Microbial Profile of the Stomach: Comparison between Normal Mucosa and Cancer Tissue in the Same Patient

Incheol Seo; Bijay Kumar Jha; Seong-Il Suh; Min-Ho Suh; Won-Ki Baek

doi:10.4167/jbv.2014.44.2.162

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Seo, Jha, Suh, Suh, and Baek: Microbial Profile of the Stomach: Comparison between Normal Mucosa and Cancer Tissue in the Same Patient

Original Article

J Bacteriol Virol 2014;44(2):162-169.

Published online: 9 February 2014

DOI: https://doi.org/10.4167/jbv.2014.44.2.162

Microbial Profile of the Stomach: Comparison between Normal Mucosa and Cancer Tissue in the Same Patient

Incheol Seo, Bijay Kumar Jha, Seong-Il Suh, Min-Ho Suh, Won-Ki Baek^*

Department of Microbiology, School of Medicine, Keimyung University, Daegu, Korea

^*Corresponding author: Won-Ki Baek, M.D., Ph.D. Department of Microbiology, Keimyung University School of Medicine, 1095 Dalgubeol-daero, Dalseo-Gu, Daegu, 704-701, Korea. Phone: +82-53-580-3843, Fax: +82-53-580-3788, e-mail: wonki@dsmc.or.kr

Received 11 April 201423 May 2014 Accepted 26 May 2014

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Gastric cancer is the third most common cancer and the third most frequent cause of cancer mortality in Asia. It is predicted that gastric cancer will remain an important cause of death at least during the next half century because of the increasing number of new cases in an aging population. However, little has been revealed about the role of gastric microbes and their reaction to gastric cancer. In this study, we identified differences in the microbial communities between gastric cancer and normal gastric mucosa by comparing the microbiomes of tissues from the same patients. The clustering analysis results showed different bacterial communities between normal gastric mucosa and gastric cancer. A comparison of bacterial communities at the species level revealed that Helicobacter pylori was significantly reduced in cancer tissue compared to that in normal gastric mucosa in the same patient. A comparison at the genus level showed that Propionibacterium spp., Staphylococcus spp., and Corynebacterium spp. had significantly reduced populations in cancer tissue, whereas Clostridium spp. and Prevotella spp. had significantly increased populations in cancer tissue.

Keywords: Gastric cancer, Helicobacter pylori, Microbiome

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Figure 1.

Clustering of the samples based on bacterial composition at the species level. Bacterial composition is different between normal gastric mucosa and gastric cancer. Y-axis represents the Bray-Curtis dissimilarity. (A) Whole bacterial species were used for analysis including Helicobacter pylori. (B) Clustering analysis result after excluding H. pylori.

Figure 2.

Relative abundances of Helicobacter pylori in normal gastric mucosa and that of gastric cancer. Normal gastric mucosa has a higher abundance of Helicobacter pylori than that of gastric cancer. Y-axis represents the relative proportion of H. pylori to all bacterial species from each sample. ‘N’ denotes normal gastric mucosa, ‘T’ denotes gastric cancer. Numbers are identification codes for each sample; the same identification code means they were obtained from the same patient.

Figure 3.

More abundant bacterial genera in normal gastric mucosa than that of gastric cancer. Presence of (A) Propionibacterium spp., (B) Staphylococcus spp., and (C) Corynebacterium spp. in normal gastric mucosa and that of gastric cancer. Y-axis represents the relative proportion of each bacterial genus to all bacterial genera from each sample. ‘N’ denotes normal gastric mucosa, ‘T’ denotes gastric cancer. Numbers are identification codes for each sample; the same identification code means they were obtained from the same patient.

Figure 4.

More abundant bacterial genera in gastric cancer than those in normal gastric mucosa. Presence of (A) Clostridium spp. and (B) Prevotella spp. in normal gastric mucosa and that of gastric cancer. Y-axis represents the relative proportion of each bacterial genus to all bacterial genera from each sample. ‘N’ denotes normal gastric mucosa, ‘T’ denotes gastric cancer. Numbers are identification codes for each sample; the same identification code means they were obtained from the same person.

Table 1.

Clinical information for the samples used in the analysis.

Patient ID^a	Sex^a	Age^a	Location^a	Size (cm)^a	Histologic subtype^a (WHO classification)	Lauren^a	Stage ^a	HP (%)^b	Select^c
43	M	51	U	7.0	WD	Gastric	IIIb	2.7
80	M	56	L	5.0	PD	Diffuse	IIIb	1.3
87	M	53	U	8.0	MD	Diffuse	IIIb	0
95	M	65	L	6.0	WD	Intestinal	IIIa	31.1	O
119	M	48	L	10.0	WD	Intestinal	IIIa	11.7	O
130	M	57	L	6.5	MD	Intestinal	IIb	0
134	M	57	L	8.5	WD	Intestinal	IIIb	31.8	O
135	M	37	L	6.0	Mucinous	Intestinal	IIb	92.0	O
136	M	55	L	4.5	MD	Diffuse	IIIa	17.5	O
195	M	67	U	6.0	Papillary	Intestinal	IIIa	30.4	O
236	F	72	L	6.5	MD	Mixed	IIa	68.1	O
849	M	64	L	5.4	PD	Intestinal	Ib	63.8	O
859	F	60	L	5.0	MD	Intestinal	Ib	74.8	O
882	F	75	L	3.5	MD	Intestinal	Ia	57.4	O
889	F	66	L	8.7	MD	Intestinal	IIa	56.6	O
917	M	73	L	7.9	MD	Intestinal	IIa	6.5

^a Information marked were obtained from Yoon et al., Comprehensive genome- and transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers, Genome Res 23 (2013) 1109-1117. HP(%)

^b Information marked with percentage of Helicobacter pylori population from entire blast results

^c Select, selected patients for analysis accroding to the presence of Helibacter pylori in the normal gastric mucosa; U, upper third; L, lower third; WD, tubular adenocarcinoma and well differentiated; MD, tubular adenocarcinoma and moderately differentiated; PD, tubular adenocarcinoma and poorly differentiated.

