February 20, 2016

Effects of ocean acidification, structural proteins in viral dark matter, and microbiome art. Also check out my new post at MicroBE.net with new papers on microbiome of the built environment.

Human respiratory tract microbiome

Review: How Recent Advances in Molecular Tests Could Impact the Diagnosis of Pneumonia – David Murdoch – Expert Review of Molecular Diagnostics

Microbiome models

In vitro fermentation of alginate and its derivatives by human gut microbiota – Miaomiao Li – Anaerobe

Plant, root, and soil microbiome

Changes of soil prokaryotic communities after clear cutting in a karst forest: evidences for cutting-based disturbance promoting deterministic processes – Xiao Zhang – FEMS Microbiology Ecology

Use of mulberry–soybean intercropping in salt–alkali soil impacts the diversity of the soil bacterial community – Xin Li – Microbial Biotechnology

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments – Lidianne L. Rocha – International Journal of Microbiology

Water and ice microbiome

Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches – Christiane Hassenrück – FEMS Microbiology Ecology

Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice – Ido Hatam – The ISME Journal

Bioreactor and waste microbiology

Biodegradation of different petroleum hydrocarbons by free and immobilized microbial consortia – Tiantian Shen – Environmental Science: Processes & Impacts

Bioinformatics and metagenomics

Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms – Ayyappa kumar Sista Kameshwar – International Journal of Biological Sciences

DUDE-Seq: Fast, flexible, and robust denoising of nucleotide sequences – Byunghan Lee – Bioinformatics

HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing – Ramin Karimi – Evolutionary Bioinformatics

FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance – Syun-ichi Urayama – Microbes and Environments

Based on my old discovery of the mycobacterial CRISPR: SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads – Eryu Xia – Genome Medicine

Microbial ecology

A tradeoff between the ecological and evolutionary stabilities of public goods genes in microbial populations – Joseph Rauch – BioRxiv

Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations – Tatiana Shashkova – PLOS ONE

Proteomics

Illuminating structural proteins in viral “dark matter” with metaproteomics – Jennifer R. Brum – PNAS

Microbes in the news

‘Unhealthy’ Microbiomes Could Promote Metabolic Disease. UCSF Symposium Explores Vulnerability and Malleability of Microbes in Human Gut – Nicholas Weiler – University of California San Francisco

Unusual sugar in leafy greens may help gut bacteria protect health – Catharine Paddock – Medical News Today

One startup’s plan to grow more crops: put the germs back in. Indigo claims it can dramatically boost yields by restoring plant’s microbiome – Ben Popper – The Verge

The intestinal microbiota—a new ally for optimum growth – Medical Xpress

Bacteria In Contact Lenses May Cause Inflammatory Response Leading To Microbial Keratitis / Gross Science Video with Anna Rothschild – Lizette Borreli – Medical Daily

Bacteria Hysteria

Tea crawling with harmful bacteria and food trays covered in faeces: The horror health threats facing airline passengers – The Sun

Microbes and art

Faces of BioArt: Sonja Bäumel’s Microbiome Portraits and Bacterial Clothing – Labiotech

Science, publishing, and career

Put the “Ph” Back in PhD. We need big thinkers, but the current system teaches students to think small – Arturo Casadevall

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