April 3, 2025

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 14, 2025

Happy Friday and see you next week at MVIF 37!

Just announced #MVIF 37 on Microbiomes in Extreme Environments!Don't miss this special event w/our guests🇩🇪 Nicole Dublier🇳🇱 Henk Bolhuis🇺🇸 Rachael Morgan-Kiss 🇺🇸 Kasthuri Venkateswaran 🇮🇹 Fabiana Canini 🇺🇸 Diana Ayala-Muñoz🇮🇹 Luca Tonietti cassyni.com/s/mvif-37

Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-03-06T14:14:27.441Z

Women’s health

Vaginal microbiota changes during a natural menstrual cycle in the Women4Health cohort highlights specific features of the Italian population – Elena Vinerbi – bioRxiv

Review: Menopausal shift on women’s health and microbial niches – Maria R. Nieto – npj Women’s Health

1/ 🚨 🧪New Research: #Menopause, #Microbiome & #WomensHealth Menopause reshapes health through hormonal, microbial, and physiological changes. 🧪📖 Explore the study: rdcu.be/d5725⬇️ Let’s dive into the key insights:

Aurea Simon-Soro (@aureasimon-soro.bsky.social) 2025-01-23T12:57:47.907Z

Gut microbiome

Review: The gut microbiota-immune-brain axis: Therapeutic implications – Kenneth J. O’Riordan – Cell Reports Medicine

Effects of oral supplementation of probiotics on body weight and visceral fat in obese patients: a meta-analysis and systematic review – Manhou Guo – Scientific Reports

Longitudinal phage–bacteria dynamics in the early life gut microbiome – Michael J. Tisza – Nature Microbiology 

Skin microbiome

Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers – Deepan Thiruppathy – Microbiome 

Animal experiments

Maternal undernutrition exacerbates microbiota-driven growth stunting through pre and postnatal effects – Yadeliz A. Serrano Matos – bioRxiv

Excited to share my lab's latest preprint and very proud of the whole team for their hard work. Check it out if you're interested in the #microbiome #maternalhealth or #undernutrition. http://www.biorxiv.org/content/10.1…

Carrie Cowardin (@ccowardin.bsky.social) 2025-03-10T13:21:21.537Z

Animal microbiome

Rumen microbiome associates with postpartum ketosis development in dairy cows: a prospective nested case–control study – Fanlin Kong – Microbiome 

Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide – Ostaizka Aizpurua – Molecular Ecology

Endometrial microbiome in mares with and without clinical endometritis – Lulu Guo – bioRxiv

Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly – Lílian Caesar – bioRxiv

New preprint out! 🐝🦠 Among the incredible diversity of bees, only a few have evolved a highly social lifestyle—honey bees and stingless bees (Apidae). We characterize for first time, using metagenomics/microbial experiments, the microbiome of a stingless bee colony

Lilian Caesar (@liliancaesar.bsky.social) 2025-03-11T08:00:43.662Z

Food microbiome

The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics – Samuel Breselge – Communications Biology

Fantastic to see this comprehensive study of water kefir pangenomes, led by Samuel Breselge, now published “The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics". @teagasc.bsky.social @apcmicrobiomeirel.bsky.social rdcu.be/ec7GT

Paul Cotter (@pauldcotter.bsky.social) 2025-03-11T20:35:16.288Z

Antimicrobial resistance

Effects of cigarette-derived compounds on the spread of antimicrobial resistance in artificial human lung sputum medium, simulated environmental media and wastewater – Peiju Fang – Environmental Health Perspectives

🚬🧬🚬🧬🚬🧬Proud to present the newest study of my PhD students Peiju and Diala in Environmental Health PerspectivesEffects of cigarette-derived compounds on the spread of #AMR in artificial human lung sputum medium, simulated environmental media and wastewaterdoi.org/10.1289/EHP1…1/9#microsky

Uli Klümper (@ulikluemper.bsky.social) 2025-03-04T15:03:48.183Z

Drinking water plumbing systems are a hot spot for antimicrobial resistant pathogens – Claire Hayward – Journal of Hospital Infection

DRAMMA: a multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data – Ella Rannon – Microbiome

Bioinformatics

LEMMIv2: Benchmarking Framework for Metagenomic and 16S Amplicon Profilers with a Catalogue of Evaluated Tools – M. Seppey – bioRxiv 

A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights – Jun Hyung Cha – bioRxiv

