Technical Note
Version 1
Preserved in Portico This version is not peer-reviewed
Metrics for Understanding the Degraded Metagenome of Stomach Cancer Patient
Version 1
: Received: 11 May 2023 / Approved: 11 May 2023 / Online: 11 May 2023 (09:25:18 CEST)
How to cite: Ng, W. Metrics for Understanding the Degraded Metagenome of Stomach Cancer Patient. Preprints 2023, 2023050835. https://doi.org/10.20944/preprints202305.0835.v1 Ng, W. Metrics for Understanding the Degraded Metagenome of Stomach Cancer Patient. Preprints 2023, 2023050835. https://doi.org/10.20944/preprints202305.0835.v1
Abstract
Metagenomics have opened our eyes to the otherwise enigmatic microbial consortia that relies on different human body niches that impact on disease pathogenesis. This work originally aims to re-analyse a public shotgun metagenomics dataset to glean insights on the microbial species that may partake in stomach cancer pathogenesis. However, a random selection of sequenced reads reveals poor percent identities (79 to 94%) of the microbial identification obtained in a BLAST search. This surprising result suggests possible stomach acid induced degradation or modification of the sequenced read that reduced the effectiveness of the metagenomics approach in microbial identification. Further analysis of the dataset highlights that poor percent identities did not arise due to highly fragmented nature of the genetic material where there is a good abundance of sequenced reads in the 100 to 1300 base pair category. More intriguingly, attempts to obtain a correlation between percent identity and read length did not reveal a correlation which meant that stomach acid did not modify all types of nucleotides. More likely, stomach acid only modified low abundance nucleotide in this case, which point to the probability of identifying a microbe in the modified gene fragment in totally unpredictable ways. Overall, data reported in this work suggests caution in the interpretation of results of shotgun metagenomics studies of stomach cancer microbiota where stomach acid likely degraded the genetic material of microbes that may result in mis-identification.
Keywords
degraded metagenome; shotgun metagenomics; stomach acid; microbial identification; percent identity
Subject
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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