How your metagenome makes you fat
This week's Nature is largely about the association of gut biota with body mass in humans, with two papers and a commentary on the subject. Both papers are from Jeffrey Gordon's lab, and to my mind they both establish a very important base for metagenomics in human biology.
It has long been known that the human gut flora can cause incredible problems when it goes wrong, but so far these problems (for example, symptomatic H. pylori, pathogenic E. coli, pathogenic Clostridium difficile) have been compartmentalized as the effects of individual pathogens. A metagenomic perspective views such health problems as imbalances in an ecosystem. Bad health outcomes might be induced by harmful invasives (such as hospital-acquired Clostridium difficile) or by long-lasting phylogeographic associations (some examples of H. pylori. In either case, if we want to control the disease, we will be best served to study its evolutionary origin -- which may owe as much to ecology as to epidemiology.
These papers are important because they show that "normal" variations in human biology -- that is, not necessarily pathological variants -- also are linked to the ecology of our metagenome. I think the introduction to the paper by Turnbaugh et al. (2006:1027) puts it well:
The human 'metagenome' is a composite of Homo sapiens genes and genes present in the genomes of the trillions of microbes that colonize our adult bodies. The latter genes are thought to outnumber the former by several orders of magnitude. 'Our' microbial genomes (the microbiome) encode metabolic capacities that we have not had to evolve wholly on our own but remain largely unexplored. These include degradation of otherwise indigestible components of our diet, and therefore may have an impact on our energy balance.
There is a complex set of interrelated observations between these two papers. They used metagenomic methods to assess the microbial population of the gut in obese and nonobese humans (that's the Ley paper). Then (the Turnbaugh paper) they looked at normal lab mice versus leptin-knockout lab mice who are genetically obese (the famous "fat" mice). They found that the microbial contrasts between obese and nonobese people were also shared by the obese and nonobese mice. But the obese and nonobese mice are difficult to compare, in terms of microbial function, because they don't have the same food intake. So finally, they took the microbial populations from the obese and nonobese mice and stuck them into germ-free mice, finding that the microbial community from the obese mice actually is more efficient at extracting calories from food -- the excreta have fewer calories remaining. And then (back to Ley), they examined humans who lost a lot of weight, and found that they had the gut microbes of nonobese people!
The power of metagenomics becomes evident when Ley and colleagues were able to show that the differences in gut ecology between obese and nonobese individuals were not simple "blooms or extinctions of specific bacterial species." Considering the rapid reproductive potential of microbes, such intermittent blooms would likely be a first hypothesis for differences between individuals; the metagenomics is able to show changes to a more complex balance of bacterial types.
This kind of alteration of a complex balance is what Bajzer and Seeley mean by "biological control systems" in their accompanying editorial. They mention that a very slight excess in caloric intake over expenditure can add up to large weight gains over time, so that relatively small differences in the efficiency of gut flora can make a large difference.
This is all really interesting, and it doesn't really solve any mysteries, it just raises new ones:
Another unknown is why and how the make-up of the microbiota is shifted by differences in body weight. Given that acquiring food from the environment can be both calorically expensive and potentially dangerous, it would seem to be most adaptive to extract as many calories from every bite of food as possible. Moreover, if caloric extraction does become more efficient, the regulatory system would dictate that the organism responds by reducing its caloric intake. If a host organism had the ability to change its microbiota so as to increase caloric extraction, it would seem most adaptive to do so when facing famine conditions and losing weight. However, the data indicate just the opposite - the microbiota seems to be more efficient in obese humans who already have the most stored energy, and shifts to being less efficient as the subjects lose weight (Bajzer and Seeley 2006:1010).
Considering that the obese mice studied here were specifically engineered to be leptin-deficient, it would seem that one likely hypothesis is that leptin serves as part of a feedback system altering the balance of the gut flora.
My hypothesis would be that obese people have more efficient gut flora because the gut flora of obese people have to be more efficient to compete for nutrients.
That's ecology again -- it would be a mistake to view the gut ecology without considering the host. I also think that time may be an important element here: one of the major factors determining digestive efficiency is gut transit time, and the effects of a change in microbial populations often include changes in the transit time of food through the digestive system. Since the human microbial samples were from stool, differences in transit time in the upper digestive tract may make an important difference to the abundance of certain microbial nutrients in the cecum or colon.
