January 12, 2017

uBiome blog

Losing Weight is the Most Popular New Year’s Resolution – Could Probiotics Help? – Julie Taylor – uBiome

Video: Young Microbiome Researchers: Celsius & Beyond – uBiome
For the uBiome team, working with other scientists is always rewarding, but we particularly enjoyed our recent collaboration with a team of researchers, many of whom were swamped by their lab coats and blue nitrile gloves.


Postdoctoral Research Fellow, Microbiology – California Academy of Sciences

Pregnancy and early life

* A molecular portrait of maternal sepsis from Byzantine Troy – Alison M Devault – eLIFE

The Generation R Study: design and cohort update 2017 – Marjolein N. Kooijman – European Journal of Epidemiology

Human oral microbiome

On the ecosystemic network of saliva in healthy young adults – Egija Zaura – The ISME Journal

Human gut microbiome

Seven brief reviews: Topical Issue of the Journal of Immunology: The Macro Influence of the Microbiome – Pamela J. Fink – The Journal of Immunology

Review: Microbiome and the future for food and nutrient security – Brajesh K. Singh – Microbial Biotechnology

Animal experiments

Neuroblastoma causes alterations of the intestinal microbiome, gut hormones, inflammatory cytokines, and bile acid composition – Christoph Castellani – Pediatric Blood & Cancer

Routine assessment of the gut microbiome to promote preclinical research reproducibility and transparency – Hannah R Wardill – Gut

Animal microbiome

Postnatal changes in the relative abundance of intestinal Lactobacillus spp. in newborn calves – Tadashi Takino – Journal of Veterinary Medical Science

Population- and growth-related differences in helminthic fauna of finless porpoises (Neophocaena asiaeorientalis) in five Japanese populations – Akira Shiozaki – Journal of Veterinary Medical Science

Antifeedants Produced by Bacteria Associated with the Gut of the Pine Weevil Hylobius abietis – Karolin Axelsson – Microbial Ecology

Plant, root, and soil microbiome

Trends in Taxonomic and Functional Composition of Soil Microbiome Along a Precipitation Gradient in Israel – Binu M. Tripathi – Microbial Ecology

Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil – Eoin Gunnigle – Scientific Report

Foliar application of the leaf-colonizing yeast Pseudozyma churashimaensis elicits systemic defense of pepper against bacterial and viral pathogens – Gahyung Lee – Scientific Reports

Response of microbial communities colonizing salt marsh plants rhizosphere to copper oxide nanoparticles contamination and its implications for phytoremediation processes – Joana P. Fernandes – Science of the Total Environment

Biodegradation of the veterinary antibiotics enrofloxacin and ceftiofur and associated microbial community dynamics – Diogo A.M. Alexandrino – Science of the Total Environment

Redox conditions and marine microbial community changes during the end-Ordovician mass extinction event – Justyna Smolarek – Global and Planetary Change

Use of plant growth promoting bacterial strains to improve Cytisus striatus and Lupinus luteus development for potential application in phytoremediation – María Balseiro-Romero – Science of the Total Environment

Response of microbial communities colonizing salt marsh plants rhizosphere to copper oxide nanoparticles contamination and its implications for phytoremediation processes -Joana P. Fernandes – Science of the Total Environment

Communication of Sedentary Plant-Parasitic Nematodes With Their Host Plants – T. Hewezi – Advances in Botanical Research

Book chapter: Application of Microbiology in Dryland Agriculture – Minakshi Grover – Innovations in Dryland Agriculture

Water and extremophile microbiome

Potential Activity of Subglacial Microbiota Transported to Anoxic River Delta Sediments – Karen A. Cameron – Microbial Ecology

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring – Laura Ward – The ISME Journal

Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics – Abraham G. Moller – PeerJ

Abundance of microorganisms and enzyme activity in the rapids-pool-benchland systems in natural Douliu River of China – Zhen Hong Wang – PeerJ Preprint

Distinct sensitivity of fungal freshwater guilds to water quality – Oliver Röhl – Mycological

Food microbiology

Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses – Jing Li – BMC Microbiology

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation – Peter R Sternes – bioRxiv

Waste and pollution microbiology

Microbial community structure in a full-scale anaerobic treatment plant during start-up and first year of operation revealed by high-throughput 16S rRNA gene amplicon sequencing – Else Marie Fykse – Bioresource Technology


* MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes – Wei Ma – Scientific Reports

Microbial ecology

Review: Where less may be more: how the rare biosphere pulls ecosystems strings – Alexandre Joussett – ISME Journal

Microbes in the news

Gut science is radically changing what we know of the human body – Pat Rich – University Affairs Canada

Renowned microbiology expert to visit West Florida. Claire Fraser will present, “The Human Gut Microbiome in Health and Disease” – SR Press Gazette

Microbiomes Move Standard Plate Count One Step Forward – Gregory Siragusa – Food Safety Tech

Researchers develop new compound to fight cytomegalovirus – EurekAlert

Eating red meat six times a week could increase chances of getting painful bowel disease – Daisy Dunne – Mirror

This looks intriguing: Microbiota and the masses: a love story – S. B. Divya – MacMillan

Microbes on the market

Gut microbiome profiling tests propelled by customer demand – Vijay Shankar – Nature Biotechnology

Bruker Announces Acquisition of CMO InVivo Biotech to Expand Molecular Biology, Microbiology and Pathology Consumables and Assay Business

Bik’s non-microbiology picks

UCSF Receives Historic Half-Billion-Dollar Donation – Lindsey Hoshaw – KQED

This is a tragic/comic read, but note that the original post contained some offending language, that was removed after protests on e.g. Twitter. The Rise and Fall of a Shrimp Biologist – David Scholnick – Scientific American

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