Today’s digest features studies on hospital-associated bacterial communities on window components, the effect of urbanization on the vaginal microbiota of Amerindians, nitrate as a potential prebiotic for oral health, and the latest news in bioinformatics. Happy reading!
General microbiome
Microbial species interactions determine community diversity in fluctuating environments – Shota Shibasaki – bioRxiv
Review: The host-associated archaeome – Guillaume Borrel – Nature Reviews Microbiology
Oral microbiome
*Nitrate as a potential prebiotic for the oral microbiome – Bob T. Rosier – Scientific Reports
Skin microbiome
Deep skin dysbiosis in vitiligo patients: link with mitochondrial and immune changes – Hanene Bzioueche – medRxiv
Gut microbiome
Review: The microbiome: An emerging key player in aging and longevity– Minhoo Kim and Bérénice A. Benayoun – Translational Medicine of Aging
Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study – Kelsey E. Huus – Microbiome
Vaginal microbiome
*Changes in the vaginal microbiota across a gradient of urbanization – Daniela Vargas-Robles – Scientific Reports
Comparison between a novel molecular tool and conventional methods for diagnostic classification of bacterial vaginosis: is integration of the two approaches necessary for a better evaluation? – Margherita Scapaticci – New Microbiologica
Genome-wide mutagenesis identifies factors involved in Enterococcus faecalis vaginal adherence and persistence – Norhan Alhajjar – bioRxiv
Association between Vaginal Bacterial Microbiota and Vaginal Yeast Colonization – McKenna C Eastment – The Journal of Infectious Diseases
Urinary microbiome
Review: The microbiome in urological diseases – Kwang Woo Lee – Investigive and Clinical Urology
Review: FimH and Anti-Adhesive Therapeutics: A Disarming Strategy Against Uropathogens – Meysam Sarshar – Antibiotics
Characterization of urinary microbiome in patients with bladder cancer: Results from a single-institution, feasibility study – Juan Chipollini – Urologic Oncology: Seminars and Original Investigations
Animal microbiome
Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage – Jolinda Pollock – Scientific Reports
Vaginal Microbiota Changes During Estrous Cycle in Dairy Heifers – Juan J. Quereda – Frontiers in Veterinary Science
Animal experiment
The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic – Eliran Kadosh – Nature
An Enteric Pathogen Subverts Colonization Resistance by Evading Competition for Amino Acids in the Gut – Gustavo Caballero-Flores – Cell Host & Microbe
Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin – Damien J. Cabral – mSystems
Water and extremophile microbiome
Determining the primary sources of fecal pollution using microbial source tracking assays combined with land-use information in the Edwards Aquifer – Jessica Hinojosa – Water Research
Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities – Tyler J. Arbour – Frontiers in Microbiology
Food microbiome
Discovering microbiota and volatile compounds of surströmming, the traditional Swedish sour herring – Luca Belleggia – Food Microbiology
Built environment
*Viable bacterial communities on hospital window components in patient rooms – Patrick F. Horve – PeerJ
Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation – Ganesh Babu Malli Mohan – mSystems
Phages and viruses
Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone – Anastasia Tsiola – Viruses
Bioinformatics
Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets – Yi Yue – BMC Bioinformatics
Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach – Christian Milani – mSystems
Automated prediction and annotation of small proteins in microbial genomes– Matthew G Durrant and Ami S Bhatt – bioRxiv
Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing data – Abigail L. Lind – bioRxiv
MicrobeAnnotator: a user-friendly, comprehensive microbial genome annotation pipeline – Carlos A. Ruiz-Perez – bioRxiv
Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra – Caroline Weis – Bioinformatics
NetCoMi: Network Construction and Comparison for Microbiome Data in R – Stefanie Peschel – bioRxiv
Review: Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses – Ana Elena Pérez-Cobas – Microbial Genomics
Podcast
Machine learning for drug development with Marinka Zitnik – Jacob Schreiber – The Bioinformatics Chat