ICU, Rudlavibizon, Flickr
Gut microbiota changes in the ICU, air microbiome of the Gobi desert, host response of human cells to gut microbiota.
Event
Synbiobeta SF2016, October 4-6, South San Francisco, CA
Human gut microbiome
Extreme Dysbiosis of the Microbiome in Critical Illness – Daniel McDonald – mSphere
Press: ICU patients lose helpful gut bacteria within days of hospital admission – Science Daily
Tracking Bacterial Imbalance in the ICU – Stephen Ornes -mBiosphere
Review: The human gut microbiome, diet, and health: “post hoc non ergo propter hoc” – Guus Roeselers – Trends in Food Science & Technology
Review: Interplay between gut microbiota, its metabolites and human metabolism: dissecting cause from consequence – A.V. Hartstra – Trends in Food Science & Technology
Animal and other model experiments
Bidirectional communication between the Aryl hydrocarbon Receptor (AhR) and the microbiome tunes host metabolism – Agata Korecka – NPJ Biofilms and Microbiomes
Temporal dynamics of bacterial microbiota in the human oral cavity determined using an in situ model of dental biofilms – Nanako Wake – NPJ Biofilms and Microbiomes
Normalizing Microbiota-Induced Retinoic Acid Deficiency Stimulates Protective CD8+ T Cell-Mediated Immunity in Colorectal Cancer – Nupur Bhattacharya – Immunity
Genetic and Transcriptional Analysis of Human Host Response to Healthy Gut Microbiota – Allison L. Richards – mSystems
Animal microbiome
Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement – Darren J Parris – PeerJ
Plant, root, and soil microbiome
Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity – Zhilin Yuan – Scientific Reports
A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities – Renee B. Johansen – Fungal Ecology
Bacterial community structure and function shift across a northern boreal forest fire chronosequence – Hui Sun – Scientific Reports
Water microbiome
Complex bacterial communities in the deep-sea sediments of the Bay of Bengal and volcanic Barren Island in the Andaman Sea – Pankaj Verma – Marine Genomics
Neutral processes and species sorting in benthic microalgal community assembly: effects of tidal resuspension – Craig J. Plante – Journal of Phycology
Air microbiome
Variations in the structure of airborne bacterial communities in Tsogt-Ovoo of Gobi desert area during dust events – Teruya Maki – Air Quality, Atmosphere & Health
Bioinformatics and metagenomics
A phylogenetic transform enhances analysis of compositional microbiota data – Justin D Silverman – bioRxiv
Higher classification sensitivity of short metagenomic reads with CLARK-S – Rachid Ounit – Bioinformatics
GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly – Cuncong Zhong – BMC Bioinformatics
Microbial ecology
Quantifying human impact on Earth’s microbiome – Stephen B. Pointing – Nature Microbiology
Synthetic microbial ecology and the dynamic interplay between microbial genotypes –
Jan Dolinšek – FEMS Microbiology Reviews
Microbes in the news
Engineered gut bacteria protect mice against obesity, improve liver function – Oliver Worsley – Fierce Biotech
You’re probably not doing metagenomics – Mick Watson – Opiniomics
Mayo Adds To Its List Of Gut Microbiome Startup Collaborators – Don Jacobson – Twin Cities Business
Nice analysis of Tweets from #ISME16 by Keith Turner – Jonathan Eisen – MicroBEnet
Peer review and science misconduct
Recognizing Peer Reviewers: a Webinar to Celebrate Editors and Researchers – September 19, 2016 – Elsevier Publishing Campus
Stop ignoring misconduct – Donald S. Kornfeld & Sandra L. Titus – Nature
Bik’s Non-Microbiology Picks
Paperfuge: An ultra-low cost, hand-powered centrifuge inspired by the mechanics of a whirligig toy – M. Saad Bhamla – bioRxiv
Microbiome Digest - Bik's Picks 