john hawks weblog

paleoanthropology, genetics and evolution

gut

  • Coprolite microbial ecology

    Thu, 2013-02-28 00:25 -- John Hawks

    The advent of metagenomic analysis of microbial communities has led to some unexpected insights about human biology. These techniques have quietly been leading to new discoveries from old archaeological contexts. One example is Alan Cooper's work demonstrating long-term changes in oral microbiota from ancient dental calculus ("Tracing teeth troubles with fossil bacteria").

    Another is a recent paper from Cecil Lewis' lab, "Insights from characterizing extinct human gut microbiomes." [1]. The paper is open access in PLoS ONE. In it, Raul Tito and colleagues recover DNA data from ancient coprolites, from three archaeological sites in the Americas. As discussed in the paper, they obtain good data from a 1400-year-old site in Mexico. Those people, who lived near present-day Durango, were contemporaries of the classic Maya and Teotihuacanos. As such, their gut microbiomes may provide a really interesting picture of health and diet from a key period in the prehistory of the Americas.

    Coprolites may seem simple, but each represents a unique history of deposition and subsequent preservation. The microbial community may shift during the early stages of this history, and subsequent DNA damage may shift estimates of microbial abundances away from their true values. They found one of their sites appeared to preserve a good signal, while the others were degraded:

    Most striking, both Rio Zape coprolites exhibited a gut microbiome signature with similarities to the children from a rural African village with the exclusion of a sample of U.S. modern adult gut microbiomes (see Figure S4 for a heat map of these data and Figure S5 for the variability in the source proportion estimates). ZA04 also harbored similarities to non-human primate gut. The coprolites from Caserones and Hinds Cave showed little similarity to a gut microbiome environment. A portion of Caserones coprolite microbial community was similar to compost, which may be explained by the post-mortem gut serving as an organic bioreactor filled with carbon and nitrogen from decaying food detritus. The microbial community assignment for Hinds Cave failed to assign well to any source environment.

    From this, we can see that any interpretation of data from a sample of ancient coprolites must be cautious. We're generally interested in how microbial communities may have changed in ancient populations, particularly in response to other factors such as shifts in diet. But as yet it's not very clear what kinds of changes we should predict in association with diet or other changes. That makes it hard to develop a convincing test of a hypothesis.

    This paper is more of a proof of principle. And in its discussion, Tito and colleagues present different ways to explain the kinds of differences that they found in the ancient coprolite microbiota. To me, the most provocative hypothesis is that changes may have more to do with parasite load than diet:

    Information from Rio Zape also supports a current hypothesis about the composition of human microbiomes in traditional communities, potentially revealing an important aspect of the ancestral human microbiome. Spirochaetes are atypical of gut microbiomes in cosmopolitan communities. However, Treponema was reported by Filippo et al. [21] in their comparative study of modern microbiota in children from Europe and rural Africa. In their study, Treponema was observed in the rural African children but was absent in the European children. They hypothesized that the Treponema may enhance the hosts ability to extract nutrients from fibrous foods and may provide anti-inflammatory capability. They raise the hypothesis that microbiota coevolved with ancient diets and that changes in food production greatly impacted the intestinal microbiota. Treponema was also observed in the published rural data for Malawi and Venezuela [22]. The results from Rio Zape provide further support for Treponema as part of the rural human microbiome. Specifically, Treponema now is observed in four rural communities from different continents, three extant communities and one community that has been extinct for over a thousand years.

    As we uncover more comparative data from living people, we will begin to have a better picture of the covariates of microbial community structure. Today's oral bacterial populations in "cosmopolitan" post-industrial peoples are uncharacteristic of past variation. The gut microbiota of cosmopolitan peoples may be just as uncharacteristic. The diversity may have had great importance to ancient health, especially at key times when pathogens were spreading through post-agricultural populations.

    References

    1. Tito RY, Knights D, Metcalf J, Obregon-Tito AJ, Cleeland L, Najar F, Roe B, Reinhard K, Sobolik K, Belknap S, et al. Insights from characterizing extinct human gut microbiomes. PLoS One. 2012;7(12):e51146.
    Tags: 
    microbiome
    gut
    diet
    America
    pathogens
    Holocene
    Synopsis: 
    A look within the gut microbiota of ancient Americans

  • Chimpanzee microbiome variation is like ours

    Tue, 2012-11-13 23:55 -- John Hawks

    A new paper by Andrew Moeller and colleagues surveys the variation in species composition of gut microbiomes in the chimpanzees from Gombe, Tanzania [1]. They found that chimpanzees have a very similar pattern of variation to that found in human populations. Here's their mini-review of the human variation in "enterotypes":

    The gut microbial communities in contemporary populations of humans have been partitioned into three clusters, termed ‘enterotypes’, each of which is characterized by a distinct set of overrepresented bacterial genera. Whereas initially no relationship was detected between enterotypes and specific features of the host (such as age, health status, body morphotype, provenance or gender), recent work has revealed associations between enterotype and long-term diet: the Bacteroides-dominant enterotype is prevalent in individuals whose diets are high in animal fat and protein, whereas the Prevotella-dominant enterotype prevails in individuals with high-carbohydrate diets.

