Jiang Fan, Li Qiang, Wang Sen, Shen Ting, Wang Hengchao, Wang Anqi, Xu Dong, Yuan Lihua, Lei Lihong, Chen Rong, Yang Boyuan, Deng Yu, Fan Wei
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.
Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, Sichuan, China.
Front Microbiol. 2023 Jan 9;13:1095497. doi: 10.3389/fmicb.2022.1095497. eCollection 2022.
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.
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 (70.5%), followed by (6.1%), and (4.7%), and the most predominant bacterial and archaeal genera were (69.1%) and (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.
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.
厌氧消化（AD）在处理食物垃圾方面很重要，并且已经为AD中的微生物群落构建了数千个宏基因组组装基因组（MAG）。然而，由于短读长测序和组装技术的局限性，这些MAG大多是通过分箱算法从数百个短重叠群中分组得到的，容易引入错误。
在本研究中，我们从一个以食物垃圾为原料的全规模沼气厂的沼渣样品中生成的64.5 Gb的PacBio高保真（HiFi）长读长序列中，总共构建了60个非冗余微生物基因组。在这60个微生物基因组中，所有基因组都至少有一个rRNA操纵子（16S、23S和5S rRNA）拷贝，54个基因组有≥18种标准tRNA基因，39个是环状完整基因组。与已发表的基于短读长的AD衍生MAG相比，我们发现有23个基因组与任何已知MAG的平均核苷酸同一性小于95%。此外，我们基于HiFi的基因组具有更高的平均重叠群N50大小、略大的平均基因组大小和更低的污染。这些基因组的GTDB-Tk分类显示，有两个基因组属于新属，四个基因组属于新物种，因为它们的16S rRNA基因与任何已知16S rRNA基因的同一性分别低于95%和97%。基于这些组装基因组的微生物群落分析表明，最主要的门类是（70.5%）, 其次是（6.1%）和（4.7%），最主要的细菌和古菌属分别是（69.1%）和（5.4%）。对从HiFi读长中鉴定出的全长16S rRNA基因的分析给出了与从60个组装基因组中得到的相似的微生物组成。
高保真测序不仅生成了质量明显提高的微生物基因组，还找回了先前基于短读长的研究中遗漏的大量新基因组，这些新基因组将加深我们对食物垃圾AD中微生物组成的理解。
