Acetate is another SCFA produced by gut bacteria through the fermentation of prebiotic fibers like inulin and GOS or unabsorbed peptides and fats. Gut-derived acetate production is tightly regulated within the microbiome and determined by the presence of prebiotic fiber and the balance between saccharolytic and proteolytic fermentation. Acetate is used for cholesterol synthesis and lipogenesis but can also be utilized by muscle tissue. Additionally, some gut bacteria like Roseburia spp and Faecalibacterium prausnitzii can convert acetate into butyrate. Excessive acetate production combined with insufficient butyrate production can lead to fat gain, particularly around the liver.
Acetate Producer
In ecology, Alpha Diversity describes a particular ecosystem by combining information about the number of species observed and their abundance. This marker evaluates your gut microbiome by looking at your own personal species diversity, which can be negatively affected by antibiotics, environmental toxins, stress, diet, or other factors. This can lead to the microbiome being dominated by only a few species. A high Alpha Diversity indicates that the ecosystem has many species and their abundance is balanced, which is typically associated with a healthy microbiome.
Ammonia Production and Detoxification in the Gut Ammonia is a normal by-product of the microbial fermentation of amino acids, particularly glutamine. This process is carried out by various commensal bacteria, including Clostridia, Enterobacteria, Bacillus spp., E. coli, Staphylococcus, and Fusobacterium. In Gram-negative gut bacteria, ammonia plays a crucial role in nitrogen anabolism, which is necessary for producing essential compounds such as amino acids, NAD, pyrimidines, purines, and amino sugars. The production of ammonia by these bacteria is associated with three key enzymes: glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH). Glutamine Synthase and Ammonia Detoxification Glutamine synthetase is also present in human tissues, including skeletal muscles, the brain, and the liver. This enzyme synthesizes glutamine from glutamate and ammonia, effectively detoxifying excess ammonia from the body. Ammonia produced in the gut is transported to the liver, where it is converted into urea and excreted through urine.Two primary detoxification processes in the liver—the urea cycle and glutamine synthetase activity—depend on a healthy gut microbiota, a well-functioning liver, and a balanced diet. While ammonia detoxification via glutamine synthetase is observed in certain microbial species, such as H. pylori, the extent of detoxification by gut microbes remains unclear.An overgrowth of ammonia-producing bacteria, combined with excessive protein intake and liver or kidney dysfunction, can lead to elevated ammonia levels in the blood, a condition known as hyperammonemia. This condition is harmful to both the brain and the liver. Bacterial strains that lack urease activity can help reduce ammonia concentrations in the gut by outcompeting ammonia-producing bacteria. The Role of Lactulose Lactulose is an effective treatment for reducing ammonia levels in the gut and bloodstream. It is a disaccharide that gut bacteria can ferment to produce monosaccharides, volatile fatty acids, hydrogen, and methane. Lactulose reduces ammonia production and absorption through three main mechanisms: Laxative Effect: Lactulose increases the excretion of ammonia by promoting bowel movements. Increased Gut Acidity: Lactulose lowers gut pH, which encourages gut bacteria to take up ammonia as a nitrogen source for protein synthesis. In an acidic environment, ammonia (NH3) is converted to ammonium (NH4+), which cannot cross the gut barrier and enter the bloodstream. Reduced Ammonia Production: The acidic pH inhibits urease-producing bacteria that contribute to ammonia production. Additionally, lactulose inhibits intestinal glutaminase activity, blocking the uptake of glutamine and its conversion to ammonia. These mechanisms highlight the importance of gut transit time, pH levels, and methane production in preventing hyperammonemia. The Role of Prebiotic Fibers Prebiotic fibers can have similar effects as lactulose by promoting the production of short-chain fatty acids (SCFAs), which lower intestinal pH and improve transit time. Butyrate, a type of SCFA, is known to scavenge ammonia. Interventions that enhance SCFA production are beneficial for controlling excessive ammonia production.Inability to clear ammonia can lead to hyperammonemia, contributing to conditions such as hepatic encephalopathy. Recent studies suggest that B. subtilis HU58 can reduce blood ammonia levels and is a safe and effective option for patients with hepatic encephalopathy. Additionally, strains like Lactobacillus casei and L. plantarum have shown significant reductions in blood ammonia levels when taken with fermentable fibers. Dietary Considerations To manage ammonia levels, it may be beneficial to restrict glutamine, the substrate for ammonia synthesis. Foods high in glutamine include beef, pork, poultry, milk, yogurt, ricotta cheese, cottage cheese, raw spinach, raw parsley, and cabbage.Gradually increasing the intake of resistant starches and cellulose can also aid in ammonia detoxification. When adding fibers to the diet, it is advisable to do so gradually for the best results. Foods rich in these fibers include plantains, green bananas, beans, peas, lentils, whole grains, bran, nuts, root vegetables, and apple skins. This version maintains the original scientific content while improving clarity and readability through shorter sentences, clear headings, and a more structured format.
