Indigenous microbes and digestion

    The term “holobiont” unites the host organism and its indigenous microbes (indibiome), the totality of the genetic material in the host-microbe system provides a more accurate description of the complex system and, due to the possibility of directional changes in the microbiota, makes it possible to correct the states characterized as distress.

    Lactose intolerance is a set of symptoms that manifest as discomfort, bloating, loose stools, and diarrhea when consuming milk or products containing lactose. Symptoms are associated with the active growth of bacteria in the lower intestine, if lactose is not digested by the enzyme (lactase) of our body in the upper divisions.

    The study of the effect of lactose intolerance (NL) prompted reflection on the evolution of digestion, revealed the presence of contradictions in the description by specialists and suggested some solutions to improve the health of the boom. In many respects, NL is not a good model for other types of reactions to products, which does not prevent us from building the most plausible hypotheses on the basis of the material below about the interaction of the genes of our body and the genes of microbes that inhabit our intestines.

    Digestion 101

    The process of digesting food in the human body begins in the mouth with an amylase enzyme that breaks down complex carbohydrates (starch) to simpler sugars, then pepsin and other enzymes in the stomach break down proteins, and then, in the duodenum, pancreatic enzymes break down fats. proteins, carbohydrates and nucleic acids, in the next section, the small intestine, enzymes are secreted by the intestinal cells themselves and are responsible for the breakdown of the remaining sugars and fats, and finally, in the colon, the bacteria are involved in the breakdown of complex polysaccharides (dietary fiber). It has evolved so that many different bacteria in the intestine are used to break down a huge number of bond options in polysaccharides. In the database of enzymes for working with polysaccharides ( CaZymes) bacteria are leading, they have 12,743 different enzymes, and eukaryotes are represented by only 243 enzymes. The simple interpretation is this: plants build their cell walls in thousands of different ways, and it’s not at all profitable for a macro-organism to evolve itself and have a new gene for each plant, it’s much more economical to carry an arsenal of bacteria whose genome capacity exceeds our orders of magnitude, and moreover , bacteria can quickly divide, and therefore mutate and exchange genetic material horizontally .

    Lactose intolerance

    Mammals lose their ability to digest lactose when they reach a certain age, due to the end of breastfeeding. One of the most important events in the development of livestock society has been the acquisition and spread of a genetic mutation that promotes the digestion of lactose in adulthood. The genetics of Europeans has been studied quite well; it has been shown that there is a characteristic genetic mutation in the European population, in the presence of which the gene of lactase, the enzyme responsible for the digestion of lactose in the small intestine, is also expressed in adulthood. According to available data, lactose intolerance may be associated with comorbidity.a wide range of diseases: from osteoporosis associated with a lack of calcium, to inflammatory bowel disease (IBD), since it is assumed that systemic irritation of the intestine increases the risk of IBD.

    Intestinal bacteria are the main factor causing the symptoms, it is assumed that the composition of the microbiota is associated with the severity of the manifestation of NL, or, conversely, a certain composition can offset the effects of lactose. Preliminary epidemiological studies have identified associations of bacterial species with the presence of symptoms. In this regard, the concept of root microbes (see. Root microbes ) takes on new facets of meaning.

    Data Analysis Field

    One of the publications (see. Indigenous microbes of the vagina ) caused a heated discussion on the relevance of such articles on Habr, I suggest colleagues interested in data analysis to join the research topic. It is interesting that systematically the issue of lactose intolerance has not been studied, since LN is not a disease and for the most part belongs to ordinary doctors in the same category as allergies to individual products.

    It is possible to systematically approach the issue from the point of view of data: hold a text of mining literature (more than 3,000 articles), select all known human genetic polymorphisms associated with lactose tolerance (estimated at least several dozen), compile a database of mutation frequencies in various ethnic groups, make using text mining approaches, a map of the area of ​​knowledge where diseases, genotypes, methods for testing NL, microbial taxa and symptoms will be related. An analysis of the genomes of intestinal bacteria and metagenomic data can be performed to create an orthology of beta-galactosidases and their occurrence in intestinal bacteria.

