Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy

Liu，Lei1,2,3; Wang，Yulin1; Yang，Yu1; Wang，Depeng4; Cheng，Suk Hang5; Zheng，Chunmiao2,3; Zhang，Tong1,3

2021-12-01

10.1186/s40168-021-01155-1

Microbiome   影响因子和分区

2049-2618

Background: Long-read sequencing has shown its tremendous potential to address genome assembly challenges, e.g., achieving the first telomere-to-telomere assembly of a gapless human chromosome. However, many issues remain unresolved when leveraging error-prone long reads to characterize high-complexity metagenomes, for instance, complete/high-quality genome reconstruction from highly complex systems. Results: Here, we developed an iterative haplotype-resolved hierarchical clustering-based hybrid assembly (HCBHA) approach that capitalizes on a hybrid (error-prone long reads and high-accuracy short reads) sequencing strategy to reconstruct (near-) complete genomes from highly complex metagenomes. Using the HCBHA approach, we first phase short and long reads from the highly complex metagenomic dataset into different candidate bacterial haplotypes, then perform hybrid assembly of each bacterial genome individually. We reconstructed 557 metagenome-assembled genomes (MAGs) with an average N50 of 574 Kb from a deeply sequenced, highly complex activated sludge (AS) metagenome. These high-contiguity MAGs contained 14 closed genomes and 111 high-quality (HQ) MAGs including full-length rRNA operons, which accounted for 61.1% of the microbial community. Leveraging the near-complete genomes, we also profiled the metabolic potential of the AS microbiome and identified 2153 biosynthetic gene clusters (BGCs) encoded within the recovered AS MAGs. Conclusion: Our results established the feasibility of an iterative haplotype-resolved HCBHA approach to reconstruct (near-) complete genomes from highly complex ecosystems, providing new insights into “complete metagenomics”. The retrieved high-contiguity MAGs illustrated that various biosynthetic gene clusters (BGCs) were harbored in the AS microbiome. The high diversity of BGCs highlights the potential to discover new natural products biosynthesized by the AS microbial community, aside from the traditional function (e.g., organic carbon and nitrogen removal) in wastewater treatment. [MediaObject not available: see fulltext.]

Activated sludge microbiome Complete genomes Haplotype-resolved Highly complex metagenomes Long-read metagenomics Nanopore long reads

SCI

英语

通讯

WOS:000707381600002

2-s2.0-85117310245

Scopus

1.Environmental Microbiome Engineering and Biotechnology Laboratory,The University of Hong Kong,Hong Kong
2.State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control,School of Environmental Science and Engineering,Southern University of Science and Technology,Shenzhen,China
3.School of Environmental Science and Engineering,Southern University of Science and Technology,Shenzhen,China
4.Nextomics Biosciences Institute,Wuhan,China
5.Department of Chemical Pathology,The Chinese University of Hong Kong,Hong Kong

Liu，Lei,Wang，Yulin,Yang，Yu,et al. Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy[J]. Microbiome,2021,9(1).

Liu，Lei.,Wang，Yulin.,Yang，Yu.,Wang，Depeng.,Cheng，Suk Hang.,...&Zhang，Tong.(2021).Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy.Microbiome,9(1).

Liu，Lei,et al."Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy".Microbiome 9.1(2021).