Open access
Applied and Industrial Microbiology
Announcement
31 May 2024

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.

ANNOUNCEMENT

Microbial communities have the potential to increase the value of agro-industrial residues by fermentation. Metagenomes reported here originate from two sets of anaerobic bioreactors and their inoculant cultures. In each experiment, three chemostats were operated anaerobically, at pH 5.5, 6-day hydraulic retention time, and either 35°C or 50°C. They were fed a 1:1 mixture of ultra-filtered milk permeate and cottage cheese acid whey and inoculated with the culture from an acid-phase digester at the local wastewater treatment plant (Madison, WI, USA) that was enriched in a similarly operated bioreactor for 23 days at 35°C. For each experiment, DNA was extracted, in duplicate, from the inoculant culture and from each bioreactor with the DNeasy PowerSoil Pro kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol. A total of 16 samples containing 1,500 ng DNA were submitted to the Joint Genome Institute (JGI) (Berkeley, USA) for sequencing, assembly, and binning, using the JGI metagenomic workflow (1). Default software parameters were used unless noted. Processing and sequencing of DNA included shearing to 300 bp fragments using a Covaris LE220 (Woburn, USA) and TotalPure NGS beads (Omega Biotek, Atlanta, USA), end repair, A-tailing, ligation of adapters using the Kapa-HyperPrep kit (Roche, USA), and sequencing of paired-end 2 × 150 bp reads using a NovaSeq S4 platform (Illumina, San Diego, USA) resulting in libraries containing 189 to 648 million 150 bp reads. Read processing and assembly included filtering, trimming, and removal of contamination using BBDuk (v38.99) and BBMap (v38.86) (2), error correction using bbcms (v38.86) (mincount=2, highcountfraction=0.6) (2), assembly into contigs with metaSPAdes (v3.15.2) (“spades.py -m 2000 --only-assembler -k 33,55,77,99,127 --meta”) (3) discarding contigs below 200 bp, and mapping the filtered reads onto the contigs with BBMap (v38.86) (“bbmap.sh build=1 fastareadlen=500 interleaved=true ambiguous=random”) (2) to determine coverage for binning purposes. Contigs were binned into metagenome-assembled genomes (MAGs) using MetaBAT (v2:2.15) (4) following the JGI IMG Annotation Pipeline (v5.1.17) (1).
Following JGI processing, MAGs were refined by identifying and removing contaminant contigs with ProDeGe (v2.3) (5) and custom scripts (“run.GC.sh” and “Calculating_TF_Correlations.R”) based on tetranucleotide frequency (6). CheckM (v1.2.2) (7) was used to obtain quality statistics for all MAGs, and MAGs under 75% completeness were discarded. Retained refined MAGs were annotated by NCBI using the Prokaryotic Genome Annotation Pipeline (v6.6) (8). MAGs from all samples were pooled and dereplicated using dRep (v3.4.5) (“dereplicate –conW 0.5 –N50W 5”) (9), whereby near-identical MAGs were clustered, and representative MAGs for each cluster were selected based on quality (Table 1). GTDB-Tk (v2.1.1, database release 214) (10) was used to assign taxonomy to representative MAGs (“gtdbtk identify”) based on concatenated bacterial marker genes (Bac120). This announcement reports 122 annotated medium-quality and high-quality MAGs, grouped into 34 dereplicated clusters representing distinct taxa (Table 1). These data advance our metagenome-based knowledge of agro-industrial residue and waste bioconverting microbiomes (6, 1120).
