July 21, 2015

Microbiome of a dead pig in the snow, two papers on oral microbiome in HIV infection, sweetener consumption and microbiome, proteomics of preterm infant colonization, sequencing platform and primer choices, and including microbial ecology in Pre-med programs.

Microbiology of death

Using Bacterial and Necrophagous Insect Dynamics for Post-Mortem Interval Estimation during Cold Season: Novel Case Study in Romania – Lavinia Iancu – Forensic Science International

Pregnancy and birth / Proteomics

Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant – Brandon Brooks

Human oral microbiome

The Oral Microbiome in HIV-positive Individuals – James O. Kistler – Journal of Medical Microbiology

Exploring salivary microbiota in AIDS patients with different periodontal statuses using 454 GS-FLX Titanium pyrosequencing – Fang Zhang – Frontiers in Cellular and Infection Microbiology

Review: Bacteria and Archaea Paleomicrobiology of the Dental Calculus: a Review – Hong T.T. Huynh – Molecular Oral Microbiology

Human urinary tract microbiome

Review: Intracellular Bacterial Communities: A Potential Etiology for Chronic Lower Urinary Tract Symptoms – Victoria C.S. Scott – Urology

Human gut microbiome

High-intensity sweetener consumption and gut microbiome content and predicted gene function in a cross-sectional study of adults in the United States – Cara L. Frankenfeld – Annals of Epidemiology

Pomegranate extract induces ellagitannin metabolite formation and changes stool microbiota in healthy volunteers – Zhaoping Li – Food & Function

Models of microbiome

Neutrophil gelatinase-associated lipocalin regulates gut microbiota of mice – Katsuya Mori – Journal of Gastroenterology and Hepatology

Effect of Dietary Protein Levels on Composition of Odorous Compounds and Bacterial Ecology in Pig Manure – Sungback Cho – Asian Australas. J. Anim. Sci

Animal microbiome

Shotgun Metagenomic Sequencing Reveals Functional Genes and Microbiome Associated with Bovine Digital Dermatitis – Martin Zinicola – PLOS ONE

Diversity and composition of the bacterial community in Amphioxus feces – Minming Pan – Journal of Basic Microbiology

Isolation, characterization, and antibiotic resistance of Vibrio spp. in sea turtles from Northwestern Mexico – Alan A. Zavala-Norzagaray – Frontiers in Microbiology

Microbial Infections Are Associated with Embryo Mortality in Arctic-Nesting Geese – Cristina M. Hansen – Applied and Environmental Microbiology

An insight into the functional role of thioredoxin reductase, a selenoprotein, in maintaining normal native microbiota in the Gulf Coast tick (Amblyomma maculatum) – K. Budachetri – Insect Molecular Biology

Chemotaxis by natural populations of coral reef bacteria – Jessica Tout – The ISME Journal

Review: Exploring the avian gut microbiota: current trends and future directions – David W. Waite – Frontiers in Microbiology

Plant, root, and soil microbiome

Lactic acid bacteria are endophytic components of durum wheat plant following the whole life cycle from plant to flour – Fabio Minervini – Applied and Environmental Microbiology

Application of mesotrione at different doses in an amended soil: Dissipation and effect on the soil microbial biomass and activity – Eva Pose-Juan – Science of The Total Environment

Plant species richness does not attenuate responses of soil microbial and nematode communities to a flood event – Daniela Wagner – Soil Biology and Biochemistry

Declined soil suppressiveness to Fusarium oxysporum by rhizosphere microflora of cotton in soil sickness – Xiaogang Li – Biology and Fertility of Soils

Water / extremophile microbiome

Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea – Yue Guan – Research in Microbiology

Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions – Christopher M. Bellas – Frontiers in Microbiology

A Paleoarchean coastal hydrothermal field inhabited by diverse microbial communities: the Strelley Pool Formation, Pilbara Craton, Western Australia – K. Sugitani – Geobiology

Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents – Daniel C Reed – The ISME Journal

Waste and bioreactor microbiology

GeoChip-based analysis of microbial community of a combined nitritation-anammox reactor treating anaerobic digestion supernatant – Jian Zhao – Water Research

Arsenic toxicity effects on microbial communities and nutrient cycling in indoor experimental channels mimicking a fluvial system – Baigal-Amar Tuulaikhuu – Aquatic Toxicology

Microbial ecology

Review: Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis – Florent Lassalle – Research in Microbiology

Microbiology and Ecology Are Vitally Important to Premedical Curricula – Val H. Smith – Evolution, Medicine, and Public Health

Bioinformatics and metagenomics
MCaVoH: A toolkit for Mining, Classification and Visualization of Human Microbiota
Maryum Nisar – Journal of Microbiological Methods

An intriguing new bacterial phylum – Naomi Attar – Nature Reviews Microbiology

Metabolic networks

A biosynthetic pathway for a prominent class of microbiota-derived bile acids – A Sloan Devlin – Nature Chemical Biology

Methanogenic food web in the gut contents of methane-emitting earthworm Eudrilus eugeniae from Brazil – Kristin Schulz – The ISME Journal

Auxotrophy and intra-population complementary in the ‘interactome’ of a cultivated freshwater model community – Sarahi L Garcia – Molecular Ecology

Techniques

Primer and platform effects on 16S rRNA tag sequencing – Julien Tremblay – Frontiers in Microbiology

Microbes in the news

Programming Bacteria to Kill Cancer Cells – Lecia Bushak – Newsweek

Scientists keep finding more evidence that bacteria in your stomach are connected to your mood – Kevin Loria – Business Insider

#BacteriaHysteriaThe even grosser cause behind gross smelling feet – Stephanie Bell-Flynt

Bik’s Picks
One Migration from Siberia Peopled the Americas: Study – Discovery

Study: Women With Mild Memory Problem Worsen Faster Than Men – Lauran Neergaard – ABC News

Marijuana helps broken bones heal, says Israeli scientific team – Ruth Schuster – Haaretz

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