    Food Allergies and Intolerances

    Estimated economic burden from food allergies and intolerances in the United States - $ 25 billion per year ( link), and this is only for children under 16 years old. It is worth distinguishing between allergies and intolerances, allergy implies that the food component becomes an antigen, and with an increase in the dose or frequency of exposure to an allergen, a developing immune system reaction can lead to death, the most common allergens are nuts and seafood. Food intolerance is manifested in the absence of a significant reaction from the immune system, however, as a result of incomplete or incorrect digestion, the components of the products cause symptoms such as nausea, diarrhea, gas formation. It is believed that intolerance of individual components is much more common and dose-dependent: up to a certain amount, the body is able to absorb the food component, and symptoms occur above a certain threshold.

    In an adult who is well absorbing milk, the enzyme responsible for the digestion of lactose (lactase) is found in the villi of enterocytes of the small intestine, in the case of NL, the enzyme is detected only in rare enterocytes inside the same villi. The possibility of lactose digestion is determined mainly by the level of gene expression, which means it is determined genetically.

    Genetics of lactose intolerance

    The frequency of NL and the age of its manifestation depends on the ethnic group (Heyman, 2006; Swallow, 2003). Among the Spaniards, the frequency is up to 8%, Ashkenazi 60-80%, Asians and Native Americans up to 100%. The opposite situation has developed among the North European ethnic groups (Johnson, 1981), where NL is found in 2%. In most studies, the same polymorphism is found to be responsible for maintaining a high level of lactase (C / T-13910). This polymorphism located upstream of the lactase gene in the genome at 13.9 thousand base pairs explains most cases of lactose tolerance in the European population (Enattah et al., 2007). At present, at least 8 unique nucleotide polymorphisms characteristic of one race or another are associated with lactose intolerance (Torniainen et al., 2009).

    Despite the fact that the symptoms themselves disappear when you refuse to consume milk, the American Society of Gastroenterologists believes that the obtained comorbidity indicators indicate the importance of research on the issue of NL.

    There is some evidence of an association of NL and diseases, in particular osteoporosis, depression, abdominal pain, irritable bowel syndrome, and fructose intolerance (Schiffner et al., 2016).

    Determination of lactose intolerance

    Clinical methods for determining lactose intolerance include the following methods:

    1. Lactose intolerance test. Blood glucose is measured two hours after drinking a drink with lactose. If the glucose level has not increased, then lactose is not digested.
    2. Hydrogen breath test. After drinking a drink with lactose, the concentration of hydrogen in the exhaled air is measured. In case of intolerance, its levels will be increased, because lactose will be metabolized in the colon to hydrogen, which is then excreted through respiration.
    3. 13C-test - a test for the concentration of modified carbon, carried out after drinking a drink with 13C-labeled lactose. If it is digested in the small intestine, 13C-labeled glucose can be detected in the blood.
    4. Fecal acidity test. For children who can not pass the above tests due to a very young age, a feces acid test is used. Fermentation of lactose in the large intestine leads to acidification of feces (due to lactic acid).

    The role of microbiota

    The role of microbiota in the development and severity of symptoms is not fully understood. Undigested lactose is thought to come from the small intestine to the colon and is fermented by the intestinal microbiota. During the fermentation process, short-chain fatty acids, hydrogen, methane and carbon dioxide are formed, thereby increasing the intestinal pressure and intestinal transit time. Acidification of the contents of the colon and an increase in the osmotic load leads to an increase in the secretion of electrolytes and fluid, which causes loose stools and diarrhea.
    There are studies that show an increase in the cytotoxicity of fecal water in individuals with NL (Windey et al., 2015). Campbell's group in the UK is developing a theory of specific bacterial toxins (Campbell et al., 2010), suggesting that a certain microflora composition, when a high-energy resource such as lactose enters, leads to the production of low- or high-molecular bacterial toxins that cause symptoms .
    The first epidemiological studies revealed (Kurilshikov et. Al 2016) a relationship between genetic polymorphism, microbiota composition, and symptoms. However, in general, the issue of the influence of the composition of microbiota as a factor in the manifestation of NL symptoms has not been studied.

