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BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis

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机构： [1]Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China. [2]AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China. [3]School of Electronic and Computer Engineering, Peking University, Shenzhen, China. [4]Peng Cheng Laboratory, Shenzhen, China. [5]Southern University of Sciences and Technology Yantian Hospital, Shenzhen, China. [6]Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China. [7]Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China. [8]Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China. [9]Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China. [10]School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China. [11]Department ofMicrobiology, University of Hong Kong, Hong Kong, China. [12]Shenzhen International Graduate School, Tsinghua University, Shenzhen, China. [13]Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China. [14]Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China. [15]Wuhan Benagen Technology Co., Ltd, Wuhan, China. [16]Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. [17]State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China. [18]College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China. [19]Department of Civil Engineering, University of Hong Kong, Hong Kong, China. [20]Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA. [21]Department of Civil and Environmental Engineering, Faculty of Engineering, University of Auckland, Auckland, New Zealand.

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Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency of binning tools in adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data. BASALT employs multiple binners with multiple thresholds to produce initial bins, then utilizes neural networks to identify core sequences to remove redundant bins and refine non-redundant bins. Using the same assemblies generated from Critical Assessment of Metagenome Interpretation (CAMI) datasets, BASALT produces up to twice as many MAGs as VAMB, DASTool, or metaWRAP. Processing assemblies from a lake sediment dataset, BASALT produces ~30% more MAGs than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that BASALT can retrieve 47.6% more non-redundant opening-reading frames than metaWRAP. These results highlight the robust handling of metagenomic sequencing data of BASALT.© 2024. The Author(s).

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第一作者机构： [1]Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China. [2]AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China.

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通讯机构： [1]Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China. [2]AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China.

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