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.
After the blog was starting to take too much toll on my personal life, a team of wonderful volunteers took over. Each of them will try to sign up a couple of times per month.
We will try to post 5 to 6 times per week. If we cannot post on a certain day, we will include papers from the previous day(s) in the most recent digest.
Search strategy
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!
Elisabeth Bik, Science Consultant – 2019
Email: eliesbik AT gmail.com
Twitter: @MicrobiomDigest (sic, without “e”)
Facebook: https://www.facebook.com/MicrobiomeDigest
My scientific publications on PubMed
ScienceIntegrityDigest.com – my other blog
Current header photo: Wall of petridishes in the Micropia museum in Amsterdam (photo by Elisabeth Bik).
Microbiome Digest - Bik's Picks 
Hi Elisabeth. Love your blog! Given your expertise in all things microbiome, I was wondering whether you’d be interested in checking out the new Nature Partner Journal Biofilms and Microbiomes Community at https://npjbiofilmscommunity.nature.com/. I’d love to hear your thoughts on it. Do feel free to contact me via the community or at the email provided. Thanks!
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Dear Dr. Elisabeth Bik,
We hope this message finds you well.
This email is foremost an expression of our lab’s gratitude to your continued efforts of your microbiome digest blog.
I keep on advising my students to include your blog in our groups journal monitoring, with particular focus on Bioinformatics (as we are a dry lab), conveniently facilitated by your categorisation. This is extremely useful, as there is – to the best of my knowledge – no proper “sub”-community for microbiome bioinformatics, i.e., no dedicated journal nor conference on this topic.
We would also thank you for your mention of our work, recently published in PLoS Comp Biol:
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004468
It is a great honour for us!
Regarding your latest post from Nov-20, the side by side figure of the amazonian fungus plot and the string ball = a clear case of “separated at birth” 😉
https://en.wikipedia.org/wiki/Separated_at_birth
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Thank you so much for this fantastic site. It’s extremely helpful to laypeople like me who wouldn’t know how to find (and appraise) these things on our own.
I don’t know if this stuff is possible on this website, or if it’s too much work, but selecting the “pregnancy and birth” category from the drop down menu on the right doesn’t really work. https://microbiomedigest.com/category/pregnancy-and-birth/
I was trying to just see everything you’ve posted under that category. It’s not too big of a deal though since I can do it similarly by using the “month” drop down menu with ctrl+f for “pregnancy and birth”.
I checked the Infant, Pregnancy, and Breast Milk collection categories here: https://microbiomedigest.com/microbiome-papers-collection/human-microbiome-paper-collection/ but I guess those are updated manually only once in a while, and only have select choices?
It also doesn’t seem possible to look through the non-study posts like these: https://microbiomedigest.com/2016/04/06/some-followers-will-need-to-sign-up-again/ – https://microbiomedigest.com/2016/04/28/microbiome-paper-collection-pages/
Again, thank you so much. This is better than reddit 🙂
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Hi Maximillian,
I know what you are asking, and I wish I could make that work, but it is currently not possible. That would mean that I post each category separately during the day, e.g. one post about “human oral microbiome”, another about “extremophiles” etc, each one labeled with its own category. I asked a while back if people would like that, but most would like to see 1 combined digest a day. So I currently will have ~10 categories per post, and you will just get to see the posts that will be flagged with that category. If I was better at programming and WordPress, I might be able to figure out how to do this, but I don’t have the knowledge to do this otherwise.
You are also correct that the “collections” are curated sets of papers, to which I will add a paper every now and then, if I have time and think about it. So they are not perfect either.
I still hope that this helps.
Cheers, Elies
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Hi Elise,
Love the blog – it helps me stay up to date with the amazing amount of stuff happening in the microbiome world.
Best,
Will
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Dear Editor
Its wonderful initiative to connect microbes to global environment. How these wonderful small tiny creature make their vauable appearnce in Nature.
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Hi Elizabeth, do you think it would be possible to convince a university’s athletic department to setup/allow something where athletes can choose to donate stool on an individual basis? Recipients could sign wavers. I’ve had an impossible time trying to find a healthy enough donor (https://redd.it/4w650j), and my state university’s (ASU) athletic department said they won’t allow me to individually ask their athletes. Athletes are going to be some of the healthiest people, and it seems like for anything other than c.diff we’re going to have to wait ~5 years to get FMT through a doctor.
Do you know of any microbiome researchers at ASU? I don’t know how to find that. Maybe one of them would let me ask their students…
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