Category Archives: Events and jobs

March 14, 2025

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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

February 14, 2025

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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

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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

October 4, 2024

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Happy Friday! And see you next week at MVIF!

Plastisphere microbiome

What harmful microbes are lurking in the world’s 7 billion tonnes of plastic waste? – Changchao Li – Nature

Respiratory microbiome

Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis – Hongbin Chen – npj Biofilms and Microbiomes

Vaginal microbiome

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

Oral microbiome

The intensive physical activity causes changes in the composition of gut and oral microbiota – Szymon Urban – Scientific Reports
⚽ “Twenty professional football players and twelve amateurs were invited to the study groups.”

Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome – Yuya Kiguchi – bioRxiv

The association between mode of childbirth delivery and early childhood caries: A comprehensive systematic review and meta-analysis – Li Xiang – PlosOne

Gut microbiome

What’s GABA got to do with it? A potential link between the microbiome, schizophrenia, and the endo-cannabinoid system – Ayala Glinert – Psychiatry Research

Changes in intestinal permeability and gut microbiota following diet-induced weight loss in patients with metabolic dysfunction-associated steatohepatitis and liver fibrosis – Dimitrios A. Koutoukidis – Gut Microbes

Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis – Yan Jia – Scientific Reports

Detailed Analysis of Prebiotic Fructo- and Galacto-Oligosaccharides in the Human Small Intestine – Mara P. H. van Trijp – Journal of Agricultural and Food Chemistry

Dietary fibers boost gut microbiota-produced B vitamin pool and alter host immune landscape – Erica T. Grant – Microbiome

Human milk microbiome

Maternal HIV infection and the milk microbiome – Nicole H. Tobin – Microbiome

Viruses and phages

Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens – Mihály Koncz – Cell

Animals

Differential interactions of Rickettsia species with tick microbiota in Rh. sanguineus and Rh. turanicus – Apolline Maitre – Scientific Reports 

Animal experiments

Disruption of the intestinal clock drives dysbiosis and impaired barrier function in colorectal cancer – Rachel C. Fellows – Science Advances

Photoperiod effects on corticosterone and seasonal clocks in cafeteria-induced obese fischer 344 rats are influenced by gut microbiota – Verónica Arreaza-Gil – Scientific Reports 

Plant, root, soil microbiome

Closing the gap: examining the impact of source habitat proximity on plant and soil microbial communities in post-mining spoil heap succession – Lenka Mészárošová – Frontiers in Microbiology

Bacterial Communities from the Antique Roman City of Carnuntum (Austria):16S r-RNA-Based Comparison of Soil Samples from Different Archaeological Horizons – Johann Michael Köhler – preprints

Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient – Viviana Freire-Zapata – Nature Microbiology

Phosphorus availability influences disease-suppressive soil microbiome through plant-microbe interactions – Yifan Cao – Microbiome

Plant diversity drives positive microbial associations in the rhizosphere enhancing carbon use efficiency in agricultural soils – Luiz A. Domeignoz-Horta – Nature Communications

Bacterial diversity of cantaloupes and soil from Arizona and California commercial fields at the point of harvest – Madison Goforth – Plos One

Drinking water microbiome

Making waves: From tap to gut- exploring the impact of drinking water on gut microbiota – Hanieh Shakeri Moghaddam – Water Research

Bioinformatics

Taxometer: Improving taxonomic classification of metagenomics contigs – Svetlana Kutuzova – Nature Communications

Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences – Yasas Wijesekara – bioRxiv

Emergent ecological patterns and modelling of gut microbiomes in health and in disease – Jacopo Pasqualini – Plos Computational Biology

Technique

Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing – Harry T. Child – Access Microbiology

Microbial community interactions on a chip – Duane S. Juang – PNAS

September 13, 2024

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Happy Friday!
And, see you next week at the MVIF and African Microbiome Day events!

