Last Modified: April 24, 2024
Introduction to Human Intestinal Bacteria
In trying to understand the epidemic of obesity much of the research has focused on two critical areas. The first is research driven by the notion that the biological and physiological interrelationships of the organ systems, primarily liver, adipose tissue, and skeletal muscle, are tightly connected and any disruption in the metabolic profile of one organ can exert a negative impact on the others. An additional avenue of more recent research is the use of modern genetic tools to scan the human genome for polymorphisms that are associated with increased risks for obesity and diabetes. However, very recently a new area of study has begun to focus on the role of the bacterial complement of the gastrointestinal system and the role these microorganisms play in altering dietary and metabolic processes.
The idea that gut bacteria can influence overall metabolism was discovered in studies using germ free mice. The full compliment of gut bacteria in an organism is referred to as gut microbiota, the compliment of living microscopic organisms of a given system.
Mice raised in a germ free environment are resistant to diet-induced obesity. The primary mechanisms underlying this resistance are decreased absorption of glucose, decreased generation of short-chain fatty acids in the gut, reductions in hepatic lipogenesis, and alterations in adipose tissue metabolism that favors reduced triglyceride accumulation and increased fatty acid oxidation.
A number of striking observations have been made in the use of animal models for studying the interaction between gut bacteria and diet-induced obesity and the development of insulin resistance and type 2 diabetes. When the guts of mice reared in a germ-free environment are colonized with bacteria from mice raised in a non-sterile environment the germ free mice amass a 60% increase in body weight and this weight gain is associated with insulin resistance.
Another important observation was made when comparing the source of the bacteria to be used for gut colonization. If bacteria are used from obese mice (the ob/ob genotype) the recipient mice have a significantly greater increase in body fat mass than in recipients that were colonized with bacteria from lean mice.
The mechanism of the weight gain in these study mice was due to increased digestion of polysaccharides resulting in higher absorption and delivery of sugars to the liver. The increased carbohydrate delivery to the liver results in increased lipogenesis. When the transcriptional profiles of the livers were analyzed it was found that germ-free mice colonized with bacteria from ob/ob mice had increased levels of expression of ChREBP and SREBP-1c, both of which drive increased fatty acid synthesis via activation of the expression of the genes encoding acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS). Although the re-colonized mice had increased fat deposition in the liver via changes in transcriptional profiles, the increase in adipose tissue mass was determined to be due to increases in the activity of lipoprotein lipase (LPL). LPL is present on the surface of vascular endothelial cells of the heart, skeletal muscles, and adipose tissue and it has a central role in lipoprotein metabolism and homeostasis.
During periods of fasting, the expression of a protein of the angiopoietin-like protein family, angiopoietin-like 4 (ANGPTL4; originally called fasting-induced adipose factor, FIAF) is stimulated by peroxisome proliferator-activated receptor alpha (PPARα) in the liver and by PPARγ in white adipose tissue. ANGPTL4 inhibits adipose tissue LPL activity by acting extracellularly as an unfolding molecular chaperone. The N-terminal coiled-coil domain of ANGPTL4 transiently binds to LPL and this interaction converts LPL from a catalytically active dimer to an inactive monomer. In the re-colonized germ-free mice the level of ANGPTL4 expression is significantly reduced allowing for increased uptake of fatty acids from circulating lipoproteins and a concomitant increase in adipose tissue triglyceride storage. These changes in lipid profiles in the liver and adipose tissue of re-colonized rodents was correlated to changes in the composition of gut microbiota such that there was a 50% reduction in the abundance of Bacteroidetes (original phylum name was Bacteroidota) and a proportional increase in Firmicutes (original name of the Firmicutes phylum was Bacillota).
The intestinal epithelium is the largest immunologically active organ system in the human body. This tissue provides defense of the host from invading pathogens. However, given that the microorganisms of the gut are essential for the metabolism of xenobiotic compounds, production of vitamins, degradation of non-digestible polysaccharides (involving fermentation of resistant starches and oligosaccharides), and absorption of nutrients there is a fine interplay between the gut immune system surveillance and maintenance of the gut microbiota.
Major Human Lower Gastrointestinal (GI) Bacteria
Discussion the human gut microbiome generally includes the stomach and the small and large intestines. The human gut contains a wide variety of microorganisms of which bacteria constitute the largest fraction. The average human gut contains numerous different types of bacteria of which anaerobic bacteria constitutes the largest proportion. There are more than 1,000 different species-level phylotypes of bacteria in the human gut microbiota (microflora). The major bacterial phyla, representing 90% of the human gut microbiome, are Bacteroidetes (Gram-negative) and Firmicutes (Gram-positive). Other major bacterial phyla of the human gut include Actinobacteria (Gram-positive) and Proteobacteria (Gram-negative). Minor bacterial phyla in the human gut include Verrucomicrobia (Gram-negative) and Fusobacteria (Gram-negative).
The predominant genera from the Bacteroidetes phylum in the human gut are Bacteroides and Prevotella. At least 23 species of Bacteroides have been identified in the human gut and these account for nearly 30% of all the bacteria of the human gut.
The Firmicutes phylum is large with over 200 different genera with the predominant genera in the human gut being Bacillus, Clostridium, Enterococcus, Lactobacillus, and Ruminicoccus where Clostridium represents roughly 95% of the total.
The Actinobacteria phylum is primarily represented by the Bifidobacterium genus. Additional genera found in the human gut include, Escherichia, Eubacterium, Fusobacterium, Peptococcus, and Peptostreptococcus.
In addition to the numerous different bacteria found in the human gut there are spatial differences as well such that the stomach, small intestines, and large intestine (colon) are colonized by distinct populations of bacteria.
Within the stomach the predominant bacteria are of the Bacteroidetes and Firmicutes phyla with the Actinobacteria, Protobacteria, and Fusobacteria contributing a much smaller number of bacteria. With respect to Firmicutes in the stomach the major genera are Lactobacillus and Streptococcus.
The small intestines are colonized with bacteria of the Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria phyla. Typical Firmicutes bacteria in the small intestine are of the genera Lactobacillus and Streptococcus. The primary Bacteroidetes bacteria within the small intestines are of the genus Bacteriodes. The predominant Actinobacteria bacteria within the small intestines are of the genus Bifidobacteria. The predominant Verrucomicrobia bacteria within the small intestines are of the genus Akkermansia.
