Table 2.

Sequencing Reads for the 27 Most Abundant Bacteria in Four Samples from Patients with Cord Colitis in the Discovery Cohort.^*

Organism	Sample No.
	5b	5c	11b	11d
	number of reads
Bradyrhizobium enterica	631,276	119,122	1,669,087	1,360,422
Delftia acidovorans	5,006	7,517	137	39
Stenotrophomonas maltophilia	2,740	3,615	130	50
Other delftia species†	2,103	2,975	371	113
Propionibacterium acnes	1,070	355	5,985	1,087
Bradyrhizobium japonicum	695	180	1,520	1,177
Ralstonia pickettii	678	148	1,295	419
Other bradyrhizobium species	542	110	1,146	887
Pseudomonas mendocina	460	76	1,276	417
Pseudomonas fluorescens	375	76	126	56
Rhodopseudomonas palustris	311	77	627	451
Acidovorax ebreus	208	101	682	290
Xanthomonas campestris	208	97	127	252
Alicycliphilus denitrificans	174	91	300	139
Ralstonia solanacearum	137	26	333	103
Other acidovorax species	123	78	349	174
Mesorhizobium opportunistum	99	94	111	50
Burkholderia gladioli	95	39	409	248
Pseudomonas aeruginosa	89	80	149	39
Methylobacterium radiotolerans	79	99	114	15
Escherichia coli	74	81	472	295
Rubrivivax gelatinosus	67	28	240	177
Other agrobacterium species†	46	11	769	269
Cupriavidus taiwanensis	46	60	29	19
Asticcacaulis excentricus	45	34	289	72
Agrobacterium tumefaciens	22	8	489	135
Fusobacterium nucleatum	8	2	142	217
Rothia mucilaginosa	5	5	313	14
Clostridium difficile	3	1	4	114
Streptococcus sanguinis	3	6	582	3
Lactobacillus reuteri	1	0	433	0

^*PathSeq taxonomic classification was performed on all four sequenced samples obtained from Patients 5 and 11 with the inclusion of the Bradyrhizobium enterica draft genome in the reference database. Organisms are listed according to their abundance in sample 5b. Additional details regarding the viral reads are provided in Table S4 in the Supplementary Appendix.

^†Only one species was identified.