February 14, 2017

Events and jobs
Postdoctoral research fellow in Microbiome Research – Karolinska Institutet

Postdoctoral Scientist ( Microbiome, Mycobiome, Mucosal Immunology) – Jill Roberts Institute for Research in IBD at Weill Cornell Medicine, New York City

Senior Lecturer in Food Microbiology – RMIT Bundoora Campus

Junior Specialist in Environmental Microbiology – University of California, Santa Cruz

General microbiome
Uncharacterized bacterial structures revealed by electron cryotomography – Megan J Dobro – bioRxiv

Pregnancy and early life
Review: Infant fungal communities: current knowledge and research opportunities – Tonya L. Ward – BMC Medicine

Human gut microbiome
A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline – B.J. Levin – Science
Also described in this short article: New tool can help researchers identify enzymes—and their abundance—in microbiomes – Phys.org

Dynamics of the human gut microbiome in inflammatory bowel disease – Jonas Halfvarson – Nature Microbiology

Inediibacterium massiliense gen. nov., sp. nov., a new bacterial species isolated from the gut microbiota of a severely malnourished infant – Maryam Tidjani Alou – Antonie van Leewenhoek

Animal microbiome
The microbiome of bulk tank milk: Characterization and associations with somatic cell count and bacterial count – M.X. Rodrigues – Journal of Dairy Science

Dynamics of the microbiota found in the vaginas of dairy cows during the transition period: Associations with uterine diseases and reproductive outcome – M.L.S. Bicalho – Journal of Dairy Science

Prophylactic use of a standardized botanical extract for the prevention of naturally occurring diarrhea in newborn Holstein calves – A.G.V. Teixeira – Journal of Dairy Science

Plant, root, and soil microbiome
Four years of experimental warming do not modify the interaction between subalpine shrub species – Alba Anadon-Rosell – Oecologia

Response to nitrogen addition reveals metabolic and ecological strategies of soil bacteria – Md Sainur Samad – bioRxiv

Water and extremophile microbiome
Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process – Andrew R.J. Curson – Nature Microbiology
This is summed up in the short article: Marine bacteria produce an environmentally important molecule with links to climate – Phys.org

Structural dynamics of microbial communities in polycyclic aromatic hydrocarbon-contaminated tropical estuarine sediments undergoing simulated aerobic biotreatment – Chioma C. Obi – Applied Microbiology and Biotechnology

Diversity and community composition of particle-associated and free-living bacteria in mesopelagic and bathypelagic Southern Ocean water masses: Evidence of dispersal limitation in the Bransfield Strait – Mathias Milici – Limnology and Oceanography

Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type – R. Heyer – Biotechnology for Biofuels

Probiotics / prebiotics
Chapter One – Antivirulence Properties of Probiotics in Combating Microbial Pathogenesis – M. Surendran Nair – Advances in Applied Microbiology

Reclamation of Chinese herb residues using probiotics and evaluation of their beneficial effect on pathogen infection – Fanjing Meng – Journal of Infection and Public Health

Probiotic dietary supplementation in Nile tilapia as prophylaxis against streptococcosis – M.M. Yamashita – Aquaculture Nutrition

Phages and viruses
Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families – Jemma L. Geoghegan – PLoS Pathogens

Plaques formed by mutagenized viral populations have elevated co-infection frequencies – Elizabeth R. Aguilera – bioRxiv

dRep: A tool for fast and accurate genome de-replication that enables tracking of microbial genotypes and improved genome recovery from metagenomes – Matthew R Olm – bioRxiv

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores – Luis H. Orellana – Nucleic Acids Research

A real-time PCR assay for accurate quantification of the individual members of the Altered Schaedler Flora microbiota in gnotobiotic mice – Joao Carlos Gomes-Neto – Journal of Microbiological Methods

Neutral and niche dynamics in a synthetic microbial community – NJ Cira – bioRxiv

Microbes in the news
“Archaea” unites University on sesquicentennial – Tess O’Brien – The Daily Illini (student newspaper at University of Illinois)

How to quickly identify sepsis-causing bacteria – melt it down – Lisa-Ann Lee – New Atlas
The paper referenced is Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping – Stephanie I. Fraley – Scientific Reports

Chemical engineers boost bacteria’s productivity – phys.org
The paper referenced is Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit – Apoorv Gupta – Nature Biotechnology

Microbes on the market
Human Microbiome Market is Expecting Worldwide Growth by 2020 – Persistence Market Research Study

Ritter Pharmaceuticals Announces Collaboration with University of British Columbia to Explore Development of Microbiome Therapeutics in Environmental Enteropathy – Yahoo Finance

Science, publishing, and career
The Troll Taunter – Andrew McMillen – BackChannel
This is an amazing piece: “But on that Friday night, Temple-Wood had an idea. For every harassing email, death threat, or request for nude photos that she received, she resolved to create a Wikipedia biography on a notable woman scientist who was previously unknown to the free online encyclopedia.”

Do’s and don’ts for scientists who want to shape policy – Erik Stokstad – Science

Scientists should be political but not partisan – Angela de Pace – Medium

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