Beta Diversity is the variation of species when comparing the composition of two separate ecosystems. This marker compares the composition of your gut microbiome to healthy populations in order to illustrate notable differences. A higher Beta Diversity is preferred.
Acetate Producer
GABA Producer
Acetate Producer
a sulfate-reducing bacterium
Butyrate is used as an energy source by intestinal epithelial cells, but it also serves numerous other functions, such as improving gut barrier function, scavenging ammonia, regulating the immune system, reducing oxidative stress, balancing blood glucose levels, and much more. Butyrate production is most commonly associated with fiber fermentation. However, butyrate formation can occur through fermentation of amino acids such as glutamate, lysine, histidine, cysteine, serine, and alanine. Amino acid fermentation typically occurs in less acidic conditions, and while it may result in some SCFA formation, it can also form potentially damaging metabolites such as phenols and ammonia. Gut pH also directly impacts butyrate production. Mildly acidic environments stunt the growth of Bacteroides, but not Firmicutes or Actinobacteria. This has the effect of limiting propionate formation and boosting butyrate formation, particularly at pH of 5.5, compared to a more neutral pH of 6.5-6.8. Lactobacillus species may indirectly boost butyrate production by increasing the acidity of the gut. A healthy carbohydrate diet (HCD) rich in cereal fibre, arabinoxylan, and resistant starch enhances Bifidobacteria and butyrate production, while diets high in refined grains can decrease the production of butyrate. Reducing sugar intake is recommended to increase butyrate production, as it is a signaling molecule for blood sugar control. Studies show that high-fat and high-sodium diets reduce butyrate concentrations. Lower fat, high carbohydrate diets, with plenty of resistant starch, boosts butyrate production and enhances abundance of Faecalibacterium and Blautia. Eubacterium spp., Roseburia spp., Faecalibacterium prausnitzii, and Clostridium cluster XIVa and IV, are primary producers of butyrate.36 Roseburia inulinivorans and Coprococcus catus, switch between butyrate and propionate production depending on the fermentation substrates. It is also worth noting that F. prausnitzii can convert acetate into butyrate, which may contribute to its anti-inflammatory reputation.
Bile Acids Metabolism
Escherichia coli, commonly known as E. coli, is a diverse group of bacteria that typically live in the intestines of humans and animals. Most strains of E. coli are harmless and play an important role in maintaining a healthy gut microbiome. However, some pathogenic strains can cause serious infections, particularly in the urinary tract, gastrointestinal system, and bloodstream. These pathogenic strains can be acquired through contaminated food or water and may result in symptoms such as diarrhea, abdominal pain, and, in severe cases, kidney failure.
The estrobolome is a network of over 60 genera of bacteria that can recycle or deconjugate inactivated estrogens for reabsorption into circulation by producing very powerful enzymes. This recycling process is handled by gut bacteria with beta-glucuronidase and beta-glucosidase activity. When the estrobolome is too abundant, the body is unable to efficiently eliminate estrogen, causing estrogens to build up and ultimately leading to estrogen dominance. On the other hand, if estrogen recycling (estrobolome) is too low, then this may lead to insufficient levels of estrogen in circulation.
Butyrate Producer
Butyrate Producer
In adults, Firmicutes and Bacteroidetes are the most abundant bacterial phyla in the gut. The Firmicutes to Bacteroidetes (F/B) abundance ratio was shown to increase from infancy to adulthood and subsequently to decrease again in the elderly. Elevated F/B ratios have been linked to obesity though the evidence is not conclusive.
