March 9, 2015

Pregnancy and birth

Association between caesarean section and childhood obesity: a systematic review and meta-analysis – S. Kuhle – Obesity Reviews

Editorial: Metabolomics, milk-oriented microbiota (MOM) and multipotent stem cells: the future of research on breast milk – Vassilios Fanos – Journal of Pediatric and Neonatal Individualized Medicine

Human oral microbiome

Detection of Mycobacterium tuberculosis DNA on the oral mucosa of tuberculosis patients – Rachel C. Wood – Scientific Reports

Human gut microbiome

Microbes-Gut-Brain Axis: A Possible Future Therapeutics Target for Gastrointestinal and Behavioral Disorder – Amit Ghosh – International Journal of Health Sciences and Research

Review: Collective unconscious: how gut microbes shape human behavior

Human microbiome after death

Seasonal variation of postmortem microbial communities – David O. Carter – Forensic Science, Medicine, and Pathology

Animal models of microbiome research

Perturbation and restoration of the fathead minnow gut microbiome after low-level triclosan exposure – Adrienne B Narrowe – Microbiome

Responses in gut microbiota and fat metabolism to a halogenated methane analogue in Sprague Dawley rats – Yong Su – Microbial Biotechnology

Animal microbiome

The oral and conjunctival microbiotas in cats with and without feline immunodeficiency virus infection – Scott J Weese – Veterinary Research

Phylogenetic distribution of symbiotic bacteria from Panamanian amphibians that inhibit growth of the lethal fungal pathogen Batrachochytrium dendrobatidis – Matthew H. Becker – Molecular Ecology

Microbial ecology in Hydra: Why viruses matter – Thomas C.G. Bosch – Journal of Microbiology

Plant microbiome

Microbial communities on flower surfaces act as signatures of pollinator visitation – Masayuki Ushio – Scientific Reports

Review: The Ecology and Natural History of Foliar Bacteria with a Focus on Tropical Forests and Agroecosystems – Eric A. Griffin, Walter P. Carson – Botanical Review

Review: Chemical diversity of microbial volatiles and their potential for plant growth and productivity – Chidananda N. Kanchiswamy – Frontiers in Plant Science

Soil and plant root microbiome

Metagenomic Assessment of the Potential Microbial Nitrogen Pathways in the Rhizosphere of a Mediterranean Forest After a Wildfire – José F. Cobo-Díaz – Microbial Ecology

Evaluation of Methyl Bromide Alternatives Efficacy against Soil-Borne Pathogens, Nematodes and Soil Microbial Community – Hongwei Xie – PLOS ONE

Relative importance of soil physico-chemical characteristics and plant species identity to the determination of soil microbial community structure – André M. Massenssini – Applied Soil Ecology

Decoupled distance-decay patterns between dsrA and 16S rRNA genes among salt marsh sulfate-reducing bacteria – Angus Angermeyer – Environmental Microbiology

Long-term nickel exposure altered the bacterial community composition but not diversity in two contrasting agricultural soils – Jing Li – Environmental Science and Pollution Research

Extreme plagiarism alert: Influence of heavy metals on earthworms, soil microbial community and mammals – Ahmad Gholamalizadeh Ahangar and Abbas Keshtehgar – Journal of Novel Applied Sciences

Water (and ice) microbiome

Dynamics of marine bacterial community diversity of the coastal waters of the reefs, inlets, and wastewater outfalls of southeast Florida – Alexandra M. Campbell – MicrobiologyOpen

Temperature affects the size-structure of phytoplankton communities in the ocean – Ángel López-Urrutia – Limnology and Oceanography

Stable microbial community composition on the Greenland Ice Sheet – Michaela Musilova – Frontiers in Microbiology

Diversity and spatial distribution of autotrophic communities within and between ice-covered Antarctic lakes (McMurdo Dry Valleys) – Jenna M. Dolhi – Limnology and Oceanography

Book chapter: Microbial Life in Volcanic Lakes – Francesca Mapelli – Volcanic Lakes

Microbiome of the built environment

Urban microbiome – Orli G. Bahcall – Nature Review Genetics

Our interface with the built environment: immunity and the indoor microbiota – Simon Lax – Trends in Immunology

Microbial evolution and ecology

Extending the Conserved Phylogenetic Core of Archaea Disentangles the Evolution of the Third Domain of Life – Céline Petitjean – Molecular Biology and Evolution

The community ecology of pathogens: coinfection, coexistence and community composition – Eric W. Seabloom – Ecology Letters