    A microbiome is a multispecies community, in which each kind of bacteria has its own distinctive metabolic role. The entire bacterial is made up of different proportions of each bacterial genus. The "enterotypes" discussed here are defined by variation in the proportions of different bacterial genera.

    A visual depiction from the paper helps to show the three enterotypes in humans and chimpanzees. Each is characterized in a principal components plot, which reduces the proportions of dozens of bacterial types into two dimensions. This reduction is possible because the bacterial communities have covariance among species abundances -- when Dialister is common for example, Ruminococcus also tends to be common. The consistent association of some of the bacterial genera suggests that the community as a whole is regulated by the host gut and immune system factors.

    Bacterial enterotypes, after Moeller et al 2012

    Figure 1 from Moeller et al. 2012. Original caption: "(a) Assortment of gut microbial communities into enterotypes in chimpanzees and humans. Shown are BCA visualizations of enterotypes (coloured ellipses), as identified by PAM clustering, with black dots representing abundance distributions of bacterial genera from an individual host and numbered white rectangles marking the centre of each enterotype. Panel (right) showing human gut enterotypes modifed from Arumugam et al.1 Bacterial taxa uniquely overrepresented in the corresponding chimpanzee and human enterotypes are listed. (b) Relative abundances of the three bacterial taxa that are principally responsible for the separation of chimpanzee enterotypes. Shown are means, ranges and first and third quartiles. Colour coding of enterotypes follows that in (a)."

    The chimpanzees have the same associations among bacterial species as humans, which suggests that the ecology within the chimpanzee gut is regulated by similar factors. The paper makes it clear that the bacterial communities of chimpanzees and humans, despite the consistent similarity of enterotypes, do differ in many ways. There are some bacterial species that are common in chimpanzees that are rare in humans, or that are overrepresented in one chimpanzee enterotype without being similarly represented in the human equivalent. The paper does not provide evidence that the chimpanzee and human microbiomes have remained static from our common ancestors. Instead, it shows that there may be ecological factors or feedbacks that keep the variability within a trimodal dynamic.

    Another interesting aspect of the paper is that the bacterial enterotypes of chimpanzees are not stable within individuals. The authors examined the microbiomes in 2000, 2001, and 2008, finding that every individual changed from one enterotype to another during that period of time. The Gombe community did not change in a directional way, and no obvious factors explain the changes in enterotypes for individuals:

    As observed in humans, there is no obvious association between chimpanzee enterotype and host genetics or geography. When sampled in 2000, the siblings, Sandi and Shelton, and their mother, Sparrow, each possessed different enterotypes, and their enterotypes changed, and still differed, in later samplings. Meanwhile, three chimpanzees that are not all members of the same family or same geographic community (Darbee, Gremlin and Kris) harboured the same enterotypes at each of the three time points sampled. In humans, diet is likely to be a major contributor to a host’s enterotype2. As the availability of different foodstuffs in Gombe can fluctuate seasonally15, 16, diet may also influence the possession of certain chimpanzee enterotypes. However, we found no consistent association between enterotype and the season in which a host was sampled. Furthermore, all three enterotypes were present during each wet season when foods were abundant and the diets among the chimpanzee hosts were the most homogenous.

    All in all, I think this is a really fascinating study. The microbiome reveals something previously hidden, which may be important to dietary adaptations or immunity in hominoids generally. We might naturally assume that human microbiomes are products of very recent dietary innovations and rapid bacterial adaptation -- particularly among human agriculturalists. The chimpanzees may be showing that the important dynamics are much older than agriculture.

    References

    1. Moeller AH, Degnan PH, Pusey AE, Wilson ML, Hahn BH, Ochman H. Chimpanzees and humans harbour compositionally similar gut enterotypes. Nature Communications. 2012;3:1179.
    Tags: 
    microbiome
    gut
    coevolution
    chimpanzees
    diet
    immune
    Synopsis: 
    A higher-order comparison of the gut bacterial community shows that some aspects of human variation may be ancient

  • Population gut metagenomics

    Fri, 2012-05-11 08:37 -- John Hawks

    The new research by Tanya Yatsunenko and colleagues examining gut microbiomes in different human populations is just incredibly cool work [1]. I don't have time to write much about it this morning, but Ed Yong's report is an excellent place to start: "Three nations divided by common gut bacteria".

    The population genomics of these gut microbes is a great topic also, but what I find most interesting is the parallel ontogenetic changes among populations from infants to adults:

    The guts of babies are dominated by Bifidobacterium – the group that’s commonly found in probiotic foods. They’re also loaded with genes for producing folate, an essential B-vitamin that’s involved in creating and repairing DNA. These folate-making genes decline as babies grow up, and get more of the vitamin from their diets. At the same time, the genes for making other vitamins, like B1, B7 and especially B12, become more common. “This similarity across cultures in building up the gut microbiome in childhood has been touched on before but it’s much more convincing here,” says Peer Bork, from the European Molecular Biology Laboratory.

    Adam Van Arsdale also has written up some thoughts about the research: "The human gut microbiome".

    References

    1. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, et al. Human gut microbiome viewed across age and geography. Nature. 2012.
    Tags: 
    metagenomics
    diet
    gut
    microbiome
Subscribe to gut

Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.