Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling

• Published in: Journal of microbiological methods 2018-04, Vol.147, p.76-86
• Main Authors: Raju, Sajan C., Lagström, Sonja, Ellonen, Pekka, de Vos, Willem M., Eriksson, Johan G., Weiderpass, Elisabete, Rounge, Trine B.
• Format: Article
• Language: English
• Subjects: Base Sequence; Community medicine, Social medicine: 801; DNA Barcoding, Taxonomic - methods; DNA Primers; Gene Expression Profiling - methods; Health sciences: 800; Helsefag: 800; High-Throughput Nucleotide Sequencing - methods; Humans; Laboratorium voor Microbiologie; Medical disciplines: 700; Medicin och hälsovetenskap; Medisinske Fag: 700; Microbiological Laboratory; Microbiologie; Microbiology; Microbiota - genetics; Reproducibility of Results; RNA, Ribosomal, 16S - genetics; Saliva - microbiology; Samfunnsmedisin, sosialmedisin: 801; VDP; VLAG; WIMEK
• ISSN: 0167-7012; 1872-8359; 1872-8359
• DOI: 10.1016/j.mimet.2018.03.003

Culture-independent molecular techniques and advances in next generation sequencing (NGS) technologies make large-scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain high reproducibility and repeatability, which is mostly attained through robust amplification. We aimed to assess the reproducibility of saliva microbiota by comparing triplicate samples. The microbiota was produced with simplified in-house 16S amplicon assays taking advantage of large number of barcodes. The assays included primers with Truseq (TS-tailed) or Nextera (NX-tailed) adapters and either with dual index or dual index plus a 6-nt internal index. All amplification protocols produced consistent microbial profiles for the same samples. Although, in our study, reproducibility was highest for the TS-tailed method. Five replicates of a single sample, prepared with the TS-tailed 1-step protocol without internal index sequenced on the HiSeq platform provided high alpha-diversity and low standard deviation (mean Shannon and Inverse Simpson diversity was 3.19 ± 0.097 and 13.56 ± 1.634 respectively). Large-scale profiling of microbiota can consistently be produced by all 16S amplicon assays. The TS-tailed-1S dual index protocol is preferred since it provides repeatable profiles on the HiSeq platform and are less labour intensive. [Display omitted] •16S assays comprised of primers with Truseq or Nextera adapters with dual index and/or 6-nt internal index all produced highly consistent saliva microbiota profiles.•Repeatability of the 16S TruSeq (TS)-tailed 1-step protocol without internal index showed little variation between nine microbiota profile measurements.•Considering reproducibility, repeatability and cost effectiveness, we recommend the 16S TruSeq (TS)-tailed 1-step protocol for large scale bacterial profiling of saliva microbiota.