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Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination
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Dinesh Aggarwal1,2
, Diana Rajan2, Katherine L. Bellis1,2, Emma Betteridge2, Joe Brennan1,2, Catarina de Sousa1,2, CARRIAGE Study Team‡, Julian Parkhill3, Sharon J. Peacock1, Marcus C. de Goffau2,4, Josef Wagner2 and Ewan M. Harrison1,2,5
Abstract
16S rRNA gene sequencing is widely used to characterize human and environmental microbiomes. Sequencing at scale facilitates better powered studies but is limited by cost and time. We identified two areas in our 16S rRNA gene library preparation protocol where modifications could provide efficiency gains, including (1) pooling of multiple PCR amplifications per sample to reduce PCR drift and (2) manual preparation of mastermix to reduce liquid handling. Using nasal samples from healthy human participants and a serially diluted mock microbial community, we compared alpha and beta diversity, and compositional abundance where the PCR amplification was conducted in triplicate, duplicate or as a single reaction, and where manually prepared or premixed mastermix was used. One hundred and fifty-eight 16S rRNA gene sequencing libraries were prepared, including a replicate experiment. Comparing PCR pooling strategies, we found no significant difference in high-quality read counts and alpha diversity, and beta diversity by Bray–Curtis index clustered by replicate on principal coordinate analysis (PCoA) and non-metric dimensional scaling (NMDS) analysis. Choice of mastermix had no significant impact on high-quality read and alpha diversity, and beta diversity by Bray–Curtis index clustered by replicate in PCoA and NMDS analysis. Importantly, we observed contamination and variability of rare species (<0.01 %) across replicate experiments; the majority of contaminants were accounted for by removal of species present at <0.1 %, or were linked to reagents (including a primer stock). We demonstrate no requirement for pooling of PCR amplifications or manual preparation of PCR mastermix, resulting in a more efficient 16S rRNA gene PCR protocol.
- Received:
- Accepted:
- Published Online:
Keyword(s):
16S rRNA gene
,
contamination
,
efficiency
,
laboratory protocol
,
mastermix
,
microbiome
,
nasal samples
,
PCR drift
and
PCR pooling
Funding
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Wellcome Trust
(Award 220540/Z/20/A)
- Principle Award Recipient: NotApplicable
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Wellcome Trust
(Award 211864/Z/18/Z)
- Principle Award Recipient: EwanM. Harrison
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Wellcome Trust
(Award 222903/Z/21/Z)
- Principle Award Recipient: DineshAggarwal