Category Archives: Microbial Ecology

April 17,2026

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See you next week at MVIF!

#MVIF 48 starts next week! Free registration: cassyni.com/s/mvif-48⭐️ Highlights:🇺🇸 Rachel R. Rock🇺🇸 @pamferretti.bsky.social ⭐️ Keynote:🇦🇺 @pam-engelberts.bsky.social and @jamesvolmer.bsky.social ⭐️ Talks: 🇨🇳 Linxing Chen🇨🇳 Zhemin Zhou🇦🇺 Hoai-An Nguyen

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2026-04-13T11:02:11.436Z


Gut microbiome

Associations of the gut microbiome and cardiometabolic risk in adolescence: the HOME study – Jennifer L. Arzu – BMC Medical Genomics 

Insect Gut Microbiota as a Reservoir of Industrially Relevant Enzymes: A Comprehensive Review – Aswin Viswan – Microbial Ecology

Respiratory Microbiome

The commensal microbiome in respiratory tract tumors: From oncogenic mechanisms to clinical translation – Jiale Yu – Journal of Advanced Research

Bacteria of the lung microbiome and health biomarkers in chronic airway disease: a systematic review and meta-analysis – Lucia Grassi – npj Biofilms Microbiomes

Animal Microbiome

Multi-omics revealed the effects of rumen to blood path on early lactation performance in transition dairy cows – Guangfu Tang – Microbiome

Spiroplasma Display an Intricate Continuum of Infection Heterogeneity and Persistence in Myrmica Ants – Diego Castillo Franco – Molecular Ecology

Oral Microbiome

Loss of salivary agglutinin induces changes in the salivary microbiome and accelerates development of oral cancer – Marcell Costa de Medeiros – Microbiome

Water Microbiome

Ecological water replenishment reshapes the river microbiome along an urban-rural gradient: Enhanced diversity but compromised stability – Hongyuan Tian – Journal of Hydrology: Regional Studies

Soil Microbiome

Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland – Linnea K. Hernandez – Microbiome

Impact of microbial consortia and fertilization regimes on the soil microbiome in maize field trials – Nils Kleinbölting – Scientific Reports

Plant Microbiome

Phenotypic resistance profiles and resistome variations between endophytic and epiphytic bacteria in apple fruits – Denis Kiplimo – Environmental Microbiome

Plant spatial compartmentalization buffers bacteriome structure and function under antibiotic stress – Caryn Kgokonyane Lenonyane – Scientific Reports

Bioinformatics

Pangenome-based design of strain-specific primers enables precise monitoring of bacteria in human microbiome intervention trials – Tom Eilers – Scientific Reports

Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies – Bianca-Maria Cosma – PLOS One

Genomic characterization of Comamonas kerstersii isolated from diarrheal patients in Bangladesh – Noshin Ibnat Rib – PLOS One

I had the joy of giving a kindergarten workshop: “Bacteria in and around us!” 🦠✨To spark their imagination and start our discussion, I showed them the beautiful @contamclub.bsky.social 2026 calendar, full of vividly colored and uniquely shaped bacterial colonies.1/3

— Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2026-04-16T10:46:01.481Z

March 19, 2026

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Gut microbiome

Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals – Gabriel Baldanzi – Nature Medicine

Spatial transcriptomics maps host–gut microbiome biogeography at high resolution – Ioannis Ntekas – Nature Microbiology

Respiratory Microbiome

Empiric azithromycin alters the upper respiratory microbiome and resistome without anti-inflammatory benefit in COVID-19 – Abigail Glascock – Nature Microbiology

Dysbiosis of the nasal microbiome is associated with prospective acute exacerbation of COPD – Cristian Roca – Microbiome

Animal Microbiome

Towards standardization in pig microbiome research based on a comprehensive twenty-year review – Samuel Onyilokwu Enokela – Animal Microbiome

Longitudinal source-sink dynamics of fecal litter and farm indoor environmental resistomes in broiler chicken and Cherry Valley ducks – Peter Fauszt –  Animal Microbiome

Oral Microbiome

Denture-associated oral microbiome in dentate and edentulous older adults living in long-term care facilities – Muhammed Manzoor – Journal of Oral Microbiology

Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia – Jun Hyung Cha – Journal of Oral Microbiology

Water Microbiome

Water mass specific genes dominate the Southern Ocean microbiome – Emile Faure – Nature Communications

Plant Microbiome

Impacts of climate extremes on plant pathogens, microbiomes and plant health – Chao Xiong – Nature Reviews Microbiology

Heritability of the Pinus radiata root microbiome – Natalie Graham – Frontiers in Plant Science

Bioinformatics

DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models – Awais Qureshi – BMC Bioinformatics

RP3Net: a deep learning model for predicting recombinant protein production in Escherichia coli – Evgeny Tankhilevich – Bioinformatics

MetaFX: feature extraction from whole-genome metagenomic sequencing data – Artem Ivanov – Bioinformatics

March 3rd ,2026

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Human Microbiome

Early risperidone exposure impairs cognitive function by perturbation of the gut microbiome and bile acids/tyrosine-PTP1B axis – Huaiyu Ye – microbiome

Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum -Chiara Mazzoni – microbiome

Animal Microbiome

Probiotic efficacy of Bacillus amyloliquefaciens TL106 from Tibetan pigs in metabolic syndrome: modulation of gut microbiota and metabolic in sows and suckling piglets – Wangyuan Yao – microbiome

Enhancing the fiber degradation efficiency in dairy cattle rumen through engineered bacterial communities – Jiayi Zhang – microbiome

Gut T cell-microbiota crosstalk orchestrates antibacterial immunity and mucosal homeostasis in teleost – Ming Geng – microbiome

Plant Microbiome

Host-driven evolution shapes the polysaccharide utilization profiles of alga-associated Flavobacteriaceae – Guanjing Cai – microbiome

Ecology-guided Bacillus SynCom from a rice–duckweed core reveals division of labor for concurrent growth promotion and sheath blight suppression – Yingjie Song – microbiome

Mikania micrantha invasion restructures rhizosphere nitrogen cycling through enzyme activation, microbial recruitment, and allelopathic regulation – Ruonan Wang – microbiome

Marine and Aquatic Environmental Microbiome

Reconstruction of coral holobionts and elucidation of the causal relationships among symbiodiniaceae, bacteria, and coral through single-cell raman spectroscopy metabolomics – Yang Shu – microbiome

Unlocking the unexplored AMPSphere in marine rare species – Shen Fan – microbiome

Potential survival strategies of novel comammox and nitrite-oxidizing Nitrospira synthesizing osmoprotectants in a wastewater microbiome treating high-ammonia brackish landfill leachate – Shohei Yasuda – microbiome

Stress-induced enrichment of Pseudomonas sp. stimulates the adaptive response of Auxenochlorella pyrenoidosa and antibiotic-resistant proliferation -Qian Liu – microbiome

Built Environment and Cultural Heritage Microbiome

Unraveling the microbiomes contributing to biodeterioration dynamics of limestone heritage at the Longmen Grottoes archeological site – Xiaoying Zhang – microbiome

February 13, 2026

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Gut microbiome

Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function – H. Krukowski – Nature Microbiology

Baby-to-baby strain transmission shapes the developing gut microbiome – Liviana Ricci – Nature

Animal Microbiome

Microbiome by transcriptome interactions triggered by a switch to an alternative diet in Nellore cattle – Anna Carolina Fernandes – Scientific Reports

Maternal supplementation with rumen-protected arginine reshapes the ileal microbiome and enhances neonatal lamb growth – Xiangjian Peng –  Animal Microbiome

Oral Microbiome

Stimuli-responsive, antimicrobial-loaded nanocarriers for oral biofilm control and microbiome restoration – Ding Chen – International Journal of Oral Science

Modulating the oral microbiome with dental biomaterials: A review of challenges, advances, and future perspectives – Woojin Choi – Biomaterials

Plant Microbiome

Large-scale multi-omics unveils host–microbiome interactions driving root development and nitrogen acquisition – Nannan Li – Nature Plants

Ecological composite fertilizer application enhances wheat yield and optimizes rhizosphere microbial community under reduced fertilization – Yu Wang – Frontiers in Plant Science