The large intestines are colonized with bacteria of the Firmicutes, Bacteroidetes, Actinobacteria, Protobacteria, and Fusobacteria phyla. Typical Firmicutes bacteria in the large intestine are of the genera Lactobacillus, Streptococcus, Clostridia, Staphylococcus, Eubacteria, and Veilonella. The primary Bacteroidetes bacteria within the large intestines are of the genus Bacteriodes. The predominant Actinobacteria bacteria within the large intestines are of the genus Bifidobacteria. The predominant Verrucomicrobia bacteria within the large intestines are of the genus Akkermansia. The predominant Protobacteria within the large intestines are of the genera Proteus, Enterobacteria, and Pseudomonads
In addition to the various bacteria constituting the gut microbiota there are methanogenic archaea (mainly Methanobrevibacter smithii), eukaryotes (mainly yeasts), and viruses (mainly bacteriophages) that colonize the human gut.
As might be expected, the predominant composition of an individuals gut microbiota is determined by the geographic location as well as the dietary composition of an individual.
Bacteroidetes
The phylum, Bacteroidetes, is composed of rod-shaped, non-spore forming, Gram-negative bacteria. The majority of the Bacteroidetes species found in the gut are represented by three genera which includes Prevotella (bile-sensitive, moderately saccharolytic, with pigmented and nonpigmented species), Porphyromonas (bile-sensitive, pigmented, asaccharolytic species), and Bacteroides (bile-resistant, nonpigmented, saccharolytic species). Additional genera in the Bacteroidetes phylum, although not typically found in the human gut microbiome, are Alistipes, Anaerorhabdus, Dichelobacter, Fibrobacter, Megamonas, Mitsuokella, Rikenella, Sebaldella, Tannerella, and Tissierella.
The most well-characterized class in the Bacteroidetes phylum is the Bacteroidia which includes the genus Bacteroides with the most commonly detected species in the human gut being Bacteroides fragilis (B. fragilis). Although, in general, the Bacteroidetes genus Prevatella is not well represented in the gut microbiome, the levels of this genus increase significantly in individuals who consume a high-carbohydrate diet.
There are some species of the Bacteroides genus that can cause opportunistic infections if the integrity of the intestinal mucosal barrier is broken even though these same species belong to the normal gastrointestinal microbiota. Some members of the genera Porphyromonas, Prevotella, and Tannerella are well-known pathogens within the mouth where they are responsible for causing periodontal disease and dental caries (cavities).
Bacteria of the Bacteroidetes phylum constitute up to 30% of the total gut microbiome. These bacteria are important in the digestion of otherwise non-digestible polysaccharides which they digest into monosaccharides and short-chain fatty acids (SCFA). The Bacteroidetes phylum bacteria may also be involved in the synthesis of vitamin K.
Firmicutes
The Firmicutes phylum (also referred to as the Bacillota phylum) is composed of Gram-positive bacteria that includes aerobic, anaerobic, spore-forming, saprophytic, and pathogenic bacteria. Firmicutes consists of over 200 genera which includes Bacillus, Clostridium, Lactobacillus, Enterococcus, Ruminicoccus, and Mycoplasma. Additional important genera within the Firmicutes phylum are Listeria, Paenibacillus, Staphylococcus, Streptococcus, Pediococcus, and Leuconostoc. Several species of the Firmicutes phylum are toxin producing bacteria and includes Clostridium botulinum, Clostridium tetani, Clostridium perfringens, and Staphylococcus aureus.
Some species of Firmicutes are involved in bile acid metabolism in the gut. Strong evidence implicates bile acid homeostasis in the gut with control of intestinal inflammation. Individuals with intestinal bowel disease (IBD) exhibit decreased microbial diversity, abnormal microbial composition, and present with depletion of bacteria of the Firmicutes phylum.
Actinobacteria
The Actinobacteria phylum (also referred to as the Actinomycetota phylum) is composed of Gram-positive bacteria and constitutes one of the largest bacterial phyla. Many strains of Actinobacteria bacteria are responsible for the production of nearly two-thirds of all naturally derived antibiotics in current clinical use. Metabolic byproducts of numerous Actinobacteria bacteria are also utilized as anticancer, anthelmintic, and antifungal drugs.
The Actinobacteria phylum includes species of the genera of Bifidobacterium, Corynebacterium, Mycobacterium, Nocardia, Propionibacteriaceae, and Streptomyces. With respect to the human gut microbiome, species of the Bifidobacterium genus represent some of the first microorganisms to colonize the intestines of newborns. These strains of bacteria play key roles in the development of the immune system and in the use of dietary components. The latter fact has led some to consider certain strains of Bifidobacterium to be probiotic microorganisms. Many foods, particularly commercial dairy products have Bifidobacterium included as bioactive ingredients.
Proteobacteria
The Proteobacteria phylum (also referred to as the Pseudomonadota phylum) is composed of Gram-negative bacteria. On the basis of phylogenetic analysis of the 16S rRNA gene, the Proteobacteria phylum is divided into six classes that includes Acidithiobacillia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilalia, and Zetaproteobacteria. Several representative Proteobacteria genera include Desulfovibrio, Escherichia, Helicobacter, Salmonella, and Shigella. There are several enteropathogenic strains of bacteria in the Proteobacteria phylum including Shigella flexneri, Shigella dysenteriae, Vibrio cholerae, Salmonella typhi, Escherichia coli, and Helicobacter pylori.
Verrucomicrobia
The Verrucomicrobia phylum (also known as the Verrucomicrobiota phylum) is composed of Gram-negative bacteria. Species of the Verrucomicrobia phylum represent a minor component of the human microbiome. The species Akkermansia muciniphila is a mucus-degrading member of the Verrucomicrobia phylum and it represents from 1% to 4% of the bacterial population in the colon. A. muciniphila degrades mucins to produce short-chain fatty acids (SCFA) which provides not only the host with energy but the bacteria itself thus, promoting colonization of the gut. The degradation of host mucins results in the increased production of mucin by colonic epithelial cells which maintains the dynamics of these proteins.
