Bacterial biota in reflux esophagitis and Barrett’s esophagus

Table 1 Clinical and pathological features of 24 patients included in this study¹

Case#	Age2	Symptoms of heartburn		Esophageal features
		Frequency (time/week)	Duration3	Endoscopic diagnosis	Histopathology4
Normal esophagus (n = 9)
248	73	0	NA	Normal	NP
251	66	0	NA	Normal	NP
256	66	0	NA	Normal	NP
259	75	3	1 Y	Hiatal hernia	NP
261	81	3	>1 Y	Esophageal ring	NP
262	65	0	NA	Esophagitis	NP
263	51	3	1 Y	Gastric erosions	NP
264	72	0	NA	Esophageal ring	NP
265	71	0	NA	Hiatal hernia	NP
Esophagitis (n = 12)
247	63	3	>1 Y	Esophagitis	AI, CI, EO
252	51	0	NA	Normal	AI, CI, EO
254	57	3	1 Y	Esophageal ring	AI, CI, EO
257	52	3	1 M	Esophagitis	AI, CI, EO
249	34	0	NA	Esophagitis	AI, CI
243	53	3	>1 Y	Esophagitis	CI, EO
255	66	3	>1 Y	Esophagitis	CI, EO
258	52	3	2–3 Y	Barrett’s esophagus	CI, EO
244	74	3	2 M	Esophagitis	CI
250	68	0	NA	Esophageal ring	CI
260	75	3	2–3 M	Esophagitis	CI
253	71	5	4 Y	Esophagitis	CI
Barrett’s esophagus (n = 3)
242	69	0	NA	BE	BE
245	70	0	NA	BE	BE
246	66	3	>1 Y	BE	BE, CI, EO

¹None of the 24 patients had a history of recent use of antibiotics, previous gastric/esophageal surgery, active infection of the oral cavity[17].

²All 24 patients are males, reflecting the veterans population.

³NA, not available; Y, year; M, month.

⁴NP: no pathologic changes; BE: Barrett’s esophagus; EO: eosinophils; CI: chronic inflammation; AI: acute inflammation.

Table 2 Analysis of 48 bacterial 16S rDNA sequences detected in the esophageal biopsies from 24 patients

		Number of sequences detected
Best matched bacterial	% Identity1	Normal esophagus	Esophageal disease		All
16S rDNA			Esophagitis	Barrett’s	patients
		(n = 9)2	(n = 12)	(n = 3)	(n = 24)
Cultivation-defined species3 (n = 14)
Prevotella veroralis	98.2	4	1		5
Streptococcal species	100	1	2		3
Pseudomonas species	100		2	1	3
Helicobacter pylori	100, 99.3, 98.6		3		3
Prevotella pallens	100	1		1	2
Streptococcus salivarius	100, 99.4	1		1	2
Actinobacillus pleuropneumoniae	99.4, 98.8	1	1		2
Acinetobacter sp. OM-E81	100			1	1
Citrobacter amalonaticus	100		1		1
Haemophilus influenzae	100		1		1
Haemophilus parainfluenzae	99.4		1		1
Veillonella atypica	99.4	1			1
Campylobacter fetus	97.9	1			1
Prevotella oulora	97		1		1
Subtotal		10	13	4	27
Unidentified species4 (n = 5)
Oral bacterium SH66	100, 99.4, 98.8	6	3	2	11
Oral bacterium RP55-18	100, 99.4		2		2
Oral bacterium SH13	100	1			1
Oral bacterium SH64	99.4	1			1
Oral bacterium AP60-12	98.3		1		1
Subtotal		8	6	2	16
Unknown5 (n = 5)
(Bacterium CEC2)	96.5		1		1
(Veillonella ratti)	93		1		1
(Cytophagales)	92.1		1		1
(Marine bacterium SS1)	89.9		1		1
(Rumen bacterium RFN91)	89.2		1		1
Subtotal			5		5

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.

²n indicates number of patients in each group.

³Cultivation-defined species: 16S rDNA sequence with equal or greater than 97% identity with 16S rDNA of cultivation-defined bacterial species[24].

⁴Unidentified species: 16S rDNA sequence with equal or greater than 97% identity with PCR-derived 16S rDNA sequence[24].

⁵Unknown: 16S rDNA sequence with <97% identity with any known 16S rDNA sequences.

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.

Table 4 Comparison of representation of bacterial phyla observed in studies of the esophagus and subgingival crevice

	Subgingival crevice			Esophagus
Phylum	Number of clones	Number of species		Number of clones	Number of species	Number of clones	Number of species
	Paster1	Paster1	Kroes2	Pei3		Present study
Clostridium group	0	0	13	0	0	0	0
Obsidian pool OB11	6	1	0	0	0	0	0
Deferribacteres	86	8	8	0	0	0	0
Spirochaetes	537	58	0	0	0	0	0
TM7	34	5	0	13	3	0	0
Fusobacteria	353	19	2	20	6	0	0
Actinobacteria	275	32	15	39	8	2	2
Firmicutes	659	113	15	626	41	18	11
Proteobacteria	338	51	14	20	14	31	11
Bacteroidetes	234	58	8	182	23	96	15
Total	2522	347	75	900	95	147	39

¹From Paster et al[14] ;

²from Kroes et al[28] ;

³from Pei et al[13].