Impact of bead-beating intensity on microbiome recovery in mouse and human stool: Optimization of DNA extraction

Bo Zhang; Matthew Brock; Carlos Arana; Chaitanya Dende; Lora Hooper; Prithvi Raj

doi:10.1101/2020.06.15.151753

Impact of bead-beating intensity on microbiome recovery in mouse and human stool: Optimization of DNA extraction

Bo Zhang, Matthew Brock, Carlos Arana, Chaitanya Dende, Lora Hooper, Prithvi Raj

Research output: Contribution to journal › Article › peer-review

Abstract

DNA extraction methods play an important role in the acquisition of accurate and reproducible 16S sequencing data in microbiome studies. In this study, we assessed the impact of bead-beating intensity during DNA extraction on microbiome recovery in mouse and human stool. We observed a higher DNA yield, better DNA integrity, higher Shannon’s entropy and Simpson’s index in samples beaten for 4 and 9 minutes as compared to unbeaten samples. 16S sequencing data showed that bead beating has a statistically-significant (p<0.05) impact on the recovery of many clinically relevant microbes that live in the mouse and human gut, including Bifidobacterium, Sutterella and Veillonella. It was observed that 4 minutes of bead beating promotes recovery of about 70% of OTUs in mouse and human stool, while the remaining 30% requires longer bead beating. In conclusion, our study indicates adjustments in bead beating treatment based on the composition of the specimen and the targeted bacteria.

Original language	English (US)
Journal	Unknown Journal
DOIs	https://doi.org/10.1101/2020.06.15.151753
State	Published - Jun 15 2020

Keywords

16S Sequencing
Bead beating
DNA extraction
Microbiome
OTU

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)
Agricultural and Biological Sciences(all)
Immunology and Microbiology(all)
Neuroscience(all)
Pharmacology, Toxicology and Pharmaceutics(all)

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title = "Impact of bead-beating intensity on microbiome recovery in mouse and human stool: Optimization of DNA extraction",

abstract = "DNA extraction methods play an important role in the acquisition of accurate and reproducible 16S sequencing data in microbiome studies. In this study, we assessed the impact of bead-beating intensity during DNA extraction on microbiome recovery in mouse and human stool. We observed a higher DNA yield, better DNA integrity, higher Shannon{\textquoteright}s entropy and Simpson{\textquoteright}s index in samples beaten for 4 and 9 minutes as compared to unbeaten samples. 16S sequencing data showed that bead beating has a statistically-significant (p<0.05) impact on the recovery of many clinically relevant microbes that live in the mouse and human gut, including Bifidobacterium, Sutterella and Veillonella. It was observed that 4 minutes of bead beating promotes recovery of about 70% of OTUs in mouse and human stool, while the remaining 30% requires longer bead beating. In conclusion, our study indicates adjustments in bead beating treatment based on the composition of the specimen and the targeted bacteria.",

keywords = "16S Sequencing, Bead beating, DNA extraction, Microbiome, OTU",

author = "Bo Zhang and Matthew Brock and Carlos Arana and Chaitanya Dende and Lora Hooper and Prithvi Raj",

note = "Publisher Copyright: The copyright holder for this preprint which was not certified by peer review) is the author/funder. It is made available under a CC-BY 4.0 International license Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",

year = "2020",

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doi = "10.1101/2020.06.15.151753",

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AU - Dende, Chaitanya

AU - Hooper, Lora

AU - Raj, Prithvi

N1 - Publisher Copyright: The copyright holder for this preprint which was not certified by peer review) is the author/funder. It is made available under a CC-BY 4.0 International license Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2020/6/15

Y1 - 2020/6/15

N2 - DNA extraction methods play an important role in the acquisition of accurate and reproducible 16S sequencing data in microbiome studies. In this study, we assessed the impact of bead-beating intensity during DNA extraction on microbiome recovery in mouse and human stool. We observed a higher DNA yield, better DNA integrity, higher Shannon’s entropy and Simpson’s index in samples beaten for 4 and 9 minutes as compared to unbeaten samples. 16S sequencing data showed that bead beating has a statistically-significant (p<0.05) impact on the recovery of many clinically relevant microbes that live in the mouse and human gut, including Bifidobacterium, Sutterella and Veillonella. It was observed that 4 minutes of bead beating promotes recovery of about 70% of OTUs in mouse and human stool, while the remaining 30% requires longer bead beating. In conclusion, our study indicates adjustments in bead beating treatment based on the composition of the specimen and the targeted bacteria.

AB - DNA extraction methods play an important role in the acquisition of accurate and reproducible 16S sequencing data in microbiome studies. In this study, we assessed the impact of bead-beating intensity during DNA extraction on microbiome recovery in mouse and human stool. We observed a higher DNA yield, better DNA integrity, higher Shannon’s entropy and Simpson’s index in samples beaten for 4 and 9 minutes as compared to unbeaten samples. 16S sequencing data showed that bead beating has a statistically-significant (p<0.05) impact on the recovery of many clinically relevant microbes that live in the mouse and human gut, including Bifidobacterium, Sutterella and Veillonella. It was observed that 4 minutes of bead beating promotes recovery of about 70% of OTUs in mouse and human stool, while the remaining 30% requires longer bead beating. In conclusion, our study indicates adjustments in bead beating treatment based on the composition of the specimen and the targeted bacteria.

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