March 20, 2015

General microbiome

Ribosomal RNA, the lens into life – Daniel McDonald, Zhenjiang Xu, Embriette R. Hyde and Rob Knight – RNA

Upcoming event: Cell Symposium: Human Immunity and the Microbiome in Health and Disease – September 27-29, 2015, Montreal, Canada

Human gut microbiome

Review: Firmicutes and Bacteroidetes involved in insulin resistance by mediating levels of glucagon-like peptide 1 – Claire Greenhill – Nature Reviews Endocrinology

Review: The impact of phytochemicals present in the diet on microbial signalling in the human gut – R.R. McCarthy – Journal of Functional Foods

Review: Targeting gut microbiota as a possible therapy for diabetes – Canxia He – Nutrition Research

Human oral microbiome

Guest editorial for special oral microbes edition – Robert Dwayne Lunsford – Microbes and Infection

Animal microbiome

Cattle: Microbial diversity analysis of subclinical mastitis in dairy cattle in Northeast China – Qingyu Jiang – African Journal of Microbiology Research

Worms: The effects of earthworms Eisenia spp. on microbial community are habitat dependent – Anna Koubová – European Journal of Soil Biology

Review: Insect Behaviour and the Microbiome – Zenobia Lewis, Anne Lizé – Current Opinion in Insect Science

Soil, sediments, and plant root microbiome

Carnivory does not change the rhizosphere bacterial community of the plant Drosera intermedia – Manuel Aira – Applied Soil Ecology

Microbial diversity and community respiration in freshwater sediments influenced by artificial light at night – Franz Hölker – Philosophical Transactions B
The biological impacts of artificial light at night: the research challenge – Kevin J. Gaston – Philosophical Transactions B

Microbial abundance and community in subsurface flow constructed wetland microcosms: role of plant presence – Qian Wang – Environmental Science and Pollution Research

Analysis of a population of magnetotactic bacteria of the Gulf of Gabès, Tunisia – Nathalie Pradel – Environmental Science and Pollution Research

Review: Linkages of plant-soil feedbacks and underlying invasion mechanisms – Inderjit and James F. Cahill Jr. – AoB Plants

Response of microbial communities to bioturbation by artificially introducing macrobenthos to mudflat sediments for in situ bioremediation in a typical semi-enclosed bay, southeast China – Ying Ma – Marine Pollution Bulletin

Water and snow microbiome

Microbial abundance and community structure in a melting alpine snowpack – Anna Lazzaro – Extremophiles

Diverse arsenic- and iron-cycling microbial communities in arsenic-contaminated aquifers used for drinking water in Bangladesh – Zahid Hassan – FEMS Microbiology Ecology

Metagenomics, proteomics, bioinformatics

Editorial: Microbial Diversity: A Bonanza of Phyla – Laura Eme, W. Ford Doolittle – Current Biology
belongs to study reconstructing Archaea genomes from metagenomic data: Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling – Cindy J. Castelle – Current Biology

Book Chapter: Evaluation of Combined Genome Assemblies: A Case Study with Fungal Genomes – Mostafa M. Abbas – Bioinformatics and Biomedical Engineering

Navigating through metaproteomics data – a logbook of database searching – Thilo Muth – Proteomics

Microbes in the news

Quorum-Sensing Molecule Modifies Gut Microbiota – Anna Azvolinsky – The Scientist

Functional Metagenomics Enables First Study of Bacterial Fitness in the Gut Microbiome – Chris Williams – Columbia Systems Biology

How to Study a Complex Microbial World- Part 1: DNA sequencing – Kevin Bonham -Scientific American

How to Study a Complex Microbial World – Part 2: Next Generation Sequencing Technology – Kevin Bonham -Scientific American

Biological oceanography: Life in the deepest depths
– Beth N. Orcutt – Nature Geoscience

1h Podcast/article: Say Cheese! Cheese history and science – GastroPod

Jailbreaking yeast could amp up wine’s health benefits, reduce morning-after headaches –

29 min podcast: Queen Bee Microbiome (starts at 8 min), Yams, Resistence To Organic Checkoff – PRX Earth Eats

The World’s First €100M Microbiome-focused Venture Fund opened in France – Labiotech

Bioinformatics tool for metagenome analysis – Nancy Ambrosiano – R&D Magazine

Andreessen-Backed uBiome Is Now Doing An Indiegogo Campaign To Check Out Dental Bacteria – Kim-Mai Cutler – TechCrunch

Science, publishing, and career

“Canadian” Open-Access Journal Doesn’t Look Very Canadian – Jeffrey Beall – ScholarlyOA

Science and art

Art project: What Bacteria And Smell Have To Do With Feminism Today – Katherine Brooks – Huffington Post

Bik’s Picks

Morphological Mutations: Lessons from the Cockscomb Major comb variants and their genetic basis – Denis Headon – PLOS GeneticsWhat’s that thing?

How to Google Something You Don’t Know How to Describe – Adrienne Lafrance – The Atlantic

New Breast Milk Products Are on the Rise, but Commercialization Troubles Many – Andrew Pollack – New York Times


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