Category Archives: General Microbiome

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 30, 2025

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See you next week at MVIF! 

Just announced! #MVIF 39 featuring groundbreaking research on the role of the Nagoya Protocol in protecting microbial diversity through fair use! Don't miss this special event!Sign up now: cassyni.com/s/mvif-391/2

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-04-24T13:46:23.487Z

Skin microbiome

Large-scale skin metagenomics reveals extensive prevalence, coordination, and functional adaptation of skin microbiome dermotypes across body sites – Chengchen Li – bioRxiv

Super thrilled to share our labor of love from the Asian Skin Microbiome Program! We collected >3,500 skin samples, built metagenomic libraries w/ >70 billion reads and >10TB of data to study heterogeneity of the skin microbiome in the general population (200 adults, 18 sites) t.co/ZylbJMpvpw

— Niranjan Nagarajan (@niranjantw.bsky.social) 2025-04-28T04:52:26.147Z

Oral microbiome

Toxic cultures: e-cigarettes and the oral microbial exposome – Michelle Lee-Scott Beverly – npj Biofilms and Microbiomes

Gut microbiome

The gut microbiota promotes pain in fibromyalgia – Weihua Cai – Neuron

Brief antibiotic use drives human gut bacteria towards low-cost resistance – Eitan Yaffe – Nature

Review: Implication of Gut Mycobiome and Virome in Type-2 Diabetes Mellitus: Uncovering the Hidden Players – Mona Kriti – Phenomics

Unravelling the causality between inflammatory bowel disease and polycystic ovary syndrome mediated by gut microbiota and blood metabolism: insights from two prospective cohort studies – Zhaoman Wan – Gut

Animal experiments

Enhanced propionate and butyrate metabolism in cecal microbiota contributes to cold-stress adaptation in sheep – Xindong Cheng – Microbiome

Animal microbiome

Social and environmental predictors of gut microbiome age in wild baboons – Mauna R Dasari – eLife

Effects of parental care on skin microbial community composition in poison frogs – Marie-Therese Fischer – eLife

Food microbiome

The effect of different milk pretreatment methods on microbiome community development during Herrgårds cheese production and ripening – Juan Antonio Rodríguez – bioRxiv

🧀 New preprint drop: adventures in the cheese microbiome! 📝We tracked microbiome dynamics across 14 production steps of industrial Herrgårds cheese (Swedish classic 🇸🇪🧐). http://www.biorxiv.org/cgi/content/…(1/7)

— Juan Antonio Rodríguez (@jrotwitguez.bsky.social) 2025-04-24T07:50:58.839Z

Bioinformatics

Assemblies of long-read metagenomes suffer from diverse errors – Florian Trigodet – bioRxiv

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,www.biorxiv.org/content/10.1…and tell you just a little bit about it in the following 🧵

— Florian Trigodet (@floriantrigodet.bsky.social) 2025-04-28T08:07:49.715Z

Enhanced semantic classification of microbiome sample origins using Large Language Models (LLMs) – Daniela Gaio – bioRxiv

argNorm is published now academic.oup.com/bioinformati…

— Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2025-04-17T04:57:42.847Z

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 11, 2025

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Happy Friday and see you next week at MVIF!

NEXT WEEK don't miss #MVIF 38 on Microbiome and Citizen Science👉https://cassyni.com/s/mvif-38& meet:🇫🇷 @patrickveiga.bsky.social & Mathieu Almeida🇮🇹Claudia Cappello 🇨🇦 @waldispuhl.bsky.social 🇺🇸Daniel McDonald🇺🇸Mikayla A. Borton🇧🇪Sarah Ahannach🇳🇱Saara Suominen🇺🇸 @gilbertjacka.bsky.social

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-04-07T14:59:29.156Z

Gut microbiome

The South American MicroBiome Archive (saMBA): Enriching the healthy microbiome concept by evaluating uniqueness and biodiversity of neglected populations – Benjamin Valderrama – bioRxiv

Excited to share our preprint on the South American MicroBiome Archive (saMBA)! 🌎🦠.We analysed one of the regions with the fewest microbiome samples but some of the highest biodiversities.📄: shorturl.at/Lmvp5 🧵: What did we find—and why? Find out 👇#microbiome #gut-microbiome (1/8)

— Ben Valderrama (@bvalderrama.bsky.social) 2025-04-09T12:50:10.653Z

Microbiome–metabolome dynamics associated with impaired glucose control and responses to lifestyle changes – Hao Wu – Nature Medicine

