July 14, 2015

Antibiotic-induced changes in mouse gut microbiome, the lichen microbiome, and what’s floating in the airplane toilet?

Human respiratory microbiome

Common Cell Shape Evolution of Two Nasopharyngeal Pathogens – Frédéric J. Veyrier – PLOS Genetics

Human gut microbiome

Trimethylamine-N -oxide: A Novel Biomarker for the Identification of Inflammatory Bowel Disease – Aze Wilson – Digestive Diseases and Sciences

Review: Roles of commensal microbiota in pancreas homeostasis and pancreatic pathologies – Camila Leal-Lopes – Journal of Diabetes Research

Animal models of microbiome research

Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile – Alyxandria M. Schubert – mBio

Animal microbiome

The Apis mellifera Filamentous Virus Genome – Laurent Gauthier – Viruses

Concentrations of viable oil-degrading microorganisms are increased in feces from Calanus finmarchicus feeding in petroleum oil dispersions – Ingvild Fladvad Størdal – Marine Pollution Bulletin

Editorial: Microbial symbiosis of marine sessile hosts- diversity and function – Suhelen Egan – Frontiers in Microbiology

Plant, root, and soil microbiome

Analyzing the antagonistic potential of the lichen microbiome against pathogens by bridging metagenomic with culture studies – Tomislav Cernava – Frontiers in Microbiology

Indigenous trees restore soil microbial biomass at faster rates than exotic species – Chun Li – Plant and Soil

MSc Thesis: Tree Islands of Fertility Structure Bacterial Community Assembly and Functional Genes Contributing to Ecosystem Processes – Tayte Paul Campbell – Brigham Young University

Rhizosphere microbiome selection by Epichloë endophytes of Festuca arundinacea – Elizabeth Lewis Roberts – Plant and Soil

Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China – W. Y. Dong – Biogeosciences Discussions

Water microbiome

Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump – S. Agusti – Nature Communications

Extremophile microbiome

Characterization of the Bacterial and Sulphate Reducing Community in the Alkaline and Constantly Cold Water of the Closed Kotalahti Mine – Malin Bomberg – Minerals

Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes – J. Comte – Biogeosciences Discussions

Built environment and waste microbiome

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance – Thomas Nordahl Petersen- Scientific Reports

Development of antibiotic resistance genes in microbial communities during long-term operation of anaerobic reactors in the treatment of pharmaceutical wastewater – Sevcan Aydin – Water Research

One-Time Addition of Nano-TiO2 Triggers Short-Term Responses in Benthic Bacterial Communities in Artificial Streams – Alexandra Ozaki – Microbial Ecology

Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure – Li Sun – Microbial Biotechnology

Characterization of the microbial community structure and the physicochemical properties of produced water and seawater from the Hibernia oil production platform – C. William Yeung – Environmental Science and Pollution Research


The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales – Zackary J. Jay – Biology Direct


Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff – Daniel K. Manter – Bioinformatics

Swarm v2: highly-scalable and high-resolution amplicon clustering – Frederic Mahe – PeerJ

Cutting edge: Anatomy of BioJS, an open source community for the life sciences – Guy Yachdav – eLIFE


Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes – Sari Peura – Scientific Reports

Metabolic networks, proteomics

A Single Host-Derived Glycan Impacts Key Regulatory Nodes of Symbiont Metabolism in a Coevolved Mutualism – Min Pan – mBIO

Extracellular protein analysis of activated sludge and their functions in wastewater treatment plant by shotgun proteomics – Peng Zhang – Scientific Reports


Scaffolding of a bacterial genome using MinION nanopore sequencing – E. Karlsson – Scientific Reports

Microbial Ecology

Biodiversity inhibits parasites: Broad evidence for the dilution effect – David J. Civitello – PNAS

Science, publishing, and career

Big Data: Astronomical or Genomical? Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. – Zachary D. Stephens – PLOS Biology

The Outrage Factor – Then and Now: There’s a lot of outrage about outrage storming around women in science and science journalism at the moment. And fear of causing it, too. – Hilda Bastian – PLOS Blogs

Microbes in the news

Aging in Microbes: bacteria are using every trick in the book to get ahead – Josh Mitteldorf

Bik’s Picks

Everything you need to know about Tuesday’s Pluto encounter – Rachel Feltman – Washington Post

Introducing the Pentaquark: Physicists Prove a New Particle Exists – Tanya Basu – Time

Neighborhood greenspace and health in a large urban center : higher health perception if you live near trees – Omid Kardan – Scientific Reports


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