Bacteria of Interest

Acidaminococcus is a genus of bacteria that digests amino acids to produce important short chain fatty acids including butyrate.

Taxonomic Level: Genus

Family: Acidaminococcaceae

Properties: Gram-negative, Anaerobic, Nonsporulating

Additional Information: Bacteria of the genus Acidaminococcus have the ability to use amino acids as their sole energy source for growth. One species of this genus is known to digest a specific type of amino acid called glutamic acid to produce butyrate, a short chain fatty acid which has many beneficial health implications, including protection against inflammatory bowel disease, diabetes, obesity, and cancer (please see the functional analysis section of your report to learn more about butyrate).

Actinobacteria is a phylum of bacteria that are common in the gastrointestinal tract, and two of their most notable genuses include Bifidobacterium and Collinsella.

Taxonomic Level: Phlyum

Properties: Gram-positive

Additional Information: Actinobacteria are abundant in the human gastrointestinal tract. One notable genus Bifidobacterium is known to have a generally beneficial effect on health. They tend to have a lower abundance in a number of diseases including vitamin K deficiency, atopic diseases, irritable bowel syndrome. They also have been noted at a lower abundance in autism spectrum disorder. Another dominant genus in the Actinobacteria phylum is Collinsella. Collinsella bacteria are capable of fermenting a wide variety of carbohydrates to produce hydrogen gas, ethanol, formate, and lactate (please see the functional analysis section of your report to learn more about the beneficial health implications of lactate). A high abundance of Collinsella has also been found to be associated with plasma cholesterol levels.

Adlercreutzia equolifaciens metabolizes a specific type of soybean isoflavone to equol, a molecule with many beneficial properties.

Taxonomic Level: Species

Family: Coriobacteriaceae

Properties: Gram-positive, Anaerobic, Nonsporulating

Additional Information: Adlercreutzia equolifaciens is known to be capable of metabolizing a specific type of soybean isoflavone called daidzeins (which is found abundantly in soy products) to equol. Equol offers many health benefits such as its antioxidative and anti-inflammatory properties which help protect your DNA, lipids, proteins, and mitochondrial function from the intracellular generation of reactive oxygen species resulting from wind, cold temperatures, and toxins/pollutants.

While the genus of Alistipes bacteria offer protective properties in some diseases, they also can be pathogenic.

Taxonomic Level: Genus

Family: Rikenellaceae

Properties: Gram-negative, Anaerobic, Nonsporulating

Additional Information: The Alistipes genus offers an interesting combination of both positive and negative health impacts. Various studies have found that Alistipes bacteria play a protective role in colitis, autism spectrum disorder, and various liver and cardiovascular fibrotic disorders. Despite having many beneficial health implications, Alistipes is also known to have a pathogenic effect in anxiety, chronic fatigue syndrome, depression, Pervasive Developmental Disorder – Not Otherwise Specified (PDD-NOS), and colorectal cancer.

Bacteroidetes is the most temporally stable phylum of bacteria in the human gastrointestinal microbiome, illuminating just how essential they are to your health.

Taxonomic Level: Phlyum

Properties: Gram-negative, Both, Nonsporulating

Additional Information: Bacteria of the phylum Bacteroidetes live in the gastrointestinal tract in high abundance, and they are essential in many degradation processes including those of proteins and complex sugar polymers. Colonization of Bacteroidetes is promoted during infantry, due to nondigestible oligosaccharides in a mother’s milk, and they represent the most stable component of the gastrointestinal microbiota over time in healthy adults. The majority of Bacteroidetes bacteria belong to certain families which produce succinic acid, acetic acid, and sometimes propionic acid (please see the functional analysis section of your report to learn more about several of these short chain fatty acids). The role of Bacteroidetes bacteria in the microbiome is somewhat complex. While low levels of this phylum of bacteria has been associated with obesity and irritable bowel syndrome, patients suffering from T1D and T2D have been found to have an increased abundance of Bacteroidetes.

Bacteroides dorei is a rod-shaped bacteria which offers an interesting mix of positive and negative health implications.

