Information

Substrate Use
Submitted by: danr October 29, 2022

Collectively, bacteria are able to consume a vast array of organic compounds. Individual groups of bacteria tend to cluster into ecological niches, specialising in the breakdown and consumption of subsets of available substrates.

The term 'substrate use' generally refers to an organism's ability to utilise a substrate for anabolic processes (growth), whereby it obtains carbon sources, nitrogen sources or both to create the building blocks required to grow. This constrasts with the oxidative/ fermentative metabolic processes employed by bacteria for the purpose of generating energy. Obviously, there can be overlap, where an organism can use a substrate for both growth and energy generation. But it is also common to see sugars, for example, used as buildilng blocks rather than as energy sources, and vice versa.

These include:

Carbohydrates

Monosaccharides and polyols

Monosaccharide
Shorthand Longhand Significance
D-Arabinose   Utilised by dominant colonic bacteria, such as Blautia wexlerae, Roseburia hominis, Blautia producta, Dorea longicatena, and Gemmiger formicilis.
L-Arabinose   Roseburia intestinalis, Klebsiella pneumoniae, Bacillus badius and numerous minor colonisers can use L-arabinose.
Fructose   Many widespread gut colonisers, such as Ruminococcus bromii, Roseburia faecis, Roseburia intestinalis, Klebsiella pneumoniae, and Gemmiger formicilis, can use fructose as a carbon source.
L-Fucose   L-Fucose can be used by these important gut microbes: Anaerostipes hadrus, Klebsiella pneumoniae, Anaerotruncus colihominis, and Subdoligranulum variabile.
D-Fucose   Some strains of Klebsiella pneumoniae, and minor coloniser Gordonibacter urolithinfaciens, along with some strains of Delftia acidovorans, are able to used D-fucose.
Galactose   Readily consumed by many gut bacteria, such as Ruminococcus bromii, Intestinimonas butyriciproducens, Klebsiella pneumoniae, and Gemmiger formicilis.
Glucose   About 40% of the widespread gut colonisers utilise glucose.
D-Lyxose   Less commonly utilised by gut bacteria. However, Enterobacter cloacae, and minor colonising Enterobacter asburiae and Hafnia alvei are successfully able to use D-lyxose.
Mannose   Used by many bacteria, including important gut colonisers, such as Blautia wexlerae, Anaerostipes hadrus, Collinsella aerofaciens, Coprococcus eutactus, Klebsiella pneumoniae and Gemmiger formicilis.
D-Psicose   D-Psicose has not been reported to be used by many gut bacteria. However, Rothia aeria and some strains of Cronobacter sakazakii, can.
Rhamnose   Used by several moderate and minor gut colonisers, such as Klebsiella pneumoniae, Subdoligranulum variabile and Lacrimispora saccharolytica.
Ribose   Consumed by important gut colonisers, such as Blautia wexlerae, Anaerobutyricum hallii, Klebsiella pneumoniae, Anaerocolumna aminovalerica and Clostridium butyricum.
Tagatose   Less important than many other sugars, some strains of Klebsiella pneumoniae, and some minor colonisers, like Bacillus clausii and some strains of Klebsiella oxytoca can utilise tagatose.
Xylose   Readily utilised by a number of widespread colonisers, such as Roseburia intestinalis, Ruminococcus gnavus, Coprococcus comes, Blautia wexlerae, and Gemmiger formicilis.
Polyols
Adonitol   Lacrimispora saccharolytica, Megasphaera elsdenii and some strains of Klebsiella pneumoniae, as well as minor colonisers Rhodococcus erythropolis and Citrobacter koseri, can consume adonitol.
D-Arabinol   Klebsiella pneumoniae and minor colonisers, such as Citrobacter koseri, Cedecea davisae and Eubacterium limosum can used D-arabinol.
L-Arabinol   Only minor colonisers, such as Serratia marcescens, Clostridium saccharoperbutylacetonicum and Enterobacter hormaechei subsp. hormaechei, can utilised L-arabinol as a carbon source.
Dulcitol   Less commonly consumed, Terrisporobacter glycolicus and a few strains of Klebsiella pneumoniae, and minor colonisers, such as Citrobacter youngae and Enterobacter hormaechei subsp. hormaechei can utilised dulcitol.
Erythritol   Rarely digested by gut bacteria. Eubacterium limosum and some strains of Bacillus clausii and Serratia marcescens are able to, however.
Glycerol   Breakdown of triglycerides in the colon liberates glycerol. Readily catabolised by important gut microbes, such as Roseburia hominis, Paraclostridium bifermentans, Staphylococcus epidermidis, and Klebsiella pneumoniae.
Inositol   Several widespread and moderately colonising bacteria, such as Dorea longicatena, Lacrimispora saccharolytica, Klebsiella pneumoniae, and Enterobacter cloacae, can use inositol as a carbon source.
Mannitol   Numerous important gut bacteria, such as Anaerobutyricum hallii, Blautia producta, Ruminococcus lactaris, Klebsiella pneumoniae, and Clostridium innocuum, can used mannitol as a carbon source.
Sorbitol   Sorbitol is readily consumed by numerous widespread gut bacteria, such as Dorea longicatena, Intestinimonas butyriciproducens, Roseburia faecis, Enterobacter cloacae, and Terrisporobacter glycolicus.
Xylitol   Only minor colonisers, such as Bacillus clausii, Enterobacter hormaechei subsp. hormaechei and Serratia marcescens, are reported to use xylitol.

