Comments on: Blood type, meet bug type: my new story for the New York Times

By: Yurtdışı Eğitim

Yurtdışı Eğitim — Wed, 27 Apr 2011 16:19:34 +0000

This is interesting…”microbes can influence their host’s behavior”…If that’s true, first of all being aware of this possibility sets great importance for each of us…This could be an answer to “why me” questions…Different races or nationalities having different group of microbes due to living, eating and geographical conditions…this is interesting too…in order to explain certain differences between cultures and behaviours…
However, research in this area is still a baby…We will see hopefully in following years, what role microbes or viruses have on human behavior both physically and mentally…

By: Ian Holmes

Ian Holmes — Mon, 25 Apr 2011 18:20:43 +0000

Although I have not studied the paper in detail, my superficial reading inclines me to agree with Joshua’s comments above. Delving into the supplementary info, the basis for the “3 enterotypes” claim in the MetaHIT Nature paper is the Calinski-Harabasz index applied to a K-medians clustering approach. This is widely-used and reasonable, but not exactly bulletproof. The determination of the best value of “K” in a “K clusters” approach is the topic of a lot of statistical methodology, and it can depend quite a lot on one’s initial assumptions and underlying model. Given the interest in this topic, I would hope to see some statistics that could e.g. provide confidence levels or error bars on K (rather than the assertion that “K=3″); I would also hope for discussion of the underlying model and its assumptions. Instead we have “K=3″ and some visually persuasive plots, which do (deliberately or not) tend to disguise the fact that these clusters are spread out, they rub shoulders, some could be split, and they are plotted in an abstract two-dimensional principal component projection (i.e. PCA) of a much higher-dimensional space of species counts.

IMO, there is nothing here (yet) that could be said to be as unambiguous as the serologic tests for blood types. It does seem to be true that there is some broad clustering, but it’s not clear to me that all of those clusters are discrete or well-defined enough to warrant the label “enterotypes”.

Having said this, I don’t mean to diminish the paper at all. It is absolutely fascinating and fundamental work, rich with data, and I will certainly be re-reading it with my students many times over.

On a somewhat related note, on the statistical methodology side of things: PCA is in my opinion a pretty blunt instrument. This high-dimensional space of counts-of-each-known-bacterial-species is not just a vector of arbitrary counts; it has structure (the phylogenetic tree of those species). I hope that metagenomics researchers will start using variations on PCA that reflect this structure, such as Erick Matsen’s “edge PCA”:
http://matsen.fhcrc.org/pplacer/demo/pca.html

By: JAShapiro

JAShapiro — Sat, 23 Apr 2011 19:24:17 +0000

I’m pretty skeptical of the claim that there are exactly three types. Identifying the number of clusters in a dataset is a very hard problem, and accuracy depends a lot on things like the number of samples, the number of dimensions, and the relationships among the measured variables. Adding more samples could easily demonstrate that there are more clusters than they claim, or fewer. Indeed, if you look at the supplementary data, in the largest cohort there appears to be nearly equal support for 2-4 samples. I think that this paper does demonstrate that there are correlations among different species of gut bacteria, but that is not the same thing as saying that there are N distinct types, and in fact it makes many of the conclusions that they draw from their simulations suspect. They simulate with uncorrelated normal distributions for the bacterial species populations, when it is clear that correlations exist, and many of the distributions are decidedly not normal.

I am also a bit annoyed by depiction in the paper of the clusters, with lines drawn from each point to the center of the cluster. Aside from making for a very busy plot that obscures the actual data points (as does writing labels over the data), it really trains the eye to accept the conclusion of clustering uncritically; points that might fall between the inferred clusters are made to look like they are clearly members of one cluster or the other, when in fact there would be quite a bit of uncertainty in their assignment. They also might represent underrepresented areas of the distribution, which would lead to changes in the conclusions about the number of types. Amplifying that concern is the fact that the authors state that many of the individuals were chosen “for diversity.” That decision might have resulted in the artificial appearance of clusters if individuals at the extremes are overrepresented.

I don’t want to sound too negative, as I think there are a lot of really good and interesting things in the paper. But I think that comparing “enterotypes” to blood types is inaccurate and misleading. If the types do exist, they are much fuzzier than blood types, and I don’t think we know yet how many there really are.

By: Ahcuah

Ahcuah — Fri, 22 Apr 2011 22:44:43 +0000

I wonder how much microbiome change as we age leads to our getting fatter as we get older. I used to be able to eat like a horse and not gain weight, even without much exercise. Now, even with vigorous hikes around twice a week, I find gaining weight effortless. Might it be that the mix of the microbiome changes as we get older, or maybe some new bug finally manages to colonize our guts, and that might be part of the obesity epidemic we are seeing these days?

By: MetaHIT

MetaHIT — Fri, 22 Apr 2011 12:29:18 +0000

Thank you Carl for your nice articles on the human microbiome. They are always very interesting and perfectly translate to the general public what our research focuses on. I would like to reproduce below the comment we posted this morning (Paris time) under the New York Times article (currently under moderation).

The enterotypes paper is the result of a wide European collaboration. The EU-funded Project MetaHIT (metagenomics of the human intestinal tract) is behind the enterotypes discovery. Many fields of expertise, teams, labs, researchers are gathered in order for this collaboration to publish such exciting results. We believe that it is more than normal that the whole consortium be thanked and its name, MetaHIT, put forward.

Congratulations to all the contributors of this wonderful adventure that is our collaboration! Stay tuned for more, it s only a beginning!

Visit our website for more information http://www.metahit.eu & Follow us on twitter, @MetaHIT

Do not hesitate to get in touch with us, we’ll be more than happy to give further details on our activities.

By: Caspar Henderson

Caspar Henderson — Thu, 21 Apr 2011 21:00:02 +0000

Fascinating! Also viruses, which outnumber bacteria by 100 to 1 in the body, play important roles in the human microbiota. See, for example ‘Going Viral: Exploring the Role Of Viruses in Our Bodies’ by
Elizabeth Pennisi, Science 25 March 2011. DOI: 10.1126/science.331.6024.1513

By: mark wisnosky

mark wisnosky — Thu, 21 Apr 2011 14:46:26 +0000

I find the quoted numbers for microbes versus number of human cells intriguing . I struggle with the numbers that I am by a factor of 10X or perhaps higher by count composed more of microbes than human cells. what is the ratio by weight? opens new questions about what it means to be human or presumably any species. take away the microbes and what is left?

By: Three Enterotypes (So Far) | Sphaerula

Three Enterotypes (So Far) | Sphaerula — Thu, 21 Apr 2011 10:40:45 +0000

[...] Excellent summaries of this research can be found on Ed Yong’s Not Exactly Rocket Science blog (“Divided by language, united by gut bacteria—people have three common gut types”) and in an article by Carl Zimmer in The New York Times (“Bacteria Divide People Into 3 Types, Scientists Say”). Carl Zimmer has further comments on his own blog, The Loom (“Blood type, meet bug type: My new story for the New York Times”). [...]

By: sp

sp — Thu, 21 Apr 2011 05:02:05 +0000

this reminded me of another paper i read about that is also mentioned in nature, about specific enzymes found only in japanese people (associated with the bacteriodes bacterium, which happens to be the basis for one of the enterotypes):

http://www.nature.com/nature/journal/v464/n7290/edsumm/e100408-14.html