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.

 

 

Advertisements

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.

Screen Shot 2017-05-20 at 2.21.56 PM.png

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

Screen Shot 2017-05-20 at 3.58.55 PM.png


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



Donna Gates – Cleansing the Microbiome

Screen Shot 2017-05-20 at 4.51.50 PM.png

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?

Screen Shot 2017-03-23 at 7.09.43 PM.png

Screen Shot 2017-03-23 at 9.28.54 PM.png

Screen Shot 2017-03-23 at 9.30.48 PM.pngScreen Shot 2017-03-23 at 9.29.47 PM

Screen Shot 2017-03-23 at 7.33.40 PM.png

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

stock-photo-human-intestine-with-intestinal-bacteria-d-illustration-442556506

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

64546996-Villi-of-small-intestine-3D-illustration-Intestinal-environment-close-up-view-Stock-Illustration.jpg

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).

500womenscientistsSanDiego.jpg

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!

Screen Shot 2017-01-26 at 10.37.47 PM.png

The new Microbiome Digest team

Microbiome Digest proudly presents: the New Microbiome Digest Team! From now on, Microbiome Digest will be taken over by a team of 21 enthusiastic scientist from all over the world.

I have tried to make this change as smoothly as possible, but I still anticipate some unanticipated SNAFU’s in the beginning. As we all need to adapt to this new style of publishing, there will probably be some irregularity in posting, some duplicate entries, or formatting issues. Or maybe you won’t notice anything at all!

Let’s give a warm welcome to the new Microbiome Digest team. Here is a short introduction to the new members (I am very short on time) – I will make a decent page with a better description in the near future.

Welcome on board!

Screen Shot 2017-01-15 at 5.03.00 PM.png

January 15, 2017

Microbes in Idiopathic Pulmonary Fibrosis, review on the female urinary microbiota, koalas with “wet bottom”, virus metagenomics of the Namib desert, biosignatures in fossils.

Jobs

Microbiome Research Associate Job – Merck Research Laboratories – Cambridge, MA – Science Careers

Human urinary tract microbiome

* Review: The female urinary microbiota, urinary health and common urinary disorders – Linda Brubaker – Annals of Translational Medicine

Human respiratory microbiome

Host-Microbial Interactions in Idiopathic Pulmonary Fibrosis – Philip L Molyneaux – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

The human gut microbiome as source of innovation for health: which physiological and therapeutic outcomes could we expect?: Human gut mibrobiome [SIC] as source of innovation for health – Joël Doré – Thérapie

In FrenchMicrobiote intestinal : qu’en attendre au plan physiologique et thérapeutique ? Le microbiote intestinal comme source d’innovation pour la santé – Joël Doré – Thérapie

Review: Seafood allergen-induced hypersensitivity at the microbiota-mucosal site: implications for prospective probiotic use in allergic response regulation – Linglin Fu – Critical Reviews in Food Science and Nutrition

Review: Impact Of Human Aging And Modern Lifestyle On Microbiota – Maria Gabriela Valle Gottlieb – Critical Reviews in Food Science and Nutrition

Review: Effects of environmental pollutants on gut microbiota – Yuanxiang Jin – Environmental Pollution

Animal experiments

Replacing corn with sorghum in the diet alters intestinal microbiota without altering chicken performance – N. S. Fagundes – Journal of Animal Physiology and Animal Nutrition

Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome – Francesco Rubino – The ISME Journal

Wolbachia Affects Reproduction and Population Dynamics of the Coffee Berry Borer (Hypothenemus hampei): Implications for Biological Control – Yobana A. Mariño – MDPI Insects

Neoagarotetraose protects mice against intense exercise induced fatigue damage by modulating gut microbial composition and function – Na Zhang – Molecular Nutrition & Food Research

Housing Systems Influence Gut Microbiota Composition of Sows but Not of Their Piglets – Tereza Kubasova – PLOS ONE

Effect of Different Lignocellulosic Diets on Bacterial Microbiota and Hydrolytic Enzyme Activities in the Gut of the Cotton Boll Weevil (Anthonomus grandis) – Emiliano Ben Guerrero – Frontiers in Microbiology

