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To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities.
- Source :
-
Briefings in bioinformatics [Brief Bioinform] 2023 Jan 19; Vol. 24 (1). - Publication Year :
- 2023
-
Abstract
- High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation. In this study, using two typical shotgun metagenome datasets recovered from geographically distant coastal sediments, the performance of different data processing approaches was comparatively investigated from both technical and biological/ecological perspectives. Microbially mediated biogeochemical cycling pathways, including nitrogen cycling, sulfur cycling and B12 biosynthesis, were analyzed. As a result, multi-sample assembly provided the most amount of usable information for targeted functional traits, at a high cost of computational resources and running time. Single-sample assembly and read-based analysis were comparable in obtaining usable information, but the former was much more time- and resource-consuming. Critically, different approaches introduced much stronger variations in microbial profiles than biological differences. However, community-level differences between the two sampling sites could be consistently observed despite the approaches being used. In choosing an appropriate approach, researchers shall balance the trade-offs between multiple factors, including the scientific question, the amount of usable information, computational resources and time cost. This study is expected to provide valuable technical insights and guidelines for the various approaches used for metagenomic data analysis.<br /> (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)
- Subjects :
- High-Throughput Nucleotide Sequencing
Metagenome
Metagenomics
Subjects
Details
- Language :
- English
- ISSN :
- 1477-4054
- Volume :
- 24
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Briefings in bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 36575570
- Full Text :
- https://doi.org/10.1093/bib/bbac594