 

Oligosaccharides and polysaccharides

Oligosaccharides
Shorthand Longhand Significance
Cellobiose   Dominant gut bacteria, such as Blautia producta, Coprococcus eutactus, Roseburia faecis, and Gemmiger formicilis can use cellobiose.
Gentiobiose   Noteable important species, such as Enterobacter cloacae, Subdoligranulum variabile, Intestinibacter bartlettii and minor colonisers, such as Enterobacter hormaechei subsp. hormaechei and Mammaliicoccus sciuri can utilise gentiobiose.
Lactose   Lactose is used by many gut bacteria. Dominant gut microbes, such as Coprococcus comes, Blautia producta, Anaerobutyricum hallii, Erysipelatoclostridium ramosum, and Gemmiger formicilis readily consume lactose as a source of carbon.
Lactulose   The consumption of lactulose is less well reported. Bacteroides cellulosilyticus and some minor colonisers, like Sphingomonas paucimobilis and Victivallis vadensis are able to use this sugar.
Isomaltose   Moderate colonisers, such as Klebsiella pneumoniae, and Subdoligranulum variabile, and rare species such as Brevibacillus brevis, are able to use isomaltose.
Maltitol   Moderate gut colonisers, Klebsiella pneumoniae, Enterobacter cloacae, and minor colonisers, Citrobacter koseri and Enterobacter ludwigii, are  able to utilise maltitol.
Maltotriose   Maltotriose can be consumed by prolific bacteria, such as Intestinimonas butyriciproducens, Megasphaera elsdenii, Enterobacter cloacae, and Anaerotruncus colihominis.
Melezitose   The sugar, Melezitose, is used by Lacrimispora saccharolytica (weak) and some strains of Enterocloster clostridioformis and Clostridioides difficile.
Melibiose   Many important bacteria, such as Roseburia faecis, Bifidobacterium adolescentis, Bacteroides caccae, Escherichia coli, and Bifidobacterium animalis can utilise melibiose as a carbon source.
Palatinose   Palatinose is consumed by Anaerotruncus colihominis, Klebsiella pneumoniae, Subdoligranulum variabile, and Enterobacter cloacae.
Raffinose   Raffinose is widely utilised by dominant bacteria, such as Blautia producta, Coprococcus comes, Ruminococcus gnavus, Roseburia intestinalis, Erysipelatoclostridium ramosum, and Lacrimispora saccharolytica.
Sucrose   Sucrose is widely utilised by dominant bacteria, such as Blautia producta, Coprococcus comes, Anaerostipes hadrus, Coprococcus eutactus, Klebsiella pneumoniae, and Gemmiger formicilis.
Trehalose   Trehalose is readily consumed by numerous well known bacteria, such as Gemmiger formicilis, Clostridium innocuum, Blautia hydrogenotrophica, Klebsiella pneumoniae, and Intestinibacter bartlettii.
Turanose   Important bacteria, such as Intestinimonas butyriciproducens, Anaerotruncus colihominis, Intestinibacter bartlettii, and Subdoligranulum variabile, can utilise turanose.
Polysaccharides
Cellulose   Surprisingly, several important gut microbes are able to process cellulose as a carbon source. Ruminococcus champanellensis, Marvinbryantia formatexigens, Ruminococcus albus and minor colonisers, Cellulosilyticum lentocellum and Lachnoclostridium phytofermentans are capable of attacking this recalcitrant fibre, but whether it can be achieved on a meaningful timescale is a different question.
Chitin   Minor colonisers, Clostridium tertium, Stenotrophomonas maltophilia and Bacillus licheniformis, can attack chitin. As with cellulose, the breakdown of chitin to useable materials in the timeframe of gut passage is questionable.
Dextrin   Dextrin, which are breakdown products of starch, can be consumed by Intestinimonas butyriciproducens, Anaerotruncus colihominis, Intestinibacter bartlettii, and Subdoligranulum variabile, and many other minor and rare colonisers.
Glycogen   Glycogen provides readily accessible glucose. Butyrivibrio crossotus, Clostridium butyricum, and minor colonisers, Bacteroides graminisolvens, Bacillus clausii and Cellulosilyticum lentocellum are able to use this glucose polymer.
Inulin   An important source of fibre, inulin is utilised by a number of important gut microbes, such as Roseburia inulinivorans, Clostridium innocuum, Gemmiger formicilis, and minor colonisers, Butyrivibrio fibrisolvens and Bacillus infantis.
Mannan   Reported to be utilised by a handful of rare gut colonisers, such as Lysinibacillus varians, Brevibacterium samyangense and Paenibacillus typhae.
Pectin   Pectin is an important dietary fibre that can be consumed by well known bacteria such as Roseburia faecis, Bacteroides pectinophilus, and Lachnospira pectinoschiza, as well as minor colonisers Monoglobus pectinilyticus, and Clostridium beijerinckii.
Starch   Starch is attacked by dominant bacteria, such as Roseburia faecis, Ruminococcus bromii, Roseburia inulinivorans, Gemmiger formicilis, Clostridium butyricum, and Butyrivibrio crossotus, as well as over 20 other moderate and minor gut colonisers.
Xylan   Important Firmicutes, including Roseburia intestinalis, and Ruminococcus champanellensis, and minor colonisers, such as Bacteroides graminisolvens and Lachnoclostridium phytofermentans, are capable of utilising the fibre xylan.

