Skip to main content
NCBI home page
Microbiology Resource Announcements logoLink to Microbiology Resource Announcements
. 2022 Jun 30;11(7):e00293-22. doi: 10.1128/mra.00293-22

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk Permeate

Kevin A Walters a,b,c, Kevin S Myers a,b, Hui Wang d, Nathaniel W Fortney a,b, Abel T Ingle a,b,d, Matthew J Scarborough e, Timothy J Donohue a,b,c, Daniel R Noguera a,b,d,✉
Editor: Irene L G Newtonf
PMCID: PMC9302107  PMID: 35770995

ABSTRACT

Fermentative microbial communities can be utilized for the conversion of various agroindustrial residues into valuable chemicals. Here, we report 34 metagenomes from anaerobic bioreactors fed lactose-rich ultrafiltered milk permeate and 278 metagenome-assembled genomes (MAGs). These MAGs can inform future studies aimed at generating renewable chemicals from dairy and other agroindustrial residues.

ANNOUNCEMENT

The metagenomes reported here originate from two anaerobic bioreactors, i.e., a continuously stirred tank reactor (CSTR) and an upflow sludge blanket reactor (USB), operated to investigate the valorization of agroindustrial residues via fermentation. Both bioreactors were inoculated with acid-phase anaerobic digester sludge from the Nine Springs Wastewater Treatment Plant (Madison, WI, USA) and fed ultrafiltered milk permeate amended with ammonium chloride as a nitrogen source. The CSTR was operated at pH 5.5 and 35°C, whereas the USB was operated at pH 5.5 and 21°C. DNA was periodically extracted from the bioreactors using a phenol-chloroform extraction procedure described by Scarborough et al. (1) but omitting the bead-beating step. DNA aliquots of 500 ng (27 samples) and 3,000 ng (7 samples) were submitted to the Joint Genome Institute (JGI) (Berkeley, CA, USA) for paired-end 2 × 150-bp NovaSeq S4 sequencing (Illumina, Inc., San Diego, CA, USA) and single-molecule real-time (SMRT), long-read sequencing using a Sequel II platform (Pacific Biosciences, Inc. [PacBio], Menlo Park, CA, USA), respectively. Illumina libraries were end repaired, A tailed, and ligated with Illumina adapters using the KAPA HyperPrep kit (Roche, USA) as described (2). PacBio library construction included shearing of genomic DNA to 6 to 10 kb (size selection with BluePippin; Sage Science, USA) and ligation using the SMRTbell Express template preparation v2.0 kit following the standard protocol (PacBio). All software used default parameters unless otherwise noted. Illumina reads were filtered and error corrected using bbcms (v38.86) (mincount=2, highcountfraction=0.6) (3), assembled with metaSPAdes (v3.14.1) (4), and mapped with BBMap (v38.86) (ambiguous=random) (3) following the JGI Metagenome Workflow (2). PacBio reads were filtered using BBtools (v38.87/38.88, rqc.filter2.sh) (3), and CCS reads were assembled using metaFlye (v2.8.1-b1676) (5), polished with subreads using GCpp (v1.0.0-SL-release-8.0.0) (https://github.com/PacificBiosciences/gcpp), and mapped using minimap2 (v2.17-r941) (6). For all libraries, contigs were binned with MetaBAT (v2:2.15) (7). The resulting Illumina libraries contained between 71 and 126 million 150-bp reads, and the PacBio libraries contained between 21,000 and 1,122,000 reads, 5 to 8 kb in average length. The resulting metagenome-assembled genomes (MAGs) were annotated using the JGI Metagenome Annotation Pipeline (MAP) (v5.0.23) (8) and the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (v6.0) (9). To improve MAG quality, contaminant contigs from all MAGs were identified and removed using ProDeGe (v2.3) (10) and custom tetranucleotide frequency analysis scripts (run.GC.sh and Calculating_TF_Correlations.R [https://github.com/GLBRC/metagenome_analysis]). All refined MAGs were dereplicated using dRep (v3.2.2) (dereplicate command with –conW 0.5 and –N50W 5 custom parameters) (11) by clustering MAGs by identity and selecting the highest-quality MAG as a representative for each cluster (Table 1). Quality statistics were obtained using CheckM (v1.0.11) (12), and MAGs with over 75% completeness were retained for further analysis. Taxonomy was assigned for dRep representative MAGs using GTDB-Tk (v1.5.1, database release 202) (13). RAxML-NG (v0.9.0) (14) and TreeViewer (v2.0.1) were used to generate and visualize a phylogenetic tree containing dRep representative MAGs (Fig. 1). We report 278 annotated MAGs from 34 samples, grouped into 123 dereplicated clusters that describe the microbial community composition of the two bioreactors (Table 1). These data contribute to the knowledgebase of microbial communities bioconverting agroindustrial residues (1, 15–25).

TABLE 1.

