March 25, 2016

A minimal bacterial genome, gut microbes/TMAO/platelets, (pro)phages and genomes, Top 50 unidentified fungi, and Propionibacterium acnes as a contaminant.

General microbiome

Review: Speciation by Symbiosis: The Microbiome and Behavior – J. Dylan Shropshire – BioRxiv

Human gut microbiome
Research highlight: Gut microbes modulate platelet function and thrombosis risk – Irene Fernández-Ruiz – Nature Reviews Cardiology

Combination of human and mouse studies: Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis Risk – Weifei Zhu – Cell

Animal microbiome

Comparison of Fecal Microbiota between German Holstein Dairy Cows with and without Left-Sided Displacement of the Abomasum – Eun-Sik Song – Journal of Clinical Microbiology

Plant, root, and soil microbiome

Infection with a Shoot-Specific Fungal Endophyte (Epichloë) Alters Tall Fescue Soil Microbial Communities – Xavier Rojas – Microbial Ecology

Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits – L Bordez – Molecular Ecology

Spatial and temporal variation of cultivable communities of co-occurring endophytes and pathogens in wheat – Morgane Comby – Frontiers in Microbiology

Plant Growth-Promoting Rhizobacteria Inoculation to Enhance Vegetative Growth, Nitrogen Fixation and Nitrogen Remobilisation of Maize under Greenhouse Conditions – Khing Boon Kuan – PLOS ONE

Microbial control of soil organic matter mineralisation responses to labile carbon in subarctic climate change treatments – Kathrin Rousk – Global Change Biology

Water microbiome

Effects of temperature and nutrients on changes in genetic diversity of bacterioplankton communities in a semi-closed bay, South Korea – Hyun Jung Kim – Marine Pollution Bulletin

Built environment microbiome

Imported anthropogenic bacteria may survive the Antarctic winter and introduce new genes into local bacterial communities – Kristian Brat – Polish Polar Research

Waste and pollution microbiome

Consistency between health risks and microbial response mechanism of various petroleum components in a typical wastewater-irrigated farmland – Juan Zhang – Journal of Environmental Management

Metagenomics and bioinformatics

DUDes: a top-down taxonomic profiler for metagenomics – Vitor C. Piro – Bioinformatics


Genetic and life-history traits associated with the distribution of prophages in bacteria – Marie Touchon – The ISME Journal

Hyperexpansion of RNA Bacteriophage Diversity – Siddharth R. Krishnamurthy – PLOS Biology


Top 50 most wanted fungi – Henrik Nilsson – MycoKeys

Book: Biology of Microfungi – Editors: De-Wei Li – Springer

Book: The Mycota: Environmental and Microbial Relationships – Editors: Irina S. Druzhinina, Christian P. Kubicek – Springer


Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing – Mohammad R. Hasan – Journal of Clinical Microbiology

Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples – Andries E. Budding – Journal of Clinical Microbiology

Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing – Sarah Mollerup

More microbiology

531 kb (473 genes): Design and synthesis of a minimal bacterial genome – Clyde A. Hutchison III – Science

How clonal are bacteria over time? – B. Jesse Shapiro – BioRxiv preprint

Microbes in the news

This man-made cell has the smallest genome ever — but a third of its genes are a mystery – Rachel Feltman – Washington Post

The Mysterious Thing About a Marvelous New Synthetic Cell – Ed Yong – The Atlantic

After 20 Year Quest, Biologists Create Synthetic Bacteria With No Extra Genes – Matthew Herper – Forbes

Scientists Create Tiniest Life Form Yet, Not Sure What It Is – Eric Roston – Bloomberg

Microbes can play games with the mind – Laura Sanders – Science News

SDSU researcher examines link between gut bacteria and metabolic disease – Adriana Millar – The Daily Aztec

What gut bacteria can teach us about cancer treatment: Studies probe link between gut bacteria and treatment effectiveness – Jenn Savedge – Mother Nature Network

ElizabethkingiaSenator seeks answers from CDC on mystery bacteria – Jonathan Stefonek – Daily Register

Study finds vast diversity among viruses that infect bacteria – EurekAlert

Bik’s Picks

Comb jelly ‘anus’ guts ideas on origin of through-gut – Amy Maxmen – Science

Funding Freeze Hits Natural History Museum Collections – Ed Yong – The Atlantic

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