September 24, 2015

Human genetic variation and microbiome composition, turmeric & travel, Nicotiana recruitment, and microbial stress in the city.

General microbiome

Editorial: Host genetic architecture and the landscape of microbiome composition: humans weigh in – Andrew K Benson – Genome Biology

Host genetic variation impacts microbiome composition across human body sites
Ran Blekhman – Genome Biology

Database of host-pathogen and related species interactions, and their global distribution – Maya Wardeh – Scientific Data

Pregnancy and birth

The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome – Paurush Praveen – Microbiome

The role of infection in miscarriage – Sevi Giakoumelou – Human Reproduction Update

Human gut microbiome

The Effect of Probiotics on Gut Microbiota during the Helicobacter pylori Eradication: Randomized Controlled Trial – Bumjo Oh – Helicobacter

Intestinal microbial communities associated with acute enteric infections and disease recovery – Pallavi Singh – Microbiome

Review: Advancing gut microbiome research using cultivation – Morten OA Sommer – Current Opinion in Microbiology

Human urinary tract microbiome

Re: The Microbiome of the Urinary Tract—A Role Beyond Infection – Alan J. Wein – The Journal of Urology

Animal models

Modulation of gut microbiota by berberine and metformin during the treatment of high-fat diet-induced obesity in rats – Xu Zhang – Scientific Reports

A small-molecule antivirulence agent for treating Clostridium difficile infection – Kristina Oresic Bender – Science Translational Medicine

Regulators of Gut Motility Revealed by a Gnotobiotic Model of Diet-Microbiome Interactions Related to Travel – Neelendu Dey – Cell

Animal microbiome

High-throughput DNA sequencing of the moose rumen from different geographical
location reveals a core ruminal methanogenic archaeal diversity and a differential
ciliate protozoal diversity – Suzanne Lynn Ishaq – Microbial Genomics

Microbial populations and fermentation profiles in rumen liquid and solids of Holstein cows respond differently to dietary barley processing – Barbara U. Metzler-Zebeli – Journal of Applied Microbiology

Culture based: Actinomycetes from the South China Sea sponges: isolation, diversity and potential for aromatic polyketides discovery – Zhiyong Li – Frontiers in Microbiology

Longitudinal study of the early-life fecal and nasal microbiotas of the domestic pig – Mackenzie Jonathan Slifierz – BMC Microbiology

Faecal microbiota characterisation of horses using 16 rdna barcoded pyrosequencing, and carriage rate of clostridium difficile at hospital admission – Cristina Rodriguez – BMC Microbiology

Essential Amino Acid Supplementation by Gut Microbes of a Wood-Feeding Cerambycid – Paul A. Ayayee – Environmental Entomology

Plant, root, and soil microbiome

RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere – Kalyan Chakravarthy Mynampati – Environmental Pollution

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features – Kayla N. Burns – Soil Biology and Biochemistry

Nicotiana Roots Recruit Rare Rhizosphere Taxa as Major Root-Inhabiting Microbes – Muhammad Saleem – Plant Microbe Interactions

Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling – Feng Wang – Scientific Reports

The coupling of the plant and microbial catabolisms of phenanthrene in the rhizosphere of Medicago sativa – Anna Muratova – Journal of Plant Physiology

Contrasting soil bacterial community structure between the phyla Acidobacteria and Proteobacteria in tropical Southeast Asian and temperate Japanese forests – Naohiko T. Miyashita – Genes & Genetic Systems

Review: Ecological importance of soil bacterivores for ecosystem functions – Jean Trap – Plant and Soil

Editorial: Microbial ecology of hydrocarbon-polluted coastal sediments – Robert Duran – Environmental Science and Pollution Research

Waste microbiology

Identification of Bacteria Synthesizing Ribosomal RNA in Response to Uranium Addition During Biostimulation at the Rifle, CO Integrated Field Research Site – Lora R. McGuinness – PLOS ONE

Microbial ecology of hydrocarbon-polluted coastal sediments – Robert Duran – Environmental Science and Pollution Research

Built environment microbiome

Urban stress is associated with variation in microbial species composition-but not richness-in Manhattan – Aspen T Reese – ISME Journal

Microbiome of death

The Search for a Volatile Human Specific Marker in the Decomposition Process – E. Rosier – PLOS ONE

Bioinformatics and metagenomics

In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database – Calum J. Walsh – BMC Microbiology

PhD thesis: Novel methods for comparing and evaluating single and metagenomic assemblies – Christopher M. Hill – University of Maryland

Microbes in the news

Metagenomic Sequencing Shows Changes in Healthy Gut Microbiome Pre- and Post-Antibiotics – Genome Web

Study shows whale microbiome shares characteristics with both ruminants and predators – Phys.org

Researchers isolate the ‘human smell of death’ – Elizabeth Pennisi – Science

Scientists find way to disarm deadly bacteria without destroying the good ones in your gut – Lena H. Sun – Washington Post

Science, publishing, and career

Failure to replicate the STAP cell phenomenon – Alejandro De Los Angeles – @nature

Make academic job advertisements fair to all: Too many university posts are given to men without proper competition – Mathias Wullum Nielsen – Nature

Gender-disparity study faces attack: A paper suggesting a Dutch grant scheme shows bias against women is criticized for a statistical flaw – Chris Woolston

Bik’s Picks

In the name of beauty: phasing out plastic microbeads found in skin scrubs – Nature

How Climate Change Shrank the Tongues of Long-Tongued Bumblebees – Ed Yong

Enamel evolved in the skin and colonized the teeth much later – EurekAlert

Giant Killer Lizards Lived Among Ice-Age Aussies – Discovery
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