A late digest today – I have been busy writing a paper and cooking for our lab’s annual holiday potluck party tomorrow. But here we go:

Human gut microbiome

Complex host genetics influence the microbiome in inflammatory bowel disease – Dan Knights – Genome Medicine

Microbiota and the human nature: know thyself – Harald Brüssow – Environmental Microbiology

Animal and bioreactor models of microbiome

Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model – Julie A.K. McDonald – Journal of Microbiological Methods

A novel method to characterize bacterial communities affected by carbon source and electricity generation in microbial fuel cells using stable isotope probing and Illumina sequencing – Yang Song – Journal of Microbiological Methods

Animal microbiome
Crab: Linking regional variation of epibiotic bacterial diversity and trophic ecology in a new species of Kiwaidae (Decapoda, Anomura) from East Scotia Ridge (Antarctica) hydrothermal vents – Katrin Zwirglmaier – MicrobiologyOpen

Soil microbiome

Minireview: The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria – Joseph Nesme and Pascal Simonet – Environmental Microbiology

The soil microbial community predicts the importance of plant traits in plant–soil feedback – Po-Ju Ke – New Phytologist

Metagenomics

Tle distribution and diversity in metagenomic datasets reveal niche specialization – Frank Egan – Environmental Microbiology Reports

Techniques

Application of a single-colony coculture technique to the isolation of unculturable gut bacteria – Yoshiki Tanaka – Microbiology and Immunology

A novel universal DNA labeling and amplification system for rapid microarray-based detection of 117 antibiotic resistance genes in Gram-positive bacteria – Christian Strauss – Journal of Microbiological Methods

Microbial Ecology

Microbial biogeography: the end of the ubiquitous dispersal hypothesis? – Christopher J. van der Gast – Environmental Microbiology

Bacteria can mobilize nematode-trapping fungi to kill nematodes – Xin Wang – Nature Communications

Microfluidic single-cell analysis links boundary environments and individual microbial phenotypes – Christian Dusny and Andreas Schmid – Environmental Microbiology

Microbes in the News

Microbiome may have shaped early human populations – Phys.org

Commensal bacteria were critical shapers of early human populations – Phys.org

Microbes played a significant role in human evolution, study says – Chuck Bednar – RedOrbit

The microbes we eat: Study investigates bacteria in different diets – Nathan Gray – NutraIngredients

Researchers source stool samples to study gut bacteria – Nicole Kwan – FOX News

Bacterial biofilms are associated with colon cancer, imaging technique reveals – Science Daily

Do Autoimmune Diseases Begin in the Gut? – Stephen Paget – Medscape

People may inherit ‘gut’ bacteria that cause Crohn’s disease and ulcerative colitis – MedicalXpress

* 2015 will be the year of the Microbiome (and 28 other predictions) – Fortune

#BacteriaHysteria: The hidden dangers lurking in your kitchen: Chopping boards harbour 200% more faecal bacteria than toilet seats and potatoes and leeks can give you food poisoning – Lizzie Parry – Daily Mail Online

Scientists Debate If It’s OK To Make Viruses More Dangerous In The Lab – Nell Greenfieldboyce – NPR Shots Health News

Science, publishing, and career

12 Unimpressed Comments From Peer Reviewers – Kristy Hamilton – IFL Science (for more entertaining quotes in Environmental Microbiology, see here)

Journalists to Catalog Retractions: Staff of the blog Retraction Watch will create a database of papers retracted from the scientific literature – Kerry Grens – The Scientist

Here’s What Happens When Female MIT PhDs Do a Reddit AMA About Computer Science – Lauren Landry – BostInno

How to be a science girl in a Barbie world – Eve Andrews – Grist.org

For Sale: “Your Name Here” in a Prestigious Science Journal – Charles Seife – Scientific American

These Beautiful Women in Science Art Prints Feature Rad As Heck Ladies – Sam Maggs – The Mary Sue

Bik’s Picks

Happy Holidays from the Corals! – Ocean Portal – Smithsonian

Science’s good, bad, ugly year – Tom Siegfried – Science News

Meet Bill Nye, The Anti-Science Guy – Robert Tracinski – The Federalist

10 Cutest Animals in Science in 2014 – Megan Gannon – Live Science

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