Blogging from SJC today on my way to Vancouver. Oral microbes correlated with food-triggered migraines, spinal cord injuries, comparison of 8 DNA extraction kits on 3 sample types, mockrobiota.

Jobs and Events

Flying to Vancouver today to give a short talk at DNA Genotek’s Microbiome Breakfast Session at #ASHG2016

Fall Mid-Atlantic Microbiome Meetup (M3) – November 1-2, University of Maryland

Human oral microbiome

Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort – Antonio Gonzalez – mSystems

Press: Migraines could be caused by gut bacteria, study suggests – Hannah Devlin – The Guardian
Scientists think they’ve found why chocolates and wine cause migraines for some very unlucky people – Katherine Ellen Foley – Quartz

Human skin microbiome

The skin is a significant but overlooked anatomical reservoir for vector-borne African trypanosomes – Paul Capewell – eLife

Human respiratory microbiome
The Prevalence of Antibiotic-resistant Staphylococcus aureus Nasal Carriage among Industrial Hog Operation Workers, Community Residents, and Children Living in their Households: North Carolina, USA – Sarah M. Hatcher – Environmental Health Perspectives

Press: Drug-resistant staph bacteria prevalence higher in young children living with hog workers – EurekAlert

Animal models

Gut dysbiosis impairs recovery after spinal cord injury – Kristina A. Kigerl – Journal of Experimental Medicine

Press: Researchers show how spinal cord injury causes profound changes in gut microbiota – News-Medical Net
Gut bacteria can aid recovery from spinal cord injury, study suggests – Science Daily

Techniques

Eight commercial kits, 16 procedures, 3 sample types: Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition – Berith E. Knudsen – mSystems

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking – Nicholas A. Bokulich – mSystems

Bioinformatics and metagenomics

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography – Stephen Nayfach – Genome Research

Press: From Genome Research: Strain-level profiling yields new insights into mother-infant microbiomes – EurekAlert

The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data – Sandeep J. Joseph – PeerJ

Microbes in the news

Tapping the Human Gut Microbiome, Part 1: The Next Frontier for Novel Therapeutics – Christian Furlan Freguia – GenEngNews
Tapping the Human Gut Microbiome, Part 2: From the Bottom Up – Christian Furlan Freguia – GenEngNews

The microbiome: Looking at microbes as more than pathogens – Ryan T. Ranallo – Healio

Harnessing The Plant Microbiome For Cleaner, Pesticide-Free Agriculture – Ben Schiller – FastCoexist

Bacteria named in Mighty Taco outbreak; chain denies fault – Food Safety News

Clemson students get bacteria named after them. New strain of Legionella named for students who studied it – Carla Field – Wyff4

Bacteria ‘alarm clock’ may cause repeat infections in patients – Kate Wighton – Imperial.ac.uk

Microbes and Money

Igniting a Microbiome Revolution: Era7 Bioinformatics Syncs with Capital Cell – Erin Hobey – CrowdFundInsider
Igenbio Inc offers metagenome analysis services for clinical and industrial applications – Reuters