TABLE 1
TABLE 1 MAG statistics and genome accession numbers
Strain nameaCodebSample of origincANImddRep scoreeGTDB-Tk classificationReference genomefANImgCompleteness (%)Contamination (%)MAG size (Mbp)No. of c ontigsN50 (Mbp)%GCNCBI genome accession numberhSRA accession numberiRelative abundance (%)jCoveragek
UW_AWMP_ACET1_1ACET1A2_r1 125d__Bacteria;p__Pseudomonadota;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter;s__Acetobacter sp012517935GCA_012517935.10.95801000.252.794280.12153.7GCA_036452275.1SRR26909978<133
UW_AWMP_ACET1_2 A1_r10.9993106   79.102.294180.21354.0GCA_036452255.1SRR26909966<1174
UW_AWMP_ACUT1_1ACUT1A3_r2 106d__Bacteria;p__Bacillota_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacterium;s__Caproicibacterium sp022483045GCA_022483045.10.999982.5501.599220.08651.3GCA_036454745.1SRR26910051<115
UW_AWMP_ACUT2_1ACUT2Series2_r2 103d__Bacteria;p__Bacillota_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacterium;s__Caproicibacterium sp902809935GCA_902809935.10.994882.70.341.580820.02342.7GCA_036454725.1SRR26909984<121
UW_AWMP_ATO1_1ATO1A2_r2 124d__Bacteria;p__Actinomycetota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter;s__Tractidigestivibacter scatoligenesGCF_001494635.10.956598.3902.241400.14162.8GCA_036454705.1SRR26909981<1158
UW_AWMP_ATO1_2 A2_r10.9990114   90.2302.062590.04862.5GCA_036454685.1SRR26909978<192
UW_AWMP_ATO2_1ATO2Series2_r1 121d__Bacteria;p__Actinomycetota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741;s__NANA98.390.272.092630.04569.7GCA_036454645.1SRR26910046<1226
UW_AWMP_ATO3_1ATO3B1_r1 118d__Bacteria;p__Actinomycetota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7748;s__UBA7748 sp900314535GCA_900314535.10.972395.970.812.022690.03560.2GCA_036454665.1SRR269099793712,486
UW_AWMP_ATO3_2 B1_r21.0000117   94.350.811.992680.03560.2GCA_036454625.1SRR269099863716,419
UW_AWMP_ATO3_3 Series1_r20.9780116   92.740.271.679620.03560.5GCA_036454605.1SRR2690996893,877
UW_AWMP_ATO3_4 Series1_r10.9793115   91.940.271.653660.03260.5GCA_036454585.1SRR26909967103,372
UW_AWMP_ATO3_5 A2_r20.9746101   79.030.91.578800.02460.4GCA_036454565.1SRR26909981<1187
UW_AWMP_ATO4_1ATO4A1_r1 107d__Bacteria;p__Actinomycetota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olegusella;s__Olegusella sp002407925GCA_002407925.10.986580.6501.49880.25355.5GCA_036454505.1SRR26909966122,610
UW_AWMP_BACIL1_1BACIL1B2_r2 115d__Bacteria;p__Bacillota;c__Bacilli;o__Bacillales;f__Bacillaceae_C;g__Weizmannia;s__Weizmannia coagulansGCF_000290615.10.983291.6102.447700.04947.9GCA_036454485.1SRR26909982243,817
UW_AWMP_BACIL1_2 B2_r10.9999111   87.5702.36690.04647.7GCA_036454545.1SRR26909987235,522
UW_AWMP_BACIL1_3 B3_r10.9525110   87.220.552.432920.03247.5GCA_036454525.1SRR26909985111,343
UW_AWMP_BACIL1_4 B3_r20.9510110   86.7602.471900.03647.4GCA_036454465.1SRR26910050102,698
UW_AWMP_BIF1_1BIF1B3_r2 130d__Bacteria;p__Actinomycetota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium mongolienseGCF_000741285.10.975799.731.142.10971.31263.2GCA_036454425.1SRR269100503752
UW_AWMP_BIF1_2 B1_r21.0000130   99.731.142.10591.25963.2GCA_036454285.1SRR26909986<1383
UW_AWMP_BIF1_3 A3_r11.0000130   99.731.142.10581.25963.2GCA_036454265.1SRR269099833640
