Metagenome-assembled genomes from microbiomes fermenting dairy coproducts

ABSTRACT To advance knowledge of microbial communities capable of fermenting agro-industrial residues into value-added products, we report metagenomes of microbial communities from six anaerobic bioreactors that were fed a mixture of ultra-filtered milk permeate and cottage cheese acid whey. These metagenomes produced 122 metagenome-assembled genomes that represent 34 distinct taxa.

Sample from which a given MAG was derived.A1-A3: samples originating from the three bioreactors operated at 35°C after 140 days of operation; B1-B3: samples originating from the three bioreactors operated at 50°C after 140 days of operation; Series1 and Series2: samples originating from the inoculant.Series1 inoculant was used for bioreactors A1, A2, and B1, while the Series2 inoculant was used for bioreactors A3, B2, and B3.The _r1 and _r2 suffixes denote extraction replicates 1 and 2, respectively.i NCBI SRA accession number for the raw reads of the metagenome for each reported MAG.
k Coverage denotes the mean number of aligned reads overlapping each position on the genome using the following equation, where read length equals 150 bp: [(number of reads mapped to a MAG) × (read length)]/(MAG size).
These values were determined for each MAG in the same manner as relative abundance, except using the "-m mean" flag when running the "coverm genome" command.

d
Average nucleotide identity (ANI) between representative MAG and otherMAGs included in the same cluster by dRep.e dRep scoring calculation: (A × completeness) − (B × contamination) + {C × [contamination × (strain heterogeneity/100)]} + [D × log(N 50 )] + [E × log(genome size)] + [F × (centrality − S_ANI)], where A to F were weighted with values 1, 0.5, 1, 5, 0, and 1, respectively.Custom dRep parameters were used to keep continuity with our previous metagenomic projects (15).f NCBI GenBank accession number of the reference genome in GTDB-Tk (10) that is closest to the representative MAG; NA represents MAGs without a closely matched reference genome when using the default minimum alignment fraction of 0.65.g Average nucleotide identity (ANI) between representative MAG and GTDB-Tk reference genome.h NCBI GenBank accession number for each reported MAG.

TABLE 1
MAG statistics and genome accession numbers

name a Code b Sample of origin c ANIm d dRep score e GTDB-Tk classification Reference genome f ANIm g
h SRA accession number i Relative abundanc e (%) j Coverag e (Continued on next page)

TABLE 1
MAG statistics and genome accession numbers (Continued)

name a Code b Sample of origin c ANIm d dRep score e GTDB-Tk classification Reference genome f ANIm g
h SRA accession number i Relative abundanc e (%) j Coverag e Announcement Microbiology Resource Announcements July 2024 Volume 13 Issue 7 10.1128/mra.00173-243

TABLE 1
MAG statistics and genome accession numbers (Continued)

name a Code b Sample of origin c ANIm d dRep score e GTDB-Tk classification Reference genome f ANIm g Completene ss (%) Contamina tion (%) MAG size (Mbp) No. of c ontigs N 50 (Mbp) %GC NCBI genome accession number h SRA accession number i Relative abundanc e (%) j Coverag e
July 2024 Volume 13 Issue 7 10.1128/mra.00173-244

TABLE 1
MAG statistics and genome accession numbers (Continued) a Code b Sample of origin c ANIm d dRep score e GTDB-

TABLE 1
MAG statistics and genome accession numbers (Continued)

name a Code b Sample of origin c ANIm d dRep score e GTDB-Tk classification Reference genome f ANIm g
h SRA accession number i Relative abundanc e (%) j Coverag e Announcement Microbiology Resource Announcements July 2024 Volume 13 Issue 7 10.1128/mra.00173-246

TABLE 1
MAG statistics and genome accession numbers (Continued)

name a Code b Sample of origin c ANIm d dRep score e GTDB-Tk classification Reference genome f ANIm g
j Coverag e Announcement Microbiology Resource Announcements July 2024 Volume 13 Issue 7 10.1128/mra.00173-247

TABLE 1
MAG statistics and genome accession numbers (Continued)

name a Code b Sample of origin c ANIm d dRep score e GTDB-Tk classification Reference genome f ANIm g
AnnouncementMicrobiology Resource Announcements July 2024 Volume 13 Issue 710.1128/mra.00173-248

TABLE 1
MAG statistics and genome accession numbers (Continued)

TABLE 1
MAG statistics and genome accession numbers (Continued)

TABLE 1
MAG statistics and genome accession numbers (Continued)

TABLE 1
MAG statistics and genome accession numbers (Continued)

name a Code b Sample of origin c ANIm d dRep score e GTDB-Tk classification Reference genome f ANIm g
Strain name assigned to each MAG.The UW_AWMP prefix stands for University of Wisconsin Acid Whey and Milk Permeate bioreactor.MAGs are clustered during dereplication using dRep (9).Strains with a numerical suffix of _1 are the highest quality dRep representative MAGs for a given cluster; nonrepresentative MAGs in each cluster are assigned the same strain name with sequential numerical suffixes (e.g., _2 and _3), assigned in order of decreasing quality, according to the dRep score.