June 29, 2015

Gut microbiome of children with Schistosoma infections, what happens to the hooves after a cow dies, and microbiomes at extremely dry or hot places.

General microbiome

Only one health, and so many omics – Nives Pećina-Šlaus – Cancer Cell International

Interchange of entire communities: microbial community coalescence – Matthias C. Rillig – Trends in Ecology and Evolution

A Vision for Investigating the Microbiology of Health and Disease – W. Ian Lipkin – The Journal of Infectious Diseases

Collateral sensitivity of antibiotic-resistant microbes – Csaba Pál – Trends in Microbiology

Personalized medicine going precise: from genomics to microbiomics – Sanjay K. Shukla – Trends in Molecular Medicine

Review: Secrets from the microbiome: molecular biology meets microbiology meets histopathology….meets clinical biochemistry – Caroline Young – Annals of Clinical Biochemistry

Human respiratory microbiome

Editorial: Infectious asthma triggers: time to revise the hygiene hypothesis? – Wilmore C. Webley – Trends in Microbiology

Human gut microbiome

Differences in the Faecal Microbiome in Schistosoma haematobium Infected Children vs. Uninfected Children – Gemma Louise Kay – PLOS Neglected Tropical Diseases

Glycan complexity dictates microbial resource allocation in the large intestine – Artur Rogowski – Nature Communications

Review: Intestinal Microbiota, Lipids, and the Pathogenesis of Intestinal Failure–Associated Liver Disease – Way Seah Lee – The Journal of Pediatrics

Review: Influence of gut bacteria on development and progression of non-alcoholic fatty liver disease – Ali Abdul-Hai – World Journal of Hepatology

Animal microbiome

Cockroaches: Aerobic Bacterial Community of American Cockroach Periplaneta americana,a Step toward Finding Suitable Paratransgenesis Candidates – Sanaz Akbari – Journal of Arthropod-Borne Diseases

Hooves from dead cows: Compost biodegradation of recalcitrant hoof keratin by bacteria and fungi – T. Reuter – Journal of Applied Microbiology

Fish: Modulation of the intestinal microbiota and morphology of tilapia, Oreochromis niloticus , following the application of a multi-species probiotic – B . T. Standen – Applied

Jellyfish: Changing company: Composition of bacterial communities associated with
Aurelia aurita changes with compartment, life stage and population – Nancy Weiland-Bräuer – Applied and Environmental Microbiology

Ants: Bacterial community composition and diversity in an ancestral ant fungus symbiosis – Katrin Kellner – FEMS Microbiology Ecology

Review: A new view of the fish gut microbiome: Advances from next-generation sequencing – Mahdi Ghanbari

Plant microbiome

Host–microbe interactions as a driver of acclimation to salinity gradients in brown algal cultures – Simon M Dittami – The ISME Journal

The olive knot disease as a model to study the role of interspecies bacterial communities in plant disease – Roberto Buonaurio – Frontiers in Plant Science

Review: Biotic Interactions in the Rhizosphere: A Diverse Cooperative Enterprise for Plant Productivity – Clelia De-la-Peña – Plant Physiology

Editorial on plants as alternative hosts for human and animal pathogens – Nicola J. Holden – Frontiers in Microbiology

Soil microbiome

Responses of bacterial communities to simulated climate changes in alpine meadow soil of
Qinghai-Tibet plateau – Junpeng Rui – Applied and Environmental Microbiology

Evaluation of bacterial communities by bacteriome analysis targeting 16S rRNA genes and quantitative analysis of ammonia monooxygenase gene in different types of compost – Rika Kitamura – Journal of Bioscience and Bioengineering

Soil conditions and land use intensification effects on soil microbial communities across a range of European field sites – Bruce C. Thomson – Soil Biology and Biochemistry

Impact of urine and the application of the nitrification inhibitor DCD on microbial communities in dairy-grazed pasture soils – Sergio E. Morales – Soil Biology and Biochemistry

Water microbiome

Metagenomic assessment of viral diversity in Lake Matoaka, a temperate, eutrophic freshwater lake in southeastern Virginia, USA – Jasmin C. Green – Aquatic Microbial Ecology

A comparison of bacterial community structure in seawater pond with shrimp, crab, and shellfish cultures and in non-cultured pond in Ganyu, Eastern China – LianTai Li – Annals of Microbiology

Extremophile microbiome

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert – Francine Piubeli – Indian Journal of Microbiology

Review: Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’ – Brian P Hedlund – Current Opinion in Microbiology

Food microbiology

Evaluation and identification of poly-microbial biofilms on natural green Gordal table olives – Antonio Benítez-Cabello – Antonie van Leeuwenhoek

Proteomic and high-throughput analysis of protein expression and microbial diversity of microbes from 30- and 300-year pit muds of Chinese Luzhou-flavor liquor – Qi Zheng – Food Research International

Bacterial communities during the process of high-temperature Daqu production of roasted sesame-like flavour liquor – Yao Su – Journal of the Institute of Brewing

Bioreactor microbiology

Sulfate Reducing Bacteria and Mycobacteria Dominate the Biofilm Communities in a Chloraminated Drinking Water Distribution System – Christa Kimloi Gomez-Smith – Environmental Science & Technology

The Microbiota and Abundance of the Class 1 Integron-Integrase Gene in Tropical Sewage Treatment Plant Influent and Activated Sludge – Magna C. Paiva – PLOS ONE

Metabolic networks

Metabolic pathway activity estimation from RNA-Seq data – Yvette Temate-Tiagueu – ISBRA abstracts

Microbes in the news

Volunteers Needed for Human Microbiota Study: prebiotic effects of certain rice bran components @UArkansas

In Defense of Fiber: How Changing Your Diet Changes Your Gut Bacteria – Mandy Oaklander – Time

Undergraduate is first author on study of Lake Matoaka’s metagenome – Joseph McClain – WM.edu

DNA Genotek Inc. announces recipients of gut microbiome grant program – Steamfeed

Indigo-Clean Is New Light Designed For Hospitals That Kills Bacteria – James Maynard – TechTimes

The ‘frightening’ rise of flesh-eating bacteria: Mystery, pain and amputations – Peter Holley – Washington Post

Fatty and sugary foods linked to lower cognitive functions: Mouse data – Nathan Gray – Food Navigator

Investors Think This Company’s Gut Bacteria Are Worth $1.9 Billion – John Tozzi – Bloomberg

What’s new in gastroenterology? Insights from BMC Medicine at #DDW2015 – Alessandro Recchioni- BioMedCentral

Science, publishing, and career

From trainee to tenure-track: ten tips – Tuuli Lappalainen – Genome Biology

What would be a suitable value for the absolute minimum proportion of female speakers at genomics/bioinformatics conferences? – Keith Bradnam? – ACGT blog

Bik’s Picks

Make it count! ‘Leap second’: Why June 30 will have one extra second – Deborah Netburn – LA Times

SpaceX Rocket Explosion Destroys Students’ Science Experiment – Alyssa Newcomb – ABC News

Rats Dream About the Places They Want to Explore – Kiona Smith-Strickland – Discover Magazine
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