UW_AWMP_BIF1_4 B2_r21.0000130   99.731.142.112101.15463.2GCA_036454305.1SRR269099822345
UW_AWMP_BIF1_5 A3_r21.0000130   99.731.142.11101.15463.2GCA_036454225.1SRR2691005131,327
UW_AWMP_BIF1_6 A1_r11.0000130   99.731.142.0791.13863.3GCA_036454245.1SRR269099661291
UW_AWMP_BIF1_7 B3_r11.0000127   99.731.142.10880.37163.2GCA_036454205.1SRR269099853381
UW_AWMP_BIF1_8 A1_r21.0000127   99.731.142.11110.26563.2GCA_036454165.1SRR269099652391
UW_AWMP_BIF1_9 B1_r11.0000126   99.731.142.066120.20963.3GCA_036454185.1SRR26909979<1279
UW_AWMP_BIF1_10 Series1_r21.0000117   88.820.231.801110.37163.3GCA_036454375.1SRR26909968<154
UW_AWMP_BIF1_11 Series2_r21.0000115   84.730.231.67941.25963.2GCA_036454405.1SRR26909984131,762
UW_AWMP_BIF1_12 Series2_r11.0000108   77.910.081.5131.20163.3GCA_036454345.1SRR26910046114,126
UW_AWMP_BIF1_13 A2_r11.0000108   77.910.081.50640.93763.4GCA_036454365.1SRR26909978<1154
UW_AWMP_BIF1_14 B2_r11.0000107   77.910.081.52340.80563.3GCA_036454325.1SRR269099872523
UW_AWMP_BIF2_1BIF2B3_r1 127d__Bacteria;p__Actinomycetota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium crudilactisGCF_000738005.10.974999.082.122.46270.50957.6GCA_036454125.1SRR26909985172,029
UW_AWMP_BIF2_2 A2_r21.0000127   99.082.122.42270.50957.7GCA_036454145.1SRR26909981153,971
UW_AWMP_BIF2_3 A3_r11.0000126   99.082.122.411100.34357.7GCA_036454105.1SRR26909983315,849
UW_AWMP_BIF2_4 A3_r21.0000117   90.361.972.19290.34357.6GCA_036454085.1SRR269100513213,341
UW_AWMP_BIF2_5 B1_r11.0000113   84.30.981.87240.56957.6GCA_036454065.1SRR2690997993,031
UW_AWMP_BIF2_6 Series1_r10.9664107   83.861.211.852490.05257.9GCA_036454025.1SRR26909967<112
UW_AWMP_BIF2_7 Series1_r20.9650103   80.781.671.75500.04657.5GCA_036454045.1SRR26909968<112
UW_AWMP_BIF3_1BIF3B1_r2 125d__Bacteria;p__Actinomycetota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium subtileGCF_000741775.10.989499.442.732.748160.28361.2GCA_036454005.1SRR26909986<1172
UW_AWMP_BIF3_2 B1_r10.9999123   98.082.582.551170.20161.1GCA_036453985.1SRR26909979<1119
UW_AWMP_BIF4_1BIF4A2_r1 125d__Bacteria;p__Actinomycetota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium thermophilumGCA_000771265.10.95511000.152.049270.11260.5GCA_036453945.1SRR26909978<120
UW_AWMP_BIF4_2 A2_r20.9994108   800.151.4760.35160.5GCA_036453925.1SRR26909981<126
UW_AWMP_BIF5_1BIF5A1_r2 123d__Bacteria;p__Actinomycetota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium sp022649135GCA_022649135.10.993498.311.532.45410.09561.5GCA_036453965.1SRR26909965<1113
UW_AWMP_BIF5_2 A1_r10.9997121   97.281.382.374460.06561.7GCA_036453885.1SRR26909966<189
UW_AWMP_COR1_1COR1Series1_r1 120d__Bacteria;p__Actinomycetota;c__Coriobacteriia;o__Coriobacteriales;f__UMGS124;g__CAIFEU01;s__CAIFEU01 sp903789505GCA_903789505.10.973595.161.412.881380.12869.5GCA_036453905.1SRR26909967<185
UW_AWMP_COR1_2 Series1_r20.9998119   93.551.493.054370.12869.4GCA_036453865.1SRR26909968<1100
UW_AWMP_EGG1_1EGG1Series2_r2 121d__Bacteria;p__Actinomycetota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAIFEB01;s__CAIFEB01 sp903789375GCA_903789375.10.967497.902.264630.04464.9GCA_036453845.1SRR26909984<118
UW_AWMP_EGG1_2 Series2_r10.9985120   95.91.72.21640.04264.9GCA_036453785.1SRR26910046<146
UW_AWMP_ENTER1_1ENTER1Series2_r1 130d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella;s__Rahnella inusitataGCF_003263515.10.989698.030.085.063102.62553.1GCA_036453825.1SRR26910046<1365
