Abstract
Purpose
The reference databases play a pivotal role in amplicon microbiome research, however these databases differ in the sequence content and taxonomic information available. Studies on mock community and human health microbiome have revealed the problems associated with the choice of reference database on the outcome. Nonetheless, the influence of reference databases in environmental microbiome studies is not explicitly illustrated.
Methods
This study analyzed the amplicon (V1V3, V3V4, V4V5 and V6V8) data of 128 soil samples and evaluated the impact of 16S rRNA databases, Genome Taxonomy Database (GTDB), Ribosomal Database Project (RDP), SILVA and Consensus Taxonomy (ConTax), on microbiome inference.
Results
The analyses showed that the distribution of observed amplicon sequence variants was significantly different (P-value < 2.647e−12) across four datasets, generated using different databases for each amplicon region. In addition, the beta diversity was also found to be altered by different databases. Further investigation revealed that the microbiome composition inferred by various databases differ significantly (P-value = 0.001), irrespective of amplicon regions. This study, found that the core-microbiome structure in environmental studies is influenced by the type of reference database used.
Conclusion
In summary, this present study illustrates that the choice of reference database could influence the outcome of environmental microbiome research.
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Data availability
Downloaded from SRA.
Code availability
Not applicable.
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Acknowledgements
I would like to thank Dr. Bhawna Dubey, Chief Scientific Officer, Reprocell Bioserve Biotechnologies Pvt. Ltd., Hyderabad for reviewing the manuscript. The effort of Soriano-Lerma et al. (2020) for making the data publicly available on SRA is highly appreciated. CSIR-NEERI is acknowledged for providing the necessary support to carry out the analyses. The manuscript draft is submitted in the Institute Repository under the KRC No.: CSIR-NEERI/KRC/2021/JUNE/HZC/1.
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Ramakodi, M.P. Influence of 16S rRNA reference databases in amplicon-based environmental microbiome research. Biotechnol Lett 44, 523–533 (2022). https://doi.org/10.1007/s10529-022-03233-2
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DOI: https://doi.org/10.1007/s10529-022-03233-2