The Tree of Life: Human microbiome project meeting (#HMP2010) Day 2 wrap up

Well, Day 2 is over now for the Human Microbiome Meeting. See my previous post for information about the meeting and about Day 1.

I enjoyed Day 2, though some things are starting to wear me down a little bit. In particular, the fact that the meeting starts at 8 AM, or 6 AM California time, has been really rough. I missed the first 1.5 talks today because of that. Not to organizers of meetings everywhere - don't start meetings so early. And don't have too many talks in one day. It is better, far better, to just have fewer talks, than it is to wear people out. Also not to meeting organizers - do not change the order of talks in concurrent sessions at the last minute. Very bad idea. Anyway - onwards.

As with Day 1, I think the best way to get a feel for the meeting would be to look at Twitter posts with the hashtag #HMP2010. Unlike what I did with my post for Day 1 I am going to put only my tweets below, not everyones.

Today was split up into one series of talks in the AM and then concurrent sessions in the PM. What lessons did I learn today? Well here are a few, with some overlap to those on Day 1 but that is OK by me.

Again - correlations ≠ causation. Those of you out there who do not get this should GTF out of science.
For statement "X manipulations of microbes help treat X ailments in X people X of the time": X="some" NOT "all"
Seems like we are really on the cusp of publications of 100s of clinical studies of microbes and their association with health status
Some of these studies are even starting to get at causation
It should be remembered that all of the methods used in microbiome studies are just methods; none are per se better than others; it is the science that should be judged not the tools themselves
With some effort it seems one can culture many more organisms from a system than might be expected
Cultures have many many uses
But culture based studies do not really get at population genetic frequencies and relative abundance information very well
Be wary of those who stick relentlessly with one idea or method
Very strange how few pharma reps there were here (more on this in my next post)
Please please please do not confuse data with knowledge. Data can be very very useful and I completely support some projects that just are focused on generating data sets. But knowledge comes from thinking about the data, and carefully analyzing it.
Microbes, I think, run our lives much more than we would like to believe

Anyway - that is a brief update. Back to preparing my talk for later this AM ...

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My tweets

Hoffman: some think probiotics overregulated (making research harder); others think underregulated (bogus stuff out there) #HMP2010 about 9 hours ago via Twitterriffc
Hoffman: FDA regulates health claims probiotics though FTC can also be involved if claims in media #HMP2010 about 9 hours ago via Twitterriffc
Many probiotics sellers make structure/function claims like "x promotes intestinal health" - these are less regulated #HMP2010 about 9 hours ago via Twitterriffc
Hoffman: whether/how to regulate probiotics depends on health claims, whether in food or not, etc. #HMP2010 about 9 hours ago via Twitterriffc
Hoffman: for most probiotics we know very little about effectiveness, safety, mechanisms and other key parameters #HMP2010 about 10 hours ago via Twitterriffc
MikeyJ

@phylogenomics ahem, it's true with larger samples too ;) http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011044 about 10 hours ago via Tweetie for Mac in reply to phylogenomics Retweeted by you

Listening to a Diane Hoffman discussing federal regulation of probiotics - there is lots of misleading stuff out there #HMP2010 about 10 hours ago via Twitterriffc
emergentnexus

Rob Knight: http://openmicrobiome.org + http://bioweathermap.org + http://qiime.sourceforge.net #HMP2010 about 10 hours ago via web Retweeted by you and 1 other

Fodor - OTU diversity (i.e., number of bacterial species) is lower in severe CF infections #HMP2010 though he notes small sample size about 11 hours ago via Twitterriffc
Fodor pronounces T-RFLP "Tee R Flip" while I and I think others usually say "Tee Riff Lip" - I think I like his more #HMP2010 about 11 hours ago via Twitterriffc
Anthony Fodor: how do infections in CF patients respond to antibiotics? Followed CF patients during exacerbation events #HMP2010 about 11 hours ago via Twitterriffc
Schmidt: in trying to culture from human microbiome have to switch methods and samples often to continue to recover new things #HMP2010 about 11 hours ago via Twitterriffc
Schmidt: to study microbes in colon they developed methods to do colonoscopies on unprepped people so microbes not flushed out #HMP2010 about 11 hours ago via Twitterriffc
Schmidt discussing nice trick for tracking oxygen in tissues - GFP only fluoresces win essence of oxygen #HMP2010 about 11 hours ago via Twitterriffc
emergentnexus

Grice: prior to wounding, have differentially expressed skin in diabetic vs normal mouse skin (inflammation from shaving fur) #HMP2010 about 12 hours ago via web Retweeted by you

