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

Oliphant, Kaitlyn; Allen-Vercoe, Emma

doi:10.1186/s40168-019-0704-8

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 pathway^I 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 pathway^I/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 pathway^I 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 pathway^I	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 pathway^I	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 pathway^I 2,3-Butanediol production Acetate production Ethanol production Lactate production Succinate pathway^I	1,2-Propanediol 2,3-Butanediol Acetate Carbon dioxide and Hydrogen Ethanol Formate Lactate Succinate

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

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ISSN: 2049-2618

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