MAG statistics and genome accession numbers

Sample originc
Strain namea Codeb Reactor Day ANImd dRepe GTDB-Tk classification Reference genomef Sequencing platform Completeness (%) Contamination (%) MAG size (Mbp) No. of contigs N50 (Mbp) GC content (%) No. of tRNAs No. of 5S rRNAs No. of 16S rRNAs No. of 23S rRNAs GenBank accession no.g SRA accession no.h No. of raw reads aligned to MAG (×1,000)i
UW_MP_ACET1_1 ACET1 CSTR 120 122 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter;s__Acetobacter lovaniensis GCF_014207635.1 Illumina NovaSeq S4 96.02 0 2.163 15 0.222 58.9 38 0 0 0 JALCMR000000000 SRX12655888 348
UW_MP_ACET1_2 CSTR 126 0.9999 107 Illumina NovaSeq S4 85.22 0.5 2.257 92 0.0302 58.5 34 0 0 0 JALCMZ000000000 SRX12655887 176
UW_MP_ACET2_1 ACET2 USB 148   121 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter;s__Acetobacter fabarum GCF_011516925.1 Illumina NovaSeq S4 95.52 0.25 2.282 10 0.2426 59.0 38 0 0 0 JALCDC000000000 SRX12657082 496
UW_MP_ACID1_1 ACID1 CSTR 44 132 d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus;s__ NA PacBio Sequel II 100 0.6 3.057 1 3.057 48.1 52 3 3 3 JAKVOM000000000 SAMN18243037 8
UW_MP_ACID1_2 CSTR 54 0.9999 118 Illumina NovaSeq S4 95.21 0 2.532 74 0.0442 48.2 50 1 0 0 JALCTG000000000 SRX12654502 922
UW_MP_ACID1_3 CSTR 49 1.0000 112 Illumina NovaSeq S4 88.62 0 2.301 63 0.046 48.5 47 1 0 0 JALCSY000000000 SRX12654484 3,262
UW_MP_ACID1_4 CSTR 36 1.0000 108 Illumina NovaSeq S4 84.43 0 2.098 57 0.0458 48.4 47 1 0 0 JALCSK000000000 SRX12654483 8,659
UW_MP_ACID2_1 ACID2 CSTR 24 122 d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__;s__ NA PacBio Sequel II 95.76 6.59 2.327 18 0.1935 40.6 50 1 1 1 JAKVOW000000000 SAMN18243588 3
UW_MP_ACID2_2 CSTR 36 0.9903 99 Illumina NovaSeq S4 77.64 0 1.455 95 0.0161 40.8 34 0 0 0 JALCSJ000000000 SRX12654483 132
UW_MP_ACID3_1 ACID3 CSTR 36   118 d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Succiniclasticum;s__Succiniclasticum sp900314855 GCA_900314855.1 Illumina NovaSeq S4 95.09 0 1.769 31 0.0707 59.7 45 1 2 1 JALCSI000000000 SRX12654483 174
UW_MP_ACID4_1 ACID4 USB 0   101 d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__;s__ NA Illumina NovaSeq S4 79.92 1.2 1.721 58 0.0383 51.9 25 4 1 0 JAKVKY000000000 SRX12655975 168
UW_MP_ACT1_1 ACT1 CSTR 78 127 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Ancrocorticia;s__ NA Illumina NovaSeq S4 99.58 0.84 2.228 16 0.2166 58.1 45 0 0 0 JALCUH000000000 SRX12655143 7,251
UW_MP_ACT1_2 CSTR 97 0.9961 126 Illumina NovaSeq S4 99.16 0 2.183 18 0.2021 58.0 45 1 0 0 JALCLX000000000 SRX12655187 366
UW_MP_ACT1_3 CSTR 72 0.9998 125 Illumina NovaSeq S4 98.74 0 2.088 19 0.2134 58.0 45 1 0 0 JALCTV000000000 SRX12655142 5,499
UW_MP_ACT1_4 CSTR 84 0.9999 121 Illumina NovaSeq S4 97.9 0.42 1.884 52 0.0475 58.3 42 0 0 0 JALCUR000000000 SRX12655158 3,985
UW_MP_ACT2_1 ACT2 CSTR 126 121 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia;s__ NA Illumina NovaSeq S4 96.68 4.1 2.988 40 0.1187 70.5 48 0 0 0 JALCMY000000000 SRX12655887 5,173
UW_MP_ACT2_2 CSTR 168 0.9997 120 Illumina NovaSeq S4 96.26 2.96 2.797 33 0.1295 70.7 45 0 0 0 JALCNR000000000 SRX12655961 2,825
UW_MP_ACT2_3 CSTR 97 0.9977 114 Illumina NovaSeq S4 92.18 3.79 2.437 47 0.0667 71.2 42 0 0 0 JALCLW000000000 SRX12655187 23,464
UW_MP_ACT2_4 CSTR 108 0.9987 114 Illumina NovaSeq S4 90.96 3.79 2.374 48 0.0935 71.2 40 0 0 0 JALCMH000000000 SRX12655904 27,582
UW_MP_ACT2_5 CSTR 120 0.9985 106 Illumina NovaSeq S4 84.55 3.95 2.26 59 0.0512 71.2 39 0 0 0 JALCMQ000000000 SRX12655888 5,493
UW_MP_ACT2_6 CSTR 192 0.9996 99 Illumina NovaSeq S4 77.38 2.61 1.811 77 0.0286 71.4 31 0 0 0 JALCOD000000000 SRX12655976 1,290
UW_MP_ACUT1_1 ACUT1 USB 42   129 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA4871;s__ NA PacBio Sequel II 98.66 0 2.467 2 1.8227 50.6 57 3 3 3 JAKVOA000000000 SAMN18243454 3
UW_MP_ACUT2_1 ACUT2 CSTR 78 113 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA4871;s__UBA4871 sp902809935 GCF_902809935.1 Illumina NovaSeq S4 90.13 0.34 1.979 74 0.0353 42.3 41 3 0 0 JALCUG000000000 SRX12655143 303
UW_MP_ACUT2_2 CSTR 72 0.9995 103 Illumina NovaSeq S4 81 1.81 1.835 92 0.0247 42.6 38 3 0 2 JALCTU000000000 SRX12655142 263
UW_MP_ACUT2_3 CSTR 84 0.9996 103 Illumina NovaSeq S4 81.71 0.56 1.732 95 0.0197 42.6 30 3 0 1 JALCUQ000000000 SRX12655158 158
UW_MP_ACUT3_1 ACUT3 CSTR 36   112 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E sp902766885 GCA_902766885.1 Illumina NovaSeq S4 90.16 0.67 1.962 78 0.0299 41.6 33 2 1 1 JALCSH000000000 SRX12655159 138
UW_MP_ACUT4_1 ACUT4 USB 63   105 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA4871;s__ NA Illumina NovaSeq S4 82.21 0 1.74 48 0.0546 48.9 32 1 1 1 JAKVJJ000000000 SRX12655160 142
UW_MP_AGRLAC1_1 AGRLAC1 USB 15   125 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Agrilactobacillus;s__ GCF_001436375.1 Illumina NovaSeq S4 99.48 1.05 3.344 25 0.2093 45.0 34 3 0 1 JAKVKU000000000 SRX12655988 494
UW_MP_ANA1_1 ANA1 CSTR 60 131 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Eubacterium_T;s__ GCF_900766045.1 PacBio Sequel II 100 0 2.563 1 2.5632 49.8 55 3 3 3 JAKVOJ000000000 SAMN18243139 7
UW_MP_ANA1_2 CSTR 78 0.9997 112 Illumina NovaSeq S4 89.36 0 2.002 56 0.0453 50.3 31 1 0 0 JALCUF000000000 SRX12655143 408
UW_MP_ANA2_1 ANA2 CSTR 12   111 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__;s__ NA Illumina NovaSeq S4 89.61 0.35 2.33 70 0.0395 48.6 48 2 1 1 JALCRY000000000 SRX12654482 281
UW_MP_ANA3_1 ANA3 CSTR 54   98 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Eubacterium_T;s__Eubacterium_T saphenum_A GCA_004555725.1 Illumina NovaSeq S4 76.9 0 1.867 92 0.0244 50.1 28 1 0 0 JALCTF000000000 SRX12654502 209
UW_MP_ATO1_1 ATO1 CSTR 97 130 d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__;s__ NA Illumina NovaSeq S4 100 0 2.025 3 1.1499 65.2 47 1 1 1 JALCLV000000000 SRX12655187 557
UW_MP_ATO1_2 CSTR 78 1.0000 130 Illumina NovaSeq S4 100 0 2.008 3 1.1446 65.3 47 1 1 1 JALCUE000000000 SRX12655143 410
UW_MP_ATO1_3 CSTR 84 1.0000 128 Illumina NovaSeq S4 100 0 2.026 6 0.3687 65.2 48 1 1 1 JALCUP000000000 SRX12655158 327
UW_MP_ATO2_1 ATO2 USB 42 129 d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__;s__ NA PacBio Sequel II 97.58 0 2.276 1 2.276 65.2 46 1 1 1 JAKVOB000000000 SAMN18243454 9
UW_MP_ATO2_2 USB 77 0.9994 125 Illumina NovaSeq S4 99.19 0 2.104 28 0.1313 65.4 47 0 0 0 JAKVIT000000000 SRX12656338 1,417
UW_MP_ATO2_3 USB 56 0.9994 124 Illumina NovaSeq S4 99.19 0 2.121 27 0.1037 65.4 48 0 0 0 JAKVJX000000000 SRX12656290 1,558
UW_MP_ATO2_4 USB 28 0.9993 122 Illumina NovaSeq S4 97.58 1.61 2.113 40 0.0603 65.4 40 0 0 0 JAKVKL000000000 SRX12656283 4,342
UW_MP_ATO2_5 USB 105 0.9992 120 Illumina NovaSeq S4 94.84 0.4 2.108 38 0.0644 65.3 48 0 0 0 JALCCP000000000 SRX12656339 284
UW_MP_ATO2_6 USB 63 0.9994 117 Illumina NovaSeq S4 94.35 0.6 1.85 67 0.0359 65.7 41 0 0 0 JAKVJK000000000 SRX12656289 814
UW_MP_ATO2_7 USB 176 0.9993 111 Illumina NovaSeq S4 87.9 1.01 1.894 72 0.0309 65.6 44 1 0 1 JALCDI000000000 SRX12657171 181
UW_MP_ATO3_1 ATO3 CSTR 108 124 d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_B;s__ NA Illumina NovaSeq S4 97.98 0 2.454 28 0.1431 61.8 46 0 0 0 JALCMG000000000 SRX12655904 20,248
UW_MP_ATO3_2 CSTR 126 0.9996 123 Illumina NovaSeq S4 97.58 0 2.434 29 0.1341 61.9 46 0 0 0 JALCMX000000000 SRX12655887 9,939
UW_MP_ATO3_3 CSTR 146 0.9997 122 Illumina NovaSeq S4 96.77 0 2.474 46 0.0912 61.7 47 0 0 0 JALCNJ000000000 SRX12655903 369
UW_MP_ATO3_4 CSTR 192 0.9994 121 Illumina NovaSeq S4 97.58 0.81 2.303 64 0.043 61.9 44 0 0 0 JALCOC000000000 SRX12655976 13,183
UW_MP_ATO3_5 CSTR 216 0.9933 121 PacBio Sequel II 92 1.61 2.589 5 0.5243 62.0 37 2 2 2 JAKVOH000000000 SAMN18243112 5
UW_MP_ATO3_6 CSTR 60 0.9883 113 PacBio Sequel II 85.48 0.81 2.449 10 0.2981 62.1 39 2 2 2 JAKVOK000000000 SAMN18243139 94
UW_MP_ATO3_7 CSTR 72 0.9931 111 Illumina NovaSeq S4 88.69 0.81 1.779 79 0.0265 62.0 40 0 0 0 JALCTT000000000 SRX12655142 46,660
UW_MP_ATO3_8 CSTR 97 0.9914 111 Illumina NovaSeq S4 88.44 0 1.79 78 0.0277 62.0 45 0 0 0 JALCLU000000000 SRX12655187 13,530
UW_MP_ATO3_9 CSTR 66 0.9932 110 Illumina NovaSeq S4 87.92 0 1.734 84 0.0238 62.1 38 0 0 0 JALCTN000000000 SRX12654503 55,155
UW_MP_ATO3_10 CSTR 84 0.9916 109 Illumina NovaSeq S4 86.42 0 1.757 75 0.0308 61.9 39 1 0 0 JALCUO000000000 SRX12655158 46,496
UW_MP_ATO3_11 CSTR 78 0.9918 107 Illumina NovaSeq S4 84.41 0 1.834 82 0.0288 61.9 39 0 0 0 JALCUD000000000 SRX12655143 35,365
UW_MP_ATO3_12 CSTR 49 0.9930 105 Illumina NovaSeq S4 82.53 0.81 1.665 81 0.0223 62.1 37 1 0 1 JALCSX000000000 SRX12654484 25,716
UW_MP_ATO3_13 CSTR 54 0.9930 104 Illumina NovaSeq S4 81.85 0 1.625 79 0.0231 62.1 38 0 0 0 JALCTE000000000 SRX12654502 36,563
UW_MP_ATO4_1 ATO4 CSTR 44   120 d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__;s__ NA PacBio Sequel II 93.71 4.95 2.611 33 0.1367 66.3 49 1 1 1 JAKVON000000000 SAMN18243037 2
UW_MP_ATO5_1 ATO5 CSTR 24 115 d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7748;s__UBA7748 sp900314535 GCA_900314535.1 PacBio Sequel II 91.13 0.81 2.448 35 0.1065 60.5 46 4 3 4 JAKVOX000000000 SAMN18243588 3