Microbial network inference for longitudinal microbiome studies with LUPINE – Saritha Kodikara, Kim-Anh Le Cao – Microbiome

Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases – Ekaterina Avershina – Microbiome

🥁We are happy to announce the release of a new version of curatedFoodMetagenomicData (cFMD)🔗 Get it here: github.com/SegataLab/cFMD🧵👇1/5

Segata Lab (@cibiocm.bsky.social) 2025-03-12T13:56:24.948Z

March 2, 2025

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

Human/General Microbiome

Gastrointestinal Tract

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

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

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

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

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

Skin

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

Oral – Respiratory Tract

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

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

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

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

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

Other Sites

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

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

Beneficial Microbes and Compounds

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

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

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

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

Environmental Microbiome / Ecology

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

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

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

Microbiome Analysis: Resources, Tools and Techniques

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

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

February 14, 2025

Check out my list of selected latest microbiome studies and see you next week at #MVIF!

It's Friday! …and a new #MVIF program is out! 🤩Registration here: cassyni.com/s/mvif-36⭐️ MicroTalks:🇯🇵 Nodoka Chiba 🇮🇩 Patsy Tasyana Fitri⭐️ Keynote: 🇯🇵 Ruixin Liu⭐️ Selected talks: 🇦🇺 @aroneys.bsky.social 🇬🇧 Maria Kardakova🇦🇺 Theo Portlock

Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-02-07T12:39:31.099Z

Gut microbiome

Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses – Puspendu Sardar – Nature Microbiology 

Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome – Nicholas Pucci – PeerJ

Though it's already a weeks ago, the newest paper from the (old) lab came out.We explored the drivers of Bifidobacterium longum subspecies dynamics in the infant gut in detail. Still fascinated by the interplay of ecology, metabolic capacity and dietpeerj.com/articles/186…

Daniel Mende (@pangenomics.bsky.social) 2025-02-12T06:54:25.656Z

Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition – Maria Luisa Savo Sardaro – Nutrients

Long-term yogurt intake and colorectal cancer incidence subclassified by Bifidobacterium abundance in tumor – Satoko Ugai – Gut Microbes

From sporulation to village differentiation: the shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia – Clarissa A. Febinia – bioRxiv

Urinary microbiome

The urinary microbiome in association with diabetes and diabetic kidney disease: A systematic review – Tiscar Graells – PlosOne

Vaginal microbiome

Quantitative profiling of the vaginal microbiota improves resolution of the microbiota-immune axis – Eric Armstrong – Microbiome

Migration and standing variation in vaginal and rectal yeast populations in recurrent vulvovaginal candidiasis – Abdul-Rahman Adamu Bukari – bioRxiv

Skin microbiome

A human skin microbiome reference catalog and the skin microbial landscape of plateau adults – Yi Liu – iMetsOmics

Animal microbiome

Exploring the impact of grazing on fecal and soil microbiome dynamics in small ruminants in organic crop-livestock integration systems – Sejin Cheong – PlosOne

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

Animal experiments

A gut-on-a-chip incorporating human faecal samples and peristalsis predicts responses to immune checkpoint inhibitors for melanoma – Mattia Ballerini – Nature Biomedical Engineering

Early-life gut mycobiome core species modulate metabolic health in mice – Mackenzie W. Gutierrez – Nature Communications

Microbiota governs host chenodeoxycholic acid glucuronidation to ameliorate bile acid disorder induced diarrhea – Zishen Lin – Microbiome

The bacterial microbiome modulates the initiation of brain metastasis by impacting the gut-to-brain axis – Matteo Massara – iScience

Excited to share a new paper from our lab 😀We investigate the tumor microenvironment – to reveal factors influencing cancer progression & therapy response 🔬🧪So we naturally wanted to ask – does the gut #microbiome influence brain #metastasis 🦠 🧠?Massara et al 2025www.cell.com/iscience/ful…

Johanna Joyce (@johannajoyce.bsky.social) 2025-02-10T14:03:22.248Z

Bacterial community assembly of specific pathogen-free neonatal mice – Elizabeth A. Kennedy – Microbiome

Antibiotic-associated changes in Akkermansia muciniphila alter its effects on host metabolic health –Yumin Han – Microbiome

Fecal microbiota transplantation modulates jejunal host-microbiota interface in weanling piglets – Shankumar Mooyottu – Microbiome

Bacterial profiles of the oral, vaginal, and rectal mucosa and colostrum of periparturient sows – Virpi Piirainen – PlosOne