Table 2.

Summary of the sequence statistics.

SRA Run^a	Patient ID^b	Sample^b	Total reads^c	Unmapped with hg19^d	Unmapped read (%)^e	Contigs^f	Matching with bacteria^g	Above threshold^h
SRR546237	43	Normal	52,088,890	13,775,741	26.4	98,994	1,722	246
SRR546236	43	Tumor	52,088,890	12,407,493	23.8	33,734	388	49
SRR825140	80	Normal	43,269,450	9,637,598	22.3	41,315	514	172
SRR546238	80	Tumor	42,996,076	12,289,307	28.6	69,175	5,567	532
SRR546239	87	Normal	44,471,834	14,136,479	31.8	93,583	1,227	190
SRR546240	87	Tumor	49,814,912	12,612,740	25.3	70,767	3,171	227
SRR825143	95	Normal	49,357,002	10,892,291	22.1	52,590	613	295
SRR825141	95	Tumor	46,801,172	8,781,017	18.8	39,856	138	69
SRR546226	119	Normal	52,088,890	14,958,865	28.7	62,186	2,739	327
SRR546225	119	Tumor	55,022,224	16,085,525	29.2	35,455	135	58
SRR825136	130	Normal	46,515,690	9,967,511	21.4	32,930	142	75
SRR825135	130	Tumor	49,181,346	10,449,965	21.2	34,317	117	58
SRR546227	134	Normal	52,400,004	12,290,105	23.5	31,281	500	97
SRR546228	134	Tumor	55,022,224	13,180,350	24.0	34,657	252	91
SRR546230	135	Normal	52,088,890	11,573,353	22.2	68,630	1,766	997
SRR546229	135	Tumor	52,266,668	10,269,450	19.6	47,252	166	43
SRR546232	136	Normal	54,755,556	14,774,615	27.0	66,951	845	177
SRR546231	136	Tumor	53,511,112	10,454,368	19.5	26,586	166	66
SRR546233	195	Normal	53,511,112	12,381,166	23.1	55,855	305	107
SRR546234	195	Tumor	52,088,890	14,704,878	28.2	47,228	499	94
SRR825139	236	Normal	41,204,902	9,277,569	22.5	44,692	857	498
SRR825137	236	Tumor	43,956,792	6,135,987	14.0	20,651	192	89
SRR801424	849	Normal	58,124,992	10,104,003	17.4	139,959	216	54
SRR801425	849	Tumor	63,880,118	7,752,423	12.1	27,819	90	6
SRR801427	859	Normal	59,019,350	10,010,433	17.0	114,625	356	104
SRR801426	859	Tumor	56,227,424	6,982,330	12.4	86,906	188	57
SRR801428	882	Normal	63,549,430	9,720,473	15.3	119,616	355	150
SRR801429	882	Tumor	59,102,148	7,322,912	12.4	75,218	354	137
SRR801430	889	Normal	44,498,444	7,450,469	16.7	88,745	412	122
SRR801431	889	Tumor	59,655,378	7,622,162	12.8	25,708	881	134
SRR801432	917	Normal	62,755,892	7,906,885	12.6	74,454	382	131
SRR801433	917	Tumor	63,306,020	8,839,289	14.0	131,114	413	162

^a SRA Run, Run number of each sample in the NCBI Sequence Read Archive

^b Information marked with obtained from Yoon et al., Comprehensive genome- and transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers, Genome Res 23 (2013) 1109-1117.

^c Total reads, Total number of sequenced reads

^d Unmapped with hg19, Number of unmapped reads after aligning with hg19 human reference genome using TopHat

^e Unmapped read (%), Percentage of unmapped reads to total sequenced reads

^f Contigs, Number of contigs de novo assembled by Vetvet

^g Matching with bacteria, Number of contigs which were matched with bacterial reference genomes

^h Above threshold, Number of contigs with E-value ≤1 × E⁻⁴⁰ and identity ≥95% to the reference sequence among matched contigs with bacterial reference genomes.

Table 3.

Microbiota with different populations between normal gastric mucosa and that of gastric cancer.

Genera	p-value
Helicobacter pylori	0.000977
Propionibacterium spp.	0.013672
Staphylococcus spp.	0.014433
Clostridium spp.	0.034611
Prevotella spp.	0.036032
Corynebacterium spp.	0.044011

Significantly different microbiota in the population by comparing normal gastric mucosa and gastric cancer from the same patient. p-value for Helicobacter pylori was analyzed by comparing all strains at the species level. Other bacterial genera were analyzed at the genus level after removing all H. pylori sequences from the blast results. The Wilcoxon signed-rank test was applied for statistical analysis.

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