Sediment-associated bacterial community and predictive functionalities are influenced by choice of 16S ribosomal RNA hypervariable region(s): An amplicon-based diversity study.
Genomics
; 112(6): 4968-4979, 2020 11.
Article
em En
| MEDLINE
| ID: mdl-32911024
ABSTRACT
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.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Bactérias
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RNA Ribossômico 16S
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Sedimentos Geológicos
Tipo de estudo:
Prognostic_studies
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Risk_factors_studies
Idioma:
En
Ano de publicação:
2020
Tipo de documento:
Article