UW_MP_ATO5_2 CSTR 12 0.9967 99 Illumina NovaSeq S4 77.3 0 1.494 72 0.0235 60.5 37 0 0 0 JALCRX000000000 SRX12654482 3,246
UW_MP_ATO6_1 ATO6 CSTR 36   112 d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_B;s__Olsenella_B sp900119625 GCF_900119625.1 Illumina NovaSeq S4 84.95 0 1.818 17 0.5024 62.7 46 0 0 0 JALCSG000000000 SRX12654483 9,573
UW_MP_BACIL1_1 BACIL1 CSTR 24 128 d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951;s__UBA4951 sp002397465 GCA_002397465.1 PacBio Sequel II 97.75 1.12 1.628 1 1.6276 48.4 48 1 1 1 JAKVOY000000000 SAMN18243588 2
UW_MP_BACIL1_2 USB 56 0.9982 107 Illumina NovaSeq S4 85.64 1.12 1.102 51 0.0242 48.7 32 0 1 0 JAKVJY000000000 SRX12656290 96
UW_MP_BACIL1_3 CSTR 12 0.9996 105 Illumina NovaSeq S4 83.15 1.4 1.051 46 0.029 48.7 31 1 2 1 JALCRW000000000 SRX12654482 151
UW_MP_BACIL1_4 USB 77 0.9977 103 Illumina NovaSeq S4 81.39 1.12 1.238 50 0.0319 48.8 38 1 1 2 JAKVIU000000000 SRX12656338 198
UW_MP_BACIL1_5 USB 63 0.9976 101 Illumina NovaSeq S4 78.65 0.56 1.146 52 0.0235 48.7 36 1 1 1 JAKVJL000000000 SRX12656289 153
UW_MP_BACIL2_1 BACIL2 CSTR 44   128 d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA7706;s__ NA PacBio Sequel II 98.31 0 1.497 2 1.482 37.9 45 1 1 1 JAKVOO000000000 SAMN18243037 1
UW_MP_BACIL3_1 BACIL3 CSTR 12   123 d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-288;g__UBA6879;s__ NA Illumina NovaSeq S4 97.75 1.5 2.094 20 0.1663 43.3 47 2 0 0 JALCRV000000000 SRX12654482 289
UW_MP_BACIL4_1 BACIL4 USB 148   110 d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951;s__ NA Illumina NovaSeq S4 85.39 0.05 1.591 15 0.2379 52.4 48 1 1 1 JALCDB000000000 SRX12657082 375
UW_MP_BACIL5_1 BACIL5 USB 63 108 d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA7706;s__ NA Illumina NovaSeq S4 85.62 0.05 1.236 57 0.0258 38.0 39 0 1 0 JAKVJM000000000 SRX12656289 173
UW_MP_BACIL5_2 USB 56 0.9996 107 Illumina NovaSeq S4 85.96 0.05 1.318 63 0.0232 37.9 41 0 0 0 JAKVJZ000000000 SRX12656290 156
UW_MP_BACIL6_1 BACIL6 CSTR 49   107 d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951;s__ NA Illumina NovaSeq S4 79.78 0 1.29 4 0.5045 54.5 46 1 1 1 JALCSW000000000 SRX12654484 230
UW_MP_BACIL7_1 BACIL7 USB 42   106 d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-288;g__UBA7642;s__ NA PacBio Sequel II 81.09 4.49 1.11 17 0.0801 49.3 28 2 2 2 JAKVOC000000000 SAMN18243454 1
UW_MP_BACIL8_1 BACIL8 CSTR 12   102 d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-451;s__CAG-451 sp000438295 GCA_000438295.1 Illumina NovaSeq S4 80.34 1.69 1.073 36 0.0438 27.9 31 2 0 0 JALCRU000000000 SRX12654482 1,424
UW_MP_BACTE1_1 BACTE1 CSTR 44 126 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900316045 GCA_900316045.1 PacBio Sequel II 96.9 1.19 3.242 4 0.8803 49.0 44 4 3 3 JAKVOP000000000 SAMN18243037 9
UW_MP_BACTE1_2 CSTR 49 0.9998 99 Illumina NovaSeq S4 77.03 1.19 2.343 81 0.0347 49.0 37 3 0 0 JALCSV000000000 SRX12654484 5,271
UW_MP_BACTE2_1 BACTE2 CSTR 126 122 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__ NA Illumina NovaSeq S4 95.24 1.19 2.426 16 0.338 43.7 41 1 1 0 JALCMW000000000 SRX12655887 701
UW_MP_BACTE2_2 CSTR 108 0.9999 97 Illumina NovaSeq S4 75.37 0.48 1.551 84 0.0231 44.0 28 0 1 1 JALCMF000000000 SRX12655904 112
UW_MP_BACTE3_1 BACTE3 CSTR 108 120 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__ NA Illumina NovaSeq S4 94.42 1.63 4.26 42 0.1502 40.0 50 0 0 0 JALCME000000000 SRX12655904 627
UW_MP_BACTE3_2 CSTR 97 0.9995 97 Illumina NovaSeq S4 75.56 1.67 2.979 166 0.0182 39.4 35 0 0 0 JALCLT000000000 SRX12655187 297
UW_MP_BACTE4_1 BACTE4 CSTR 120 118 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__UBA1232;s__ NA Illumina NovaSeq S4 95 0.95 2.367 56 0.0637 41.8 39 1 3 1 JALCMP000000000 SRX12655888 208
UW_MP_BACTE5_1 BACTE5 CSTR 36 117 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900316045 GCA_900316045.1 Illumina NovaSeq S4 91.43 0.95 2.926 27 0.192 48.3 40 0 1 1 JALCSF000000000 SRX12654483 7,427
UW_MP_BACTE5_2 CSTR 49 0.9987 100 Illumina NovaSeq S4 77.48 0.95 2.445 66 0.0431 48.3 31 0 2 0 JALCSU000000000 SRX12654484 3,692
UW_MP_BACTE6_1 BACTE6 CSTR 49 117 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__;s__ NA Illumina NovaSeq S4 91.79 0 2.185 23 0.1385 48.4 42 1 2 0 JALCST000000000 SRX12654484 425
UW_MP_BACTE6_2 CSTR 36 0.9999 115 Illumina NovaSeq S4 90.48 0.48 2.089 34 0.0966 48.4 36 1 3 1 JALCSE000000000 SRX12654483 403
UW_MP_BACTE6_3 CSTR 54 0.9999 103 Illumina NovaSeq S4 82.13 0 1.744 92 0.0217 48.8 29 0 1 0 JALCTD000000000 SRX12654502 129
UW_MP_BACTE7_1 BACTE7 CSTR 24   117 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__;s__ NA PacBio Sequel II 91.84 0 1.881 23 0.1506 29.7 34 1 2 1 JAKVOZ000000000 SAMN18243588 1
UW_MP_BACTE8_1 BACTE8 CSTR 12   101 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp000432515 GCA_000432515.1 Illumina NovaSeq S4 80.01 1.9 2.392 109 0.0251 49.2 31 1 2 0 JALCRT000000000 SRX12654482 346
UW_MP_BIF1_1 BIF1 CSTR 49 130 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium breve GCF_001025175.1 Illumina NovaSeq S4 100 0 2.182 4 1.1285 58.8 53 2 0 0 JALCSS000000000 SRX12654484 731
UW_MP_BIF1_2 CSTR 54 1.0000 127 Illumina NovaSeq S4 99.92 0 2.179 10 0.3004 58.8 53 2 1 0 JALCTC000000000 SRX12654502 370
UW_MP_BIF2_1 BIF2 USB 42 130 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium tibiigranuli GCF_009371885.1 PacBio Sequel II 99.12 4.36 3.1 3 3.0762 60.6 50 2 2 2 JAKVOD000000000 SAMN18243454 27
UW_MP_BIF2_2 USB 56 0.9999 122 Illumina NovaSeq S4 97.39 3.14 2.673 16 0.2331 60.5 45 2 2 2 JAKVKB000000000 SRX12656290 27,953
UW_MP_BIF2_3 USB 77 0.9999 122 Illumina NovaSeq S4 97.39 3.14 2.654 19 0.2026 60.5 45 0 0 0 JAKVIV000000000 SRX12656338 16,783
UW_MP_BIF2_4 USB 105 0.9883 120 Illumina NovaSeq S4 95.12 3.37 2.656 24 0.1768 60.5 42 0 0 0 JALCCO000000000 SRX12656339 19,505
UW_MP_BIF2_5 USB 126 0.9893 118 Illumina NovaSeq S4 95.74 3.83 2.535 57 0.0713 60.6 40 0 0 0 JALCCS000000000 SRX12656446 25,167
UW_MP_BIF2_6 CSTR 146 0.9952 117 Illumina NovaSeq S4 91.94 1.48 2.326 35 0.1149 60.6 39 0 0 0 JALCNI000000000 SRX12655903 11,592
UW_MP_BIF2_7 CSTR 126 0.9918 112 Illumina NovaSeq S4 88.7 2.39 2.316 48 0.0776 60.7 37 0 0 0 JALCMV000000000 SRX12655887 2,983
UW_MP_BIF2_8 USB 28 0.9992 103 Illumina NovaSeq S4 80.75 4.28 2.398 47 0.074 60.5 42 0 0 0 JAKVKM000000000 SRX12656283 3,617
UW_MP_BIF2_9 USB 176 0.9929 103 Illumina NovaSeq S4 78.95 1.7 1.894 40 0.0758 60.7 32 0 0 0 JALCDG000000000 SRX12657171 26,915
UW_MP_BIF2_10 USB 148 0.9934 100 Illumina NovaSeq S4 77.81 2.31 1.878 55 0.048 61.1 28 0 0 0 JALCCZ000000000 SRX12657082 34,329
UW_MP_BIF3_1 BIF3 USB 197   129 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__ NA PacBio Sequel II 98.86 0.91 2.342 1 2.3423 48.8 46 2 2 2 JALCLM000000000 SRX12729151 9
UW_MP_BIF4_1 BIF4 CSTR 192   127 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium crudilactis GCF_000738005.1 Illumina NovaSeq S4 98.32 1.82 2.253 3 1.3824 57.8 48 0 1 0 JALCOB000000000 SRX12655976 670
UW_MP_BIF5_1 BIF5 CSTR 72 124 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium crudilactis GCF_000738005.1 Illumina NovaSeq S4 99.23 1.93 2.313 25 0.1431 57.5 50 2 2 2 JALCTS000000000 SRX12655142 1,206
UW_MP_BIF5_2 CSTR 66 1.0000 117 Illumina NovaSeq S4 93.11 1.44 2.062 49 0.0643 57.5 42 0 0 0 JALCTM000000000 SRX12654503 666
UW_MP_BIF6_1 BIF6 CSTR 78 124 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium psychraerophilum GCF_000741705.1 Illumina NovaSeq S4 98.41 1.97 2.494 22 0.218 59.2 46 0 0 0 JALCUB000000000 SRX12655143 1,025
UW_MP_BIF6_2 CSTR 84 0.9998 122 Illumina NovaSeq S4 97.05 2.73 2.466 34 0.1047 59.1 46 0 0 0 JALCUN000000000 SRX12655158 283
UW_MP_BIF6_3 CSTR 146 0.9999 120 Illumina NovaSeq S4 96.44 1.67 2.401 44 0.0765 59.1 44 0 0 0 JALCNH000000000 SRX12655903 220
UW_MP_BIF6_4 CSTR 108 1.0000 105 Illumina NovaSeq S4 82.86 0.67 2.142 73 0.034 59.0 42 0 0 0 JALCMC000000000 SRX12655904 487
UW_MP_BIF7_1 BIF7 USB 126   124 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium crudilactis GCF_000738005.1 Illumina NovaSeq S4 99.17 1.67 2.32 16 0.2279 57.7 45 0 0 0 JALCCR000000000 SRX12656446 3,089
UW_MP_BIF8_1 BIF8 CSTR 168 123 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__ NA Illumina NovaSeq S4 98.57 2.2 2.367 33 0.0991 61.8 44 0 0 0 JALCNP000000000 SRX12655961 422
UW_MP_BIF8_2 CSTR 192 0.9994 115 Illumina NovaSeq S4 92.02 1.29 1.991 61 0.0429 62.4 38 1 0 1 JALCOA000000000 SRX12655976 2,179
UW_MP_BIF9_1 BIF9 CSTR 84 123 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium tibiigranuli GCF_009371885.1 Illumina NovaSeq S4 94.82 2.58 2.669 10 0.7116 60.6 46 0 0 0 JALCUM000000000 SRX12655158 1,485
UW_MP_BIF9_2 CSTR 78 1.0000 122 Illumina NovaSeq S4 95.73 2.5 2.555 22 0.2925 60.8 45 0 0 0 JALCUA000000000 SRX12655143 1,512
UW_MP_BIF9_3 CSTR 97 0.9998 107 Illumina NovaSeq S4 84.22 2.5 2.23 61 0.0601 60.7 37 0 0 0 JALCLR000000000 SRX12655187 1,353
