Figure 6. Firmicutes favor dietary protein while Bacteroidetes prefer secreted host protein. See also^{Figure S6,S7}.

(A) Nitrogen contribution of dietary algal protein across bacterial genera. Mean±s.e., N = 6 mice.

(B) Nitrogen contribution of circulating urea across bacterial genera. Mean±s.e., N = 6 mice.

(C) Experimental scheme of 72 hr urea infusion followed by 16S rRNA gene amplicon sequencing.

(D) Urea infusions increased urea concentration in systemic circulation. N = 5 mice. ***P<0.001 by two-sided Student’s t-test.

(E) Genus-level microbiota composition changes after urea infusion. The genera increased after urea infusion prefer urea in (B). Mean±s.e., N=5 mice. *P<0.05 by two-sided Student’s t-test.

(F) Correlation between genera abundance changes and nitrogen-source preference.

(G) Experimental schematic of long-term ¹⁵N-lysine and ¹⁵N-arginine infusion to probe the contribution of secreted host proteins to different bacterial genera.

(H) Nitrogen contribution of secreted host proteins across bacterial genera. Mean±s.e., N = 5 mice.

(I) Negative correlation between f_{genus←dietary proteins N} and f_{genus←secreted proteins N}.

(J) Summary of carbon and nitrogen inputs to different gut bacteria. Firmicutes prefer dietary carbon sources (fiber and protein) and nitrogen from host circulating urea. Bacteroidetes heavily use dietary fiber, while using on host secreted proteins for nitrogen. Verrucomicrobia prefers host secreted nutrients, both protein and circulating small molecules (lactate, urea).