Gut microbiome profiling and colorectal cancer in African Americans and Caucasian Americans

Table 1 General characteristics of African American and Caucasian American patients

Race	Gender	Age	Height (inches)	Weight (lbs)	Body mass index	Polyp	Adenoma
AA	Male	65.2	70.4	181	28.9	4.6	3.8
CA	Male	62.6	69.0	194	31.0	1.43	1.0

AA: African Americans; CA: Caucasian Americans.

Table 2 List of primers for bacterial genes specific for family, genus and species

Bacterial gene	Forward primer (5’-3’)	Reverse primer (5’-3’)	Ref.
Clostridium cluster XI	TGACGGTACYYNRKGAGGAAGCC	CTACGGTTRAGCCGTAGCCTTT	[63]
Clostridium cluster XIVa	GCGGTRCGGCAAGTCTGA	CCTCCGACACTCTAGTMCGAC	[64]
Clostridium cluster IV	GCACAAGCAGTGGAGT	CTTCCTCCGTTTTGTCAA	[65]
Bifidobacterium genus	GATTCTGGCTCAGGATGAACGC	CTGATAGGACGCGACCCCAT	[66]
Lactobacillus spp.	AGCAGTAGGGAATCTTCCA	CACCGCTACACATGGAG	[66]
Enterobacter (Family)	CATTGACGTTACCCGCAGAAGAAGC	CTCTACGAGACTCAAGCTTGC	[66]
Fusobacterium (genus)	GGATTTATTGGGCGTAAAGC	GGCATTCCTACAAATATCTACGAA	[67]
Fusobacterium nucleatum	CAACCATTACTTTAACTCTACCATGTTCA	GTTGACTTTACAGAAGGAGATTATGTAAAAATC	[68]
Clostridium sordelli	CTGAGACACGTCCAAACTCTAC	CCTCCTCAAGTACCGTCATTATC	-
Total bacteria	CGTGCCAGCAGCCGCGG	TGGACTACCAGGGTATCTAATCCTG

Table 3 Abundance of microbiota in colonic effluents from African Americans and Caucasian Americans (green, black, blue and red color represent phylum, family, genus and species, respectively)

Phylum	Family	Genus	Species	AA (%)	CA (%)
Bacteroidetes				70.74	43.17
	Bacteroidaceae			56.75	29.94
		Bacteroides		56.8	29.9
			Unclassified	30.3	17.8
			Caccae	13.6	5.5
			Massiliensis	6.7	1.7
			Uniformis	2.8	1.5
			Fragilis	1	2
	Rikenellaceae			6.44	5.47
		Allistipes	Putredinis	6.4 (3.9)	5.4 (3.0)
	Porphymonadaceae			6.4	6.95
		Parabacteroides	Distasonis	4.9 (3.4)	3.2 (1.0)
		Barnesiella	Intestinihominis	0.16 (0.16)	2.7 (2.6)
	Prevotellaceae			1.9	1.1
		Paraprevotella	Clara	1.0 (0.9)	0.6 (0.6)
Firmicutes				26.74	36.25
	Ruminococaceae			11.35	15.7
		Faecalibacterium	Prausinitzii	4.5 (4.5)	3.1 (3.1)
		Unclassified	Unclassified	2.5 (2.5)	2.9 (3.0)
		Gemmiger	Formicilis	1.9 (1.6)	6.1 (6.0)
		Clostridium IV	Unclassified	0.3 (0.3)	1.5 (1.5)
	Lachnospiraceae			11.19	13.7
		Ruminococcus 2	Unclassified	3.4 (3.4)	4.7 (4.7)
		Clostridium XIVa	Unclassified	2.05 (2.0)	1.03 (1.0)
		Unclassified	Unclassified	1.6 (1.7)	2.4 (2.4)
		Blautica	Producta	0.22 (0.06)	1.2 (0.0)
		Dorea	Unclassified	1.8 (0.8)	1.3 (1.0)
		Roseburia	Unclassified	0.5 (0.3)	1.3 (0.9)
	Steptococaccae	Steptococcus	Faecium	0.9 (0.9) (0.8)	3.2 (3.2) (3.2)
	Acidaminococcaceae	Phascolarctobacterium	Unclassified	1.8 (1.9) (1.4)	0.9 (0.9) (1.3)
	Peptostreptococcaceae	Clostridium XI	Unclassified	0.02 (0.02) (0.02)	0.01 (0.008) (0.008)
	Veillonellaceae	Veillonella	Atypica	0.81 (0.03) (0.03)	1.27 (0.02) (0.02)
			Unclassified	0.6 (0.6)	0.5 (0.5)
		Dialister	Invisus	0.002 (0.0)	0.68 (0.65)
	Lactobacillaceae	Lactobacillus	Sanfrancisecnsis	0.035 (0.02) (0.004)	0.01 (0.01) (0.001)
Proteobacteria				2.02	5.9
	Desulfovibrionaceae	Biophila	Unclassified	0.16 (0.12) (0.12)	0.07 (0.07) (0.01)
	Sutterrellaceae	Parasuttrella	Excrementihomis	0.50 (0.76) (0.4)	0.24 (1.9) (0.1)
	Pasteurellaceae	Haemophilus	Parainfluenza	0.57 (0.9) (0.4)	1.98 (1.9) (1.9)
	Enterobacteiaceae	Escherichia/Shigella	Unclassified	0.92 (0.8) (0.9)	3.14 (3.1) (3.1)
		Klebsiella	Unclassified	(0.09) (0.02)	0.003 (0.01)
Fusobacteria				0.18	0.58
	Fusobactereaceae	Fusobacterium	Unclassified	0.18 (0.15) (0.15)	0.58 (0.6) (0.6)
Verrucomicrobia				0.04	1.9
	Verrucomicrobiaceae	Akkermansia	Muciniphila	0.04 (0.04)	1.9 (1.9)
Bacteria-unclassified	Unclassified	Unclassified	Unclassified	0	5.4 (5.4) (5.4)
Unclassified-unclassified	Unclassified	Unclassified	Unclassified	0	4.6 (4.6) (4.6)

AA: African Americans; CA: Caucasian Americans.