UW_MP_BIF10_1 BIF10 USB 197   122 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium crudilactis GCF_000738005.1 PacBio Sequel II 92.41 1.21 2.062 1 2.0624 57.7 42 0 0 0 JALCLO000000000 SRX12729151 34
UW_MP_BIF11_1 BIF11 CSTR 120 121 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium tibiigranuli GCF_009371885.1 Illumina NovaSeq S4 94.88 2.88 2.706 17 0.3076 60.6 42 0 0 0 JALCMO000000000 SRX12655888 13,270
UW_MP_BIF11_2 CSTR 108 0.9996 118 Illumina NovaSeq S4 93.19 2.88 2.543 26 0.1275 60.5 41 0 0 0 JALCMD000000000 SRX12655904 6,115
UW_MP_BIF11_3 CSTR 168 0.9957 102 Illumina NovaSeq S4 79.42 2.12 2.297 55 0.0569 60.4 42 0 0 0 JALCNQ000000000 SRX12655961 12,520
UW_MP_BIF12_1 BIF12 USB 126 118 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__ NA Illumina NovaSeq S4 94.72 2.27 2.15 53 0.0569 60.7 41 2 0 0 JALCCV000000000 SRX12656446 327
UW_MP_BIF12_2 USB 56 0.9999 117 Illumina NovaSeq S4 92.34 2.12 2.131 34 0.141 60.7 46 1 1 1 JAKVKA000000000 SRX12656290 337
UW_MP_BIF13_1 BIF13 USB 21 114 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__ NA Illumina NovaSeq S4 88.64 1.36 2.037 24 0.1459 48.6 41 0 0 0 JAKVKQ000000000 SRX12655989 976
UW_MP_BIF13_2 USB 15 1.0000 110 Illumina NovaSeq S4 85.71 1.36 1.999 25 0.1141 48.6 38 0 0 0 JAKVKV000000000 SRX12655988 992
UW_MP_BIF14_1 BIF14 USB 148 112 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium subtile GCF_000741775.1 Illumina NovaSeq S4 89.48 3.03 2.186 50 0.0601 61.2 39 0 1 0 JALCDA000000000 SRX12657082 2,259
UW_MP_BIF14_2 USB 126 0.9975 106 Illumina NovaSeq S4 83.66 1.06 2.076 70 0.0367 61.3 33 0 0 0 JALCCU000000000 SRX12656446 2,424
UW_MP_BIF14_3 USB 176 0.9995 100 Illumina NovaSeq S4 77.67 1.36 1.81 54 0.0516 61.2 36 0 1 0 JALCDH000000000 SRX12657171 975
UW_MP_BIF15_1 BIF15 USB 197   111 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium crudilactis GCF_000738005.1 PacBio Sequel II 84.03 0.98 1.751 5 0.4795 57.6 39 0 0 0 JALCLN000000000 SRX12729151 9
UW_MP_BIF16_1 BIF16 CSTR 97   111 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium crudilactis GCF_000738005.1 Illumina NovaSeq S4 90.81 2.23 1.957 84 0.0266 57.9 43 1 0 1 JALCLS000000000 SRX12655187 322
UW_MP_BIF17_1 BIF17 USB 15   111 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium minimum GCF_000741645.1 Illumina NovaSeq S4 89.08 0.66 1.488 68 0.0271 63.2 38 0 0 0 JAKVKW000000000 SRX12655988 243
UW_MP_BIF18_1 BIF18 CSTR 78   109 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium thermophilum GCF_000771265.1 Illumina NovaSeq S4 87.44 0.95 1.802 63 0.0375 60.5 32 1 0 1 JALCUC000000000 SRX12655143 9,522
UW_MP_BIF19_1 BIF19 USB 126   105 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__ NA Illumina NovaSeq S4 81.29 1.21 1.761 22 0.1391 58.8 40 0 1 0 JALCCT000000000 SRX12656446 509
UW_MP_BUL1_1 BUL1 USB 56 120 d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ NA Illumina NovaSeq S4 96.05 0.79 2.075 40 0.0737 45.2 38 1 1 1 JAKVKC000000000 SRX12656290 4,421
UW_MP_BUL1_2 USB 77 1.0000 118 Illumina NovaSeq S4 94.15 0.79 2.163 40 0.0737 44.9 41 0 0 0 JAKVIW000000000 SRX12656338 3,071
UW_MP_BUL1_3 USB 63 1.0000 116 Illumina NovaSeq S4 92.24 0.32 2.041 36 0.0751 45.2 41 0 0 0 JAKVJN000000000 SRX12656289 4,322
UW_MP_BUL1_4 USB 42 0.9990 106 PacBio Sequel II 78.01 0.79 2.313 7 0.4212 44.9 42 1 1 1 JAKVOE000000000 SAMN18243454 8
UW_MP_BUL2_1 BUL2 CSTR 66   116 d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__Bulleidia massiliensis_B GCF_900290205.1 Illumina NovaSeq S4 94.29 0.32 2.418 54 0.0627 50.1 43 0 0 0 JALCTL000000000 SRX12654503 3,619
UW_MP_BUL3_1 BUL3 USB 56 103 d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__ NA Illumina NovaSeq S4 81.19 1.27 1.989 85 0.0305 48.8 35 1 0 0 JAKVKD000000000 SRX12656290 207
UW_MP_BUL3_2 USB 63 0.9998 100 Illumina NovaSeq S4 77.78 0.32 1.731 80 0.0275 49.1 31 0 0 0 JAKVJO000000000 SRX12656289 146
UW_MP_BUL3_3 USB 77 0.9997 99 Illumina NovaSeq S4 77.14 0.32 1.882 82 0.0273 49.0 30 1 0 0 JAKVIX000000000 SRX12656338 161
UW_MP_BURK1_1 BURK1 USB 77 123 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kerstersia;s__Kerstersia gyiorum GCF_004216755.1 Illumina NovaSeq S4 98.33 0 3.756 67 0.0811 62.6 49 1 1 1 JAKVIY000000000 SRX12656338 373
UW_MP_BURK1_2 USB 105 0.9998 121 Illumina NovaSeq S4 96.68 0.54 3.569 73 0.0612 62.6 43 0 0 0 JALCCN000000000 SRX12656339 444
UW_MP_BURK2_1 BURK2 CSTR 146   120 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter;s__Achromobacter ruhlandii GCF_902859695.1 Illumina NovaSeq S4 97.25 0.23 5.869 141 0.058 67.9 52 2 1 1 JALCNG000000000 SRX12655903 588
UW_MP_BURK3_1 BURK3 CSTR 108   116 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mesosutterella;s__Mesosutterella multiformis GCF_003402575.1 Illumina NovaSeq S4 93.33 0 1.739 42 0.0581 57.9 45 2 1 0 JALCMB000000000 SRX12655904 930
UW_MP_BURK4_1 BURK4 USB 63   101 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes;s__Alcaligenes aquatilis GCF_003076515.1 Illumina NovaSeq S4 79.99 0.18 3.138 131 0.0268 56.1 40 0 0 0 JAKVJP000000000 SRX12656289 1,134
UW_MP_CARN1_1 CARN1 CSTR 168   116 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium;s__Carnobacterium maltaromaticum GCF_000744945.1 Illumina NovaSeq S4 95.63 7.19 3.399 79 0.0624 34.4 35 4 0 0 JALCNO000000000 SRX12655961 272
UW_MP_CAUL1_1 CAUL1 USB 77   127 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas;s__Brevundimonas sp002386585 GCA_002386585.1 Illumina NovaSeq S4 100 0.39 3.598 15 0.4877 67.4 49 1 1 1 JAKVIZ000000000 SRX12656338 736
UW_MP_CLOS1_1 CLOS1 CSTR 216 132 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B;s__ NA PacBio Sequel II 99.83 0 3.567 1 3.5672 35.0 66 7 6 6 JAKVOI000000000 SAMN18243112 10
UW_MP_CLOS1_2 CSTR 126 1.0000 127 Illumina NovaSeq S4 99.83 0 3.434 23 0.3067 34.9 61 4 3 0 JALCMU000000000 SRX12655887 34,895
UW_MP_CLOS1_3 CSTR 120 1.0000 127 Illumina NovaSeq S4 99.83 0 3.385 23 0.2571 34.9 61 4 3 0 JALCMN000000000 SRX12655888 29,082
UW_MP_CLOS1_4 CSTR 146 1.0000 127 Illumina NovaSeq S4 99.83 0 3.381 22 0.2535 34.9 61 4 3 0 JALCNF000000000 SRX12655903 36,752
UW_MP_CLOS1_5 CSTR 192 1.0000 127 Illumina NovaSeq S4 99.83 0 3.39 23 0.2535 34.9 61 4 2 0 JALCNZ000000000 SRX12655976 33,252
UW_MP_CLOS1_6 CSTR 84 1.0000 122 Illumina NovaSeq S4 98.91 0 3.34 87 0.0504 35.0 58 4 3 0 JALCUL000000000 SRX12655158 309
UW_MP_CLOS2_1 CLOS2 USB 197 132 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B;s__Clostridium_B tyrobutyricum GCF_000359585.1 PacBio Sequel II 99.49 0.23 3.062 1 3.0624 31.0 63 7 6 6 JALCLL000000000 SRX12729151 18
UW_MP_CLOS2_2 USB 77 0.9999 123 Illumina NovaSeq S4 98.11 0.36 3.17 49 0.1032 30.5 59 3 1 0 JAKVJA000000000 SRX12656338 1,461
UW_MP_CLOS2_3 USB 56 0.9998 117 Illumina NovaSeq S4 93.6 0.27 3.01 109 0.0384 30.6 52 3 1 0 JAKVKE000000000 SRX12656290 415
UW_MP_CLOS2_4 USB 63 0.9995 106 Illumina NovaSeq S4 84.24 0.33 2.377 119 0.0242 31.0 43 3 1 0 JAKVJQ000000000 SRX12656289 193
UW_MP_CLOS2_5 USB 148 1.0000 105 Illumina NovaSeq S4 79.59 0.23 2.664 32 0.152 31.0 32 0 0 0 JALCCY000000000 SRX12657082 713
UW_MP_EGG1_1 EGG1 USB 63 113 d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA5808;s__UBA5808 sp002417975 GCA_002417975.1 Illumina NovaSeq S4 89.85 0.81 1.734 62 0.0349 46.5 41 0 0 0 JAKVJR000000000 SRX12656289 193
UW_MP_EGG1_2 USB 56 0.9997 102 Illumina NovaSeq S4 79.61 0.27 1.656 58 0.0307 46.6 37 0 0 0 JAKVKF000000000 SRX12656290 330
UW_MP_ENTER1_1 ENTER1 CSTR 168 127 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella;s__Ewingella americana GCF_000735345.1 Illumina NovaSeq S4 97.7 0.25 4.882 10 0.7672 53.9 65 3 0 1 JALCNN000000000 SRX12655961 3,203
UW_MP_ENTER1_2 CSTR 192 1.0000 126 Illumina NovaSeq S4 98.36 0.25 4.911 17 0.4431 53.9 66 3 0 1 JALCNY000000000 SRX12655976 1,154
UW_MP_ENTER1_3 CSTR 84 1.0000 126 Illumina NovaSeq S4 98.54 0.27 4.929 24 0.3563 53.8 64 3 1 0 JALCUK000000000 SRX12655158 712
UW_MP_ENTER1_4 CSTR 97 1.0000 126 Illumina NovaSeq S4 97.7 0.25 4.853 14 0.5036 53.9 65 3 0 0 JALCLQ000000000 SRX12655187 1,440
UW_MP_ENTER1_5 CSTR 72 1.0000 122 Illumina NovaSeq S4 97.14 0.41 4.791 59 0.1111 53.9 65 3 0 0 JALCTR000000000 SRX12655142 571
UW_MP_ENTER1_6 CSTR 66 0.9999 119 Illumina NovaSeq S4 93.57 1.18 4.507 42 0.1385 54.0 56 5 0 0 JALCTK000000000 SRX12654503 540
UW_MP_ENTER2_1 ENTER2 USB 148 126 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia;s__Serratia liquefaciens GCF_000422085.1 Illumina NovaSeq S4 98.21 0.56 5.147 22 0.479 55.5 75 2 0 0 JALCCX000000000 SRX12657082 1,977
UW_MP_ENTER2_2 CSTR 168 1.0000 126 Illumina NovaSeq S4 98.76 0.45 5.136 26 0.3624 55.5 74 3 0 0 JALCNM000000000 SRX12655961 947
UW_MP_ENTER2_3 USB 126 1.0000 126 Illumina NovaSeq S4 98.21 0.56 5.15 20 0.4788 55.5 74 2 0 0 JALCCQ000000000 SRX12656446 3,786
UW_MP_ENTER2_4 USB 105 1.0000 126 Illumina NovaSeq S4 98.21 0.56 5.151 21 0.3835 55.5 75 2 0 0 JALCCM000000000 SRX12656339 1,995
UW_MP_ENTER2_5 CSTR 0 1.0000 125 Illumina NovaSeq S4 98.21 0.45 5.139 29 0.2433 55.5 74 3 0 0 JALCRN000000000 SRX12654481 886
UW_MP_ENTER2_6 USB 77 1.0000 123 Illumina NovaSeq S4 96.8 1 5.032 37 0.2053 55.6 73 3 1 0 JAKVJB000000000 SRX12656338 619
