Still catching up from my trip abroad – lots of new papers to share, so I will do two blog posts today.

General microbiome

Elucidating microbial codes to distinguish individuals – Allyson L. Byrd and Julia A. Segre – PNAS

Human oral microbiome

Periodontal status and pathogenic bacteria after gastric bypass: a cohort study – Sílvia Helena de Carvalho Sales-Peres – Journal of Clinical Periodontology

Inflammation-associated microbiota in pediatric eosinophilic esophagitis – Alain J Benitez – Microbiome

Global transcription of CRISPR loci in the human oral cavity – Andrew G Lum – BMC Genomics

Oral and Gastric Helicobacter Pylori: Effects and Associations – Nélio Veiga – PLOS ONE

Book Chapter: Obesity and Periodontal Disease – Simon D. Tran – Environmental Metagenomics

Human gut microbiome

Investigation of the Association Between the Fecal Microbiota and Breast Cancer in Postmenopausal Women: a Population-Based Case-Control Pilot Study – James J. Goedert – Journal of the National Cancer Institute

Review: The art of targeting gut microbiota for tackling human obesity – Marisol Aguirre, Koen Venema – Genes and Nutrition

Review article: dietary fibre–microbiota interactions – H. L. Simpson and B. J. Campbell – Alimentary Pharmacology & Therapeutics

Animal and other microbiome models

Evolutionary transition in symbiotic syndromes enabled diversification of phytophagous insects on an imbalanced diet – Sailendharan Sudakaran – ISME Journal

Fecal Microbial Transplant After Ileocolic Resection Reduces Ileitis but Restores Colitis in IL-102/2 Mice – Troy Perry – IBD Journal

Alteration of gut microbiota by vancomycin and bacitracin improves insulin resistance via glucagon-like peptide 1 in diet-induced obesity – Injae Hwang – The FASEB Journal

Pheromone killing of multidrug-resistant Enterococcus faecalis V583 by native commensal strains – Michael S. Gilmore – PNAS

Human Microbiota-Associated Swine: Current Progress and Future Opportunities – Mei Wang and Sharon M. Donovan – ILAR Journal

Animal microbiome

Marked seasonal variation in the wild mouse gut microbiota – Corinne F Maurice – ISME Journal

Evolution of host specialization in gut microbes: the bee gut as a model – Waidan K Kwong – Gut Microbes

Soil microbiome

Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China – Yuguang Zhang – Microbial Biotechnology

High resolution dynamics of microbial communities during dissimilatory selenate reduction in an anoxic soil – Ronald Ragudo Navarro – Environmental Science & Technology

Study and assessment of microbial communities in natural and commercial bioleaching – Arevik Vardanyan – Minerals Engineering

Benefactor and allelopathic shrub species have different effects on the soil microbial community along an environmental severity gradient – S. Hortal – Soil Biology and Biochemistry

Evaluation of soil microbial communities as influenced by crude oil pollution – Eucharia Oluchi Nwaichi and Magdalena Frac – African Journal of Biotechnology

Water microbiome

Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management – William Van Bonn – Zoo Biology

Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations – Sergio Pulido-Tamayo – Nucleic Acids Research

Manganese and iron as structuring parameters of microbial communities in Arctic marine sediments from the Baffin Bay – Camelia Algora – FEMS Microbial Ecology

Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level – Mounira Smati – Microbiology Open

Manganese cycling microbial communities inside deep-sea manganese nodules – Marco Blöthe – Environmental Science & Technology

Effects of Misgurnus anguillicaudatus and Cipangopaludina cathayensis on Pollutant Removal and Microbial Community in Constructed Wetlands – Pengfei Li – Water

Thesis: Evaluating changes in diversity and functional gene abundance of denitrifying microbe communities and nutrient concentrations in runoff following the implementation of low-grade weirs in agricultural drainage systems – Beth Baker – Mississippi State University/ Gradworks

Bioreactor microbiome

Lipid hydrolysis products affect the composition of infant gut microbial communities in vitro – Rikke G. Nejrup – British Journal of Nutrition

Effect of phospholipid on pyrite oxidation and microbial communities under simulated acid mine drainage (AMD) conditions – Andro-Marc Pierre-Louis – Environmental Science & Technology

Antibiotic resistome and its association with bacterial communities during sewage sludge composting – Jianqiang Su – Environmental Science & Technology

Food microbiology

Microbiota dynamics associated with environmental conditions and potential roles of cellulolytic communities in traditional Chinese cereal starter solid-state fermentation – Pan Li- Applied and Environmental Microbiology

Bioinformatics and metagenomics

Note: not metagenomics but Single Locus Sequencing / OTU defining: MICCA: a complete and accurate software for taxonomic profiling of metagenomic data – Davide Albanese – Scientific Reports

An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data: GotCloud – Goo Jun – Genome Research

GITIRBio: A Semantic and Distributed Service OrientedArchitecture for Bioinformatics Pipeline – Luis F. Castillo – Journal of Integrative Bioinformatics

mmnet: an R package for metagenomics systems biology analysis: community-level metabolic network reconstruction – Yang Cao – BioMed Research International

Techniques

How to evaluate PCR assays for the detection of low-level DNA – Frederik Banch Clausen – APMIS
http://onlinelibrary.wiley.com/doi/10.1111/apm.12405/full

A Novel Microbial Source Tracking Microarray for Pathogen Detection and Fecal Source Identification in Environmental Systems – Xiang Li – Environmental Science & Technology

Functional Foods

Programmable probiotics for detection of cancer in urine – Tal Danino – Science Translational Medicine

Microbes in the news

Alterations to the eye microbiome of contact lens wearers may increase infections – Medical News Today

U.S. defense chief monitoring military anthrax investigation – Reuters

Deadly Bacteria Now a Proven Cancer Detector? – Samantha Solomon – Wall Street Daily’

Gut Bacteria Impacts Toddlers’ Behavior, Particularly Boys – Traci Pederson – PsychCentral

Cervicovaginal Bacteria May Increase the risk of HIV Acquisition in Women – University of Kwazulu – Natal

DNA Genotek’s microbiome collection and stabilization blog: Microbiome learnings from the Weizmann Institute – Cindy MacCullough – DNA Genotek

Scientists probe mysterious wave of antelope deaths – Rory Galloway – BBC News

Bacteria may cause Type 2 diabetes – University of Iowa Now

Should we care about fungi? The mycobiome: an emerging field of the human microbiome research – Human Microbiome Club

Hardy bacteria thrive under hot desert rocks – Nola Taylor Redd – Phys.org

Colon Cancer Diagnosis With Lumninescent Bacteria: Modified Probiotics Can Successfully Detect Tumors In Liver – Colon Cancer News Today

Scientists Find Link Between Ocean Bacteria and Atmosphere – Simon Yu – UCSD Guardian

Woman goes blind after cat licks her and transmits rare bacteria that could affect the brain, eyes, heart, and internal organs – Daily Mail

Science, career, and publishing

This poor advice blog post was retracted from Science today, but the internet never forgets.

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