Gamma-aminobutyric acid (GABA) is a neurotransmitter, or chemical messenger, in the brain that blocks specific signals in the central nervous system in order to slow down the brain. This provides a protective and calming effect on the brain and body. High fat diets are shown to reduce GABA levels in the prefrontal cortex by 40% which can result in various mood imbalances and difficulty sleeping.
Glutathione Production on a BiomeFx Panel Glutathione is a powerful antioxidant produced in the body, playing a critical role in protecting cells from oxidative stress and maintaining overall cellular health. On a BiomeFx panel, the marker for glutathione production indicates the capacity of the gut microbiota to contribute to the synthesis of this vital molecule. Adequate glutathione levels are essential for detoxification processes, immune function, and the neutralization of free radicals. Low levels of glutathione production can be associated with increased susceptibility to chronic diseases, inflammation, and compromised immune response. Factors influencing glutathione production include diet, lifestyle, gut health, and genetic predispositions. Monitoring and supporting glutathione production through nutritional interventions, such as increasing intake of sulfur-rich foods (e.g., garlic, onions, cruciferous vegetables), antioxidants, and specific supplements, can enhance the body’s antioxidant defenses and promote overall well-being.
an overall score for gut microbiome health
Histamine can be produced in the gut and travel to distant areas of the body, where it may induce unfavorable symptoms. Patients with an overabundance of histamine-producing bacteria should focus on strengthening intestinal barrier function, as a leaky gut can allow gut derived histamines to enter circulation and promote dietary intolerances or disruption in healthy allergic responses. High levels of gut derived histamine are associated with high abundance of Proteobacteria, Roseburia, Morganii morganii, and Klebsiella pneumoniae and decreased abundance of Bifidobacterium.
Hydrogen sulfide (H2S) is a byproduct of dietary sulfur and hydrogen gas. The bacteria that produce H2S are known as hydrogen sulfide producers or sulfate-reducing bacteria (SRB). H2S can be produced by numerous bacterial species of the Proteobacteria and Firmicutes phylum, including genera such as Clostridium, Escherichia, Salmonella, Klebsiella, Streptococcus, Desulfovibrio, and Enterobacter. High-protein diets are believed to increase H2S by supplying the sulfide-rich amino acid, cysteine, which can be easily converted to H2S. Additionally, cruciferous vegetables (cabbage, cauliflower, kale, broccoli, etc) and durian fruit can directly release H2S during digestion. At low concentrations, hydrogen sulfide is protective for the gut barrier. However, too much hydrogen sulfide leads to a disruption in ATP synthesis within mitochondria, which can destabilize the gut mucosal layer and promote inflammation. Interestingly, sulfate reduction, acetogenesis, and methanogenesis compete for H2, which is produced by hydrogenotrophic microbes. The end-product is dependent on substrate availability, hydrogenotrophic microbes. The end-product is dependent on substrate availability, thermodynamics, and pH. The human gut environment favors methanogenesis, due to the neutral pH of stool and low sulfate levels in diet.88 However, if consuming high amounts of dietary sulfate (i.e. bread, beer, wine) with low stomach acid, sulfate reduction may overtake methanogenesis.88 As with many things in the human body, balance is key. Overproduction of hydrogen sulfide is detrimental to intestinal health. Reducing H2S production can be accomplished by limiting cysteine and homocysteine in diet, which are sulfur containing amino acids. Increasing H2S production can be accomplished through amino acid supplementation and cruciferous vegetable intake.
Indole is a byproduct of the microbial degradation of tryptophan that can be utilized in a variety of ways in the gut microbiome. Indole can bind to serotonin receptors in order to regulate behavior, gut motility, and food intake, and it can support immune and intestinal health by interacting with gut microbes, scavenging free radicals, and increasing the expression of xenobiotic-metabolizing enzymes like cytochrome P450. Indole also functions as a signaling molecule that may be increased during latent infections. Indole production must be balanced, as too much indole may produce unwanted changes in mood or cognition, yet insufficient indole production may damage the gut barrier.
