Trash to treasure: exploring the wastewater system with high quality MAGs from large-scale Nanopore data

Research output: Contribution to conference without publisher/journalConference abstract for conferenceResearch

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Abstract

Improvements to wastewater resource recovery and treatment efficiency are essential for fulfilling the UN sustainable development goals for both sustainable cities (goal 11) and responsible production and consumption (goal 12). Microbes are central to the processes underpinning wastewater treatment, however knowledge of this complex community is limited to isolates, marker genes or incomplete genomes. To improve our capacity to characterise this community at the genome level, we conducted large-scale long-read sequencing of 23 Danish full-scale wastewater treatment plant (WWTP) metagenomes using the Nanopore PromethION platform, producing >1 Tbp (or 17 TB raw) of long-read data. These data enabled the recovery of 987 metagenome-assembled genomes (MAGs), including 36 circular genomes, after short-read data polishing (>0.9 Tbp Illumina). The recovered MAGs met stringent high-quality draft requirements of >90% completeness, <5% contamination and full-length rRNA genes. The MAGs included known and uncharacterised, abundant and rare lineages, and accounted for 25% of the populations present in the metagenomes. With these MAGs we present a HQ reference database for WWTP systems that will facilitate the connection of genomic potential to historical and future amplicon studies.
Original languageEnglish
Publication date11 Nov 2019
Publication statusPublished - 11 Nov 2019
EventDanish Microbiological Society Congress 2019 - Eigtveds Pakhus , Copenhagen, Denmark
Duration: 11 Nov 201911 Nov 2019
https://dms.dk/congress/

Conference

ConferenceDanish Microbiological Society Congress 2019
LocationEigtveds Pakhus
CountryDenmark
CityCopenhagen
Period11/11/201911/11/2019
Internet address

Fingerprint

Nanopores
Metagenome
Waste Water
Genome
United Nations
Conservation of Natural Resources
rRNA Genes
Databases

Keywords

  • Nanopore
  • Long-read
  • Metagenomics
  • Microbial community
  • Wastewater

Cite this

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title = "Trash to treasure: exploring the wastewater system with high quality MAGs from large-scale Nanopore data",
abstract = "Improvements to wastewater resource recovery and treatment efficiency are essential for fulfilling the UN sustainable development goals for both sustainable cities (goal 11) and responsible production and consumption (goal 12). Microbes are central to the processes underpinning wastewater treatment, however knowledge of this complex community is limited to isolates, marker genes or incomplete genomes. To improve our capacity to characterise this community at the genome level, we conducted large-scale long-read sequencing of 23 Danish full-scale wastewater treatment plant (WWTP) metagenomes using the Nanopore PromethION platform, producing >1 Tbp (or 17 TB raw) of long-read data. These data enabled the recovery of 987 metagenome-assembled genomes (MAGs), including 36 circular genomes, after short-read data polishing (>0.9 Tbp Illumina). The recovered MAGs met stringent high-quality draft requirements of >90{\%} completeness, <5{\%} contamination and full-length rRNA genes. The MAGs included known and uncharacterised, abundant and rare lineages, and accounted for 25{\%} of the populations present in the metagenomes. With these MAGs we present a HQ reference database for WWTP systems that will facilitate the connection of genomic potential to historical and future amplicon studies.",
keywords = "Nanopore, Long-read, Metagenomics, Microbial community, Wastewater",
author = "Singleton, {Caitlin Margaret} and Andersen, {Martin Hjorth} and Kirkegaard, {Rasmus Hansen} and {Yssing Michaelsen}, Thomas and Karst, {S{\o}ren Michael} and Dueholm, {Morten Simonsen} and Nielsen, {Per Halkj{\ae}r} and Mads Albertsen",
year = "2019",
month = "11",
day = "11",
language = "English",
note = "Danish Microbiological Society Congress 2019, DMS Congress 2019 ; Conference date: 11-11-2019 Through 11-11-2019",
url = "https://dms.dk/congress/",

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Trash to treasure: exploring the wastewater system with high quality MAGs from large-scale Nanopore data. / Singleton, Caitlin Margaret; Andersen, Martin Hjorth; Kirkegaard, Rasmus Hansen; Yssing Michaelsen, Thomas; Karst, Søren Michael; Dueholm, Morten Simonsen; Nielsen, Per Halkjær; Albertsen, Mads.

2019. Abstract from Danish Microbiological Society Congress 2019, Copenhagen, Denmark.

Research output: Contribution to conference without publisher/journalConference abstract for conferenceResearch

TY - ABST

T1 - Trash to treasure: exploring the wastewater system with high quality MAGs from large-scale Nanopore data

AU - Singleton, Caitlin Margaret

AU - Andersen, Martin Hjorth

AU - Kirkegaard, Rasmus Hansen

AU - Yssing Michaelsen, Thomas

AU - Karst, Søren Michael

AU - Dueholm, Morten Simonsen

AU - Nielsen, Per Halkjær

AU - Albertsen, Mads

PY - 2019/11/11

Y1 - 2019/11/11

N2 - Improvements to wastewater resource recovery and treatment efficiency are essential for fulfilling the UN sustainable development goals for both sustainable cities (goal 11) and responsible production and consumption (goal 12). Microbes are central to the processes underpinning wastewater treatment, however knowledge of this complex community is limited to isolates, marker genes or incomplete genomes. To improve our capacity to characterise this community at the genome level, we conducted large-scale long-read sequencing of 23 Danish full-scale wastewater treatment plant (WWTP) metagenomes using the Nanopore PromethION platform, producing >1 Tbp (or 17 TB raw) of long-read data. These data enabled the recovery of 987 metagenome-assembled genomes (MAGs), including 36 circular genomes, after short-read data polishing (>0.9 Tbp Illumina). The recovered MAGs met stringent high-quality draft requirements of >90% completeness, <5% contamination and full-length rRNA genes. The MAGs included known and uncharacterised, abundant and rare lineages, and accounted for 25% of the populations present in the metagenomes. With these MAGs we present a HQ reference database for WWTP systems that will facilitate the connection of genomic potential to historical and future amplicon studies.

AB - Improvements to wastewater resource recovery and treatment efficiency are essential for fulfilling the UN sustainable development goals for both sustainable cities (goal 11) and responsible production and consumption (goal 12). Microbes are central to the processes underpinning wastewater treatment, however knowledge of this complex community is limited to isolates, marker genes or incomplete genomes. To improve our capacity to characterise this community at the genome level, we conducted large-scale long-read sequencing of 23 Danish full-scale wastewater treatment plant (WWTP) metagenomes using the Nanopore PromethION platform, producing >1 Tbp (or 17 TB raw) of long-read data. These data enabled the recovery of 987 metagenome-assembled genomes (MAGs), including 36 circular genomes, after short-read data polishing (>0.9 Tbp Illumina). The recovered MAGs met stringent high-quality draft requirements of >90% completeness, <5% contamination and full-length rRNA genes. The MAGs included known and uncharacterised, abundant and rare lineages, and accounted for 25% of the populations present in the metagenomes. With these MAGs we present a HQ reference database for WWTP systems that will facilitate the connection of genomic potential to historical and future amplicon studies.

KW - Nanopore

KW - Long-read

KW - Metagenomics

KW - Microbial community

KW - Wastewater

M3 - Conference abstract for conference

ER -