October 20, 2015

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.


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


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

Gut Microbiome Insights; Obesity and Digestive Health Risks; Delivery Options and Predictors of Failure for Fecal Microbiota Transplantation; among Featured Topics Presented at the American College of Gastroenterology’s 80th Annual Meeting – PR NewsWire

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


One thought on “October 20, 2015

  1. 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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