This blog is a (almost) daily digest with scientific papers about microbiome research and other interesting microbiology papers. The “Bik’s non-microbiology Picks” at the end can be about any topic!
In each post, I will cover the microbiome papers that came out in the previous days. I will try to sort them in the same order, covering these broad groups:
1. Human microbiome: scientific papers on microbiome studies on human samples (oral, skin, gut, and other anatomical sites) as well as studies using animal or bioreactor models of human microbiome and disease.
2. Non-human microbiome: scientific papers on microbiomes of animals, plants, soil, sediments, water, acid mine drainage, and the built environment.
3. General microbiology and science: general metagenomics and metabolomics papers, techniques (primers, DNA extraction, sequencing), bioinformatics tools, antibiotic resistance, general microbiology, microbes in the news, science and publishing, women in science, and Bik’s Picks.
Please note that inclusion of a paper in this blog does not necessarily mean that I endorse the paper or vouch for its quality. There would not be enough time to read all of papers and give each a critical evaluation. The purpose of this blog is to be inclusive, not exclusive, so listing here simply means that the paper’s subject is about a microbial community, not that it is a good paper.
How it started
It all started with a daily email to members of the lab I work in, with papers that came out about the topics that interest us, but as this list grew longer and longer every day, I thought I’d share with others as well. And so I created this blog in May 2014 to let others be able to access this information too. The first post online was on May 21, 2014.
I will try to post 5 to 6 times per week. If I cannot post on a certain day, I will include papers from the previous day(s) in the most recent digest, so even if I skip posting on a particular day, I will not skip any microbiome papers.
Microbiome Digest is enabled by a bunch of Google alerts, Google Scholar alerts, electronic Table of Contents (eTOCs) and other search alerts. I have listed most of them here. But please let me know if you feel I am missing a particular journal or topic. Feel free to contact me about other topics / key words that I should include, or ones you feel you see too much of.
I owe a big thanks to Tomer Altman for helpful suggestions and positive feedback!
MicroBE.net, blog with papers on the microbiology of the Built Environment, for which I write regular guest posts
Current header photo: Wall of petridishes in the Micropia museum in Amsterdam (photo by Elisabeth Bik).