries among Turkish children: A cross-sectional study – Ozge Yesildemir – PLOS ONE

Molecular biology & immunity

LIPL-1 and LIPL-2 are TCER-1-regulated lysosomal lipases with distinct roles in immunity and fertility – Laura Bahr – PLOS Genetics

November 27, 2025

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Human gut microbiome

Weifuchun alleviates MNNG-induced chronic atrophic gastritis by improving the gastric and intestinal microbiota homeostasis – Yingying Chen – PLOS ONE

Microbiota-supportive diets and hyperlipidemia: The mediating role of systemic inflammation – Wenjing Wang – PLOS ONE

Toxoplasma gondii disrupts intestinal microbiota and host metabolism in a rat model – Ji-Xin Zhao – PLOS NTDs

Body mass index distinctly modulates the associations between Alistipes and CRP/IL-6 – Lourdes Chero-Sandoval – PLOS ONE

Dogs with advanced myxomatous mitral valve disease have evidence of gastrointestinal bacterial translocation – Maria C Jugan – PLOS ONE

Predicting postoperative constipation in middle-aged and elderly fracture patients using machine learning – Xiaoyan Yang – PLOS ONE

Animal microbiome

Cecal microbiota of broilers responds similarly to black soldier fly larvae fat and conventional fat sources – Muhammad Rumman Aslam – PLOS ONE

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

Oral / GI cancer microbiome

Serum IgG titer for Fusobacterium nucleatum and clinical outcome in esophageal squamous cell carcinoma – Toru Yoshikawa – PLOS ONE

Phages & bacterial pathogenesis

Structural determinants of SlpA-mediated phage recognition in Clostridioides difficile – Alexia LM Royer – PLOS Pathogens

Disruption of yqhG attenuates virulence in MRSA by compromising membrane stability – Jianhua Liao – PLOS ONE

Host range of generalist and specialist phages in capsule-diverse Klebsiella hosts – Celia Ferriol-González – PLOS Biology

Immunology / human disease

Large-scale seroepidemiology uncovers nephro-urological pathologies with tau autoimmunity – Andreia D Magalhães – PLOS Biology

Plant, soil & ecological microbiome

Root-associated Streptomyces strains enriched during drought reveal diverse functional traits – Citlali Fonseca-Garcia – PLOS Biology

Co-infections shaping Chlamydia pecorum infection outcomes in northern koalas – Yasmine S S Muir – PLOS Pathogens

Trade-offs between yields and sustainability in winter wheat systems under climate change – Jennifer Michel – PLOS Climate

Clinical microbiology

Clinical impact of prophylactic antibiotics in kidney transplantation – Sang Ah Lee – PLOS ONE

Microbial interactions

Veillonella species increase Listeria monocytogenes growth in broth and biofilms – Fanie Shedleur-Bourguignon – PLOS ONE

October 24, 2025

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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

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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

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

November 17, 2024

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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 13, 2024

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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

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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

November 3, 2024

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Human and General Microbiome

Gut microbiota and metabolic profile changes unveil the deterioration of alveolar bone inflammatory resorption with aging induced by D-galactose – Fangzhou Liu – Scientific Reports

The human gut symbiont Ruminococcus gnavus displays strain-specific exopolysaccharides modulating the host immune response – Victor Laplanche – Carbohydrate Polymers

Stage dependent microbial dynamics in hepatocellular carcinoma and adjacent normal liver tissues – Hee Eun Jo – Scientific Reports

Intestinal microflora and metabolites affect the progression of acute pancreatitis (AP) – Zhenjiang Wang – Gut Pathogens

Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients – Angeli D G Macandog – Cell Host & Microbe

Review: A pathophysiologic framework for the overlap of disorders of gut-brain interaction and the role of the gut microbiome – Ayesha Shah – Gut Microbes

Review: AI in microbiome-related healthcare – Niklas Probul – Microbial Biotechnology

