Social Media for Scientists: YouTube One Channel

If you have videos posted to youtube, then you should definitely check out the new layout design. In the span of ten minutes, you can customize your "YouTube One Channel" as they now call it with a banner from your gallery or theirs, feature video, and a list of videos that you can customize according to theme, recency, popularity, etc. If you do not post videos to youtube, then you should. Its a great way to give wings to your science to other scientists and the public. Consider it a broader impact if you will. Video pages are on the rise, like twitter and facebook. They are here to stay as an online footprint of your life or profession, whatever you may choose. For scientists or educators, lectures, seminars, news features, TED talks, etc are all great things to post. Ive gotten immense benefit from watching research seminars on youtube because there are always meetings that you miss or talks you would like to hear twice. If you set up a channel, let me know so I can subscribe to it!

http://www.youtube.com/user/sbordenstein

Diet Cures Multiple Sclerosis

Source

I am fascinated by how changes in the gut microbiome can alter the course and even reverse human disease. Take the recent surge of fecal transplants for instance to treat chronic diseases such as IBD, Clostridium difficile, Crohn's, and multiple sclerosis (blog post). I am also intrigued by how plant strong and paleo diets seem to be increasingly beneficial for health.

Here is an inspirational TEDx talk by Dr. Terry Wahls (@TerryWahls) on how she used pubmed.gov to research and develop a hunter gatherer diet rich in phytonutrients that cured her multiple sclerosis - an autoimmune disease of the central nervous system. Note that her approach focussed on the beneficial vitamins and phytonutrients from these foods. She did not mention the changes in the gut bacteria that are also occurring on this diet and that can have positive repercussions on the body's metabolites. I hope her message helps others.

Diet changes the gut microbiome, which in turn changes the metabolic, neuronal, and inflammatory networks that may cause or cure many chronic 'Western' diseases. Nothing short of awesome. The regenerative power of the gut microbiome is akin to stem cells and here to stay.

Animated 3D Video of Human Microbiome

A quick post on a really good video from the Knight Lab on how the Human Microbiome (wiki) varies across body space (skin, mouth, vagina, gut) and across time (from infant to adult). Its a really nice way to sum up years of data in three minutes! I can also imagine that we all can immediately use this video in teaching the microbiome. Hence, this is why I am posting to the blog rather than twitter, where it may get lost in the twittersphere feed.

Can A Fecal Transplant Cure IBD, Colitis, Crohn's, C. difficile, Multiple Sclerosis..?

Some call it a fecal transplantation. Others, fecal bacteriotherapy. Call it what you want, but there is regenerative power in poop for severe, bowel problems. Seriously? Yes. Cure rates are generally above 90% for Clostridium difficile; treatments for Crohn's Disease and Multiple Sclerosis are not as well studied, but appear promising. Everyone should know about fecal transplants as C. difficile infections have risen 400% since 2000 (largely due to hospitals spreading them). Just in the past year, I have had one family member and one friend come down with C. diff infection. Doctors are recalcitrant to prescribe fecal transplants, but that appears to be due to lack of knowledge rather than success.