Plant microbiome

Comparative analysis of grape berry microbiota uncovers sour rot associates from a Maryland vineyard – Blaise Jumbam – PlosOne

Drinking water microbiome

Building plumbing influences the microdiversity and community assembly of the drinking water microbiome – Huanqi He – Water Research

Bioinformatics

Intraspecies associations from strain-rich metagenome samples – Evan B. Qu – bioRxiv

Excited to share my preprint describing a new microbiome analysis method, PHLAME, for detecting strain-level associations in difficult sample types. 🧵www.biorxiv.org/content/10.1…This work was done with my great coauthors and my amazing advisor @contaminatedsci.bsky.social

Evan Qu (@quevan.bsky.social) 2025-02-11T23:06:43.624Z

Techniques

De-biasing microbiome sequencing data: bacterial morphology-based correction of extraction bias and correlates of chimera formation – Luise Rauer – Microbiome

Internships

Outreachy–a 3 month paid internship in open source and open science–applications for the June 2025 cohort are ongoing.

It was an awesome #Outreachy chat! Thanks for all your (detailed) questions, hope I answered them all…Recording available here: I enjoyed it a lot!www.youtube.com/live/PiOm6nq…

Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2025-02-05T16:46:07.001Z

January 17, 2025

Starting the new year with a new digest out, full of interesting findings.
Check it out and see you at MVIF next week!

It's a new year! …and a new #MVIF program is out! 🤩Registration here: cassyni.com/s/mvif-35⭐️MicroTalks: Minna Chang@hariszaf.bsky.social⭐️ Keynote: @chmoei.bsky.social⭐️Selected talks: Pratyay Sengupta@fatimacpereira.bsky.social@cladigar.bsky.social

Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-01-08T14:53:12.804Z

Human gut microbiome

Early life microbial succession in the gut follows common patterns in humans across the globe – Guilherme Fahur Bottino – Nature Communications 

Epigenetic phase variation in the gut microbiome enhances bacterial adaptation – Mi Ni – bioRxiv 

Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals – Gloria Fackelmann – Nature Microbiology 

Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations – Qi Yin – Nature Microbiology

Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: http://www.nature.com/articles/s41… @naturemicrobiol.bsky.social

Alexandre Almeida (@alexmsalmeida.bsky.social) 2025-01-10T10:06:52.895Z

Interconnected pathways link faecal microbiota plasma lipids and brain activity to childhood malnutrition related cognition – T. Portlock – Nature Communications

Environmental microbiome, human fungal pathogens, and antimicrobial resistance – Zhen-Zhen Yan – Trends in Microbiology

An RNase III–processed sRNA coordinates sialic acid metabolism of Salmonella enterica during gut colonization – Ziying Chen – PNAS

Happy to share our latest work published in @pnas.org In collaboration with @yjchao.bsky.social , we uncovered an RNase III-processed sRNA, ManS, that orchestrates sialic acid metabolism in Salmonella enterica during gut colonization.Link: doi.org/10.1073/pnas…

Chuan Wang (@chuanwangfdu.bsky.social) 2025-01-11T10:54:15.040Z

Metagenome-guided culturomics for the targeted enrichment of gut microbes – Jeremy Armetta – Nature Communications

The gut microbiota-SCFA-inflammation axis in patients with AECOPD – Hengjing Zhu – PlosOne

Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study – Gertrude Ecklu-Mensah – Scientific Reports

Vaginal microbiome

Cervicovaginal microbiome and natural history of Chlamydia trachomatis in adolescents and young women – Mykhaylo Usyk – Cell

Nasal microbiome

Nasal microbiota predictors for methicillin resistant Staphylococcus colonization in critically ill children – Kathleen Zani – PlosOne

Animal experiments

Fecal Microbiota Transplantation (FMT) From a Human at Low Risk for Alzheimer’s Disease Improves Short-Term Recognition Memory and Increases Neuroinflammation in a 3xTg AD Mouse Model – Claire Chevalier – Genes, Brain and Behavior 

Short-chain fatty acid metabolites propionate and butyrate are unique epigenetic regulatory elements linking diet, metabolism and gene expression – Michael Nshanian – Nature Metabolism

The efficacy of Lacticaseibacillus paracasei MSMC39-1 and Bifidobacterium animalis TA-1 probiotics in modulating gut microbiota and reducing the risk of the characteristics of metabolic syndrome: A randomized, double-blinded, placebo-controlled study – Wongsakorn Luangphiphat – PlosOne

