May 4, 2016

Note: If you enjoy this blog, I would very much appreciate a comment here below. Without your support, I might not be able to continue MicrobiomeDigest in its current form and frequency. So please, show your love by leaving a sign of support at the end of this blog. Thank you from the bottom of my heart! – Elies

Culturing the unculturables, a review on social bee microbiotas, the needle mycobiome, and an improved phage search tool.

Jobs and events

Faculty Position – Phage Biology and Microbiome Research, McMaster University, Ontario – Science Careers

Postdoctoral Fellow in Mucosal Immunology and Host-Microbiome Interactions
Jill Roberts Institute for Research in Inflammatory Bowel Disease at Weill Cornell Medicine – New York City, United States of America

General microbiome

Review: Microbial contributions to chronic inflammation and metabolic disease – Shanahan, Fergus – Current Opinion in Clinical Nutrition and Metabolic Care

Review: The microbial-mammalian metabolic axis: a critical symbiotic relationship – Chilloux, Julien – Current Opinion in Clinical Nutrition and Metabolic Care

Human gut microbiome

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation – Hilary P. Browne – Nature

(Also oral samples) The role of the gastrointestinal microbiome in infectious complications during induction chemotherapy for acute myeloid leukemia – Jessica R. Galloway-Peña – Cancer

Ecological Effect of Solithromycin on the Normal Human Oropharyngeal and Intestinal Microbiota – Mamun-Ur Rashid – Antimicrobial Agents and Chemotherapy

Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production – David Endesfelder – Microbiome

Clostridium difficile Infection in Patients with Inflammatory Bowel Disease – Nancy Fu – Current Infectious Disease Reports

Review: Interplay between diet, gut microbiota, epigenetic events, and colorectal cancer – Scott J. Bultman – Molecular Nutrition & Food Research

Animal microbiome

Cecal microbiota of Tibetan Chickens from five geographic regions were determined by 16S rRNA sequencing – Xueyan Zhou – Microbiology Open

Variability of Bacterial Communities in the Moth Heliothis virescens Indicates Transient Association with the Host – Heike Staudacher – PLOS ONE

Review: Gut microbial communities of social bees – Waldan K. Kwong and Nancy A. Moran – Nature Reviews Microbiology

Plant, root, and soil microbiome

Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing – L. C. Kelly – Microbial Ecology

Habitat conditions and phenological tree traits overrule the influence of tree genotype in the needle mycobiome–Picea glauca system at an arctic treeline ecotone – Pascal Eusemann – New Phytologist

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes
Philip E. Long – Trends in Microbiology

Extremophile microbiome

Twenty-Three Species of Hypobarophilic Bacteria Recovered from Diverse Ecosystems Exhibit Growth under Simulated Martian Conditions at 0.7 kPa – Andrew C. Schuerger – Astrobiology


Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains – Yemin Lan – Microbiome

Phages and viruses

Inferring phage-bacteria infection networks from time series data – Luis Jover – bioRxiv preprint

PHASTER: a better, faster version of the PHAST phage search tool – David Arndt – Nucleic Acids Research


Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples – Minsoung Rhee – PLOS ONE

Microbial Ecology

A conceptual framework for invasion in microbial communities – Marta Kinnunen – The ISME Journal

Microbes in the news

Most Gut Microbes Can Be Cultured. Contrary to the popular thought that many species are “unculturable,” the majority of bacteria known to populate the human gut can be grown in the lab, scientists show – Jyoti Madhusoodanan – The Scientist

Capturing the vast diversity of bacteria in our bodies – Megan Thielking – STAT News

A bitter pill. Josiah Zayner’s gut was making his life hell — so he embarked on an extreme DIY fecal transplant – Arielle Duhaime-Ross – The Verge

Article with video: Your mouth is full of bacteria blooming. And it’s beautiful – Hyacinth Empinado – STAT news

Explore this interactive map of the Gowanus Canal’s slightly scary microbiology – Jason Sayer – Architects Newspaper

The Friendly Viruses, and how they can help with the looming antimicrobial resistance crisis – Peter Speck and Anthony Smithyman – OUP blog

How the Gut Microbiome May be Key in Post-Surgery Organ Failure after Heart Surgery in Children – University of Arizona

Bugs as drugs: Harnessing novel gut bacteria for human health – Medical Xpress

Bacteria carrying bug threatens wine industry – John Bartell – ABC

Autonomous Super Mario-Themed Sewer Robots Live-Stream Neighborhood Microbiome Data – The answer to our health is in our excrement – Nickolaus Hines – Inverse

Bay Area Scientists Join Forces To Help Contain Zika Virus – CBS San Francisco

Breast milk hormones found to impact bacterial development in infants’ guts
Intestinal microbiome of children born to obese mothers significantly different from those born to mothers of healthy weight, CU Anschutz researchers find – EurekAlert

Science, publishing, and career

Dealing with retractions – Paul van der Vet – BioMed Central blog

Propagation of errors in citation networks: a study involving the entire citation network of a widely cited paper published in, and later retracted from, the journal Nature – Paul E. van der Vet and Harm Nijveen – Research Integrity and Peer Review


39 thoughts on “May 4, 2016

  1. Read you every day, please keep on the good work, love your blog
    Charles Morin pediatrician province of Quebec, Canada.


