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Table 1 Major genera present in the human gut microbiome and their metabolisms

From: Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health

Phylum Family Genus Substrates Metabolism End products
Actinobacteria Bifidobacteriaceae Bifidobacterium Dietary carbohydrates
HMO
Mucin
Bifid shunt pathway Acetate
Ethanol
Formate
Lactate
Bacteroidetes Bacteroidaceae Bacteroides Dietary carbohydrates
HMO
Mucin
Proteins
Succinate
1,2-Propanediol pathwayI
Acetate production
Ethanol production
Succinate pathway
1,2-Propanediol
Acetate
Carbon dioxide and Hydrogen
Ethanol
Formate
Propionate
Succinate
  Porphyromonadaceae Parabacteroides W Dietary carbohydrates
Proteins
Succinate
Acetate production
Succinate pathway
Acetate
Carbon dioxide and Hydrogen
Formate
Propionate
Succinate
  Prevotellaceae Prevotella NW Dietary carbohydrates
Proteins
Succinate
Acetate production
Succinate pathwayI/A
Acetate
Formate
Propionate
Succinate
  Rikencellaceae Alistipes W Dietary carbohydrates
Proteins
Succinate
Acetate production
Succinate pathway
Acetate
Carbon dioxide and Hydrogen
Formate
Propionate
Succinate
Firmicutes Clostridiaceae Clostridium
(Clostridium cluster I)
Ethanol and Propionate
Lactate
Proteins
Saccharides
1,2-Propanediol pathwayI
Acetate production
Acrylate pathway
Butyrate kinase pathway
Ethanol production
Lactate production
Valerate production
1,2-Propanediol
Acetate
Carbon dioxide and Hydrogen
Ethanol
Formate
Lactate
Propionate
Butyrate
Valerate
  Eubacteriaceae Eubacterium Acetate
Carbon dioxide and hHydrogen
Formate
Lactate
Methanol
Proteins
Saccharides
Acetogenesis
Acetate production
Butyryl c CoA transferase pathway
Ethanol production
Lactate production
Acetate
Butyrate
Carbon dioxide and Hydrogen
Ethanol
Formate
Lactate
  Erysipelotrichaceae Erysipelatoclostridium Proteins
Saccharides
Acetate production
Lactate production
Acetate
Carbon dioxide and Hydrogen
Formate
Lactate
  Lachnospiraceae Blautia
(Clostridium cluster XIVa)
1,2-Propanediol
Carbon dioxide and Hydrogen
Dietary carbohydrates
Formate
Mucin
1,2-Propanediol pathway
Acetogenesis
Acetate production
Ethanol production
Lactate production
Succinate pathwayI
Acetate
Carbon dioxide and Hydrogen
Ethanol
Formate
Lactate
Propanol
Propionate
Succinate
   Coprococcus
(Clostridium cluster XIVa)
Acetate
Dietary carbohydrates
Lactate
Acrylate pathway
Butyrate kinase pathway
Butyryl CoA:acetyl CoA transferase pathway
Ethanol production
Lactate production
Acetate
Butyrate
Ethanol
Carbon dioxide and Hydrogen
Formate
Lactate
Propionate
   Dorea
(Clostridium cluster XIVa)
Dietary carbohydrates Acetate production
Ethanol production
Lactate production
Acetate
Carbon dioxide and Hydrogen
Ethanol
Formate
Lactate
   Lachnoclostridium
(Clostridium cluster XIVa)
Proteins
Saccharides
Acetate production
Butyrate kinase pathway
Ethanol production
Lactate production
Acetate
Butyrate
Carbon dioxide and Hydrogen
Ethanol
Formate
Lactate
   Roseburia
(Clostridium cluster XIVa)
1,2-Propanediol
Acetate
Dietary carbohydrates
1,2-Propanediol pathway
Acetate production
Butyryl CoA:acetyl CoA transferase pathway
Ethanol production
Lactate production
Acetate
Butyrate
Carbon dioxide and Hydrogen
Ethanol
Formate
Lactate
Propanol
Propionate
  Lactobacillaceae Lactobacillus 1,2-Propanediol
Saccharides
1,2-Propanediol pathway
Acetate production
Ethanol production
Lactate production
Acetate
Ethanol
Formate
Lactate
Propanol
Propionate
  Ruminococcaceae Faecalibacterium
(Clostridium cluster IV)
Acetate Butyryl CoA:acetyl CoA transferase pathway Butyrate
Carbon dioxide and Hydrogen
Formate
   Ruminiclostridium W
(Specifically Clostridium cluster IV, which is currently grouped with Clostridium cluster III)
Dietary carbohydrates
Proteins
Acetate production
Butyrate kinase pathway
Ethanol production
Lactate production
Acetate
Butyrate
Carbon dioxide and Hydrogen
Ethanol
Formate
Lactate
   Ruminococcus
(Clostridium cluster IV)
Dietary carbohydrates Acetate production
Ethanol production
Lactate production
Succinate pathwayI
Acetate
Ethanol
Formate
Lactate
Succinate
  Streptococcaceae Streptococcus NW Mucin
Saccharides
Acetate production
Ethanol production
Lactate production
Acetate
Ethanol
Formate
Lactate
  Veillonellaceae Veillonella 1,2-Propanediol
Lactate
Proteins
Saccharides
Succinate
1,2-Propanediol pathway
Acetate production
Lactate production
Succinate pathway
Acetate
Carbon dioxide and Hydrogen
Formate
Lactate
Propanol
Propionate
Succinate
Proteobacteria Enterobacteriaceae Escherichia Proteins
Saccharides
1,2-Propanediol pathwayI
2,3-Butanediol production
Acetate production
Ethanol production
Lactate production
Succinate pathwayI
1,2-Propanediol
2,3-Butanediol
Acetate
Carbon dioxide and Hydrogen
Ethanol
Formate
Lactate
Succinate
  1. Taxa that are listed as part of a ‘core’ gut microbiota found by Falony et al. are in bold [31]. Those genera that were core components of exclusively the ‘Western’ cohorts are denoted with a ‘W’ superscript, whereas the exclusively ‘non-Western’ ones are denoted with a ‘NW’ superscript. If the core taxon could not be resolved to the genus level, the bacterial families are bolded. For the bacterial families that do not already contain several core genera, the most commonly described genus of the human gut microbiome for that family is also listed as a representative. Additionally, genera found to be highly prevalent among the human population, yet typically present in low abundance, are underlined [32]. The possible substrates consumed, metabolisms, and metabolites for each genus are listed. These metabolisms were inferred from the following articles [28, 33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61]. Note that many of these metabolisms are species-specific, and only the substrates commonly utilized among species of the genus are listed. Further, only the most abundant metabolites produced from pyruvate catabolism (i.e., saccharolytic processes) are given. When a particular metabolic pathway is denoted with an ‘I’ superscript, the microorganisms do not possess the full enzymatic pathway, but rather produce the typical intermediate as an end-product instead. Likewise, an ‘I/A’ indicates species of that genus may possess either the full or half pathway