Play along for a moment.
The year is 2015 and all hell has broken loose. You’re part of a small band of people wondering the post-apocalyptic streets of downtown Atlanta – staying one step ahead of the flesh-eating “walkers.” If spending all day trying to avoid being infected or possibly eaten by a zombie wasn’t bad enough, months on the run drinking iffy water and eating what you could scrounge, have taken its toll on your gut – or at least you thought. You are doubled-over most of the time, and good day is measured by your ability to keep the tiniest nibble of food in your gut. You’re wasting away.
As luck would have it, your small band finds itself standing outside an unassuming building among a sea of unassuming buildings slung across a sprawling campus on the outskirts of Atlanta. Ground zero – you have found the Centers for Disease Control and its Primate Biomedical Research Center – aka chimp asylum. After some discussion, sympathetic researchers inside grant you entrance.
If government employees who specialize in the world’s nastiest infectious diseases know how to do anything, that’s how to hunker down during a zombie apocalypse. Completely self-contained with their own water supply and electricity – and a pile of shelf stable food – the group of a dozen researchers could probably make it a few years if need be – or however long it takes Will Smith and Bruce Willis to solve this little zombie problem.
Amid the various offices and laboratories in the building, are rows of caged chimpanzees “participating” in biomedical research. Throughout the zombie ordeal, the researchers have dutifully cared for the animals, continuing daily feeding and medications. Amazingly, in the center of the building sits a lush, park-like enclosure half the size of a football field. Amongst the trees and dense tropical-like foliage, maintained with mechanically controlled humidity and rainfall, are two-dozen common chimpanzees (Pan troglodytes) roaming about eating familiar foods. This recent population had been captured near Gombe in Tanzania and had arrived at the CDC days before the zombie invasion and had not transitioned into the biomedical program – yet.
One of your new hosts notices that you are ill and inquiries as to your problem (seems your two visits to the bathroom in one hour gave you away). After listening to you recount your symptoms, one of the researchers who had gathered with the others to hear your story suggests you might have a nasty bug, possibly even Clostridium difficile – or C Diff. He inquiries if you had been recently hospitalized or taken broad-spectrum antibiotics – either of which, or a combination of, could be contributing to your problem. Turns out, days before the apocalypse you had some minor surgery at a local hospital and indeed had taken several courses of antibiotics.
As the days wore on at the chimp asylum, your frequent visits to the bathroom had only gotten worse – even after the researchers had given you more antibiotics. The antibiotics in fact, had made things worse. One of the researchers, who was a microbiologist tasked with screening stool samples from new chimps arriving from the “wild” for problematic viruses and pathogens using metagenomic tools, suggested you might consider a fecal transplant.
As the name implies, a fecal transplant is just that – following a high volume enema deep into your colon from the business end of your GI tract to clean things out, a small sample of a donor stool from a presumably healthy individual is inserted (nasogastric tube from the top end is used in some instances – more of a European thing). The donor sample, teeming with trillions of presumably healthy bacterial cells, then sets up shop in your colon and reinstates balance in an ecosystem sent into a tailspin by an opportunistic pathogen(s) that bloomed following a perturbation – presumably from the scorched earth effect of said broad-spectrum antibiotic. By doing a number on the diversity and abundance of microbes in your gut – both friend and foe and everything in between – broad-spectrum antibiotics have the potential to significantly shift the composition of your gut microbial community and provide opportunities for low abundance pathogens to rise up. As mounting research suggests, fecal transplants are impressively effective in solving recurrent C. diff infections – one such opportunistic pathogen.
Given your current state – and the researchers explanation of the procedure, along with his assurance he could pull it off, and the evidence to support its potential success in solving your problem – the only question remaining is who the donor would be. More to the point, how do you define a healthy gut microbiome in a potential donor – especially among a rag tag bunch of apocalyptic survivors just trying to make it to the next day? Do you pick the old guy, the 20-something female you been traveling with, or maybe her 14-year old little brother? The Mexican guy looks healthy, but so does the Asian couple – though he’s a bit on the heavy side. But does that even matter? What about the researchers? A mixed bag of gender, age, body-type, race, and attitude – maybe one of them would be suitable?
Maybe you could ask the potential donors for a sample of test poo for the microbiologist to evaluate, you’re in a biomedical research facility after all. The prescreening of samples with high-throughput sequencing technology would provide a snapshot of the microbes in the guts of your comrades and allow you to weed out any obvious bad donors based on any nasty bugs they may be carrying. But alas, while the researcher has all the equipment to pull this off, they had run out of some critical supplies just before the coming of the “walkers” and had not been resupplied. Prescreening was out.
As you scan over the faces and bellies of your potential donors, the doe-eyed primate handler blurts out, “what about one of the chimps that just came in from Tanzania?” A little taken back at first, you press your face to the glass of the football field-sized jungle enclosure and consider the possibility.
Even though we differ in some aspects of appearance and behavior, humans share 99% of the same DNA with common chimpanzees (and about the same with their close cousins the bonobo it turns out). And when you consider that some of those DNA differences are responsible for things like hair and sensory perception and having nothing to do with diet and immunity (and microbes), we are even more similar than that 99% figure suggests.
