Today’s quite diverse digest features: the role of gut commensal fungi mycobiota in shaping the human protective IgG antibody repertoire, Mouse Microbial Genome Collection, gut microbiome – lymphocytes – diet link, competition between Gardnerella species, microbiota-derived bile acids pool as a mediator of host–microbiota interactions, multiscale variation in genome graphs, and a list of awesome webinars, courses and podcasts. Check out two cool science and art projects, Bacterial Alphabet and Microbe Crayon. Happy Friday!
Gut microbiome
*Human gut mycobiota tune immunity via CARD9-dependent induction of anti-fungal IgG antibodies – Itai Doron – Cell
*Functional and taxonomic comparison of mouse and human gut microbiotas using extensive culturing and metagenomics – Benjamin S. Beresford-Jones – bioRxiv
*High intake of vegetables is linked to lower white blood cell profile and the effect is mediated by the gut microbiome – Cristina Menni – BMC Medicine
The Reactobiome Unravels a New Paradigm in Human Gut Microbiome Metabolism – Gholamreza Bidkhori – bioRxiv
Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer – Kellyanne Duncan – Gut Microbes
Review: Diversity and dynamism of IgA−microbiota interactions – Kelsey E. Huus – Nature Reviews Immunology
Antibiotic-associated dysbiosis affects the ability of the gut microbiota to control intestinal inflammation upon fecal microbiota transplantation in experimental colitis models – Francesco Strati – Microbiome
Adherent-invasive E. coli metabolism of propanediol in Crohn’s disease regulates phagocytes to drive intestinal inflammation – Monica Viladomiu – Cell Host & Microbe
Adults with Prader–Willi syndrome exhibit a unique microbiota profile – Wendy J. Dahl – BMC Research Notes
Vaginal microbiome
*Population density affects the outcome of competition in co-cultures of Gardnerella species isolated from the human vaginal microbiome – Salahuddin Khan and Janet E. Hill – bioRxiv
Review: Lactic acid-containing products for bacterial vaginosis and their impact on the vaginal microbiota: A systematic review – Erica L. Plummer – PlosOne
Urinary microbiome
Functional and Taxonomic Dysbiosis of the Gut, Urine, and Semen Microbiomes in Male Infertility – Scott D. Lundy – European Urology
Review: The microbiome and host mucosal interactions in urinary tract diseases – Bernadette Jones-Freeman – Mucosal Immunology
Epidemiology of urinary tract infections in children: Causative bacteria and antimicrobial therapy – Yuhei Tanaka – Paediatrics International
Human milk microbiome
Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota – Shirin Moossavi – Microbiome
Respiratory microbiome
Review: Respiratory microbiome in mechanically ventilated patients: a narrative review – Mélanie Fromentin – Intensive Care Medicine
Animal microbiome
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes – Xuefeng Peng – Nature Microbiology
Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics – Paiboon Tunsagool – Applied and Environmental Microbiology
Unravelling the Role of Rumen Microbial Communities, Genes, and Activities on Milk Fatty Acid Profile Using a Combination of Omics Approaches – Sokratis Stergiadis – Frontiers in Microbiology
Evaluation of the ocular surface mycobiota in clinically normal horses – Mary L. Walsh – PlosOne
Animal experiments
Colonization at birth with human CST IV cervicovaginal microbiota alters development and increases neonatal mortality in mice – Eldin Jašarević – bioRxiv
Novel gut pathobionts confound results in a widely used mouse model of human inflammatory disease – Samuel C Forster – bioRxiv
Low-dose exposure of glyphosate-based herbicides disrupt the urine metabolome and its interaction with gut microbiota – Jianzhong Hu – Scientific Reports
Microbiota control of maternal behavior regulates early postnatal growth of offspring – Yujung Michelle Lee – Science Advances
Probiotics
Minireview: Lactic acid bacteria as probiotics for the nose? – Ilke De Boeck – Microbial Biotechnology
*Lactobacillus bile salt hydrolase substrate specificity governs bacterial fitness and host colonization – Matthew H. Foley – PNAS
Probiotic nasal spray development by spray drying – Katarina Jokicevic – European Journal of Pharmaceutics and Biopharmaceutics
Water microbiome
Microbiota analysis of rural and urban surface waters and sediments in Bangladesh identifies human waste as driver of antibiotic resistance – Ross S. McInnes – bioRxiv
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika – Patricia Q. Tran – The ISME Journal
Soil microbiome
Trace gas oxidizers are widespread and active members of soil microbial communities – Sean K. Bay – Nature Microbiology
Bacterial communities regulate temporal variations of the antibiotic resistome in soil following manure amendment – Jianhua Cheng – Environmental Science and Pollution Research
Techniques
Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method – Pascal M. Frey – mSystems
Bioinformatics
*Enabling multiscale variation analysis with genome graphs – Brice Letcher – bioRxiv
HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes – Yu Li – Microbiome
BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence – Benjamin Hepp – Bioinformatics
Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN) – Renaud Van Damme – Plos Computational Biology
PATO: Pangenome Analysis Toolkit – Miguel D. Fernández-de-Bobadilla – bioRxiv
Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets – Nicholas D. Youngblut and Ruth E. Ley – bioRxiv
Webinars
UCC Science Society STEMinar: The Gut Microbiome, Health & Disease. You truly are what you eat – Paul O’Toole – 15 February
SGBUG (Singapore Bacterial Ultra Group) seminar: Human Gut Bacteria, Bile Acids, and Host Physiology – Sloan Devlin – 18 February
MicroSeminars 2021 – Free Web-based Microbiology Seminar Series
Biofilm Baithak – An India-specific Meetup – India Biofilms Society- 20-27 February 2021.
Klebsiella Virtual Seminar Series 2021 #KlebClub2021 – Department of Microbiology and Immunology, University of Michigan
Courses
Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R – The Wellcome Genome Campus
Next Generation Sequencing Bioinformatics course – Wellcome Genome Campus Advanced Courses & Scientific Conferences – H3Abionet
Biobanking – Institut Pasteur
Podcasts
Season 2, Ep. 2: Building Biomes with Jack Gilbert – Ruairi Robertson – Biomes
Reverse mentoring with Martin Dougherty – Alice Matimba – Your Digital Mentor
Episode 17: Post-docs Part 2: Hiring – Stephanie Hicks and John Muschelli – The Corresponding Author
Episode 235: Green algae and fatty acids – Vincent Racaniello, Elio Schaechter, Michele Swanson, and Michael Schmidt – This week in microbiology podcast
Dr. Heer Mehta: Antibiotic Resistance and Experimental Evolution – Leo Elworth – The Bioinformatics and Beyond Podcast
Science and Art
Microbe Crayon Project – Anne A. Madden
Drawing the #BacterialAlphabet – Noémie Matthey
Microbiome Digest - Bik's Picks 