Lactate is an intermediate of carbohydrate metabolism, produced from pyruvate during lactic acid fermentation. Lactate also plays important roles in immunomodulation and inflammation modulation. These species use lactate as a substrate for SCFA production. However, if there is an overabundance of lactate producers paired with low abundance of lactate utilizers (SCFA producers) this will cause a surge of lactate in the gut which can be toxic and harmful to host tissues.
Lactate Producer
Methane production, measured on the BiomeFx testing panel, provides critical insights into the activity of methanogens—a group of microbes that convert compounds like acetate, ammonia, hydrogen gas, and trimethylamines (TMA) into methane gas. Methanogens are a normal part of the gut microbiome, but their activity can significantly influence digestive health and gut function. How Methane Impacts the Gut Methane gas plays a key role in modulating gut motility. Elevated methane production can slow intestinal transit, which may result in: Constipation or altered bowel movements, due to delayed gut motility. Increased nutrient absorption, as food spends more time in the intestines. Digestive discomfort, often linked to an imbalance in microbial populations. Methanogens also compete with acetate-producing microbes for available substrates. This competition may disrupt normal metabolic processes and is indirectly associated with digestive issues such as bloating, gas, or irregular bowel habits.
Oxalate Degradation
Phenols, including phenol and p-cresol, are aromatic compounds that result from the microbial fermentation of aromatic amino acids, such as tryptophan and tyrosine. These compounds are cytotoxic and may cause damage to the gut, skin, vascular system, kidneys, and more. Tyrosine tends to be metabolized to phenol by Escherichia coli, Proteus spp., and Streptococcus faecalis, whereas it tends to be metabolized to p-cresol by strictly anaerobic gut bacteria such as Bacteroides fragilis, Fusobacterium spp., and Clostridium spp. Tryptophan is abundant in foods such as cheese, poultry, red meat, egg whites, and seeds; and therefore, these foods can increase phenol production in the gut. Similarly, tyrosine is also present in protein-rich foods including beef, pork, chicken, fish, chicken, tofu, milk, cheese, beans, seeds, nuts, and whole grains. When paired with a diet low in fermentable fibers, these foods have the potential to dramatically increase phenol and p-cresol production, as gut microbes are forced to use amino acids for energy. Increasing gut acidity through the intake of resistant starches, galactooligosaccharides, and fructooligosaccharides may reduce the production of these toxic metabolites.
Bile Acids Metabolism
Bile Acids Metabolism
Low levels of pathogens can be normal and characteristic of a healthy, diverse gut microbiome. Increased levels of pathogens, however, could indicate that a pathogen is playing a role in symptoms you are experiencing. The Pathogen Control Index compares the relative abundances (RA) of specific pathogens to normal levels present in the healthy gut. Note: BiomeFx is NOT a diagnostic test. If your Pathogen Control Index is low, consult your physician who can make a diagnosis and provide treatment if needed.
Propionate Producer
Polyamines like putrescine, spermidine, and cadaverine are metabolites of arginine and tyrosine that have many important roles in the gut like stabilizing RNA and DNA structures, supporting protein synthesis, and scavenging free radicals. However, high amounts of polyamines can be toxic to the gut microbiome. Gut bacteria primarily synthesize amines from amino acids. Generally speaking, Gram-positive bacteria tend to reduce the concentration of amines, while Gram-negative species produce amines and increase their concentration.
High Prevotella:Bacteroides ratios are associated with lower BMI and reduced incidence of chronic, inflammatory disease. Low Prevotella:Bacteroides ratios are associated with metabolic imbalances and are positively correlated with high intake of protein and animal fat as typical for a Western diet. Higher abundance of Prevotella is observed in individuals that consume diets rich in carbohydrates and fiber. Bacteroides is increased by sugar and saturated fat intake, while Prevotella generally thrives on fiber rich foods, like fruit, vegetables, beans, and whole grains. Levels of Prevotella tend to decrease with age.
Propionate is a SCFA that can be produced by gut bacteria through the fermentation of key fibers or the metabolism of lactate. Propionate supports a healthy immune system by encouraging regulatory T cell differentiation in gut associated lymphoid tissues (GALT), and it also promotes gluconeogenesis in the liver, supports insulin sensitivity, and improves gut hormone production. Propionate and butyrate both work together to support healthy inflammatory responses by inhibiting histone deacetylases (HDACs) in macrophages and dendritic cells.
