March 24, 2015

General microbiome

Review: Biomarkers for the 21st Century: Listening to the Microbiome – Rodney Reynolds Dietert* and Ellen Kovner Silbergeld – Toxicological Sciences

Nice overview [PDF]: FASEB Releases “The Human Microbiome: Your Own Personal Ecosystem” – FASEB

Microbiome of pregnancy and birth

Bacterial diversity and Clostridia abundance decrease with increasing severity of necrotizing enterocolitis – Valarie E McMurtry – Microbiome

Human vaginal microbiome

Vaginal Microbiota of Adolescent Girls Prior to the Onset of Menarche Resemble Those of Reproductive-Age Women – Roxana J. Hickey – mBio

Human gut microbiome

The detection of vector-borne-disease-related DNA in human stool paves the way to large epidemiological studies – Alpha Kabinet Keita – European Journal of Epidemiology

Animal and other models

A Modified R-Type Bacteriocin Specifically Targeting Clostridium difficile Prevents Colonization of Mice without Affecting Gut Microbiota Diversity – Dana Gebhart – mBio

Effects of Irradiation on Epithelial Wound Healing and Microbial Diversity in an
in-vitro Oral Mucosa Model – Tine De Ryck – Nuclear Medicine & Radiation

Microbes on Mars? Carbon monoxide as a metabolic energy source for extremely halophilic microbes: Implications for microbial activity in Mars regolith – Gary M. King – PNAS USA

Animal microbiome

Rabbit: The bacterial communities associated with fecal types and body weight of rex rabbits – Bo Zeng – Scientific Reports

Plant microbiome

Lots of omics words in this book: Microbiomics: An Approach to Community Microbiology – Pankaj Sharma – In: PlantOmics

Soil and plant root microbiome

The Soil Microbiome Influences Grapevine-Associated Microbiota – Iratxe Zarraonaindia – mBio

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem – Jinbo Xiong – Scientific Reports

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust – Ulisses Nunes da Rocha – Frontiers in Microbiology

Nucleotide Sequences of Giant Viruses Found in Soil Samples of the Mojave Desert, the Prairie, the Tundra and the Antarctic Dry Valleys – Csaba Kerepesi – ArXiv

Impacts of bulk soil microbial community structure on rhizosphere microbiomes of Zea mays – Matthew G. Bakker – Plant and Soil

Pyrosequencing Reveals Changes in Soil Bacterial Communities after Conversion of Yungas Forests to Agriculture – Marcela S. Montecchia – PLOS ONE

Priority effects during fungal community establishment in beech wood – Jennifer Hiscox – The ISME Journal

Water microbiome

Very cool, with longitudinal plots: The Source of the River as a Nursery for Microbial Diversity – Luiz Felipe Valter de Oliveira, Rogério Margis – PLOS ONE

Evidence of active methanogen communities in shallow sediments of the Sonora Margin cold seeps – Adrien Vigneron – Applied and Environmental Microbiology

Site history and edaphic features override the influence of plant species on microbial communities in restored tidal freshwater wetlands – Christine E. Prasse – Applied and Environmental Microbiology

Multivariate and Phylogenetic Analyses Assessing the Response of Bacterial Mat Communities from an Ancient Oligotrophic Aquatic Ecosystem to Different Scenarios of Long-Term Environmental Disturbance – Silvia Pajares – PLOS ONE

Physiological and evolutionary potential of microorganisms from the Canterbury Basin subseafloor, a metagenomic approach – Frédéric Gaboyer – FEMS Microbiology Ecology

Biosurfactant production from marine hydrocarbon-degrading consortia and pure bacterial strains using crude oil as carbon source – Eleftheria Antoniou – Frontiers in Microbiology

Built environment microbiome

Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments – Christine Moissl-Eichinger – Scientific Reports

Effect of Monochloramine Treatment on the Microbial Ecology of Legionella and Associated Bacterial Populations in a Hospital Hot Water System – Julianne L. Baron – Systematic and Applied Microbiology

Non-culturable bioaerosols in indoor settings: impact on health and molecular approaches for detection – Pascale Blais-Lecours – Atmospheric Environment


Development and Utility of the FDA “GutProbe” DNA Microarray for Identification, Genotyping, and Metagenomic Analysis of Commercially Available Probiotics – Jennifer N. Patro – Journal of Applied Microbiology


Global trends in antimicrobial use in food animals – Thomas P. Van Boeckel – PNAS USA

Metagenomics and bioinformatics

Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly – Tarini Shankar Ghosh – Journal of Bioinformatics and Computational Biology

Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors – Jeremy G. Owen – PNAS USA

Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis – Pushpendra Singh – PNAS USA

Metabolomics / Ecology

Species interactions differ in their genetic robustness – Lon M. Chubiz – Frontiers in Microbiology

Microbes in the news

With a picture you will never forget: Acne and the Microbiome: Christi Investigates – Alexandra Carmichael

Vineyard’s soil microbes shape grapes’ microbial community – Science Daily

Crohn’s Disease: Gut Microbial Collaborations Trigger Inflammatory Diseases – PR NewsWire

Feed the microbes so they don’t feed on you: Fiber-Famished Gut Microbes Linked to Poor Health – Katherine Harmon Courage – Scientific American

Harnessing The Microbiome To Curb Hunger – Chemical and Engineering News

New Research On Appetite-Suppressing Bacteria Could Help Fight Obesity – Anna Almendrala

The MinION Access Programme (MAP) for portable DNA sequencing – Science Daily

Viruses, Archaea Self-mutate to Survive – Laboratory Equipment

Engineering and waterborne bacteria in building water systems – Colum Ó Bric -EngineersJournal

Gut and Mood: The Microbiome in Anxiety and Depression – Nina Weisbroth – Translational Microbiome

Not so fast, FastTree – Darling lab

SatireEach bioinformatician to have their own personal short-read aligner by 2016 – The Science Web

Not about Dr. WhoThe Doctor Who Tested Infectious Bacteria On Himself, And Won A Nobel – Ria Misra

Comparing the genomes of the leprosy bacteria –

#BacteriaHysteria: “Beer Pong” Associated with Frequent Bacterial Transmissions – Jacquelyn Gray – HCPlive

#BacteriaHysteria: Clean machines: how to look after your tech and avoid bacteria bombs – David Howell – TechRadar

Science and art

Workshop, April 6, 2015: Paint with Bacteria – GenSpace, New York City’s Community Biolab

Science, publishing, and career

Opinion: Lay summaries needed to enhance science communication – Lauren M. Kuehne and Julian D. Olden – PNAS USA

50 min podcast: Women in Oceanography: Lots of Students, Not So Many Professors – Heather Goldstone –

This is why you shouldn’t believe that exciting new medical study – Julia Belluz –

Stubborn Pay Gap Is Found in Nursing – Catherine Saint Louis – Catherine Saint Louis – New York Times

It’s time to reboot bioinformatics education – Todd Harris

Bik’s Picks

Macaques Exhibit a Naturally-Occurring Depression Similar to Humans – Fan Xu – Scientific Reports

Earth’s most powerful physics machine gets back in action – Marcus Woo –

Scientists want museums to cut their ties with David Koch – Science Recorder


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