Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing
Numerous studies have correlated dysbiosis in stool microbiota with colorectal cancer (CRC); however, fewer studies have investigated the mucosal microbiome in pre-cancerous bowel polyps. The short-read sequencing of variable regions in the 16S rRNA gene has commonly been used to infer bacterial tax...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-10-01
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| Series: | Cancers |
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| Online Access: | https://www.mdpi.com/2072-6694/15/20/5045 |
| _version_ | 1797574337587314688 |
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| author | Zoe Welham Jun Li Alexander F. Engel Mark P. Molloy |
| author_facet | Zoe Welham Jun Li Alexander F. Engel Mark P. Molloy |
| author_sort | Zoe Welham |
| collection | DOAJ |
| description | Numerous studies have correlated dysbiosis in stool microbiota with colorectal cancer (CRC); however, fewer studies have investigated the mucosal microbiome in pre-cancerous bowel polyps. The short-read sequencing of variable regions in the 16S rRNA gene has commonly been used to infer bacterial taxonomy, and this has led, in part, to inconsistent findings between studies. Here, we examined mucosal microbiota from patients who presented with one or more polyps, compared to patients with no polyps, at the time of colonoscopy. We evaluated the results obtained using both short-read and PacBio long-read 16S rRNA sequencing. Neither sequencing technology identified significant differences in microbial diversity measures between patients with or without bowel polyps. Differential abundance measures showed that amplicon sequence variants (ASVs) associated with <i>Ruminococcus gnavus</i> and <i>Escherichia coli</i> were elevated in mucosa from polyp patients, while ASVs associated with <i>Parabacteroides merdae</i>, <i>Veillonella nakazawae</i>, and <i>Sutterella wadsworthensis</i> were relatively decreased. Only <i>R. gnavus</i> was consistently identified using both sequencing technologies as being altered between patients with polyps compared to patients without polyps, suggesting differences in technologies and bioinformatics processing impact study findings. Several of the differentially abundant bacteria identified using either sequencing technology are associated with inflammatory bowel diseases despite these patients being excluded from the current study, which suggests that early bowel neoplasia may be associated with a local inflammatory niche. |
| first_indexed | 2024-03-10T21:21:35Z |
| format | Article |
| id | doaj.art-61d18c3c04f24dc381c03bd9dbfa366b |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-10T21:21:35Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-61d18c3c04f24dc381c03bd9dbfa366b2023-11-19T15:59:47ZengMDPI AGCancers2072-66942023-10-011520504510.3390/cancers15205045Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA SequencingZoe Welham0Jun Li1Alexander F. Engel2Mark P. Molloy3Bowel Cancer and Biomarker Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, AustraliaBowel Cancer and Biomarker Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, AustraliaColorectal Surgical Unit, Royal North Shore Hospital, Sydney 2065, AustraliaBowel Cancer and Biomarker Laboratory, School of Medical Sciences, The University of Sydney, Sydney 2065, AustraliaNumerous studies have correlated dysbiosis in stool microbiota with colorectal cancer (CRC); however, fewer studies have investigated the mucosal microbiome in pre-cancerous bowel polyps. The short-read sequencing of variable regions in the 16S rRNA gene has commonly been used to infer bacterial taxonomy, and this has led, in part, to inconsistent findings between studies. Here, we examined mucosal microbiota from patients who presented with one or more polyps, compared to patients with no polyps, at the time of colonoscopy. We evaluated the results obtained using both short-read and PacBio long-read 16S rRNA sequencing. Neither sequencing technology identified significant differences in microbial diversity measures between patients with or without bowel polyps. Differential abundance measures showed that amplicon sequence variants (ASVs) associated with <i>Ruminococcus gnavus</i> and <i>Escherichia coli</i> were elevated in mucosa from polyp patients, while ASVs associated with <i>Parabacteroides merdae</i>, <i>Veillonella nakazawae</i>, and <i>Sutterella wadsworthensis</i> were relatively decreased. Only <i>R. gnavus</i> was consistently identified using both sequencing technologies as being altered between patients with polyps compared to patients without polyps, suggesting differences in technologies and bioinformatics processing impact study findings. Several of the differentially abundant bacteria identified using either sequencing technology are associated with inflammatory bowel diseases despite these patients being excluded from the current study, which suggests that early bowel neoplasia may be associated with a local inflammatory niche.https://www.mdpi.com/2072-6694/15/20/5045bowel polypsgut microbiome16S rRNA sequencingPacBio long-read sequencing |
| spellingShingle | Zoe Welham Jun Li Alexander F. Engel Mark P. Molloy Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing Cancers bowel polyps gut microbiome 16S rRNA sequencing PacBio long-read sequencing |
| title | Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing |
| title_full | Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing |
| title_fullStr | Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing |
| title_full_unstemmed | Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing |
| title_short | Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing |
| title_sort | mucosal microbiome in patients with early bowel polyps inferences from short read and long read 16s rrna sequencing |
| topic | bowel polyps gut microbiome 16S rRNA sequencing PacBio long-read sequencing |
| url | https://www.mdpi.com/2072-6694/15/20/5045 |
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