Yi Yue1,2,3, Hao Huang4,5,6, Zhao Qi4,7, Hui-Min Dou7, Xin-Yi Liu7, Tian-Fei Han4,6, Yue Chen4,6, Xiang-Jun Song4,6, You-Hua Zhang8,9,10, Jian Tu11,12,13. 1. Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, China. yyyue@ahau.edu.cn. 2. School of Information & Computer, Anhui Agricultural University, Hefei, 230036, China. yyyue@ahau.edu.cn. 3. School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China. yyyue@ahau.edu.cn. 4. Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, China. 5. School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China. 6. School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China. 7. School of Information & Computer, Anhui Agricultural University, Hefei, 230036, China. 8. Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, China. zhangyh@ahau.edu.cn. 9. School of Information & Computer, Anhui Agricultural University, Hefei, 230036, China. zhangyh@ahau.edu.cn. 10. School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China. zhangyh@ahau.edu.cn. 11. Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036, China. tujian1980@126.com. 12. School of Information & Computer, Anhui Agricultural University, Hefei, 230036, China. tujian1980@126.com. 13. School of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China. tujian1980@126.com.
Abstract
BACKGROUND: Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assembled sequences into individual groups, which represent microbial genomes, is the key step and a major challenge in metagenomic research. Both supervised and unsupervised machine learning methods have been employed in binning. Genome binning belonging to unsupervised method clusters contigs into individual genome bins by machine learning methods without the assistance of any reference databases. So far a lot of genome binning tools have emerged. Evaluating these genome tools is of great significance to microbiological research. In this study, we evaluate 15 genome binning tools containing 12 original binning tools and 3 refining binning tools by comparing the performance of these tools on chicken gut metagenomic datasets and the first CAMI challenge datasets. RESULTS: For chicken gut metagenomic datasets, original genome binner MetaBat, Groopm2 and Autometa performed better than other original binner, and MetaWrap combined the binning results of them generated the most high-quality genome bins. For CAMI datasets, Groopm2 achieved the highest purity (> 0.9) with good completeness (> 0.8), and reconstructed the most high-quality genome bins among original genome binners. Compared with Groopm2, MetaBat2 had similar performance with higher completeness and lower purity. Genome refining binners DASTool predicated the most high-quality genome bins among all genomes binners. Most genome binner performed well for unique strains. Nonetheless, reconstructing common strains still is a substantial challenge for all genome binner. CONCLUSIONS: In conclusion, we tested a set of currently available, state-of-the-art metagenomics hybrid binning tools and provided a guide for selecting tools for metagenomic binning by comparing range of purity, completeness, adjusted rand index, and the number of high-quality reconstructed bins. Furthermore, available information for future binning strategy were concluded.
BACKGROUND: Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assembled sequences into individual groups, which represent microbial genomes, is the key step and a major challenge in metagenomic research. Both supervised and unsupervised machine learning methods have been employed in binning. Genome binning belonging to unsupervised method clusters contigs into individual genome bins by machine learning methods without the assistance of any reference databases. So far a lot of genome binning tools have emerged. Evaluating these genome tools is of great significance to microbiological research. In this study, we evaluate 15 genome binning tools containing 12 original binning tools and 3 refining binning tools by comparing the performance of these tools on chicken gut metagenomic datasets and the first CAMI challenge datasets. RESULTS: For chicken gut metagenomic datasets, original genome binner MetaBat, Groopm2 and Autometa performed better than other original binner, and MetaWrap combined the binning results of them generated the most high-quality genome bins. For CAMI datasets, Groopm2 achieved the highest purity (> 0.9) with good completeness (> 0.8), and reconstructed the most high-quality genome bins among original genome binners. Compared with Groopm2, MetaBat2 had similar performance with higher completeness and lower purity. Genome refining binners DASTool predicated the most high-quality genome bins among all genomes binners. Most genome binner performed well for unique strains. Nonetheless, reconstructing common strains still is a substantial challenge for all genome binner. CONCLUSIONS: In conclusion, we tested a set of currently available, state-of-the-art metagenomics hybrid binning tools and provided a guide for selecting tools for metagenomic binning by comparing range of purity, completeness, adjusted rand index, and the number of high-quality reconstructed bins. Furthermore, available information for future binning strategy were concluded.
Authors: Gleb Goussarov; Jürgen Claesen; Mohamed Mysara; Ilse Cleenwerck; Natalie Leys; Peter Vandamme; Rob Van Houdt Journal: Environ Microbiome Date: 2022-03-05