UW_AWMP_ENTER1_2 B1_r21.0000130   98.030.085.063102.62553.1GCA_036453645.1SRR269099861498
UW_AWMP_ENTER1_3 B2_r11.0000130   97.870.085.063112.62553.1GCA_036453605.1SRR26909987<1135
UW_AWMP_ENTER1_4 Series2_r21.0000130   97.870.085.063102.62553.1GCA_036453565.1SRR26909984<1130
UW_AWMP_ENTER1_5 B2_r21.0000128   98.030.085.064111.18853.1GCA_036453585.1SRR26909982<195
UW_AWMP_ENTER1_6 A1_r21.0000128   97.870.085.063111.18853.1GCA_036453525.1SRR26909965<188
UW_AWMP_ENTER1_7 B1_r11.0000128   97.870.085.067121.11453.1GCA_036453545.1SRR269099791382
UW_AWMP_ENTER1_8 A1_r11.0000127   97.870.085.034120.63453.1GCA_036453505.1SRR26909966<157
UW_AWMP_ENTER1_9 B3_r20.9999126   98.20.085.059200.37753.1GCA_036453485.1SRR26910050<130
UW_AWMP_ENTER1_10 A3_r21.0000126   97.870.085.04170.41753.1GCA_036453805.1SRR26910051<149
UW_AWMP_ENTER1_11 A3_r10.9999125   98.520.085.025300.24553.1GCA_036453765.1SRR26909983<124
UW_AWMP_ENTER1_12 Series1_r21.0000125   97.70.085.042210.3553.1GCA_036453715.1SRR26909968<136
UW_AWMP_ENTER1_13 A2_r21.0000125   98.20.085.019280.27853.2GCA_036453725.1SRR26909981<123
UW_AWMP_ENTER1_14 Series1_r11.0000125   97.870.195.045280.25553.1GCA_036453695.1SRR26909967<131
UW_AWMP_ENTER1_15 B3_r10.9998123   97.870.084.819580.1353.4GCA_036453665.1SRR26909985<116
UW_AWMP_ENTER1_16 A2_r11.0000123   97.70.084.84760.09553.4GCA_036453625.1SRR26909978<115
UW_AWMP_ERY1_1ERY1A2_r2 120d__Bacteria;p__Bacillota;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__NANA96.190.452.114590.0547.9GCA_036453465.1SRR26909981<135
UW_AWMP_ERY1_2 A2_r10.9994111   89.520.451.8251000.01948.2GCA_036453445.1SRR26909978<114
UW_AWMP_ERY2_1ERY2Series1_r1 115d__Bacteria;p__Bacillota;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__Bulleidia sp900319505GCA_900319505.10.952392.520.321.691660.0347.9GCA_036453425.1SRR26909967176,142
UW_AWMP_ERY2_2 Series1_r20.999598   75.370.321.462540.03147.9GCA_036453385.1SRR26909968167,190
UW_AWMP_LAC1_1LAC1A1_r1 119d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus delbrueckiiGCF_001433875.10.975995.7801.797540.04650.1GCA_036453405.1SRR2690996692,072
UW_AWMP_LAC1_2 B1_r10.9995116   93.1801.573560.03150.6GCA_036455785.1SRR26909979<1107
UW_AWMP_LAC1_3 A2_r20.9994115   93.1801.531640.02550.8GCA_036455715.1SRR26909981<115
UW_AWMP_LAC1_4 B3_r20.9830114   88.8501.597290.08850.6GCA_036455765.1SRR2691005051,304
UW_AWMP_LAC1_5 B1_r20.9995114   90.5801.712590.03850.1GCA_036455695.1SRR26909986<1166
UW_AWMP_LAC2_1LAC2A1_r2 102d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus absianaGCA_017309015.10.978279.990.971.392750.01952.7GCA_036455685.1SRR26909965<1177
UW_AWMP_LAC2_2 B1_r10.9943101   78.3501.374420.03852.2GCA_036455705.1SRR2690997941,195
UW_AWMP_LAC2_3 B1_r20.994198   75.1101.351400.03952.1GCA_036453365.1SRR2690998641,588
UW_AWMP_LAC3_1LAC3A1_r2 100d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus amylovorusGCF_002706375.10.975679.280.091.343730.02238.6GCA_036453345.1SRR26909965<117
UW_AWMP_LACCAS1_1LACCAS1A3_r1 125d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus;s__Lacticaseibacillus paracaseiGCF_000829035.10.983699.4602.788390.10246.5GCA_036453305.1SRR2690998391,765
UW_AWMP_LACCAS1_2 A3_r21.0000124   98.9102.787380.10246.5GCA_036453325.1SRR2691005183,476
UW_AWMP_LACCAS1_3 B1_r10.9905111   87.4702.185510.0646.6GCA_036453275.1SRR26909979<1157
