May 22, 2015

Several special issues this week: Science features results from the Tara ocean plankton biodiversity expedition, Microbes and Infection has a special on the oral microbiome, and Frontiers bundled several papers under the not-so-pretty name The Human Gutome.

General microbiome

The Microbiome and Autoimmune Disease: Report from a Noel R. Rose Colloquium – Jobert G. Barin – Clinical Immunology

New developments providing mechanistic insight into the impact of the microbiota on allergic disease – Kathy D. McCoy – Clinical Immunology

Review: Self or non-self? The multifaceted role of the microbiota in immune-mediated diseases – Martin A. Kriegel – Clinical Immunology

Human oral microbiome

Special issue of Microbes and Infection (7 papers but most have already been posted in this blog). Editorial with links to 7 papersA New Frontier: Oral Microbes without Borders – Özlem Yilmaz
Extracellular DNA in oral microbial biofilms – Nicholas S. Jakubovics

Not microbiome but cool: The Diet of Three Medieval Individuals from Caravate (Varese, Italy). Combined Results of ICP-MS Analysis of Trace Elements and Phytolith Analysis Conducted on Their Dental Calculus – A. M. B. Lazzati – International Journal of Osteoarchaeology

Human gut microbiome

Frontiers Research Topic (papers have been posted previously in this blog): The Human Gutome: Nutrigenomics of Host-Microbiome Interactions

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes – Stefanía Magnúsdóttir – Frontiers in Genetics

Model: Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico – Almut Heinken – Applied and Environmental Microbiology

Review: Intestinal microbiota and allergic diseases: A systematic review – L.C.F.L. Melli – Allergologia et Immunopathologia

Human urogenital microbiome

Editorial: Cervicovaginal Microbiota: Simple Is Better – Smita Gopinath – Immunity

Cervicovaginal Bacteria Are a Major Modulator of Host Inflammatory Responses in the Female Genital Tract – Melis N. Anahtar – Immunity

The New World of the Urinary Microbiome in Women – Linda Brubaker, Alan J Wolfe – American Journal of Obstetrics and Gynecology

Plant and soil microbiome

Root-associated bacterial endophytes from Ralstonia solanacearum resistant and susceptible tomato cultivars and their pathogen antagonistic effects – Reshmi Upreti and Pious Thomas – Frontiers in Microbiology

Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types – Brian Reavy – Applied and Environmental Microbiology

Water microbiome

Special Science issue: Tara Oceans studies plankton at Planetary Scale – P. Bork- Science

pH levels drive bacterial community structure in sediments of the Qiantang River as determined by 454 pyrosequencing – Shuai Liu – Frontiers in Microbiology

Distribution and diversity of fungi in freshwater sediments on a river catchment scale – Jie Liu – Frontiers in Microbiology

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction
Ping Zhang – Applied and Environmental Microbiology

Extremophile microbiome

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms – Young-Mo Kim – Frontiers in Microbiology

Abundance and Distribution of Dimethylsulfoniopropionate Degradation Genes and the Corresponding Bacterial Community Structure at Dimethyl Sulfide Hot Spots in the Tropical and Subtropical Pacific Ocean – Yingshun Cui – Applied and Environmental Microbiology

Built environment microbiome

Feasibility study involving the search for natural strains of microorganisms capable of degrading graffiti from heritage materials – Patricia Sanmartín – International Biodeterioration & Biodegradation

Bioreactor microbiology

Next-Generation Pyrosequencing Analysis of Microbial Biofilm Communities on Granular Activated Carbon in Treatment of Oil Sands Process-Affected Water – M. Shahinoor Islam – Applied and Environmental Microbiology

Metagenomics

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes – Stefanía Magnúsdóttir – Frontiers in Genetics

Metabolomics

Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters – Tina Netzker – Frontiers in Microbiology

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

Functional foods

Probiotics for Weight Loss: A Systematic Review and Meta-Analysis – Sunmin Parka, Ji-Hyun Baeb – Nutrition Research

Viruses and phages

Badger, mongoose, otterFecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses – Nádia Conceição-Neto – Virology Journal

Review: The Virome in Host Health and Disease – Ken Cadwell – Immunity

More microbiology

Editorial: recent discoveries in evolutionary and genomic microbiology – Anton G. Kutikhin and Arseniy E. Yuzhalin – Frontiers in Microbiology

Financial evaluations of antibiotic stewardship programs—a systematic review – Jan-Willem H. Dik – Frontiers in Microbiology

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach – Román Zapién-Campos – Frontiers in Microbiology

Microbes in the news

What’s Next for the Microbiome? – Jo Handelsman and Elizabeth R. Stulberg – Whitehouse.gov
The White House wants input on the future of microbiome research (by June 15) – Jonathan Eisen – Microbe.net

Ocean’s microbiome has incredible diversity – and human likeness – Colin Barras – New Scientist
Three-year ocean voyage discovered thousands of new, unfamiliar virusesA study of plankton reveals just how little we know about the ocean – Arielle Duhaime-Ross – The Verge
Scientists Map 5,000 New Ocean Viruses – Carl Zimmer – Quanta Magazine

Help fund koala microbiome study – Andy Fell – Egghead Research at UC Davis

Nurturing a baby’s microbiome, before and after birth – Kate Gammo – Populair Science

Meet the caesarean mums who are ‘seeding their baby’s microbiome’ – Best Daily

Long-gone bacteria blows the whistle on gold deposits – Geology Page

Microbes and money

Why bacteria is becoming big business – Stephen Valdivia – Fortune
Danone’s big bet on tiny bacteria – Erica Fry – Fortune

uBiome Partners with PicnicHealth: Participants diagnosed with Inflammatory Bowel Disease (IBD) will receive a complementary PicnicHealth account as well as a complementary uBiome research kit. – PR Rocket

Science, publishing, and career

(Satire) The Allium Top Tips For Scientists and Engineers – The Allium
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