Taxonomic Level: Species

Family: Bacteroidaceae

Properties: Gram-negative, Anaerobic, Nonsporulating

Additional Information: Like many other gut microbes, Bacteroides dorei has an interesting mix of positive and negative health implications. High levels of B. dorei and a related microbe B. vulgatus have been shown to be associated with inflammation in several gut diseases such as ulcerative colitis, irritable bowel disease, and celiac disease. Contrastingly, an increased abundance of B. dorei has also been implicated in a future immunity for T1D.

Bacteroides uniformis plays a role in the degradation of a specific type of soybean isoflavone called genistein.

Taxonomic Level: Species

Family: Bacteroidaceae

Properties: Gram-negative, Anaerobic, Nonsporulating

Additional Information: Bacteroides uniformis is a gut bacterium that likely contributes to the degradation of a specific type of soybean isoflavone called genistein (found abundantly in soy products) in individuals who degrade genistein rapidly. The chemical structure of B. uniformis resembles the naturally occurring hormone estrogen, which is why scientists believe it has so many health implications, including properties which may reduce the risk of some forms of cancer and atherosclerosis. This microbe also plays a unique role in butanoate metabolism, enhancing the process through the use of pectin (a polysaccharide commonly present in ripe fruits). This enhancement increases the production of butyrate and the inhibitory neurotransmitter GABA, contributing to the strength of the gut barrier and even mental health (please see the functional analysis section of your report to learn more about butyrate and GABA).

Bacteroides vulgatus is generally part of a healthy gut but has been associated with diseases such as Crohn’s disease and inflammation in several other gut diseases.

Taxonomic Level: Species

Family: Bacteroidaceae

Properties: Gram-negative, Anaerobic, Nonsporulating

Additional Information: Some amount of Bacteroides vulgatus in the gut is generally healthy, however many of the known health effects of abnormal levels of this microbe are detrimental. For instance, some studies have implicated E. coli and B. vulgatus in the development of Crohn’s disease, and high levels of B. vulgatus and a related microbe B. dorei have been shown to be associated with inflammation in several gut diseases such as ulcerative colitis, irritable bowel disease, and celiac disease.

Bilophila wadsworthia is known to produce hydrogen sulfide, a molecule implicated in many different health conditions, good and bad.

Taxonomic Level: Species

Family: Desulfovibrionaceae

Properties: Gram-negative, Anaerobic, Nonsporulating

Additional Information: One of the most important processes that occurs in Bilophila wadsworthia is producing hydrogen sulfide through the respiration of bisulfite released from organosulfonate substrates, including a molecule known as taurine (commonly ingested through meat and fish). The production of hydrogen sulfide is implicated in many different health conditions, good and bad. Hydrogen sulfide can act as a signaling molecule, resulting in beneficial effects such as cardioprotection. Some of the more negative impacts of hydrogen sulfide production in the gut include disrupting the gut epithelial’s barrier function, playing a role in inflammatory bowel disease, and it is also known to induce antibiotic resistance, which can lead to bacterial blooms during antibiotic treatment.

Blautia is a genus of bacteria known for contributing to the maintenance of intestinal immune homeostasis, and it may also play a role in stimulating serotonin release.

Taxonomic Level: Genus

Family: Lachnospiraceae

Properties: Gram-positive, Anaerobic, Nonsporulating

Additional Information: Blautia is a genus of microbes known to contribute to the maintenance of intestinal immune homeostasis. According to a study on the microbiota of obese children, a decreased abundance of B. luti and B. wexlerae species in the gut is often associated with obesity and metabolic issues such as resistance to insulin and related inflammatory markers. Furthermore, a decreased abundance of Blautia was significantly associated with visceral (abdominal) fat accumulation in adults. It has also been proposed that Blautia contains a specific enzyme which can convert tryptophan into tryptamine. Tryptamine then stimulates specialized cells in the GI tract to release serotonin.

Clostridioides difficile, often called C. difficile or C. diff, is a commensal bacteria that is often seen in patients with diarrhea and can lead to life-threatening inflammation of the colon.

Taxonomic Level: Species

Family: Peptostreptococcaceae

Properties: Gram-positive, Anaerobic, Spore forming

Additional Information: Clostridioides difficile produces toxins, enterotoxin A and cytotoxin B, that impede signal transduction of the cytoskeleton, which can disrupt certain gene expression and destroy cells. Additionally, Clostridioides difficile infections are mostly found after the patient has been on antibiotics, and it often leads to watery diarrhea. This connection to antibiotics is due to Clostridioides difficile’s production of p-cresol, which inhibits the growth of other microbes and allows Clostridioides difficile to thrive.