 

Miscellaneous related carbohydrates

Shorthand Longhand Significance
Aesculin   Widespread colonisers, Dorea longicatena and Roseburia intestinalis, as well as various moderate and minor commensals can utilise aesculin.
Amygdalin   The important commensal, Dorea longicatena, along with various moderate and minor taxa can use amygdalin as a carbon source.
Arbutin   Anaerotruncus colihominis and Subdoligranulum variabile, as well as some minor Proteobacteria can use arbutin as a carbon source.
Butanol   Of little relevance to gut bacteria.
Ethanol   A number of Proteobacteria residing in the gut can use ethanol as a carbon source.
Ethanediol   Aside from the important gut commensal, Terrisporobacter glycolicus, few other gut bacteria of significance utilise ethanediol.
Propanediol 1,2-Propanediol Aside from the important gut commensal, Terrisporobacter glycolicus, few other gut bacteria of significance utilise propanediol.
2,3-Butanediol   Delftia acidovorans and Rothia mucilaginosa metabolise 2,3-butanediol.
2-Ketogluc 2-Ketogluconate Numerous moderate and minor gut colonisers from Proteobacteria can use 2-ketoglutarate.
5-Ketogluc 5-Ketogluconate Turicibacter sanguinis and a handful of minor colonisers can use 5-ketoglutarate.
L-Gal-lactone L-Galactono-1,4-lactone Of little relevance to gut bacteria.
Gluconate   Important colonisers, such as Bacteroides pectinophilus, Enterobacter cloacae, Klebsiella pneumoniae and Enterococcus faecalis, as well as over 30 other minor gut colonisers, can use gluconate.
Me-α-Glc Methyl-α-glucoside Over 20 gut colonising Proteobacteria and a few minor colonising Firmicutes can use this sugar.
Me-β-Glc Methyl-β-glucoside Important Firmicutes, such as Anaerotruncus colihominis and Intestinibacter bartlettii, as well as important Proteobacteria, such as Klebsiella pneumoniae and Enterobacter cloacae can use this glucose derivative.
Me-α-Gal Methyl-α-galactoside Several (mainly) Proteobacteria can use this sugar.
Me-β-Gal Methyl-β-galactoside More than 15 (mainly) Proteobacteria can use this sugar.
3-Me-α-Glc 3-Methyl-α-glucose Important colonisers, such as Intestinimonas butyriciproducens, Anaerotruncus colihominis, Intestinibacter bartlettii and Subdoligranulum variabile, as well as a number of other minor colonisers can utilise this sugar.
Me Mannoside Methyl mannoside Of little relevance to gut bacteria.
Me Xyloside Methyl xyloside Of little relevance to gut bacteria.
Glc-1-P Glucose-1-phosphate (G1P) Subdoligranulum variabile and Kosakonia cowanii can use G1P as a carbon source. Few others do, however.
Glc-6-P Glucose-6-phosphate (G6P) Important colonisers, such as Intestinimonas butyriciproducens, Subdoligranulum variabile and Intestinibacter bartlettii can utilise G6P.
Glycerol-P Glycerol-1-phosphate (Glyc1P) Moderate coloniser, Megasphaera elsdenii, and minor gut colonisers, Cronobacter sakazakii and Rothia mucilaginosa can us Glyc1P as a carbon source.
Fruct-6-P Fructose-6-phosphate (F6P) Minor gut colonisers, Lysinibacillus fusiformis and Gordonibacter urolithinfaciens can use F6P as a carbon source.
Methanol   Minor gut colonisers, Eubacterium limosum and Methanosphaera stadtmanae can use methanol.
Propanol   Aside from Delftia acidovorans, propanol is of little significance to gut microbes.
Salicin   More than 40 moderate and minor gut colonising bacteria can use salicin as a carbon source.

