February 6, 2015

Pregnancy and birth microbiome

The composition of the gut microbiota throughout life, with an emphasis on early life – Juan Miguel Rodríguez – Microbial Ecology in Health and Disease

Review: Antenatal lower genital tract infection screening and treatment programs for preventing preterm delivery – Ussanee S Sangkomkamhang – Cochrane Library

Animal models of microbiome research

Barcoded pyrosequencing-based metagenomic analysis of the faecal microbiome of three purebred pig lines after cohabitation – Edward Alain B. Pajarillo – Applied Microbiology and Biotechnology

Animal microbiome

Microbial interactions and the ecology and evolution of Hawaiian Drosophilidae –
Timothy K. O’Connor – Frontiers in Microbiology

Plant microbiome

Agricultural probiotics enter spotlight – Jeffrey L Fox – Nature

Soil microbiome

Inorganic fungicides as routinely applied in organic and conventional agriculture can increase palatability but reduce microbial decomposition of leaf litter – Jochen P. Zubrod – Journal of Applied Ecology

Effect of diesel-oil addition on soil microbiological parameters in systems with and without plants – MC Petenello – Terra Latinoamericana

Does long-term use of mineral fertilizers affect the soil microbial biomass? – D Geisseler – Better Crops with Plant Food

News and views: Microbes: The chief ecological engineers in reinstating equilibrium in degraded ecosystems – Jay Shankar Singh – Agriculture, Ecosystems & Environment

Review: Impact of engineered nanoparticles on the activity, abundance, and diversity of soil microbial communities: a review – Marie Simonin, Agnès Richaume – Environmental Science and Pollution Research

Water microbiome

Phaeocystis antarctica blooms strongly influence bacterial community structures in the Amundsen Sea polynya – Tom O. Delmont – Frontiers in Microbiology

Biogeographic patterns of bacterial microdiversity in Arctic deep-sea sediments (HAUSGARTEN, Fram Strait) – Pier Luigi Buttigieg – Frontiers in Microbiology

Aquifer environment selects for microbial species cohorts in sediment and groundwater – Laura A Hug – The ISME Journal

Fate of the Herbicide Alachlor Exposed to Different Microbial Consortia in Aquatic Systems – Armelle Paule – Water, Air, & Soil Pollution

Microbial community structure and methane-cycling activity of subsurface sediments at Mississippi canyon 118 before the Deepwater Horizon disaster – Sarah Underwood – Deep Sea Research Part II: Topical Studies in Oceanography

Air microbiome

Molecular characterization of microbial communities in bioaerosols of a coal mine by 454 pyrosequencing and real-time PCR – Min Wei – Journal of Environmental Sciences

Bioreactor and wastewater microbiology

Processing barley grain with lactic acid and tannic acid ameliorates rumen microbial fermentation and degradation of dietary fibre in vitro – Kathrin Deckardt – Journal of the Science of Food and Agriculture

Microbial community dynamics associated with veterinary antibiotics removal in constructed wetlands microcosms – Joana P. Fernandes – Bioresource Technology

Analysis of microbial community structure and composition in leachates from a young landfill by 454 pyrosequencing – Thorsten Köchling – Applied Microbiology and Biotechnology

Metabolomics and proteomics

Review: Nutriproteomics: Facts, concepts, and perspectives – Sascha Sauer and Toni Luge – Proteomics

Microbial Ecology

Dispersal among local communities does not reduce historical contingencies during metacommunity assembly – Zhichao Pu and Lin Jiang – Oikos

Functional dissimilarity across trophic levels as a driver of soil processes in a Mediterranean decomposer system exposed to two moisture levels – Mathieu Coulis – Oikos

Modeling evolution of spatially distributed bacterial communities: a simulation with the haploid evolutionary constructor – Alexandra Igorevna Klimenko – BMC Evolutionary Biology


Recent infections are associated with decreased risk of rheumatoid arthritis: a population-based case-control study – Maria EC Sandberg – Annals of the Rheumatic Diseases

Viruses and phages

Assembly of viral genomes from metagenomes – Saskia L. Smits – Frontiers in Microbiology

Sorting of small infectious virus particles by flow virometry reveals distinct infectivity profiles – Raphaël Gaudin & Natasha S Barteneva – Nature Communications

Metagenomics and chromosomal organization

Novel assay to measure the plasmid mobilizing potential of mixed microbial communities – Uli Klümper – Frontiers in Microbiology

Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria – Ryan C. Lynch – Frontiers in Microbiology

Review: Evolution of small prokaryotic genomes – David J. Martínez-Cano – Frontiers in Microbiology


A Quick Guide for Building a Successful Bioinformatics Community – Aidan Budd – PLOS Computational Biology

Microbes in the news

Bacteria help breastfed babies digest solid food – Mark Derewicz – Futurity

From fourth-century soup to 21st-century procedure, fecal transplantation proves its worth against stubborn bacteria – VA Research Currents (HT: Inder Perkash)

Mapping the Microbes of the New York City Subway – Marcus Woo – Wired.com

Age-related hepatitis B infection and the gut microbiome – Heather Zeiger – Medical Xpress

Researchers Uncover Infant Gut Microbiome Alterations Linked to Type 1 Diabetes – GenomeWeb

Gut Bacteria Link Between Heart and Kidney Disease Strengthened – WH Wilson Tang – MedicalResearch.com

Nine ways your gut can protect your heart – Giovanni Campanile – Mens Fitness

New clinical study to focus on gut, autism connection (with James Versalovic) – Baylor College of Medicine

Science, publishing, and career

Frontiers for Young Minds – non-profit scientific journal for 8-15 year olds – Frontiers

A classroom experiment – Jeffrey Mervis – Science

Undergraduate research experiences: Impacts and opportunities – Marcia C. Linn – Science

Science by any means necessary (interview with Erich Jarvis) – Rachel Bernstein – Science

The Scientist’s Toolbox: Last Call – Name and describe a currently nonexistent invention that would make you a more effective scientist – Science

Breaking bad science – Joel Best – Science

Science and art

Cute pathology pictures – Seriously Science – Discover Magazine

Bik’s Picks

This college student is eating bugs for 30 days so you will too – Rachel Feltman – Washington Post

Where is Silicon Valley? – Jorge Guzman, Scott Stern – Science

Fire Department Saves Woman From Robot Vacuum Attack. It Begins. – Dan Van Winkle – The Mary Sue


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