Animal microbiome

Microbiota assembly of specific pathogen-free neonatal mice – Elizabeth Kennedy – bioRxiv

Organ-Specific Microbiomes of Biomphalaria Snails – Lauren V Carruthers – bioRxiv

Approaching the sterile womb theory in dogs and cats: A multi-technique investigation – Penelope Banchi – Theriogenology

Altered microbiome and metabolome profiling in fearful companion dogs: An exploratory study – Luigi Sacchettino – PlosOne

Bioinformatics

microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data – Engy Nasr – bioRxiv 

Our new preprint "microGalaxy: A gateway to tools, workflows, and training for accessible, reproducible, and FAIR microbial data analysis" is live! 🎉 📝 Read it here: http://www.biorxiv.org/content/10.1…#Microbiome #FAIRdata #usegalaxy @galaxyproject.bsky.social

Bérénice Batut (@bebatut.bsky.social) 2025-01-08T12:16:20.185Z

Podcasts

I’ve been regularly updating this repo https://github.com/SvetlanaUP/Microbiome-etc-Podcasts with podcasts related to microbiome science: science, microbiology and bioinformatics. If I missed your favorite one, feel free to add it. Thanks!

I co-host The Bioinformatics Lab podcast with @kevinlibuit.bsky.social and the other day we had a great chat about our job hunting experiences, the importance of professional networks and making genuine connections. Its on all the podcasting apps & youtube soundcloud.com/the_bioinfor…

Andrew Page (@andrewjpage.bsky.social) 2025-01-14T11:33:40.738Z

December 10, 2024

General microbiome

[COMMENT]The role of pharmacomicrobiomics in HIV prevention, treatment, and women’s health – Swanson, Basting & Klatt

Early life

Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy – Roth et al. – Nutrients

Human gut microbiome

[REVIEW]A systematic review of the relationship between gut microbiota and prevalence of pancreatic diseases – Jankowski, Fichna & Tarasiuk-Zawadzka – Microbial Pathogenesis

Beneficial microbiome and diet interplay in early-onset colorectal cancer – Zhou et al. – EMBO Molecular Medicine

Age-stratification reveals age-specific intestinal microbiota signatures in juvenile idiopathic arthritis – Budzinski et al. – Molecular and Cellular Pediatrics

[PREPRINT]Human gut archaea collection from Estonian population – Pantiukh & Org – bioRxiv

Analysis of early childhood intestinal microbial dynamics in a continuous-flow bioreactor – Granato et al. – Microbiome

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Increase in body weight is lowered when mice received fecal microbiota transfer from donor mice treated with the AT1 receptor antagonist telmisartan – Freschi et al. – Frontiers in Pharmacology

Plant, root, and soil microbiome

Interaction between root exudates and PFOS mobility: Effects on rhizosphere microbial health in wetland ecosystems – Lu et al. – Environmental Pollution

[PREPRINT]The activity of soil microbial taxa in the rhizosphere predicts the success of root colonization – Harris et al. – bioRxiv

[PREPRINT]Fertilization impacts microbiomes along the grassland trophic chain – Jetter et al. – bioRxiv

Waste

Shallow shotgun sequencing of healthcare waste reveals plastic-eating bacteria with broad-spectrum antibiotic resistance genes – Siew et al. – Environmental Pollution

Bioinformatics

EURYALE: A versatile Nextflow pipeline for taxonomic classification and functional annotation of metagenomics data – Cavalcante et al. – IEEE Xplore
EURYALE

[PREPRINT]MCSPACE: inferring microbiome spatiotemporal dynamics from high-throughput co-localization data – Uppal et al. – bioRxiv

December 6, 2024

Gut Microbiome

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

Animal experiments 

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

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

Oral and respiratory microbiomes

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

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

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

Plant and environmental microbiomes

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

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

Bioinformatics

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

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

November 29, 2024

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

Human and General Microbiome

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Animal Model Microbiome

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

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

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

Animal Microbiome

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

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

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

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

Plant Microbiome

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

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

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

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

Environmental Microbiome

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

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

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

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

Viruses

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

Microbiome Analysis

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

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

November 17, 2024

Human and General Microbiome

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

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

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

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

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

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

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

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

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

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

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

Beneficial Microbes and Compounds

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

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

Animal Models

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

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

Non-Model Animal Microbiome

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

Plant and Soil Microbiome

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

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

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

Environmental Microbiome

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

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

Other Microbes

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

Microbiome Analysis: Tools, Procedures and Resources

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

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

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

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