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High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure

Singh, Abhijeet and Nylander, Johan A. A. and Schnürer, Anna and Bongcam-Rudloff, Erik and Müller, Bettina (2020). High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure. Frontiers in Microbiology. 11 , 2066
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Abstract

The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline "AcetoScan" presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at.

Authors/Creators:Singh, Abhijeet and Nylander, Johan A. A. and Schnürer, Anna and Bongcam-Rudloff, Erik and Müller, Bettina
Title:High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure
Year of publishing :2020
Volume:11
Article number:2066
Number of Pages:13
ISSN:1664-302X
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Microbiology (Microbiology in the medical area to be 30109)
Keywords:FTHFS, acetogens, AcetoScan, AcetoBase, high-throughput sequencing
URN:NBN:urn:nbn:se:slu:epsilon-p-108119
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-108119
Additional ID:
Type of IDID
DOI10.3389/fmicb.2020.02066
Web of Science (WoS)000570698400001
ID Code:17824
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
VH - Faculty of Veterinary Medicine and Animal Science
Department:(NL, NJ) > Department of Molecular Sciences
(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:14 Oct 2020 16:40
Metadata Last Modified:14 Oct 2020 16:41

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