Fusobacteria
The Fusobacteria phylum (also known as the Fusobacteriota phylum) is composed of Gram-negative, nonmotile, rod-shaped bacteria. These bacteria have a spindle shaped (fusiform) morphology accounting for the name of the phylum. Species within the Fusobacteria phylum are facultative aerobic to obligately anaerobic, fermentative bacteria. Fusobacteria strains have been found predominantly in the jejunum, ileum, and the colon.
Human Microbiome of the Upper Gastrointestinal (GI) Tract
Although the microbiome of the human lower gastrointestinal tract has been most extensively studied there are relevant bacteria in the upper gastrointestinal tract that includes the oral cavity and the esophagus.
Microbiota of the Oral Cavity
The oral cavity is comprised of several microbial environments including the tonsils, teeth, gums, tongue, cheeks, hard and soft palates. It is the opening to the GI tract where food enters and is mixed with saliva. More than 1000 taxa have been found in the oral cavity. Six major phyla comprise 96% of the taxa including Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes, and Fusobacteria. In saliva of healthy patients, the predominant genera are Gemella, Veillonella, Neisseria, Fusobacterium, Streptococcus, Prevotella, Pseudomonas, and Actinomyces.
Microbiota of the Esophagus
The most abundant bacteria in the human esophagus belong to the phylum Firmicutes and the genus Streptococcus, likely derived from the oral cavity. Shotgun sequencing has revealed three distinct community types in the esophagus of healthy subjects. Communities are dominated either by Streptococcus (S. mitis, S. oralis, and S. pneumoniae), Prevotella (P. melaninogenica and P. pallens) and Veillonella, or Haemophilus (H. parainfluenzae) and Rothia (R. mucilaginosa).
Dietary Influences on Composition of Gut Microbiota
Numerous factors contribute to the composition of an individuals gut microbiota. These factors include mode of birth (vaginal versus caesarian), age, health status, genetics, and lifestyle. Of these factors, the major contributor to gut microbiota composition is dietary habit. However, dietary habit represents a complex entity owing to the differences in dietary components such as macronutrients, micronutrients, salt, and food additives. Due to these differences, the precise mechanisms that account for variability in an individuals gut microbiota are still being determined. Nonetheless, numerous studies have identified dietary fats and proteins as major contributors to the overall composition of gut microbiota.
Dietary fats, not carbohydrates, have been shown to be the major contributors of adiposity and the development of obesity. Nonetheless, both fats and carbohydrates have been shown to induce specific changes in the abundance levels of various bacterial taxa.
Consumption of a high fat diet has been found to lead to a reduction in the level of bacteria of the Actinobacteria, Bacteroidetes, and Firmicutes phyla in the gut. Specifically bacteria of the Bifidobacterium and Eubacterium genera of the Actinobacteria phylum, Bacteroides and Prevotella genera of the Bacteroidetes phylum, and the Clostridium genus of the Firmicutes phylum.
The consumption of a diet that contains mostly saturated and omega-6 polyunsaturated fatty acids (PUFA) leads to changes in the composition of gut microbiota that are correlated with the development of obesity. The significance of the high-fat diet-induced changes in gut microbiota to the development of obesity has been demonstrated in laboratory mice. When fed a high-fat diet enriched in saturated and omega-6 PUFA along with broad-spectrum antibiotics, mice are partially resistant to development of obesity. Not only were these mice resistant to obesity, they were also less likely to develop insulin resistance and had a reduced level of inflammation, both of which contribute to the development of the metabolic syndrome in humans. Additional experiments have shown that mice raised in a germ-free environment are also partially resistant to the development of metabolic dysfunction associated with consumption of a high-fat diet.
Of significance to dietary composition, mice that are fed a high-fat diet that contains omega-3 PUFA, and no saturated or omega-6 PUFA, are found to be protected from the development of obesity, insulin resistance, and inflammation, even when the diet contains the same caloric content to mice fed the high-fat diet composed of saturated and omega-6 PUFA. When the gut microbiota are analyzed in omega-3 fed mice there is found to be an increase in Akkermansia muciniphila (Verrucomicrobia phylum), Bifidobacteria (Actinobacteria phylum), and Lactobacillus (Firmicutes phylum). The levels of these same bacteria are elevated in the gut of individuals consuming inulin-type fructans such as oligofructose. Oligofructose is called a prebiotic which is any substance that is non-digestible by humans but can be fermented by gut bacteria thereby promoting their growth and activity.
Of significance to the relationship between gut microbiota and obesity, studies have shown that obese individuals had lower levels of Bacteroidetes and more Firmicutes than lean control subjects. When obese patients are placed on either a carbohydrate restricted low calorie diet or a fat restricted diet their ratios of Bacteroidetes to Firmicutes approached those of lean control subjects after several months.
Gut Microbiota Metabolites in Host Homeostasis
The brain, in particular the hypothalamus, plays a central role in the regulation of energy metabolism, nutrient partitioning, and the control of feeding behaviors. The gastrointestinal tract is intimately connected to the actions of the brain in metabolic and appetite control, in a large part, through interactions with the hypothalamic-pituitary axis. These gut-brain interactions occur via the release of gut peptides that exert responses within the brain as well as through neuroendocrine and sensory inputs from the gut.
In addition, gut microbiota-derived metabolites, in particular the short-chain fatty acids (SCFA), acetic acid, propionic acid, and butyric acid, as well as the bile acid metabolites, are significant contributors to the interconnections between the gut and the brain. The generation of SCFA by gut microbiota occurs primarily through metabolism of non-digestible fibers and resistant starches.
The synthesis of SCFA and the metabolism of bile acids are the major processes by which gut microbiota influence host homeostasis, but they do not reflect the only bacterial processes that contribute to host homeostasis. Gut microbiota metabolism of tryptophan generates several compounds that influence functions within the brain and gut microbiota also produce numerous neurotransmitters and neuroactive compounds that influence brain functions such as feeding behaviors.
