Metagenomes Assembles Genomes from cultivated freshwater bacterial communities

This dataset represents 122 Metagenomes-Assembled Genomes (MAGs) that were reconstructed from 20 individual microcosms in the context of understanding microbial community assembly processes. The cultivation media consisted in Artificial Lake Water (ALW) enriched with glucose and cellobiose (See details in Le Moigne et al., 2023, Ecology). The microcosms (200 mL) were inoculated with lake bacteria.

The DNA from each microcosm was collected from 100 mL, exracted with DNeasy PowerBiofilm Kit (Qiagen) and shotgun sequenced on Illumina Hiseq platform (paired end 150bp, 5GB per microcosms).Raw paired-end Illumina shotgun reads were pre-processed to remove low-quality bases and reads. Briefly, Trimmomatic v.0.36 was used to interleave paired-end reads, perform quality trimming (Phred score = 33) and to remove sequencing adaptors. Additional checks (i.e. de novo adapter identification with “bbmerge.sh” (“BBMap v.37.02) were performed in order to ensure that the datasets met the quality threshold necessary for assembly. The pre-processed reads were assembled with “metaSPAdes” v3.11.1 using the k-mer sizes 21, 33, 55, 77, 99, 127. Curated metagenomic datasets were mapped using “bbwrap.sh” (BBMap v. 37.02) (parameters: kfilter=31, subfilter=15, maxindel=80) against the assembled contigs (longer than 2.5 Kb) in a sample-dependent fashion. The resulting BAM files were used to generate contig abundance profiles with “jgi_summarize_bam_contig_depths” from “MetaBAT2” v2.12.1 (parameter percentIdentity = 97). The contigs and their abundance files were used for binning with “MetaBAT2” (default settings). Bin completeness, contamination and strain heterogeneity were estimated using “CheckM” v1.0.3 (using the “lineage_wf” workflow). Bins with estimated completeness above 40% and contamination below 5% were denominated as metagenome assembled genomes (MAGs, n = 122).