June 20, 2015

Catching up after spending all day in the lab on Friday, and all day working on figures and text today…. Here’s your weekend digest, with the microbiome of sport schools, phasing of Illumina sequencing, and happy endings for preterm infants.

Pregnancy and birth microbiome

Preterm infant gut colonization in the Neonatal ICU and Complete Restoration two years later – Laura Moles – Clinical Microbiology and Infection

Clostridium butyricum strains and dysbiosis linked to necrotizing enterocolitis in preterm neonates – Nadim Cassir – Clinical Infectious Diseases

Human respiratory microbiome

The microbiome of the human lower airways: a next generation sequencing perspective – Velma T. E. Aho – World Allergy Organization Journal

Human skin microbiome

Poster: Noma disease: 10 years of research in the quest of a microbial etiology – P François – Antimicrobial Resistance and Infection Control

Human oral microbiome

Oral Mucositis in Pediatric Acute Lymphoblastic Leukemia Patients: Evaluation of Microbiological and Hematological Factors – Regina Maria Holanda de Mendonça – Pediatric Hematology-Oncology

Human gut microbiome

Composition and temporal stability of the gut microbiota in older persons – Ian B Jeffery – The ISME Journal

The Host Genotype and Environment Affect Strain Types of Bifidobacterium longum subsp. longum Inhabiting the Intestinal Tracts of Twins – Min Zhang – Applied and Environmental Microbiology

The Influence of the Gut Microbiome on Obesity, Metabolic Syndrome and Gastrointestinal Disease – Parth J Pareck – Clinical and Translational Gastroenterology

Editorial: About the gut microbiome as a pharmacological target in atherosclerosis – Julia.J. Witjes – European Journal of Pharmacology

Editorial: Diabetes, More on Merde, the Microbiome, and the Dung Beetle – Richard I. Shader – Clinical Therapeutics

Review: Effect of Dietary Resistant Starch on Prevention and Treatment of Obesity-related Diseases and Its Possible Mechanisms – Lei Zhang – Biomedical and Environmental Sciences

Animal models

In pigs: Influence of genotype and feeding strategy on pig performance, plasma concentrations of micro nutrients, immune responses and fecal microbiota composition of growing-finishing pigs in a forage-based system – A.G. Kongsted – Livestock Science

In rats: Prenatal Stress-Induced Alterations in Major Physiological Systems Correlate with Gut Microbiota Composition in Adulthood – Anna V. Golubeva – Psychoneuroendocrinology

In mice: The genetic architecture of NAFLD among inbred strains of mice – Simon T Hui – eLIFE

Animal microbiome

Cows: Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency – Kelsea A. Jewell – Applied and Environmental Microbiology

Thesis: The earthworm microbiome – Daniel Antony Pass – Cardiff University

Thesis: Gut microbiota of migratory passerines at stopover – William Lewis – University of Southern Mississippi

Plant microbiome

PERN: an EU–Russia initiative for rhizosphere microbial resources – Stéphane Declerck – Trends in Biotechnology

Review: Biological control in the microbiome era: challenges and opportunities – Haissam Jijakli – Biological Control

Plant root and soil microbiome

Impact of plant domestication on rhizosphere microbiome assembly and functions
Juan E. Pérez-Jaramillo – Plant Molecular Biology

16S rRNA-based bacterial community structure is a sensitive indicator of soil respiration activity – Rongxiao Che – Journal of Soils and Sediments

Built environment microbiome

Athletic equipment microbiota are shaped by interactions with human skin – Mariah Wood – Microbiome

Food microbiology

Bacteriophages Isolated from Chicken Meat and the Horizontal Transfer of Antimicrobial Resistance Genes – Amira Shousha – Applied and Environmental Microbiology

Microbiological diversity associated with the spontaneous wet method of coffee fermentation – Suzana Reis Evangelista – International Journal of Food Microbiology

Chemical and microbiological characteristics of traditional homemade fresh goat cheeses from Northern Morocco – Ouiam El Galiou – Small Ruminant Research

Metagenomics and bioinformatics

Microbial bioinformatics for food safety and production – Wynand Alkema – Briefings in Bioinformatics

Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review – Felipe H. Coutinho – Peer J

Ultra-large alignments using phylogeny-aware profiles – Nam-phuong D Nguyen – Genome Biology


Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis – Liyou Wu – BMC Microbiology

Microbes in the news

Medicine’s next frontier: The microbiome – Meg Tirrell – CNBC

Microbes could be key for better yields, stronger plants – Michigan State University – AG Professional

Berkeley balcony collapse: A failure at the intersection of building science and microbiology – Brent Stephens – Microbe.net

Science, publishing, and career

Gender Differences in Physicians’ Financial Ties to Industry: A Study of National Disclosure Data – Susannah L. Rose – PLOS ONE

“If you think it’s rude to ask to look at your co-authors’ data, you’re not doing science” – C. K. Gunsalus and Drummond Rennie – Retraction Watch

Bik’s Picks

An Ant With the Right Coat for 158-Degree Weather – Sindya N. Bhanoo – New York Times

8 million mummified animals, mostly dogs, in catacombs at Egypt site – Greg Botelho – CNN

Blind Americans can now ‘see’ with a device that uses their tongues – Michelle Cortez – Mashable



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