August 11, 2015

Several reviews on human gut microbiome, two papers on coral microbiome, gut microbiota of wild mice, ancient sea microbes found in gold mine stalactites, and an update on the tree of life.

Microbiome of Death

Not a microbiota paper, but cannot leave out: A Longitudinal Study on Human Outdoor Decomposition in Central Texas – Joanna K. Suckling – Journal of Forensic Sciences

Human gut microbiome

Anti-tumour Necrosis Factor Treatment with Adalimumab Induces Changes in the Microbiota of Crohn’s Disease – David Busquets – Journal of Crohn’s and Colitis

Reduced Levels of D-dimer and Changes in Gut Microbiota Composition after Probiotic Intervention in HIV-infected Individuals on Stable ART – Birgitte Stiksrud – Journal of Acquired Immune Deficiency Syndromes

The human gut microbiome as a transporter of antibiotic resistance genes between continents – Johan Bengtsson-Palme – Antimicrobial Agents and Chemotherapy

Review: The gut microbiota in human energy homeostasis and obesity – Michael Rosenbaum – Trends in Endocrinology & Metabolism

Review: Understanding probiotics’ role in allergic children: the clue of gut microbiota profiling – Pamela Vernocchi – Current Opinion in Allergy and Clinical Immunology

Editorial: The Role of Bacteria in Necrotizing Enterocolitis: Understanding the Forest for the Trees – McElroy S.J – Neonatology

Review: Implications of microbiota and bile acid in liver injury and regeneration – Hui-Xin Liu – Journal of Hepatology

Animal and bioreactor models

Metagenomic Analysis of Antibiotic Resistance Genes in Dairy Cow Feces following Therapeutic Administration of Third Generation Cephalosporin – Lindsey Chambers – PLOS ONE

Increased Butyrate Production During Long-Term Fermentation of In Vitro-Digested High Amylose Cornstarch Residues with Human Feces – Li Li – Journal of Food Science

Bacterial diversity in bovine rumen by metagenomic 16S rDNA sequencing and scanning electron microscopy – Raphael Barbetta de Jesus – Acta Scientiarum

Animal microbiome

The Gut Microbiota of Wild Mice – Laura Weldon – PLOS ONE

Necrotizing Enterocolitis in Preterm Pigs Is Associated with Increased Density of Intestinal Mucosa-Associated Bacteria Including Clostridium perfringens – Støy A.C.F. – Neonatology

Cecal drop reflects the chickens’ cecal microbiome, fecal drop does not – J. Pauwels – Journal of Microbiological Methods

Evidence for host specificity among dominant bacterial symbionts in temperate gorgonian corals – Marie La Rivière – Coral Reefs

Identification of Candidate Coral Pathogens on White Band Disease-Infected Staghorn Coral – Sarah A. Gignoux-Wolfsohn – PLOS ONE

Bacteria detected in the honeybee parasitic mite Varroa destructor collected from beehive winter debris – J. Hubert – Journal of Applied Microbiology

Plant, root, and soil microbiome

Remediation of diesel-contaminated soil using in situ chemical oxidation (ISCO) and the effects of common oxidants on the indigenous microbial community: a comparison study – Ku-Fan Chen – Journal of Applied Microbiology

Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition – An Yang – Frontiers in Microbiology

Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans – Anish Bhattacharyya – Archaea

Seasonal effect and anthropogenic impact on the composition of the active bacterial community in Mediterranean orchard soil – Sammy Frenk – FEMS Microbial Ecology

Effects of biochar on copper immobilization and soil microbial communities in a metal-contaminated soil – Sebastián Meier – Journal of Soils and Sediments

Factors associated with the diversification of the microbial communities within different natural and artificial saline environments – Shilong He – Ecological Engineering

Review: Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead? – Aimée T. Classen – Ecosphere

Water microbiome

Deep subsurface mine stalactites trap endemic fissure fluid Archaea, Bacteria, and Nematoda possibly originating from ancient seas – Gaëtan Borgonie – Frontiers in Microbiology

Drivers of the dynamics of diazotrophs and denitrifiers in North Sea bottom waters and sediments – Haoxin Fan – Frontiers in Microbiology

Waste treatment microbiology

Denitrifying capability and community dynamics of glycogen accumulating organisms during sludge granulation in an anaerobic-aerobic sequencing batch reactor – Zhang Bin – Scientific Reports


Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data – Laurence Yang – PNAS

Colonic metaproteomic signatures of active bacteria and the host in obesity – Carolin A. Kolmeder – Proteomics

More microbes

The universal tree of life: an update – Patrick Forterre – Frontiers in Microbiology

How Do Microbial Populations and Communities Function as Model Systems? – Maureen O’Malley – The Quarterly Review of Biology

Impact of space flight on bacterial virulence and antibiotic susceptibility – Peter William Taylor – Infection and Drug Resistance

Microbes in the news

Look Up! There’s an Invisible Zombie Highway Right Above You – Robert Krulwich – National Geographic

uBiome Invites Health Care Providers to Join New Clinical Microbiome Consortium – Global News Wire

Our microbiome: Separating hype from health – Nicholas Staropoli – Genetic Literacy Project

Poop Transplants And Microbiome Makeovers: How We’ll Engineer Our Bacteria To Feel Better – Jessica Leber – FastCoExist

Researchers Offer New Insights Into the Pulmonary Microbiota of Cystic Fibrosis Patients – Patricia Silva – Cystic Fibrosis News Today

Conflict and Co-operation in Bacterial Communities – MicrobePost

Can Your Body’s Bacteria Cause Cancer? – Charis Eng – Cleveland Clinic

British Ministry of Defense released potentially lethal bacteria on London Tube (in 1963), chemically experimented on soldiers – Russell Boyce – RT

Engineered Bacteria Send A Signal When Water Gets Polluted – Tracy Staedter – Discovery

JGI to Grant $1.2 Million to Genomic Technology Projects – Genome Web

Science, publishing, and career

Science: The Story of Me – Morgan Pak – Huffington Post

4 Ways to Help Everyone Find Their Inner Scientist – Imogen Coe – Huffington Post

Tech Women in India’s Startup Boom Reach Out – Gagandeep Kaur – WomensEnews

Bik’s Picks

Magnetosensitive neurons mediate geomagnetic orientation in Caenorhabditis elegans – Andrés Vidal-Gadea – eLIFE

Here’s why coffee makes you poop – Rachel Feltman – Washington Post

Why You’re More Likely To Be Killed By a Bee Than a Bear: Our fear of bear attacks is far greater than the actual risk of being mauled or killed, experts say. – Carrie Arnold – National Geographic



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