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Carbohydrates
| Monosaccharides | ||
|---|---|---|
| Shorthand | Longhand | Significance |
| Arabinose | Arabinose, unspecified chirality | Widespread and dominant gut bacteria, such as Bacteroides thetaiotaomicron, Blautia producta, Coprococcus comes, Phocaeicola vulgatus and Ruminococcus gnavus are able to ferment arabinose. The description, 'arabinose', is often reported without assigned chirality, especially in the older literature. |
| D-Arabinose | Widespread and dominant gut bacteria, such as Blautia obeum, Blautia massiliensis, Bacteroides eggerthii, Enterococcus avium and Bacteroides finegoldii, can ferment D-arabinose. | |
| L-Arabinose | Dorea longicatena, Bacteroides caccae, Phocaeicola vulgatus, Bifidobacterium adolescentis and most strains of Anaerostipes hadrus can ferment L-arabinose. | |
| Fructose | Over 50% of widespread gut bacteria can ferment or oxidise fructose. | |
| L-Fucose | Numerous dominant bacteria, such as Bacteroides ovatus, Phocaeicola vulgatus, Blautia obeum, Ruminococcus gnavus and Escherichia coli, can ferment or oxidise L-fucose. | |
| D-Fucose | Fewer gut bacteria consume D-fucose as an energy source. However, Blautia massiliensis and minor colonisers, Micrococcus lylae, Serratia marcescens and some strains of Enterobacter hormaechei subsp. hormaechei are able to do so. | |
| Galactose | 40% of widespread gut bacteria can ferment or oxidise galactose. | |
| Glucose | Over 70% of widespread gut bacteria can ferment or oxidise glucose. | |
| D-Lyxose | Fermentation of D-lyxose can occur with strains from Dorea longicatena (weak), Blautia massiliensis, Enterococcus avium and Anaerostipes caccae. | |
| Mannose | About 50% of all widespread gut bacteria can ferment mannose, including Bacteroides uniformis, Collinsella aerofaciens, Bacteroides stercoris, Alistipes shahii and Fusicatenibacter saccharivorans. | |
| Rhamnose | Roughly 30% of widespread gut microbes can ferment rhamnose, including Alistipes finegoldii, Bacteroides thetaiotaomicron, Blautia obeum, Parabacteroides distasonis and Phocaeicola vulgatus. | |
| Ribose | A diverse number of widespread gut bacteria, such as Bifidobacterium longum subsp. infantis, Bacteroides caccae, Bifidobacterium longum subsp. longum, Blautia obeum and Escherichia coli, can ferment ribose. | |
| Sorbose | A handful of important microbes, such as widespread colonisers, Anaerostipes caccae and most strains of Anaerostipes hadrus, and moderate colonisers, such as Enterococcus avium and Blautia coccoides, can ferment sorbose. | |
| Tagatose | Blautia massiliensis and Anaerostipes caccae, and moderate colonisers, such as Enterococcus durans, Lactobacillus gasseri and Mitsuokella multacida are able to ferment tagatose. | |
| D-Xylose | Over half of all widespread colonisers can ferment or oxidise D-xylose. | |
| L-Xylose | The dominant gut bacterium, Blautia massiliensis, is reported to consume L-xylose, as does moderate coloniser Enterocloster lavalensis (weak), and some rare bacteria from various taxa. | |
| Polyols | ||
| Adonitol | The widespread coloniser, Anaerostipes caccae, the moderate coloniser, Enterococcus avium, and most strains of Klebsiella pneumoniae are able to ferment or oxidise adonitol. | |
| D-Arabinol | Dominant coloniser, Anaerostipes caccae, moderate colonisers, Klebsiella pneumoniae and Enterococcus avium, and minor colonisers, such as Lactiplantibacillus plantarum and Escherichia fergusonii can ferment D-arabinol. | |
| L-Arabinol | Widespread colonisers Dorea longicatena (weak) and Anaerostipes caccae, moderate coloniser, Enterococcus avium, and minor colonisers, Providencia alcalifaciens and Clostridium saccharoperbutylacetonicum are able to ferment L-arabinol. | |
| Dulcitol | Dulcitol can be fermented or oxidised by widespread coloners, like Blautia massiliensis and Anaerostipes caccae, and moderate colonisers, Enterococcus avium, Blautia coccoides and Terrisporobacter glycolicus. | |
