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Metabolites Produced by Bacteria
Submitted by: danr November 07, 2022

Metabolites Produced by Bacteria Table

Short-Chain Fatty Acids (SCFA)
Shorthand Full name Significance
Formate Formic acid Around 30% of widespread gut commensals produce formate as a product of fermentation. While most of these are Firmicutes bacteria, Bacteroides stercoris and Bacteroides pectinophilus produce it as well.
Acetate Acetic acid Two thirds of all widespread gut bacteria produce at least minor amounts of acetate during the fermentation process. In addition, over 70 moderate gut colonisers also produce this byproduct.
Propionate Propionic acid, propanoic acid The biggest producers of propionate by dominant gut bacteria are from the Bacteroidetes phylum. These include Odoribacter splanchnicus, Bacteroides cellulosilyticus, Bacteroides stercoris, Bacteroides xylanisolvens and Parabacteroides distasonis. Other common bacteria that can produce propionate are Akkermansia muciniphila, Coprococcus catus and Faecalitalea cylindroides.
Butyrate Butyric acid, butanoic acid Butyrate, arguably the most important product made by gut bacteria, is produced from fermentation by dominant Firmicutes (30% of all widespread bacteria) and many more moderate colonisers (>24 species) mainly from Firmicutes. Exceptions are Butyricimonas virosa, which is a Bacteroidetes species, and Gemmiger formicilis, which is a Proteobacteria species.
Isobutyrate Isobutyric acid, 2-methylpropanoic acid The fermentation product, isobutyrate, is made by a number of common gut bacteria, such as Butyricimonas virosa, Catenibacterium mitsuokai, Intestinibacter bartlettii and Megasphaera elsdenii.
Valerate Valeric acid, pentanoic acid Valerate, a product of fermentation, is made only by the common Megasphaera elsdenii, but also by minor commensals, Oscillibacter valericigenes and Anaerococcus octavius.
Isovalerate Isovaleric acid, 3-methylbutanoic acid IVA is a fermentation product made in minor amounts by a handful of widespread gut commensals, but is a significant product of some other common bacteria, such as Butyricimonas virosa, Intestinibacter bartlettii and Terrisporobacter glycolicus.
Polar Acids
Citrate   Citrate is not reported to be produced by any significant gut commensal.
Lactate Lactate, unassigned chirality Lactate (either D, L or both) is produced in at least minor amounts by over 50% of the widespread gut bacteria.
Malate Malate, unassigned chirality Malate is not reported to be produced by any significant gut commensal.
Pyruvate   With the exception of Gemmiger formicilis, pyruvate is not reported to be produced by any significant gut commensal.
Succinate   Over 40% of widespread gut bacteria, such as Phocaeicola vulgatus, Bacteroides xylanisolvens and Alistipes putredinis, produce at least a trace of succinate during fermentation. The major producers are almost all Bacteroidetes.
Vitamins (predicted)
Biotin    
Cobalamin    
Folate    
Riboflavin    
Vitamin K    
Miscellaneous
Acetoin Acetoin, 3-hydroxybutanone, acetylmethyl carbinol A single widespread coloniser, Coprococcus eutactus, produces acetoin from the fermentation of glucose, although over 20 moderate colonisers, mostly Firmicules, are able to.
Butanol   The production of butanol, presumeably from butyrate, is rare by gut bacteria. Minor coloniser, Clostridium fallax, is able to generate it, as well as a number of other Clostridium species.
Ethanol   A number of common gut bacteria, including Escherichia coli, Ruminococcus bicirculans, Blautia obeum, Dorea longicatena and Lachnospira eligens produce ethanol during carbohydrate fermentation.
Indole   Over 16 common Bacteroidetes species produce indole. Slightly less prevalent are a handful of Firmicutes (e.g. Anaerotruncus colihominis, Enterocloster citroniae and Ruminococcus torques) that produce indole also.
Pigment   Pigments would be expected to be less common for bacteria acclimatised with the gut. The reduced oxygen level and lack of solar radiation lessen the reasons to develop pigments. However, there are exceptions: common gut bacteria, Alistipes finegoldii, Alistipes onderdonkii and Alistipes shahii produce brown pigments, as does Bacteroides cellulosilyticus. Others produce green-yellow colours (Megasphaera elsdenii) or are fluorescent (Clostridioides difficile).
Volatiles
NH3 Ammonia Ammonia can come from several sources, but most commonly via the hydrolysis of arginine or urea. While dominant gut bacteria are not reported to release ammonia, a number of moderate colonisers from the Firmicutes, do, including Acidaminococcus fermentans, Clostridium symbiosum, Finegoldia magna, Lactococcus lactis subsp. lactis and Parvimonas micra.
CO2 Carbon dioxide Several widespread colonisers, namely Anaerostipes caccae and Escherichia coli, have been reported to produce carbon dioxide. Campylobacter concisus, and a handful of Firmicutes (e.g. Hungatella hathewayi and Parvimonas micra) also make it.
H2 Hydrogen Numerous carbohydrate-fermenting bacteria produce hydrogen as a byproduct. This is the case for widespread bacteria, such as Anaerostipes caccae, Anaerostipes hadrus and Eubacterium rectale, as well as moderate colonisers, Anaerococcus hydrogenalis, Clostridium butyricum and Ruminococcus torques. An additional >50 moderate and minor colonisers also produce hydrogen.
H2S Hydrogen sulfide Around 8% of all gut bacteria produce H2S. This can be a byproduct from the breakdown of sulfur-containing proteins or the complete reduction of sulfate, sulfite, elemental sulfur or thiosulfate. Of the widespread colonisers, Bacteroides thetaiotaomicron, Parabacteroides distasonis and Phocaeicola vulgatus, plus most strains of Flavonifractor plautii and Blautia obeum produce it.

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