Table 1.

Description of functional features shown in figure 5

Module	Description
M00064	DP-L-glycero-D-manno-heptose biosynthesis
M00079	Keratan sulphate degradation
M00191	Thiamine transport system
M00229	Arginine transport system
M00233*	Glutamate transport system
M00287	PTS system, galactosamine-specific II component
M00316	Manganese transport system
M00326	RTX toxin transport system
M00339	RaxAB-RaxC type I secretion system
M00358*	Coenzyme M biosynthesis
M00373	Ethylmalonyl pathway
M00434	PhoR-PhoB (phosphate starvation response) two-component regulatory system
M00442	Putative hydroxymethylpyrimidine transport system
M00443	SenX3-RegX3 (phosphate starvation response) two-component regulatory system
M00447	CpxA-CpxR (envelope stress response) two-component regulatory system
M00448	CssS-CssR (secretion stress response) two-component regulatory system
M00499	HydH-HydG (metal tolerance) two-component regulatory system
M00456	ArcB-ArcA (anoxic redox control) two-component regulatory system
M00472	NarQ-NarP (nitrate respiration) two-component regulatory system
M00566*	Dipeptide transport system
M00571	AlgE-type Mannuronan C-5-Epimerase transport system
M00601	Putative chitobiose transport system
M00696	Multidrug resistance, efflux pump AcrEF-TolC
M00697	Multidrug resistance, efflux pump MdtEF-TolC
M00713*	Fluoroquinolone resistance, efflux pump LfrA
M00714*	Multidrug resistance, efflux pump QacA
M00720	Multidrug resistance, efflux pump VexEF-TolC
M00739	Cationic peptide transport system

All KEGG modules found to be significantly different between baseline and week 1 samples are shown, includingall modules identified in samples with reads from dominant taxa present (those in figure 5B), as well as the 20 modules identified with the largest effect size after reads from dominant taxa were removed (figure 5D). Asterisks indicate modules identified in the analyses shown in both figure 5B,D.