UW_MP_ENTER2_7 USB 56 1.0000 123 Illumina NovaSeq S4 97.67 0.62 5.06 62 0.1217 55.6 72 2 0 0 JAKVKG000000000 SRX12656290 513
UW_MP_ENTER2_8 CSTR 146 1.0000 122 Illumina NovaSeq S4 94.64 0.45 5.068 17 0.4056 55.5 71 2 0 0 JALCNE000000000 SRX12655903 4,113
UW_MP_ENTER2_9 CSTR 192 1.0000 118 Illumina NovaSeq S4 95.04 1.49 4.95 106 0.0672 55.6 73 3 1 0 JALCNX000000000 SRX12655976 517
UW_MP_ENTER2_10 USB 63 1.0000 115 Illumina NovaSeq S4 91.75 1.34 4.824 127 0.0527 55.7 68 4 0 0 JAKVJS000000000 SRX12656289 393
UW_MP_ENTER2_11 CSTR 12 1.0000 113 Illumina NovaSeq S4 90.54 0.51 4.755 155 0.0372 55.7 66 3 0 0 JALCRS000000000 SRX12654482 422
UW_MP_ENTER3_1 ENTER3 USB 77   125 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus;s__Proteus vulgaris GCF_901472505.1 Illumina NovaSeq S4 99.46 0 3.912 30 0.2166 37.8 74 2 0 0 JAKVJC000000000 SRX12656338 913
UW_MP_ENTER4_1 ENTER4 CSTR 108 125 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter;s__Citrobacter braakii GCF_002075345.1 Illumina NovaSeq S4 98.4 0.71 4.924 34 0.2174 52.1 74 2 0 0 JALCMA000000000 SRX12655904 8,904
UW_MP_ENTER4_2 CSTR 146 1.0000 125 Illumina NovaSeq S4 98.63 0.75 4.96 43 0.18 52.1 74 2 0 0 JALCND000000000 SRX12655903 3,163
UW_MP_ENTER5_1 ENTER5 CSTR 192 117 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia;s__ NA Illumina NovaSeq S4 94.44 1.07 4.58 116 0.0513 52.8 72 4 0 0 JALCNW000000000 SRX12655976 587
UW_MP_LAC1_1 LAC1 USB 63 119 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus delbrueckii GCF_001433875.1 Illumina NovaSeq S4 96.43 0 1.8 62 0.037 50.2 46 4 0 1 JAKVJT000000000 SRX12656289 229
UW_MP_LAC1_2 USB 77 0.9998 116 Illumina NovaSeq S4 92.53 0 1.657 50 0.0451 50.4 51 4 0 1 JAKVJD000000000 SRX12656338 350
UW_MP_LAC1_3 USB 98 0.9997 110 PacBio Sequel II 80.84 0 1.681 2 0.866 49.9 77 7 8 7 JAKVNX000000000 SAMN18243097 1
UW_MP_LAC2_1 LAC2 CSTR 108 113 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus delbrueckii GCF_001433875.1 Illumina NovaSeq S4 90.15 0.22 1.512 49 0.0383 50.8 34 1 0 0 JALCLZ000000000 SRX12655904 207
UW_MP_LAC2_2 CSTR 120 0.9999 113 Illumina NovaSeq S4 90.15 0.22 1.62 57 0.0347 50.7 51 2 1 0 JALCMM000000000 SRX12655888 208
UW_MP_LAC2_3 CSTR 146 0.9999 111 Illumina NovaSeq S4 88.2 0.22 1.58 50 0.0389 50.5 55 3 0 0 JALCNC000000000 SRX12655903 413
UW_MP_LAC3_1 LAC3 USB 148 106 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus delbrueckii GCF_001433875.1 Illumina NovaSeq S4 83.77 0.09 1.338 41 0.0473 50.7 51 4 0 0 JALCCW000000000 SRX12657082 430
UW_MP_LCO1_1 LCO1 CSTR 44 130 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis GCF_000020605.1 PacBio Sequel II 99.3 0.24 3.246 4 1.6305 41.9 58 5 5 5 JAKVOQ000000000 SAMN18243037 3
UW_MP_LCO1_2 CSTR 36 0.9997 111 Illumina NovaSeq S4 85.99 0 2.152 31 0.1489 41.8 53 0 1 3 JALCSD000000000 SRX12654483 3,051
UW_MP_LCO1_3 CSTR 49 0.9996 110 Illumina NovaSeq S4 87.99 1.21 2.129 92 0.028 42.2 51 0 1 3 JALCSR000000000 SRX12654484 183
UW_MP_LCO2_1 LCO2 CSTR 108 123 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I;s__Eubacterium_I sp000270305 GCF_000270305.1 Illumina NovaSeq S4 97.99 1.15 2.509 32 0.1097 51.1 43 0 0 0 JALCLY000000000 SRX12655904 564
UW_MP_LCO2_2 CSTR 97 1.0000 122 Illumina NovaSeq S4 97.41 1.15 2.476 27 0.1253 51.2 43 0 0 0 JALCLP000000000 SRX12655187 1,796
UW_MP_LCO2_3 CSTR 84 1.0000 115 Illumina NovaSeq S4 89.94 1.15 2.304 22 0.1545 50.9 43 0 0 0 JALCUJ000000000 SRX12655158 1,513
UW_MP_LCO3_1 LCO3 USB 56   116 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio;s__ NA Illumina NovaSeq S4 94.33 3.01 3.574 60 0.0732 45.1 39 0 0 1 JAKVKH000000000 SRX12656290 427
UW_MP_LCO4_1 LCO4 CSTR 66   114 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_H;s__Eubacterium_H sp003488475 GCA_003488475.1 Illumina NovaSeq S4 89.17 0.64 1.907 25 0.1356 50.5 46 0 0 1 JALCTJ000000000 SRX12654503 460
UW_MP_LCO5_1 LCO5 CSTR 0   109 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791;s__ NA Illumina NovaSeq S4 84.34 0 2.67 27 0.1657 55.0 30 0 0 0 JALCRM000000000 SRX12654481 905
UW_MP_LENLAC1_1 LENLAC1 USB 15   112 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus;s__Lentilactobacillus diolivorans GCF_001434255.1 Illumina NovaSeq S4 92.81 3.07 3.131 149 0.0245 40.0 33 3 1 0 JAKVKX000000000 SRX12655988 389
UW_MP_LEUC1_1 LEUC1 CSTR 60 131 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc;s__Leuconostoc mesenteroides GCF_000014445.1 PacBio Sequel II 99.74 0 1.856 1 1.856 37.9 71 4 4 4 JAKVOL000000000 SAMN18243139 2
UW_MP_LEUC1_2 CSTR 54 0.9987 123 Illumina NovaSeq S4 98.24 0.53 1.643 39 0.0796 37.8 36 1 0 0 JALCTB000000000 SRX12654502 1,187
UW_MP_LEUC1_3 CSTR 78 0.9933 123 Illumina NovaSeq S4 98.94 0.53 1.863 35 0.0736 37.7 53 0 0 0 JALCTZ000000000 SRX12655143 314
UW_MP_LEUC1_4 CSTR 49 0.9990 115 Illumina NovaSeq S4 89.95 0 1.426 22 0.103 37.9 37 1 0 0 JALCSQ000000000 SRX12654484 988
UW_MP_LEUC1_5 CSTR 72 0.9933 111 Illumina NovaSeq S4 88.29 1.06 1.668 65 0.0316 37.6 35 0 0 0 JALCTQ000000000 SRX12655142 244
UW_MP_LEUC1_6 CSTR 120 0.9970 109 Illumina NovaSeq S4 86.45 1.3 1.496 79 0.0233 37.9 39 0 0 0 JALCML000000000 SRX12655888 134
UW_MP_LEUC1_7 CSTR 44 0.9983 104 PacBio Sequel II 79.39 0 1.571 28 0.0738 37.8 47 1 1 1 JAKVOR000000000 SAMN18243037 1
UW_MP_LIQLAC1_1 LIQLAC1 USB 197 129 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus;s__Liquorilactobacillus nagelii GCF_001434225.1 PacBio Sequel II 98.95 1.31 2.447 1 2.4466 36.9 57 6 6 6 JALCLK000000000 SRX12729151 4
UW_MP_LIQLAC2_1 LIQLAC2 CSTR 120 119 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus;s__Liquorilactobacillus nagelii GCF_001434225.1 Illumina NovaSeq S4 95.29 0 2.032 32 0.0932 36.9 51 3 1 0 JALCMK000000000 SRX12655888 1,105
UW_MP_MEG1_1 MEG1 USB 56 115 d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera;s__ NA Illumina NovaSeq S4 92.22 0.6 1.903 47 0.0574 45.7 43 2 0 0 JAKVKI000000000 SRX12656290 7,120
UW_MP_MEG1_2 USB 63 0.9993 112 Illumina NovaSeq S4 88.62 0.6 1.91 48 0.0736 45.6 45 2 0 0 JAKVJU000000000 SRX12656289 6,875
UW_MP_MEG1_3 USB 21 0.9994 106 Illumina NovaSeq S4 82.53 0 1.754 49 0.0527 45.4 34 3 0 0 JAKVKR000000000 SRX12655989 1,008
UW_MP_MEG2_1 MEG2 CSTR 168 111 d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera_A;s__ GCF_900103535.1 Illumina NovaSeq S4 89.24 1.4 2.097 97 0.0283 39.8 45 1 0 0 JALCNL000000000 SRX12655961 252
UW_MP_MEG2_2 CSTR 146 0.9995 107 Illumina NovaSeq S4 84.43 0.9 1.792 88 0.0272 40.0 38 0 0 0 JALCNB000000000 SRX12655903 144
UW_MP_MEG3_1 MEG3 USB 176 107 d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera;s__ NA Illumina NovaSeq S4 84.28 0.6 1.687 73 0.0311 46.9 45 1 0 0 JALCDF000000000 SRX12657171 221
UW_MP_MEG3_2 USB 28 0.9989 106 Illumina NovaSeq S4 83.71 0.6 1.669 66 0.0366 46.9 41 1 0 0 JAKVKN000000000 SRX12656283 1,028
UW_MP_MEG4_1 MEG4 USB 28   105 d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera;s__Megasphaera sp000417505 GCF_000417505.1 Illumina NovaSeq S4 84.22 0 1.63 64 0.0352 55.2 50 3 0 0 JAKVKO000000000 SRX12656283 4,503
UW_MP_MEG5_1 MEG5 USB 197   103 d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera;s__Megasphaera cerevisiae GCF_001045675.1 PacBio Sequel II 76.05 1.87 1.705 7 0.3397 44.5 29 3 3 3 JALCLJ000000000 SRX12729151 17
UW_MP_METH1_1 METH1 CSTR 49 126 d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__Methanomethylophilus;s__Methanomethylophilus sp001481295 GCF_001481295.1 Illumina NovaSeq S4 98.39 0.81 1.744 9 0.3894 60.5 46 2 1 1 JALCSP000000000 SRX12654484 219
UW_MP_METH1_2 CSTR 36 1.0000 124 Illumina NovaSeq S4 97.58 0.81 1.696 9 0.2547 60.5 46 2 1 1 JALCSC000000000 SRX12654483 247
UW_MP_METH1_3 CSTR 44 0.9998 122 PacBio Sequel II 95.97 2.42 1.51 20 0.1119 60.7 41 1 1 1 JAKVOS000000000 SAMN18243037 1
UW_MP_MIC1_1 MIC1 USB 105 105 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__;s__ NA Illumina NovaSeq S4 83.82 0.58 1.208 53 0.0324 66.2 36 0 0 0 JALCCL000000000 SRX12656339 106
UW_MP_MIC1_2 USB 77 0.9993 103 Illumina NovaSeq S4 81.98 0 1.286 65 0.0223 66.2 38 1 0 1 JAKVJE000000000 SRX12656338 97
UW_MP_MORAX1_1 MORAX1 USB 77 121 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter;s__Acinetobacter populi GCF_002174125.1 Illumina NovaSeq S4 97.48 0 3.317 62 0.0823 40.3 55 5 0 0 JAKVJF000000000 SRX12656338 361
UW_MP_MORAX2_1 MORAX2 USB 77   109 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter;s__Acinetobacter gerneri GCF_000368565.1 Illumina NovaSeq S4 84.98 0.86 4.041 48 0.1192 37.6 68 1 0 0 JAKVJG000000000 SRX12656338 670
UW_MP_MUR1_1 MUR1 USB 0   108 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__ NA Illumina NovaSeq S4 85.97 0.57 2.948 93 0.0394 44.6 40 0 2 0 JAKVKZ000000000 SRX12655975 301
UW_MP_MYC1_1 MYC1 USB 176   122 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium;s__Corynebacterium provencense GCF_900049755.1 Illumina NovaSeq S4 96.62 1.91 2.996 29 0.2017 67.1 57 3 0 0 JALCDE000000000 SRX12657171 633
UW_MP_OSCL1_1 OSCL1 CSTR 12   119 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Oscillibacter;s__ NA Illumina NovaSeq S4 96.98 1.34 2.253 69 0.0428 55.4 43 2 0 0 JALCRR000000000 SRX12654482 213
