August 31, 2016

Screen Shot 2016-08-31 at 10.36.09 PM

ICU, Rudlavibizon, Flickr

Gut microbiota changes in the ICU, air microbiome of the Gobi desert, host response of human cells to gut microbiota.


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


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