Review: The oncomicrobiome: new insights into microorganisms in cancer – Yingying Ma – Microbial Pathogenesis

Viewpoint: Gut microbiome: a biomedical revolution – Maria Carmen Collado – Nature Reviews Gastroenterology & Hepatology

Research Highlight: Microbiome-colonizing RNAs – Andrea Du Toit – Nature Reviews. Microbiology

Beneficial Microbes and Compounds

Effects of Limosilactobacillus reuteri DSM 17938 in neonates exposed to antibiotics: a randomised controlled trial – J Lozar Krivec – Beneficial Microbes

Lactobacillus rhamnosus 1.0320 Postbiotics Ameliorate Dextran Sodium Sulfate-Induced Colonic Inflammation and Oxidative Stress by Regulating the Intestinal Barrier and Gut Microbiota – Jing Zhang – Journal of Agricultural and Food Chemistry

Oral administration of Lactobacillus casei DG® after ileostomy closure in restorative proctocolectomy: a randomized placebo-controlled trial (microbiota and immune microenvironment in pouchitis -MEP1) – Imerio Angriman – Gut Microbes

Development of interleukin-27 recombinant Lactococcus lactis and its efficacy in treating psoriasis and colitis in mice – Shaoju Qian – International Journal of Biological Macromolecules

Animal Models

The gut microbiome in patients with Cushing’s disease affects depression- and anxiety-like behavior in mice – Ding Nie – Microbiome

Alpha-synuclein overexpression and the microbiome shape the gut and brain metabolome in mice – Livia H Morais – NPJ Parkinson’s Disease

Transfer of microbiota from lean donors in combination with prebiotics prevents excessive weight gain and improves gut-brain vagal signaling in obese rats – Dulce M Minaya – Gut Microbes

Animal Microbiome (non-models)

Microbiome divergence of marine gastropod species separated by the Isthmus of Panama – Alexander T Neu – Applied and Environmental Microbiology

Plant and Soil Microbiome

Planting density effect on poplar growth traits and soil nutrient availability, and response of microbial community, assembly and function – Rongye Qiao – BMC Plant Biology

Plant growth-promoting fungi improve tobacco yield and chemical components by reassembling rhizosphere fungal microbiome and recruiting probiotic taxa – Mingzi Shi – Environmental Microbiome

Review: Community standards and future opportunities for synthetic communities in plant-microbiota research – Trent R Northen – Nature Microbiology

Review: Alpine and subalpine plant microbiome mediated plants adapt to the cold environment: A systematic review – Mengyan Hou – Environmental Microbiome

Environmental Microbiome

Arctic’s hidden hydrocarbon degradation microbes: investigating the effects of hydrocarbon contamination, biostimulation, and a surface washing agent on microbial communities and hydrocarbon biodegradation pathways in high-Arctic beaches – Ya-Jou Chen – Environmental Microbiome

SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas – Lei Gao – Microbial Ecology

Resistome analysis of wastewater treatment plants in Agadir city, Morocco, using a metagenomics approach – Maryem Wardi – Scientific Reports

Comparative genomic analysis and characterization of novel high-quality draft genomes from the coal metagenome – Arunmozhi Bharathi Achudhan – World Journal of Microbiology & Biotechnology

October 27, 2024

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Human and General Microbiome

Gut

A human gut Faecalibacterium prausnitzii fatty acid amide hydrolase – Jiye Cheng – Science

A ubiquitous mobile genetic element changes the antagonistic weaponry of a human gut symbiont – Madeline L Sheahan – Science

Exploring alterations of gut/blood microbes in addressing iron overload-induced gut dysbiosis and cognitive impairment in thalassemia patients – Kanokphong Suparan – Scientific Reports

Effects of bile acids on the growth, composition and metabolism of gut bacteria – Yi-Lei Peng – NPJ Biofilms and Microbiomes

Gut-first Parkinson’s disease is encoded by gut dysbiome – Mário F Munoz-Pinto – Molecular Neurodegeneration

