Category Archives: Plant Root Soil microbiome

November 21, 2025

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prepared by Bugembe Allan

Human gut microbiome

Effects of ascorbic acid on intestinal flora and metabolites of C57 mice exposed to formaldehyde in the digestive tract – Xin Ling – PLOS ONE

Consumption of non-sugar sweeteners by Brazilian adolescents and adults in 2017–2018: Socioeconomic distribution and food sources – Luisa Gazola Lage – PLOS ONE

The impact of day care attendance on antibiotic use among children aged 0–12 years: A population-based register study – Tapio Räsänen – PLOS ONE

Continuous Glucose Monitoring under standardised conditions regarding diet, exercise and stress in Healthy Young People (CGM-HYPE study) – Florian Kinny – PLOS Digital Health

Animal microbiome

Triadic relationships between pasture exposure, gastrointestinal parasites, and hindgut microbiomes in grazing lambs – Jack Jefferson – PLOS ONE

Prevalence and antimicrobial resistance of multidrug-resistant Staphylococcus epidermidis from raw milk of dairy cattle and ewes – Inamullah – PLOS ONE

Fate of Trypanosoma cruzi in bed bugs after oral ingestion or intrathoracic injection – Sanam Meraj – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Salmonella enterica exploits the auxin signaling pathway to overcome stomatal immunity – Brianna Fochs – PLOS Pathogens

Microbial Ecology

Bacterial immune systems as causes and consequences of microbiome structure – Rafael Custodio – PLOS Biology

Human respiratory microbiome

Non-canonical metatranscriptomic analysis of COVID-19 and Dengue reveals an expanded microbial and AMR landscape in COVID-19 mortality patients – Aanchal Yadav – PLOS Pathogens

Metagenomics & Bioinformatics

tvsfglasso: Time-varying scale-free graphical lasso for network estimation from time-series data – Markku Kuismin – PLOS Computational Biology

Quantifying microbial interactions based on compositional data with generalized Lotka-Volterra equations – Yue Huang – PLOS Computational Biology

Water microbiome

Diverse biophysical and molecular mechanisms drive phytoplankton sinking in response to starvation – Yanqi Wu – PLOS Biology

Phages & Viruses

ATG-3 limits Orsay virus infection in C. elegans and regulates collagen pathways – Gowri Kalugotla – PLOS Pathogens

Animal experiments

Antioxidant and antidiabetic effects of Angylocalyx oligophyllus leaves aqueous extract in pregnant diabetic rats – Christian Tenezogang Takoukam – PLOS ONE

October 24, 2025

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Gut & Human Microbiome

The microbiome and gut–lung axis in nontuberculous mycobacterial pulmonary disease – Ria N. Thompson – PLOS Pathogens

Alterations in the gut microbiota of alcoholic cirrhosis patients infected with Clonorchis sinensis in the Pearl River Delta region of China – Aijun Huang – PLOS ONE

Association between dietary B vitamins intake and age-specific blood pressure: A cross-sectional study in American adults – Xianfeng Li – PLOS ONE

Animal & Environmental Microbiomes

Cuts or carcasses? Diet form affects fecal microbial and animal fiber fractions in a large carnivore, the Asiatic lion – Mengmeng Sun – PLOS ONE

From pre-oral secretions to gut digestion: How do Lucilia sericata (Diptera: Calliphoridae) larvae handle Leishmania major? – Azam Malekian – PLOS ONE

Pathogenicity and transmission of Morganella morganii in honey bees – Yijun Chen – PLOS Pathogens

Mitogenomics of the tropical bont tick Amblyomma variegatum reveals vertical and horizontal transmission of Rickettsia africae – Elisha Chatanga – PLOS Neglected Tropical Diseases

Regulation of lipid metabolism in Spodoptera frugiperda by the symbiotic bracovirus of the gregarious parasitoid Cotesia ruficrus – Xian Li – PLOS Pathogens

The genome of Gallaecimonas pentaromativorans strain 10A, isolated from a Pacific oyster, sheds light on an environmentally widespread genus with remarkable metabolic potential – Yasmine Gouin – PLOS ONE

Plant, Soil & Microbial Ecology

Starve or share? Phosphate availability shapes plant–microbe interactions – Maja Schmidt – PLOS Pathogens

