This time of year seems to be nonstop conferences, symposiums, presentations, meetings, and chats. I’ve been trying to catch up with the Storify collections for all of the ones I’ve been attending or lurking in recently. The Microbiome Symposium was a HUGE one!
In case you didn’t know, I’m fascinated by the microbiome, and have been for years. I’ve been tracking research about it, playing with personal microbiome testing services, finagled my way into being the liaison librarian to the Host-Microbiome Initiative here on campus, and doing my level best to make myself a useful collaborator with them. This all gained me access to the day-long Microbiome Symposium sponsored by Cayman Chemistry, where a few of us live-tweeted. I want to take just a brief moment to talk about some of the highlights. But in case you don’t have time, here is the number one most important critical thing to remember (the rest are in no particular order):
NUMBER ONE: Eat fiber. Lots of fiber. Many kinds.
2. What we don’t know about the microbiome is how all the species interact.
3. Microbes are sort of little factories that make all sorts of chemicals, drugs and poisons (which aren’t regulated by the FDA).
4. Liver and bile are way more important than we expected. To the gut. Yeah, really.
5. Nutrients from food are not one-size-fits-all. What you get out of your food is tailored by your microbiome.
6. The reverse is also true! What you eat tailors your microbiome!
7. What we don’t know about the microbiome is how it interacts with the rest of what our body does, say, for example, exercise.
8. We might be able to predict different diseases by watching changes to our microbiome, like cancer and diabetes.
9. If we can spot predictive changes early enough, we might be able to head them off by changing diet.
10. Most of the bacteria that show colon cancer seem to come via the mouth. So brush your teeth!
11. Don’t eat fiber? Changes your microbiome. Degrades mucosa. Erodes protection from mucus, first line defense. Triggers inflammation. OOPS!
12. It’s complicated.
13. Complexity is important. Eat the rainbow.
14. Fiber is IMPORTANT. Especially eating a diversity of fiber. Try counting how many different plants are in your meals.
15. A diet poor in what make the bacteria happy (fiber, a.k.a. microbiota-accessible carbohydrates, a.k.a. MACs) has immediate impacts on them, long term impacts on us.
16. Diet is a tool to engineer (program) our bodies to meet our goals. What are your goals? Optimize yourself, your health, and your mood, with food!
17. Break the chain, it stays broken. (Once you kill off the diversity of bacteria in your body through poor diet, they don’t tend to come back.)
18. How do you get a diversity of bugs in your gut again? Fecal transplants.
19. Avoid antibiotics whenever possible. but especially early in life.
20. Bugs I want to remember: FLVR = Faecalibacterium prausnitzii, Lachnospira multipara, Veillonella parvula, Rothia mucilaginosa.
21. High fiber diets help protect against allergies, and allergens, and asthma.
22. High fiber diets help protect against different types of gut pain.
23. About probiotics: Dead bacteria don’t work. They have to be live, the kind you keep in the fridge.
24. This isn’t regulated territory yet, the FDA has little sway. Be cautious about product claims.
Now, those were the official take aways, but there were some deeply intrigued nuggets in the hallways conversations and posters as well. There was a lot of unofficial buzz around fungus, and worms (helminth therapy). Things to watch for in the future. Here’s the Storify, if you want to dig into this more deeply.
— PF Anderson @pfanderson@disabled.social (@pfanderson) October 1, 2015
And in the meantime, I found ANOTHER Storify from a symposium that focused on microbiomics, so here’s that (from Cell Symposia as #CSMicrobiome) as a bonus.
The image above is from one of the earliest studies on the genetics of clefting done here at the University of Michigan School of Dentistry. Those were the days, weren’t they? You had to track signs and symptoms across generations, for decades, trying to deduce large scale patterns. Now we spit in a tube and mail it off.
The Future of Genomic Medicine was just happening. It was being actively tweeted by a number of leading figures in healthcare and science — Eric Topol, Carl Zimmer, Dr. Khoury from the CDC, Magdalene Skipper from Nature, and (uh) Al Gore, just for starters. It was so active that the original hashtag, #FOGM14, had to be dropped because of spammers, and they group switched to #FOGM2014. It was so active that even though it happened two weeks ago, the hashtags are still active on Twitter with people continuing the conversations around the conference. Here are just a highly selected few tweets with interesting thoughts, resources, and take-aways from this important conference.