 

Organic acids

Short and medium chain fatty acids

Shorthand Longhand Significance
Formate (C1)   More than 15 moderate and minor gut colonising bacteria and archaea can use formate as a carbon source.
Acetate (C2)   Short-chain fatty acid. About 20% of widespread gut colonisers (mainly Firmicutes), and another ~50 moderate and minor gut colonisers of various taxa (including Archaea) can utilise acetate as a carbon source.
Propionate (C3) Propanoate Short-chain fatty acid. Hungatella effluvii and some minor gut colonising Firmicutes and Proteobacteria can use propionate.
Butyrate (C4) n-Butanoate Short-chain fatty acid. Important Paraclostridium bifermentans, other Firmicutes, such as Desulfitobacterium hafniense and Allisonella histaminiformans can use butyrate as a carbon source. Several moderate and minor gut colonising Proteobacteria can also use this substrate.
Isobut. (C4) Isobutyrate Short-chain fatty acid. Some minor gut colonising Proteobacteria can use isobutyrate.
Valerate (C5) n-Valerate Medium-chain fatty acid. Minor colonising Firmicutes, such as Eubacterium ruminantium, Selenomonas ruminantium and Selenomonas sputigena, as well as some minor gut colonising Proteobacteria can utilise valerate.
Isoval. (C5) Isovalerate Medium-chain fatty acid. Some minor gut colonising Proteobacteria and some strains of Butyrivibrio fibrisolvens can utilise isovalerate.
Caproate (C6) n-Hexanoate Medium-chain fatty acid. Some strains of several minor gut colonising Proteobacteria can utilise hexanoate.
Heptanoate (C7)   Medium-chain fatty acid. Some strains of several minor gut colonising Proteobacteria can utilise heptanoate.
Caprylate (C8) n-Octanoate Medium-chain fatty acid. Some strains of several minor gut colonising Proteobacteria can utilise octanoate.
Nonan. (C9) n-Nonanate, Pelagonate Medium-chain fatty acid. Some strains of several minor gut colonising Proteobacteria can utilise nonanate.
Caprate (C10) n-Decanoate Medium-chain fatty acid. Aside from Bacillus badius, some minor gut colonising Proteobacteria can utilise caprate.

