Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/163813
Title: Recovery of high quality metagenome-assembled genomes from full-scale activated sludge microbial communities in a tropical climate using longitudinal metagenome sampling
Authors: Haryono, Mindia A. S.
Law, Ying Yu
Arumugam, Krithika
Liew, Larry C. W.
Nguyen, Thi Quynh Ngoc
Drautz-Moses, Daniela Isabel
Schuster, Stephan Christoph
Wuertz, Stefan
Williams, Rohan B H
Keywords: Science::Biological sciences
Issue Date: 2022
Source: Haryono, M. A. S., Law, Y. Y., Arumugam, K., Liew, L. C. W., Nguyen, T. Q. N., Drautz-Moses, D. I., Schuster, S. C., Wuertz, S. & Williams, R. B. H. (2022). Recovery of high quality metagenome-assembled genomes from full-scale activated sludge microbial communities in a tropical climate using longitudinal metagenome sampling. Frontiers in Microbiology, 13, 869135-. https://dx.doi.org/10.3389/fmicb.2022.869135
Project: 1102-IRIS-10-02 
11000984 
Journal: Frontiers in Microbiology 
Abstract: The analysis of metagenome data based on the recovery of draft genomes (so called metagenome-assembled genomes, or MAG) has assumed an increasingly central role in microbiome research in recent years. Microbial communities underpinning the operation of wastewater treatment plants are particularly challenging targets for MAG analysis due to their high ecological complexity, and remain important, albeit understudied, microbial communities that play ssa key role in mediating interactions between human and natural ecosystems. Here we consider strategies for recovery of MAG sequence from time series metagenome surveys of full-scale activated sludge microbial communities. We generate MAG catalogs from this set of data using several different strategies, including the use of multiple individual sample assemblies, two variations on multi-sample co-assembly and a recently published MAG recovery workflow using deep learning. We obtain a total of just under 9,100 draft genomes, which collapse to around 3,100 non-redundant genomic clusters. We examine the strengths and weaknesses of these approaches in relation to MAG yield and quality, showing that co-assembly may offer advantages over single-sample assembly in the case of metagenome data obtained from closely sampled longitudinal study designs. Around 1,000 MAGs were candidates for being considered high quality, based on single-copy marker gene occurrence statistics, however only 58 MAG formally meet the MIMAG criteria for being high quality draft genomes. These findings carry broader broader implications for performing genome-resolved metagenomics on highly complex communities, the design and implementation of genome recoverability strategies, MAG decontamination and the search for better binning methodology.
URI: https://hdl.handle.net/10356/163813
ISSN: 1664-302X
DOI: 10.3389/fmicb.2022.869135
Schools: School of Biological Sciences 
Research Centres: Singapore Centre for Environmental Life Sciences and Engineering (SCELSE) 
Rights: © 2022 Haryono, Law, Arumugam, Liew, Nguyen, Drautz-Moses, Schuster, Wuertz and Williams. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SBS Journal Articles
SCELSE Journal Articles

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