April 11, 2015

Another new paper on gorilla gut microbiome, reviews on role of microbes in obesity, and finding the microbial equivalent of cockroaches.

Pregnancy and birth microbiome

Pathogenesis of neonatal necrotizing enterocolitis – Joanna C. Lim – Pediatric Surgery International

Human oral microbiome

Differentiation of salivary bacterial profiles of subjects with periodontitis and dental caries – Daniel Belstrøm – Journal of Oral Microbiology

Secretome of gingival epithelium in response to subgingival biofilms – N. Bostanci – Molecular Oral Microbiology

Human gut microbiome

Perspective: Integrating host gene expression and the microbiome to explore disease pathogenesis – Allyson L Byrd and Julia A Segre – Genome Biology

Review: Recent Advances in Characterizing the Gastrointestinal Microbiome in Crohn’s Disease: A Systematic Review – Emily K Wright – Inflammatory Bowel Diseases

Review: Dietary effects on human gut microbiome diversity – Zhenjiang Xu and Rob Knight – British Journal of Nutrition

Review: Obesity and the gastrointestinal microbiota: a review of associations and mechanisms – Catherine Graham – Nutrition Reviews

Review: Gut Microbiome and Obesity: A Plausible Explanation for Obesity – Claudia Sanmiguel – Current Obesity Reports

Animal model microbiome

Distinct Commensals Induce Interleukin-1β via NLRP3 Inflammasome in Inflammatory Monocytes to Promote Intestinal Inflammation in Response to Injury – Sang-Uk Seo – Immunity
Animal microbiome

Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology – Andres Gomez – Molecular Ecology

Soil and plant root microbiome

Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests – Cedar N. Hesse – Frontiers in Microbiology

Parent materials have stronger effects than land use types on microbial biomass, activity and diversity in red soil in subtropical China – Huan Deng – Pedobiologia

Changes in soil microbial functional diversity and biochemical characteristics of tree peony with amendment of sewage sludge compost – Xiangdong Huang – Environmental Science and Pollution Research

16S rRNA study, not metagenomics: Cataloguing the bacterial diversity of the Sundarbans mangrove, India in the light of metagenomics – Pijush Basak – Genomics Data

Relationships among bulk soil physicochemical, biochemical, and microbiological parameters in an organic alfalfa-rice rotation system – Ana R. Lopes – Environmental Science and Pollution Research

Soil microbial responses over 2 years following biochar addition to a north temperate forest – Genevieve L. Noyce – Biology and Fertility of Soils

Water microbiome

Temporal Dynamics of Active Prokaryotic Nitrifiers and Archaeal Communities from River to Sea – Mylène Hugoni – Microbial Ecology

Extremophile microbiome

Finding the microbial equivalent of cockroachesThe impact of gamma radiation on sediment microbial processes – Ashley R. Brown – Applied and Environmental Microbiology

Built environment microbiome

Methods to Assess Human Occupancy and Occupant Activity in Hospital Patient Rooms – Sandra Dedesko – Building and Environment

Bioreactor microbiology

Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing – Jiemin Zhou – Journal of Hazardous Materials

Microbial Ecology

Antimicrobial Resistance: The Major Contribution of Poor Governance and Corruption to This Growing Problem – Peter Collignon – PLOS ONE

Local–global overlap in diversity informs mechanisms of bacterial biogeography – Joshua A Livermore and Stuart E Jones – The ISME Journal

Metagenomics and bioinformatics

Inference of Markovian Properties of Molecular Sequences from NGS Data and Applications to Comparative Genomics – Jie Ren – ArXiv

Techniques

Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members – J.-B. Ramond – Letters in Applied Microbiology

Estimating Protistan Diversity using High-throughput Sequencing – Sarah K. Hu – Journal of Eukaryotic Microbiology

Microbes in the news

Connecting Indoor Microbiome Studies with Indoor Chemistry – Jonathan Eisen – MicroBE.net

Smart Sewers Will Reveal What’s in Cambridge Citizens’ Guts – Elie Dolgin – IEEE Spectrum

Microbes disprove long-held assumption that all organisms share a common vocabulary – Science Daily

Scientists study mystery of Lake Erie toxic bacteria – Detroit Free Press

Jessica Cofield puts degrees in microbiology to good use – Crystal Garrett – Sun Journal

MRSA Bacteria From Borrowed Makeup Brush Paralyzes 27-Year-Old Woman – Lecia Bushak – Medical Daily

Science, publishing, and career

Virginia student earns admission to all eight Ivy League schools, and others – T. Rees Shapiro – Washington Post

China’s medical research integrity questioned – The Lancet

The seven sins of peer review – Technologist

Bik’s Picks

Review: Innovations in Health Value and Functional Food Development of Quinoa (Chenopodium quinoa Willd.) – Brittany L. Graf – Comprehensive Reviews in Food Science and Food Safety

In Hawaii, Chickens Gone Wild – Kenneth Chang – New York Times

Komodo dragon named Smaug gets a leg up from a new prosthetic – Rachel Feltman – Washington Post

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