 

Polyacidic compounds

Dicarboxylic Acids
Shorthand Longhand Significance
Oxalate (C2)   Apart from the important moderate coloniser, Oxalobacter formigenes, only a few rare colonisers can use oxalate.
Malonate (C3)   Priestia megaterium and some colonising Proteobacteria can use malonate.
Fumerate (C4)   Over 40 gut colonising Proteobacteria, Firmicutes, such as Bacillus badius, and a couple of minor colonising Actinobacteria can utilise fumerate. Some strains of the widespread Flavonifractor plautii can use fumerate, also.
Maleate (C4)   Some minor gut colonising Proteobacteria can utilise maleate.
Succinate (C4)   Over 40 gut colonising Proteobacteria, Firmicutes, such as Dialister succinatiphilus and Megasphaera elsdenii, and some minor colonising Actinobacteria can use succinate.
Citracon (C5) Citraconate Some minor gut colonising Proteobacteria can utilise citraconate.
Glutarate (C5)   Some minor gut colonising Proteobacteria can utilise glutarate.
2-Ketoglt (C5) 2-Ketoglutarate (2KG) Some minor gut colonising Proteobacteria can utilise 2-ketogluconate.
Itacon (C5) Itaconate Some minor gut colonising Proteobacteria can utilise itaconate.
Mesacon (C5) Mesaconate Some minor gut colonising Proteobacteria can utilise mesaconate.
Adipate (C6)   Bacillus badius and some minor gut colonising Proteobacteria can utilise adipate.
Pimelate (C7)   Some minor gut colonising Proteobacteria can utilise pimelate.
Suberate (C8)   Some minor gut colonising Proteobacteria can utilise suberate.
Azelate (C9)   Some minor gut colonising Proteobacteria can utilise azelate.
Sebacate (C10)   Some minor gut colonising Proteobacteria can utilise sebacate.
Hydroxy Dicarboxylic Acids
Malate (C4) Malate, chirality unassigned Peribacillus simplex, Corynebacterium propinquum and numerous minor gut colonising Proteobacteria can use malate. The chirality is unspecified, but is presumably the most common enantiomer.
L-Malate (C4)   Anaerotruncus colihominis, Megasphaera elsdenii and more than 20 moderate and minor gut colonising Proteobacteria can use L-malate.
D-Malate (C4)   Klebsiella pneumoniae and some other minor gut colonising Proteobacteria can use D-malate.
D-Tartr (C4) D-Tartrate Some minor gut colonising Proteobacteria can use D-tartrate.
L-Tartr (C4) L-Tartrate Some minor gut colonising Proteobacteria can use L-tartrate.
m-Tartr (C4) meso-Tartrate Megasphaera elsdenii and some minor gut colonising Proteobacteria can use meso-tartrate.
Mucate (C6)   A handful of moderate and minor gut colonising Proteobacteria can use mucate. This substrate can also be fermented for energy.
Sacchar (C6) Saccharate A handful of moderate and minor gut colonising Proteobacteria can use saccharate.
Tricarboxylic Acids
Aconitate cis or trans-aconitate Peribacillus simplex and numerous gut colonising Proteobacteria can use aconitate (cis-version).
Citrate   Over 50 gut moderate and minor gut colonisers can use citrate.
Tricarballylate   Peribacillus simplex and some minor gut colonising Proteobacteria can use tricarballylate.

 

