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

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 13, 2024

Today we are highlighting a recent call to action by leading scientists and scientific organizations around the globe aimed at drawing attention to the increasingly urgent climate catastrophe. The authors argue for the use of microbe-based solutions that could be promising in addressing the crisis, and yet are not used effectively at scale. Here we’ve included links to the press release and the journals which have jointly published the paper:

[PRESS RELEASE] Scientists issue call to action underlining importance of microbial solutions to tackle climate crisis – Linda Stewart – The Microbiologist by Applied Microbiology International

Microbial solutions must be deployed against climate catastrophe – Raquel Peixoto, Christian R Voolstra, Lisa Y Stein, Philip Hugenholtz, Joana Falcao Salles, Shady A Amin, Max Häggblom, Ann Gregory, Thulani P Makhalanyane, Fengping Wang, Nadège Adoukè Agbodjato, Yinzhao Wang, Nianzhi Jiao, Jay T Lennon, Antonio Ventosa, Patrik M Bavoil, Virginia Miller, Jack A Gilbert – Sustainable Microbiology

The paper can also be found in journals published by FEMS, ISME, ASM, and Nature.

Human gut microbiome

Predictable regulation of gut microbiome in immunotherapeutic efficacy of gastric cancer – Wei Gao et al – Genes & Immunity

Multimodal analysis identifies microbiome changes linked to stem cell transplantation-associated diseases – Alejandro Artacho et al – BMC Microbiome

Human oral microbiome

Large-scale metagenomic analysis of oral microbiomes reveals markers for autismspectrum disorders – Paolo Manghi et al – Nature Communications

[REVIEW] Viral infection and antiviral immunity in the oral cavity – Heather D. Hickman & Niki M. Moutsopoulos – Nature Reviews Immunology

Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized – Eria P. Ryu et al – BMC Microbiome

Human respiratory microbiome

Major alteration of lung microbiome and the host responses in critically ill COVID-19 patients with high viral load – Ingrid G. Bustos et al – Scientific Reports

Human skin microbiome

The healing process of diabetic ulcers correlates with changes in the cutaneous microbiota – Emanuele Bruni et al – Scientific Reports

Soil microbiome

Microplastic diversity increases the abundance of antibiotic resistance genes in soil – Yi-Fei Wang et al – Nature Communications

Built environment microbiome

Moving beyond species: fungal function in house dust provides novel targets for potential indicators of mold growth in homes – Neeraja Balasubrahmaniam et al – BMC Microbiome

Animal microbiome

Reef site and habitat influence effectiveness of Acropora palmata restoration and its microbiome in the Florida Keys – Stephanie M. Rosales et al – Nature Communications Earth & Environment

Melatonin alleviates heat stress-induced spermatogenesis dysfunction in male dairy goats by regulating arachidonic acid metabolism mediated by remodeling the gut microbiota – Xinrui Guo et al – BMC Microbiome

Pathobiont and symbiont contribute to microbiota homeostasis through Malpighian tubules-gut countercurrent flow in Bactrocera dorsalis – Yanning Liu et al – ISME Journal

Medium-chain fatty acid triglycerides improve feed intake and oxidative stress of finishing bulls by regulating ghrelin concentration and gastrointestinal tract microorganisms and rumen metabolites – Jiaming Luan et al – BMC Microbiome

Intestinal commensal bacteria promote Bactrocera dorsalis larval development through the vitamin B6 synthesis pathway – Jian Gu et al – BMC Microbiome

Water & extremophile microbiome

Latitudinal gradients and ocean fronts strongly influence protist communities in the southern Pacific Ocean – Daniela Sturm et al – FEMS Microbial Ecology

Urea assimilation and oxidation support activity of phylogenetically diverse microbial communities of the dark ocean – Nestor Arandia-Gorostidi et al – ISME Journal

Bioinformatics & tools

MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes – Annabel Cansdale & James P.J. Chong – BMC Microbiome

January 27, 2023

General Microbiome

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies – Kennedy et al. Nature

Microbial foods for improving human and planetary health – Jahn et al. Cell

A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy – Mayer et al. Science Advances

Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults – Larson et al. Nature Aging

Bacteriophage / Virome

Phage therapy: From biological mechanisms to future directions – Strathdee et al. Cell

Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs – Lee et al. Cell

Water and extremophile microbiome

High-resolution metagenomic reconstruction of the freshwater spring bloom – Kavagutti et al. Microbiome

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria – Sereika et al. ISME

Bioinformatics

Enhanced correlation-based linking of biosynthetic gene clusters to their metabolic products through chemical class matching – Louwen et al. Microbiome

PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data – Wang & Cao. Briefings in Bioinformatics

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine – Heinken et al. Nature Biotechnology

Non-Microbiome picks

Infection infidelities drive innate immunity – Kagan. Science

Functional T cells are capable of supernumerary cell division and longevity – Soerens et al. Nature

Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe – Kerner et al. Cell Genomics

June 8, 2022

Happy Friday! Today’s digest includes articles about Gardnerella vaginalis clades in pregnancy, how a Japanese herbal medicine may alleviate a leaky gut, and a feasibility study of the impact of oral activated charcoal on healthy volunteers.

