{"id":1038,"date":"2020-04-22T14:38:12","date_gmt":"2020-04-22T18:38:12","guid":{"rendered":"http:\/\/haidut.me\/?p=1038"},"modified":"2020-04-22T14:38:12","modified_gmt":"2020-04-22T18:38:12","slug":"bacteria-in-colon-microbiome-more-exception-than-rule-in-nature","status":"publish","type":"post","link":"https:\/\/haidut.me\/?p=1038","title":{"rendered":"Bacteria in colon (microbiome) more exception than rule in nature"},"content":{"rendered":"

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<\/a>. 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<\/strong><\/span> function, without which the animal cannot survive. Our microbiome does NOT fit any of those requirements<\/strong><\/span>. 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<\/a>.<\/p>\n

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<\/em><\/span> “that obligate, fixed and functional symbioses were universal<\/strong>” 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.<\/p>\n

https:\/\/science.sciencemag.org\/content\/200\/4346\/1157<\/a><\/p>\n

https:\/\/academic.oup.com\/icb\/article\/57\/4\/705\/4049474<\/a><\/p>\n

https:\/\/mbio.asm.org\/content\/11\/1\/e02901-19<\/a><\/p>\n

https:\/\/www.quantamagazine.org\/why-is-the-microbiome-important-in-some-animals-but-not-others-20200414\/<\/a><\/p>\n

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

“…In some of those ant species, he saw \u201cthis amazing, dense, packed cloud. It was like a galaxy of microbes<\/strong>,\u201d he said. \u201cThey\u2019d explode in your eyes when you looked at them\u201d 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 \u2014 for processing food that we can\u2019t 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\u00a0the sum of their microbial parts<\/a>. But when Sanders turned to the rest of the ants \u2014 about two-thirds of the different colonies <\/strong>and species he had collected \u2014 he was surprised to find that \u201cyou would be hard-pressed to find any cells in the gut that you could readily identify as bacteria<\/strong>,\u201d he said. Food, debris, the cells of the insects\u2019 gut lining \u2014 all were present. Microbes<\/span> that might be engaged in the symbiotic relationships we take for granted \u2014 not so much<\/span><\/strong>.”<\/p>\n

“…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\u2019t 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 \u2014 as in\u00a0a 1978 report in\u00a0<\/a>Science<\/em><\/a> that tiny wood-eating crustaceans, unlike termites, had no stable population of gut bacteria \u2014 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<\/span><\/strong>: 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<\/strong><\/span>. \u201cAgain and again there have been authors who insist that endosymbiosis is an elementary principle of all organisms<\/strong>,\u201d 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.”<\/p>\n

\u201cThe human microbiome has completely driven a lot of our thinking about how microbes work<\/strong><\/span>,\u201d said\u00a0Tobin Hammer<\/a>, a postdoctoral researcher in ecology and evolutionary biology at the University of Texas, Austin. \u201cAnd we often project from ourselves outwards<\/strong><\/span>.\u201d<\/p>\n

“…A transient, almost nonexistent relationship with bacteria was what Sanders saw in his tropical ants<\/strong>. He brought his samples back to his lab (then at Harvard University, although he is now at Cornell), where he sequenced the insects\u2019 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\u2019s worth<\/strong>. \u201cIt\u2019s really a profound difference.\u201d<\/p>\n

That difference<\/strong><\/span>,\u00a0reported in\u00a0<\/a>Integrative & Comparative Biology<\/em><\/a> in 2017, seemed to be associated with diet<\/strong>: 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<\/span><\/strong>. Some of the herbivorous ants also lacked a microbiome. And the ants that did have one didn\u2019t 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.”<\/p>\n

“..Repeated experiments that\u00a0disrupted the butterflies\u2019 microbial populations<\/a> yielded no effect on the hosts\u2019 growth or development. Neither did reintroducing the bacteria to their guts. \u201cReally,\u201d Agashe said, \u201cthey don\u2019t seem to care about their microbes at all<\/span>\u201d<\/strong> \u2014 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, \u201cinitially we were scratching our heads,\u201d Agashe said. \u201cIt was a surprising result, and actually it took us a while to wrap our heads around it.\u201d But maybe it shouldn\u2019t be so surprising. As the scientists realized, when microbiomes are present, they\u2019re often found in specific tissues \u2014 and they involve specific bacteria that influence specific traits at specific times<\/strong><\/span>. The bobtail squid, for example, has a symbiosis that\u2019s\u00a0limited to one species of luminous bacteria<\/a>, which is sequestered in a single light-producing organ while the squid\u2019s gut and skin remain microbe-free. Adult honeybees have important relationships with their bacteria, but the larvae don\u2019t. So it\u2019s not such a leap to think there could be animals that don\u2019t have such relationships at all<\/strong>, or that have relationships that play by different rules. \u201cI think there\u2019s now an increasing realization that there\u2019s this whole spectrum of kinds of associations that you might find<\/strong>,\u201d Agashe said. Hammer agreed. \u201cWe\u2019re just getting a glimpse at the tip of the iceberg,\u201d he said.”<\/p>\n

“…Even in humans, she points out, the microbiome (including transient microbes) can shift with changes in diet or behavior<\/strong><\/span>. Studying living systems that don\u2019t 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<\/strong> and gain new insights into its evolution.”<\/p>\n

“…Even among mammals, there\u2019s diversity in how the microbiome<\/span> presents itself. Although most mammalian species seem to associate predictably with specific bacteria, a recent study by Sanders and his colleagues<\/a> found that bats do not<\/span><\/strong>. In fact, their microbiomes were more transient and random \u2014 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\u2019t afford to carry any additional baggage.”<\/p>\n

“…\u201cWe need to keep our eyes and ears open<\/strong>,\u201d he added. \u201cThere\u2019s still a lot to learn from natural variation and diversity.\u201d”<\/p>\n","protected":false},"excerpt":{"rendered":"

One of the criticisms against Peat’s views that I most commonly hear is that his ideas on…<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[2],"tags":[1225,105,56,1223,1226,106,1224,615],"class_list":["post-1038","post","type-post","status-publish","format-standard","hentry","category-science","tag-assumption","tag-bacteria","tag-colon","tag-exception","tag-fraudulent","tag-microbiome","tag-pathogenic","tag-wrong","wpcat-2-id"],"_links":{"self":[{"href":"https:\/\/haidut.me\/index.php?rest_route=\/wp\/v2\/posts\/1038","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/haidut.me\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/haidut.me\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/haidut.me\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/haidut.me\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1038"}],"version-history":[{"count":1,"href":"https:\/\/haidut.me\/index.php?rest_route=\/wp\/v2\/posts\/1038\/revisions"}],"predecessor-version":[{"id":1039,"href":"https:\/\/haidut.me\/index.php?rest_route=\/wp\/v2\/posts\/1038\/revisions\/1039"}],"wp:attachment":[{"href":"https:\/\/haidut.me\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1038"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/haidut.me\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1038"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/haidut.me\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1038"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}