1. CNN raised the profile of fecal transplants a trillion fold when it posted this article on the front page of its website a couple of days ago: Little known fecal transplant cures woman's bacterial infection. If anyone was previously skeptical, this article basically legitimizes fecal transplantation.
2. The Henry Ford Hospital in Detroit, MI recently found that 43/49 patients with C. difficile infections were cured after fecal transplants; they had no problems up to three months later. Fecal transplant from mom cures ailing toddler.
3. A 2011 literature review found that 92% of 317 patients with recurrent C. difficile infection or pseudomembranous colitis had disease resolution upon fecal transplant. 
4. Clinics and retreats are offered! For instance in the US, the Bright Medicine Clinic in Portland, Oregon performs Fecal Transplants for many conditions discussed below.
5. There's a blog called Fecal Microbiota Transplant that reports seemingly unpublished data on transplants improving Multiple Sclerosis in patients with bowel syndromes. At a minimum, patients were able to walk again!
6. Two papers on inflammatory bowel disease indicate that of nine patients who were non-responsive to standard treatment, all nine of them responded dramatically well to fecal transplant therapy.  Bacteriotherapy Using Fecal Flora (2004) and Treatment of Ulcerative Colitis Using Fecal Bacteriotherapy (2003)
7. We NEED a site that provides location information on fecal transplants. I can not seem to find one and people will clearly be asking for more information. Googling around appears to come up with specific instances, so if you search hard enough, you may find something in your neck of the woods. (There is a partial list of USA fecal transplant places here); if you're in TN, Vanderbilt's clinical chief, Dr. Michael Vaezi of Gastroenterology is doing fecal transplants in response to refractory Clostridium difficult; In Virginia at the Virginia Commonwealth University, Dr. Michael Edmond is doing fecal transplants for C. diff [news link]; In Nevada, Gastroenterology Consultants in Carson City offers fecal transplantation for C. diff
8. There's a Facebook Page that appears to be a good social media resource, aptly named Fecal Bacteriotherapy is "The Bomb"
9. There are reports on the internet of do-it-yourself fecal transplants. Clinics can be hard to find and the treatment is not typically covered under insurance, especially for IBD. Understandably, these barriers to a treatment have led some to pursue self-treatment with enema kits. Probiotic Therapy Home Infusion Protocol and Success of Self-Administered Home Fecal Transplantation for C. difficile Infection. 
10. A University of Guelph lab in Canada has developed a Robogut machine to simulate the human gut conditions in vitro. They have successfully used it to grow a cocktail of bacteria that cured C. diff infections from two elderly patients. What a breakthrough! Symbionticism Blog Post Link

Background: Despite the conventional lexicon that poop is dirty, an agent of infection, and should be left for one place and one place only - the toilet, poop may be as powerful in its regenerative capacity as stem cells. Perhaps better. Roughly 40% of your feces is made up of bacteria living inside and shed from your gut. These species help us digest food, develop intestinal tissue, and fight off infections among many other things.

Disease: The bacteria in your gut are as much a part of you as your genes. The fact that some fraction of them come out in your waste is fortunate because these symbiotic bacteria can be used in the purest form of recycling that humans may ever know. Friends or family that are suffering month-to-month, or year-to-year, with debilitating or deadly diseases such as Crohn's disease, ulcerative colitis (these first two are often referred to as IBD or inflammatory bowel disease), Clostridium difficile, etc know all too well the long and painful aspects of these diseases. In many cases, antibiotics are prescribed over and over, with each one that fails leading to more expensive ones that are also more difficult to get. The irony of the antibiotic ferris wheel is that antibiotics may be buying a little more time or even exacerbating the problem, while the solution happens to be right in front of us, or behind us to be technically accurate. The healthy bacteria in poop from a friend or family member can be "transplanted" into the gut of a sick patient and fully cure them in many cases.

Professor Thomas Borody (MD, PhD) is one of the leading physician scientists in this area and this video is definitely worth watching and sharing to classrooms, friends, and family.

Further Reading: Fecal Microbiota Transplantation and Emerging Applications. Borody and Khoruts 2012. Nature Reviews Gastroenterology and Hepatology 9: 88-96.

ASM's "Small Things Considered" Spotlights Our Article, Speciation By Symbiosis

Over at ASM's Small Things Considered Blog, a very popular blog on all things microbes, Elio Schaechter discusses our recent review entitled Speciation by Symbiosis. I'll start this post by saying that I think the review (coauthored by my student Rob Brucker, @liveinsymbiosis) is one of the most important pieces that Ive contributed to. I'll explain more about that opinion below. Elio is favorable to the article. He highlights some of the key aspects of the review, including:

1. Some of the examples they cite are startling. For one, Wolbachia, like some other bacterial symbionts of insects, induces parthenogenesis in the insect host, a form of asexual reproduction that does not involve fertilization and leads to what is called “asexual speciation

2. For another, Drosophila flies reared on different diets house different microbiota, and show strong mating discrimination; ergo, the symbionts dictate who mates with whom. 

3. Bacterial symbionts that we could classify as vertically-transmitted, nutritional mutualists (e.g., insect symbionts in the genus Buchnera) assist in resource exploitation, thereby creating new ecological opportunities for their host

4. Endosymbionts can also induce cytoplasmic incompatibility.  Here the offspring of infected males and uninfected females are sterile, therefore, unproductive. 

5. In other cases, the offspring of hybrid matings become more susceptible to infection than non-hybrids, which may reduce their fertility and viability. We are working on this very issue right now and plan to have a paper ready in the next few weeks.

