Sediment-associated bacterial community and predictive functionalities are influenced by choice of 16S ribosomal RNA hypervariable region(s): An amplicon-based diversity study

• Published in: Genomics (San Diego, Calif.) Calif.), 2020-11, Vol.112 (6), p.4968-4979
• Main Authors: Rajeev, Meora, Sushmitha, T.J., Toleti, Subba Rao, Pandian, Shunmugiah Karutha
• Format: Article
• Language: English
• Subjects: 16S hypervariable regions; Amplicon sequencing; Marine sediments; Predictive functionality
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2020.09.006

Meta-omics approaches such as high-throughput sequencing of 16S hypervariable region(s) [HVR(s)] is extensively applied for profiling microbial community. Several studies have deciphered the influence of HVR(s) on bacterial diversity; most of these were devoted to human body habitats. Extent to which targeted HVR(s) influences the diversity estimates of environmental samples is rather unclear. Here, we evaluated the performance of five widely used universal primer pairs spanning V1-V3, V3-V4, V4, V5-V6 and V7-V9 HVRs to characterize bacterial diversity and predictive functionality of complex marine sediments. Obtained results revealed that the HVR(s) V4 and V5-V6 represented the higher species richness than others while, V1-V3 and V7-V9 were unsuccessful to detect Bacteroidetes and Planctomycetes. Further, PICRUSt analysis showed that the selected HVR(s) also had significant impact on the predictive functional profile. Conclusively, this study proved that HVR selection has a profound effect on overall results and thus should be selected with utmost caution. •Evaluated the performance of 16S hypervariable regions in marine sediment.•Hypervariable regions significantly influence the amplicon-based diversity study.•Region(s) V5-V6 & V4 provide ideal diversity estimates than others.•V7-V9 regions failed to detect abundant phylum Bacteroidetes & Planctomycetes.•Study highlights the importance of selecting appropriate hypervariable region.