Short-Chain Fatty Acids (SCFA) from Gut Microbiota Metabolism
The bacterial digestion of polysaccharides into short-chain fatty acids (SCFA) involves a process called saccharolytic fermentation. Gut microbiota produce significant quantities of the SCFA, acetate, propionate, and butyrate. The average molar ration of these three SCFA is 60:20:20 for acetate, propionate, and butyrate, respectively. Anaerobic fermentation of undigestible fibers represents the predominant source of bacterially derived SCFA. However, metabolism of amino acids, predominantly by bacteria within the distal large intestines, is also a source of these three SCFA. Bacteria can also convert the acetyl-CoA byproduct of glycolysis into acetate and then into butyrate.
Upon their synthesis, SCFA are absorbed by colonocytes via the actions of H+-dependent transporters of the monocarboxylate transporter (MCT) family or via Na+-dependent transporters of the Na+-monocarboxylate transporter (SMCT) family. The MCT family of transporters are encoded by genes of the SLC16 family while the SMCT family transporters are encoded by genes of the SLC5 family.
Upon uptake by colonocytes the SCFA can be metabolized for production of energy. SCFA that are not metabolized by colonocytes are transported into the portal circulation where they are primarily picked up by hepatocytes and metabolized for energy production. The exception to this latter fate of gut microbiota-derived SCFA is acetate which cannot be oxidized by hepatocytes due to the lack of expression of the gene (OXCT1) encoding 3-oxoacid-CoA transferase 1 which is also known as succinyl-CoA:3-oxoacid-CoA transferase (SCOT). Due to the metabolism of acetate, propionate, and butyrate by gut microbiota and subsequently by the liver, there is very little metabolism of gut-derived SCFA by other peripheral tissues.
Following absorption, propionic acid aids the liver in the production of ATP by being converted to propionyl-CoA and then to succinyl-CoA followed by oxidation in the TCA cycle. Butyrate is used for energy production by intestinal epithelial cells and also has anti-inflammatory properties in the gut.
In addition to energy production, gut-derived SCFA are very important for the maintenance of overall gut health. These effects include, but are not limited to, maintenance of the barrier integrity of the intestines, enhancement of mucus production, and likely most importantly aid in the protection against inflammation to which can reduce the overall risk of colorectal cancers. Gut-derived SCFA also exert effects in peripheral tissues such as the pancreas, immune system, and central nervous system, CNS.
The mechanisms by which SCFA exert effects in the gut are the result of binding to and activating a variety of cell surface and nuclear receptors in gut epithelial cells. Important G-protein coupled receptors in intestinal epithelial cells that respond to bacterially derived SCFA include FFAR2 and FFAR3. FFAR2 was originally identified as GPR43 and FFAR3 was originally identified as GPR41. Many of the receptors that are activated by SCFA are indicated in the Table below entitled Gut Microbiota Metabolites Involved in Host Homeostasis.
Within the gut the activation of these various receptors leads to increased synthesis and release of various neuropeptides such as glucagon-like peptide 1 (GLP-1) and peptide YY (PYY) both of which are produced by intestinal enteroendocrine L cells. These gut-derived neuropeptides then exert effects within the periphery in tissues such as the pancreas and the CNS.
The gut-derived SCFA can also exert effects in the periphery that involve the regulation of gene expression through inhibition of histone deacetylase (HDAC) activity as well as by serving as substrates for histone lysine modifications that include acetylation, propionylation, and β-hydroxybutyrylation.
Gut-derived SCFA exert numerous effects within the brain that includes within neurons, astrocytes and microglial cells. Within neurons gut-derived SCFA modulate the level of expression of neurotransmitters and neurotrophic factors. These effects are exerted, in part, via the regulated expression of genes encoding enzymes responsible for neurotransmitter synthesis such as tyrosine hydroxylase and tryptophan hydroxylase 1. Tyrosine hydroxylase is rate-limiting for the synthesis of epinephrine and norepinephrine, whereas tryptophan hydroxylase 1 is one of the two forms of the tryptophan hydroxylase enzymes that are rate-limiting for the synthesis of serotonin.
Gut Microbiota Metabolism of Bile Acids
As described in detail in the Bile Acid Synthesis, Metabolism, and Biological Functions page, the liver is the site of bile acid synthesis. The liver produces the primary bile acids, cholic acid (CA) and chenodeoxylcholic acid (CDCA) from cholesterol. Following their synthesis, the amino acids glycine or taurine are conjugated to the primary bile acids forming the bile salts. The conjugation increases the amphipathic nature of the bile acids making them much less toxic as well as more easily secreted into the bile canaliculi. These conjugated primary bile acids are transported within the bile canaliculi to the gallbladder and stored for secretion following the consumption of fats and proteins.
Once bile salts are secreted into the duodenum and carry out their emulsification role, around 95% are reabsorbed into the distal ileum. The remainder of the bile acids then enter the colon where the majority of the gut microbiota reside. Within the colon the amino acids conjugated to the bile acids are removed by colonic bacteria. These amino acids represent energy generating substrates for the gut microbiota. Removal of the conjugated amino acid is the function of bacterial bile salt hydrolases. The major phyla that are responsible for the hydrolysis of amino acids from bile salts are Bacteroides, Firmicutes, and Actinobacteria.
Gut microbiota carry out several additional bile acid metabolic reactions that includes dehydroxylation of the hydroxy groups on the steroid backbone. Dehydroxylation of the bile acids generates the secondary bile acids. Dehydroxylation of CA yields deoxycholic acid (DCA) while dehydroxylation of CDCA yields lithocholic acid (LCA).
In addition to dehydroxylation, gut microbiota bacterial carry out numerous additional modifications that includes oxidation, epimerization, desulfation, esterification, and conjugation. Oxidation or reduction reactions are primarily the result of bacterial hydroxysteroid dehydrogenases. Epimerization of CDCA yields ursodeoxycholic acid (UDCA), an important bile acid metabolite involved in regulating the composition of gut microbiota as well as being important for fat soluble vitamin absorption.
One of the major functions of gut microbiota-derived bile acid metabolites is the result of their interaction with host cell receptors that includes both cell surface receptors and nuclear receptors. The primary cell surface receptors to which bile acids bind are the G-protein coupled bile acid receptor 1, GPBAR1 (originally identified as TGR5 and also known as GPR131) and the sphingosine-1-phosphate receptor 2 (S1PR2). The nuclear receptors to which bile acids bind include the farnesoid X receptors (FXR), the vitamin D receptor (VDR), the pregnane X receptor (PXR), and the constitutive androstane receptor (CAR).