Bioinformatics

argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO) – Svetlana Ugarcina Perovic – Bioinformatics

A negative binomial latent factor model for paired microbiome sequencing data – Hyotae Kim – BMC Bioinformatics

January 23, 2026

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Animal microbiome

Bacterial-archaeal co-occurrence in honey bee gut microbiomes across host species and management regimes -Jian-Ping Ying –PLOS ONE

Bacterial community associated with the surface and inside of centipede forcipules: Identification and characterization -Yasutaka Tanaka – PLOS ONE

Human reproductive & urinary microbiome

Vaginal chlorhexidine gluconate versus fluconazole for recurrent vulvovaginal candidiasis: A randomized noninferiority trial – Cathrin Alvendal – PLOS ONE

Infection and transplantation / Host–microbe interactions

DnaK supports intracellular persistence of Staphylococcus xylosus and confers mechanical resilience to a human breast cancer cell line – Lei Ye – PLOS ONE

Investigation of a viable but non-culturable state in Porphyromonas gingivalis and host cell invasion – Adenrele Oludiran – PLOS ONE

Microbial ecology & symbiosis

Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis – Sunnyjoy Dupuis – PLOS ONE

Oral microbiome & animal experiments

Effects of glycyrrhizin on healing and prevention of recurrent aphthous stomatitis in hamster models – Fumie Shiba – PLOS ONE

Plant, soil & ecological microbiome

Tree species-specific strategies of soil aggregation driven by SOC–GRSP coupling under nitrogen addition and precipitation reduction -Mingxin Zhou – PLOS ONE

Microbial genomics & bioremediation

Genomic analysis of Acinetobacter baumannii DUEMBL6 reveals diesel bioremediation potential and biosafety concerns – Nizam Uddin – PLOS ONE

Human gut & inflammatory disease

Identification of hypoxia- and mitophagy-related diagnostic biomarkers for ulcerative colitis based on bioinformatic analysis and machine learning – Zewei Sheng – PLOS ONE

Oral & dental archaeology / Ancient microbiome

Paleo-proteomic analysis of Iron Age dental calculus provides direct evidence of Scythian reliance on ruminant dairy – Jaruschka Pecnik – PLOS ONE

Cancer & clinical oncology

Radiomics profiling combined with clinical risk factors for preoperative lymphatic metastasis prediction in colorectal cancer: A multicenter study – Fangda Guo – PLOS ONE

Toxicology & respiratory health

Potential mechanisms and effects of AFB1-induced asthma: A comprehensive analysis based on network toxicology and molecular docking – Zhiyue Yu – PLOS ONE

Human development & diet (archaeology / isotopes)

Fed the same way? Exploring the influence of breastfeeding, weaning, and childhood diet on adult sex ratios through stable isotope analysis of incremental dentine in Medieval Tuscany – Alessio Amaro – PLOS ONE

January 16, 2026

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Human Microbiome

The testobolome in microbial testosterone metabolism and human health – Liisa Veerus –  
npj biofilms and microbiomes 

Multi-omic definition of metabolic obesity through adipose tissue–microbiome interactions – Rima M. Chakaroun – Nature Medicine

Gut microbiome

The microbiome at the centre of NAD+ supplementation – Youngjae Jo – Nature Metabolism

Meta-analysis of H. pylori and the gut microbiome interactions and clinical outcomes – Xiongjian Wu – Frontiers in Cellular and Infection Microbiology

Environmental Microbiome

High microbial diversity in glacial habitats uncoupled from the specialized microbiomes of resident chironomid fauna – Valeria Lencioni – PLOS One

Bacterial communities show distinctive spatial diversity patterns in productive truffle orchards amended with peat-based substrate – Pedro Marco –  Environmental Microbiome

Plant Microbiome

Root Triterpenoid Metabolites Drive the Assembly and Feedback Regulation of the Rhizosphere Microbiome During Flowering to Senescence in Rhododendron hybridum – Fei Shan – Frontiers in Microbiology

Drought-Tolerant Rhizobacterial Consortia Enhance Grapevine Growth and Tolerance to Water Deficit – Ginevra Canavera – Frontiers in Plant Science

Bioinformatics

Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study – Tanya T. Karagiannis – PLOS Computational Biology