Animal microbiome

Variation in the microbiome of the urogenital tract of koalas (Phascolarctos cinereus) with and without “wet bottom” – Alistair Raymond Legione – bioRxiv

Plant, root, and soil microbiome

* Fossils: Carbonaceous biosignatures of diverse chemotrophic microbial communities from chert nodules of the Ediacaran Doushantuo Formation – Yuangao Qu – Precambrian Research

Plant, soil and microbial controls on grassland diversity restoration: A long-term, multi-site mesocosm experiment – Ellen L. Fry – Journal of Applied Ecology

Pyrosequencing reveals bacterial communities and enzyme activities differences after application of novel chiral insecticide Paichongding in aerobic soils – Jie Chen – Applied Soil Ecology

Cedar and bamboo plantations alter structure and diversity of the soil bacterial community from a hardwood forest in subtropical mountain – Yu-Te Lin – Applied Soil Ecology

The differentiation of soil bacterial communities along a precipitation and temperature gradient in the eastern Inner Mongolia steppe – Minjie Yao – CATENA

Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands – Julia Kyaschenko – The ISME Journal

Association between Grape Yeast Communities and the Vineyard Ecosystems – João Drumonde-Neves – PLOS ONE

Water microbiome

High growth potential and activity of 0.2 µm filterable bacteria habitually present in coastal seawater – Yumiko Obayashi – Biogeosciences Discuss

Chronic exposure effects of silver nanoparticles on stream microbial decomposer communities and ecosystem functions – Ahmed Tlili – Environmental Science & Technology

Waste and pollution microbiology

Global profiling of metabolite and lipid soluble microbial products in anaerobic wastewater reactor supernatant using UPLC/MSe – Phornpimon Tipthara – Journal of Proteome Research

Food microbiology

Rapid concentration detection and differentiation of bacteria in skimmed milk using surface enhanced Raman scattering mapping on 4-mercaptophenylboronic acid functionalized silver dendrites – Panxue Wang – Analytical and Bioanalytical Chemistry

Metagenomics and bioinformatics / Viruses and phages

Robust inference of genetic exchange communities from microbial genomes using TF-IDF – Yingnan Cong – Frontiers in Microbiology

Virome assembly and annotation: a surprise in the Namib Desert – Uljana Hesse – Frontiers in Microbiology

Metaviromes of Extracellular Soil Viruses along a Namib Desert Aridity Gradient – Olivier Zablocki – Genome Announcements

Metagenome Sequencing of Prokaryotic Microbiota Collected from Rivers in the Upper Amazon Basin – Célio Dias Santos-Júnior – Genome Announcements

Restoring the Duality between Principal Components of a Distance Matrix and Linear Combinations of Predictors, with Application to Studies of the Microbiome – Glen A. Satten – PLOS ONE

New approach for studying mobile genes using metagenomic analysis – Kazuyuki Ishihara – Oral Diseases

Archaea

New insights into marine group III Euryarchaeota, from dark to light – Jose M Haro-Moreno – The ISME Journal

Techniques

MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling – Kristin Burnum-Johnson – Analyst

An explanation of the Nagoya Protocol and Access and Benefit Sharing, and its implication for microbiology – David Smith – Microbiology

Microbes in the news

You’re probably showering way too often – Rafi Letzter – Business Insider

Viruses May Be Responsible For Life As We Know It – Ryan F. Mandelbaum – Gizmodo

Boost your intake of resistant starch to help your gut thrive – Leslie Beck – The Globe and Mail

We now know bacteria can communicate electrically, and we should be worried
They’re organised – David Nield – Science Alert

Proceed with caution: Autism Causes Update: The Gut-Brain Connection And How A Common Probiotic May Ease Symptoms – Lizette Borreli – Medical Daily

Study provides fundamental insights into functioning of microbiota and human-gut flora symbiosis – News Medical

Microbes on the market

Bristol-Myers Squibb and Enterome Announce Immuno-Oncology Collaboration Focused on Microbiome-Derived Biomarkers, Drug Targets and Bioactive Molecules – SAT Press Releases

Bik’s non-microbiology picks

The Physics of Everyday Life. Why popcorn pops and ducks don’t freeze when swimming in icy water. John Gribbin reviews “Storm in a Teacup” by Helen Czerski – Wall Street Journal