Gene-by-environment interactions modulate the infant gut microbiota in asthma and atopy – Sara A. Stickley – Journal of Allergy and Clinical Immunology

Mutualistic interactions between Escherichia coli and Bifidobacterium bifidum enable degradation of human milk oligosaccharides in healthy infants – David Seki – bioRxiv

Excited to finally share results from my first post-doc @halllab.bsky.social 🫡E.coli commonly occurs in infant gut microbiota, yet its role during healthy development has been disregarded. In our pre-print, we reveal its fundamental involvement in HMO-degradation.www.biorxiv.org/content/10.1…

— David Seki (@sekid.bsky.social) 2025-04-09T15:12:35.525Z

Delivery Mode Impacts Gut Bacteriophage Colonization During Infancy – Poorani Subramanian – Gut Microbes Report

Our paper on #bacteriophages in the infant gut #microbiome came out earlier this year.This work was a long time coming, and I'm super proud to be first author alongside Suchi Hourigan and Hector Romero Soto of the Clinical Microbiome Unit at NIAID.doi.org/10.1080/2993…

— poorani (@poorani.bsky.social) 2025-04-09T17:08:33.195Z

Animal microbiome

Humpback whales harbor a highly novel and endemic gut microbiome that adapts to periods of fasting during migration – Ryan Bos – bioRxiv

Wild house mice have a more dynamic and aerotolerant gut microbiota than laboratory mice – Eveliina Hanski – BMC Microbiology

Animal experiments

Acute stress enhances synaptic plasticity in male mice via a microbiota-dependent mechanism – Cristina Rosell-Cardona – Neuropharmacology

First paper from my PD at @apcmicrobiomeirel.bsky.social out! 🥳Do you want to know how acute stress enhances synaptic plasticity?Our latest study shows that the gut microbiota is essential.@jfcryan.bsky.social @kjdoriordan.bsky.socialsciencedirect.com/science/article/pii/S0028390825001406?s=08

— Cristina Rosell Cardona (@crosellcardona.bsky.social) 2025-04-05T15:13:41.606Z

Built environment

Assessing microbial diversity in open-pit mining: Metabarcoding analysis of soil and pit microbiota across operational and restoration stages – Priscila Heredia Reto – PlosOne

Bioinformatics

Commentary: Mixing microbiomes in vitro reveals rules of community assembly – Alyssa H. Mitchell and Tami D. Lieberman – PNAS

CoverM: Read alignment statistics for metagenomics – Samuel T N Aroney – Bioinformatics

Excited to introduce the preprint for CoverM: the Swiss Army knife of coverage calculators for metagenomics! 🧬🖥️ DOI: doi.org/10.48550/arX…@benjwoodcroft.bsky.social @viralinstruction.bsky.social @apcamargo.bsky.social

— Samuel Aroney (@aroneys.bsky.social) 2025-01-22T06:11:42.303Z

Investigating statistical power of differential abundance studies – Michael Agronah and Benjamin Bolker – PlosOne

MetaDAVis: An R shiny application for metagenomic data analysis and visualization – Sankarasubramanian Jagadesan and Chittibabu Guda – PlosOne 

Anita & I chatted abt #opensource tools, dbs and **community** around the microbiome science in #OpenSourceDiaries!I mentioned @bioconductor.bsky.social @microbiomevif.bsky.social & @merenbey.bsky.social’s anvi’o & other important tools for microbiome data analysis.www.youtube.com/watch?v=7yii…

— Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2025-04-07T17:17:29.063Z

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 29, 2024

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NEWS: ” Researchers say the social-media platform — an alternative to X — offers more control over the content they see and the people they engage with.” Source: https://www.nature.com/articles/d41586-024-03784-6

INVITATION: MVIF’s last event of the year is coming up! Quick, register now :https://cassyni.com/s/mvif-34
Looking forward to seeing you next week!