FXR represents a major bile acid receptor being activated by free and conjugated CA, CDCA, DCA, and LCA. Within enterocytes in the ileum, the activation of FXR by bile acids results in the activation of FGF19 expression. The secretion of FGF19 into the portal circulation leads to suppression of hepatic bile acid synthesis. Bile acid-mediated activation of hepatic FXR also leads to reduced bile acid synthesis via inhibition of expression of the CYP7A1 (cholesterol 7α-hydroxylase) and CYP8B1 (sterol 12α-hydroxylase) genes. FXR also induces expression of the BAAT (bile acid-CoA:amino acid N-acetyltransferase) gene allowing for increased conjugation of bile acids thereby suppressing the accumulation of toxic unconjugated bile acids. An additional mechanism by which bile acid induction of FXR reduces hepatic accumulation of toxic bile acids is by activation of the ABCB11 gene, which encodes the canalicular bile salt export pump (BSEP), allowing a higher rate of bile salt export from hepatocytes. FXR also reduces expression of the SLCOB1 gene, which encodes the Na+-independent organic anion transporting polypeptide 1B1 (OATP1B1), which is normally responsible for transport of bile acids into hepatocytes.
Lactic Acid Producing Bacteria of the Gut
The term, lactic acid bacteria (LAB) refers to the numerous genera of bacteria that utilize carbohydrates as their only (or primary) source of energy and in the context of metabolism generate lactic acid as a major byproduct. LAB are Gram-positive and non-spore-forming bacteria. LAB are important in the food industry as the production of lactic acid results in the inhibition of the growth of spoilage agents. In addition, some LAB produce bacteriocins (peptide toxins) that prevent the growth of pathogenic microorganisms.
The major bacterial phylum to which the LAB genera belong is Firmicutes and within this phylum the LAB belong to the Bacilli class. There are over 60 genera that constitute the LAB with the principal genera being Aerococcus, Carnobacterium, Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Oenococcus, Pediococcus, Streptococcus, Tetragenococcus, Vagococcus, and Weissella. The major LAB of significance for humans, both for their use in the food industry, as well as constituting major constituents of gut microbiota that are classified as “good” bacteria, are Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and Streptococcus. Lactobacillus represents the largest LAB genus with over 100 identified species.
Due to the original size of the classified Lactobacillus genus, there has been a reclassification such that what was once a single genus has been divided into 25 distinct genera. These 25 genera are Lactobacillus, Paralactobacillus, Amylolactobacillus, Acetilactobacillus, Agrilactobacillus, Apilactobacillus, Bombilactobacillus, Companilactobacillus, Dellaglioa, Fructilactobacillus, Furfurilactobacillus, Holzapfelia, Lacticaseibacillus, Lactiplantibacillus, Lapidilactobacillus, Latilactobacillus, Lentilactobacillus, Levilactobacillus, Ligilactobacillus, Limosilactobacillus, Liquorilactobacillus, Loigolactobacilus, Paucilactobacillus, Schleiferilactobacillus, and Secundilactobacillus. The reclassification of the Lactobacillus genus was reported in Int. J. Syst. Evol. Microbiol. 2020, vol 70, pp. 2782–2858.
Within the human gut the most common LAB genera are Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and Streptococcus. Nearly all of the identified Lactobacillus species have been found residing within the human gut.
Table of Several Gut Microbiota Metabolites Involved in Host Homeostasis
| Acetate | short-chain fatty acid (SCFA) | represents the major SCFA produced by gut microbiota; daily ratio of acetate, butyrate, and propionate is 60:20:20; SCFA absorption is primarily accomplished via the monocarboxylate transporter 1 (MCT1) encoded by the SLC5A8 gene; luminal SCFA also activate numerous receptors on small intestinal enterocytes (FFAR2, FFAR3, HCA1, OR51E2) resulting in the activation of PYY, GLP-1, serotonin, and GABA secretion that then exert effects in the brain that include satiety; interacts with histone deacetylases HDAC1 and HDAC3; contributes to gut barrier integrity; regulates appetite and overall energy homeostasis; inhibits proinflammatory cytokines |
| Acetylcholine | neurotransmitter | more details in Biochemistry of Nerve Transmission page |
| Butyrate | short-chain fatty acid (SCFA) | one of three major SCFA produced by gut microbiota; daily ratio of acetate, butyrate, and propionate is 60:20:20; SCFA absorption is primarily accomplished via the monocarboxylate transporter 1 (MCT1) encoded by the SLC5A8 gene; butyrate provides 60%–70% of the energy demands of enterocytes of the large intestine; luminal SCFA also activate numerous receptors on small intestinal enterocytes (FFAR2, FFAR3, HCA1, OR51E2) resulting in the activation of PYY, GLP-1, serotonin, and GABA secretion that then exert effects in the brain; interacts with histone deacetylases HDAC1 and HDAC3; contributes to gut barrier integrity; regulates appetite and overall energy homeostasis; inhibits proinflammatory cytokines |
| Chenodeoxycholic acid (CDCA) | bile acid | more details in Bile Acid Metabolism page; activates numerous nuclear receptors such as FXR, PXR, VDR (vitamin D receptor), and CAR (constitutive androstane receptor); also binds to several GPCR including GPBAR1 (G-protein coupled bile acid receptor), S1PR2 (sphingosine-1-phosphate receptor 2), formyl peptide receptors, and muscarinic acetylcholine receptors; involved in regulation of the composition of gut microbiota; facilitation of lipid and vitamin absorption; induction of gut hormone secretion; modulation of gut immunity |
| Cholesterol | contributes to bile acid synthesis | |
| Cholic acid | bile acid | more details in Bile Acid Metabolism page; activates numerous nuclear receptors such as FXR, PXR, VDR (vitamin D receptor), and CAR (constitutive androstane receptor); also binds to several GPCR including GPBAR1 (G-protein coupled bile acid receptor), S1PR2 (sphingosine-1-phosphate receptor 2), formyl peptide receptors, and muscarinic acetylcholine receptors; involved in regulation of the composition of gut microbiota; facilitation of lipid and vitamin absorption; induction of gut hormone secretion; modulation of gut immunity |
