The best microbiome papers of 2017

Happy New Year again!

Last week, I asked you all to vote for the best microbiome papers of 2017. And just like the previous year, we have a very clear winner. A paper that had some obvious help from the author’s Facebook friends, who all wrote in to vote 🙂

Full disclosure: I was the handling editor of this paper.

The winner is…. (drumroll)….

Second place was won by:

And in shared third/fourth place:

Other nominees were:

I wish you all the best for the new year! Hopefully, 2018 will bring even more great microbiome science papers.

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Vote for the best microbiome papers of 2017

It’s that time again, where we look back on what happened in the past year. Like last year, I thought it would be nice to choose the best microbiome papers of the year.  Here is a form where you can fill out your top 3 (#1 being the best, and – optional – your second and third choice). I will post the results on January 1, so you can vote until December 31, midnight, Pacific Time. Below the poll are a ton of ideas for papers that I thought were news-worthy. I probably forgot a lot, so feel free to add your own choice. Happy voting and all the best wishes for the New Year.

Update December 28: I have added Kiran Gurung’s favorite papers, so there are even more to choose from!

January 2017

February 2017

March 2017 

April 2017

May 2017

June 2017

July 2017

August 2017

September 2017

October 2017

November 2017

December 2017

The Microbiome Digest Team

Hi all, it’s Elisabeth Bik, doing a rare blog post here, after having run this blog for 3 years in a row. I am having a blast working at uBiome, but as I wrote in January, with my long commute and continuing science integrity work I can not spend much time here at Bik’s Picks. Fortunately, the Microbiome Digest has been able to continue to run through the fantastic work of a group of 20 people from all over the world. In the last couple of months, some new people joined, and some other people left, so it was time for a update on the team members and their background and interest. I am so grateful that this team could take over from me, and that they are running the blog so I can currently focus on other things.

So here is the new Microbiome Digest Team page where you can read more about the fantastic group of scientists who are currently writing the Microbiome Digest posts.

Thank you all, team, for providing this continuous stream of new microbiome papers and articles.

 

 

Microbiome Medicine Summit 2017

Last year I wrote about the Microbiome Medicine Summit, which was not really a summit/conference but rather a collection of interviews with “nutrition specialists” and “microbiome experts” – some real, others not so much – conducted by Raphael Kellman, who has been trained as an MD but is very eager to believe and report on non-scientific statements involving the human microbiome. RK has been award the “Overselling the Microbiome” Award by Jonathan Eisen.

Most of the talks at last year’s Microbiome Medicine Summit provided very little science, a lot about “nurturing your microbes” , some crazy stuff, and lots of promotions to buy overpriced probiotic drinks, minerals, and self-help books. Even more telling, there were very few interviews with real microbiome experts or scientists.

I wrote about some of these talks in my blog posts from last year: Microbiome Medicine Summit with Deepak Chopra et al, part 2 with Donna Gates, part 3 with Ann Louise Gittleman, part 4 with Joseph Mercola, and part 5 with Larry Dossey.

This year, the Microbiome Medicine Summit returned in its second edition, with lots of new interviews, but basically the same strange mix of a tiny bit of science and lots of quackery, snake oil, alternative facts, and of course links to dubious websites selling products claiming to cure diseases. As in last year’s collection, most of these interviews were with nutritionists and holistic doctors. And again, most interviews were conducted by Raphael Kellman, who sometimes talks more than the person he is interviewing, and never, ever, seems to ask a critical question.  The schedule can be found here.

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I took on the (at times painful) task of sitting through several of these talks so that I could share with you what they were about. Some of these talks were not too bad, with lots of “feed your microbes by eating healthy” types of messages, but some were outright weird or even dangerous. I reported about these talks on Twitter and compiled the tweets and some responses on Storify.

Here are my reports on Storify.