I’ve been blogging elsewhere about microbiome research, and collecting a ridiculous number of links and articles about it. I’ve been lucky enough to have long conversations with some of our faculty who are publishing in this area. This week one of the faculty asked me to proofread a chapter they are writing about the microbiome, which was a great treat for me. Beautifully written, engaging and educational, I’m really looking forward to seeing it in print.
Midway through the process of writing about the microbiome, the faculty member was asked to include the virome. Oh. Well, let’s mix things up a bit, shall we? By the time I saw the draft, the mycobiome had also been added in. A brief ‘glossary’ for those not currently working in this space. Also note that because of the lack of a true glossary for some of these terms, I am intuiting definitions from a scan of the writings using the term. In other words, doing the best I can, but part of this is sort of made up, even though the terms exist and are being used*. While we don’t have enough for an alphabet book, there were enough that I felt compelled to alphabetize.
Biome = community of living things in a particular space or habitat Exobiome = a community of living things external to the Earth’s air space Exposome = measuring and assessing health impacts of environmental exposures external to the individual (beginning in utero) Genome = genes of an organism Metabolome = “small-molecule metabolites (such as metabolic intermediates, hormones and other signaling molecules” [Wikipedia] Microbiome = genomes of a community of microbial or bacterial living things etc. Mycobiome = genomes of the community of fungi … Parisitome = genomes of the community of parisites … Pathobiome = genomes of the pathological components of a microbiome; behaviors and changes in a microbiome that lead it toward a pathological state Proteome = proteins produced by a genome Retrovirome = genomes of the community of retroviruses … Transcriptome = a subset of the genome comprised of the transcripts or various types of RNA fragments from a given cell Virome = genomes of the community of viruses … Xenome = genomes of microbiomes involved in xenografts or xenotransplants
And then there are the specific microbiomes for body regions, such as the vaginal biome, oral microbiome, aural microbiome, nasal microbiome, and the skin microbiome. I’m not aware of specialized terms for microbiomes of external locations (hospital, home, school, jungle, waterways, etc.) and other species (canine, feline, various bird species, various rodent species, etc). Most of the other Omes also are studied across species and locations. And there are more.
Here’s a tutorial for an introduction to just the genomics part.
The Human Genome, DNA, Chromosomes & Gene Structure – Excellent genomics tutorial & figs by Dr. Carol Guzé – http://t.co/puUDdgJi7T
And while this isn’t a tutorial, these are videos from the recent conference on Human Microbiome Science: Vision for the Future. That should give you an overview of that portion.
So let’s take a look via Twitter at some of the other “Ome”s and omics. As you might guess, these are BUSY topics, with formal Twitter chats discussing fine points of methods, sharing articles, conference presentations, news, and general buzz.
Image Credit: National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH)
Interested in the human microbiome? There is an upcoming lecture on this from the Department of Computational Medicine & Bioinformatics (CCMB) as part of their lecture series. (Don’t know much about microbiomes? Introductory information at the end of the post.)
Dynamics of the Microbiome Patrick Schloss
Palmer Commons, Forum Hall (4th Floor)
Wednesday, March 27
3:30 – 4:30 PM
If you don’t know much about the Human Microbiome, or want to have resources to explain it to others, here are some places to start from last week at the Emerging Technologies Librarian blog.
To start off, let’s look at Larry Smarr’s video of how he is studying his own personal microbiome, what he has learned about his own health, and how it has changed his life.
If you are remotely intrigued by what Larry said, then you might want to check into the uBiome project, a citizen science endeavor allowing you to explore your own microbiome.
Now, more videos about the Human Microbiome Project itself. The first is an interview with Dr. Julie Segre, who has oversight of the project; the second from University of Michigan faculty member, Dr. Vincent Young.
The NIH Common Fund’s Human Microbiome Project. No Longer Germ Warfare. An interview with Dr. Julie Segre, NIH Intramural Researcher, The NIH Common Fund’s Human Microbiome Project. http://www.youtube.com/watch?v=LfeNTQxxn0w
Three videos describing more about the concepts behind idea of the human microbiome. One is a lecture from Stanford faculty member Julie Theriot, another by the most expert Julie Segre, and the third just because I like it and find it one that is relatively easy for people to understand.
Last but not least, a selection of videos looking at implications of the human microbiome in specific areas of the body or of our health, from bowels to brain.
