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Monday, April 20, 2015

A Microbiome Three-Conference Summary

During the month of March, I've been pleased to cover three great microbiome-related conferences for the Gut Microbiota for Health website. I heard about interesting things happening in the field -- research both deep and broad -- and talked to scientists and clinicians from around the world.

Here are the conferences I attended:

Keystone Symposium - Gut Microbiota Modulation of Host Physiology: The Search for Mechanism

Gut Microbiota for Health World Summit 2015

Experimental Biology 2015

It's hard to summarize the mass of information from these conferences, but here are some of the important messages I heard about gut microbiota:

"Lactobacillus spp Sauerkraut 1" by A doubt - Own work.
Licensed under CC BY-SA 3.0 via Wikimedia Commons -
https://commons.wikimedia.org/wiki/File:Lactobacillus_spp_
Sauerkraut_1.jpg#/media/File:Lactobacillus_spp_Sauerkraut_1.jpg


The gut microbiota are constantly changing; in a single person, composition varies from day to day and over the course of the day.

Diet has a huge impact on (a subset of) the microbiota, with effects on long-term health; the impact of fibre is among the hottest areas of investigation.

Bacterial viruses (bacteriophages) are an important part of the gut community, and may have a role in diseases like Crohn's and AIDS.

Bacterial species are often interesting to note, but it's the metabolites they produce that may be doing the key work in the body.

The immune system is extremely sensitive, responding to slight shifts in the gut community and maybe even suffering long-term 'scarring' from environmental factors.

Clinical trials with therapies (e.g. fecal microbiota transplantation or probiotics) are useful, but it's even more important to investigate mechanisms that are making them work, so we can match therapies to patients with perfect precision.

So far, the established, concrete clinical applications of microbiota research are few (for example, fecal microbiota transplantation for C. difficile), but the intangible clinical applications are many!





I also talk about these three conferences in this podcast interview with the great guys at the American Microbiome Institute.

You can find Storify summaries of the live tweets from Keystone and Experimental Biology here:

Keystone Day 1
Keystone Day 2
Keystone Day 3
Keystone Day 4

Experimental Biology Day 1
Experimental Biology Day 2
Experimental Biology Day 3
Experimental Biology Day 4

Get in touch if you want to know more details about the science!

Monday, March 30, 2015

"Speaking of Microbiota" - Important ideas in gut microbiota research - Emeran Mayer of UCLA

Emeran Mayer (left) at the Experimental Biology 2015 session, "Gut Microbes and the Brain"

When discussing research about components of the diet that affect the gut microbiota and possibly affect disease risk:

"...we have to look at how we eat and what we eat, and take care of it. Not that people eat what they want to eat, and then put drugs on top of it."

- Emeran Mayer, UCLA

Mayer said this in an interview at the 2014 Harvard Probiotics Symposium. Read more of this interview here.

Later this year, Mayer will release a book on the mind-gut connection.


Sunday, March 29, 2015

"Speaking of Microbiota" - Important ideas in gut microbiota research - Mark Smith of OpenBiome


Currently, science shows that fecal microbiota transplantation (FMT) is clearly effective only in the case of recurrent C. difficile infection. OpenBiome, which supplies donor stool to hospitals all over the United States, is positioned to expand FMT access to other types of patients, but only if the science justifies it. By email, OpenBiome co-founder Mark Smith told me:

"There is an enthusiasm for projecting the success of [fecal microbiota transplation] in [C. difficile infection] onto other indications, but the mechanism is likely quite different and the efficacy is very unlikely to be as high."

- Mark Smith, co-founder of OpenBiome stool bank


See the original article here.



Sunday, November 16, 2014

Microbiomania, microbophobia, and getting excited about the microbiome

Jonathan Eisen at UC Davis famously polices news and academic articles that oversell the microbiome on his blog, The Tree of Life. He provides a valuable service to the field of microbiome research, since it benefits neither the researchers nor the public when writers convey wishful or wrong messages.

Recently on his blog, Eisen "rediscovered" two new words that I think capture some important concepts:

1) Microbiomania:
The overselling of the impact (beneficial or detrimental or otherwise) of microbiomes without the evidence to support such impact.

and

2) Microbophobia:
The overwhelming and unreasonable fear of microbes (of any kinds).

One example of microbiomania from Eisen's blog is this:

Gut bacteria health may be the key to living longer, disease-free lives, U.S. fruit fly study reveals

...because extending the life span of a fruit fly in a study is a loooooong way off from making humans live "longer, disease-free lives".

One of my favourite examples of microbophobia is the "healthing" campaign of a major cleaning products company (critically analyzed in this blog post) that equates zealous cleaning with being healthy.

The terms zero in on two common mistakes in writing about the microbiome. In both cases, the problem is not sticking to the facts. Microbiomania is going beyond the facts and building up microbiome research to be something it is not, while microbophobia is letting existing fears and preconceptions about bacteria act as a filter through which we see the facts. Neither makes for good science writing.

I want to make sure, however, that no one equates microbiomania with simply getting excited about the microbiome. They are not the same thing.

Say someone reports on a study that found jet-lagged mice have a different gut microbiota and messed-up metabolism compared with normal mice. In microbiomania, there's conjecture: saying that jet lag is the cause of obesity, or that probiotics can cure jet lag. Not okay.

But it is completely okay to just get excited about the jet-lagged mouse study because it's interesting and awesome. The field will advance best if the researchers see that people are enthusiastic about their research.

By Douglas P. Perkins (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons



For more, see this sciencewriters.ca post:

Hail the Gut: Why it’s okay to get excited about the microbiome


Tuesday, July 1, 2014

What's on the menu at your local long-term care facility?