| Choline | serves as a precursor for the synthesis of acetylcholine, phosphatidylcholines, and betaine (trimethylglycine) | |
| p-Cresol | neurotransmitter | derived from phenylalanine and tyrosine metabolism; impairs dopamine neuron excitability in the ventral tegmental area (VTA); induces autism spectrum-like behaviors; levels of p-cresol are higher in patients with autism spectrum disorders; increased intestinal p-cresol results in increased levels of Duncaniella dubosii, Barnesiella, Muribaculaceae, Anaerobium, and Turicimonas muris and decreased levels of Eisenbergiella, Lacrimispora saccharolytica, Clostridiaceae, Ruthenibacterium lactatiformans, and Anaerobium |
| Deoxycholic acid (DCA) | bile acid | more details in Bile Acid Metabolism page; activates numerous nuclear receptors such as FXR, PXR, VDR (vitamin D receptor), and CAR (constitutive androstane receptor); also binds to several GPCR including GPBAR1 (G-protein coupled bile acid receptor), S1PR2 (sphingosine-1-phosphate receptor 2), formyl peptide receptors, and muscarinic acetylcholine receptors; involved in regulation of the composition of gut microbiota; facilitation of lipid and vitamin absorption; induction of gut hormone secretion; modulation of gut immunity |
| Dimethylglycine | choline metabolite | inhibits bile acid synthesis; contributes to mitochondrial dysfunction; promotes inflammation |
| Dopamine | neurotransmitter | regulates gut motility; more details in Biochemistry of Nerve Transmission page |
| Ethanol | affects intestinal immune responses; damages gut barrier functions | |
| GABA | neurotransmitter | more details in Biochemistry of Nerve Transmission page |
| Homovanillic acid (HVA) | tyrosine metabolism | primarily produced by Bifidobacterium longum (phylum Actinobacteria) and Roseburia intestinalis (phylum Firmicutes); increases production of brain-derived growth factor (BDNF) in the hippocampus; reduces autophagy and promotes synaptic plasticity; higher levels of HVA corelate with reduced incidence of depression |
| Hippuric acid | benzoate metabolism | primarily derived by metabolic actions of LAB on hydroxycinnamic acids (polyphenols) found in many plants; binds to and activates the GPCR originally identified as GPR109A but is now known as hydroxycarboxylic acid receptor 2 (HCA2) which is encoded by the HCAR2 gene; suppresses the activation of NF-κB which is a critical transcription factor in the activation of the immune system; contributes to reduced gut inflammation; hippurate is also formed as a byproduct of one method for the treatment of urea cycle disorders |
| Histamine | neurotransmitter | more details in Biochemistry of Nerve Transmission page |
| 5-Hydroxyindoleacetic acid | tryptophan derivative | primarily derived from serotonin; interacts with and activates the aryl hydrocarbon receptor (AHR); enhancement of oxidative stress and inflammation as a result of increased expression of the cytochrome P450 enzymes encoded by the CYP1A1 and CYP1B1 genes, the interleukin-6 (IL-6) gene, and the transforming growth factor beta 1 (TGFB1) gene |
| 4-Hydroxyphenyllactic acid | tryptophan derivative | primarily derived from serotonin; interacts with and activates the aryl hydrocarbon receptor (AHR); enhancement of oxidative stress and inflammation as a result of increased expression of the cytochrome P450 enzymes encoded by the CYP1A1 and CYP1B1 genes, the interleukin-6 (IL-6) gene, and the transforming growth factor beta 1 (TGFB1) gene |
| Indole | tryptophan derivative | interacts with and activates the aryl hydrocarbon receptor (AHR); enhancement of oxidative stress and inflammation as a result of increased expression of the cytochrome P450 enzymes encoded by the CYP1A1 and CYP1B1 genes, the interleukin-6 (IL-6) gene, and the transforming growth factor beta 1 (TGFB1) gene |
| Indole-3-lactic acid | tryptophan derivative | interacts with and activates the aryl hydrocarbon receptor (AHR); enhancement of oxidative stress and inflammation as a result of increased expression of the cytochrome P450 enzymes encoded by the CYP1A1 and CYP1B1 genes, the interleukin-6 (IL-6) gene, and the transforming growth factor beta 1 (TGFB1) gene |
| Indolepropionic acid (IPA) | tryptophan derivative | also identified as indole-3-propionic acid; interacts with and activates the aryl hydrocarbon receptor (AHR); enhancement of oxidative stress and inflammation as a result of increased expression of the cytochrome P450 enzymes encoded by the CYP1A1 and CYP1B1 genes, the interleukin-6 (IL-6) gene, and the transforming growth factor beta 1 (TGFB1) gene; elevated levels of IPA associated with lower risk for steatohepatitis, chronic kidney disease, and atherosclerosis; IPA has been tested as a therapeutic for Alzheimer disease |
| Isobutyric acid | short-chain fatty acid (SCFA) | activates numerous receptors on small intestinal enterocytes (FFAR2, FFAR3, HCA1, OR51E2) resulting in the activation of PYY, GLP-1, serotonin, and GABA secretion that then exert effects in the brain; interacts with histone deacetylases HDAC1 and HDAC3; contributes to gut barrier integrity; regulates appetite and overall energy homeostasis; inhibits proinflammatory cytokines |
| Isovaleric acid | short-chain fatty acid (SCFA) | activates numerous receptors on small intestinal enterocytes (FFAR2, FFAR3, HCA1, OR51E2) resulting in the activation of PYY, GLP-1, serotonin, and GABA secretion that then exert effects in the brain; interacts with histone deacetylases HDAC1 and HDAC3; contributes to gut barrier integrity; regulates appetite and overall energy homeostasis; inhibits proinflammatory cytokines |
| Kynurenic acid | tryptophan derivative | interacts with and activates the aryl hydrocarbon receptor (AHR); enhancement of oxidative stress and inflammation as a result of increased expression of the cytochrome P450 enzymes encoded by the CYP1A1 and CYP1B1 genes, the interleukin-6 (IL-6) gene, and the transforming growth factor beta 1 (TGFB1) gene |