Miscellaneous related acids

Hydroxy and Oxy-acids
Shorthand Longhand Significance
2-Ketobutyrate   Intermediate in the Ile biosynthetic pathway. A small number of important gut colonisers (Intestinibacter bartlettii, Anaerotruncus colihominis and Gordonibacter urolithinfaciens) can use 2-ketobutyrate.
3-Ketovalerate   A small number of important gut colonisers (Anaerotruncus colihominis and Gordonibacter urolithinfaciens) can use 3-ketovalerate.
Glycerate Glycerate, chirality unassigned Several Proteobacteria can use glycerate (probably racemic mixture - see below).
DL-Glycerate Glycerate, racemic mixture More than 10 Proteobacteria (minor colonisers) can use the racemic mixture of glycerate.
Glycolate   Paraclostridium bifermentans, plus a handful of minor gut colonisers from Proteobacteria can use glycolate.
Levulinate   Levulinate, obtained from lignocellulosic biomass, is mainly attacked by α-Proteobacteria and Pseudomonas species. Minor colonisers from Proteobacteria, such as Ralstonia pickettii Biovar Va-1&2, Delftia acidovorans and Comamonas testosteroni can also use levulinate.
 Quinate   Part of the quinate/shikimate biochemical pathway. Lactiplantibacillus plantarum (Whiting1971) and Klebsiella pneumoniae, plus a few minor colonisers can utilise quinate.
Pyruvate   Intestinimonas butyriciproducens and over 60 moderate and minor gut colonisers can utilise pyruvate. Can be oxidised or fermented source of energy.
Me Pyruvate Methyl pyruvate A handful of moderate and minor gut colonisers, such as Intestinibacter bartlettii, Anaerotruncus colihominis, Gordonibacter pamelaeae and Rothia mucilaginosa can use methyl pyruvate.
2-HO-Butyrate 2-Hydroxybutyrate Aside from Rothia aeria, of little relevance to gut bacteria.
3-HO-Butyrate 3-Hydroxybutyrate Utilised by a number of important gut commensals, such as Intestinimonas butyriciproducens, Brevundimonas diminuta, Megasphaera elsdenii and about 15 other moderate or minor gut colonising Proteobacteria.
4-HO-Butyrate 4-Hydroxybutyrate Of little relevance to gut bacteria.
Lactate Lactate, chirality unassigned Anaerostipes hadrus (weak response) plus over 20 moderate and minor gut colonisers utilise lactate (unassigned chirality).
L-Lactate   Aside from Rothia aeria, L-lactate is not specifically reported as being used much. Default chirality is probably unassigned 'lactate'.
D-Lactate   By itself, of little relevance to gut bacteria. Default chirality is probably unassigned 'lactate', or DL racemate.
DL-Lactate Lactate, racemic mixture Intestinimonas butyriciproducens and over 25 (mainly Proteobacteria) moderate and minor gut colonising bacteria utilise DL-lactate.
Me Lactate Methyl lactate Aside from Intestinimonas butyriciproducens, of little relevance to gut bacteria.
Aromatic Acids
Benzoate    
4-HO-Benzoate 4-Hydroxybenzoate Several minor gut colonising Actinobacteria (Rhodococcus erythropolis and Micrococcus lylae) as well as numerous Proteobacteria (e.g. Klebsiella pneumoniae and Citrobacter amalonaticus) can utilise 4-hydroxybenzoate.
3-HO-Benzoate 3-Hydroxybenzoate Peribacillus simplex and a handful of minor gut colonising Proteobacteria and Actinobacteria can use 3-hydroxybenzoate.
L-Mandelate   A small handful of minor gut colonising Proteobacteria can use L-mandelate.
Phenylacetate   Peribacillus simplex and a handful of Proteobacteria can use phenylacetate.
4-HO-PhAc 4-Hydroxyphenylacetic acid Of little relevance to gut bacteria.
m-Coumarate meta-Coumarate Terrisporobacter glycolicus and Peribacillus simplex from Firmicutes, and Klebsiella pneumoniae plus a number of minor colonising Proteobacteria utilise m-coumarate.

 

Amino acids

The 20 typical amino acids

Shorthand Longhand Significance
Ala L-Alanine Over 30 moderate and minor gut colonisers from various taxa can use L-alanine.
Arg L-Arginine More than 20 moderate and minor gut commensals can use arginine, including Acidaminococcus fermentans, Paraclostridium bifermentans, Lactococcus lactis subsp. lactis and Adlercreutzia equolifaciens.
Asn L-Asparagine A handful of bacteria have been reported to use asparagine (e.g. Klebsiella pneumoniae and Stomatobaculum longum).
Asp L-Aspartate Asp is used by a large number (>40) of moderate and minor gut commensals.
Cys L-Cysteine Acidaminococcus fermentans and Lactococcus lactis subsp. lactis consume cysteine, but numerous other minor taxa do also.
Glu L-Glutamate Glutamate is used by a large number (>50) of moderate and minor gut commensals.
Gln L-Glutamine Glutamine is utilised by Prevotella intermedia and Stomatobaculum longum, but these are not particularly widespread gut bacteria.
Gly L-Glycine Gly is consumed by over 15 moderate and minor gut colonisers from various taxa.
His L-Histidine His is consumed by over 30 moderate and minor gut colonisers from various taxa.
Ile L-Isoleucine Ile is consumed by over 15 moderate and minor gut colonisers from various taxa.
Leu L-Leucine Leu is consumed by over 20 moderate and minor gut colonisers from various taxa.
Lys L-Lysine Lys is used by Lactococcus lactis subsp. lactis and Terrisporobacter glycolicus, as well as numerous minor gut colonisers.
Met L-Methionine Met is utilised by Clostridioides difficile, Intestinibacter bartlettii, Lactococcus lactis subsp. lactis and Terrisporobacter glycolicus, among others.
Phe L-Phenylalanine Phe is utilised by over 15 moderate and minor gut colonisers from various taxa.
Pro L-Proline Pro is utilised by over 30 moderate and minor gut colonisers from various taxa.
Ser L-Serine Intestinimonas butyriciproducens, as do a number of other Firmicutes (e.g. Anaerotruncus colihominis, Clostridioides difficile and Enterococcus faecalis), consumes L-serine. Others include Enterobacter cloacae and Klebsiella pneumoniae.
Thr L-Threonine Intestinimonas butyriciproducens from the Firmicutes, consumes L-threonine, as does Lactococcus lactis subsp. lactis, Clostridioides difficile, Intestinibacter bartlettii and Anaerotignum lactatifermentans.
Trp L-Tryptophan Aside from Lactococcus lactis subsp. lactis and Acidaminococcus fermentans, only occasional gut colonisers utilise tryptophan.
Tyr L-Tyrosine Numerous important gut bacteria use valine, including Delftia acidovorans, Clostridium subterminale, Lactococcus lactis subsp. lactis and Ralstonia pickettii Biovar Va-1&2.
Val L-Valine Numerous important gut bacteria use valine, including Clostridioides difficile, Acidaminococcus fermentans, Lactococcus lactis subsp. lactis and Terrisporobacter glycolicus.

