May 14, 2016

Your weekend microbiome update.

Human Respiratory microbiome

The significance of oral streptococci in patients with pneumonia with risk factors for aspiration: the bacterial floral analysis of 16S ribosomal RNA gene using bronchoalveolar lavage fluid – Kentaro Akata – BMC Pulmonary Medicine

The cystic fibrosis lower airways microbial metagenome – Patricia Moran Losada – ERJ Open Research

Nasopharyngeal Microbiome in Respiratory Syncytial Virus Resembles Profile Associated with Increased Childhood Asthma Risk – Christian Rosas-Salazar – American Journal of Respiratory and Critical Care Medicine

Enumerating Virus-Like Particles and Bacterial Populations in the Sinuses of Chronic Rhinosinusitis Patients Using Flow Cytometry – Jessica A. P. Carlson-Jones – PLOS ONE

Human ear microbiome

MALDI-TOF mass spectrometry reveals a highly complex bacterial profile of otitis media with effusion – Zoltán Papp – International Journal of Pediatric Otorhinolaryngology

Human gut microbiome

Editorial: Heartbeat: The gut microbiota and heart failure – Catherine M Otto – Heart

Editorial: Dietary metabolism, gut microbiota and acute heart failure – WH Wilson Tang – Heart

Trimethylamine N-oxide and prognosis in acute heart failure – Toru Suzuki – Heart

Animal experiments

Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium – Ting-Chin David Shen – PLOS ONE

Effects of alternative plant-based feeds on hepatic and gastrointestinal histology and the gastrointestinal microbiome of sablefish (Anoplopoma fimbria) – Linda D. Rhodes – Aquaculture

Addendum: Rebooting the Microbiome – Sean Munoz – Gut Microbes

Typos, horrible experiment, and controversial findings. Proceed with care: An investigation into blood microbiota and its potential association with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers – Rabindra K. Mandal – Scientific Reports

Animal microbiome

Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits – Yuliaxis Ramayo-Caldas – The ISME Journal

Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta) – Genevieve Bennett – American Journal of Primatology

Jellyfish: Aurelia aurita ephyrae reshape a coastal microbial community – Luca Zoccarato – Frontiers in Microbiology

Mosquito C-type lectins maintain gut microbiome homeostasis – Xiaojing Pang – Nature Microbiology

Plant, root, and soil microbiome

D-Amino Acid Catabolism Is Common Among Soil-Dwelling Bacteria – Atanas D Radkov – Microbes and Environments

MycoDB, a global database of plant response to mycorrhizal fungi – V. Bala Chaudhary – Scientific Data

Effects of soil substrate quality, microbial diversity and community composition on the plant community during primary succession – Jan Frouz – Soil Biology and Biochemistry

Deciphering the Bacterial Microbiome in Huanglongbing-Affected Citrus Treated with Thermotherapy and Sulfonamide Antibiotics – Chuanyu Yang – PLOS ONE

Fire-severity effects on plant–fungal interactions after a novel tundra wildfire disturbance: implications for arctic shrub and tree migration – Rebecca E. Hewitt – BMC Ecology

Water and extremophile microbiome

The symbiotic relationship of sediment and biofilm dynamics at the sediment water interface of oil sands industrial tailings ponds – T. Reid – Water Research

Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai Trough – Taiki Katayama – FEMS Microbiology Ecology

The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions – Sergei V. Bukin – Frontiers in Microbiology

The diversity and biogeography of the communities of Actinobacteria in the forelands of glaciers at a continental scale – Zhang, Binglin – Environmental Research Letters

Microbial dynamics of the extreme-thermophilic (70 °C) mixed culture for hydrogen production in a chemostat – Fang Zhang – International Journal of Hydrogen Energy

Dense microbial community on a ferromanganese nodule from the ultra-oligotrophic South Pacific Gyre: Implications for biogeochemical cycles – Fumito Shiraishi – Earth and Planetary Science Letters

Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge – Likui Zhang – Scientific Reports

Biofilm transplantation in the deep sea – Irene Wagner-Döbler – Molecular Ecology

Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting – Weipeng Zhang – Molecular Ecology

Food microbiology

Composition and function of sourdough microbiota: From ecological theory to bread quality – Michael Gänzle – International Journal of Food Microbiology

Comparison of DNA-based techniques for differentiation of production strains of ale and lager brewing yeast – J. Kopecká – Journal of Applied Microbiology

Infection microbiology

Review: Polymicrobial-Host Interactions During Infection – Hong Tay Wei – Journal of Molecular Biology

Bioinformatics and metagenomics

A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology – Jesús A. Ballesteros – Molecular Biology and Evolution

Evaluating techniques for metagenome annotation using simulated sequence data (CC) – Richard J. Randle-Boggis – FEMS Microbiology Ecology

Computational methods for predicting genomic islands in microbial genomes – Bingxin Lu – Computational and Structural Biotechnology Journal

Microbial ecology

Quorum Sensing Communication Modules for Microbial Consortia – Spencer R. Scott – ACS Synthetic Biology

Ecological Opportunity, Evolution, and the Emergence of Flea-borne Plague – B. Joseph Hinnebusch – Infection and Immunity

Microbes in the news

NOAA Research on Microbial Communities Contributes to National Microbiome Initiative – Edward Pritchard – NOAA

Parasites Influence Makeup of Human Gut Microbiome, BoG Speaker Reports – GenomeWeb

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