Collinsella is a genus that plays an important role in developing gut microbiota and regulating metabolism.

Taxonomic Level: Genus

Family: Coriobacteriaceae

Properties: Gram-positive, Anaerobic, Nonsporulating, Fermentative

Additional Information: At high levels, Collinsella has been associated with type 2 diabetes, rheumatoid arthritis and cholesterol metabolism. Collinsella in high abundance is also known to cause high insulin circulation, which can lead to atherosclerosis. Increasing dietary fiber consumption may help you reduce your abundance of Collinsella.

Coprococcus comes is a beneficial bacteria at healthy levels but has been known to exist in abundance in individuals with Crohn's disease. C. comes is a butyrate producer.

Taxonomic Level: Species

Family: Lachnospiraceae

Properties: Gram-positive, Anaerobic , Nonsporulating, Fermentative

Additional Information: Coprococcus comes has a few notable advantages such as helping with the acute immune response and producing AAT, a protein that protects lungs from environmental stressors. Coprococcus comes also produces butyrate, a short chain fatty acid which has many beneficial health implications, including protection against inflammatory bowel disease, diabetes, obesity, and cancer (please see the functional analysis section of your report to learn more about butyrate).

Dorea formicigenerans is a commensal bacteria that is common to the gut, meaning it can be harmful if found outside the intestinal tract.

Taxonomic Level: Species

Family: Lachnospiraceae

Properties: Gram-positive, Anaerobic , Nonsporulating, Fermentative

Additional Information: Dorea formicigenerans directly impacts the immune system, with a positive correlation to the presence of inflammatory markers, which aids the body’s inflammatory and innate immune response. At higher levels of Dorea formicigenerans, it has been known to also increase the IFNγ levels in response to C. albicans hyphae. IFNγ is produced by specialized cells of the innate immune system.

Eggerthella is a genus of bacteria containing the species Eggerthella lenta, which is a pathogen.

Taxonomic Level: Genus

Family: Coriobacteriaceae

Properties: Gram-positive, Anaerobic , Nonsporulating, Non-fermentative

Additional Information: Eggerthella has not been researched much because of its complex phenotype, but members of its genus are known to be pathogenic. In vaginal samples, it’s been noted that an abundance of Eggerthella exists in women who have bacterial vaginosis. Additionally, members of the Eggerthella, specifically Eggerthella lenta, have been related to cases of ulcerative colitis, abscesses of the liver and anal, and systemic bacteremia- bacteria in the blood.

Firmicutes is a one of the major phyla in the human gut with many beneficial bacteria but some problematic bacteria at high levels.

Taxonomic Level: Phlyum

Properties: Mostly gram-positive, Spore forming

Additional Information: Firmicutes is known to have the highest abundance of gut bacteria, but too much is unsafe for a number of reasons. Firmicutes is a Sulphate Reducing Bacteria- which produces hydrogen sulfide; hydrogen sulfide is toxic outside of healthy levels and can cause colonocyte apoptosis, degradation of mucous, and can inhibit butyrate production (please see the functional analysis section of your report to learn more about hydrogen sulfide). Butyrate is a short chain fatty acid which has many beneficial health implications, including protection against inflammatory bowel disease, diabetes, obesity, and cancer (please see the functional analysis section of your report to learn more about butyrate). There are certain species of Firmicutes with benefits to your metabolism, such as Faecalibacterium prausnitzii, which reduces chronic inflammation. However, high levels of other species of Firmicutes have been seen in patients with obesity, type II diabetes, and irritable bowel syndrome. Eating foods rich in fiber has been seen to increase Firmicutes abundance.

Lachnospiraceae is a family of bacteria that is one of the main contributors to the production of short-chain fatty acids, such as butyrate.