General microbiome

Clinical Burkholderia pseudomallei isolates from north Queensland carry diverse bimABm genes that are associated with central nervous system disease and are phylogenomically distinct from other Australian strains – Burnard et al. – PLOS Neglected Tropical Diseases

Preprint: The energy requirements of ion homeostasis determine the lifespan of starving bacteria – Schink et al. – bioRxiv

Preprint: A novel bacterial speciation process observed in a symbiotic marine population – Wang et al. – bioRxiv

Human vaginal microbiome

Gardnerella vaginalis clades in pregnancy: New insights into the interactions with the vaginal microbiome – Severgnini et al. – PLOS One

Human gut microbiome

Saireito, a Japanese herbal medicine, alleviates leaky gut associated with antibiotic-induced dysbiosis in mice – Ozaka et al. – PLOS One

A dose-finding safety and feasibility study of oral activated charcoal and its effects on the gut microbiota in healthy volunteers not receiving antibiotics – Rashidi et al. – PLOS One

Water and extremophile microbiome

The microbial community and functional potential in the Midland Basin reveal a community dominated by both thiosulfate and sulfate-reducing microorganisms – Tinker et al. – Microbiology Spectrum

Techniques

Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in asymptomatic and symptomatic populations – Ganz et al.- PLOS One

June 3, 2022

Happy Friday!

Today’s digest has articles on COVID-19 vaccine hesitancy, a new R package to extract network backbones, and a class of novel antibiotics that targets a Mycobacterium tuberculosis PE-PGRS protein. There also preprints on biofilm winkling in Bacillus subtilis, the dental calculus microbiome, and the relationship between eukaryotic genomes and ocean plankton in a global metagenomic dataset.

Events

Next week is ASM Microbe! I’ll be there, wearing a KN-95 and clutching a box of rapid tests. Feel free to comment or reach out if you’re also attending.

COVID-19

Oro-facial mucocutaneous manifestations of Coronavirus Disease-2019 (COVID-19): A systematic review – Fakhruddin et al. – PLOS ONE

Preprint: The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity – Kim et al. – bioRxiv

Determinants of the COVID-19 vaccine hesitancy spectrum – Piltch-Loeb et al. – PLOS ONE

General microbiome

Preprint: Fatty acid synthesis knockdown promotes biofilm wrinkling and inhibits sporulation in Bacillus subtilis – Arjes et al. – bioRxiv

Association of Strongyloides stercoralis infection and type 2 diabetes mellitus in northeastern Thailand: Impact on diabetic complication-related renal biochemical parameters – Yingklang et al. – PLOS ONE

Analysis of secondary metabolite gene clusters and chitin biosynthesis pathways of Monascus purpureus with high production of pigment and citrinin based on whole-genome sequencing – Zhang et al. – PLOS ONE

Human respiratory microbiome

A novel class of antimicrobial drugs selectively targets a Mycobacterium tuberculosis PE-PGRS protein – Seo et al. – PLOS Biology

Human oral microbiome

Preprint: Assessing the influence of the Mediterranean diet on dental calculus microbiome composition: a pilot study – Innocenti et al. – bioRxiv

Human gut microbiome

Lactobacillus plantarum improves LPS-induced Caco2 cell line intestinal barrier damage via cyclic AMP-PKA signaling – Wei et al. – PLOS ONE

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Preprint: Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton – Alexander et al. – bioRxiv

Bioinformatics

backbone: An R package to extract network backbones – Neal – PLOS ONE


March 3, 2022

Today’s digest is heavy on studies focused on the gut and soil microbiomes. It also includes articles focused on microbial indoor air quality as well as bacterial vaginosis and aerobic vaginitis among pregnant women. If you’d still like more, I’ve also included several preprints.

Happy reading!