This review article was actually a decade in the making for me. Speciation by symbiosis was the topic of my Ph.D. thesis at the University of Rochester and along with Jack Werren, we helped put Wolbachia on the map as one of the first cases by which symbionts drive the evolution of reproductive isolation between species. This work was later followed by several other important studies on Wolbachia and speciation and came on the heels of intense evangelizing by Lynn Margulis that symbionts were important to speciation; though I contend that she actually provided little evidence that directly linked symbionts to speciation. In my opinion, Lynn was more interested in showing that symbionts drive adaptations, an undeniable legacy that she has left behind.

After the Wolbachia-associated speciation work came out, there seemed to be a lull in the pace of work on symbionts and speciation. Within the last few years however and the uptick in microbiome studies in all organisms, it has since become clearer that speciation by symbionts in general is a robust field with many new insights to be gleaned in the future. Symbionts drive mate discrimination in Drosophila, rapid evolution of immune genes that in turn cause hybrid maladies in plants, and directly prevent gene flow between closely related species - all discussed in the paper. Our hope is that the review revitalizes the topic for new and old investigators alike, and that as the merger between speciation genetics and symbiosis become seamless, the pioneer of the idea that symbionts drive speciation, Ivan Wallin, be formally recognized. More on Ivan in our article and ASM Small Things Considered Blog.

Finally, we tried to publish this article as open access at various journals, but it ended up in TREE's hands. If anyone needs a full copy of the pdf, do not hesitate to email me. My email is readily available by google search or the lab home page.

Related blog posts:
1. The story behind Speciation by Symbiosis? (April 26, 2012)
2. Is the microbiome part of the organism or the environment?
3. Is the microbiota species specific? (June 23, 2012)

Quantified Self and The Microbiome One Year in The Making

With a custom iPhone app and a year of daily gut microbiome data from Eric Alm et al. at MIT, this video from the 2012 GET Conference (recorded April 25, 2012) shows:

• His human microbiome is stable over a year
• Temporal variation within his microbiome is lower than human-to-human variation
• Fiber has an effect on microbial community structure
• Travel affects gut microbiome 

A panel of pioneers in "The Quantified Self" movement (self-tracking of health/disease) then meet at the GET Conference to talk about what they have done and learned in the process of self-tracking, including Eric and Larry Smarr. Eric talks more about how the gut microbiome surprisingly stays stable over time. Its resilient. One of the most interesting points in the panel discussion occurs at 7:57 by Larry. He raises the prospect that self-tracking can become the norm and its benefit is that we'll see the onset of disease way before symptoms ever occur. I agree with this. The microbial flora will unquestionably show changes prior to our body ever feeling the negative outcomes. The upshot is that this could lead to preventive medicine in which doctors and patients tweek the microbiome back to normal before something makes us feel ill. Fascinating.

After watching this, you will see that "Medicine 2.0" (web 2.0 + participatory, self-tracking + doctors) is on the horizon.

Is the Microbiota Species Specific? Cell paper weighs in.

A just published Cell paper, Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota, weighs in on the growing evidence that the gut microbiota is specific to a host. In this case, the study shows that non-native microbiotas, including human and rat, colonize a mouse gut, but those bacterial species do not work with the resident mouse cells to mount a proper immune response. Simply stated, you can put non-native microbes in an animal, but you dont get a fit animal back.

Highlights from the paper:

• Mouse and human microbiota differ in bacterial species, primarily within Firmicutes
• Human microbiota (HMb) colonized mice have a global immunodeficiency like GF mice
• HMb induced less T cell proliferation and activation than mouse microbiota (MMb)
• HMb mice are more susceptible to enteric and disseminated infection than MMb mic

Video link of the senior author and Harvard professor, Dennis Kasper, describing the paper:

This work contributes to an emerging body of literature that supports the hypothesis that a minor or major part of the assemblage of the OTUs in the microbiota interact with the host in a specific manner. The consequence of this specificity is that assemblages of bacteria in related species may actually change in composition over time in parallel with the phylogeny of the host species. Thus, the bacterial OTUs could be a general extension of the host's genes, and there is an evolutionary footprint in the changes in both. We saw this in Nasonia wasps (Evolution paper here) and have summarized other evidence in Box 1 of this review (Trends in Ecology and Evolution paper here).

All this makes me wonder how important symbiosis will turn out to be in speciation. If the pace of new discoveries is any indication, it is looking like the old ideas of the 80's and 90's (that symbionts do not assist speciation in any grand way) is going to be entirely reassessed.

