A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016

Table 1 Microorganisms, microbial substrates, and microbial products under study, FY2012–2016

Body region	Commensal microbial isolates	Microbial products		Microbial substrates
Body region	Commensal microbial isolates	Cellular	Metabolic	Microbial substrates
GI tract—lumen	Bacteroids fragilis	Lipopolysaccharide	Indole	Fiber
	B. thetaiotamicron	Flagellin	Short-chain fatty acids (butyrate, acetate, proprionate)	Human milk oligosaccharides
	B. ovatus	Bacteriocins	Corrinoids (B vitamins)	Plant pectin glycans
	Bacteriodes spp.	Amyloids	Hydrogen sulfide	Fructans
	Methanobrevibacter smithii	Polysaccharide A	Secondary bile acids	Host mucin glycans
	Escherichia coli	Sphingolipids	Pyrazinones, dihydropyrazinones	Polyphenols
	Oxalobacter formigenes	CRISPRs	Trimethylamine N-oxide	Inulin
	Akkermansia mucinophila	Type IV pili	Thiopeptides
	Enterococcus faecium		Oxalate
	Candida albicans
GI tract—lymphoid	Alcaligenes spp.
	Achromobacter spp.
	Ochrobacter spp.
	Bordetella spp.
	Bifidobacterium adolescentis
Skin	Corynebacterium spp.
Skin	Staphylococcus epidermidis
Oral	Proprionibacterium spp.
Vagina	Clostridiales spp.
Nares	S. aureus
Body-wide	Neisseria spp.

This table summarizes the commensal microorganisms, microbial growth substrates, and bioactive microbial products which were the subject of study in the microbiome-related projects over FY12–16. The first two columns indicate the body region from which the commensal microorganism was isolated, and the name of the isolate. The next two columns list the microbial products which were the subject of study and which are either cellular in nature or a byproduct of microbial metabolism. The final column lists the microbial growth substrates which were a subject of study

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