  2. Hi Elizabeth,
    I love this blog. I follow all of the updates and it’s incredibly useful for staying up to date in the field.


  3. Hi Elies, I love reading through your blog! In addition to helping me keep up to date on research relevant to my own, I find that it also exposes me to interesting and important research or research-related topics that I would probably not otherwise be exposed to. I hope you keep it going!


  4. Dear Elies,
    I greatly appeciate your efforts in making these concise and well structured overviews. I check them on regular basis and it helps me to stay informed. Great job!
    Greetings from Amsterdam,


  5. Please, going on with this wonderful compilation of microbiome advances.
    Without your help, I could not be updated with all new publications

    Thank you so much for your amazing work and effort!!


  6. Oh man that would be terrible if this blog was discontinued. This blog is such a gem for laypeople like me who couldn’t find and evaluate this stuff elsewhere. I check it everyday! I understand it probably takes a ton of time to sift through the hundreds of articles & studies per day though. Maybe you could bring in other people willing to help?


  7. This blog is amazing! I start my day every day reading the new blog post. Thank you for all the work you put into this blog.
    Greetings from Germany 🙂


  8. This blog is really a valuable resource! I appreciate your effort to keep it up. Every day I check my email just because of your blog :). Please keep it coming!


  9. Elies,
    Your blog is an invaluable tool that I use every day to keep up to date with literature on all things microbiome! I particularly love the Pregnancy & Birth, Bioinformatics, Microbial Ecology and News sub-headings. Please keep up the awesome work!!

    PhD student, UK


  10. Your blog and your tweets help me a lot in my first steps in micro biome research. Not only to find but also to evaluate new research. A thank you is long overdue!


  11. As an ignorant layperson I am greatly indebted to you for the knowledge and insights that you so freely share. As I am now an old man I often think if I had my time again this is what I would be doing/studying. Fascinating stuff and a daily delight.


  12. This blog is the best source of new microbiome papers I have found anywhere, including journal feeds, and dedicated microbiome news sites, a view I’ve heard from multiple different researchers. It is an invaluable resource for anyone in the microbiome field.


  13. Please keep your blog coming! I read it daily and regularly recommend it to others. It’s an incredible resource for the microbiome community!


  14. Please keep the blog alive for the sake of our microbiome-dependent lives. It is a tremendous resource for researchers that is unmatched. I wish there was something like this for the other disciplines my research touches. I second the idea of additional support to the make this process more efficient for yourself. Thanks for all your efforts!


  15. Today is the first time I’ve seen this blog. It is truly useful and s-o-o-o-o interesting. Thanks for taking the time and effort to compile it. BTW, I was told about it by our VP of Business Development in my company — you’ve really got something when you can get the commercial guys interested in a scientific blog!

    Liked by 1 person

  16. I guess I’m sort of addicted to your postings as I’m wondering in some late afternoon when there is no posting. I can’t imagine how you manage to do this, but it is very useful and helps me tremendous to keep up with all the microbiome studies. Thanks a lot!


  17. Lots of love from a postdoc fresh to this field. My boss is constantly astonished how in tune I am with the literature, given that my background is in evolutionary ecology and philosophy of science. I’ve mentioned to my team many times that we should provide similar services. Thank you, thank you, thank you.


  18. Before I saw this post I was just thinking of reaching out to you to thank you for this work! Your dedication to this blog is amazing, through thick and thin in your life. It’s a very valuable service to the field and often I think it helps bring attention to researchers whose work is good but who wouldn’t otherwise get much attention. I really hope you are able to continue the blog.


  19. Hi Elizabeth! I love these digests, you really help me stay on top of the literature. Please funders, keep this lady going and give her more!


  20. These posts have helped me tremendously to get background in the field. Absolutely invaluable. I hope they keep coming! Wonderful way to access and keep abreast of the tsunami of information emerging from the field. Plus humor! Total bonus.

    Liked by 1 person

  21. I read the blog every day and it has been super useful for keeping on top of the microbiome literature across fields. Keep the posts coming and thank you!


  22. Elis. without your blog I couldn’t keep up with microbiome literature. Thanks for the amazing job and updates.


  23. You have greatly increased my ability to stay informed of all the microbiome research and have recommended the site to my colleagues. It is very valuable work!


  24. I agree with others who have said this blog is an invaluable way to keep up with the tremendous volume of microbiome literature. Thanks for all you work to put it together, and please keep it coming!


    • Great, thanks! There might be an ad every now and then, but so far the amount has been very reasonable. I won’t get any money from the ads, but I’ll get free hosting. Otherwise I’ll need to pay $$ for hosting, out of my own pocket. Thanks!


  25. What you do is amazing! Thank you on behalf of everyone who follows your Twitter feed – it’s the best source of microbiome information I’m aware of.


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