UW_MP_OSCL2_1 OSCL2 CSTR 12 114 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Oscillibacter;s__ NA Illumina NovaSeq S4 93.74 3.02 1.796 63 0.0293 61.7 30 1 0 1 JALCRQ000000000 SRX12654482 183
UW_MP_OSCL3_1 OSCL3 CSTR 36 114 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas;s__ NA Illumina NovaSeq S4 89.09 0.34 2.054 28 0.1131 53.8 38 2 0 0 JALCSB000000000 SRX12654483 1,146
UW_MP_PREV1_1 PREV1 USB 98 128 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__ NA PacBio Sequel II 97.64 2.11 3.412 1 3.412 43.8 54 4 4 4 JAKVNY000000000 SAMN18243097 3
UW_MP_PREV2_1 PREV2 USB 42 125 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002409785 GCA_002409785.1 PacBio Sequel II 97.94 1.86 3.131 13 0.3543 44.5 54 4 4 4 JAKVOF000000000 SAMN18243454 7
UW_MP_PREV2_2 CSTR 120 0.9929 121 Illumina NovaSeq S4 97.64 1.6 2.978 54 0.0875 44.2 45 0 1 0 JALCMJ000000000 SRX12655888 699
UW_MP_PREV2_3 CSTR 54 0.9918 121 Illumina NovaSeq S4 97.64 2.11 3.056 49 0.0759 44.2 45 1 0 0 JALCTA000000000 SRX12654502 1,437
UW_MP_PREV2_4 CSTR 49 0.9917 119 Illumina NovaSeq S4 95.61 2.03 3.027 59 0.0706 44.1 39 1 0 0 JALCSO000000000 SRX12654484 455
UW_MP_PREV2_5 CSTR 66 0.9949 117 Illumina NovaSeq S4 94.09 0.68 2.507 63 0.0545 44.9 45 1 0 0 JALCTI000000000 SRX12654503 2,330
UW_MP_PREV2_6 USB 77 0.9980 116 Illumina NovaSeq S4 94.02 1.18 2.298 94 0.0295 45.2 40 0 0 0 JAKVJH000000000 SRX12656338 5,405
UW_MP_PREV2_7 USB 63 0.9980 113 Illumina NovaSeq S4 91.22 1.35 2.266 91 0.0295 45.0 33 0 0 0 JAKVJV000000000 SRX12656289 9,265
UW_MP_PREV2_8 CSTR 192 0.9942 112 Illumina NovaSeq S4 90.26 1.18 2.544 105 0.0299 44.7 43 1 0 0 JALCNV000000000 SRX12655976 1,069
UW_MP_PREV2_9 USB 56 0.9980 111 Illumina NovaSeq S4 89.3 1.69 2.298 90 0.0338 45.3 40 0 0 0 JAKVKJ000000000 SRX12656290 4,804
UW_MP_PREV2_10 CSTR 168 0.9935 111 Illumina NovaSeq S4 89.5 1.53 2.566 114 0.0271 44.4 38 1 0 0 JALCNK000000000 SRX12655961 275
UW_MP_PREV2_11 CSTR 72 0.9943 111 Illumina NovaSeq S4 87.92 0.34 2.374 93 0.0358 44.9 43 1 0 0 JALCTP000000000 SRX12655142 1,346
UW_MP_PREV2_12 CSTR 126 0.9939 110 Illumina NovaSeq S4 86.71 1.1 2.521 63 0.0507 44.4 37 0 0 0 JALCMT000000000 SRX12655887 333
UW_MP_PREV2_13 CSTR 84 0.9952 109 Illumina NovaSeq S4 87.09 1.76 2.21 114 0.0242 45.0 37 0 0 0 JALCUI000000000 SRX12655158 1,338
UW_MP_PREV2_14 CSTR 78 0.9964 108 Illumina NovaSeq S4 85.57 0.68 2.115 92 0.0287 45.2 41 0 0 0 JALCTY000000000 SRX12655143 1,522
UW_MP_PREV2_15 CSTR 146 0.9930 106 Illumina NovaSeq S4 84.82 2.14 2.501 128 0.0234 44.4 41 0 0 0 JALCNA000000000 SRX12655903 539
UW_MP_PREV3_1 PREV3 CSTR 44 124 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900316015 GCA_900316015.1 PacBio Sequel II 94.29 1.07 3.459 6 0.9289 46.9 48 4 4 4 JAKVOT000000000 SAMN18243037 2
UW_MP_PREV3_2 CSTR 49 0.9997 117 Illumina NovaSeq S4 95 0.71 2.917 85 0.0392 47.0 41 0 0 0 JALCSN000000000 SRX12654484 792
UW_MP_PREV3_3 CSTR 36 0.9996 117 Illumina NovaSeq S4 94.29 0.71 2.84 83 0.0393 47.0 37 0 0 0 JALCSA000000000 SRX12654483 611
UW_MP_PREV4_1 PREV4 USB 63 113 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__ NA Illumina NovaSeq S4 89.67 1.01 2.933 73 0.0684 40.2 45 1 1 1 JAKVJW000000000 SRX12656289 514
UW_MP_PREV4_2 USB 56 0.9995 113 Illumina NovaSeq S4 89.86 2.36 2.945 99 0.0482 40.2 48 2 1 0 JAKVKK000000000 SRX12656290 280
UW_MP_PREV4_3 USB 77 0.9991 110 Illumina NovaSeq S4 84.97 1.77 2.998 69 0.0938 40.2 45 0 1 0 JAKVJI000000000 SRX12656338 714
UW_MP_PREV5_1 PREV5 USB 0 110 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__ NA Illumina NovaSeq S4 84.68 0.66 2.611 37 0.1869 43.7 40 2 0 0 JAKVLA000000000 SRX12655975 1,748
UW_MP_PREV6_1 PREV6 USB 98 107 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002409785 GCA_002409785.1 PacBio Sequel II 82.21 1.71 2.42 24 0.1166 44.7 48 3 3 3 JAKVNZ000000000 SAMN18243097 2
UW_MP_PREV7_1 PREV7 USB 197 106 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__ NA PacBio Sequel II 77.7 4.48 2.524 15 0.32 40.5 51 4 4 4 JALCLI000000000 SRX12729151 17
UW_MP_PREV8_1 PREV8 USB 176 101 d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__ NA Illumina NovaSeq S4 80.41 2.45 1.952 82 0.0302 44.8 43 0 0 0 JALCDD000000000 SRX12657171 1,995
UW_MP_PROP1_1 PROP1 USB 197 117 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium;s__ NA PacBio Sequel II 91.48 1.32 3.682 26 0.2395 67.8 55 1 1 1 JALCLH000000000 SRX12729151 7
UW_MP_RUM1_1 RUM1 CSTR 12 118 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__ NA Illumina NovaSeq S4 93.88 0 2.218 35 0.1048 56.5 46 1 1 0 JALCRP000000000 SRX12654482 535
UW_MP_SACCH1_1 SACCH1 USB 0 126 d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans;s__ NA Illumina NovaSeq S4 99.65 0 1.923 12 0.2265 46.7 42 2 0 1 JAKVLB000000000 SRX12655975 432
UW_MP_SACCH1_2 CSTR 0 0.9997 111 Illumina NovaSeq S4 86.88 0 1.394 21 0.078 46.2 37 1 1 0 JALCRL000000000 SRX12654481 269
UW_MP_SCHLAC1_1 SCHLAC1 CSTR 192 126 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Schleiferilactobacillus;s__Schleiferilactobacillus harbinensis GCF_000425885.1 Illumina NovaSeq S4 98.69 1.05 3.131 16 0.3078 53.5 60 3 0 0 JALCNU000000000 SRX12655976 579
UW_MP_SCHLAC1_2 CSTR 126 0.9998 110 Illumina NovaSeq S4 85.69 1.05 2.478 55 0.0637 53.8 42 1 1 0 JALCMS000000000 SRX12655887 379
UW_MP_SCHLAC1_3 CSTR 120 0.9995 109 Illumina NovaSeq S4 85.42 0.52 2.468 79 0.0426 53.7 26 1 0 0 JALCMI000000000 SRX12655888 243
UW_MP_SCHLAC2_1 SCHLAC2 CSTR 78   119 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Schleiferilactobacillus;s__Schleiferilactobacillus perolens GCF_001435585.1 Illumina NovaSeq S4 95.29 0.79 2.837 42 0.108 49.4 25 2 0 0 JALCTX000000000 SRX12655143 290
UW_MP_SELEN1_1 SELEN1 USB 42 115 d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A;s__ NA PacBio Sequel II 90.69 1.87 2.941 22 0.2326 51.7 71 8 6 8 JAKVOG000000000 SAMN18243454 6
UW_MP_SPH1_1 SPH1 CSTR 44 130 d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__RZYO01;s__ NA PacBio Sequel II 98.85 0 3.468 3 3.4088 44.4 55 6 5 5 JAKVOU000000000 SAMN18243037 4
UW_MP_SPH2_1 SPH2 CSTR 44 125 d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__RUG023;s__ NA PacBio Sequel II 97.63 2.3 2.472 20 0.1891 55.9 44 2 2 1 JAKVOV000000000 SAMN18243037 17
UW_MP_SPH2_2 CSTR 24 0.9952 123 PacBio Sequel II 96.48 1.15 2.251 14 0.2435 56.2 46 4 3 3 JAKVPA000000000 SAMN18243588 11
UW_MP_SPH2_3 CSTR 54 0.9962 116 Illumina NovaSeq S4 94.19 0 1.763 75 0.0264 56.9 31 2 0 0 JALCSZ000000000 SRX12654502 2,865
UW_MP_SPH2_4 CSTR 49 0.9958 111 Illumina NovaSeq S4 88.44 0 1.721 64 0.0348 57.0 26 2 0 0 JALCSM000000000 SRX12654484 5,420
UW_MP_SPH2_5 CSTR 36 0.9956 106 Illumina NovaSeq S4 83.84 0 1.538 64 0.0255 56.9 27 2 0 0 JALCRZ000000000 SRX12654483 1,0252
UW_MP_SPH2_6 CSTR 12 0.9976 100 Illumina NovaSeq S4 78.09 0 1.336 76 0.0202 56.9 27 0 0 0 JALCRO000000000 SRX12654482 1,119
UW_MP_SPH2_7 CSTR 66 0.9947 98 Illumina NovaSeq S4 76.37 0 1.635 91 0.0202 56.7 34 2 1 1 JALCTH000000000 SRX12654503 343
UW_MP_SPHING1_1 SPHING1 USB 0 122 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium;s__ NA Illumina NovaSeq S4 98.11 0.78 2.808 48 0.0789 63.3 46 1 1 1 JAKVLC000000000 SRX12655975 488
UW_MP_SPHING1_2 CSTR 0 0.9999 121 Illumina NovaSeq S4 97.69 1.64 3.059 62 0.0623 63.2 49 1 2 2 JALCRK000000000 SRX12654481 405
UW_MP_SPOR1_1 SPOR1 CSTR 192 120 d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus;s__Sporolactobacillus sp900543345 GCA_900543345.1 Illumina NovaSeq S4 96.74 1.94 3.636 39 0.1143 49.1 41 5 2 0 JALCNT000000000 SRX12655976 510
UW_MP_STREP1_1 STREP1 CSTR 78 122 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus;s__Lactococcus lactis GCF_900099625.1 Illumina NovaSeq S4 98.71 0.57 2.274 67 0.0391 35.0 51 3 0 0 JALCTW000000000 SRX12655143 206
UW_MP_STREP1_2 CSTR 49 0.9999 120 Illumina NovaSeq S4 97.16 0.57 2.402 84 0.0436 34.9 39 1 0 0 JALCSL000000000 SRX12654484 220
UW_MP_STREP1_3 CSTR 72 0.9997 109 Illumina NovaSeq S4 87.08 0.82 2.106 95 0.0273 35.0 43 2 0 0 JALCTO000000000 SRX12655142 216
UW_MP_STREP2_1 STREP2 USB 28 118 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__MMGLQ5-1;s__ NA Illumina NovaSeq S4 94.04 0.66 2.517 41 0.0783 35.1 42 1 0 0 JAKVKP000000000 SRX12656283 238
UW_MP_STREP2_2 USB 21 0.9999 104 Illumina NovaSeq S4 78.81 0.66 2.101 30 0.1097 35.2 4 1 0 0 JAKVKS000000000 SRX12655989 491
UW_MP_STREP3_1 STREP3 CSTR 192   115 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus;s__Lactococcus lactis_E GCF_002078765.2 Illumina NovaSeq S4 91.32 0 2.102 39 0.0881 35.7 43 2 0 0 JALCNS000000000 SRX12655976 250
UW_MP_STREP4_1 STREP4 USB 21   114 d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus_A;s__Lactococcus_A raffinolactis GCF_001591765.1 Illumina NovaSeq S4 90.57 0.5 1.911 37 0.0827 40.4 29 1 0 0 JAKVKT000000000 SRX12655989 579
UW_MP_TREP1_1 TREP1 USB 105   107 d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D;s__ NA Illumina NovaSeq S4 84.62 0.35 2.692 95 0.0361 44.8 43 0 0 0 JALCCK000000000 SRX12656339 367
Open in a new tab
a