UW_AWMP_LACCAS2_1LACCAS2B1_r2 107d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus;s__Lacticaseibacillus rhamnosusGCF_900636965.10.974980.9802.071230.13346.8GCA_036453285.1SRR26909986<162
UW_AWMP_LACCAS2_2 B1_r11.0000101   75.6901.992230.13346.8GCA_036453265.1SRR26909979<145
UW_AWMP_LCO1_1LCO1Series2_r2 121d__Bacteria;p__Bacillota_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor;s__Bilifractor sp900319355GCA_900319355.10.993497.130.322.31400.08152.5GCA_036453235.1SRR26909984<130
UW_AWMP_LCO2_1LCO2A2_r1 118d__Bacteria;p__Bacillota_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791;s__CAG-791 sp900315055GCA_900315055.10.988994.910.42.9061060.03855.9GCA_036453225.1SRR26909978<128
UW_AWMP_LCO2_2 A2_r20.9999118   94.910.42.9151050.03755.9GCA_036453185.1SRR26909981<143
UW_AWMP_LCO3_1LCO3Series1_r1 116d__Bacteria;p__Bacillota_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor;s__NANA91.561.272.395170.17450.6GCA_036453165.1SRR26909967<1130
UW_AWMP_LCO4_1LCO4A2_r1 114d__Bacteria;p__Bacillota_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066;s__NANA89.8102.176670.05455.1GCA_036453195.1SRR269099784617
UW_AWMP_LCO4_2 A2_r20.9999114   89.8102.162650.05455GCA_036453145.1SRR2690998141,050
UW_AWMP_LCO4_3 Series1_r10.9989113   88.5401.992400.08655GCA_036453125.1SRR26909967227,869
UW_AWMP_LCO4_4 Series1_r20.9989113   88.5401.994400.08655GCA_036453075.1SRR26909968229,531
UW_AWMP_LENLAC1_1LENLAC1B1_r2 125d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus;s__Lentilactobacillus sunkiiGCF_001435575.10.96698.8902.749250.14342.1GCA_036453105.1SRR26909986<121
UW_AWMP_LENLAC1_2 B1_r11.0000124   98.9102.623450.08842.3GCA_036453065.1SRR26909979<115
UW_AWMP_LEUC1_1LEUC1B2_r1 128d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc;s__Leuconostoc gelidumGCF_000166715.10.987599.440.191.87180.44336.6GCA_036453045.1SRR26909987<1150
UW_AWMP_LEUC1_2 B2_r21.0000128   99.440.191.87980.44236.6GCA_036453025.1SRR26909982<1102
UW_AWMP_LEUC1_3 B3_r21.0000128   99.440.191.87870.44236.6GCA_036452995.1SRR26910050<1158
UW_AWMP_LEUC1_4 A3_r11.0000128   99.440.191.8860.44236.6GCA_036452985.1SRR26909983<180
UW_AWMP_LEUC1_5 B3_r10.9999128   99.440.191.8880.44236.6GCA_036452945.1SRR26909985<165
UW_AWMP_LEUC1_6 Series2_r10.9999120   90.450.191.79741.04136.6GCA_036452965.1SRR26910046<1101
UW_AWMP_LEUC1_7 A3_r20.9999119   90.450.191.78860.44236.6GCA_036452925.1SRR26910051<1145
UW_AWMP_LEUC1_8 Series2_r20.9999116   90.450.191.786170.12536.6GCA_036452905.1SRR26909984<132
UW_AWMP_LEUC2_1LEUC2A2_r1 125d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc;s__Leuconostoc mesenteroidesGCF_000014445.10.990310001.801240.09337.7GCA_036452885.1SRR269099781186
UW_AWMP_LEUC2_2 A3_r20.9995123   97.8801.595200.10337.8GCA_036452855.1SRR26910051<143
UW_AWMP_LEUC2_3 B2_r20.9995123   97.8801.625200.09837.9GCA_036452825.1SRR26909982<143
UW_AWMP_LEUC2_4 B2_r10.9995123   97.8801.572170.09837.9GCA_036452785.1SRR26909987<168
UW_AWMP_LEUC2_5 A3_r11.0000108   83.601.294180.08737.7GCA_036452815.1SRR26909983<122
UW_AWMP_PROP1_1PROP1A3_r1 126d__Bacteria;p__Actinomycetota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium;s__Acidipropionibacterium acidipropioniciGCF_001441165.10.988310003.48290.18868.9GCA_036452805.1SRR26909983<170
UW_AWMP_PROP1_2 A3_r21.0000126   99.3403.482290.17868.9GCA_036452765.1SRR26910051<1147
