Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes

ABSTRACT The gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures required, specifically the isolation of DNA and gener...

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Autores principales:	Elin Videvall, Maria Strandh, Anel Engelbrecht, Schalk Cloete, Charlie K. Cornwallis
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	16S rRNA DNA extraction direct PCR library preparation microbiota repeatability Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/1ee1c7be94dc4c4ebc91bd2dbab2acc0
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spelling	oai:doaj.org-article:1ee1c7be94dc4c4ebc91bd2dbab2acc02021-12-02T19:48:49ZDirect PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes10.1128/mSystems.00132-172379-5077https://doaj.org/article/1ee1c7be94dc4c4ebc91bd2dbab2acc02017-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00132-17https://doaj.org/toc/2379-5077ABSTRACT The gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures required, specifically the isolation of DNA and generation of amplicon libraries. Recently, direct PCR kits have been developed that circumvent conventional DNA extraction steps, thereby streamlining the laboratory process by reducing preparation time and costs. However, the reliability and efficacy of direct PCR for measuring host microbiomes have not yet been investigated other than in humans with 454 sequencing. Here, we conduct a comprehensive evaluation of the microbial communities obtained with direct PCR and the widely used Mo Bio PowerSoil DNA extraction kit in five distinct gut sample types (ileum, cecum, colon, feces, and cloaca) from 20 juvenile ostriches, using 16S rRNA Illumina MiSeq sequencing. We found that direct PCR was highly comparable over a range of measures to the DNA extraction method in cecal, colon, and fecal samples. However, the two methods significantly differed in samples with comparably low bacterial biomass: cloacal and especially ileal samples. We also sequenced 100 replicate sample pairs to evaluate repeatability during both extraction and PCR stages and found that both methods were highly consistent for cecal, colon, and fecal samples (rs > 0.7) but had low repeatability for cloacal (rs = 0.39) and ileal (rs = −0.24) samples. This study indicates that direct PCR provides a fast, cheap, and reliable alternative to conventional DNA extraction methods for retrieving 16S rRNA data, which can aid future gut microbiome studies. IMPORTANCE The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA library preparation and compared it with a standard DNA extraction method. We used both techniques on five different gut sample types collected from 20 juvenile ostriches and sequenced samples with Illumina MiSeq. The methods were highly comparable and highly repeatable in three sample types with high microbial biomass (cecum, colon, and feces), but larger differences and low repeatability were found in the microbiomes obtained from the ileum and cloaca. These results will help microbiome researchers assess library preparation procedures and plan their studies accordingly.Elin VidevallMaria StrandhAnel EngelbrechtSchalk CloeteCharlie K. CornwallisAmerican Society for Microbiologyarticle16S rRNADNA extractiondirect PCRlibrary preparationmicrobiotarepeatabilityMicrobiologyQR1-502ENmSystems, Vol 2, Iss 6 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	16S rRNA DNA extraction direct PCR library preparation microbiota repeatability Microbiology QR1-502
spellingShingle	16S rRNA DNA extraction direct PCR library preparation microbiota repeatability Microbiology QR1-502 Elin Videvall Maria Strandh Anel Engelbrecht Schalk Cloete Charlie K. Cornwallis Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
description	ABSTRACT The gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures required, specifically the isolation of DNA and generation of amplicon libraries. Recently, direct PCR kits have been developed that circumvent conventional DNA extraction steps, thereby streamlining the laboratory process by reducing preparation time and costs. However, the reliability and efficacy of direct PCR for measuring host microbiomes have not yet been investigated other than in humans with 454 sequencing. Here, we conduct a comprehensive evaluation of the microbial communities obtained with direct PCR and the widely used Mo Bio PowerSoil DNA extraction kit in five distinct gut sample types (ileum, cecum, colon, feces, and cloaca) from 20 juvenile ostriches, using 16S rRNA Illumina MiSeq sequencing. We found that direct PCR was highly comparable over a range of measures to the DNA extraction method in cecal, colon, and fecal samples. However, the two methods significantly differed in samples with comparably low bacterial biomass: cloacal and especially ileal samples. We also sequenced 100 replicate sample pairs to evaluate repeatability during both extraction and PCR stages and found that both methods were highly consistent for cecal, colon, and fecal samples (rs > 0.7) but had low repeatability for cloacal (rs = 0.39) and ileal (rs = −0.24) samples. This study indicates that direct PCR provides a fast, cheap, and reliable alternative to conventional DNA extraction methods for retrieving 16S rRNA data, which can aid future gut microbiome studies. IMPORTANCE The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA library preparation and compared it with a standard DNA extraction method. We used both techniques on five different gut sample types collected from 20 juvenile ostriches and sequenced samples with Illumina MiSeq. The methods were highly comparable and highly repeatable in three sample types with high microbial biomass (cecum, colon, and feces), but larger differences and low repeatability were found in the microbiomes obtained from the ileum and cloaca. These results will help microbiome researchers assess library preparation procedures and plan their studies accordingly.
format	article
author	Elin Videvall Maria Strandh Anel Engelbrecht Schalk Cloete Charlie K. Cornwallis
author_facet	Elin Videvall Maria Strandh Anel Engelbrecht Schalk Cloete Charlie K. Cornwallis
author_sort	Elin Videvall
title	Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
title_short	Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
title_full	Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
title_fullStr	Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
title_full_unstemmed	Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
title_sort	direct pcr offers a fast and reliable alternative to conventional dna isolation methods for gut microbiomes
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/1ee1c7be94dc4c4ebc91bd2dbab2acc0
work_keys_str_mv	AT elinvidevall directpcroffersafastandreliablealternativetoconventionaldnaisolationmethodsforgutmicrobiomes AT mariastrandh directpcroffersafastandreliablealternativetoconventionaldnaisolationmethodsforgutmicrobiomes AT anelengelbrecht directpcroffersafastandreliablealternativetoconventionaldnaisolationmethodsforgutmicrobiomes AT schalkcloete directpcroffersafastandreliablealternativetoconventionaldnaisolationmethodsforgutmicrobiomes AT charliekcornwallis directpcroffersafastandreliablealternativetoconventionaldnaisolationmethodsforgutmicrobiomes
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Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes

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