| Lactate | organic acid | predominantly produced by lactic acid bacteria (LAB); LAB includes those genera that use carbohydrates as their only (or primary) source of energy; LAB include more than 60 genera with the most common in human gut being Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, Streptococcus, and Enterococcus; LAB are common in fermented milk products such as yogurt; binds to and activates the GPCR originally identified as GPR81 but is now known as hydroxycarboxylic acid receptor 1 (HCA1) which is encoded by the HCAR1 gene; in the periphery lactate modulates lipid metabolism in adipose tissue and inhibits ghrelin secretion from the stomach A (X-like) cells |
| Lithocholic acid (LCA) | bile acid | more details in Bile Acid Metabolism page; activates numerous nuclear receptors such as FXR, PXR, VDR (vitamin D receptor), and CAR (constitutive androstane receptor); also binds to several GPCR including GPBAR1 (G-protein coupled bile acid receptor), S1PR2 (sphingosine-1-phosphate receptor 2), formyl peptide receptors, and muscarinic acetylcholine receptors; involved in regulation of the composition of gut microbiota; facilitation of lipid and vitamin absorption; induction of gut hormone secretion; modulation of gut immunity |
| Menaquinone | vitamin K | commonly identified as vitamin K2 |
| Norepinephrine | neurotransmitter | more details in Biochemistry of Nerve Transmission page |
| Phenylethylamine (PEA) | neurotransmitter | most common form of PEA in humans in β-phenylethylamine (β-PEA); functions by binding to and activating receptors of the trace amine receptor family, predominantly TAAR1; likely activates aminergic neurons in the CNS leading to elevation in mood and and energy level as well as enhanced aggression |
| Phylloquinone | vitamin K | commonly identified as vitamin K1 |
| Propionate | short-chain fatty acid (SCFA) | one of three major SCFA produced by gut microbiota; daily ratio of acetate, butyrate, and propionate is 60:20:20; SCFA absorption is primarily accomplished via the monocarboxylate transporter 1 (MCT1) encoded by the SLC5A8 gene; luminal SCFA also activate numerous receptors on small intestinal enterocytes (FFAR2, FFAR3, HCA1, OR51E2) resulting in the activation of PYY, GLP-1, serotonin, and GABA secretion that then exert effects in the brain; interacts with histone deacetylases HDAC1 and HDAC3; contributes to gut barrier integrity; regulates appetite and overall energy homeostasis; inhibits proinflammatory cytokines |
| Serotonin | neurotransmitter | regulates gut motility; more details in Biochemistry of Nerve Transmission page |
| Taurine | amino acid | one of the most abundant amino acids in skeletal muscle, brain, and retina; in the retina taurine functions in photoreceptor development; in the brain taurine serves as a cytoprotectant against stress-related neuronal damage and other pathological conditions; is also an organic osmolyte involved in the regulation of cell volume; plays important roles in the modulation of intracellular free calcium concentration and in the protection from mitochondrial stress |
| Taurocholic acid (TCA) | bile acid | more details in Bile Acid Metabolism page; activates numerous nuclear receptors such as FXR, PXR, VDR (vitamin D receptor), and CAR (constitutive androstane receptor); also binds to several GPCR including GPBAR1 (G-protein coupled bile acid receptor), S1PR2 (sphingosine-1-phosphate receptor 2), formyl peptide receptors, and muscarinic acetylcholine receptors; involved in regulation of the composition of gut microbiota; facilitation of lipid and vitamin absorption; induction of gut hormone secretion; modulation of gut immunity |
| Trimethylamine N-oxide | choline metabolite | inhibits bile acid synthesis; contributes to mitochondrial dysfunction; promotes inflammation |
| Tryptamine | neurotransmitter | derived from tryptophan; more details in Biochemistry of Nerve Transmission page; interacts with trace amine receptors (TAAR1, TAAR2, TAAR5, TAAR6, TAAR8, and TAAR9) in brain; negative control of dopaminergic neural activity |
| Ursodeoxycholic acid (UDCA) | bile acid | more details in Bile Acid Metabolism page; activates numerous nuclear receptors such as FXR, PXR, VDR (vitamin D receptor), and CAR (constitutive androstane receptor); also binds to several GPCR including GPBAR1 (G-protein coupled bile acid receptor), S1PR2 (sphingosine-1-phosphate receptor 2), formyl peptide receptors, and muscarinic acetylcholine receptors; involved in regulation of the composition of gut microbiota; facilitation of lipid and vitamin absorption; induction of gut hormone secretion; modulation of gut immunity |
Gut Bacteria: Roles in Metabolism, Obesity, and Immunity
Given that obesity, insulin resistance, and type 2 diabetes are all associated with low-grade systemic inflammation of unclear etiology, it has been proposed that one mechanism leading to this state involves inflammatory modulation by gut bacteria. High-fat diet-induced obesity has been shown to be correlated with the increased expression of several pro-inflammatory cytokines including IL-1, IL-6, MCP-1, and TNF-α. In particular, TNF-α is known to cause insulin resistance and the levels of TNF-α are elevated in individuals with non-alcoholic fatty liver disease, NAFLD.
Bacterial lipopolysaccharide (LPS) evokes an inflammatory response triggering the secretion of many pro-inflammatory cytokines. LPS is continuously produced by gut bacteria through the lysis of dead and dying Gram-negative bacteria. LPS binds to a complex of CD14 and the toll-like receptor 4 (TLR4) on cells of the innate immune system resulting in the secretion of pro-inflammatory cytokines. LPS is also transported from the gut to peripheral tissues via interaction with chylomicrons. Since the rate of chylomicron synthesis is elevated in response to a high-fat and/or high-carbohydrate diet there will be more LPS uptake in obese individuals due to the elevated intake of lipids and carbohydrates.
The fat-induced increase in LPS uptake is referred to as metabolic endotoxemia. The role of a high-fat diet in triggering metabolic endotoxemia can be mimicked in the absence of dietary fat by direct infusion of LPS. When these experiments are carried out in mice fed a fat-restricted diet, LPS infusion resulted in fasting hyperglycemia, obesity, steatosis, infiltration of macrophages into adipose tissue, insulin resistance and hyperinsulinemia. These are the same conditions that are observed in mice fed a high-fat diet.