UW_AWMP_PSEU1_1PSEU1Series2_r1 98d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E;s__Pseudomonas_E helleriGCF_001043025.10.972875.7905.1591310.05358.6GCA_036452715.1SRR26910046<154
UW_AWMP_STREP1_1STREP1A2_r1 127d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus;s__Lactococcus lactisGCF_900099625.10.98461000.282.51200.23434.9GCA_036452675.1SRR269099782290
UW_AWMP_STREP1_2 A2_r20.9999127   1000.282.606210.23435GCA_036452555.1SRR269099812563
UW_AWMP_STREP1_3 Series2_r20.9999127   1000.282.552190.23434.9GCA_036452575.1SRR269099843543
UW_AWMP_STREP1_4 Series1_r10.9999127   1000.282.552190.23434.9GCA_036452605.1SRR26909967<1331
UW_AWMP_STREP1_5 B3_r11.0000127   1000.282.491190.2334.9GCA_036452545.1SRR269099853355
UW_AWMP_STREP1_6 B3_r21.0000127   1000.282.51200.22334.9GCA_036452585.1SRR269100504941
UW_AWMP_STREP1_7 A1_r11.0000127   1000.282.506240.22334.9GCA_036452505.1SRR269099662509
UW_AWMP_STREP1_8 B2_r11.0000126   99.620.282.511230.22334.9GCA_036452485.1SRR2690998771,642
UW_AWMP_STREP1_9 A1_r21.0000108   81.510.281.919160.2335GCA_036452465.1SRR269099653609
UW_AWMP_STREP1_10 Series1_r21.0000108   81.510.281.937180.2334.9GCA_036452705.1SRR269099681540
UW_AWMP_STREP1_11 Series2_r11.0000108   81.510.281.938170.2334.9GCA_036452685.1SRR2691004631,296
UW_AWMP_STREP1_12 A3_r21.0000108   81.510.281.919160.2335GCA_036452655.1SRR269100511603
UW_AWMP_STREP2_1STREP2B1_r2 109d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus;s__Lactococcus cremorisGCF_001591705.10.982685.850.381.744560.03735.7GCA_036452495.1SRR2690998621,047
UW_AWMP_STREP2_2 B1_r10.999897   75.630.381.589810.02135.9GCA_036452445.1SRR269099792774
a
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.
b
ACET, Acetobacteraceae; ACUT, Acutalibacteraceae; ATO, Atopobiaceae; BACIL, Bacillaceae; BIF, Bifidobacteriaceae; COR, Coriobacteriales; EGG, Eggerthellaceae; ENTER, Enterobacteriaceae; ERY, Erysipelotrichaceae; LAC, Lactobacillus; LACCAS, Lacticaseibacillus; LCO, Lachnospiraceae; LENLAC, Lentilactobacillus; LEUC, Leuconostoc; PROP, Propionibacteriaceae; PSEU, Pseudomonadaceae; STREP, Streptococcaceae.
c
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.
d
Average nucleotide identity (ANI) between representative MAG and other MAGs included in the same cluster by dRep.
e
dRep scoring calculation: (A × completeness) − (B × contamination) + {C × [contamination × (strain heterogeneity/100)]} + [D × log(N50)] + [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.
i
NCBI SRA accession number for the raw reads of the metagenome for each reported MAG.
j
Relative abundance calculation: [(mean coverage of MAG of interest)/(sum of mean coverages of each MAG used in mapping)] × (proportion of reads that were mapped to MAGs). These values were determined for each MAG by first using Bowtie2 (v2.4.1; “bowtie2” command) (21) to map BBDuk-filtered reads from each metagenome’s FASTQ file to a concatenated FASTA file of the MAGs generated from that metagenome. Then, resulting SAM files were converted to BAM files and sorted using samtools (v1.10; “samtools view” and “samtools sort” commands) (22). Lastly, CoverM (v0.4.0; “coverm genome” command) (https://wwood.github.io/CoverM/coverm-genome.html) to generate relative abundance statistics from the mapped reads.
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.