Gram-negative Proteobacteria are a source of lipopolysaccharide associated with metabolic endotoxemia. Bifidobacterium species within Actinobacteria produce health-promoting metabolites like IL-10, SCFA, and GABA. Consuming a balanced diet with a wide variety of fibers, polyphenols, and a healthy level of fat can help balance this ratio.
This section explores the presence and abundance of a panel of antibiotic resistance genes in the gut microbiome, and compares that to healthy population. The resistome is the sum of antimicrobial resistance genes in your gut. High number of resistance functions in your gut will make pathogens less likely to be sensitive to antibiotics and may be an indication that virulent strains are flourishing.
Butyrate Producer
Cellulose Degrader
Sutterella wadsworthensis is a fascinating microbe that's part of the normal gut flora in many people. This gram-negative, non-spore-forming bacterium is known for its ability to thrive in bile-rich environments, which explains its presence in the intestines and bile ducts. While S. wadsworthensis is found in about 50-60% of healthy individuals, its role in gut health is still being explored. On a BiomeFX report, elevated levels of S. wadsworthensis might catch your attention. This could indicate potential changes in your gut microbiome balance, possibly linked to dietary factors like high consumption of saturated fats or taurine-rich foods. Some studies have associated higher levels of S. wadsworthensis with conditions like inflammatory bowel disease and autism spectrum disorders, though the exact relationship is still under investigation. It's important to note that while its presence isn't inherently harmful, an overgrowth might be worth discussing with your healthcare provider, especially if you're experiencing any digestive issues or have concerns about your metabolic health.
Thiamin is a vitamin that plays a critical role in energy metabolism, especially in the brain and nervous system. Thiamin also plays an important role in muscle contraction and nerve conduction. Faecalibacterium spp utilize thiamine but do not produce it, indicating that there is a competition for vitamins within the gut microbiome.
Vitamin B12 (cobalamin) is a cobalt-containing vitamin that catalyzes the synthesis of the amino acid methionine. B12 is also crucial for healthy red blood cells, brain and nervous system function, DNA regulation, and metabolism. B12 can be found in animal products, such as meat and eggs, but it can also be produced by gut bacteria and rapidly absorbed into the intestines. In fact, gut-derived B12 production contributes up to 31% of the daily recommended intake for this nutrient. Bacterial vitamin B12 is synthesized by Pseudomonas denitrificans, Bacillus megaterium, Propionibacterium freudenreichii, Bacteroides fragilis, Prevotella copri, Clostridium difficile, Faecalibacterium prausnitzii, Ruminococcus lactaris, Bifidobacterium animalis, B. infantis, B.longum, and Fusobacterium varium. Furthermore, Lactobacillus plantarum and L. coryniformis isolated from fermented food produce vitamin B12, and Bifidobacterium animalis synthesizes vitamin B12 during milk fermentation.
Vitamin B2 (riboflavin) is a cofactor for the TCA cycle and fatty acid beta-oxidation. Therefore, it helps with extracting energy from nutrients. In addition, research suggests that vitamin B2 is associated with the differentiation and function of immune cells through the regulation of fatty acid beta-oxidation. Bacteroides fragilis and Prevotella copri (Bacteroidetes); Clostridium difficile, Lactobacillus plantarum, L. fermentum, and Ruminococcus lactaris (Firmicutes) express factors essential for vitamin B2 synthesis, suggesting that these bacteria are an important source of vitamin B2 in the large intestine.
Pantothenic acid is a precursor of coenzyme A (CoA), an essential cofactor for the TCA cycle and fatty acid beta-oxidation. Vitamin B5 is thus essential for gaining energy from food as well as generating energy for immune cells. Vitamin B5 is found in foods such as liver, eggs, chicken, and fermented soybeans. Vitamin B5 derived from gut bacteria exists as free pantothenic acid, which is directly absorbed in the large intestine, converted to CoA, and distributed in the same way as dietary vitamin B5. Bacteroides fragilis, Prevotella copri, Ruminococcus lactaris, Ruminococcus torques, Salmonella enterica, and Helicobacter pylori produce vitamin B5 endogenously. In contrast, most Fusobacterium, Bifidobacterium spp., Faecalibacterium spp., Lactobacillus spp., and some strains of Clostridium difficile are not able to produce B5, yet they need it for their growth, suggesting that these bacteria compete with the host for vitamin B5 utilization.