It's Wednesday! …and #MVIF 34 program is out! 🤩⭐️MicroTalks: 🇹🇼 Ha T. Doan🇦🇺 Vedanth Ramji⭐️ Keynote: 🇺🇸 Sean Gibbons @gibbological.bsky.social ⭐️Selected talks: 🇯🇵 Yuya Kiguchi🇦🇺 Kurtis Budden🇨🇭 Amit Halkhoree (#Roche)Registration: cassyni.com/s/mvif-34

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2024-11-20T08:57:41.034Z

Citizen science

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

General

Perspective: A framework for understanding collective microbiome metabolism – Matthias Huelsmann – Nature Microbiology 

Thrilled to announce that Matthias Hülsmann's new perspective is now out in @naturemicrobiol.bsky.social! This exciting work is shaping how our group thinks about collective microbiome metabolism. Check it out! http://www.nature.com/articles/s41…

— Microbial Systems Ecology Lab (@micsysecolab.bsky.social) 2024-11-26T12:45:51.587Z

Gut microbiome

Large scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome –  Tatiana Borodovich – bioRxiv

Gut microbiota markers in early childhood are linked to farm living, pets in household and allergy – Annika Ljung – Plos One

Gut physiology and environment explain variations in human gut microbiome composition and metabolism – Nicola Procházková – Nature Microbiology

Today we publish an (in my opinion) important paper in @naturemicrobiol.bsky.social 🍾 showing that gut physiology and environment are factors explaining substantial variations in human gut #microbiome composition and #metabolism🦠Fantastic work Procházková et al. 👏www.nature.com/articles/s41…

— Henrik M. Roager (@hroager.bsky.social) 2024-11-27T10:36:53.274Z

Significant difference in gut microbiota Bifidobacterium species but not Lactobacillus species in colorectal cancer patients in comparison with healthy volunteers using quantitative real-time PCR – Fahime Esfandiari – Plos One

Gut microbiome strain-sharing within isolated village social networks – Francesco Beghini – Nature

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

🥁 New Publication Alert:Our manuscript on the ☕️ and #microbiome relationship is out in #NatureMicrobiology:www.nature.com/articles/s41…1/12

— Segata Lab (@cibiocm.bsky.social) 2024-11-18T11:24:44.554Z

Respiratory microbiome

Insights into respiratory microbiome composition and systemic inflammatory biomarkers of bronchiectasis patients – Aleksandras Konovalovas – Clinical Microbiology

Urinary microbiome

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

Distinct maternofetal immune signatures delineate preterm birth onset following urinary tract infection – Samantha Ottinger – bioRxiv

Glucose alters the evolutionary response to gentamicin in uropathogenic Escherichia coli – Shalini Choudhary – bioRxiv

🚨 New preprint 🚨 With two excellent students Shalini Choudhary and Jacob Smith, we started looking at how the metabolic microenvironment of the urinary tract might affect uropathogenic E. coli evolution and response to antibiotics.www.biorxiv.org/content/10.1…

— Rebecca J Hall (@drrebeccajhall.bsky.social) 2024-11-27T08:11:55.853Z

Animal microbiome

Ileal microbial microbiome and its secondary bile acids modulate susceptibility to nonalcoholic steatohepatitis in dairy goats – Yue Wang – Microbiome

Effects of prebiotic and multispecies probiotic supplementation on the gut microbiota, immune function, and growth performance of weaned piglets – Soimer Omar Baldera Huaman – Plos One

Animal and model experiments

Western diet promotes endometriotic lesion growth in mice and induces depletion of Akkermansia muciniphila in intestinal microbiota – Guillaume Parpex – BMC Medicine 

In vitro validation of colon delivery of vitamin B2 through a food grade multi-unit particle system – R.E. Steinert – Beneficial Microbes

Development of a novel complex inflammatory bowel disease mouse model: Reproducing human inflammatory bowel disease etiologies in mice – Sun-Min Seo – Plos One

Marine microbiome

Applications of marine microbial community models in the nature-based economy – Semidán Robaina-Estévez and Jay Gutiérrez – Plos Sustainability and Transformation

Soil microbiome

Soil microbiomes show consistent and predictable responses to extreme events – Christopher G. Knight – Nature

Bioinformatics

A metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics – Ye Peng- Cell Host & Microbe

Lefser: Implementation of metagenomic biomarker discovery tool, LEfSe, in R – Asya Khleborodova – Bioinformatics

Technique

Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection – Srinithi Purushothaman – Scientific Reports

#microbiome starter pack 1 & 2 by @claesengroup.bsky.social:—-bsky.app/starter-pack…bsky.app/starter-pack…#human #microbiome starter pack by @ruairirobertson.bsky.social:—bsky.app/starter-pack…#MVIF starter pack by @microbiomevif.bsky.social:—-bsky.app/start/did:pl…

— Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2024-11-21T21:55:47.051Z

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