Human microbiome

Gut Microbiome

Transient colonizing microbes promote gut dysbiosis and functional impairment – Sunjae Lee – npj Biofilms and Microbiomes

Cataloging metagenome-assembled genomes and microbial genes from the athlete gut microbiome – Laura Wosinska – Microbiome Research Reports

Gut microbiome and schizophrenia: insights from two-sample Mendelian randomization – Keer Zhou – Schizophrenia

Disease-associated microbiome signature species in the gut – Junhui Li – PNAS Nexus

Nasal microbiome

E-Cigarette Use, Cigarette Smoking, and Sex Are Associated With Nasal Microbiome Dysbiosis Get access Arrow – Elise Hickman – Nicotine & Tobacco Research

Urinary microbiome

Review: Synthesis of current pediatric urinary microbiome research – Layla M. Jeries – Frontiers in Pediatrics

Skin microbiome

The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival – Philipp Licht – npj Biofilms and Microbiomes

Animal microbiome

Antibiotics damage the colonic mucus barrier in a microbiota-independent manner – Jasmin Sawaed – Science Advances

Host diet drives gut microbiome convergence between coral reef fishes and mammals – Samuel Degregori – Molecular Ecology

Functional insights into the effect of feralisation on the gut microbiota of cats worldwide – Ostaizka Aizpurua – bioRxiv

Animal experiments

Diet-microbiome interactions promote enteric nervous system resilience following spinal cord injury – Adam M. Hamilton – npj Biofilms and Microbiomes

Ketogenic interventions restore cognition and modulate peripheral metabolic dysfunctions in Alzheimer’s disease mouse models – Paule E. H. M’Bra – bioRxiv

Plant microbiome

The influence of plant traits on soil microbial communities varies between arid and mesic grasslands – Eleonora Egidi – Plant and Soil

Enrichment of novel entomopathogenic Pseudomonas species enhances willow resistance to leaf beetles – Haitao Wang – Microbiome

Microbial colonisation rewires the composition and content of poplar root exudates, root and shoot metabolomes – F. Fracchia – Microbiome

Built environment

Predicting how varying moisture conditions impact the microbiome of dust collected from the International Space Station – Nicholas Nastasi – Microbiom

The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches – Kenneth Wasmund – Environmental Microbiology

Bioinformatics

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

June 7, 2024

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Today’s digest features AMPSphere, Candida pathogenesis, rhizosphere microbiome in the Himalayas, imaging of oral microbiome, and more.
See you at #MVIF special event on women’s health!

Global microbiome

Discovery of antimicrobial peptides in the global microbiome with machine learning – Célio Dias Santos-Júnior and Marcelo D.T. Torres – Cell

Bioenergetic mapping of ‘healthy microbiomes’ via compound processing potential imprinted in gut and soil metagenomes – Craig Liddicoat – Science of The Total Environment

Infant microbiome

The impact of perinatal maternal stress on the maternal and infant gut and human milk microbiomes: A scoping review protocol – Niamh Ryan – Plos One

Oral microbiome

Improved Visualization of Oral Microbial Consortia – S.T. Ramirez-Puebla – Journal of Dental Research

Animal microbiome

Changes of faecal bacterial communities and microbial fibrolytic activity in horses aged from 6 to 30 years old – Marylou Baraille – Plos One

Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization – Ke Zhang – Microbiome

Animal experiments

Bacteroides uniformis CECT 7771 requires adaptive immunity to improve glucose tolerance but not to prevent body weight gain in diet-induced obese mice – Marina Romaní-Pérez – Microbiome

The impact of microplastics polystyrene on the microscopic structure of mouse intestine, tight junction genes and gut microbiota – Qi-Ling Su – Plos One

Epithelial hypoxia maintains colonization resistance against Candida albicans – Hannah P. Savage – Cell Host & Microbe

Viruses and phages

Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs – Jun Hu – Microbiome

Water microbiome

Deep long-read metagenomic sequencing reveals niche differentiation in carbon cycling potential between benthic and planktonic microbial populations – Tomeu Viver – bioRxiv

Root, soil, plant microbiome

Altitude-Dependent Influence of Artemisia brevifolia on its Rhizosphere Microbiome in Ladakh Region of the Western Himalayas – Manzoor Hussain – Rhizosphere

Bioinformatics

Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet – Nicolae Sapoval – bioRxiv

Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion – Xiaofan Jin – bioRxiv

May 17, 2024

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Today’s digest features bioinformatics binning methods, healthy dogs, lakes in South Africa, and more. For the human gut microbiome studies, check out the latest digest (May 15, 2024) by Grace Deitzler.