It sure seems like an interesting problem, and one that we increasingly have the tools to tackle. Human microbial anthropology might be a stretch, but who knows?
References:
Bajzer M, Seeley RJ. 2006. Obesity and gut flora. Nature 444:1009-1010. DOI link
Ley RE, Turnbaugh PJ, Klein S, Gordon JI. 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444:1022-1023. DOI link
Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027-1031. DOI link
Microbiomic metagenomics
At the movies last night I saw a preview for Superman, and now Science tells me that humans are superorganisms!
Metagenomic Analysis of the Human Distal Gut Microbiome
Steven R. Gill et al.
The human intestinal microbiota is composed of 1013 to 1014 microorganisms whose collective genome ("microbiome") contains at least 100 times as many genes as our own genome. We analyzed 78 million base pairs of unique DNA sequence and 2062 polymerase chain reaction-amplified 16S ribosomal DNA sequences obtained from the fecal DNAs of two healthy adults. Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes. Our microbiome has significantly enriched metabolism of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-D-erythritol 4-phosphate pathway-mediated biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes.
This is really important stuff -- our nutrition is very dependent on these microbes, and there is every reason to think that their ecology affects our overall health status as well. And we know very little about them -- heck, these guys are using the same metagenomic techniques to fine organisms in our bodies that are used to find new unidentified ocean life!
But notice that even this study with all its comparisons of gross gene function among all these microbes has only included two humans. The next step will be finding the variability among people in intestinal ecologies, how humans have adapted to their microbes by means of genetic evolution, and how different people have different health susceptibilities as a result.
The metagenomic technique gives two assessments at once -- the genes of the microbes and their relative abundances (through the relative numbers of reads). I wonder if there is some sense in treating the entire community as an evolutionary unit -- one that can shift its proportions of different parts over time and in different hosts.
There should be much of interest here, considering the dietary and other evolutionary changes within humans during the Late Pleistocene and Holocene.
References:
Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312:1355-1359. DOI link
Probing for the alien within
Laura MacConaill and Matthew Meyerson present a cool short review in Nature Genetics of metagenomics applications in pathogen discovery.
The basic principle is to extract DNA from a tumor or sore, do intensive sequencing of all the DNA in it, and use the computers to subtract out everything human. What's left after you subtract out the human DNA is any pathogen that might be in the sample:
The two recent studies combined computational subtraction with microreactor-based pyrosequencing to identify viral signatures associated with human disease. Feng et al. used high-throughput pyrosequencing15 and comparison to the human transcriptome to identify a viral sequence in a library of cDNAs generated from individuals with Merkel cell carcinoma, a rare but aggressive human skin cancer. The authors sequenced over 395,000 reads of 150-200 bp in length. After digital transcriptome subtraction, 2,395 sequences remained. Among these, conceptual translation of one sequence showed similarity to a polyomavirus. By cloning the complete viral genome and carrying out further analyses, the authors found that the Merkel cell polyomavirus sequence was present in eight of ten Merkel cell carcinomas.
A second group used the same high-throughput DNA sequencing technology to identify a previously undiscovered arenavirus that likely caused the deaths of three transplant recipients who all received organs from a single donor.
I don't know if sequencing will ever get so cheap that this will become practical diagnostic method, but it really doesn't need to be. As soon as you suspect a pathogen, you can probe directly for that pathogen's DNA in a sample -- and there's no barrier to testing for hundreds of pathogens at once. Heck, there ought to be a SNP chip for it.
But this is a potentially important way of identifying new pathogens in unknown samples from scratch. The article mentions that the current cost of this kind of sequencing is around $10,000 per sample, and that is rapidly falling. For that cost, you get the sequence on your computer, even if you can't identify it yet, and who knows -- it might pop up two years later when somebody else finds it in some unexpected place.
References:
MacConaill L, Meyerson M. 2008. Adding pathogens by genomic subtraction. Nat Genet 40:380-382. doi:10.1038/ng0408-380
John Hawks Department of Anthropology
University of Wisconsin—Madison
Copyright © 2007 John Hawks