After Science’s Microbiome Issue yesterday, today’s digest features Genome Biology’s special Translational Microbiome issue. Papers on detecting colon cancer, Clostridium difficile infection, high-fat diets in mice. Also check out papers on H2 metabolism in the colon, no effects of temperature rise on soil microbiome of wet tropical forests, and ultra-basic springs.
Jobs and events
Nice speaker line-up: May 16-18, Michigan Meeting on Microbial Communities: a deep dive into the world of microbes – University of Michigan
Job opening in our lab: Life Science Research Professional – Stanford
Pregnancy and birth
Gestational age, mode of birth and breastmilk feeding all influence acute early childhood gastroenteritis: a record-linkage cohort study – Jason P. Bentley – BMC Pediatrics
Human gut microbiome
Special issue Genome Medicine: Translating the microbiome: health and disease, Guest Editor: Curtis Huttenhower
Editorial: A roadmap to translating the microbiome – Rabia Begum – Genome Medicine
Detecting colon cancer using microbiota: Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions – Nielson T. Baxter – Genome Medicine
Dynamics of the fecal microbiome in patients with recurrent and nonrecurrent Clostridium difficile infection – Anna Maria Seekatz – Genome Medicine
Use of Shotgun Metagenome Sequencing to Detect Fecal Colonization with Multi-Drug Resistant Bacteria in Children – Heidi Andersen – Journal of Clinical Microbiology
Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection – Emmanuel Montassier – Genome Medicine
Impact of Helminth Infection on the Clinical and Microbiological Presentation of Chagas Diseases in Chronically Infected Patients – Fernando Salvador – PLOS Neglected Tropical Diseases
Malaria, helminths and malnutrition: a cross-sectional survey of school children in the South-Tongu district of Ghana – Patrick Ferdinand Ayeh-Kumi – BMC Research Notes
Review: The Microbiome and Mental Health: Looking Back, Moving Forward with Lessons from Allergic Diseases – Alan C. Logan – Clinical Psychopharmacology and Neuroscience
Review: Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology – Mukesh Verma – Technology in Cancer Research & Treatment
Animal models
Effects of Isoflavone-Enriched Feed on the Rumen Microbiota in Dairy Cows – Jitka Kasparovska – PLOS ONE
Deep-fried oil consumption in rats impairs glycerolipid metabolism, gut histology and microbiota structure – Zhongkai Zhou – Lipids in Health and Disease
Dietary supplementation of Rosmarinus officinalis L. leaves in sheep affects the abundance of rumen methanogens and other microbial populations – Gabriella Cobellis – Journal of Animal Science and Biotechnology
Microorganisms in the rumen and reticulum of buffalo (Bubalus bubalis) fed two different feeding systems – Raul Franzolin – BMC Research Notes
Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet – Douglas Mahana – Genome Medicine
A fish, not the bird: Combined effects of dietary mannan- and fructo-oligosaccharide on growth indices, body composition, intestinal bacterial flora and digestive enzymes activity of regal peacock (Aulonocara stuartgranti) – S. S. Mirzapour-Rezaee – Aquaculture Nutrition
Plant, root, and soil microbiome
The composition, localization and function of low-temperature adapted microbial communities involved in methanogenic degradations of cellulose and chitin from Qinghai-Tibetan Plateau wetland soils – Yumei Dai – Journal of Applied Microbiology
Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce – Jian-Gang Li – Scientific Reports
Pichia kudriavzevii as a representative yeast of North Patagonian winemaking terroir – Silvana M. del Mónaco – International Journal of Food Microbiology
Increases in mean annual temperature do not alter soil bacterial community structure in tropical montane wet forests – Paul C. Selmants – Ecosphere
Water and extremophile microbiome
A role for fungi as parasites in the black box of marine trophic interactions – Thomas A. Richards – Environmental Microbiology Reports
Exploring the metabolic potential of microbial communities in ultra-basic, reducing springs at The Cedars, CA, USA: Experimental evidence of microbial methanogenesis and heterotrophic acetogenesis – Lukas Kohl – Journal of Geophysical Research
Viruses and phages
Minireview: Virus-host interplay in high salt environments – Nina S. Atanasova – Environmental Microbiology Reports
Metagenomics and bioinformatics
Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques – Disha Tandon – PLOS ONE
Metabolomics
H2 metabolism is widespread and diverse among human colonic microbes – Patricia G. Wolf – Gut Microbes
Localizing metabolic synthesis in microbial cultures with kinetic mass spectrometry imaging (kMSI) – Katherine Louie – bioRxiv
Viruses and phages
The virome: a missing component of biological interaction networks in health and disease – Scott A. Handley – Genome Medicine
Microbial ecology
Commentary: Bacteriophages or bacteriovores – that is the question: variations on the theme of eating Stenotrophomonas maltophilia – Harald Brüssow – Environmental Microbiology Reports
Microbes in the news
Lots of press coverage for the Science and Genome Medicine special issues today!
Scientists think they’ve found the secret to better poop transplants – Rachel Feltman – The Washington Post
Why Are Your Gut Microbes Different From Mine? To find out, scientists collected poop from thousands of people—but they ended up with more questions than answers – Ed Yong – The Atlantic
Food you eat and medicines you take can alter your gut bacteria in both good and bad ways – Emma Tiller – NH Voice
Special microbiome issue – Science Codex
Gut Microbiome Makeup Influenced by Medication Use, Other Factors – Genome Web
In Dutch: Zijn koffie, rode wijn en chocola nou wel of niet goed voor je? – Sander Voormolen – NRC
Title fail: World’s first microbiome study reveals links between lifestyle and gut flora – EurekAlert
Lifestyle has a strong impact on intestinal bacteria – Medical Xpress
The “Friendly” Bacteria In Your Gut Isn’t As Set At Birth As We Thought – Tom Chivers – BuzzFeed
Gut bacteria may predict risk of life-threatening infections following chemotherapy – Science Daily
What Can Happen When You’re Way Too Clean – Alice Park – Time
10 Bizarre (and Wonderful) Facts About Microbes:truly amazing facts about the human microbiome – Dawn Field – TopTenz
Vancouver couple develops slime-free water dishes for dogs – Eric MacKenzie – Vancouver 24h
Podcast: Microbe Talk, April 2016, Can parasitic worms treat inflammatory diseases?
Some superbugs literally explode when they die, making them even more deadly
Ticking time bomb – Jacinta Bowler – Science Alert
Science, publishing, and career
Unconditional data sharing, plus peer review transparency, is key to research reproducibility – Leonid Schneider – The Winnower
Featuring our paper: Seeing double: Duplicated images plague research papers – Ivan Oransky and Adam Marcus – STAT News
Paper linking fecal transplants to obesity in rats retracted for faked data – Dalmeet Singh Chawla – Retraction Watch