PMA-qPCA: Accelerating the market release of high-quality Bradyrhizobium diazoefficiens inoculant – Mariana Cap – PLOS ONE

Ancient & Evolutionary Microbiomes

Targeted pathogen profiling of ancient feces reveals common enteric infections in the Rio Zape Valley, 725–920 CE – Drew Capone – PLOS ONE

Health, Disease & Microbial Interactions

Differential regulation of the eicosanoid biosynthesis pathway in response to Enterocytozoon hepatopenaei infection in Litopenaeus vannamei – Wananit Wimuttisuk – PLOS ONE

Microplastic exposure and allergic rhinitis: Network toxicology and molecular docking insights – Yaojun Wang – PLOS ONE

Comparative evaluation of the antimicrobial, antioxidant, and cytotoxic properties of essential oils from vetiver, lemongrass, and clove buds with implications for topical application – Acharawan Thongmee – PLOS ONE

October 13, 2025

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General Microbiome

Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research – Imane Allali – Microbiome

Gut microbiome

Gut microbiota alterations are linked to COVID-19 severity in North African and European populations – Marius Bredon – Nature

Expanding the human gut microbiome atlas of Africa -Dylan G. Maghini – Nature

Vaginal microbiome

Changes in the vaginal microbiome in female patients with condyloma acuminatum and its impact on persistent HPV infection – Zhiyu Liu – Nature

Associations among HPV persistence, the vaginal microbiome, and cervical cancer recurrence – Despina Tsementzi – Journal of Translational Medicine

Respiratory Microbiome

Impact of RNA extraction on respiratory microbiome analysis using third-generation sequencing – Alice Michel – BMC Genomics

Animal microbiome

UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog – Shuang Liu – Nature

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

Water Microbiome

Decoding the genetic drivers of marine bacterial blooms through comparative genomics – Xavier Rey-Velasco – Microbiome

Bioinformatics

Influence of creatine pyruvate on newly received cattle: insights from metagenomics and metabolomics – Kang Mao – BMC Microbiology

Computational microbiome pharmacology analysis elucidates the anti-cancer potential of vaginal microbes and metabolites – Damilola C Lawore  – Frontiers

October 3, 2025

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See you at the MVIF 42!

NEW #MVIF program is out! 🤩Free registration: cassyni.com/s/mvif-42⭐️ Highlights:🇦🇺 @gbouras13.bsky.social🇺🇸 Danica Schmidtke⭐️ Keynote:🇺🇸 Peter Turnbaugh⭐️ Talks: 🇸🇬 Minghao Chia🇺🇸 @arzamasovalex.bsky.social 🇳🇿 Brooke Wilson

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-09-23T14:27:57.484Z

Human gut microbiome

Micro-scale spatial metagenomics: revealing high-resolution spatial biogeography of gut microbiomes – Carlotta Pietroni – bioRxiv

Animal microbiome

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort – Anna Cuscó – bioRxiv

Finally, the results of my postdoc at the @bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs.See our new preprint:www.biorxiv.org/content/10.1…

— Anna Cusco (@annacusco.bsky.social) 2025-09-23T11:23:52.836Z

Genome-resolved metagenomics reveals microbiome diversity across 48 tick species – Li-Feng Du – Nature Microbiology

The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media – Alice M. Buckner – Microbiology Spectrum

Animal experiments

The microbiota extends the reproductive lifespan by safeguarding the ovarian reserve – Sarah K. Munyoki – bioRxiv

Comment: From gut to gamete: how the microbiome influences fertility and preconception health – Sarah K. Munyoki – Microbiome

Review: Microbiome in heritage: how maternal microbiome transmission impacts next generation health – Clara Delaroque & Benoit Chassaing – Microbiome

Water microbiome

Metagenomics reveal allopatric speciation and higher connectivity among coastal vs. inland hypersaline lakes and solar salterns – Tomeu Viver – bioRxiv

Bioinformatics

microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis – Haris Zafeiropoulos – Genome Biology

our software, microbetag, for the annotation of microbial co-occurrence networks with phenotypic traits & metabolic complementarities was just publishedA Cytoscape app is also available to make your life easier (and prettier)#microbiome #metabolic-modeling #networks

