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MicrobiomeDigest – your daily fix of microbiome literature

Microbiomes are everywhere. Not only inside and around us, but also in the scientific literature.

Not too many years ago, only a handful of microbiology laboratories were analyzing the composition of the invisible communities that surround us. Today, it feels as if every other scientist is doing something microbiome-related. New techniques such as high-throughput sequencing and bioinformatic tools have enabled us to explore the microbial world like never before. Microbial communities have been implicated in all kinds of fields, from diseases such as Alzheimers, autism, and obesity, to agriculture, bio-conservation, and pollution research.

Microbiome-related articles are no longer just published in certain specialized microbiology journals, but are nowadays found in a wide variety of scientific publications ranging from clinical journals to publications in plant and soil biology and environmental research. In addition, there is an ever-increasing amount of news articles in the popular press covering the microbiome.

On one side, this is really nice – microbes have finally gotten the attention they deserve. Many old hypotheses and assumptions have been confirmed – or shattered. I no longer have to explain to my non-scientist friends that our bodies and surroundings are covered in microbes, and that this is completely normal and important for our health. However, on the other hand, the larger publication range and the sheer amount of microbiome-related papers make it increasingly hard to keep up with the literature in our field.

That is why I started MicrobiomeDigest, an almost daily blog listing the new scientific papers and news articles about host-associated and environmental microbiomes. It started by a sending out a daily email with some interesting papers, just to my coworkers. But when that list became longer every day, it made sense to share this with a much broader audience by posting the papers onto a blog.

Every day, I scan hundreds of papers and news articles, pick out the relevant articles, bin them into categories (I love binning!) and post them on MicrobiomeDigest so that everyone can enjoy them. I try to keep the lay-out very simple, with just the title of each paper, the first author, the journal in which it was published, and the link. No ads, pop-up windows, or required registration (although you can sign up to receive updates if you like). So, if you are interested in microbiome literature and news articles, come on over to MicrobiomeDigest to take a look. The more readers, the better! You can also follow me on Twitter, @MicrobiomDigest (without the “e”; unfortunately Twitter handles can only be up to 15 characters long).

From now on, I will try to regular write here about some new papers that were included in the most recent MicrobiomeDigest posts. Here we go:

The Best of MicrobiomeDigest

Characterisation of the Physical Composition and Microbial Community Structure of Biofilms within a Model Full-Scale Drinking Water Distribution System — Katherine E. Fish — PLOS ONE

The quality of drinking water can be hindered by microbial biofilm formation within pipes and other parts of the drinking water distribution systems (DWDS). Here, fluorescent confocal laser scanning microscopy shows that the extracellular polymeric substances (EPS) matrix produced by these microbes is almost 5 times as thick as the microbial layer itself. In addition, the authors used T-RFLP and ARISA to characterize the composition of these biofilm communities.

Our interface with the built environment: immunity and the indoor microbiota — Simon Lax — Trends in Immunology

This short review describes the human colonization with microbes after birth, and how this process might be influenced by microbes in the environment.

Presence of oxygen and aerobic communities from sea floor to basement in deep-sea sediments — Steven D’Hondt — Nature Geoscience

Although oxygen does not appear to penetrate very deeply into deep-sea sediments, this study found evidence for aerobic respiration and live microbial cells to the incredible depth of 75 meters (almost 250 feet!) below the sea floor.


That’s it for this time!

Elisabeth Bik, Stanford University


Elisabeth Bik

After receiving my PhD at Utrecht University in The Netherlands, I worked at the Dutch National Institute for Health and the St. Antonius Hospital in Nieuwegein. In 2001, I joined the Department of Microbiology and Immunology at Stanford, where I have worked on the characterization of the microbiome of human oral, gastric, and intestinal samples, as well as samples from marine mammals. Since November 2016, I am the new Science Editor at uBiome, a microbiome genomics company enabling citizen science. But you might also find me working on the detection of science misconduct, at my blog Microbiome Digest , an almost daily compilation of scientific papers in the rapidly growing microbiome field, on Twitter at @MicrobiomDigest.

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