Human vaginal microbiome

Prevalence of bacterial vaginosis and aerobic vaginitis and their associated risk factors among pregnant women from northern Ethiopia: A cross-sectional study – Yalew et al. – PLOS One

Human gut microbiome

Systematically assessing microbiome–disease associations identifies drivers of inconsistency in metagenomic research – Tierney et al. – PLOS Biology

Preprint: Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation – Venzon et al. – bioRxiv

Hydrogen-producing small intestinal bacterial overgrowth is associated with hepatic encephalopathy and liver function – Yokoyama et al. – PLOS One

Plant, root, and soil microbiome

Preprint: Deciphering the potential niche of two novel black yeast fungi from a biological soil crust based on their genomes, phenotypes, and melanin regulation – Carr et al. – bioRxiv

Bacterial age distribution in soil—Generational gaps in adjacent hot and cold spots – Borer & Or – PLOS Computational Biology

Deciphering the influence of Bacillus subtilis strain Ydj3 colonization on the vitamin C contents and rhizosphere microbiomes of sweet peppers – Liang et al. – PLOS One

Antimicrobial effect and mechanism of bovine lactoferrin against the potato common scab pathogen Streptomyces scabiei – Nakamura et al. – PLOS One

Preprint: Arbuscular mycorrhizal fungal composition across US citrus orchards, management strategies, and disease severity spectrum – Xi et al. – bioRxiv

Built environment

Comprehensive health risk assessment of microbial indoor air quality in microenvironments – Kumar et al. – PLOS One

Phages and viruses

Preprint: Modelling the synergistic effect of bacteriophage and antibiotics on bacteria: killers and drivers of resistance evolution – Leclerc et al. -bioRxiv

Bioinformatics

Preprint: Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution – Kiefl et al. – bioRxiv

January 7, 2022

Today’s digest covers a range of topics including a duplex qPCR assay to detect lung infections, an investigation into sand fly symbionts, and a characterization of a fermented soybean food (Pe poke). If you want to end the week on a good note, I’d suggest reading the two articles I’ve highlighted below. One demonstrates that flooding and ecological restoration of former cranberry farmland also restores wetland microbial communities and soil function. The second provides a new barcoding strategy for the phenotypic screening of mosquitos that can be applied towards malaria research.

Happy reading!

General microbiome

Controlled spatial organization of bacterial growth reveals key role of cell filamentation preceding Xylella fastidiosa biofilm formation – Anbumani et al. – npj Biofilms and Microbiomes

Bacteria can be selected to help beneficial plasmids spread – Dimitriu et al. – PLOS Biology

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network – Urchueguía et al. – PLOS Biology

Human respiratory microbiome

Detection of Pneumocystis jirovecii and Toxoplasma gondii in patients with lung infections by a duplex qPCR assay – Wu et al. – PLOS Neglected Tropical Diseases

Animal experiments

***Barcoded Asaia bacteria enable mosquito in vivo screens and identify novel systemic insecticides and inhibitors of malaria transmission – Sturm et al. – PLOS Biology

Molecular phylogeny of heritable symbionts and microbiota diversity analysis in phlebotominae sand flies and Culex nigripalpus from Colombia – Vivero-Gomez – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar – Tamang et al. – PLOS One

***Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland – Rubin et al. – PLOS One

Water and extremophile microbiome

Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment – Remple et al. – npj Biofilms and Microbiomes

December 20, 2021

Today’s digest is a grab bag that includes research articles on the vaginal microbiota, the gut microbiota of dairy calves, microbial loads in medical waste, and more! I’ve also highlighted a non-microbiology article that found that pet dog owners were significantly less depressed than non-pet owners during the pandemic. So if you’re looking for more reasons to adopt a new furry friend, you can add this one to the list!

General microbiome

Genomic comparison and phenotypic profiling of small colony variants of Burkholderia pseudomallei – Zulkefli et al. – PLOS One

Human vaginal microbiome

Vaginal microbiota of American Indian women and associations with measures of psychosocial stress – Borgogna et al. – PLOS One

Human gut microbiome

Gut microbiota features associated with Clostridioides difficile colonization in dairy calves – Redding et al. – PLOS One

Animal microbiome

Culicoides Latreille (Diptera: Ceratopogonidae) as potential vectors for Leishmania martiniquensis and Trypanosoma sp. in northern Thailand – Sunantaraporn et al. – PLOS Neglected Tropical Diseases

Migratory wild birds carrying multidrug-resistant Escherichia coli as potential transmitters of antimicrobial resistance in China – Yuan et al. – PLOS One

Plant, root, and soil microbiome

Characterization of soils conducive and non-conducive to Prunus replant disease – Khan et al. – Plos One

Built environment

Disposal habits and microbial load of solid medical waste in sub-district healthcare facilities and households in Yilo-Krobo municipality, Ghana – Egbenyah et al. – PLOS One

Phages and viruses

A systematic review and meta-analysis of the potential non-human animal reservoirs and arthropod vectors of the Mayaro virus – Celone et al. – PLOS Neglected Tropical Diseases

Bioinformatics

Genomic prediction using low-coverage portable Nanopore sequencing – Lamb et al. – PLOS One

Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations – Lim et al. – PLOS One

Kara’s non-microbiology pick

***Depression, anxiety, and happiness in dog owners and potential dog owners during the COVID-19 pandemic in the United States – Martin et al. – PLOS One