Humans have lived in caves and rock shelters for millions of years. Over time – long periods of time – the detritus of daily life mixed with sediments that blew in from the outside and the floor of the cave literally rose beneath their ancient feet, sealing below evidence of past activities. And if we are lucky, these sheltered homes stayed dry allowing organic remains to preserve until dug up and cataloged by archaeologist’s eons later.
This is precisely what happened in a series of caves and rock shelters in the Trans Pecos region of what is now west Texas. For nearly 10,000 years, this arid environment preserved an extraordinary record of sandals, baskets, bedding, food scraps, bones, wooden tools, weapons, and every organic fragment imaginable – and in some cases, the actual bodies of the inhabitants themselves. But perhaps the most interesting item preserved was their poo – that is, coprolites.
Coprolites can provide amazing insight into what our ancestors ate. Seeds, food fragments, tiny bones, fur, insects and so on can be, well, picked out of these ancient droppings. But since a majority of their (and your) stool is – by dry weight – made up of bacteria, then it’s also possible get a glimpse of the ancient microbiome (bacteria + their genes) of the person from which said coprolite came. Assuming you can control for contamination. By channeling our ancestors and their poo, we might get a better understanding of what microbes we may have lost or how our modern diet and lifestyle has shifted the composition of our gut microbiome in some not-so-good ways. And that’s what some researchers just did.
Writing in the journal PLOS, researchers looked at six coprolites from sites in the U.S., Mexico and South America. The two samples from the U.S. came from that Trans Pecos area of west Texas – specifically from deposits dating to around ~8,000 year ago; the two samples from South America came from the intestines of an intact ~1,600 year old mummy (yup, last meals still inside so to speak); and the two samples from Mexico came from a ~1,400 year old sealed deposit at a site called Cueva de los Chiquitos Muerto – which translates as ‘cave of the dead kids.’ For comparison (and fun), they also compared these ancient samples to some previous data on Ötzi the Iceman and an Austrian soldier killed and frozen in a glacier in 1918.
After some special handling and processing, DNA was extracted from the sample and referenced to gene databases – allowing for the taxonomic identification of the microbes present in the ancient samples. The figure below shows the various archaeological sites and the bacterial diversity of each sample (at the higher phyla level).
In short, the samples from South America (Caserones) and west Texas (Hinds Cave) were a bust. That is, we know the modern gut microbiome across the world – regardless of geographic region, age, gender, etc – looks different than the microbiome of soil microbes which further looks different than the gut microbiome of non human primates, like chimpanzees. When the researchers tallied the microbes for the two samples from Caserones (South America), a few bacteria dominated and very little diversity – a hallmark of the human gut microbiome – existed. The researchers suspect that since the samples were derived from an actual mummy, the results may be “explained by the post-mortem gut serving as an organic bioreactor filled with carbon and nitrogen from decaying organic matter.” They even suggested the samples looked more like microbial communities from your run of the mill compost pile.
As for the west Texas samples, post-depositional contamination by surrounding sediment and who knows what else altered them beyond recognition as being derived from a human gut. Interestingly, something the authors didn’t discuss in the paper, is the presence of Actinobacteria (the blue wedge on the pie chart). This particular group (phyla) of bacteria contains species that are known to thrive on inulin-type fructans that are abundant in desert succulents like agave and were consumed in large quantities by these arid region hunter-gatherers. Inulin-type fructans, if you will recall, are potent prebiotics known to selectively stimulate Bifidobacterium and other healthful lactic acid bacteria. Though the west Texas samples were highly contaminated, the presence of Actinobacteria may suggest some remnants of the original – and ancestral – gut microbiome remained.
But the most interesting results were obtained from the two samples from El Zape in Mexico. When the diversity of bacteria in each of these samples was matched against known human gut microbiome samples from modern populations, the researchers were stunned to find they exhibited a gut microbiome signature similar to one identified from children in a rural African village in Burkina Faso. In addition, the El Zape samples “harbored similarities to non human primate gut.” And if that wasn’t enough, they also matched more closely with Ötzi the Iceman, our frozen Austrian soldier, and with rural populations in Malawi and South America than they did with gut microbiomes from folks living in the U.S. today. In one final note, one of the samples from El Zape (ZA23) also contained Bifidobacterium breve, a species known to occur almost exclusively in breastfed infants (remember, this was the ‘cave of the dead kids’ after all). The presence of B. breve suggests that this sample almost certainly came from an infant. (Note also this sample ‘kinda’ matched some infant microbiomes from the US – but only slightly).
What’s emerging from studies of ancient poo and sampling among rural populations in places like Africa and South America is a glimpse at our ancient – and what might be our preferred or target – gut microbiome for optimal health and wellness. These ancient and rural populations carried/carry in their guts bacterial species that are all but missing from our modern gut. With names like Butyrivibrio, Treponema and Xylanibacter you would hardly know they were missing. Like the once mighty gastric inhabitant H. pylori and the numerous intestinal parasites of our ancestral past – who trained and educated our immune system – they are or have totally disappeared.
In the case of H. pylori and intestinal worms, their disappearance and others like them, are ‘likely’ sitting at the root (along with the removal of dirt and its associated organisms from our modern life) of our immune dysfunction (allergies and autoimmune disease). The disappearance of our rural or ancient bugs, like those still teaming in some guts in Africa, may have provided services – ecological services that is – that we are only beginning to know we are missing. In these case of the microbes mentioned above, their known ability to assist in the degradation of plant matter – and thus the production of beneficial short chain fatty acids in the process – may be contributing to our epidemic of reduced pathogen resistance and gut permeability (think leaky gut) in their absence. When the gut leaks, bad things happen, the least of which is increased inflammation that is linked to obesity and type 2 diabetes and likely many other metabolic disorders. (Join American Gut project to see what’s in your gut)
So when we hear about those studies that talk about how second and third generation immigrants in a new land suffer from diseases unknown to their parents and grandparents – and fast food and diet in general are blamed – we might also want to ask if their gut microbiome is missing some important ‘old friends.’ Has their birth in a new land – presumably one that is less wormy and less likely to promote the transfer of ancestral microbes between family members – shifted their gut microbiome just enough to invite some truly human-made diseases.