Category Archives: Events and jobs

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

November 10, 2023

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Read about new species discovered in the female genitourinary tract Lactobacillus isalae, Gardnerella pickettii and Gardnerella greenwoodii, and important UTI and other latest microbiome science news.
Happy Friday! And see you next week at MVIF!

Urinary microbiome

A human urothelial microtissue model reveals shared colonization and survival strategies between uropathogens and commensals – Carlos Flores – Science Advances

Gardnerella pickettii sp. nov. (formerly Gardnerella genomic species 3) and Gardnerella greenwoodii sp. nov. (formerly Gardnerella genomic species 8) isolated from female urinary microbiome – Márcia Sousa – International Journal of Systematic and Evolutionary Microbiology

Vaginal microbiome

Lactobacillus isalae sp. nov., isolated from the female reproductive tract – Tom Eilers – International Journal of Systematic and Evolutionary Microbiology

Identification of a DNA-cytosine methyltransferase that impacts global transcription to promote group B streptococcal vaginal colonization – Haider S. Manzer – mBio

Gut microbiome

Aggression: A gut reaction? The effects of the gut microbiome on aggression – Atara Uzan-Yulzari – bioRxiv

Oral microbiome

Establishment of tongue microbiota by 18 months of age and determinants of its microbial profile – Shinya Kageyama – mBio

Animal microbiome

Pet cats may shape the antibiotic resistome of their owner’s gut and living environment – Yiwen Yang – Microbiome

The impact of kit, environment and sampling contamination on the observed microbiome of bovine milk – Christopher J Dean – bioRxiv

Animal experiments

Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease – Lola Holcomb – mSystems

Daily fluctuation of colonic microbiome in response to nutrient substrates in a pig model – Hongyu Wang – npj Biofilms and Microbiomes

Water microbiome

Assessing the impact of anti-microbial showerheads on the prevalence and abundance of opportunistic pathogens in shower water and shower water-associated aerosols – Sarah Pitell, Sarah-Jane Haig – Frontiers in Microbiomes

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants – Huifeng Hu – bioRxiv

Technique

A high-throughput and low-waste viability assay for microbes – Christian T. Meyer – Nature Microbiology

Bioinformatics

Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses – Saioa Manzano-Morales – Genome Biology

ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool – Hoon Je Seong – Briefings in Bioinformatics


October 13, 2023

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Today’s digest features the Chinese Gut Microbiome Resource, plate readers in the anaerobic chamber, seasonal stability of sponge microbiomes, and more.

Also, you can support the outreachy bugsigdb project by sharing your study to be curated (more info here https://www.outreachy.org/apply/project-selection/#bioconductor or contact me). See you at #MVIF next week!

General

From hype to hope: considerations in conducting robust microbiome science – Amelia J McGuinness – Brain, Behavior, and Immunity

Global

Unraveling the functional dark matter through global metagenomics – Georgios A. Pavlopoulos – Nature

Human gut microbiome

Integration of 168,000 samples reveals global patterns of the human gut microbiome – Richard J. Abdill – bioRxiv

Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets – Anna C. Salvador – Microbiome

Gut microbial genomes with paired isolates from China signify probiotic and cardiometabolic effects – Pan Huang – bioRxiv

Gut microbiota profiles in feces and paired tumor and non-tumor tissues from Colorectal Cancer patients. Relationship to the Body Mass Index – Sofía Tesolato – PlosOne

Tracking gut microbiome and bloodstream infection in critically ill adults – Christopher H. Gu – PlosOne

Human milk

Human milk oligosaccharides modify the strength of priority effects in the Bifidobacterium community assembly during infancy – Martin F. Laursen & Henrik M. Roager – The ISME Journal

Antibiotic Resistome

Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments – Jessica Subirats – Applied and Environmental Microbiology

Plant microbiome

Characterization of Differences of Seed Endophytic Microbiome in Conventional and Organic Rice by Amplicon-based Sequencing and Culturing Methods – Sabin Khana – bioRxiv

Animal microbiome

Microbiome species diversity and seasonal stability of two temperate marine sponges Hymeniacidon perlevis and Suberites massa – Claire E. Lamb & Joy E. M. Watts – Environmental Microbiome

An observational study of the presence and variability of the microbiota composition of goat herd milk related to mainstream and artisanal farm management – Rita A. H. Hoving-Bolink – PlosOne

Technique

Cultivating efficiency: High-throughput growth analysis of anaerobic bacteria in compact microplate readers – Oona L.O. Snoeyenbos-West – bioRxiv

Bioinformatics

On the relationship between protist metabarcoding and protist metagenome-assembled genomes – Daryna Zavadska – bioRxiv

Track, Analyze, Visualize: Unravel Your Microbiome’s Temporal Tale with MicrobiomeStat – Chen Yang & MicrobiomeStat team

September 15, 2023

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Today’s digest features the BugSigDB, AMPSphere and more. Also, you can check out my tips for online conferencing and how to do it better. See you at #MVIF next week!

Respiratory microbiome

The landscape of antibiotic resistance genes in the nasopharynx of preterm infants: Prolonged signature of hospitalization and effects by antibiotics – Achal Dhariwal – bioRxiv

Breast cancer microbiome

Integrating current analyses of the breast cancer microbiome – Sidra Sohail and Michael B. Burns – Plos One

Vaginal microbiome

Diet influences community dynamics following vaginal group B Streptococcus colonization – Christina J. Megli – bioRxiv

Gut microbiome

Gut microbes exacerbate systemic inflammation and behavior disorders in neurologic disease CADASIL – Sheng Liu – Microbiome

Water microbiome

Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean – Mirna Vázquez Rosas Landa – mSystems

Insect microbiome

Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions – Francesca De Filippis – Microbiome

Animal experiment

Enhancing Recovery from Gut Microbiome Dysbiosis and Alleviating DSS-Induced Colitis in Mice with a Consortium of Rare Short-Chain Fatty Acid-Producing Bacteria – Achuthan Ambat – bioRxiv

Bioinformatics

BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures – Ludwig Geistlinger – Nature Biotechnology

Computational exploration of the global microbiome for antibiotic discovery – Célio Dias Santos-Júnior – bioRxiv

June 13, 2023

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Today’s microbiome digest includes quite a few host-microbe studies, including one published by my colleague and highlighted below which focuses on the hindgut microbiome of the American cockroach.

Human gut microbiome

Gut microbiota interspecies interactions shape the response of Clostridioides difficile to clinically relevant antibiotics – Hromada – and Venturelli – PLOS Biology

Construction of model animals to explore intestinal microbiome for detection of breast cancer – Ji et al. – PLOS One

Animal experiments

**Disentangling hindgut metabolism in the American cockroach through single-cell genomics and metatranscriptomics – Dukes et al. – Frontiers in Microbiology

Evaluation of microbial and vancomycin treatments in ulcerative colitis in murine models – Hasan and Yang – PLOS One

Animal microbiome

Geography, not lifestyle, explains the population structure of free-living and host-associated deep-sea hydrothermal vent snail symbionts – Hauer et al. – Microbiome

Insect phylogeny structures the bacterial communities in the microbiome of psyllids (Hemiptera: Psylloidea) in Aotearoa New Zealand – Martoni et al. – PLOS One

Water and extremophile microbiome

In the right place, at the right time: the integration of bacteria into the Plankton Ecology Group model – Park et al. – Microbiome

Phages and viruses

Beyond pathogenesis: Detecting the full spectrum of ecological interactions in the virosphere – Jurburg et al. – PLOS Biology

Phage therapy and the public: Increasing awareness essential to widespread use – McCammon et al. – PLOS One