I recently came across the work of Paul O'Toole, of University College Cork (in Ireland). He works with the Alimentary Pharmabiotic Centre, which focuses on developing "bench-to-bedside solutions focusing on gut health". O'Toole was interviewed about one of his recent presentations here.

Some of O'Toole's recent work has to do with the relationship between diet and gut microbiota in elderly people. I recently wrote an article about nutrition for seniors that piqued interest here in Canada, so O'Toole's major findings are really interesting to me:

- The setting where an elderly person lives appears to determine his/her gut microbiota: based on microbial species in fecal samples, scientists could predict which seniors lived in the community, a day-hospital, a rehab setting, or a long-term care facility

- The difference in gut microbiota in each setting could be because of different diets

- In general, seniors living in the community has diverse gut microbiota, and seniors in long-term care had less diverse microbiota

- Low-diversity gut microbiota correlated with poor health: sarcopenia (muscle loss), inflammation, and even lower cognitive function
Source: Wikimedia Commons (Siobhan from Upstate New York)

Like any human research, it's not easy to tease apart cause and effect here. This issue of causality has been controversial on at least one other paper that O'Toole co-authored. But the bottom line is that seniors in care facilities have a less diverse microbiota and poorer health.

It could be the case that by the time a person is ready to go into long-term residential care, he/she is already naturally in a state of declining health, regardless of diet. But we have converging evidence from other places that diet can indeed affect health through the microbiota. The other major possibility is more intriguing: what if the poor diet of a senior in a long-term care facility was the thing that caused poorer health from the day they entered? This isn't so far-fetched, as those who study geriatric populations (like Keller, below) will tell you.

I, for one, wouldn't be so keen to support an elderly parent going into a care facility if the menu was going to guarantee a health decline.

The problem would seem to have such a simple solution: change the menus in these care facilities. But I doubt it's as easy as it looks. There are all kinds of social and cultural factors to consider when creating menus, not to mention the pressure of keeping down costs. Dr. Heather Keller at University of Guelph is knowledgeable about some of these factors.

A word to the wise here, if you happen to be checking out the menu at your local long-term care facility: macaroni and cheese won't cut it. Elderly folks need protein, protein, and more protein.



Friday, May 9, 2014

Babies in the womb are not sterile after all

Previously I've written about how infants become colonized with microbes. I, like many others, took it as gospel that babies were sterile in the womb, and got their first (literal) taste of microbes on their way through the birth canal during labour. C-section babies, of course, picked up their initial microbes from whatever things touch them in the operating room.

Now, however, scientists are challenging the truth of the "sterile womb paradigm". Studies (reviewed here) are beginning to suggest that babies do indeed acquire a collection of microbes before birth. The birth process and breastfeeding are ways of "copious supplementation" afterward.

Imagine that: when I had my daughter two years ago, I went through the pregnancy thinking that she was more or less shrink-wrapped from the microbes inside of me. I only had to start consuming lots of probiotics when I got close to the "big day" when she'd finally emerge into the great microbial world. 

But when I had my son this year, the scientific picture had changed. I thought of him in more of a mesh bag inside of me: vulnerable to, and benefitting from, the microbes that I encountered throughout the pregnancy.

Take-home message of the day: the womb is more of a mesh bag. Exactly what that means for pregnant mothers is still to come. 

Wednesday, July 10, 2013

How the microbiome is (slowly) making its way into clinical practice

If you follow my Twitter feed (@bykriscampbell) or read this blog, it will be obvious to you that the microbiome impacts our day-to-day health. The research, granted, is in an early-ish phase where certainties are few and far between (as I mention in this podcast interview). But still, there are myriad studies that say things like "administer probiotics", "avoid prescribing antibiotics to kids", and "consider c-sections only in emergency situations".

What has me puzzled lately is this: if lots of good evidence is already out there, how come it's being incorporated so slowly into clinical practice?

Well, it's Good News Day on this blog. Because here are a few examples where health professionals are taking the information on the microbiome and using it to immediately help patients:

1) Fecal transplants are moving from the realm of weird voodoo cure, into a respectable treatment option. The most likely reason for this is that they work ridiculously well a lot of the time. In a recent NEJM study, for example, fecal transplants were used to treat recurrent C. difficile infection, and were so effective that the study had to be discontinued because it was unethical to withhold the treatment from the control group.

In the US, the FDA recently tried to put up a barrier for doctors wanting to use this treatment with their patients: requiring an Investigational New Drug application for fecal transplants. Recently, though, the requirement was thankfully overturned.

2) I was having another dinner-table conversation about feces the other day (wait, not all families do that??), when I heard from a Winnipeg doctor that the formulary in his hospital carries probiotics, and that he and his colleagues often administer probiotics when antibiotics are given to inpatients. Since then, I've heard that Quebec's Pierre-Le-Gardeur hospital does the same, as do several others in Quebec and Ontario. (And probably more that I haven't heard about.)

3) Should you be fortunate enough to have access to a clinic that does bacterial sequencing, the data can be used to personalize your treatment experience. As explained in the video below (with helpful hand gestures) by Nicholas Chia, Ph.D., at Mayo Clinic, a patient with refractory bacterial vaginosis could get a bacterial swab and have it sequenced. This would help the doctors know what antibiotics she is resistant to, and which bacterial takeovers she'd be susceptible to. Based on that, the doctor could find a treatment that would work better than the repeated rounds of antibiotics she might have had in the past. Here's the video with the full explanation:

Using "the firehose of information that comes down off of sequencers"


Those are three examples that make me happy. But the job is far from done. Anyone can do their part to advance "the cause" by bringing up the microbiome at their next doctor's appointment. Even if the doctor doesn't know much about it, she or he might go home and catch up on the topic by reading a few journal articles.

The microbiome is going to change healthcare, but it'll be one doc and one patient at a time.