Strain name assigned to each MAG. The UW_MP prefix stands for University of Wisconsin Milk Permeate bioreactor. MAGs are clustered during dereplication using dRep (11). 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, Acetobacter; ACID, Acidaminococcaceae; ACT, Actinomycetaceae; ACUT, Acutalibacteraceae; AGRLAC, Agrilactobacillus; ANA, Anaerovoracaceae; ATO, Atopobiaceae; BACIL, Bacilli; BACTE, Bacteroidales; BIF, Bifidobacterium; BUL, Bulleidia; BURK, Burkholderiaceae; CARN, Carnobacteriaceae; CAUL, Caulobacteraceae; CLOS, Clostridium; EGG, Eggerthellaceae; ENTER, Enterobacteriaceae; LAC, Lactobacillus; LCO, Lachnospiraceae; LENLAC, Lentilactobacillus; LEUC, Lecuonostoc; LIQLAC, Liquorilactobacillus; MEG, Megasphaera; METH, Methanomethylophilus; MIC, Microbacteriaceae; MORAX, Moraxellaceae; MUR, Muribaculaceae; MYC, Mycobacteriaceae; OSCL, Oscillospiraceae; PREV, Prevotella; PROP, Propionibacteriaceae; RUM, Ruminococcaceae; SACCH, Saccharofermentans; SCHLAC, Schleiferilactobacillus; SELEN, Selenomonadaceae; SPH, Sphaerochaetaceae; SPHING, Sphingobium; SPOR, Sporolactobacillaceae; STREP, Streptococcaceae; TREP, Treponema.