Related Blog Posts:

• Speciation by symbiosis (April 26, 2012)
• Is the microbiome part of the organism or the environment? (May 11, 2012)

The Story Behind Our New Review: "Speciation by Symbiosis"

This post is a behind-the-scenes look at our new review, entitled Speciation by Symbiosis, by graduate student Robert Brucker and I. The review is online today in Trends in Ecology and Evolution. If anyone needs a copy, Ill happily send you one. Here are four points that motivated us to write the review.

1. The study of microbial symbionts in speciation has an interesting history: One of the central questions in evolutionary biology remains how do new species arise. What types of genes and evolutionary forces spur one species to split into two, ultimately to form the 1.8 million species on the planet? While we clearly have answers today that shed some light on these questions, debate remains about what types of heritable factors are important in promoting speciation. Specifically, these factors include two possibilities: (i) the genes on an organism's chromosomes versus (ii) the microbial symbionts that inhabit that same organism. The controversy over this topic actually began a century ago among evolutionary biologists and geneticists.  The main demarcation in the debate was best represented by two books, one of which was nearly forgotten to history and is the inspiration for the review, as well as our grant (press release) from the National Science Foundation's Dimensions of Biodiversity Program.

The forgotten book and the famous book that complements it are:

• by microbiologist Ivan Wallin - Symbionticism and the Origin of Species (1927), and 
• by geneticist Theodosius Dobzhansky - Genetics and the Origin of Species (1937)

Given the uncanny similarities in titles and the time frame of their publications, I think it is likely that Dobzhansky "copied"  Wallin's title and replaced Symbionticism (meaning intracellular symbioses with microorganisms) with the word Genetics.

A 1920 photo of Ivan E. Wallin. Wallin was a professor in the Department of Anatomy at the Univ. of Colorado Medical School, Boulder and was most well known for recognizing that mitochondria as bacteria. Credit: Archives, University of Colorado at Boulder Libraries. Colorado, U.o. (1920) Junior Class. In College of Liberal Arts, Univ of Colorado, Boulder.

2. Ivan Wallin's Hypothesis Was Ahead of His Time: Wallin’s central thesis was that the universality of bacterial-derived organelles (i.e., mitochondria) reflected the importance of bacterial symbionts as building blocks of evolutionary change and ultimately new species. Despite Wallin’s effort to put microbial symbiosis into the mainstream of evolutionary biology in the early 1900's, it was Dobzhansky’s work that would have a lasting influence. From the Biological Species Concept to the Dobzhansky-Muller-Bateson model of postzygotic isolation, Dobzhansky et al laid a solid foundation for the study of the genetics of speciation. Experimental and theoretical investigations of symbiont-assisted speciation were far and few between as speciation genetics took off in the 80's and 90's by many science idols of mine.

 

3. Today's biotechnology and thinking are up to the task: With the advent of high throughput sequencing techniques that make the identification of bacterial symbionts simple, and today's recognition of microbial symbiosis as a requirement for complex eukaryotes, Wallin’s ideas on the symbiotic origin of species are primed for a full reassessment. Indeed, the emergence of the bacterial symbiont Wolbachia in topical discussions of speciation (book chapter) was a beginning to reviving Wallin’s silenced ideas. The emerging story supported by the latest science in our review is that biologists have even farther to go with symbiont-assisted speciation. It appears to be almost a given that studies of the general microbial community of animals and plants will reveal even grander ways in which microorganisms act as causative agents of their host's speciation.

  

4. A new phase in the study of symbiont-assited speciation is happening now: Our article begins begins with a rich, historical controversy in evolution and genetics. Where that debate goes in the future is up for scientific discourse and experimentation. Rob Brucker (@liveinsymbiosis) and I suggest in the review that the current evidence for symbiont-induced speciation is far more solid than many speciation geneticists appreciate, and a new phase of speciation by symbiosis is likely to spur many exciting new insights.

We suggest that as studies of microbe-assisted speciation march forward, Ivan Wallin should be recognized for his pioneering and imaginative work on the microbial basis of speciation. Here is arguably his greatest quote:

“It is a rather startling proposal that bacteria, the organisms which are popularly associated with disease, may represent the fundamental causative factor in the origin of species.” (Ivan E. Wallin, 1927)