Vitamin B6 is an incredibly versatile nutrient that supports immunity, brain function, and protein metabolism. It is also a necessary, rate limiting cofactor for neurotransmitter production, including dopamine, serotonin, gamma-aminobutyric acid (GABA), noradrenaline, and the hormone melatonin. This nutrient is found abundantly in foods, particularly fish, chicken, tofu, sweet potato, and avocado. B6 can also be produced by commensal gut species including Bacteroides fragilis, Prevotella copri, Bacillus clausii, Corynebacterium glutamicum, Listeria monocytogenes, Streptococcus mutans, Bifidobacterium longum, Collinsella aerofaciens, and Helicobacter pylori. Human gut microflora contribute up to 86% of the daily recommended intake of B6.
Biotin is a water soluble vitamin necessary for growth, development, and energy production and may support healthy hair, skin, and nails. Biotin also acts as a cofactor for 5 carboxylases and plays an important role in balancing immune responses. Biotin is synthesized from tryptophan by intestinal bacteria and can also be found in foods such as meat, beans, milk, and cereal grains. Interestingly, when the human body is deficient in biotin, intestinal cells can actually increase the biotin uptake process, allowing the human host to feed off of biotin produced by the gut microbiome. Bacteroides fragilis, Prevotella copri, and several members of the Proteobacteria phylum possess a vitamin B7 biosynthesis pathway. In contrast, species belonging to Prevotella, Bifidobacterium, Clostridium, Ruminococcus, Faecalibacterium, and Lactobacillus are unable to produce biotin yet need it for survival, suggesting that these bacteria may compete with the host for biotin utilization. Free biotin in the gut can change the composition of the gut microbiome and is linked to the overgrowth of Lactobacillus murinus and unfavorable outcomes. Furthermore, Bifidobacterium longum produces a B7 precursor that enhances vitamin B7 production by other intestinal bacteria. Gut bacteria only contribute about 5% of the daily recommended intake of B7 for adults, so it is important to ensure adequate biotin intake from the diet and/or supplementation.
Vitamin B9 (folate or tetrahydrafolate), is essential for healthy blood cells. Gut-derived folate is directly absorbed into the colon, contributing up to 37% of the daily recommended intake. If vitamin B9 producers are low, there could be low levels of this nutrient available to the body. -------------------- A balanced and healthy gut microbiome is necessary for the proper digestion of food and the production of essential nutrients. Gut bacteria synthesize vitamin K2 and many of the B vitamins including biotin, cobalamin, folates, nicotinic acid, pantothenic acid, pyridoxine, riboflavin, and thiamine. Bacteroidetes synthesize the majority of B vitamins, however Fusobacteria, Proteobacteria, Firmicutes, and Actinobacteria are also capable of completing this task. Vitamin K2 is produced by many members of gut bacteria including Bacillus subtilis, E. coli, certain species of Lactobacillus, and others. It appears that the most important factor in a well-rounded vitamin synthesis microbial network is the diversity of microbial species. For example, antibiotic usage is linked to poor vitamin K status, yet during periods of low vitamin K intake, a diverse and balanced gut microbiome can make up for dietary insufficiencies. In addition, vitamin synthesis requires a complex cross-feeding relationship among various bacterial species, underscoring the importance of diversity for vitamin production. Generally speaking, Bacteroidetes produce the greatest number of B vitamins. Riboflavin and biotin are produced by nearly all members of Bacteroidetes, Fusobacteria, and Proteobacteria, while Firmicutes and Actinobacteria produce very little. Fusobacteria produces the greatest amount of vitamin B12. These biologically important bacteria can help you understand your unique vitamin needs based on the status of your gut microbiome.
Vitamin K2 is a fat-soluble vitamin necessary for calcium metabolism and critical for the health of teeth, bones, nerves, and the cardiovascular system. Most K2 comes from dietary sources, however, gut bacteria including Escherichia coli, Bacteroides vulgatus, Bacillus subtilis and Bacteroides fragilis can also produce K2 endogenously. However, microbially derived K2 has protective role against oxidative tissue damage in the gut.