Novel artificial selection method improves function of simulated microbial communities – Bjorn Vessman – PLOS Computational Biology

January 13 , 2026

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Environmental & Wastewater Microbiomes

Viral and eukaryotic drivers of prokaryotic and antibiotic resistance gene diversity in wastewater microbiomes – Antonia Weiss – Springer nature

Correction: Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants – Huifeng Hu – Springer nature

Ruminant & Livestock Gut Microbiomes

The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows – Jianhao Yang – Springer nature

Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation – Moli Li – Springer nature

Rumen microbiota inoculation indicates collaborative mechanisms enhancing propionate supply to alleviate weaning stress in lambs – Tianrong Chen – Springer nature

Host-Associated Gut Microbiomes (Non-Human Models)

Ningxiang pig-derived Enterococcus hirae protects against E. coli-induced gut dysbiosis and inflammation via acetate/propionate-MyD88-NF-κB axis in piglets – Longlin Zhang – Springer nature

Insect & Evolutionary Microbiomes

Gut microbiome convergence and functional adaptation underlie the evolution of predation in stink bugs (Heteroptera Pentatomidae) –Jingjing Sun – Springer nature

December 12, 2025

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Animal microbiome

Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation – Cervantes-Echeverría – PLOS ONE

TTSS-2 virulence drives inflammatory destruction of the gut epithelial barrier and modulates inflammatory response profiles in the Salmonella-infected mouse gut – Enz – PLOS Pathogens

Aspartic protease 2 from Trichinella spiralis excretion/secretion products hydrolyzes tight junctions of intestinal epithelial cells – Long – PLOS NTDs

Endosymbiont hijacking of acylcarnitines regulates insect vector fecundity by suppressing the viability of stored sperm – Weiss – PLOS Genetics

Development and validation of a quantitative real-time PCR assay for enumeration of Clostridium sporogenes in meat products – Schuller – PLOS ONE

Rooting for data: A FAIR research data management environment for Plant-Microbe collaboration – Dröst – PLOS Pathogens (Plant microbiome)

Prolonged starvation deepens quiescence in Vasa2/Piwi1-expressing cells of a sea anemone – Pascual-Carreras – PLOS Biology

Host–microbe interactions / Immunology

Gut bacteria induce heterologous immune priming in Rhodnius prolixus encompassing humoral and cellular responses – Gilliland – PLOS Pathogens

Dietary flavonoids may improve insulin resistance: NHANES + in vitro – Sui – PLOS ONE

Antiviral and immune-modulatory activities of STING agonists in persistent HBV infection – Wang – PLOS Pathogens

Endosymbiont metabolic manipulation affecting insect reproduction – Weiss – PLOS Genetics

Human clinical studies / Metabolism

Effects of risperidone on amino acid metabolism, glucose & kidney function – Oshima – PLOS ONE

Association between Anti-H. pylori IgG and coronary heart disease – Wang – PLOS ONE

Benefits of psychosocial support for adolescent mothers in Uganda – Nakyaze – PLOS ONE

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

Exposure to polystyrene nanoparticles disrupts trophoblast mitochondrial homeostasis – Hao – PLOS ONE

Molecular mechanisms of lipid metabolism abnormalities driving sepsis & atrial fibrillation – Ou – PLOS ONE

Multi-dimensional analysis of global colorectal cancer burden (1990–2021) – Sun – PLOS ONE

Computational / Modeling

Identification of dynamic models of microbial communities – Paredes-Vázquez – PLOS Comp Biol

Accuracy limits of the Lotka–Volterra model in strongly coupled microbial systems – Mustri – PLOS Comp Biol

Plant, soil & ecological microbiome

High-resolution melting assays for discrimination of fungal pathogens in grapevine trunk disease – Azevedo-Nogueira – PLOS ONE

Rooting for data: FAIR data environment for plant–microbe collaboration – Dröst – PLOS Pathogens

Environmental health / Climate / Water

Bridging water, health and climate: A call to action – Hedke – PLOS Water

December 05, 2025

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See you at MVIF next week!

Join us in December for #MVIF 44!We will discuss diverse #microbiome topics:human urinary, gut, oral and nasal microbiomes, extreme environments, anda new sequence alignment tool.

