The gut microbiome, stomach acidity, sloths, and you.
In recent years we’ve seen an explosion in the research on the importance of the collection of trillions of bacteria, viruses, and fungi living in the human body, collectively known as the microbiome. We now know that a vast array of health conditions such as obesity, mood disorders, type 2 diabetes, and autoimmune disease are at least in part associated with imbalances in the microbiome, leading researchers and healthcare providers to consider the causes of microbial imbalances. The more we learn about the microbiome, the more the factors that may influence it become evident or further refined. This include dietary choices, age, regional location,, race, maternal microbiome and type of infant birth (namely vaginal vs. C-section), among other things. Even medications without distinct effects on the gastrointestinal system such as statins and antidepressants have been shown to affect the gut microbiome.
One factor worth carefully considering is that of stomach acid, which we now know plays a critical role in determining what kinds of microbes live in our bodies, and in what quantities. Stomach acid is necessary for the role it plays in digestion, but also to protect us from gastrointestinal infection. An acidic environment is necessary to denature proteins, that is, to allow the protein structure to relax so it can be further degraded by enzymes in subsequent phases of digestion. The infectious microbes that we potentially encounter in the foods we consume or in other activities leading to exposure also are killed when exposed to the acidic environment of the stomach.
The infectious microbes that we potentially encounter in the foods we consume or in other activities leading to exposure also are killed when exposed to the acidic environment of the stomach.
Stomach acid levels are dramatically variable, particularly with age and medication use. In an investigation of the stomach acid level of healthy elderly people, it was found that 12 of 15 (80%) individuals ranging in age from 80 to 91 years old had low stomach acid levels, with an average pH of 6.6. Stomach acidity also can be affected by medications, in particular those which are prescribed to for this purpose like antacids. Unfortunately, many individuals end up on these medications for a longer period of time than their intended use.
Interspecies differences in stomach acidity
From an evolutionary perspective, stomach acid secretion also may be related to diet. One way to understand the evolution of stomach acidity is to look at the variation between different species, and how stomach acidity is related to dietary choices. Mammals and birds that are herbivores (vegans) have a lower risk of infection, and also rely upon certain microbes (which would be killed by an acidic environment) to help breakdown and ferment the plant fibers from their diet. On the opposite end of the spectrum, mammals and birds that feed on the decaying flesh of animals are at a high risk of being exposed to pathogens in the food they consume.
Surveying many species these concepts were found to hold true – birds which are scavengers and almost exclusively fed on carrion such as the turkey vulture, buzzard, and red-tailed hawk had very low stomach pH (< 2) (higher acidity) whereas the species which were herbivores, particularly the foregut fermenters such as the colobus monkey, sheep, llama, and the sloth had a much higher average pH (around 6). The stomach acidity of omnivores, such as humans, baboons, and some monkeys, came in at an average of about 2.5. Interestingly, the sloth was found to have the highest stomach pH of 7.4, perhaps reflecting the low energy which is exerted by the sloth’s physiology overall.
(Fun fact: the sloth, being a very unique creature, also has a very slow fermentation rate and a gastric transit time of 150 hours, with a significantly greater percentage of weight attributed to the gut than other similarly sized animals.)
Stomach acidity and microbiota diversity
One might think that humans with less acidic stomachs would have greater microbial diversity. After all, they lack the acid needed to degrade microbes, so it would make sense that more microbes would survive in the stomachs of those with lower acidity, and those microbes would then pass on to other parts of the gastrointestinal tract.
A decrease in microbial diversity has been noted in stool samples collected from individuals on proton-pump inhibiting medications.
However, in actuality, we see the opposite of this in settings where stomach acidity is reduced through the use of acid-suppressing medications. A decrease in microbial diversity has been noted in stool samples collected from individuals on proton-pump inhibiting medications. The change in microbial composition seen in these individuals may furthermore predispose them to development of Clostridium difficile (“C-diff”) infection, a hard to treat and potentially life-threatening condition., With the significant amount of people who are on proton-pump inhibitors long term, and a continuously larger aging population, the impact of stomach acidity on health begs further study for greater understanding. But one thing is clear: when it comes to microbial balance in humans, stomach acid is a good thing.
Click here to see References
 Bouter KE, et al. Role of the Gut Microbiome in the Pathogenesis of Obesity and Obesity-Related Metabolic Dysfunction. Gastroenterology. 2017 Feb 9.
 Foster JA, McVey Neufeld KA. Gut-brain axis: how the microbiome influences anxiety and depression. Trends Neurosci. 2013 May;36(5):305-12.
 Long J, et al. Association of oral microbiome with type 2 diabetes risk. J Periodontal Res. 2017 Feb 8.
 Chen B, et al. Integration of microbiome and epigenome to decipher the pathogenesis of autoimmune diseases. J Autoimmun. 2017 Mar 23.
 Sheflin AM, et al. Linking dietary patterns with gut microbial composition and function. Gut Microbes. 2016 Dec 14:1-17.
 Jeffery IB, et al. Composition and temporal stability of the gut microbiota in older persons. ISME J. 2016 Jan;10(1):170-82.
 Laursen MF, et al. First Foods and Gut Microbes. Front Microbiol. 2017 Mar 6;8:356.
 O’Keefe SJ, et al. Fat, fibre and cancer risk in African Americans and rural Africans. Nat Commun. 2015 Apr 28;6:6342.
 Hester CM, et al. Fecal microbes, short chain fatty acids, and colorectal cancer across racial/ethnic groups. World J Gastroenterol. 2015 Mar 7;21(9):2759-69.
 Power ML, et al. Reproductive Microbiomes. Reprod Sci. 2017 Jan 1:1933719117698577.
 Rutayisire E, et al. The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants’ life: a systematic review. BMC Gastroenterol. 2016 Jul 30;16(1):86.
 Imhann F, et al. The influence of proton pump inhibitors and other commonly used medication on the gut microbiota. Gut Microbes. 2017 Jan 24:1-8.
 Silk DB, et al. Protein digestion and amino acid and peptide absorption. Proc Nutr Soc. 1985 Feb;44(1):63-72.
 Martinsen TC, et al. Gastric juice: a barrier against infectious diseases. Basic Clin Pharmacol Toxicol. 2005 Feb;96(2):94-102.
 Husebye E, et al. Fasting hypochlorhydria with gram positive gastric flora is highly prevalent in healthy old people. Gut. 1992 Oct;33(10):1331-7.
 Rohof WO, et al. Proton pump inhibitors reduce the size and acidity of the acid pocket in the stomach. Clin Gastroenterol Hepatol. 2014 Jul;12(7):1101-1107.
 Lambert JE. Primate digestion: interactions among anatomy, physiology, and feeding ecology. Evol Anthr. 1998; 7: 8–20.
 Beasley DE, et al. The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome. PLoS One. 2015 Jul 29;10(7):e0134116.
 Foley WJ, Engelhardt WV, Charles‐Dominique P. The passage of digesta, particle size, and in vitro fermentation rate in the three‐toed sloth Bradypus tridactylus (Edentata: Bradypodidae). Journal of Zoology. 1995 Aug 1;236(4):681-96.
 Imhann F, et al. Proton pump inhibitors affect the gut microbiome. Gut. 2016 May;65(5):740-8.
 Clooney AG, et al. A comparison of the gut microbiome between long-term users and non-users of proton pump inhibitors. Aliment Pharmacol Ther. 2016 May;43(9):974-84.
 Pohl D, et al. Do we need gastric acid? Digestion. 2008;77(3-4):184-97.