| Erythritol | Erythritol is poorly digested by bacteria. However, Blautia massiliensis and Anaerostipes caccae, in addition to minor colonisers, such as Cutibacterium avidum, Eubacterium limosum and Streptococcus pneumoniae, are able to do so. | |
| Glycerol | Glycerol, the product of triglyceride hydrolysis, can be oxidised or fermented by the widespread gut bacteria, Escherichia coli and Blautia massiliensis, and moderate colonisers, Butyricimonas virosa, Enterocloster bolteae and Ruminococcus torques. | |
| Inositol | Inositol can be attacked by important gut bacteria, such as Dorea longicatena, Dysosmobacter welbionis, Anaerostipes caccae and some strains of Bifidobacterium longum subsp. infantis. | |
| Mannitol | Mannitol can be fermented by a number of important gut bacteria, such as Bacteroides xylanisolvens, Bifidobacterium adolescentis, Escherichia coli, Anaerostipes caccae and Blautia massiliensis. | |
| Sorbitol | Widespread gut bacteria, such as Dorea longicatena, Fusicatenibacter saccharivorans, Escherichia coli, Anaerostipes caccae and Blautia massiliensis, can process sorbitol for energy. | |
| Xylitol | Less well documented, xylitol can be fermented by the dominant bacteria, Eubacterium rectale and Dorea longicatena (weak), plus the moderate coloniser, Enterococcus avium, as well as minor colonisers, like Staphylococcus aureus subsp. aureus and Serratia marcescens. | |
Oligosaccharides and polysaccharides
| Oligosaccharides | ||
|---|---|---|
| Shorthand | Longhand | Significance |
| Cellobiose | About 40% of widespread gut bacteria can use cellobiose and ferment the glucose derived from it. | |
| Gentiobiose | Dominant gut microbes, such as Bacteroides caccae, Bifidobacterium adolescentis, Bifidobacterium angulatum, Blautia massiliensis and Dorea longicatena catabolise gentiobiose and all ferment the glucose derived from it. | |
| Lactose | At least half the strains of 60% of widespread gut bacteria break down lactose to galactose and glucose. In only one reported case (Lachnospira eligens), most strains fermented lactose and glucose, but not galactose. | |
| Maltose | Maltose, made up of two glucose units, is hydrolysed and the glucose fermented in over 60% of dominant gut bacteria. | |
| Melezitose | While 20% of widespread gut bacteria can use melezitose, the sugar is rarely found in nature. | |
| Melibiose | At least some strains of about 30% of widespread gut microbes can use melibiose (disaccharide of glucose and galactose), and, where data is recorded, ferment the resulting monosaccharides. | |
| Raffinose | Over 50% of dominant gut bacteria can break down raffinose to glucose, fructose and galactose, then, in all data that was reported, ferment each of these monosaccharides. | |
| Sucrose | Over 50% of dominant gut microbes consume sucrose. All of these also ferment glucose, while all reported activities against fructose (not all had data) were also positive. | |
| Trehalose | At least some strains from about 30% of the widespread gut colonisers can ferment trehalose (or cleave trehalose and ferment glucose). All consumers of trehalose also ferment glucose. | |
| Turanose | A handful of important Bifidobacteria, Bifidobacterium angulatum, Bifidobacterium adolescentis, and variable results for Bifidobacterium longum subsp. infantis and Bifidobacterium longum subsp. longum, as well as Anaerostipes caccae, can ferment turanose. | |
| Polysaccharides | ||
| Amygdalin | A number of widespread gut colonisers, such as Bifidobacterium adolescentis, Coprococcus eutactus, Parabacteroides distasonis, Dorea longicatena and Bacteroides uniformis, can process and ferment amygdalin. | |
| Cellulose | Cellulose can be fermented by widespread colonisers, such as Bacteroides cellulosilyticus and Eubacterium rectale, and moderate ones, like Ruminococcus albus and Ruminococcus champanellensis. | |
