Recovery of metagenome-assembled microbial genomes from a full-scale biogas plant of food waste by pacific biosciences high-fidelity sequencing

Fan Jiang; Qiang Li; Sen Wang; Ting Shen; Hengchao Wang; Anqi Wang; Dong Xu; Lihua Yuan; Lihong Lei; Rong Chen; Boyuan Yang; Yu Deng; Wei Fan

doi:10.3389/fmicb.2022.1095497

Recovery of metagenome-assembled microbial genomes from a full-scale biogas plant of food waste by pacific biosciences high-fidelity sequencing

Front Microbiol. 2023 Jan 9:13:1095497. doi: 10.3389/fmicb.2022.1095497. eCollection 2022.

Authors

Fan Jiang¹, Qiang Li^{2

3}, Sen Wang¹, Ting Shen^{2

3}, Hengchao Wang¹, Anqi Wang¹, Dong Xu¹, Lihua Yuan¹, Lihong Lei¹, Rong Chen¹, Boyuan Yang¹, Yu Deng^{2

3}, Wei Fan¹

Affiliations

¹ Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.
² Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China.
³ Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China.

Abstract

Background: Anaerobic digestion (AD) is important in treating of food waste, and thousands of metagenome-assembled genomes (MAGs) have been constructed for the microbiome in AD. However, due to the limitations of the short-read sequencing and assembly technologies, most of these MAGs are grouped from hundreds of short contigs by binning algorithms, and the errors are easily introduced.

Results: In this study, we constructed a total of 60 non-redundant microbial genomes from 64.5 Gb of PacBio high-fidelity (HiFi) long reads, generated from the digestate samples of a full-scale biogas plant fed with food waste. Of the 60 microbial genomes, all genomes have at least one copy of rRNA operons (16S, 23S, and 5S rRNA), 54 have ≥18 types of standard tRNA genes, and 39 are circular complete genomes. In comparison with the published short-read derived MAGs for AD, we found 23 genomes with average nucleotide identity less than 95% to any known MAGs. Besides, our HiFi-derived genomes have much higher average contig N50 size, slightly higher average genome size and lower contamination. GTDB-Tk classification of these genomes revealed two genomes belonging to novel genus and four genomes belonging to novel species, since their 16S rRNA genes have identities lower than 95 and 97% to any known 16S rRNA genes, respectively. Microbial community analysis based on the these assembled genomes reveals the most predominant phylum was Thermotogae (70.5%), followed by Euryarchaeota (6.1%), and Bacteroidetes (4.7%), and the most predominant bacterial and archaeal genera were Defluviitoga (69.1%) and Methanothrix (5.4%), respectively. Analysis of the full-length 16S rRNA genes identified from the HiFi reads gave similar microbial compositions to that derived from the 60 assembled genomes.

Conclusion: High-fidelity sequencing not only generated microbial genomes with obviously improved quality but also recovered a substantial portion of novel genomes missed in previous short-read based studies, and the novel genomes will deepen our understanding of the microbial composition in AD of food waste.

Keywords: PacBio HiFi reads; food waste; full-length 16S rRNA genes; full-scale biogas plants; metagenome.