Taxonomic Level: Family

Family: Lachnospiraceae

Properties: Gram-positive, Anaerobic , Spore forming, Fermentative

Additional Information: The Lachnospiraceae family makes up a large amount of the gut microbiome, and it has many benefits to human health. Butyrate may protect against inflammatory bowel diseases, diabetes, obesity, and cancer, and it has been noted that the production of butyrate by Lachnospiraceae may protect the colon from cancer (please see the functional analysis section of your report to learn more about butyrate). Additionally, the presence of Lachnospiraceae family bacteria has been known to correlate with ammonium production (ammonium helps digest food but in large amounts can lead to seizures or death), indole production (people with indole are more prone to develop mood disorders), and p-cresol production (p-cresol inhibits the growth of other microbes).

Oscillibacter is a genus of bacteria that can have certain mental benefits at high abundances.

Taxonomic Level: Genus

Family: Oscillospiraceae

Properties: Gram-negative, Anaerobic, Nonsporulating, Fermentative

Additional Information: The Oscillibacter genus, specifically Oscillibacter valericigenes, produces valeric acid. Valeric acid resembles γ-aminobutyric acid, also known as GABA (please see the functional analysis section of your report to learn more about GABA). The absence of GABA has been seen in patients with depression, so the presence of Oscillibacter valericigenes to produce GABA is beneficial to your mental health. Having a diverse diet and limiting the amount of fatty foods you eat will help increase your abundance of Oscillibacter.

Phascolarctobacterium is a genus of bacteria that is a part of the healthy gut microbiome and produces the short-chain fatty acids acetate and propionate.

Taxonomic Level: Genus

Family: Acidaminococcaceae

Properties: Gram-negative, Anaerobic, Nonsporulating, Non-fermentative

Additional Information: Phascolarctobacterium is a major contributor to the production of the short-chain fatty acids acetate and propionate. Acetate and propionate help regulate your metabolism, can affect your mood, and can be increased with the addition of berberine and metformin to your diet (please see the functional analysis section of your report to learn more about acetate and propionate). Studies have shown that physical exercise may also help increase the abundance of Phascolarctobacterium.

Proteobacteria is a phylum of bacteria that ranges from commensal bacteria to pathogenic bacteria.

Taxonomic Level: Phlyum

Properties: Gram-negative

Additional Information: Proteobacteria is the most diverse phylum with many pathogens including Escherichia (E. coli), Salmonella, Vibrio, and Helicobacter. Therefore, a high abundance of Proteobacteria are generally found in patients with metabolic diseases, inflammatory bowel diseases, and irritable bowel syndrome. Additionally, Proteobacteria is a Sulphate Reducing Bacteria- which produces hydrogen sulfide; hydrogen sulfide is toxic outside of healthy levels and can cause colonocyte apoptosis, degradation of mucous, and can inhibit butyrate production (please see the functional analysis section of your report to learn more about hydrogen sulfide). Butyrate is a short chain fatty acid which has many beneficial health implications, including protection against inflammatory bowel disease, diabetes, obesity, and cancer (please see the functional analysis section of your report to learn more about butyrate).

Ruminococcus torques produces butyrate at healthy levels but has been seen in high quantities in children with autism spectrum disorder (ASD).

Taxonomic Level: Species

Family: Lachnospiraceae

Properties: Gram-positive, Anaerobic, Fermentative

Additional Information: Ruminococcus torques is normally seen with an average percentage abundance of 42%, but has been seen in Crohn’s disease patients at lower levels and has been seen in circadian disruption patients at higher levels. Ruminococcus torques’s low presence in patients with Crohn’s disease is due to its inability to create sufficient butyrate: a short chain fatty acid which has many beneficial health implications, including protection against inflammatory bowel disease, diabetes, obesity, and cancer (please see the functional analysis section of your report to learn more about butyrate).

Sutterella wadsworthensis is a commensal bacteria that is common to the gut and can be related to pediatric autism spectrum disorder (ASD).

Taxonomic Level: Species

Family: Sutterellaceae

Properties: Gram-negative, Anaerobic, Nonsporulating

Additional Information: Sutterella wadsworthensis hasn’t been researched extensively because of its complex properties. It has been found in children with ASD but is also found at 79% abundance in the healthy cohort, meaning the presence of Sutterella wadsworthensis does not indicate pediatric ASD. Similarly, Sutterella wadsworthensis has been detected in patients with and without ulcerative colitis, which shows Sutterella wadsworthensis is unlikely related to inflammatory bowel diseases. Sutterella wadsworthensis may be resistant to the antibiotic metronidazole but is 95% of the time susceptible to amoxicillin.