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-11-24T10:34:26.363Z

General microbiome

Consensus Statement: STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies – Julia M. Kelliher – Nature Microbiology

Urinary microbiome

Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection – Michael L. Neugent – NPJ Biofilms and Microbiomes

Thrilled to share that our recent work is out in npj Biofilms and Microbiomes. 🧵 (1/4)www.nature.com/articles/s41…

— Mike Neugent PhD (@mikeneugent.bsky.social) 2025-11-24T17:49:26.272Z

Vaginal microbiome

Microbial and seminal traces of sexual intercourse and forensic implications – Sarah Ahannach – Microbiome

Ambient temperature affects the composition of the vaginal microbiome, and temperature-sensitive vaginal microbes influence assisted reproductive technology outcomes – Zheng Liu –  – Microbiome

Gut microbiome

HGMT: a database of human gut microbiota for tumors and immunotherapy response – Jinxin Liu – Genome Biology

Review: Circadian rhythms as a modulator of gut microbiota-tumor microenvironment crosstalk – Qinglong Xu – Cellular and Molecular Life Sciences

Dynamics of gut metabolome and microbiota maturation during early life – Anna-Katariina Aatsinki – iScience

Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk – Pamela Ferretti – Nature Communications

Animal microbiome

Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function – Omar E. Tovar-Herrera – Nature Ecology & Evolution

Longitudinal changes in gut microbiota across reproductive states in wild baboons – Chelsea A. Southworth – bioRxiv

Probiotic effect of B. subtilis PS-216 in broiler chickens: modulation of weight, feed conversion, short chain fatty acids, microbiota and meat quality – Katarina Šimunović – Animal Microbiome

Animal experiments

The microbial metabolite imidazole propionate modulates hypothalamic activity and stress-induced behaviors – Gulistan Agirman – Cell Host & Microbe

Excited to share new work by Guli Agirman + co that identifies a direct mechanism linking gut microbial imidazole propionate to stress! 🧠🦠 Btw this image was made by Nano Banana Pro 🍌. First time I've gotten a model to accurately generate a science graphic 🤯 authors.elsevier.com/a/1mA5M6t8JE…

— Elaine Hsiao (@pipethero.bsky.social) 2025-11-25T17:45:03.571Z

Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function – Yi Wang – PNAS

Selection and transmission of the gut microbiome alone can shift mammalian behavior – Taichi A. Suzuki – Nature Communications

Postbiotics

Review: Postbiotics as microbial-derived therapeutics for wound healing disorders: from molecular mechanisms to future application – Miroslav Dinić – Home  Cell Communication and Signaling

Phages and viruses

Unveiling the global urban virome through wastewater metagenomics – Nathalie Worp – Nature Communications 

Soil, root and plant microbiome

Rare taxa modulate the emergence of dominants in microbial communities – Jianing Wang – mBio

Integrated effects of anaerobic soil disinfestation and beneficial microbes in strawberry production – Baker D. Aljawasim – PlosOne

Food microbiome

Exploring diversity and functional contribution of the microbiome of traditional Italian dry-cured hams – Giulia Longhi – Current Research in Microbial Sciences

Environmental microbiome

The Microflora Danica atlas of Danish environmental microbiomes – C. M. Singleton – Nature

Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬www.nature.com/articles/s41…

— Morten Kam Dahl Dueholm (@mkddueholm.bsky.social) 2025-12-03T20:50:16.284Z

Bioinformatics

TAGINE: Fast Taxonomy-based Feature Engineering for Microbiome Analysis – Shiri Baum – bioRxiv

Creating unity: linking 16S rRNA gene sequence information to the core taxonomy of genomes – Hilde Vinje – Environmental Microbiome

LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation – Wei Xue – Nature Communications

cFMD v1.3.0 is here! 🚀We're thrilled to announce the release of the latest version of the curatedFoodMetagenomicData (cFMD) github.com/SegataLab/cFMDWhile we're keeping the same core datasets & samples, we've packed this release w/ significant improvements under the hood.1/4

— Segata Lab (@cibiocm.bsky.social) 2025-11-26T13:09:52.484Z

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