Long-read metagenome-assembled genomes improve identification of novel complete biosynthetic gene clusters in a complex microbial activated sludge ecosystem

Roberto Sánchez-Navarro, Matin Nuhamunada, Omkar Mohite, Kenneth Wasmund, Mads Albertsen, Lone Gram, Per Hostrup Nielsen, Tilmann Weber, Caitlin M. Singleton

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Abstract

Microorganisms produce a wide variety of secondary/specialized metabolites (SMs), the majority of which are yet to be discovered. These natural products play multiple roles in microbiomes and are important for microbial competition, communication, and success in the environment. SMs have been our major source of antibiotics and are used in a range of biotechnological applications. In silico mining for biosynthetic gene clusters (BGCs) encoding the production of SMs is commonly used to assess the genetic potential of organisms. However, as BGCs span tens to over 200 kb, identifying complete BGCs requires genome data that has minimal assembly gaps within the BGCs, a prerequisite that was previously only met by individually sequenced genomes. Here, we assess the performance of the currently available genome mining platform antiSMASH on 1,080 high-quality metagenome-assembled bacterial genomes (HQ MAGs) previously produced from wastewater treatment plants (WWTPs) using a combination of long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies. More than 4,200 different BGCs were identified, with 88% of these being complete. Sequence similarity clustering of the BGCs implies that the majority of this biosynthetic potential likely encodes novel compounds, and few BGCs are shared between genera. We identify BGCs in abundant and functionally relevant genera in WWTPs, suggesting a role of secondary metabolism in this ecosystem. We find that the assembly of HQ MAGs using long-read sequencing is vital to explore the genetic potential for SM production among the uncultured members of microbial communities.
Original languageEnglish
Number of pages15
JournalmSystems
Early online date29 Nov 2022
DOIs
Publication statusEarly online - 29 Nov 2022

Keywords

  • biosynthetic gene cluster
  • secondary metabolite
  • wastewater treatment plant
  • activated sludge
  • metagenome-assembled genome

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