This is a metagenome-assembled genome (MAG) that was assembled with FLYE v2.9.1-b1780 (settings: --nano-corr –meta –no-alt-contigs) from combined long- and short-read sequencing (Oxford Nanopore and Illumina NovaSeq). Contigs ≥3 kbp were used for hybrid binning (tetranucleotide frequencies and coverage data using cross-mapping of reads gained from the same lake, i.e., 12 samples in the case of Lake Malawi) using MaxBin-2.2.7, MetaBAT and MetaBAT2 and DAS Tool-1.1.3 to combine their predictions. Bins were manually curated and CheckM v1.1.3 was used to estimate bin completeness, contamination, and strain heterogeneity. rRNA genes were predicted with barrnap v0.9, tRNA genes were predicted with tRNAscan v1.4. Although the fragmentation of this long-read MAG is low (it consists of only 7 contigs), and it is highly complete (95.2%) it contains only a 5S rRNA gene, but no 16S or 23S rRNA genes.