Metaproteomics reveals diet-induced changes in gut microbiome function according to Crohn’s disease location – Stefano Levi Mortera – Microbiome

Review: Examining the healthy human microbiome concept – Raphaela Joos – Nature Reviews Microbiology

Review: Host-pathobiont interactions in Crohn’s disease – Roberta Caruso – Nature Reviews Gastroenterology & Hepatology

Early Microbiome

Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy – Samuel S Minot – Gut Microbes

Metal availability shapes early life microbial ecology and community succession – Joshua Soto Ocaña – mBio

Virome

Oral reovirus reshapes the gut microbiome and enhances antitumor immunity in colon cancer – Won Suk Lee – Nature Communications

Oral Cavity

Pooled analysis of oral microbiome profiles defines robust signatures associated with periodontitis – Assem Soueidan – mSystems

Animal Microbiome (Model and Non-Model Organisms)

Type VI secretion systems promote intraspecific competition and host interactions in a bee gut symbiont – Erick V S Motta – PNAS

Gut bacteria facilitate leaf beetles in adapting to dietary specialization by enhancing larval fitness – Meiqi Ma – NPJ Biofilms and Microbiomes

The dietary effects of two strain probiotics (Leuconostoc mesenteroides, Lactococcus lactis) on growth performance, immune response and gut microbiota in Nile tilapia (Oreochromis niloticus) – Assel Paritova – PloS One

Effects of Lactiplantibacillus plantarum CBT LP3 and Bifidobacterium breve CBT BR3 supplementation on weight loss and gut microbiota of overweight dogs – Jihee Choi – Scientific Reports

Maternal gastrointestinal microbiome shapes gut microbial function and resistome of newborns in a cow-to-calf model – Yimin Zhuang – Microbiome

Integrated analysis of metabolome and microbiome in a rat model of perimenopausal syndrome – Yanqiu Wei – mSystems

Maternal dysbiosis produces long-lasting behavioral changes in offspring – Jacob Hudobenko – Molecular Psychiatry

DNA metabarcoding analyses reveal fine-scale microbiome structures on Western Canadian bat wings – Chadabhorn Insuk – Microbiology Spectrum

Plant and Environmental Microbiome

Aquificae overcomes competition by archaeal thermophiles, and crowding by bacterial mesophiles, to dominate the boiling vent-water of a Trans-Himalayan sulfur-borax spring – Nibendu Mondal – PloS One

Metagenome-assembled genomes of Macrocystis-associated bacteria – Emily G Aguirre – Microbiology Resource Announcements

Metagenomic time-series reveals a western English Channel viral community dominated by members with strong seasonal signals – Luis M Bolaños – The ISME Journal

Volatile-mediated interspecific plant interaction promotes root colonization by beneficial bacteria via induced shifts in root exudation – Xingang Zhou – Microbiome

Other Microbes

Microbial community acclimation during anaerobic digestion of high-oil food waste – Yangqing Hu – Scientific Reports

The choice of 16S rRNA gene sequence analysis impacted characterization of highly variable surface microbiota in dairy processing environments – Sarah E Daly – mSystems

Microbiome Analysis: Tools, Techniques and Resources

A single-stranded based library preparation method for virome characterization – Xichuan Zhai – Microbiome

Microbiome-based correction for random errors in nutrient profiles derived from self-reported dietary assessments – Tong Wang – Nature Communications

Fecal samples and rectal swabs adequately reflect the human colonic luminal microbiota – Julia Rode – Gut Microbes

Optimal 16S rRNA gene amplicon sequencing analysis for oral microbiota to avoid the potential bias introduced by trimming length, primer, and database – Takahiko Nagai – Microbiology Spectrum

Moving Toward Metaproteogenomics: A Computational Perspective on Analyzing Microbial Samples via Proteogenomics – Franziska Singer – Methods in Molecular Biology