In today’s digest read about ureteral stent microbiota, metagenomic growth estimators, social transmission as a major shaper of gut microbiota in wild mice [spoiler: mice with many friends in separate social circles have the richest microbiota], and give a listen to the first episode of Lonely Pipette, a brand new podcast about doing better science!
General microbiome
Review: Searching for principles of microbial physiology – Frank J Bruggeman – FEMS Microbiology Reviews
Metagenomics
*Benchmarking microbial growth rate predictions from metagenomes – Andrew M. Long – The ISME Journal
Metabolomics
Review: Gut microbial metabolites as multi-kingdom intermediates – Kimberly A. Krautkramer – Nature Reviews Microbiology
Multi-omics
Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes – Francesco Delogu – Nature
Behind the paper: What can absolute multi-omics add to microbial ecology?
Gut microbiome
Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption – Aleksandra S. Chikina – Cell
Review: Anorexia nervosa and gut microbiota: A systematic review and quantitative synthesis of pooled microbiological data – Laura Di Lodovico – Progress in Neuro-Psychopharmacology and Biological Psychiatry
In search for interplay between stool microRNAs, microbiota and short chain fatty acids in Crohn’s disease – a preliminary study – Filip Ambrozkiewicz – BMC Gastroenterology
Vaginal microbiome
Slipped strand mispairing in the gene encoding cell wall associated sialidase NanH3 in Gardnerella spp – Shakya P. Kurukulasuriya – bioRxiv
The vaginal microbiome in pregnant women: knowledge gaps in relation to clinical relevance – Steven S. Witkin – BJOG: An International Journal of Obstetrics and Gynaecology
Urinary microbiome
*Ureteral Stent Microbiota Is Associated with Patient Comorbidities but Not Antibiotic Exposure – Kait F. Al – Cell Reports Medicine
Novel Antibiotic-Loaded Particles Conferring Eradication of Deep Tissue Bacterial Reservoirs for the Treatment of Chronic Urinary Tract Infection – Wai Lau – Journal of Controlled Release
Respiratory microbiome
Altered respiratory microbiota composition and functionality associated with asthma early in life – Mohammad T. AL Bataineh – BMC Infectious Diseases
Oral microbiome
Comparative evaluation of microbial profiles of oral samples obtained at different collection time points and using different methods – Michi Omori – Clinical Oral Investigations
Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment – Xiaoyu Sun – Scientific Reports
Animal microbiome
Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog – Randall R. Jiménez – BMC Microbiology
Lactobacillus spp. attenuate antibiotic-induced immune and microbiota dysregulation in honey bees – Brendan A. Daisley – Communications Biology
Animal experiment
Antibiotics increase aggression behavior and aggression-related pheromones and receptors in Drosophila melanogaster – Michal Grinberg – bioRxiv
*Social networks strongly predict the gut microbiota of wild mice – Aura Raulo – bioRxiv
Plant/root/soil microbiome
Insights into the diversity and survival strategies of soil bacterial isolates from the Atacama Desert – Alicyn Reverdy – bioRxiv
Rhizobacterial species richness improves sorghum growth and soil nutrient synergism in a nutrient-poor greenhouse soil – Mohammad Radhi Sahib – Scientific Reports
Water microbiome
Bacterial Opportunistic Pathogen Gene Markers in Municipal Drinking Water are Associated with Distribution System and Household Plumbing Characteristics – Sarah Haig – Environmental Science: Water Research & Technology
Collection system investigation microbial source tracking (CSI-MST): Applying molecular markers to identify sewer infrastructure failures – Dana Gonzalez – Journal of Microbiological Methods
New insights into the vertical distribution and microbial degradation of microplastics in urban river sediments – Lihua Niu – Water Research
Unveiling dynamics of size-dependent antibiotic resistome associated with microbial communities in full-scale wastewater treatment plants – Kaifeng Yu – Water Research
Aerobic microbial communities in the sediments of a marine oxygen minimum zone – Sabyasachi Bhattacharya – FEMS Microbiology Letters
Phages and viruses
Identification of Bacteriophages in the Vagina of Pregnant Women: A Descriptive Study – Antonio Charlys da Costa – BJOG: An International Journal of Obstetrics and Gynaecology
The Protective Effect of Staphylococcus epidermidis Biofilm Matrix against Phage Predation – Luís D.R. Melo – Viruses
Bioinformatics
Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation – Dileep Kishore – bioRxiv
GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure – Yu Wan – BMC Genomics
A network approach to elucidate and prioritize microbial dark matter in microbial communities – Tatyana Zamkovaya – The ISME Journal
Podcast
*TLP #1: Navigating the path to team leader, guest: Maxim Greenberg – Renaud Pourpre and Jonathan Weitzman – The Lonely Pipette: helping scientists do better science
Burnout Syndrome, guest: Beth Thompson – Christine Boinett – Your Digital Mentor Podcast
August 2020 Pod: From the deep sea to the lost sense of smell – Bengtsson-Palme Lab – Microbiology Lab Pod
Events &c
Black In Microbiology Week [September 28 – October 4]
a vibrant celebration of Black microbiologists, with talks & panels featuring microbiologists across career stages and subdisciplines
How CHROMagar™ Revolutionized Microbe Identification – Andrea Prinzi – ASM
*Submit a Masterpiece to ASM Agar Art 2020!
The National Summer Undergraduate Research Project (NSURP) #nolabnoproblem initiative – Projects & Presentations
