November 25, 2015 – another digest

Two digests today, to catch up with all literature that came out earlier this week. Gut microbiota of patients with stroke or TIAs, symbiosis within symbiosis, the coffee-machine microbiome, and chocolate making with yeasts.

Human gut microbiome

Dysbiosis of Gut Microbiota With Reduced Trimethylamine‐N‐Oxide Level in Patients With Large‐Artery Atherosclerotic Stroke or Transient Ischemic Attack – Jia Yin – Journal of the American Heart Association

Siri, What Should I Eat? – Reiner Jumpertz von Schwartzenberg, Peter J. Turnbaugh – Cell

Human skin microbiome

Microbiologic Safety of the Transareolar Approach in Breast Augmentation – Dana Mihaela Jianu – Aesthetic Surgery Journal

Microbiome models

Microbiota’s No Wasting Policy – Miguel P. Soares – Cell

Animal microbiome

Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis
Mateus Laguardia-Nascimento – PLOS ONE

Review: The natural occurrence of secondary bacterial symbionts in aphids – Sharon E. Zytynska – Ecological Entomology

Plant, root, and soil microbiome

Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts
Philippe Remigi – Trends in Microbiology

Soil microbial response to tetracycline in two different soils amended with cow manure – Luigi Chessa – Environmental Science and Pollution Research

Reviews: Friends or foes? Emerging insights from fungal interactions with plants – Susanne Zeilinger – FEMS Microbiology Reviews

Review: Extinction risk of soil biota – worrying paucity of existing information – Stavros D. Veresoglou – Nature Communications

Extremophile microbiome

Integrated ‘Omics’, Targeted Metabolite and Single-cell Analyses of Arctic Snow Algae Functionality and Adaptability – Stefanie Lutz – Frontiers in Microbiology

Water microbiome

Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members – Graham G. Willsey – PLOS ONE

Built environment microbiome

The coffee-machine bacteriome: biodiversity and colonisation of the wasted coffee tray leach – Cristina Vilanova – Scientific Reports

Food microbiology

Tuning chocolate flavor through development of thermotolerant Saccharomyces cerevisiae starter cultures with increased acetate ester production – Esther Meersman – Applied and Environmental Microbiology

Microbial genomes and ecology

Migration and horizontal gene transfer divide microbial genomes into multiple niches
Rene Niehus – Nature Communications

The Good, the Bad, and the Tiny: A Simple, Mechanistic-Probabilistic Model of Virus-Nutrient Colimitation in Microbes – B. B. Cael – PLOS ONE

Microbes are trophic analogs of animals – Shawn A. Steffan – PNAS

Animal–microbe interactions and the evolution of nervous systems – Heather L. Eisthen – Philosophical Transactions B

Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi – Martin Ryberg – Molecular Ecology

Review: Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome – Maayan Levy – Genome Medicine

Metagenomics and bioinformatics

Large-scale Machine Learning for Metagenomics Sequence Classification – Kévin Vervier – Bioinformatics


Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing – Marcia L. Hart – PLOS ONE

Bacteria in the news

Your gut bacteria are controlling your appetite, study finds – Bec Crew – ScienceAlert

Beastly bacteria on extinct ancient carcasses offers ‘cure’ for modern oil pollution – Vera Salnitskaya – The Siberian Times

This ‘Plant Lamp’ uses bacteria to generate electricity – Sean Buckley – EnGadget


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