RT Journal Article
SR Electronic
T1 Impact of bead-beating intensity on microbiome recovery in mouse and human stool: <em>Optimization of DNA extraction</em>
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.06.15.151753
DO 10.1101/2020.06.15.151753
A1 Zhang, Bo
A1 Brock, Matthew
A1 Arana, Carlos
A1 Dende, Chaitanya
A1 Hooper, Lora
A1 Raj, Prithvi
YR 2020
UL http://biorxiv.org/content/early/2020/06/15/2020.06.15.151753.abstract
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&lt;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.