    Dairy products

    An interesting way of influencing indigenous microbes is to explain the ability of people with NL to digest dairy products. Most fermented milk products (kefir, yogurt) do not differ much from milk in terms of the amount of lactose, however, their use even in the presence of NL does not lead to the appearance of symptoms.

    Important note.
    Since the topic is not discussed in textbooks, often colleagues give unsubstantiated statements, without evidence, believing that only the absence of lactose allows you to drink kefir.
    For example, in the Journal “Chemistry and Life” it is stated that there is no lactose in kefir. Moreover, the respected magazine also trolls to Malyshev (we already have a common past with her on Habr ( link )).
    In principle, asking a question to “Dr. Google” one can come across various interpretations, most of the colleagues apparently think that since kefir does not cause a reaction, then there is no lactose in it. 

    Actually there is.
    Original article with measurement (milk 5 g of lactose, kefir 3.7 g) ( link )
    Most of the works cite Renner and Renz-Schaven, 1986 or Hallé et al., 1994, where 100 g of kefir 4 g of lactose.
    Conclusion : there is enough lactose in kefir.
    Honestly, I myself was surprised that there is so much lactose in the fermented milk product. The more interesting it was to figure out the details. The work (de Verse et al., 2001) discloses a mechanism according to which the microbial beta-galactosidase contained in fermented dairy products avoids digestion in the stomach, as it is in the cell membrane of bacteria and, when it enters the upper intestines, hydrolyzes lactose.

    Again. Microbes from fermented foods give us their enzymes, bringing them to the upper intestines in their bodies. In the small intestine, bacterial enzymes help us digest lactose, and it does not enter the large intestine, and therefore there are no symptoms of NL.


    The same reasoning applies to many fermented products, for which the conditions of fermentation were selected during the development of mankind. Most often, plant foods can be fermented by indibiom living directly on the leaves, such as sauerkraut. Fermentation is an external (relative to the human) digestion, and more fermented foods contain a mixture of enzymes for the best assimilation of foods within our intestines.

    Another observation: bacteria are a factor that can both positively and negatively affect food intolerance. And, apparently, there is an optimal combination of intestinal microbiome and product microbiome, in which there will be no negative reactions.


    The problem described above is largely not paid enough attention, since NL is not officially considered a disease and the data on economic burden, comorbidity and disease statistics are quite fragmented. While many issues are being addressed today by national or international societies or consortia, the issue of lactose intolerance is left unattended. A related fact is the dissociation of researchers and research: different assessment technologies or NL assessment protocols are used, individual polymorphisms are considered, there is no standardized validated questionnaire and coordination in the direction of epidemiological studies.

    Why is it important

    The ability to use milk for food is considered a powerful evolutionary impetus in the development of mankind, the appearance of a mutation allowing digestion of lactose according to calculations (Bersaglieri, T. et al. 2004) increased the number of healthy offspring by its owners. So far, there is no data, but it is obvious that the microbial part of the holobiont also co-evolved with human digestion, possibly also compensating for the lack of lactase in individuals with NL. Deciphering the mechanisms of microbial adaptation in the case of NL would allow us to proceed to the study of coevolution processes.

    Data on comorbidity also indicate the importance of LD in the pathogenesis of multifactorial diseases, here microbial compensation and proper monitoring of intolerance would lead to direct economic consequences - an increase in the number of able-bodied people.

    A study of fermented foods will potentially allow microbiota to be corrected without the use of drugs or food additives. Work with food intolerances using fermented products is undoubtedly in the sphere of interests not only of healthcare, but also of pharmaceuticals and food companies.

    Lactose intolerance is a good model for the study and resolution of food intolerance issues in general. Although the mechanisms may differ in the case of other intolerances, the approach to the study of the issue may be expanded to other problems: detection of genetic dependencies, determination of the mechanisms of regulation of enzyme activity, search for relationships with the intestinal microbiota, and correction of the microbiota in order to reduce the negative effects of intolerance.

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