Good morning/afternoon all microbiome lovers!
Coming back from 4th Thunen Sumposium on Soil Metagenomics (11-13.12, Germany), the first section of today’s digest will highlight some work emphasized during the conference. Pay special attention to Amy Willis work (UoW) dealing with amplification bias in 16S analyses, among else. You are more than welcome to check the conference and the bioinformatic workshops schedule, as you’ll find interesting, inspiring and useful studies and tools that are relevant even if you’re not working on soil-associated habitats.
Have a great day!
Soil Metagenomics insights
Rigorous Statistical Methods for Rigorous Microbiome Science, Amy Willis, mSystems. I highly recommended to be familiar with the Willis lab works and tools, for all of us working with amplicon-sequencing and metagenomics. Amy was kind enough to upload her conference materials to github, using this link.
Additionally, They just started a bio-statistics blog, so check this as well.
Consistent and correctable bias in metagenomic sequencing experiments, Michael R. McLaren, bioRxiv
These two papers are from Benjamin Callahan group (NCSW). Even though he wasn’t at the conference, his work (et al.) were mentioned several times by other speakers, so I decided to emphasize these two papers.
The MG-RAST API explorer: an on-ramp for RESTful query composition, Tobias Paczian, BMC Bioinformatics. Folker Meyer, one of the developers of MG-RAST and its head, was actually at the conference with a great talk about both MG-RAST and the importance of pipelines and common workflow language in computational biology. Check this link and the MG-RAST API explorer, making it so much simpler to search, filter and efficiently use MG-RAST.
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes, Felipe B Correa, bioRxiv. An amazing tool for searching and filtering soil-associated metagenomes in different databases, plus simple codes for downloading. Take a look at more papers from the de-Rocha group.
**Molecular messages in human microbiota, Matthew T. Henke and Jon Clardy, Science
Resident microbes of lactation rooms and daycares, Diana H. Taft, PeerJ
Female genital tract microbiota affecting the risk of preterm birth: What do we know so far? A Review, O. Tsonis, European J OBG & Reproductive Biology
Differences in Fecal Microbiomes and Metabolomes of People With vs Without Irritable Bowel Syndrome and Bile Acid Malabsorption, Ian B. Jeffery, Gastroenterology
Soil and Plant microbiome
Comparison of Microbial Community of Rhizosphere and Endosphere in Kiwifruit, Min-Jung Kim, Plant Patho J.
Soil exposed to silver nanoparticles reveals significant changes in community structure and altered microbial transcriptional profiles, Matthew J. Meier, Env. Pollution
Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax), Danila Rosado, Scientific Reports