Today’s digest is super diverse (read cool!): novel genes from uncultivated prokaryotes, a new Latilactobacillus species isolated from leaves of a strawberry plant (read the full 🍓 story behind the paper!), the benchmarking study of taxonomic profilers for long-read shotgun metagenomic datasets, and more. The first Issue of a new international peer-reviewed, open access, microbiome-oriented journal – the Microbiome Research Reports – is out with one original article, one perspective and four reviews.
And, a bit of shameless self-promotion, check out my preprint on urinary microbiome of healthy European women!
Happy Friday!
Global microbiome
*Functional and evolutionary significance of unknown genes from uncultivated taxa – Alvaro Rodríguez – bioRxiv
Ear microbiome
The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes – Maria Burton – PlosOne
Respiratory microbiome
Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer – Lisa Derosa – Nature Medicine
Associations and recovery dynamics of the nasopharyngeal microbiota during influenza‑like illness in the aging population – Sudarshan A. Shetty – Scientific Reports
Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways – Kasey A. Webb – Microbial Genomics
Gut microbiome
Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project – Esteban A. Lopera-Maya – Nature Genetics
The gut bacterial community potentiates Clostridioides difficile infection severity – Nicholas A Lesniak – bioRxiv
Emergent evolutionary forces in spatial models of microbial growth in the human gut microbiota – Olivia M. Ghosh and Benjamin H. Good – bioRxiv
Review: Microbiome-based therapeutics – Matthew T. Sorbara and Eric G. Pamer – Nature Reviews Microbiology
Review: Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota –Anna E. Lindell – Nature Reviews Microbiology
Review: Gut microbiome and health: mechanistic insights – Willem M de Vos – Gut
Vaginal microbiome
Gardnerella vaginalis induces matrix metalloproteinases in the cervicovaginal epithelium through TLR-2 activation – Kristin D. Gerson – American Journal of Obstetrics & Gynecology/SMFM 42nd Annual Meeting: The Pregnancy Meeting
Urinary microbiome
*Extended bacterial diversity of the urinary microbiome of reproductive-age healthy European women captured by culturomics and long-read amplicon sequencing – Svetlana Ugarcina Perovic – bioRxiv
Phylogenetic analysis and antimicrobial susceptibility profile of uropathogens – Hanif Ullah – PlosOne
Multidrug-resistant Uro-associated Escherichia coli Populations and Recurrent Urinary Tract Infections in Patients Performing Clean Intermittent Self-catheterisation – Catherine Mowbray – European Urology Open Science
Plant microbiome
*Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa) – Marie Legein – International Journal of Systematic and Evolutionary Microbiology
Ecology and potential functions of plant-associated microbial communities in cold environments – Malek Marian – FEMS Microbiology Ecology
Animal microbiome
Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides – Lucelia Cabral – Nature Communications
Review: Pesticide-induced disturbances of bee gut microbiotas – Michelle Z Hotchkiss – FEMS Microbiology Reviews
Animal experiments
Effect of a freeze-dried coffee solution in a high-fat diet-induced obesity model in rats: Impact on inflammatory response, lipid profile, and gut microbiota – Marilia Hermes Cavalcanti – PlosOne
Gut microbiota and butyrate contribute to nonalcoholic fatty liver disease in premenopause due to estrogen deficiency – Limin Liu – PlosOne
Techniques
BIOME-Preserve: A novel storage and transport medium for preserving anaerobic microbiota samples for culture recovery – Embriette R. Hyde – PlosOne
Species-targeted sorting and cultivation of commensal bacteria from the gut microbiome using flow cytometry under anaerobic conditions – Samuel Bellais – Microbiome
Bioinformatics
*Evaluation of taxonomic profiling methods for long-read shotgun metagenomic sequencing datasets – Daniel M Portik – bioRxiv
AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite – Giorgos Skoufos – Genome Biology
McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems – André Bogdanowski – Plos Computational Biology
VeChat: Correcting errors in long reads using variation graphs – Xiao Luo – bioRxiv
ReadBouncer: Precise and Scalable Adaptive Sampling for Nanopore Sequencing – Jens-Uwe Ulrich – bioRxiv
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Microbiome Digest - Bik's Picks 