Short of the tranquilizer shot into their rump back in Tanzania, the chimps in the jungle enclosure had not been exposed to any medication or funky monkey chow fed to the chimps already enrolled in the biomedical program. To ease the transition into western life and biomedical research, they were enjoying (as much as a captive chimp could) familiar foods and vegetation in the enclosure. They were as close to pure or untainted as any chimp could be in Atlanta – or anywhere in the US for that matter. And lucky for you, the first thing the microbiologist did when the new batch of chimps arrived, was to collect stool samples and analyzed them – no nasty viruses, nothing out of the ordinary. Pure, unadulterated monkey poo from the birthplace of humanity – East Africa.
You weigh the pros and cons. As with humans, 80-90% of all the bacteria in the chimp gut belong to the major phyla of Firmicutes or Bacteroidetes. As with chimps, humans have simple guts and like other mammalian fermenters, our gut microbes are necessary to break down and release sugars from plant polysaccharides. We are also omnivores – in that we eat plants and animals – so too, are chimps. In fact, the chimps currently in jungle asylum are from the Gombe region of Tanzania, made famous by Jane Goodall. Like all chimps, the Gombe chimps hunt and kill other animals including bushpig, bushbuck, rodents, birds, baboons, and even other chimpanzees (and the occasional human infant). But at the top of the menu are the abundant red colobus monkeys. Though the amount of hunting and meat consumption among chimp communities throughout Africa varies based on habitat and access to prey (and from season to season), it can reach staggering levels. During one season in 1992, the chimp community at Gombe (45 individuals) successfully killed more than 1,300 pounds of red colobus, bushpigs, and bushbucks – which included more than 100 red colobus monkeys. Given the researchers are unable to witness every hunt, the estimates for 1992 are thought to be much higher.
As pointed out by anthropologist and primate researcher Craig Stanford, “The percentage of the chimpanzee diet that is meat is therefore quite substantial and approaches the figures for the low end of the range of some human foragers.” On top of that, in the west-African country of Senegal, savannah chimps are known to fashion sticks into spears to hunt and kill small, nocturnal bushbabies. Good heavens, a Charlton Heston-like nightmare come true!
Even below the phylum level, we share many of the same genus level bacteria with chimps as well including bacteroides, prevotella, faeocalbacterium, dialester, bifidobacterium, ruminococcus and so on. Though there are differences in human-chimp immunity associated with susceptibility to infectious diseases, chimps and humans share the same adaptive immunity, which tolerates the presence of select gut microbial communities and is rooted deep in our shared evolutionary past.
The variability in the gut microbes of humans is tremendous – people from Malawi don’t look much like people from the U.S., kids in Burkina Faso looked different than kids from Italy, and while you might share 99.9% of the DNA with your neighbor down the street, your gut microbiomes can be as much as 80-90% unique. In other words, as the Human Microbiome Project and others teach us that genetics can contribute to the shaping the composition of your gut microbiota, environmental factors such as diet and lifestyle play a significant role. That said, while there are differences in the gut microbiota of chimps and humans, geography, diet and lifestyle may be contributing to those differences – more so than underlying genetics, which we share more or less anyway.
So, who shall your poo donor be? Among the human choices, you have to give serious thought to the inescapable fact that every single person standing before you was born and raised in a world of medications, chlorinated water, antibiotics, chemicals, and funky and weird diets unknown to our ancestors and their microbes. As westerners, we spend 90% of our time inside our homes, offices, and cars – walled off from the natural world and its diverse metacommunity of microbes. By reducing our exposure to the terra firma of nature and its microbes, and carpet-bombing our guts with medications and monotonous diets by evolutionary standards, we likely harbor a less diverse and thus less resilient gut microbiome of any generation in human history. All of us, every last one of us, are in varying stages of gut dysbiosis. In fact, we may be so compromised as a generation that any attempt to model a normal or optimal gut microbiome from our ranks would be a fool’s errand.
Months hunkering down or on the run from the zombie hoards appears to be taking its toll on the group as a whole, further calling into question the appropriateness of any of these humans as a potential donor. Your choice might (should) start becoming easier. I also put this question of healthy chimp versus sick human to Jonathan Eisen, a microbiologist who works on the ecology and evolution of microbial communities at UC-Davis. Though in our e-mail exchange we didn’t define what sick was in a human or how one defines healthy in chimp, his conclusion was, nevertheless:
“Given the incredibly close relationship we have with chimps I think it is reasonable to hypothesize that a healthy person might have more similarities in the microbiome with a health chimp than with a sick person. And therefore I would choose to get my FT [Fecal Transplant] if I needed it from a chimp rather than from a sick person.”
So next time you are at the zoo, maybe one that houses chimps just off the boat from Africa that have not been westernized in anyway (not that is realistic in the real world), and you find yourself on the receiving end of some poo flying your way, you might catch a little and take it home and pop it the freezer. You never know when the zombie apocalypse might hit.
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