Computational prediction of molecular pathogen-host interactions based on dual transcriptome data – Sylvie Schulze – Frontiers in Microbiology

Genetic isolation between two recently diverged populations of a symbiotic fungus
Sara Branco – Molecular Ecology

Review: Ecology and exploration of the rare biosphere – Michael D. J. Lynch & Josh D. Neufeld – Nature Reviews Microbiology

Metagenomics and bioinformatics

Metaxa2: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data – Johan Bengtsson-Palme – Molecular Ecology Resources

RITA: Rapid Identification of HighConfidence Taxonomic Assignments for Metagenomic Data – Norman J. MacDonald – Genes, Genomes and Metagenomes

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets – Matthias Scheuch – BMC Bioinformatics

Poster: Possibilities and obstacles in recovery of genomes from elusive microbes in complex metagenomes – Søren M. Karst

Beyond research: a primer for considerations on using viral metagenomics in the field and clinic – Richard J. Hall – Frontiers in Microbiology

Whole genome sequencing in clinical and public health microbiology – Kwong, J. C – Pathology


Genome-Wide Association Study of Metabolic Traits Reveals Novel Gene-Metabolite-Disease Links – Rico Rueedi – PLOS Genetics


International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons – Nathan D. Olson – Biomolecular Detection and Quantification

The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations – Fiona Fouhy – PLOS ONE

Parallel DNA polymerase chain reaction: Synthesis of two different PCR products from a DNA template – Vikash Bhardwaj1, Kulbhushan Sharma2 – F1000 Research

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island – Philip M Ashton- Nature Biotechnology

Microbes in the news

1h podcast with Jonathan Eisen: The Tiny World of Microbes Inside You – Inquiring Minds at Soundcloud

20m podcast: The Straight Poop – Transistor

Beyond Probiotics: Can You “Hack” Your Microbiome? – Beth Skwarecki – Vitals

The unseen world: reflections on Leeuwenhoek (1677) ‘Concerning little animals’ – Nick Lane – Royal Society

Drugging the gut microbiome – Ken Garber – Nature Biotechnology

Tummy Troubles? Your Microbiome Can Help – Isabel Smith

Sewage Bacteria Reveal Cities’ Obesity Rates – Brian Owens – Inside Science

Trend of colon cleansing generally unnecessary – Denise Cedar and Marilyn Bacon – Statesman Journal

Health focus shifts to gut microbiome and nurturing ‘good’ bacteria – Peg Moline – LA Times

How Microbes Keep Us Healthy – Scientific American

Understanding psychobiotics: John F. Cryan – Catherine Lawson – Wired

“Thinking from the Gut” – Rob Wipond – Mad In America

Prediabetes Patients Have Fewer Gut Bugs – Parker Brown – MedPageToday

Fecal microbiota present target for glucose tolerance assessment – Elena Barengolts – Healio

How gut microbiota could play a key role in protecting the brain – Nina Weisbroth – Translational Microbiome

Hand-Wringing Over Bacteria – C. Claiborne Ray – New York Times

Beer Makers To Produce Beer Replicas of 170-Year-Old Brews – Jenny Michelle Panganiban – International Business News

Gut check: With bacteria in us and all over us, researchers are finding ways to take advantage of them – Kyle Peveto – The Advocate

First Detailed Microscopy Evidence of Bacteria at the Lower Size Limit of Life – Lab Manager

Autism’s bacteria link gains credence – Jonathan Sher – LF Press

Nestlé’s research on nutrition and the human gut microbiome – Enea Rezzonico – Scientific American

Fine Focus: Microbiology Research Journal for Undergraduate Students

Science and art

New Drawings Show the Strange Beauty of Phages, the Bacteria Slayers – Brian Handwerk – Smithsonian’

Cosmos: Abstract Images Created by Destroying Star Photo Film Slides with Bacteria – Michael Zhang – Peta Pixel

Science, publishing, and career

Keys to the kingdom (academic bioentrepreneurs) – Sybil C K Wong- Nature Biotechnology

My Most Informative Error – Ami Schattner – JAMA Internal Medicine

We need post-publication peer review of journals – Lenny Teytelman – The Spectroscope

Bik’s Picks: The science of aging edition

Cavers Find Ancient Hoard of Coins and Jewelry in Israel – Megan Gannon – Live Science

Book Review: Rust’ Offers an Engrossing Look at Corrosion – Gregory Cowles – New York Times

Achieving Immortality: How Science Seeks to End Aging – Josh Nilaya – WNPR



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