| Dextrin | Dextrins, mixture; non-cyclic | Dextrin is broken down and fermented by important Bacteroidetes, such as Bacteroides stercoris, Phocaeicola vulgatus and Bacteroides fragilis and moderate colonisers from various taxa, such as Bacteroides eggerthii, Bifidobacterium animalis and Enterococcus gallinarum. |
| Aesculin | About 30% of the widespread gut bacteria (Firmicutes and Bacteroidetes) can hydrolyse aesculin and ferment the glucose derived from it. | |
| Glycogen | Several dominant Bacterioides species, such as Bacteroides thetaiotaomicron, Bacteroides stercoris, Bacteroides uniformis and Bacteroides ovatus, as well as the related Phocaeicola vulgatus, can break down and ferment glycogen. | |
| Inulin | Around 30% of widespread gut colonisers can break down and ferment inulin. | |
| Pectin | The dominant gut bacteria, Bacteroides cellulosilyticus, Bacteroides pectinophilus, Bacteroides thetaiotaomicron and most strains of Lachnospira eligens, as well as the moderate gut colonisers, Erysipelatoclostridium ramosum and Faecalicatena contorta, can ferment this important dietary fibre. | |
| Pullulan | Minor gut colonisers, such as Streptococcus sanguinis, Priestia megaterium and Streptococcus infantarius, can ferment or oxidise pullulan. | |
| Starch | Almost 40% of at least half the strains of widespread gut colonisers can ferment starch. | |
| Xylan | The widespread gut bacteria, Bacteroides xylanisolvens, Roseburia intestinalis, most strains of Bifidobacterium longum subsp. infantis, and Bacteroides cellulosilyticus, and moderate bacteria, Ruminococcus albus and Ruminococcus callidus, can ferment xylan. | |
Miscellaneous related carbohydrates
| Shorthand | Longhand | Significance |
|---|---|---|
| Arbutin | Anaerostipes caccae, Blautia massiliensis, Blautia obeum, Dorea longicatena and some strains of Bifidobacterium adolescentis | |
| Ethanol | Only fermented by rare gut bacteria. | |
| Gluconate | Bacteroides pectinophilus, Bifidobacterium longum subsp. infantis, Blautia massiliensis, Escherichia coli and Lachnospira pectinoschiza | |
| 2-Ketogluc | 2-Ketogluconate | The common facultative anaerobes, Enterococcus avium, Enterococcus pseudoavium and Raoultella ornithinolytica, can oxidise or ferment 2KG. |
| 5-Ketogluc | 5-Ketogluconate | Strictly anaerobic and prolific Blautia massiliensis, Mitsuokella multacida and Turicibacter sanguinis, as well as minor colonising facultative anaerobes, such as Citrobacter koseri and Micrococcus lylae can ferment or oxidise 5KG. |
| Me-α-Glc | Methyl-α-D-glucoside | Important gut commensals Anaerostipes caccae, Blautia obeum, Bifidobacterium longum subsp. infantis, Bifidobacterium longum subsp. longum and some strains of Bifidobacterium adolescentis are able to ferment Me-α-Glc. |
| Me-β-Glc | Methyl-β-D-glucoside | Numerous moderate gut colonising Entercoccus species can ferment Me-β-Glc, as can Erysipelatoclostridium ramosum and Streptococcus anginosus. |
| MDM | Methyl-D-mannoside | Moderate coloniser, strictly anaerobic Blautia coccoides and minor, facultative anaerobic Enterococcus hirae, as well as numerous rarer Listeria and other taxa are capable of oxidising or fermenting MDM. |
| MDX | Methyl-D-xyloside | Only dominant Blautia obeum and minor Bacillus circulans, along with numerous rarer Paenibacillus species can ferment or oxidise MDX. |
| NAGA | N-Acetylglucosamine | Important gut bacteria, such as Anaerostipes caccae, Blautia obeum, Streptococcus parasanguinis, Eubacterium rectale and Escherichia coli are capable of fermenting or oxidising NAGA. |
| Salicin | At least some strains of about 50% of widespread gut commensals can ferment salicin. | |
| Mucate | Only moderate and minor gut commensals from Proteobacteria can ferment or oxidise mucate. These include most strains of Enterobacter cloacae, as well as Atlantibacter hermannii, Citrobacter amalonaticus and Kluyvera ascorbata. | |
| Pyruvate | Only two moderate and minor gut commensals can ferment pyruvate, namely Erysipelatoclostridium ramosum and Eubacterium barkeri. |
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