ACKNOWLEDGMENTS

This material is based upon work supported in part by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Biological and Environmental Research Program under Award Number DE-SC0018409, funding from the National Dairy Council under project MSN214606, and an award from the University of Wisconsin-Madison Office of the Vice Chancellor for Research and Graduate Education. The work (award DOI: 10.46936/10.25585/60008808) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337) is supported by the Office of Science of the U.S. Department of Energy operated under contract no. DE-AC02-05CH11231. We thank collaborators at the Center for Dairy Research (https://www.cdr.wisc.edu/) and Meister Cheese (Muscoda, WI, USA) for providing the ultra-filtered milk permeate and collaborators at WW Homestead Dairy LLC (Waukon, IA, USA) for providing the cottage cheese acid whey.

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Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Online First
eLocator: e00173-24
Editor: Frank J. Stewart, Montana State University, Bozeman, Montana, USA
PubMed: 38819152

History

Received: 20 February 2024
Accepted: 1 May 2024
Published online: 31 May 2024

Keywords

  1. microbiome
  2. fermentation
  3. dairy

Data Availability

Raw metagenomic sequence data and annotated MAGs for each sample are available at NCBI GenBank under accession number PRJNA1040840. Links and accession numbers for individual MAGs (NCBI) and raw sequence data (SRA) are presented in Table 1. Custom scripts are available on GitHub (https://github.com/GLBRC/metagenome_analysis).

Contributors

Authors

Kevin A. Walters
Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
Author Contributions: Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Writing – original draft, and Writing – review and editing.
Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
Author Contributions: Data curation, Formal analysis, Methodology, Software, and Writing – review and editing.
Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
Author Contributions: Conceptualization, Funding acquisition, Methodology, Project administration, Supervision, and Writing – review and editing.
Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
Author Contributions: Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Supervision, and Writing – review and editing.

Editor

Frank J. Stewart
Editor
Montana State University, Bozeman, Montana, USA

Notes

The authors declare no conflict of interest.

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