It has long been known that humans have a very acidic stomach but some will be surprised to learn just how acidic it is - as acidic as other carnivores and scavengers.

The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome - DeAnna E. Beasley , Amanda M. Koltz, Joanna E. Lambert, Noah Fierer, Rob R. Dunn Published: July 29, 2015

Gastric acidity is likely a key factor shaping the diversity and composition of microbial communities found in the vertebrate gut. The study conducted a systematic review to test the hypothesis that a key role of the vertebrate stomach is to maintain the gut microbial community by filtering out novel microbial taxa before they pass into the intestines. The study proposes that species feeding either on carrion or on organisms that are close phylogenetic relatives should require the most restrictive filter (measured as high stomach acidity) as protection from foreign microbes. Conversely, species feeding on a lower trophic level or on food that is distantly related to them (e.g. herbivores) should require the least restrictive filter, as the risk of pathogen exposure is lower. Comparisons of stomach acidity across trophic groups in mammal and bird taxa show that scavengers and carnivores have significantly higher stomach acidities compared to herbivores or carnivores feeding on phylogenetically distant prey such as insects or fish. In addition, the study found when stomach acidity varies within species either naturally (with age) or in treatments such as bariatric surgery, the effects on gut bacterial pathogens and communities are in line with our hypothesis that the stomach acts as an ecological filter. Together these results highlight the importance of including measurements of gastric pH when investigating gut microbial dynamics within and across species.

Because maintaining an acidic pH environment is costly, acidic stomachs should be present primarily in those cases where it is adaptive (or where it was adaptive in a recent ancestor). The cost of stomach acidity is twofold. The host must invest significant energy for both acid production and protecting the stomach from acid-related damage [17]. In addition, the acidity of the stomach may preclude, or at least make more difficult, chance acquisition of beneficial microbes. At the opposite extreme are those specialized herbivores in which stomach morphology is derived to include an alkaline chamber (forestomach or pre-saccus) that house microbes critical for fermenting a plant diet [18–22]. In these animals, an acidic stomach is not only of limited value (because the risk of foodborne pathogens in plant material is low), it may also remove those microbes that aid in the breakdown of plant material. Broadly then, we expect stomach acidity to mirror animal diets in ways that reflect pathogen risk. We expect that animals feeding on carrion will have the most restrictive filter, i.e. higher stomach acidity. Carrion has the potential to sustain high pathogen loads because the dead host’s body has stopped suppressing bacterial growth. Similarly, carnivores and omnivores would be expected to have higher stomach acidities than herbivores with specialized fermenting forestomachs because pathogens found in prey are more likely to be capable of infecting the predator than plant-associated microbes [23]. However, we would also expect the acidity of the carnivore and omnivore stomach to also depend on the phylogenetic distance between predator and prey. Pathogens are far more likely to be able to infect related hosts [23], such that a bird consuming an insect should face a lower risk of a foodborne infection than a bird consuming a bird. To test these hypotheses, we compare the stomach acidity of mammals and birds across a diversity of diet types.

In light of the results, we then revisit the ecology of the human stomach, its role as a filter and the likely consequences of this role within the context of modern human lifestyles and medical interventions. If stomach acidity acts as a strong filter, we expect that when acidity levels are reduced, the influence of diet-associated microbes on the intestinal microbiota will be greater. It is known that stomach acidity decreases with age and as a consequence of some medical treatments [24–26]. Thus, as acidity decreases and the filter’s effectiveness is reduced, we would expect to see increases in both the diversity of microbial lineages and pathogen loads in the gut. We also expect that animals, such as humans, with very acidic filters should be particularly predisposed to negative consequences of the loss of gut symbionts because the odds of chance re-colonization are low.

Based on the available data, our analysis illustrates a general pattern in which species feeding on carrion and animals have significantly higher stomach acidities compared to species feeding on insects, leaves, or fruit. On their own, the patterns are in line with the hypothesis that one role of the stomach is to inhibit microbial entry into the gut, though these patterns might also be explained by other phenomena. Carnivores need more acidic stomachs in order to lyse the protein in their meat-based diets. For example, secretion of pepsinogen and its activation to pepsis in the stomach is modulated by an acid pH (2–4) [30]. Also, activity of proteases in a simple acid stomach depends on an acidic environment (pH 2–4) [31]. However, while this might explain differences between predators and herbivores, it does not account for the very high acidity in the stomachs of scavengers, especially considering that the meat consumed by scavengers is not likely to be much harder to digest than that of predators. We suggest that these scavengers rely on the high acidity of their stomach to prevent colonization of their guts by foodborne pathogens [32]. Omnivores and piscivores were most variable in stomach acidities, which is to be expected as both diets differ greatly from species to species. Insectivores may use diverse means to digest insect chitin, with acidity playing a role in some but not other cases.