Schmidt - cultured organisms very valuable for working on functions in communities #HMP2010 about 11 hours ago via Twitterriffc
Schmidt: Great Plate Count Anomaly misinterpreted to mean most microbes are unculturable - means most don't grow in one condition #HMP2010 about 11 hours ago via Twitterriffc
Tom Schmidt now up talking about culturing the human microbiome #HMP2010 about 11 hours ago via Twitterriffc
Here is a link to Gail Rosens Naive Bayesian Classifier tool for metagenomics analysis http://nbc.ece.drexel.edu/ #HMP2010 about 11 hours ago via Twitterriffc
@ianholmes yes i think kmer classification though got in late about 12 hours ago via Twitterriffc in reply to ianholmes
Listening to Gail Rosen talk about naive bayesian classifiers for metagenomic data #HMP2010 about 12 hours ago via Twitterriffc
Oh no - #HMP2010 has concurrent sessions - where to go? Where to go? about 12 hours ago via Twitterriffc
Fortenberry discussing ethical issues w/ genomic research on young people; especially on sexual behavior #HMP2010 about 13 hours ago via Twitterriffc
Those bloggers are wild: RT @DrBondar oh the drama!! "PZ Myers will reveal his decision on free blogagency on live TV" http://bit.ly/9QBHtx about 13 hours ago via Twitterriffc
TheGenomeCenter

Fortenberry: obtained urine samples from young men; showed urine is appropriate sample to study urethral #microbiome #HMP2010 about 13 hours ago via TweetDeck Retweeted by you and 1 other

Fortenberry: need to train teens "amazing the things teenage males will do with specimen cups that does no involve peeing in cup" #HMP2010 about 13 hours ago via Twitterriffc
Fortenberry on difficulty studying microbe-sexual activity connection in teens "These are free-ranging adolescents" #HMP2010 about 13 hours ago via Twitterriffc
Fortenberry discussed scanner image of MF sex, how microbes could exchange, ended w/ "don't how how they got them in scanner" #HMP2010 about 13 hours ago via Twitterriffc
TheGenomeCenter

Fortenberry: multiple microbiomes of the penis - in areas where pass urine and areas used during sex #HMP2010 about 14 hours ago via TweetDeck Retweeted by you and 2 others

Fortenberry "for those of you who have not been thinking about male sexual anatomy this morning, here is a primer" #HMP2010 about 13 hours ago via Twitterriffc
Dennis Fortenberry: urethral & coronal sulcus microbiome studies of adolescent males; offers caution for sexual nature of talk #HMP2010 about 14 hours ago via Twitterriffc
@andyfell well, the talk here said the hard part was getting large collection of stools associated with NEC, so worth looking into about 14 hours ago via Twitterriffc in reply to andyfell
Those interested in IBD/microbes might want to look at ileal transplant study from my lab/Georgetown http://bit.ly/XFRWf #HMP2010 about 14 hours ago via Twitterriffc
Young looking at "pouchitis" to develop in IBD patients who get inflammation of diverting intestinal pouch #HMP2010 about 14 hours ago via Twitterriffc
Young: complexities in IBD microbe studies incl. lack of time zero, diversity of host history/genetics, no info on microbe function #HMP2010 about 14 hours ago via Twitterriffc
Young: many studies suggesting possible connection between microbes and IBD; but emphasizes these are associations not causal proof #HMP2010 about 14 hours ago via Twitterriffc
Next up Vince Young on the role of gut microbiota in ulcerative colitis, IBD #HMP2010 about 14 hours ago via Twitterriffc
Tarr doing a great job of saying who did the analysis for which he presents results #HMP2010 #willtrytodothisbetter about 14 hours ago via Twitterriffc
@andyfell does he still have it? about 14 hours ago via Twitterriffc in reply to andyfell
Tarr: high throughput, barcoded, quick collection of all stools of premies in hospital, then if some get NEC will do sequencing #HMP2010 about 14 hours ago via Twitterriffc
Phil Tarr doing "massively parallel stool collection" for necrotizing enterocolitis study "all stools all the time" #HMP2010 about 14 hours ago via Twitterriffc
Phil Tarr telling a very sad story of a premature infant dying of necrotizing enterocolitis - which is alas very common #HMP2010 about 14 hours ago via Twitterriffc
I have created a PaperLi newspaper on the human microbiome meeting tweets - see http://www.paper.li/tag/HMP2010 #HMP2010 about 14 hours ago via Twitterriffc
Next up - Philip Tarr on the infant microbiome and necrotizing einterocolitis #HMP2010 about 14 hours ago via Twitterriffc
Petrosino working on a viral metagenomic sequencing pipeline including isolation, concentration strategies #HMP2010 about 14 hours ago via Twitterriffc
Note of caution: For statement "X manipulations of microbes help treat X ailments in X people X of the time": X="some" NOT "all" #HMP2010 about 15 hours ago via Twitterriffc
Petrosino doing some interesting analysis of the risks/benefits of assembly in metagenomics #HMP2010 about 15 hours ago via Twitterriffc
Petrosino has interesting results on sequencing mock community, I note we have study like this in PLoSone http://bit.ly/cPaIKF #HMP2010 about 15 hours ago via Twitterriffc
Petrosino: key ?s: what are biases, how do new sequencing platforms perform, what is gained/lost from assemblies #HMP2010 about 15 hours ago via Twitterriffc
Petrosino - reminds people that not only is HMP producing data and science, but also spin off benefits akin to space program #HMP2010 about 15 hours ago via Twitterriffc
Joe Petrosino from Baylor giving overview of role of Baylor in HMP #HMP2010 about 15 hours ago via Twitterriffc
TheGenomeCenter