— Haris Zafeiropoulos (@hariszaf.bsky.social) 2025-09-23T09:42:39.741Z

A roadmap for equitable reuse of public microbiome data – Laura A. Hug – Nature Microbiology

Reference-guided assembly of metagenomes with MetaCompass – Tu Luan – Cell Reports Methods

👏 “To promote more inclusive scientific discussions with international colleagues at our conferences, virtual delegates based in Lower and Middle-Income Countries can register for free”

— Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2025-09-30T07:09:00.327Z

September 19, 2025

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prepared by Bugembe Allan

Gut microbiome

Iron-saturated bovine lactoferrin preserves microbiota diversity and healthy ageing-associated taxa in an in vitro colon model of elderly gut microbiota – María Ruiz-Rico – PLOS ONE

Repopulation of the gut microbiota after a screening colonoscopy – Yezaz A. Ghouri – PLOS ONE

Gut microbiome signatures in iNPH: Insights from a shotgun metagenomics study – Rahel Park – PLOS ONE

Animal microbiome

Bacterial assemblages on eggs reflect nesting strategies in wetland-associated birds – Wouter F. D. van Dongen – PLOS ONE

Substrate degradation and black soldier fly larvae bioconversion performance profile on co-digested oil palm biomass-based feedstock – Mulki Salendra Kusumah – PLOS ONE

Soil microbiome

Mycelial traits and GRSP in enhancing soil stability on cold region highway slopes: Comparative effects of three shrub species – Yibo Li – PLOS ONE

Food microbiome

Investigation of bacterial community and histamine production in fresh mackerel at low temperature storage – Grace Margareta – PLOS ONE

Combinatorial effects of Zingiber officinale and Citrus limon juices: Hypolipidemic and antioxidant insights from in vivo, in vitro, and in silico investigations – Oussama Bekkouch – PLOS ONE

Human Health & Disease

Maternal-infant rotavirus-specific antibody kinetics to inform timing of vaccine boosting in Malawi: An observational study – Jonathan Mandolo – PLOS Medicine

Mother-child autonomic nervous system interaction as an indication of parental stress: 24-hour cross recurrence plot analysis – Jiarui Li – PLOS ONE

Pre-infection cerebral cortex structure predicts murine sepsis outcome – Robert M. Gallant – PLOS ONE

Optimized processing of Gardenia Fruits with ginger juice: Unveiling therapeutic mechanisms for cholestatic liver injury through TLR4/NF-κB, FXR/PPAR-α, and PI3K/AKT/GSK-3β – Chenzi Lyu – PLOS ONE

Pathogens & Virulence

How Klebsiella pneumoniae controls its virulence – To Nguyen Thi Nguyen – PLOS Pathogens

Coronavirus M protein impairs cilium during early infection by enhancing the AurA-HDAC6 axis – Tenghan Zhuang – PLOS Pathogens

Virulence gene profile and antimicrobial resistance patterns of Aeromonas hydrophila in farmed catfishes – Farjana Ferdousi – PLOS ONE

Chimeric PRR T-cell-engager targeting cell surface β-1,3-glucan for invasive candidiasis – Yu Fang Sun – PLOS Pathogens

September 5, 2025

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See you next week at #GloMiNe2025!

Program for #GloMiNe2025 "Preservation of microbial diversity” by @microbiotavault.bsky.social ‬and #MVIF is OUT:cassyni.com/s/mvif-glomi…1/3

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-08-22T11:42:37.937Z

Gut microbiome

Gut fungi are associated with human genetic variation and disease risk – Emily P. Van Syoc – Plos Biology

The resident gut microbiome modulates the effect of synbiotics on the immunogenicity after SARS-COV-2 vaccination in elderly and diabetes patients – Lin Zhang – npj Biofilms and Microbiomes

Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research – Matija Tričković – Cell Host & Microbe

New paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.

