April 22, 2019

(Posting for our new team member, Zehra Tüzün Güvener.)

Good Morning! Highlights from Monday’s digest include a widely distributed efflux pump in saprophytic soil bacteria, genomic analysis of plant-growth-promoting rhizobacteria, identification of novel mammalian viruses from bats, rectal swabs to study gut microbiomes and TrueBiome’s solution to reduce variability in animal experiments.

General Microbiology

Efflux pumps in Chromobacterium species and their involvement in antibiotic tolerance and survival in a co-culture competition model – Benomar et al. – BioRxiv

Muropeptides Stimulate Growth Resumption from Stationary Phase in Escherichia coli – Joers et al. –  BioRxiv
Human oral microbiome

Current Understanding of the Gut Microflora in Subjects with Nutrition-Associated Metabolic Disorder Such as Obesity and/or Diabetes: Is There Any Relevance with Oral Microflora? – Yumoto et al. –  Current Oral Health Reports
Human skin microbiome

Scalp bacterial shift in Alopecia areata – Pinto et al. –  PLOS ONE
Human gut microbiome

Factors influencing the gut microbiome in children: from infancy to childhood – Kumbhare et al. – Journal of Biosciences
Animal microbiomes

Defining Escherichia coli as a health-promoting microbe against intestinal Pseudomonas aeruginosa – Christofi et al. – BioRxiv

Glyphosate, but not its metabolite AMPA, alters the honeybee gut microbiota – Blot et al. – PLOS ONE
Plant, root and soil microbiome

**MiniReview: Gene mobility in microbiomes of the mycosphere and mycorrhizosphere –role of plasmids and bacteriophages – Pratama et al. –  FEMS Microbial Ecology

**Review: Response of microbial communities to biochar-amended soils: a critical review – Palansooriya et al. –  Biochar

The effects of soil phosphorous content on microbiota are driven by the plant phosphate starvation response – Finkel et al. – – BioRxiv

Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis – Du et al. – BMC Genomics

Are drivers of root-associated fungal community structure context specific? – Alzarhani et al. –  The ISME Journal
Water and extremophile microbiome

Impact of NaCl, nitrate and temperature on the microbial community of a methanol-fed, denitrifying marine biofilm – Villemur et al.  – BioRxiv

Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments – Dong et al. – Nature Communications
Probiotics / prebiotics

Screening of single or combined administration of 9 probiotics to reduce ammonia emissions from laying hens – Mi et al. – Poultry Science
Phages and viruses

A viral metagenomic survey identifies known and novel mammalian viruses in bats from Saudi Arabia – Mishra et al. – PLOS ONE
Techniques

Metaproteomics of Freshwater Microbial Communities – Russo et al. –  Mass Spectometry of Proteins (Methods in Molecular Biology)

Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate – Gonzales et al. –  The ISME Journal

Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR – Gobbi et al. — PLOS ONE

Usability of rectal swabs for microbiome sampling in a cohort study of hematological and oncological patients – Biehl et al. –  PLOS ONE
Microbes in the news

** Report – North America Human Microbiome Market to 2025 – Regional Analysis and Forecasts by Product, Disease, Application, and Country –  Research and Markets
Microbes on the market

** Newsletter – Addressing experimental variability: Taconic launches TruBiome – Outsourcing-Pharma.com

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