TABLE 3.

Description of main stimulated phylotypes and group phylotypes as shown in Fig. 6^a

GPTb	PTc	Description
GPT-1	A4, T3, R96	Group phylotype GPT-1 (99% to 100% identity to Aeromonas hydrophila) was significantly stimulated by ribose and aspartate (Fig. 6). The facultative aerobe A. hydrophila ferments pentoses to acetate, ethanol, lactate, succinate, formate, CO2, and H2 (100–104). Consistent with its response to ribose, this fermentative phylotype was shown previously to respond to RNA and RNA-rich cell lysate (40). Although A. hydrophila is not known to ferment aspartate, it and closely related Aeromonas media harbor (i) aspartate ammonia lyase that transforms aspartate into the electron acceptor fumarate which reductively forms succinate (105, 106) and (ii) aspartate carbamoyltransferase that is utilized in the synthesis of pyrimidine precursors (107). Group phylotype GPT-1 was also responsive to glucose, a finding consistent with its responsiveness to diverse polymeric and nonpolymeric saccharides (8, 108).
GPT-2	A6, R5, T6	Based on 16S rRNA gene sequences, the Enterobacteriaceae-affiliated group phylotype GPT-2 (99% to 100% identity to the facultative aerobes Buttiauxella gaviniae and Enterobacter aerogenes) displayed a broad response in glutamate, aspartate, threonine, Casamino Acids, ribose, and formate treatments (Fig. 6). B. gaviniae produces fatty acids and gases when fermenting sugars such as ribose, and several Buttiauxella-associated species can utilize amino acids, including glutamate, aspartate, and threonine as sole carbon and energy sources (109). The Buttiauxella- and Enterobacter-affiliated phylotypes were also stimulated in gut contents supplemented with RNA or cell lysate (40).
GPT-3	A129, A1526	Sequences of the Yokenella-affiliated group phylotype GPT-3 (97% to 99% identity to the facultative aerobe Yokenella regensburgei) displayed an apparent net increase in relative abundance in glutamate, aspartate, and threonine treatments. We are unaware of information on the ability of Y. regensburgei to ferment amino acids, but its occurrence in human wounds and infection is suggestive of its potential ability to use amino acids (110, 111).
GPT-4	A25, T7	The group phylotype GPT-4 (99% to 100% identity to Terrisporobacter glycolicus) was stimulated in threonine and formate treatments (Fig. 6). This is consistent with (i) the ability of T. glycolicus to convert threonine to propionate (112) and (ii) the potential for this acetogen to from acetate from formate (113). Acetogen-affiliated phylotypes also responded positively in cell lysate treatments that produced large amounts of transient formate (40). Acetogens are capable of diverse dissimilatory processes, including fermentation (114, 115); thus, the stimulation of a potential acetogen is not strictly dependent on acetogenesis.
GPT-5	A1, T2	The Fusobacteriaceae were represented by group phylotype GPT-5 (96% identity to Cetobacterium somerae), which was responsive in the glutamate, aspartate, valine/glycine, and Casamino Acids treatments (Fig. 6), findings consistent with this group phylotype being strongly stimulated by protein (40). Although a 96% sequence identity is relatively low for species-level classification, C. somerae occurs in gastrointestinal systems and ferments amino acids and peptides to acetate, propionate, and butyrate, products detected in the aforementioned amino acid treatments (116, 117). Group phylotype GPT-5 was more distantly related to species of the strictly anaerobic genus Propionigenium that are able to utilize succinate for growth and produce propionate (66, 118), properties consistent with the product profile of the succinate treatment (Fig. 4) in which this group phylotype was also responsive (Fig. 6).
	A8	Peptostreptococcaceae-affiliated phylotype A8 (99% identity to the amino acid fermenter Paraclostridium bifermentans) responded in the co-amino acid treatments (Fig. 6), which was indicative of Stickland fermentation (60). In this regard, P. bifermentans isolated from the human gut can be cultivated on co-amino acids such as the alanine/glycine treatment utilized in the present study (53), which is consistent with phylotype A8 facilitating Stickland fermentation. Phylotype A8 was also weakly responsive in the Casamino Acids treatment (Fig. 6), and P. bifermentans-affiliated phylotypes are also strongly stimulated by protein and cell lysate (40), activities consistent with the ability of P. bifermentans to ferment numerous amino acids (53).
	A14	Glutamate-stimulated phylotype A14 (Fig. 6) was closely related to Clostridium pascui (100% identity), a proteolytic spore-forming anaerobe that ferments glutamate (119). This phylotype is also stimulated by protein-rich cell lysate (40), reinforcing the likelihood that this phylotype can ferment certain amino acids.

^aSee Table S10 in the supplemental material for statistical analyses of the phylotypes.

^bGPT, group phylotype.

^cPT, stimulated phylotype.