 

Unusual amino acids

Shorthand Longhand Significance
Alaninamide L-Alaninamide Aside from the important Intestinibacter bartlettii, L-alaninamide is not used by many gut bacteria.
D-Ala D-Alanine Of any signficant gut colonisers, only Proteobacteria consume D-alanine. These include Citrobacter, Enterobacter, Serratia and Klebsiella species.
beta-Ala β-Alanine, 3-Aminopropionic acid Used by some minor Proteobacteria gut colonisers, like Ralstonia pickettii Biovar Va-1&2.
2-Aminobenz 2-Aminobenzoate Of little relevance to gut bacteria.
3-Aminobenz 3-Aminobenzoate Of little relevance to gut bacteria.
4-Aminobenz 4-Aminobenzoate Cedecea davisae and Acidaminococcus fermentans consume 4-aminobenzoate.
2-Aminobut. 2-Aminobutyrate Aside from Delftia acidovorans, 2-aminobutyrate is of little relevance to gut bacteria.
3-Aminobut. 3-Aminobutyrate Of little relevance to gut bacteria.
4-Aminobut. 4-Aminobutyrate Apart from Peribacillus simplex and Rhodococcus erythropolis 4-aminobutyrateis used by Proteobacteria.
5-Aminoval. 5-Aminovalerate Apart from a few important Firmicutes (Peribacillus simplex, Anaerocolumna aminovalerica) 5-aminovalerate is used by Proteobacteria, particularly Citrobacter species.
Betaine   Relevant to minor gut colonisers from Proteobacteria, such as Enterobacter hormaechei subsp. hormaechei and Sphingomonas paucimobilis.
Casamino Casamino acids A handful, but diverse set of gut colonisers can use Casamino acids. These include Bifidobacterium pseudolongum (Actinobacteria), Cetobacterium somerae (Fusobacteria), Cloacibacillus evryensis (Synergistetes) and Terrisporobacter glycolicus (Firmicutes).
L-Citrulline   Of little relevance to gut bacteria.
Glucosaminate   Of little relevance to gut bacteria.
Hippurate   Utilised by many Enterococcus species, such as Enterococcus faecalis and Streptococcus agalactiae.
Histamine L-Histamine Enterobacter hormaechei subsp. hormaechei, a minor gut coloniser, can use histimine.
L-HOPro L-Hydroxyproline Relevant to minor gut colonisers from Proteobacteria, such as Serratia marcescens.
DL-Kyn Kynurenine, racemic mixture Relevant to minor gut colonisers from Proteobacteria, such as Ralstonia pickettii Biovar Va-1&2.
Norleucine L-Norleucine Minor gut colonisers from Proteobacteria, such as Delftia acidovorans, Alcaligenes faecalis and some strains of Comamonas testosteroni, can use norleucine
Norvaline L-Norvaline Brevundimonas diminuta, a common Proteobacteria species, can use norvaline.
Ornithine L-Ornithine Used by gut colonising Proteobacteria, such as Serratia marcescens and Klebsiella pneumoniae.
PyroGlu L-Pyroglutamate Of little relevance to gut bacteria.
Sarcosine   Of little relevance to gut bacteria.
Trigonelline   Relevant to minor gut colonisers from Proteobacteria, such as Enterobacter hormaechei subsp. hormaechei and some strains of Delftia acidovorans.
Tryptamine L-Tryptamine Relevant to minor gut colonisers from Proteobacteria, such as Enterobacter hormaechei subsp. hormaechei and some strains of Alcaligenes faecalis.