Gut bacteria have also been shown to play a role in the secretion of gastrointestinal hormones that function in digestion and appetite control. One very important gut hormone is glucagon-like peptide-1 (GLP-1). GLP-1 is called an incretin which is a term referring to a substance that promotes pancreatic insulin secretion in response to food intake. For detailed information on GLP-1 see the Gut-Brain Interrelationships and Control of Feeding Behavior page. The role of GLP-1 in the regulation of digestion, insulin secretion, and appetite is precisely the reason it is a current pharmaceutical target in the treatment of hyperglycemia and type 2 diabetes. GLP-1 is secreted from specialized enteroendocrine cells (L-cells) of the ileum and colon and the composition of the diet affects the release of this hormone. Dietary fat and glucose stimulate GLP-1 release but dietary proteins do not appear to be involved in its secretion.
When animals are fed a high fiber diet composed of non-digestible oligofructose, which can be fermented by gut bacteria, there is an increase in GLP-1 release. In addition, feeding animals oligofructose results in increased enteroendocrine L-cell proliferation in the proximal colon and this contributes to a higher level of GLP-1 release. When rats are fed a high-fat diet which also includes oligofructose there is an improvement in the diabetes induced by the high-fat diet alone. In humans, the consumption of oligofructose protects against weight gain, reduces fat accumulation, reduces serum triglyceride accumulation, and promotes satiety. These effects are presumably due, in part, to changes in the composition of gut microbiota as is seen in experimental animals.
Numerous experiments have identified both direct and indirect effects of gut microbiota and their metabolites on overall host metabolism and control of body mass. Some of these direct effects include alteration in the amount of calories that are made available from the diet and how readily they are absorbed from the gut. Indirect mechanisms include the modification of host-derived compounds that then modulate host metabolic processes.
Major gut microbiota derived metabolites that exert significant effects on host metabolism and neurological functions, such as appetite regulation, are the short-chain fatty acids (SCFA), predominantly acetate, butyrate, and propionate. As indicated in the Table above, gut microbiota produce these three SCFA in a molar ratio of approximately 60:20:20.
SCFA produced by gut microbiota are involved in the regulation of luminal pH and mucus production, and modulate mucosal immune functions. Gut microbiota-derived SCFA are major fuels for energy production by intestinal epithelial cells. The SCFA also enter the systemic circulation where they contribute to metabolic processes of peripheral tissues and contribute to overall energy homeostasis as a result of inducing a reduction in hepatic glucose and lipid production.
Gut microbiota-derived SCFA bind to numerous receptors on the surface of intestinal epithelial cells leading to increased synthesis and release of neuropeptides that then affect functions in the central nervous system, in particular the regulation of feeding behaviors. These actions of gut-derived SCFA constitute a significant arm of the gut-brain axis.
The lipid-sensing receptors that bind SCFA include FFAR2 (GPR43), FFAR3 (GPR41), HCAR1 (GPR109A), and olfactory receptor family 51 subfamily E member 2 (OR51E2; homolog of murine OLFR78 gene). Sensing of the SCFA by these receptors, results in the modulation of a variety of physiological and hormonal processes that ultimately contribute to whole body energy sensing. FFAR2 is expressed on enteroendocrine A (X-like) cells of the stomach that secrete ghrelin and on enteroendocrine L cells that secrete GLP-1, GLP-2, PYY, OXM, and serotonin. FFAR3 is also expressed on enteroendocrine L cells.
The enhancement of GLP-1 and PYY release from intestinal enteroendocrine cells, in response to gut microbiota produced SCFA, contributes to control of feeding behaviors via effects in the hypothalamus. Experiments performed in mice have shown that administration of SCFA exhibits a direct benefit with respect to the control of overall appetite and body weight. Despite the fact that there is, as yet, no conclusive evidence that similar results occur in humans, there is evidence that increasing colonic propionate reduces appetite in humans and contributes to the prevention of weight gain. Methods to increase SCFA production in human gut may very well prove a useful strategy for the non-pharmacologic prevention of obesity.
OR51E2, expressed in renal juxtaglomerular cells, is responsible for renin release in response to SCFA. This effect of gut bacteria-derived SCFA on renal function plays an important role in overall regulation of blood pressure.
The primary bile acids, cholic acid (CA) and chenodeoxycholic acid (CDCA), are produced from cholesterol in the liver. These primary bile acids are conjugated to amino acids, primarily glycine or taurine, to facilitate their solubility. The liver then transports the bile acids into the bile canaliculi where they are transported for storage in the gallbladder. Upon their release into the small intestine they facilitate dietary fat digestion and absorption and fat-soluble vitamin absorption.
Bile acids are metabolized by gut microbiota releasing the amino acids which the bacteria utilize for energy production. The action of gut bacterial enzymes generates what are referred to as the secondary bile acids which includes, but is not limited to, deoxycholic acid (DCA), lithocholic acid (LCA), and ursodeoxycholic acid (UDCA). These gut microbiota-derived bile acid metabolites serve as signaling molecules that function as key regulators of systemic metabolism.
Bile acids and their metabolites bind to and activate nuclear receptors that includes the farnesoid X receptor (FXR), the vitamin D receptor (VDR), the pregnane X receptor (PXR), and the constitutive androstane receptor (CAR). Bile acids and metabolites also bind to and activate plasma membrane localized receptors of the GPCR family that includes G-protein coupled bile acid receptor 1 (GPBAR1). GPBAR1 was also identified as GPR131 and as TGR5 (Takeda G protein-coupled receptor 5).
Within the gut the activation of receptor signaling by bile acids results in increased synthesis and secretion of PYY, GLP-1, and fibroblast growth factor 19 (FGF19). The release of PYY and GLP-1 contribute to satiety effects elicited by the hypothalamus as well as to modulation of systemic energy expenditure. GLP-1 also activates the pancreas to increase the synthesis and release of insulin. Intestinal FGF19 enters the portal circulation where it activates hepatocyte FGF receptors resulting in reduced synthesis of bile acids. The activation of GPBAR1 in brown adipose tissue results in activation of uncoupling protein 1, UCP1 (thermogenin) leading to enhanced energy expenditure.