Colonic Mucosal Microbiota in Colorectal Cancer: A Single-Center Metagenomic Study in Saudi Arabia

Al-Omair, Ameen; Masoodi, Ibrahim; Alyamani, Essam J.; Al-Lehibi, Abed; Qutub, Adel; Alsayari, Khalid; Altammami, Musaad A.; Alshanqeeti, Ali S.

doi:10.1155/2018/5284754

Cited by 31 publications

(18 citation statements)

References 20 publications

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“…Red meat was widely recognized as a dietary factor linked to the development of colorectal cancer ( Brenner et al, 2014 ). B. finegoldii and B. dorei can cause bacteremia ( Lee et al, 2015 ), along with B. Stercoris ( Lucas et al, 2017 ; Alomair et al, 2018 ), B. uniformis , and B. ovatus ( Liang et al, 2014 ), and they were all reported to be correlated with colorectal cancer.…”

Section: Resultsmentioning

confidence: 99%

Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data

Guo

2019

Front. Genet.

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Colorectal cancer is the third most common cancer worldwide with abysmal survival, thus requiring novel therapy strategies. Numerous studies have frequently observed infiltrating bacteria within the primary tumor tissues derived from patients. These studies have implicated the relative abundance of these bacteria as a contributing factor in tumor progression. Infiltrating bacteria are believed to be among the major drivers of tumorigenesis, progression, and metastasis and, hence, promising targets for new treatments. However, measuring their abundance directly remains challenging. One potential approach is to use the unmapped reads of host whole genome sequencing (hWGS) data, which previous studies have considered as contaminants and discarded. Here, we developed rigorous bioinformatics and statistical procedures to identify tumor-infiltrating bacteria associated with colorectal cancer from such whole genome sequencing data. Our approach used the reads of whole genome sequencing data of colon adenocarcinoma tissues not mapped to the human reference genome, including unmapped paired-end read pairs and single-end reads, the mates of which were mapped. We assembled the unmapped read pairs, remapped all those reads to the collection of human microbiome reference, and then computed their relative abundance of microbes by maximum likelihood (ML) estimation. We analyzed and compared the relative abundance and diversity of infiltrating bacteria between primary tumor tissues and associated normal blood samples. Our results showed that primary tumor tissues contained far more diverse total infiltrating bacteria than normal blood samples. The relative abundance of Bacteroides fragilis, Bacteroides dorei, and Fusobacterium nucleatum was significantly higher in primary colorectal tumors. These three bacteria were among the top ten microbes in the primary tumor tissues, yet were rarely found in normal blood samples. As a validation step, most of these bacteria were also closely associated with colorectal cancer in previous studies with alternative approaches. In summary, our approach provides a new analytic technique for investigating the infiltrating bacterial community within tumor tissues. Our novel cloud-based bioinformatics and statistical pipelines to analyze the infiltrating bacteria in colorectal tumors using the unmapped reads of whole genome sequences can be freely accessed from GitHub at https://github.com/gutmicrobes/UMIB.git.

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Section: Resultsmentioning

confidence: 99%

Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data

Guo

2019

Front. Genet.

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“…Finally, 50 ml of the washes, obtained from each colonoscopy, were collected in four (15 ml) test tubes and immediately stored at −80 C for further processing as discussed in our previous metagenomic studies. 11,12 DNA extraction for Total metagenomic sequencing. DNA samples were centrifuged at 5000 × g for 15 min, and the supernatants were discarded.…”

Section: Methodsmentioning

confidence: 99%

“…The pellet was resuspended in 10-ml lysis buffer (0.5 M Tris-HCl; 20 mm EDTA; 10 mm NaCl; 0.1% SDS; pH 9.0), and the mixtures were homogenized by centrifuging and shaking for 5-10 min as discussed in our previous metagenomic studies. 11,12 Samples were then diluted (1: 2) with a 10-ml lysis buffer and homogenized for another 5 min. Genomic DNA (gDNA) was precipitated by adding 5 ml of 7.5 M ammonium acetate and 25 mL of ice-cold ethanol (95-100%).…”

Section: Methodsmentioning

confidence: 99%

Microbial dysbiosis in irritable bowel syndrome: A single‐center metagenomic study in Saudi Arabia

Masoodi

Alshanqeeti²,

Alyamani

et al. 2020

JGH Open

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Background The focus of this study was to explore potential differences in colonic mucosal microbiota in irritable bowel syndrome (IBS) patients compared to a control group utilizing a metagenomic study. Methods Mucosal microbiota samples were collected from each IBS patient utilizing jet‐flushing colonic mucosa in unified segments of the colon with distilled water, followed by aspiration, during colonoscopy. All the purified dsDNA was extracted and quantified before metagenomic sequencing using an Illumina platform. An equal number of healthy age‐matched controls were also examined for colonic mucosal microbiota, which were obtained during screening colonoscopies. Results The microbiota data on 50 IBS patients (31 females), with a mean age 43.94 ± 14.50 (range19–65), were analyzed in comparison to 50 controls. Satisfactory DNA samples were subjected to metagenomics study, followed by comprehensive comparative phylogenetic analysis. Metagenomics analysis was carried out, and 3.58G reads were sequenced. Community richness (Chao) and microbial structure in IBS patients were shown to be significantly different from those in the control group. Enrichment of Oxalobacter formigenes , Sutterella wadsworthensis , and Bacteroides pectinophilus was significantly observed in controls, whereas enrichment of Collinsella aerofaciens , Gemella morbillorum , and Veillonella parvula Actinobacteria was observed significantly in the IBS cohort. Conclusion The current study has demonstrated significant differences in the microbiota of IBS patients compared to controls.

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“…Tissue microbiome analysis revealed Burkholderia predominance among BC patients, with no significant gender differences. Interestingly, Burkholderia species have been linked with colorectal and gastric cancer, however its potential significance in carcinogesis remains to be established [ 90 , 91 ]. Despite obvious limitations, such as lack of control for well-known BC risk factors (e.g., smoking, environmental exposure, and diet) and disease-specific factors (stage, grade), these represent the first step to recognize gender-related differences in BC patients [ 79 ].…”

Section: Sex Related Urinary Microbiome Differences In Bladder Canmentioning

confidence: 99%

Urobiome in Gender—Related Diversities of Bladder Cancer

Bilski¹,

Dobruch²,

Kozikowski³

et al. 2020

IJMS

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Bladder cancer (BC) remains the most common malignancy of urinary tract. Sex-related differences in BC epidemiology, diagnosis, therapy, and outcomes have been reported. Throughout the recent years, extensive research has been devoted to genetic and molecular alterations in BC. Apart from the molecular background, another related concept which has been speculated to contribute to gender diversities in BC is the role of urinary pathogens in bladder carcinogenesis. Microbiome studies, fueled by the availability of high-throughput DNA-based techniques, have shown that perturbation in the microbiome is associated with various human diseases. The aim of this review is to comprehensively analyze the current literature according to sex-related differences in the microbiome composition in BC.

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Colonic Mucosal Microbiota in Colorectal Cancer: A Single-Center Metagenomic Study in Saudi Arabia

Cited by 31 publications

References 20 publications

Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data

Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data

Microbial dysbiosis in irritable bowel syndrome: A single‐center metagenomic study in Saudi Arabia

Urobiome in Gender—Related Diversities of Bladder Cancer

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