Human evolution and stomach pH

It is interesting to note that humans, uniquely among the primates so far considered, appear to have stomach pH values more akin to those of carrion feeders than to those of most carnivores and omnivores. In the absence of good data on the pH of other hominoids, it is difficult to predict when such an acidic environment evolved. Baboons (Papio spp) have been argued to exhibit the most human–like of feeding and foraging strategies in terms of eclectic omnivory, but their stomachs–while considered generally acidic (pH = 3.7)–do not exhibit the extremely low pH seen in modern humans (pH = 1.5) [38]. One explanation for such acidity may be that carrion feeding was more important in humans (and more generally hominin) evolution than currently considered to be the case (although see [39]). Alternatively, in light of the number of fecal-oral pathogens that infect and kill humans, selection may have favored high stomach acidity, independent of diet, because of its role in pathogen prevention.

The special risk to juvenile and elderly humans

If, in carnivores and carrion-feeders, the stomach’s role is to act as an ecological filter then we would also expect to see higher microbial diversity and pathogen loads in cases where stomach pH is higher. We see evidence of this in age-related changes in the stomach. Baseline stomach lumen pH in humans is approximately 1.5 (Table 1). However, premature infants have less acidic stomachs (pH > 4) and are susceptibility to enteric infections [40]. Similarly, the elderly show relatively low stomach acidity ([41], pH 6.6 in 80% of study participants) and are prone to bacterial infections in the stomach and gut [42]. It is important to note that these differences may be related to differences in the strength of the immune system however we argue here that the stomach needs more consideration when studying these patterns.

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Comparison of the gastrointestinal anatomy, physiology, and biochemistry of humans and commonly used laboratory animals (ePDF)

The gastric acid and fluid secretion rates, gastric volume, and pH values for humans, beagle dogs, pigs, and Rhesus monkeys are given in Table 4. In dogs, the gastric acid secretion rate at the basal state is low. Therefore, the stomach pH of the dog can be as high as its duodenal contents in the unstimulated state.I9 Following stimulation (i.e., food, histamine), gastric acid secretion rates in dogs exceed those of the human and pig (Table 4). In humans, the stomach pH after food is initially higher due to the strong buffering action of food. However, the pH returns to a low value after about one hour (Table 4).

The Internal, External and Extended Microbiomes of Hominins

We hypothesize that the stomachs of chimpanzees are likely somewhat acidic, but less so than those of humans. We also propose that the extreme acidity of human stomachs evolved after our split with the LCA with chimpanzees. If this is the case, it raises the question of what factors favored such acidity. One possible explanation is scavenging prey items abandoned by carnivores and/or the consumption of prey items too big to eat all at once. Chimpanzees in all habitats where they are found in the wild eat meat (Moore et al., 2017), as do bonobos (Wakefield et al., 2019), leading many to think that the LCA did as well. Sometimes the meat chimpanzees consumed Is scavenged (Nakamura et al., 2019) but relatively rarely (compared to other foods in their diet). More often the meat is eaten fresh from kills, though chimpanzees exhibit great variability between communities in success, technique, and seasonality of hunting behavior (Moore et al., 2017; Figure 2). Given that several chimpanzee communities target mammalian prey, and may do so using tools (Pruetz and Bertolani, 2007; Nakamura and Itoh, 2008), it is likely that species of Australopithecus, Homo habilis or Homo erectus also targeted and consumed meat, but also that how much meat they consumed, how fresh the meat was and how much was excess varied. While there is broad consensus among paleoanthropologists and evolutionary anthropologists that meat-eating played a role in the evolution of Homo, the relative importance of hunted and scavenged meat is contested. At least some of the meat that early hominins were eating was carrion (Pante et al., 2018). Some bones, for example, from the time during which H. erectus was extant, show evidence both of cut marks by stone tools and, in a layer beneath the cuts from those tools, tooth marks from hyenas (Blumenschine, 1995). The obvious inference is that such bones were scavenged by our ancestors after being killed by another mammal (maybe hyena, maybe something else). Any hominins that scavenged for prey before the advent of fire may have avoided food borne pathogens if their stomachs were acidic. As a result, it is possible that the acidity of the hominin stomach may have played a role in human foraging behavior and diet. That said, we note that the question of how much hominins scavenged, and how central it was to social evolution, is the subject of intense debate (Dominguez-Rodrigo and Pickering, 2017). An alternate (but not mutually exclusive) hypothesis is that acidic stomachs became advantageous once our ancestors began to hunt large prey. This might be expected if the meat from such a prey items was often more than could be eaten in a sitting such that meat was eaten later (after it had begun to rot) even though it had not been scavenged.