March 26, 2015

General microbiome

Note: not about metagenomics but 16S rRNA gene: The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies – J Paul Brooks – BMC Microbiology

Human respiratory microbiome

Spatial Variation in the Healthy Human Lung Microbiome and the Adapted Island Model of Lung Biogeography – Robert P. Dickson – Annals ATS

A metagenomic approach to characterize temperate bacteriophage populations from Cystic Fibrosis and non-Cystic Fibrosis bronchiectasis patients – Mohammad A. Tariq – Frontiers in Microbiology

Perspective: Meningitis in adolescents: the role of commensal microbiota – James W.B. Moir – Trends in Microbiology

Human gut microbiome

An n=1 case report of a child with autism improving on antibiotics and a father’s quest to understand what it may mean – John Rodakis – Microbial Ecology of Health and Disease

Animal microbiome

Sponges: Culturable associated-bacteria of the sponge Theonella swinhoei show tolerance to high arsenic concentrations – Ray Keren – Frontiers in Microbiology

Soil, sediment, and plant root microbiome

Community Dynamics of Arbuscular Mycorrhizal Fungi in High-Input and Intensively Irrigated Rice Cultivation Systems – Yutao Wang – Applied and Environmental Microbiology

Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes – Zhichao Zhou – Frontiers in Microbiology

Isolation and characterization of culturable bacteria from bulk soil samples and the rhizosphere of arid-adapted Tylosema esculentum (Burchell). A. Schreiber (Marama bean) in Namibia – Olaf S. Kandjimi – African Journal of Biotechnology

Water microbiome

Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea – Ching-Hung Tseng – BMC Genomics

Spatial distribution of bacterial communities driven by multiple environmental factors in a beach wetland of the largest freshwater lake in China – Xia Ding- Frontiers in Microbiology

Review: Advancing the science of microbial symbiosis to support invasive species management: a case study on Phragmites in the Great Lakes – Kurt P. Kowalski – Frontiers in Microbiology

Extremophile microbiome (by special request!)

Colonization of plant substrates at hydrothermal vents and cold seeps in the northeast Atlantic and Mediterranean and occurrence of symbiont-related bacteria – Kamil M. Szafranski – Frontiers in Microbiology

Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines) – Kristin M. Woycheese – Frontiers in Microbiology

Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China – Brian P. Hedlund – Frontiers in Microbiology

Fatty Acids Profile of Microbial Populations in a Mining Reclaimed Region Contaminated with Metals: Relation with Ecological Characteristics and Soil Respiration – Ramya Narendrula and Kabwe K. Nkongolo – Journal of Bioremediation & Biodegradation

Bioreactor microbiome

Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities – Anthony S. Amend – Frontiers in Microbiology

Food microbiology

Lipidomics as an important key for identification of beer-spoilage bacteria – Tomáš Řezanka – Letters in Applied Microbiology

Metabolomics

Combining reverse genetics and NMR-based metabolomics unravels trypanosome-specific metabolic pathways – Frédéric Bringaud – Molecular Microbiology

Resource niche overlap promotes stability of bacterial community metabolism in experimental microcosms – Ellard R. Hunting – Frontiers in Microbiology

Techniques

Enriching distinctive microbial communities from marine sediments via an electrochemical-sulfide-oxidizing process on carbon electrodes – Shiue-Lin Li and Kenneth H. Nealson – Frontiers in Microbiology

Microbes in presentations

Video: Dissertation seminar for Suzanne Ishaq – comparative analysis of the moose rumen microbiota

Video: Vance Kramer of Syngenta discussing microbiome research and comparing soil microbe communities across the US, Europe, and Brazil.

Video: Dr. Jan Jones from AgBiome discussing the plant-soil microbiome

Microbes in the news
Hidden Life Forms: Investigating Microbial Diversity on Our Bodies and in Our Homes – Jennifer Cutraro – New York Times

My uBiome Sleep Hacking Update – Alexandra Carmichael – uBiome

Antimicrobial CRISPR-Cas systems may be better weapons against bacteria than antibiotics – The Conversation

Secret Science Club Post-Lecture Recap: Big Data, Genomics and Urban Microbiomes – Big Bad Bald Bastard

Antibiotics For Gut Bacteria Show Surprising Results In Treating Autism – Dianne Depra – Tech Times

Harmless bacteria may be helpful against meningococcal outbreaks – Eureka Alert

New Software Offers Improved Read-based Identification in Metagenome Studies – Andrew P. Han – Genome Web

Not sure which one, but here it is: I am the bacterium that lives in your intestine – MicrobeWorld

FMTUpdate on OpenBiome – Paul Levy – Not Running A Hospital

Workshop on Planetary Protection Knowledge Gaps for Human Extraterrestrial Missions (Intro) – Jenna Lang – Microbe.net

Microbes and art

A Dress Made From Beer And Bacteria: C’est Chic Or C’est Ick? – Charles Poladian – IB Times

Science, publishing, and career

Developing microbiological learning materials for schools: best practice – James Redfern – FEMS Microbiology Letters

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights – Claire Bertelli – Frontiers in Microbiology

Calling attention to poor speaker gender ratio – even when it hurts – Jonathan Eisen – The Tree of Life

The 5 Biases Pushing Women Out of STEM – Joan C. Williams – Harvard Business Review

Bik’s Picks

Jurrassic Park, but then with more furWoolly mammoth could be revived after scientists paste DNA into elephant’s genetic code – Andrew Griffin – The Independent

The Fitness Guru of the Trucking Industry – The Atlantic

On Friday, half a pair of twins leaves for a year in space. Here’s why that’s awesome. – Rachel Feltman – Washington Post

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