 

Other sources

Nitrogen-containing compounds

Shorthand Longhand Significance
Ethanolamine   Relevant to minor gut colonisers from Proteobacteria, such as Enterobacter hormaechei subsp. hormaechei and most strains of Citrobacter koseri.
Butylamine   Of little relevance to gut bacteria.
Benzylamine   Of little relevance to gut bacteria.
2-Aminobenzoate   Of little relevance to gut bacteria.
3-Aminobenzoate   Of little relevance to gut bacteria.
4-Aminobenzoate   The important Firmicute, Acidaminococcus fermentans, can utilise 4-aminobenzoate. Other minor colonisers from Proteobacteria (Cedecea davisae and Delftia acidovorans) are also able to use it.
Putrescine   Consumed by gut colonising Proteobacteria, such as Cronobacter sakazakii, Enterobacter cloacae and Klebsiella pneumoniae.
Acetamide   Several minor gut colonisers (Achromobacter xylosoxidans and Delftia acidovorans) and some strains of Rhodococcus erythropolis can use acetamide.
Urea   Of little relevance to gut bacteria.
Lactamide Lactamide, chirality unassigned Of little relevance to gut bacteria.
Succinamate   Of little relevance to gut bacteria.
Creatine   Of little relevance to gut bacteria.
DL-Carnitine Carnitine, racemic mixture Of little relevance to gut bacteria.
Nicotinate   Several minor gut colonisers (Delftia acidovorans and Eubacterium barkeri) and most strains of Serratia marcescens can use nicotinate.
Urocanate   Of little relevance to gut bacteria.
Histamine L-Histimine Enterobacter hormaechei subsp. hormaechei, a minor gut coloniser, can use histimine.
Tryptamine L-Tryptamine Enterobacter hormaechei subsp. hormaechei, a minor gut coloniser, can use tryptamine.
Adenosine   Of little relevance to gut bacteria.
Inosine   Metabolised by Intestinimonas butyriciproducens and Anaerotruncus colihominis, otherwise unremarkable in terms of gut bacteria.
Thymidine   Metabolised by Intestinimonas butyriciproducens, Megamonas hypermegale and Anaerotruncus colihominis, otherwise unremarkable in terms of gut bacteria.
Uridine   Metabolised by Intestinimonas butyriciproducens and Anaerotruncus colihominis, otherwise unremarkable in terms of gut bacteria.
AMP Adenosine monophosphate Several rare gut microbes are able to use AMP (Brevibacterium samyangense and Lysinibacillus boronitolerans).
TMP Thymidine monophosphate Metabolised by Intestinimonas butyriciproducens, otherwise unremarkable in terms of gut bacteria.
UMP Uridine monophosphate Metabolised by Intestinimonas butyriciproducens, otherwise unremarkable in terms of gut bacteria.
Glucosamine D-Glucosamine Commonly utilised by Bacteroidetes, such as Bacteroides ovatus, Phocaeicola vulgatus and Parabacteroides distasonis.
N-AcGlcamine N-Acetyl-D-glucosamine Utilised by important bacteria, such as Intestinimonas butyriciproducens, Anaerotruncus colihominis and Enterobacter cloacae.
N-AcGalamine N-Acetylgalactosamine Metabolised by Cloacibacillus porcorum, otherwise unremarkable in terms of gut bacteria.
N-AcMannamine N-Acetylmannosamine A few important bacteria, such as Subdoligranulum variabile, Cetobacterium somerae and Lysinibacillus fusiformis, can metabolise this substrate.
N-AcNeuram N-Acetylneuraminate Metabolised by Cloacibacillus porcorum, otherwise unremarkable in terms of gut bacteria.
Glucuronamide β-D-glucopyranuronamide (IUPAC) Metabolised by Gordonibacter urolithinfaciens.
D-Glucosaminate 2-Acetamido-2-deoxy-D-gluconate (IUPAC) Can be used to differentiate E. coli from Salmonella enterica strains. Synthesised via D-glucosaminate-6-phosphate ammonia-lyase. Little relevance to gut bacteria.

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