Now Joseph Petrosino from Baylor on improved metagenomic sequencing and analysis for healthy and diseased individuals #HMP2010 about 15 hours ago via TweetDeck Retweeted by you

Zhao wants to encourage marriage of metagenomics and metabolomics in gut studies #HMP2010 about 15 hours ago via Twitterriffc
Zhao emphasizes benefits of having reference genomes to sort through metagenomic data #HMP2010 about 15 hours ago via Twitterriffc
Zhao: diet / excercise differences -> lifespan differences + microbiota differences; though I note just correlations right now #HMP2010 about 15 hours ago via Twitterriffc
Zhao: what is connection between diet, microbiome and longevity? Doing experiment in mice over four years #HMP2010 about 16 hours ago via Twitterriffc
Good to sea some old school TFLP Data here from Zhao mixed in with sequence data #HMP2010Z about 16 hours ago via Twitterriffc
Zhao: who is right? Grandma: you are what you eat; Geneticists: you are your genes #HMP2010 about 16 hours ago via Twitterriffc
Zhao: multiple models could explain connection between microbes and obesity #HMP2010 about 16 hours ago via Twitterriffc
TheGenomeCenter

Now Liping Zhao from Shanghai Center of Systems Biomedicine on re-eng. gut microbiota with TCM foods to prevent metab. syndrome #HMP2010 about 16 hours ago via TweetDeck Retweeted by you and 2 others

Jeff Gordon has electrified the crowd w/ his discussion of model organisms & model communities #HMP2010 #modelorganisms about 16 hours ago via Twitterriffc
Gordon - much of OTU diversity in human gut microbes can be captured via culturing #HMP2010; though this ignores w/in species diversity about 16 hours ago via Twitterriffc
Gordon: Goal .. use "personal" culture collections isolated from people to get a collection that has coevolved w/ each other #HMP2010 about 16 hours ago via Twitterriffc
Gordon : using RNAseq to track gene expression patterns in model microbial communities #HMP2010 about 16 hours ago via Twitterriffc
@mikethemadbiol explain more .. Why is what they are using not abundance? about 16 hours ago via Twitterriffc
in reply to mikethemadbiol
Gordon: using defined communities of microbes to test microbiota response to different diets #HMP2010 - track changes in abundance, txn, etc about 16 hours ago via Twitterriffc
After brief delay now at #HMP2010 - Jeff Gordon up: creating artificial communities of many species & introducing to germ free animals about 16 hours ago via Twitterriffc
TheGenomeCenter

Gordon: took fecal microbe community from healthy donor and graft it into gut of germ-free mice successfully #HMP2010 about 16 hours ago via TweetDeck Retweeted by you and 1 other

TheGenomeCenter

Next talk Jeff Gordon from @wustl on the marriage of comparative metagenomics and gnotobiotics #HMP2010 about 16 hours ago via TweetDeck Retweeted by you and 1 other

yowino

RT @MetaHIT: #HMP2010 feed integrated to our dashboard dedicated to the Human Microbiome http://ow.ly/2xmNL about 21 hours ago via HootSuite Retweeted by you

TheGenomeCenter

By the way, for those interested, I am @TheGenomeCenter's communication coordinator Gaia Remerowski http://bit.ly/9Qa3o2 #HMP2010 about 17 hours ago via TweetDeck Retweeted by you and 1 other