If you are still hungry for microbiome videos, Jonathan Eisen has a fantastic collection in a playlist, there is another playlist from Fora.TV at the Compass Summitt conference in 2011, and Yohanan Winogradsky’s entire Youtube channel is devoted to the topic.
I’ve been tracking the Human Microbiome Project for a few years now. I was going to blog about it, and then the New York Times published articles about it, and I assumed that meant I didn’t need to say anything. Last week I was talking with a few friends about the human microbiome, and absolutely blasted their minds into outer space. Not only had they not heard about it, the very idea was hard for them to wrap their minds around. So, here is a very brief intro, grabbing wonderful pieces from other folk. Brief take-aways.
1. Most of our body, say roughly 99% (by cell count), is comprised of critters that don’t have any human DNA. Surprise!
2. The groups of critters, a.k.a. microbes, that make up most of our bodies are surprisingly different from person to person.
3. The whole idea of antibiotics might turn out to be one of those really really bad social experiments, in that while killing the “bad” microbes, the antibiotics are also killing our good ones, the ones that we need to live and be healthy.
4. The research into what microbes make up part of different people, and how this impacts on physical and mental health, is provocative, potentially quite valuable, and extremely complicated.
5. This area of research brings up yet more challenges to the ideas of personal privacy and transparency in healthcare.
“Before the Human Genome Project was completed, some researchers predicted that ~100,000 genes would be found. So, many were surprised and perhaps humbled by the announcement that the human genome contains only ~20,000 protein-coding genes, not much different from the fruitfly genome. However, if the view of what constitutes a human is extended, then it is clear that 100,000 genes is probably an underestimate. The microorganisms that live inside and on humans (known as the microbiota) are estimated to outnumber human somatic and germ cells by a factor of ten. Together, the genomes of these microbial symbionts (collectively defined as the microbiome) provide traits that humans did not need to evolve on their own. If humans are thought of as a composite of microbial and human cells, the human genetic landscape as an aggregate of the genes in the human genome and the microbiome, and human metabolic features as a blend of human and microbial traits, then the picture that emerges is one of a human ‘supraorganism’.”
Elizabeth K. Costello, Christian L. Lauber, Micah Hamady, Noah Fierer, Jeffrey I. Gordon, Rob Knight. Bacterial Community Variation in Human Body Habitats Across Space and Time. Science (18 December 2009) 326(5960):1694-1697. http://www.sciencemag.org/content/326/5960/1694.abstract
“Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. … Within habitats, interpersonal variability was high, whereas individuals exhibited minimal temporal variability. Several skin locations harbored more diverse communities than the gut and mouth, and skin locations differed in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease.”
Chris S. Smillie, Mark B. Smith, Jonathan Friedman, Otto X. Cordero, Lawrence A. David, Eric J. Alm. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:241–244 (08 December 2011). http://www.nature.com/nature/journal/v480/n7376/full/nature10571.html
“Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution1, 2. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence3, antibiotic resistance4 and xenobiotic metabolism5 to spread through the human microbiome. Recent anecdotal studies providing snapshots of active gene flow on the human body have highlighted the need to determine the frequency of such recent transfers and the forces that govern these events4, 5. … We show that within the human microbiome this ecological architecture continues across multiple spatial scales, functional classes and ecological niches with transfer further enriched among bacteria that inhabit the same body site, have the same oxygen tolerance or have the same ability to cause disease. This structure offers a window into the molecular traits that define ecological niches, insight that we use to uncover sources of antibiotic resistance and identify genes associated with the pathology of meningitis and other diseases.”
Kjersti Aagaard, Joseph Petrosino, Wendy Keitel, Mark Watson, James Katancik, Nathalia Garcia, Shital Patel, Mary Cutting, Tessa Madden, Holli Hamilton, Emily Harris, Dirk Gevers, Gina Simone, Pamela McInnes, James Versalovic. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB Journal March 2013 27(3):1012-1022. http://www.fasebj.org/content/27/3/1012.abstract
“In the future, human microbiomes will be defined at many body sites and during different periods in the human life span. A metagenomic survey alone can describe the microbial communities present, but clinical data are required to understand the factors that affect community composition. Studies must consider the role of sex, diet, race/ethnicity, age, residence location, use of medications, dietary supplements, and hygiene products, and many other factors that shape and cause fluctuations in individual microbiomes. Current NIH-funded demonstration projects are exploring differences in microbial communities and whole metagenomes in disease states.”
Emerging Technologies Librarian 