February 17, 2015

Too little time to cover everything from this 3-day weekend, but hopefully I can catch up tomorrow.

Microbiome of pregnancy and birth

Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome – Amanda L. Thompson – Frontiers in Cellular and Infection Microbiology

Human oral microbiome

Dynamic Changes in the Subgingival Microbiome and Their Potential for Diagnosis and Prognosis of Periodontitis – Baochen Shi – mBio

The hidden ‘mycobacteriome’ of the human healthy oral cavity and upper respiratory tract
Lilia Macovei – Journal of Oral Microbiology

Human vaginal microbiome

The Vaginal Microbiota over an 8- to 10-Year Period in a Cohort of HIV-Infected and HIV-Uninfected Women – Supriya D. Mehta – PLOS ONE

Human gut microbiome

Effects of polysaccharopeptide from Trametes versicolor and amoxicillin on the gut microbiome of healthy volunteers – Kumar Pallav – Gut Microbes

Animal models of microbiome research

Vertically transmitted faecal IgA levels determine extra-chromosomal phenotypic variation – Clara Moon – Nature

Voluntary and forced exercise differentially alter the gut microbiome in C57BL/6J mice – Jacob M. Allen – Journal of Applied Physiology

Commentary: Secret behind commensal resilience revealed – Christina Tobin Kåhrström – Nature Reviews Microbiology

Animal microbiome

Community structure of gut fungi during different developmental stages of the Chinese white pine beetle (Dendroctonus armandi) – Xia Hu – Scientific Reports

Persistent Shifts in Caribbean Coral Microbiota are Linked to the 2010 Warm Thermal Anomaly – Allison Tracy – Environmental Microbiology Reports

Review: Pathogenesis of canine atopic dermatitis: skin barrier and host–micro-organism interaction – Domenico Santoro – Veterinary Dermatology

Plant microbiome

Whose truffle is this? Distribution patterns of ectomycorrhizal fungal diversity in Tuber melanosporum brûlés developed in multi-host Mediterranean plant communities – Elisa Taschen – Environmental Microbiology

The composition of arbuscular mycorrhizal fungal communities differs among the roots, spores and extraradical mycelia associated with five Mediterranean plant species – Sara Varela-Cervero – Environmental Microbiology

Plant and soil effects on bacterial communities associated with Miscanthus ×giganteus rhizosphere and rhizomes – Dongfang Li – GCB bioenergy

Soil microbiome

Plant diversity, soil biota and resistance to exotic invasion – Huixuan Liao – Diversity and Distributions

Global biogeographic sampling of bacterial secondary metabolism – Zachary Charlop-Powers – eLife

Water microbiome

Illumina sequencing-based analysis of free-living bacterial community dynamics during an Akashiwo sanguine bloom in Xiamen sea, China – Caiyun Yang – Scientific Reports

Transient Changes in Bacterioplankton Communities Induced by the Submarine Volcanic Eruption of El Hierro (Canary Islands) – Isabel Ferrera – PLOS ONE

Bioreactor microbiology

Analysis of microbial community composition in a lab-scale membrane distillation bioreactor – Q. Zhang – Journal of Applied Microbiology

Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters – Inka Vanwonterghem – Scientific Reports

Phages and viruses

Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus – Yunzhou Wei – Nucleic Acids Research

Microbial Ecology

Patterns, causes and consequences of defensive microbiome dynamics across multiple scales – Andrew H. Smith – Molecular Ecology

Niche construction by growth forms is as strong a predictor of species diversity as environmental gradients – Kari Anne Bråthen and Virve Tuulia Ravolainen – Journal of Ecology

Comment: The importance of soil archives for microbial ecology – Jan Dolfing & Youzhi Feng – Nature Reviews Microbiology

Editorial: Metabolites in differentiation – Andrea Du Toit – Nature Reviews Microbiology

Bioinformatics, metagenomics

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes – Thomas Brettin – Scientific Reports

An improved method to set significance thresholds for β diversity testing in microbial community comparisons – Arda Gülay and Barth F. Smets – Environmental Microbiology

Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses – Marie Lisandra Zepeda Mendoza – Briefings in Bioinformatics

Correcting Illumina sequencing errors for human data – Heng Li – ArXiv

Not really microbial, but of possible interest: ModuleBlast: identifying activated sub-networks within and across species – Guy E. Zinman – Nucleic Acids Research


A high-resolution 2D J-resolved NMR detection technique for metabolite analyses of biological samples – Yuqing Huang – Scientific Reports

Pseudomonas aeruginosa manipulates redox and iron homeostasis of its microbiota partner Aspergillus fumigatus via phenazines – Benoit Briard – Scientific Reports

An overview of fecal preparation for global metabolic profiling – O. Deda – Journal of Pharmaceutical and Biomedical Analysis

Increased urinary indoxyl sulfate (indican): new insights into gut dysbiosis in Parkinson’s Disease – Cassani Erica – Parkinsonism & Related Disorders

Microbes in the news

Overselling the microbiome award: CBC Fresh Air & JA Tetro on kissing microbiomes – Jonathan Eisen – Phylogenomics / The Tree of Life Blog

A (not so!) Surprising Comparison of Male vs. Female Microbiomes – Alexandra Carmichael – uBiome

Microbes in the Gut Are Essential to Our Well-Being – David Grogan – Scientific American

Inflammatory Bowel Disease May Be from Mom’s Bacteria, not DNA – Christopher Wanjek – LiveScience

Mothers can pass traits to offspring through bacteria’s DNA, mouse study shows – Science Daily (about the Clara Moon paper in Nature; see above)

How Can Rivers And Streams Be Sources Of Antibiotic Resistant Bacteria? – James Maynard – TechTimes

Cooperative Control: With the help of a virus that infects its prey’s nervous system, a parasitoid wasp coerces a lady beetle to protect its young – Sandhya Sekar – The Scientist

Scientists turn the tables on drug-resistant bacteria by infecting them with bacteriophages – Phys.org

Science and career

Seven myths about scientists debunked – Jeffrey Craig, Marguerite Evans-Galea – the Conversation

Science and art

Microbial Masterpieces: Artist Anicka Yi explores the beauty of bacteria – Jenny Rood – The Scientist

2015 Year of the Phage – Life in our Phage World (Book, download)

Bik’s Picks

Demographic Clusters Identified within the Northern Gulf of Mexico Common Bottlenose Dolphin (Tursiops truncates) Unusual Mortality Event: January 2010 – June 2013 – Stephanie Venn-Watson – PLOS ONE

BP cherry-picks study to dodge blame for massive deaths of gulf dolphins – Michael Hiltzik – Los Angeles Times

Satire: Study Finds Jack Shit – The Onion


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