Cohabitation of helminths, bacteria, and host in the gut, diurnal sampling bias in plankton biodiversity, contaminant influence on groundwater microbiome, volatile affairs, and new tools for metagenomics.
Events
Postdoc and grad student Summit — preceding the EMBO Symposium on Aquatic Microeukaryotes: Abstract deadline October 22 – Jonathan Eisen – MicroBEnet
Human oral microbiome
Periodontal clinical and microbiological characteristics in healthy versus generalized aggressive periodontitis families – Mabelle de F. Monteiro – Journal of Clinical Periodontology
Masters Thesis: Caries and the Oral Microbiome of a Native American Population – Michael Tuan – Ohio State University
Human gut microbiome
Review: Cohabitation in the Intestine: Interactions among Helminth Parasites, Bacterial Microbiota, and Host Immunity – Lisa A. Reynolds – The Journal of Immunology
Review: Influences of diet and the gut microbiome on epigenetic modulation in cancer and other diseases – Bidisha Paul – Clinical Epigenetics
Review: Intestinal Microbiota Metabolism and Atherosclerosis – Tian-Xing Liu – Chinese Medical Journal
Animal models
Colonic Lesions, Cytokine Profiles, and Gut Microbiota in Plasminogen-Deficient Mice – Bill Vestergaard – Comparative Medicine
Plant, root, and soil microbiomes
Cyanobacterial composition and spatial distribution based on pyrosequencing data in the Gurbantunggut Desert, Northwestern China – Bingchang Zhang – Journal of Basic Microbiology
Disease in apple orchards: Different bacterial communities in heat and gamma irradiation treated replant disease soils revealed by 16S rRNA gene analysis – contribution to improved aboveground apple plant growth? – Bunlong Yim – Frontiers in Microbiology
A fragrant neighborhood: Volatile mediated bacterial interactions in soil – Kristin Schulz-Bohm – Frontiers in Microbiology
Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing – Lin Chen – Frontiers in Microbiology
Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California – A. C. Hollowell – Plant Microbe Interactions
Water microbiome
Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique – Satoshi Nagai – Gene
Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations – Xiaofen Wu – The ISME Journal
Viral impact on prokaryotic and microalgal activities in the microphytobenthic biofilm of an intertidal mudflat (French Atlantic coast) – Hélène Montanié – Frontiers in Microbiology
Comparative metagenomics reveals impact of contaminants on groundwater microbiomes – Christopher L. Hemme – Frontiers in Microbiology
Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes – Guillem Salazar – Molecular Ecology
Effects of Seasonal Thermal Stratification on the Functional Diversity and Composition of the Microbial Community in a Drinking Water Reservoir – Xiao Yang – Water
Extremophile microbiology
Review: Extremely Thermophilic Microorganisms as Metabolic Engineering Platforms for Production of Fuels and Industrial Chemicals – Benjamin M. Zeldes – Frontiers in Microbiology
Metagenomics and bioinformatics
Snowball: Strain aware gene assembly of Metagenomes – I. Gregor – ArXiv
PEPR: Pipelines for Evaluating Prokaryotic References – Nathan D. Olson – PeerJ preprint
cualid: globally unique, correctable, and humanfriendly sample identifiers for
comparative omics studies – John H Chase – PeerJ preprint
Why we need more algal metagenomes – Linda E. Graham – Journal of Phycology
Phages and viruses
Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters – Jeremy J. Barr – PNAS
Microbial Ecology
Interspecies interactions are an integral determinant of microbial community dynamics –
Fatma A. A. Aziz – Frontiers in Microbiology
Differentiating between niche and neutral assembly in metacommunities using null models of β-diversity – Caroline M. Tucker – Oikos
Review: Role of the Environment in the Transmission of Antimicrobial Resistance to Humans: A Review – Patricia M. C. Huijbers – Environmental Science & Technology
More microbiology
Self-Protected Nitrate Reducing Culture for Intrinsic Repair of Concrete Cracks –
Yusuf C. Ersan – Frontiers in Microbiology
Metabolomics
Review: Volatile affairs in microbial interactions – Ruth Schmidt – The ISME Journal
Microbes in the news
Society for Neuroscience meeting in Chicago : Probiotic bacteria may aid against anxiety and memory problems – Ian Sample – The Guardian
ID Week: How Babies’ Gut Bacteria May Help Find Treatments for C. Diff – Rachael Rettner – Live Science
Video: Speaking of Chemistry: What is the Gut Microbiome? Matt Davenport – American Chemical Society
Study reveals a key role your gut bacteria play in body’s self-defense – David Callahan – Medical Xpress
MS conference, Barcelona: Q&A With Helen Tremlett From the University of British Columbia: Gut Microbiome And Its Role In Multiple Sclerosis -HCP Live
Virginia Tech scientists reveal more about how body copes with common gut bacterium – Augusta Free Press
High Starch Diets’ Effects on Stress Response in Horses – Casie Bazay – The Horse
These Bacteria Could Live in Europa’s Ocean – Irene Klotz – Discovery
Local news: Dozens Sick With Shigella Bacteria After Eating At San Jose Restaurant – CBS Local
The Phage is a Lonely Hunter: New research reveals that bacteriophages use slow, staccato movements to hunt bacteria on cell surfaces – Michael Price – SDSU
Creating Healthier Microbiomes, from Conception to Childhood: A Clinical Conversation with Geeta Maker-Clark, MD, and Robert Rountree, MD -Alternative and Complementary Therapies
Microbes and art
Very cool: A Microbiologist Recreated ‘Starry Night’ With Bacteria In A Petri Dish And it’s not too shabby – Priscilla Frank – Huffington Post
Bik’s Picks
Poo turns naked mole rats into better babysitters – Oestrogen in queen mole rat’s faeces drives subordinates to care for her pups – Sara Reardon – Nature News
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Microbiome Digest - Bik's Picks 
Those gastroenterology guys who were talking about constipation were utterly useless. There were a couple of papers a few months back on the Microbiome Digest which suggested that constipation is linked to issues with bile salts affecting the microbiome (also issues with gall stone formation and gall duct blocking IIRC), and can be driven by the liver and gall bladder microbiota. I could swear I read that here.
These gastro guys need to read your blog every day Elizabeth!
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