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Abundance Tracking by Long-Read Nanopore Sequencing of Complex Microbial Communities in Samples from 20 Different Biogas/Wastewater Plants

Brandt, Christian and Bongcam-Rudloff, Erik and Müller, Bettina (2020). Abundance Tracking by Long-Read Nanopore Sequencing of Complex Microbial Communities in Samples from 20 Different Biogas/Wastewater Plants. Applied Sciences. 10 , 7518
[Research article]

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Abstract

Anaerobic digestion (AD) has long been critical technology for green energy, but the majority of the microorganisms involved are unknown and are currently not cultivable, which makes abundance tracking difficult. Developments in nanopore long-read sequencing make it a promising approach for monitoring microbial communities via metagenomic sequencing. For reliable monitoring of AD via long reads, we established a robust protocol for obtaining less fragmented, high-quality DNA, while preserving bacteria and archaea composition, for a broad range of different biogas reactors. Samples from 20 different biogas/wastewater reactors were investigated, and a median of 20.5 Gb sequencing data per nanopore flow cell was retrieved for each reactor using the developed DNA isolation protocol. The nanopore sequencing data were compared against Illumina sequencing data while using different taxonomic indices for read classifications. The Genome Taxonomy Database (GTDB) index allowed sufficient characterisation of the abundance of bacteria and archaea in biogas reactors with a dramatic improvement (1.8- to 13-fold increase) in taxonomic classification compared to the RefSeq index. Both technologies performed similarly in taxonomic read classification with a slight advantage for Illumina in regard to the total proportion of classified reads. However, nanopore sequencing data revealed a higher genus richness after classification. Metagenomic read classification via nanopore provides a promising approach to monitor the abundance of taxa present in a microbial AD community as an alternative to 16S ribosomal RNA studies or Illumina Sequencing.

Authors/Creators:Brandt, Christian and Bongcam-Rudloff, Erik and Müller, Bettina
Title:Abundance Tracking by Long-Read Nanopore Sequencing of Complex Microbial Communities in Samples from 20 Different Biogas/Wastewater Plants
Series Name/Journal:Applied Sciences
Year of publishing :2020
Volume:10
Article number:7518
Number of Pages:14
Publisher:MDPI
ISSN:2076-3417
Language:English
Publication Type:Research 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 > 102 Computer and Information Science > 10203 Bioinformatics (Computational Biology) (applications to be 10610)
Keywords:nanopore, sequencing, DNA extraction, metagenome, abundance, GTDB, nanopore
URN:NBN:urn:nbn:se:slu:epsilon-p-109360
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-109360
Additional ID:
Type of IDID
DOI10.3390/app10217518
Web of Science (WoS)000589167800001
ID Code:22420
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:18 Feb 2021 08:03
Metadata Last Modified:18 Feb 2021 08:11

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