Bacterial biota in reflux esophagitis and Barrett’s esophagus

Table 3 Prevalence of specific 16S rDNA in 99 subclones from a single biopsy from patient #242 with Barrett’s esophagus

Best matched bacterial 16S rDNA	% Identity1	Number of sequences
Cultivation-defined species2 (n = 10)
Neisseria flavescens	98.8, 98.2	11
Prevotella pallens	100	6
Porphyromonas sp oral clone CW034	100, 99.4, 97.6	3
Gemella morbillorum	100	2
Prevotella sp oral clone BI027	100	1
Campylobacter fetus	99.4	1
Rothia mucilaginosa	99.4	1
Veillonella sp oral clone AA050	98.8	1
Veillonella parvula	98.2	1
Catonella morbi	98.1	1
Subtotal		28
Unidentified species3 (n = 5)
Oral bacterium SH66	100, 99.4	50
Oral bacterium SH25	99.4	4
Oral bacterium SH13	100	1
Oral bacterium AP60-12	98.7	1
Oral bacterium AP60-35	98.2, 97.6	2
Subtotal		58
Unknown4 (n = 7)
(Prevotella sp oral clone FO45)	95	3
(Rumen bacterium JW17)	93.9	3
(Rumen bacterium RFN91)	88.4, 89	3
(Rumen bacterium 30-15)	94.5, 93.9	2
(Rumen bacterium JW17)	96.3	1
(Prevotella sp oral clone AH125)	93.9	1
Subtotal		13

¹Multiple numbers indicate that sequences were obtained from more than one clone, and that the identity to the specified best matching bacteria varied between clones.

²Cultivation-defined species: 16S rDNA sequence with equal or greater than 97% identity with 16S rDNA of cultivation-defined bacterial species[24].

³Unidentified species: 16S rDNA sequence with equal or greater than 97% identity with PCR-derived 16S rDNA sequence[24].

⁴Unknown: 16S rDNA sequence with <97% identity with any known 16S rDNA sequences.