June 10, 2016

Volunteers taking ETEC, 3 new E. coli phages, oral microbiomes of cats and dogs, skin microbes in Japanese amphibians, fungi and bacteria in floor dust.

Human oral microbiome

The oral microbiome of patients with axial spondyloarthritis compared to healthy individuals – Jordan E. Bisanz – PeerJ

Human vaginal microbiome

Association of Sexual Debut in Adolescents With Microbiota and Inflammatory Markers – Jespers, Vicky – Obstetrics & Gynecology

Human blood ‘microbiome’

Rapid identification of fungi in culture-negative clinical blood and respiratory samples by DNA sequence analyses – Farida Sidiq – BMC Research Notes

Human gut microbiome

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment – Mihai Pop – BMC Genomics

Mucosa-Associated Ileal Microbiota in New-Onset Pediatric Crohn’s Disease – Assa, Amit – Inflammatory Bowel Diseases

Three New Escherichia coli Phages from the Human Gut Show Promising Potential for Phage Therapy – Marion Dalmasso – PLOS ONE

“Free living females” sounded… weird. Soluble Corn Fiber Increases Calcium Absorption Associated with Shifts in the Gut Microbiome: A Randomized Dose-Response Trial in Free-Living Pubertal Females – Corrie M Whisner – Journal of Nutrition

Similar Fecal Microbiota Signatures in Patients With Diarrhea-predominant Irritable Bowel Syndrome and Patients With Depression – Yixuan Liu – Clinical Gastroenterology and Hepatology

DGGE: Differences in the Biodiversity of the Fecal Microbiota of Infants With Rotaviral Diarrhea and Healthy Infants – Peng Fei – Jundishapur Journal of Microbiology

Opinion: How Our Other Genome Controls Our Epi-Genome – Antonella Celluzzi – Trends in Microbiology

Review: The role of the gut microbiota in NAFLD – Christopher Leung – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Diet may influence the oral microbiome composition in cats – Christina J. Adler – Microbiome

Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules – James E. McDonald – PLOS ONE

Bacterial microbiomes from vertically-transmitted fungal inocula of the leaf-cutting ant Atta texana – Lucas A. Meirelles – Environmental Microbiology Reports

Defensive insect symbiont leads to cascading extinctions and community collapse – Dirk Sanders – Ecology Letters

Plant, root, and soil microbiome

Subalpine conifers in two different geographic locations host highly similar foliar bacterial endophyte communities – Alyssa A. Carrell – FEMS Microbiology Ecology

Effect of plant growth-promoting bacteria on the growth and fructan production of Agave americana L. – Neyser De La Torre-Ruiz – Brazilian Journal of Microbiology

Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region – Joana Sabino-Pinto – Microbial Ecology

Water and extremophile microbiome

Benthic protists: the under-charted majority – Dominik Forster – FEMS Microbiology Ecology

Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance – Maren Bornemann – FEMS Microbiology Ecology

Review: How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes – Elena Kazamia – Ecology Letters

Review: All ecosystems potentially host electrogenic bacteria – Nicolas Chabert – Bioelectrochemistry

Pollution and waste and bioreactor microbiology

Arsenic metabolism and toxicity influenced by ferric iron in simulated gastrointestinal tract and the roles of gut microbiota – Haiyan Yu – Environmental Science & Technology

Pyrosequencing analysis of bacterial diversity in soils contaminated long-term with PAHs and heavy metals: Implications to bioremediation – Saranya Kuppusamy – Journal of Hazardous Materials

A strange combination of samples: Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies – Simon Güllert – Biotechnology for Biofuels

Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing – S. Festa – FEMS Microbiology Ecology

Built environment microbiome

Fungal and bacterial growth in floor dust at elevated relative humidity levels – Karen C. Dannemiller – Indoor Air

Bioinformatics and statistics

An Introduction to Programming for Bioscientists: A Python-Based Primer – Berk Ekmekci – PLOS Computational Biology

Ten Simple Rules for Effective Statistical Practice – Robert E. Kass – PLOS Computational Biology

Bipartite Graphs for Visualization Analysis of Microbiome Data – Karel Sedlar – Evolutionary Bioinformatics


The source of SYBR green master mix determines outcome of nucleic acid amplification reactions – Jianxin Yang – BMC Research Notes

More microbiology

Ancestral Tryptophan Synthase Reveals Functional Sophistication of Primordial Enzyme Complexes – Florian Busch – Cell Chemical Biology

Press: Ancient enzyme resurrected from the ancestor of all bacteria – Conor Gearin – New Scientist
Bacteria perfected protein complexes more than 3.5 billion years ago – Science Daily

Microbes in the news

Tufts microbiologist Cecilia A. Silva-Valenzuela, Ph.D., named Pew Latin American Fellow
Silva-Valenzuela, in Andrew Camilli’s lab, will investigate novel approaches to prevent cholera outbreaks – EurekAlert

Bio-statistician Albert Parker with MSU’s Center for Biofilm Engineering earns top EPA award – Amanda Eggert – Montana State University

Video series with James Hamblin – The Atlantic
Should You Map Your Microbiome? A visit to uBiome
Your Probiotics Aren’t Doing Anything (Yet)
You Probably Don’t Need to Shower – James Hamblin – The Atlantic

Banking on stool despite an uncertain future – Tina Amirtha – Science

Science, publishing, and career

In effort to understand continuing racial disparities, NIH to test for bias in study sections – Jeffrey Mervis – Science

Triplicated paper with multiplicated cells and images – Leonid Schneider – For Better Science
Author denies accusations of blatant duplication – Shannon Palus – Retraction Watch

Bik’s Picks (it’s not microbiology, but pretty cool)

RhizoTubes as a new tool for high throughput imaging of plant root development and architecture: test, comparison with pot grown plants and validation – Christian Jeudy – Plant Methods

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