Bacteria in colon (microbiome) more exception than rule in nature

One of the criticisms against Peat’s views that I most commonly hear is that his ideas on the pathogenicity of colon bacteria is plain wrong, and that having a vibrant microbiome is key to good health. I have been told by biologists that apparently the presence of a microbiome is the norm in mammals and, without it, we will be left without immune system – defenseless against evil pathogens all around us. Never mind the recent studies exposing such views as little more than wishful thinking. As the article below explains, a consistent presence of microbiome is more of an oddity in nature than a rule. Even in the species where it is present, the symbiotic relationship between a host and its microbiome seems to either depend on diet or on the bacteria performing a very feature- and time-specific vital function, without which the animal cannot survive. Our microbiome does NOT fit any of those requirements. We are not herbivorous, so one major reason (according to the studies discussed below) for having a microbiome is absent. The bacteria in our gut also do not perform any vital survival function, unlike in other species. There have been multiple studies on humans with sterilized guts demonstrating no ill-effects. To the contrary, recent studies have suggested that gut sterilization can treat “incurable” diseases.

As such, the totality of evidence seems to point to the current (wrong) ideas about the human microbiome being the result of the advocacy of a few persistent, loud voices who polluted the scientific literature back in the 1960s and 1970s when this topic was first beginning to emerge. Due to minority of scientists having the time/resources to oppose it, this assumption “that obligate, fixed and functional symbioses were universal” gradually became accepted as self-evident truth in the collective scientific mind. Interestingly, a very similar (but much more authoritarian) process engulfed medicine in the 20th century and managed to completely exclude the role of environment in human health. The dominant theory (wrong, again) that “won” due to the advocacy of vocal (and well-funded) proponents was that genes were the beginning and the end of the story of human health. As it seems, the evidence for yet another major assumption related to human physiology is wrong/fraudulent and needs to be discarded so that science can embark on a more truthful path.

“…To stay healthy, humans and some other animals rely on a complex community of bacteria in their guts. But research is starting to show that those partnerships might be more the exception than the rule.”

“…In some of those ant species, he saw “this amazing, dense, packed cloud. It was like a galaxy of microbes,” he said. “They’d explode in your eyes when you looked at them” under the microscope. Which is what you might expect to find, given the extent to which we and so many other animals depend on the trillions of bacterial cells that reside within us — for processing food that we can’t otherwise digest, for providing key nutrients, for training our immune system to act effectively against infections. The microbiome is so critical to our health and survival that some researchers even find it useful to think of animals as the sum of their microbial parts. But when Sanders turned to the rest of the ants — about two-thirds of the different colonies and species he had collected — he was surprised to find that “you would be hard-pressed to find any cells in the gut that you could readily identify as bacteria,” he said. Food, debris, the cells of the insects’ gut lining — all were present. Microbes that might be engaged in the symbiotic relationships we take for granted — not so much.”

“…In the early 20th century, biologists began to uncover fascinating relationships between complex organisms and their microbes: in tubeworms that had no mouth, anus or gut; in termites that fed on tough, woody plants; in cows whose grassy diet significantly lacked protein. Such observations generated excitement and prompted follow-up experiments. In those years, the absence of microbial helpers in an animal wasn’t considered particularly surprising or interesting, and it often received little more than a passing nod in the literature. Even when it was thought to merit more than that — as in a 1978 report in Science that tiny wood-eating crustaceans, unlike termites, had no stable population of gut bacteria — it ended up flying under the radar. And so expectations quietly began to shift to a new norm, that every animal had a relationship with bacteria without which it would perish. A few voices protested this oversimplification: As early as 1953, Paul Buchner, one of the founders of symbiosis research, wrote with exasperation about the notion that obligate, fixed and functional symbioses were universal. “Again and again there have been authors who insist that endosymbiosis is an elementary principle of all organisms,” he seethed. But counterexamples drowned in the flood of studies on the importance of host-microbe symbioses, especially those that drew connections between human health and our own microbiome.”

The human microbiome has completely driven a lot of our thinking about how microbes work,” said Tobin Hammer, a postdoctoral researcher in ecology and evolutionary biology at the University of Texas, Austin. “And we often project from ourselves outwards.”

“…A transient, almost nonexistent relationship with bacteria was what Sanders saw in his tropical ants. He brought his samples back to his lab (then at Harvard University, although he is now at Cornell), where he sequenced the insects’ bacterial DNA and quantified how many microbes were present. The ant species with dense, specialized microbiomes had approximately 10,000 times more bacteria in their guts than Sanders found in the many other species he had captured. Put another way, Sanders said, if the ants were scaled to human size, some would carry a pound of microbes within them (similar to what humans harbor), others a mere coffee bean’s worth. “It’s really a profound difference.”

That differencereported in Integrative & Comparative Biology in 2017, seemed to be associated with diet: Strictly herbivorous tree-dwelling ants were more likely to have an abundant microbiome, perhaps to make up for their protein-deficient diet; omnivorous and carnivorous ground-dwelling ants consumed more balanced meals and had negligible amounts of bacteria in their gut. Still, this pattern was inconsistent. Some of the herbivorous ants also lacked a microbiome. And the ants that did have one didn’t seem to have widespread, predictable associations with particular species of bacteria (although some sets of microbes were common to individual genera of the insects). That result marked a clear departure from mammalian microbiomes like our own, which tend to be very specific to their hosts.”

“..Repeated experiments that disrupted the butterflies’ microbial populations yielded no effect on the hosts’ growth or development. Neither did reintroducing the bacteria to their guts. “Really,” Agashe said, “they don’t seem to care about their microbes at all — even though the butterflies feed on toxic plants and seem like perfect candidates for a full-fledged, functional microbiome that could detoxify their meals. Like Hammer and Sanders, “initially we were scratching our heads,” Agashe said. “It was a surprising result, and actually it took us a while to wrap our heads around it.” But maybe it shouldn’t be so surprising. As the scientists realized, when microbiomes are present, they’re often found in specific tissues — and they involve specific bacteria that influence specific traits at specific times. The bobtail squid, for example, has a symbiosis that’s limited to one species of luminous bacteria, which is sequestered in a single light-producing organ while the squid’s gut and skin remain microbe-free. Adult honeybees have important relationships with their bacteria, but the larvae don’t. So it’s not such a leap to think there could be animals that don’t have such relationships at all, or that have relationships that play by different rules. “I think there’s now an increasing realization that there’s this whole spectrum of kinds of associations that you might find,” Agashe said. Hammer agreed. “We’re just getting a glimpse at the tip of the iceberg,” he said.”

“…Even in humans, she points out, the microbiome (including transient microbes) can shift with changes in diet or behavior. Studying living systems that don’t depend on a stable microbiome could help scientists disentangle the effects of those shifts. It could also allow them to better pinpoint the costs of having a microbiome and gain new insights into its evolution.”

“…Even among mammals, there’s diversity in how the microbiome presents itself. Although most mammalian species seem to associate predictably with specific bacteria, a recent study by Sanders and his colleagues found that bats do not. In fact, their microbiomes were more transient and random — and bore a far closer resemblance to the microbiomes of birds than to those of fellow mammals. The researchers posit that this difference might relate to an evolved need for both bats and birds to be as light as possible to enable powered flight. Perhaps they couldn’t afford to carry any additional baggage.”

“…“We need to keep our eyes and ears open,” he added. “There’s still a lot to learn from natural variation and diversity.””

Author: haidut