— Silas Kieser (@silask.bsky.social) 2025-08-29T10:06:18.408Z

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants – Raymond Kiu – Nature Communications

A defined microbial community reproduces attributes of fine flavour chocolate fermentation – David Gopaulchan – Nature Microbiology

Gut microbiome alterations precede graft rejection in kidney transplantation patients – Johannes Holle – American Journal of Transplantation

Adolescent girls at familial risk for depression with more advanced adrenarche have altered gut microbiota – A. Kolobaric – bioRxiv

Effects of a combined energy restriction and vigorous-intensity exercise intervention on the human gut microbiome: A randomised controlled trial – Russell G. Davies – The Journal of Physiology

Resistome

Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort – Katariina Pärnänen – Nature Communications

Oral microbiome

Complementary Predictors for Asthma Attack Prediction in Children: Salivary Microbiome, Serum Inflammatory Mediators, and Past Attack History – Shahriyar Shahbazi Khamas – Allergy

Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study – Cong Zhu – Microbiology Spectrum

SANA-Biome: A Protocol for a Cross-Sectional Study on Oral Health, Diet, and the Oral Microbiome in Romania – Sterling L. Wright – Healthcare 

🧬🪥 Just published! Our new paper introduces the SANA-biome, a biocultural study exploring how diet, lifestyle, and the oral microbiome shape periodontal health in Romania.📰 Read the open-access protocol in Healthcare: 👉 http://www.mdpi.com/2227-9032/13…

— Sterling L. Wright (@anthbyte.bsky.social) 2025-08-27T16:01:43.887Z

Animal microbiome

Metagenomics reveals fibre fermentation and AMR pathways in red grouse (Lagopus scotica) microbiota – Anum Ali Ahmad – BMC Microbiology

Thrilled that our new paper on the Red Grouse microbiota has now been published in BMC Microbiology: doi.org/10.1186/s128…! A really rewarding collaboration between our team and Nick Hesford and Kathy Fletcher from the Game & Wildlife Conservation Trust @gwct.org.uk.

— Laura Glendinning (@microbes4ever.bsky.social) 2025-08-19T14:12:37.569Z

Establishment of the early gut microbiota in vaginally delivered infants: the influence of maternal gut microbiota outweighs vaginal microbiota – Haishan Xie – Microbiology Spectrum

Integrative multi-omics analysis of dietary fibre-induced modulations in the composition and function of chicken caecal microbiota – Anum Ali Ahmad – bioRxiv

Vaginal microbiome

Degradation of Resistant α-1,4-glucan by Vaginal Gardnerella Species is Associated with Bacterial Vaginosis – Rosanne Hertzberger – Current Microbiology 

Animal experiments

The microbiome is associated with obesity-related metabolome signature in the process of aging – Dana Binyamin – npj Biofilms and Microbiomes

Evidence for an indigenous female mouse urobiome – Sidra Sohail – bioRxiv 

Food microbiome 

Microbiome profiling of Grana Padano and Parmigiano Reggiano cheeses reveals cheese-specific biomarkers, psychobiotic potential, and bioprotective activities – Vincenzo Valentino – npj Biofilms and Microbiomes

Metabolomics

Microbes release lower-value metabolites at higher rates – Snorre Sulheim – bioRxiv

So excited to share this new paper by @sulheim.bsky.social and others! It's rare that you find a pattern, propose a hypothesis and the more you look, the more data you find that fits! Snorre's intuition, hard work and rigour to put it all together have been inspiring! Let us know what you think…

— Sara Mitri (@saramitri.bsky.social) 2025-08-22T14:05:47.584Z

Soil microbiome

236 metagenome-assembled microbial genomes from rivers along a latitudinal gradient – Xiang Xiong – Scientific Data 

Bioinformatics

StrainFacts accurately quantifies both endogenous and live biotherapeutic product strain abundances in simulated and clinical vaginal microbiota samples – Johnathan Shih – bioRxiv

Comparison of iSeq and Miseq in 16S rRNA sequencing-based human gut microbiome analysis – Yanling Wang – bioRxiv 

Podcast

Biopolis – into the microbiome A young scientist is looking for answers in the human microbiome.

Food systems are teeming with complex microbial networks, carried from soil and water to crops, animals, and humans. Can we better track and steer these networks to enhance ecosystem health and food security? Find out more at this #FrontiersForum webinar ➡️ fro.ntiers.in/NfcCnmIEkWb

— Paul Cotter (@pauldcotter.bsky.social) 2025-09-05T13:25:35.039Z

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

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

December 10, 2024

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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

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