See you at #MVIF!

Skin microbiome

Intraspecies warfare restricts strain coexistence in human skin microbiomes – Christopher P. Mancuso – bioRxiv

Oral microbiome

Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study – Memduh Bingöl – Journal of Clinical Periodontology

Urinary microbiome

Microbroth dilution method for antibiotic susceptibility testing of fastidious and anaerobic bacteria of the urinary microbiome – Wilson Geaman – Microbiology Spectrum

Respiratory tract

Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease – Nick Quinn-Bohmann – BMC Biology

Food microbiome

Microbial community structure of plant-based meat alternatives – Franz-Ferdinand Rochn – pj Science of Food

Plan, root, soil

Functional team selection: a framework for local adaptation in plants and their belowground microbiomes – Nancy Collins Johnson and César Marín – ecoevoRxiv

Life on the edge: microbial diversity, resistome, and virulome in soils from the Union Glacier cold desert – Patricio Arros – bioRxiv

Animal microbiome

Microbiota of healthy dogs demonstrate a significant decrease in richness and changes in specific bacterial groups in response to supplementation with resistant starch, but not psyllium or methylcellulose, in a randomized cross-over trial – Silke Salavati Schmitz – Access Microbiology

Early-life factors shaping the gut microbiota of Common buzzard nestlings – Hugo Pereira – Animal Microbiome

Animal experiment

13C-Stable isotope resolved metabolomics uncovers dynamic biochemical landscape of gut microbiome-host organ communications in mice – Xia Xiao – Microbiome

Water microbiome

Metagenomics datasets of water and sediments from eutrophication-impacted artificial lakes in South Africa – Grace Nkechinyere Ijoma – Scientific Data

Bioinformatics

Fairy: fast approximate coverage for multi-sample metagenomic binning – Jim Shaw and Yun William Yu – bioRxiv

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods – Daniel M Portik – biorXiv

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level – Amy S Graham – bioRxiv

Full factorial construction of synthetic microbial communities – Juan Diaz-Colunga – bioRxiv

ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences – Yao Pei – Microbiome

February 23, 2024

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Today’s digest features the MetaPhlAn v4.1 & viral module, early life gut microbiome and diabetes, human milk oligosaccharides study, and more.

NEWS
MVIF has launched their crowdfunding campaign https://www.gofundme.com/f/me-mvif

See you at #MVIF next week!

Oral microbiome

Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases – Davide Bazzani – npj Biofilms and Microbiomes

Nasal microbiome

Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability – Y Zhao – bioRxiv

Semen microbiome

Characterisation and comparison of semen microbiota and sperm function in men with infertility, recurrent miscarriage, or proven fertility – Shahriar Mowla – bioRxiv

Gut microbiome

CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei – Sivan Kijner – Nature Communications

Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study – Kinga Humińska-Lisowska – Plos One

The impact of iron supplementation on the preterm neonatal gut microbiome: A pilot study – Matthew VanOrmer – Plos One

Early-life exposures to specific commensal microbes prevent type 1 diabetes – Jamal Green – bioRxiv

Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing – Philipp Spohr – Scientific Reports

Donor-recipient intermicrobial interactions impact transfer of subspecies and fecal microbiota transplantation outcome – Qiyi Chen – Cell Host & Microbe

Animal experiment

The gut ileal mucosal virome is disturbed in patients with Crohn’s disease and exacerbates intestinal inflammation in mice – Zhirui Cao – Nature Communications

Animal microbiome

Gut microbiome diversity and function during hibernation and spring emergence in an aquatic frog – Ji-Eun Lee – Plos One