John Gray – Healthy Microbiome and Personal Relationships

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Marco Ruggiero – The Study of Brain Microbiota and HealthScreen Shot 2017-05-20 at 4.34.09 PM.png



Donna Gates – Cleansing the Microbiome

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Microbiome stock photo fails

Sometimes I come across a stock photo that is unintentionally funny. Here is another one.

An artist’s rendition of how microbes grow in the intestinal tract. Here you can see bacteria circling around microvilli. Or are they shiny pills in straight lines circling around sausages, or decaying fingers in plastic gloves?

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Same villi but different bacteria. It’s a Fecal Microbiota Transplant!

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And this one has no bacteria at all. I guess it represents the Germ Free Mouse.

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Wageningen Microbiology Centennial – a very male celebration

Wageningen University, in my home country of the Netherlands, will be holding a 2.5-day symposium in October 2017 to celebrate 100 years of microbiology research at this institute, called Microbiology Centennial. At first glance, the program looked great; many talks about microbial ecology, microbial physiology and bacterial genetics.

But alas, the list of keynote speakers is very low-diversity. All 10 keynote speakers are men.

  1. 029ded60-4bf6-43a0-8ecf-882f52167d67_microbiology_849fee03_183x196Jan Roelof van der Meer
  2. Mark van Loosdrecht
  3. Hauke Harms
  4. Bernhard Schink
  5. Thijs J. G. Ettema
  6. Mike Jetten
  7. Hauke Smidt
  8. Alfons J.M. Stams
  9. John van der Oost
  10. Willem M. de Vos

In addition, there are opening remarks by Alex Zehnder.

That is 11 men. No women.

The program states:

“The keynote lectures include eminent scientists (see below) who have been interacting with the Laboratory of Microbiology throughout the years. The program also features the present research group leaders of the Laboratory of Microbiology as well as the present and past chair who all have contributed to the success of the last decades. “

I guess no women have contributed to the success of the Laboratory of Microbiology in the last decades. Thanks ladies for all your hard work. Now move over, please, so that the guys can present your fantastic research!

Sadly, this lack of women in academic positions or keynote lecturers is not unique for my home country. The Netherlands, a country that likes to think its very modern, is lacking in the participation of women in science. Less than 20% of professors at Dutch Universities are women. According to this article at Times Higher Education:

“Wageningen University, one of the country’s top-ranked universities in 2016-17, has significantly improved its gender diversity in recent years, although just 12 per cent of its professors were women in 2016, the report says.”

A recent report entitled “Monitor Women Professors 2016” published by the Dutch Network of Women Professors, stated that women account for 43% of PhD students and 39% of University Lecturers, but only 18% of professors. The report states:

“not only do female academics earn less, they are also systematically awarded lower job levels”….“There is a ruthlessly thick glass ceiling between job levels,” it adds, saying the barrier stopping women progressing from a grade 1 professor to a grade 2 professor is “sky-high”.

 

Storify of the Human Microbiome Congress

(Crossposting from the NPJ Biofilms and Microbiome Community website)

This week I visited the Human Microbiome Congress in San Diego, where Kisaco Research brought together a splendid group of academic and industry researchers, who talked about their latest research. I really enjoyed listening to all these great speakers, and wanted to share this great event with the rest of the world, so I live-tweeted all the talks from my Twitter account @MicrobiomDigest. In case you missed it, here is a Storify with all my ~400 tweets. So grab a beer (or a kombucha) and some popcorn, and enjoy.

Storify of the Human Microbiome Congress in San Diego

We also held a 500WomenScientists meeting organized by Jessica Metcalf (who tweeted the first photo below).

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And uBiome was represented at the poster session too! This was the first time I ordered a fabric poster, and it was great. Arrived folded up at my house (sort of like a t-shirt), and fitted easily in my luggage. I could have done a slightly better job ironing it (which is how you get rid of the wrinkles) but it was so much easier than traveling with a glossy print in a big tube. I ordered my poster at MakeSigns; poster + shipping (3 days after ordering) was $120. Recommended!

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