June 17, 2015

After a long day in the hood having fun with stool samples (Ha! I hope you are not reading this during breakfast), finally time for the digest.

Microbiome of pregnancy and birth

Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case – Jacque C. Young – Proteomics

Mouse model: Alterations in the Vaginal Microbiome by Maternal Stress Are Associated With Metabolic Reprogramming of the Offspring Gut and Brain – Eldin Jašarević- Endocrinology

Human oral microbiome

Subgingival microbiome in patients with healthy and ailing dental implants – Hui Zheng – Scientific Reports

Human gut microbiome

EditorialThe Interactions between Innate Immunity and Microbiota in Gastrointestinal Diseases – Danilo Pagliari – Journal of Immunology Research

Animal microbiome

Microbial diversity associated with copepods in the North Atlantic subtropical gyre – Katyanne M. Shoemaker – FEMS Microbiology Ecology

Plant microbiome

Bacterial populations on the surfaces of organic and conventionally grown almond drupes – J.A. McGarvey – Journal of Applied Microbiology

Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific – Tao Zhang – PLOS ONE

Plant root and soil microbiome

High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy – Hyo Jung Lee – Frontiers in Microbiology

Profiling microbial community structures across six large oilfields in China and the potential role of dominant microorganisms in bioremediation – Weimin Sun – Applied Microbiology and Biotechnology

Influence of Pre-Emergence Herbicides on the Soil Microflora during the
Crop growth of Blackgram, Vigna mungo.L – N.Trimurtulu – Int.J.Curr.Microbiol.App.Sci

Metagenomics and Bioinformatics

GenomePeek—an online tool for prokaryotic genome and metagenome analysis – Katelyn McNair – PeerJ

Deconvolving molecular signatures of interactions between microbial colonies – Y.-C. Harn – Bioinformatics

Reconstructing 16S rRNA genes in metagenomic data – Cheng Yuan – Bioinformatics

Microbes in the news

Below Our Feet, a World of Hidden Life – Elizabeth Svoboda – Quanta Magazine

Maternal stress alters offspring gut, brain through vaginal microbiome – Science Daily

Big Shoulders STEM Scholars – Dr Jack Gilbert explains the latest microbiome research to students; A short artwork project with artist Katharine Gilbert was completed at the end. – YouTube


This reminded me of the door scene from Office SpaceGerm-Zapping Doorknob Could Get a Handle on Bathroom Bacteria – TakePart

Bik’s Picks

An Estimate of the Total DNA in the Biosphere – Hanna K. E. Landenmark – PLOS Biology

New NASA data show how the world is running out of water – Todd C. Frankel – The Washington Post

Tiny Octopus Is So Cute Scientists Might Name It ‘Adorabilis’ – Carl Enkelking – Discover Magazine


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