Unraveling the gut microbiota of Tibetan chickens: insights into highland adaptation and ecological advantages – Tao Zeng – bioRxiv

Water microbiome

A difficult coexistence: resolving the iron-induced nitrification delay in groundwater filters – Francesc Corbera-Rubio – bioRxiv

Human virome

Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples – Moreno Zolfo – bioRxiv

January 8, 2024

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The microbiome digest team, Juan Pablo Cardenas Astudillo, Axel Künstner and Svetlana Ugarcina Perovic (it’s me), wishes you happy and healthy 2024! Also, we wish to have more members in our team in order to cover all daily microbiome science news: if you are interested in reviewing microbiome papers at your convenience (with our support!) and digest them for the community, feel free to contact us. We are happy to welcome you!

And, yes, see you at MVIF #25!

Vaginal microbiome

Vaginal Lactobacillus fatty acid response mechanisms reveal a novel strategy for bacterial vaginosis treatment – Meilin Zhu – bioRxiv

Gut microbiome

BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen – Brantley Hall – Nature Microbiology

Influence of feeding practices in the composition and functionality of infant gut microbiota and its relationship with health – Misael Martínez-Martínez – PlosOne

Mucin-degrading gut bacteria promote anti-parasitic immunity – Mathis Wolter – bioRxiv

Host genetic regulation of human gut microbial structural variation – Daria V. Zhernakova – Nature

Animal microbiome

Deciphering the gut microbiome of grass carp through multi-omics approach – Ming Li – Microbiome

Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus – Chloe G. Shaw – BMC Microbiology

Animal experiments

Desulfovibrio vulgaris interacts with novel gut epithelial immune receptor LRRC19 and exacerbates colitis – Runxiang Xie – Microbiome

Individualized microbiotas dictate the impact of dietary fiber on colitis sensitivity – Erica Bonazzi – Microbiome

A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice – Rachel M. Bleich – Microbiome

Environmental microbiome

A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes – Victor Borin Centurion – Environmental Microbiome

Plant, root, soil microbiome

Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet – Abdelrahman Alahmad – Microbiome

Methods

mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome – Lei Cao – Nature Methods

Bioinformatics

A catalogue of small proteins from the global microbiome – Yiqian Duan – bioRxiv

December 15, 2023

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Today’s digest features house mice gut microbiome, infant gut DNA bacteriophage strain persistence, maternal gut microbiome in pregnancy, and more.

Do not miss Francine Marques’s opinion on rethinking culture to unlock the potential of research.

See you at #MVIF next week!

Respiratory microbiome

Review: Winds of change a tale of: asthma and microbiome – David Galeana-Cadena – Frontiers in Microbiology

Gut microbiome

Review: The maternal gut microbiome in pregnancy: implications for the developing immune system – Omry Koren – Nature Reviews Gastroenterology & Hepatology

Bioactive glycans in a microbiome-directed food for children with malnutrition – Matthew C. Hibberd – Nature

Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients – Zixuan Xie – Microbiome

Gut microbiota-related metabolite alpha-linolenic acid mitigates intestinal inflammation induced by oral infection with Toxoplasma gondii – Jing Yang – Microbiome

Fiber-deficient diet inhibits colitis through the regulation of the niche and metabolism of a gut pathobiont – Peter Kuffa – Cell Host & Microbe

Animal microbiome

Subspecies divergence, hybridisation and the spatial environment shape phylosymbiosis in the microbiome of house mice – Susana C. M. Ferreira – bioRxiv

Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers – Gilles L. C. Baud – Genome Biology

Seasonal and environmental factors contribute to the variation in the gut microbiome: a large-scale study of a small bird – Martta Liukkonen – bioRxiv

Plant-Root-Soil microbiome

Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota – Nathan Vannier – Nature Communications

Virome

Infant gut DNA bacteriophage strain persistence during the first 3 years of life – Yue Clare Lou – Cell Host & Microbe

Techniques

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities – Patrick Müller – Nature Protocols

Bioinformatics

MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes – James P.J. Chong – bioRxiv