c

Sample from which a given MAG was derived, described as the bioreactor of origin and the sampling day, where day 0 is designated as the day the bioreactor was inoculated. Each bioreactor was fed ultrafiltered milk permeate amended with 400 mg/L of N, in the form of NH4Cl. The CSTR was operated at pH 5.5 and 35°C, with a 6-day solids/hydraulic retention time. The USB was operated at pH 5.5 and 21°C, with a 1.4-day hydraulic retention time and with dynamic solids removal.

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 – ANI)], where A to F were weighted with values of 1, 0.5, 1, 5, 0, and 1, respectively.

f

NCBI GenBank accession number of the reference genome in GTDB-Tk (13) that is closest to the representative MAG. NA, not applicable, i.e., MAGs without a closely matched reference genome when using the default minimum alignment fraction of 0.65.

g

NCBI GenBank accession number for each reported MAG.

h

NCBI SRA accession number for the raw reads of the metagenome for each reported MAG. For PacBio samples that utilized multiple runs, the NCBI BioSample for the experiment is provided.

i

The number of raw reads that aligned to each reported MAG with BBMap or minimap2 for Illumina and PacBio reads, respectively. These reads originated from the metagenome in which the MAG was assembled.

FIG 1.

FIG 1

Open in a new tab

Phylogenic tree of dRep representative bacterial MAGs and their presence in two bioreactors (CSTR and USB) fermenting ultrafiltered milk permeate. ACET, Acetobacter; ACID, Acidaminococcaceae; ACT, Actinomycetaceae; ACUT, Acutalibacteraceae; AGRLAC, Agrilactobacillus; ANA, Anaerovoracaceae; ATO, Atopobiaceae; BACIL, Bacilli; BACTE, Bacteroidales; BIF, Bifidobacterium; BUL, Bulleidia; BURK, Burkholderiaceae; CARN, Carnobacteriaceae; CAUL, Caulobacteraceae; CLOS, Clostridium; EGG, Eggerthellaceae; ENTER, Enterobacteriaceae; LAC, Lactobacillus; LCO, Lachnospiraceae; LENLAC, Lentilactobacillus; LEUC, Lecuonostoc; LIQLAC, Liquorilactobacillus; MEG, Megasphaera; MIC, Microbacteriaceae; MORAX, Moraxellaceae; MUR, Muribaculaceae; MYC, Mycobacteriaceae; OSCL, Oscillospiraceae; PREV, Prevotella; PROP, Propionibacteriaceae; RUM, Ruminococcaceae; SACCH, Saccharofermentans; SCHLAC, Schleiferilactobacillus; SELEN, Selenomonadaceae; SPH, Sphaerochaetaceae; SPHING, Sphingobium; SPOR, Sporolactobacillaceae; STREP, Streptococcaceae; TREP, Treponema. Higher taxonomic levels are labeled, from left to right, family (F), order (O), class (C), and phylum (P). Spiro., Spirochaetota; Alphapr., Alphaproteobacteria; Spiro., Spirochaetia; Acida., Acidaminococcales; Clos., Clostridiales; Erys., Erysipelotrichales; Lachno., Lachnospirales; Pepto., Peptostreptococcales; Veillonella., Veillonellales; Acida., Acidaminococcaceae; Acutali., Acutalibacteraceae; Anaer., Anaerovoracaceae; Clos., Clostridiaceae; Erys., Erysipelotrichaceae; Lachno, Lachnospiraceae; Megasph., Megasphaeraceae; Oscil., Oscillospiraceae; Strep., Streptococcaceae. The phylogenetic tree was generated in RAxML-ng (14) with 500 bootstraps using the concatenation of 120 bacterial single-copy marker genes (Bac120) identified by GTDB-Tk (13). Bootstrap values greater than 50 are shown. The scale bar represents evolutionary distance and indicates the number of nucleotide substitutions per sequence site.

Data availability.

Raw metagenomic sequence data and MAGs for each sample are available at NCBI GenBank under BioProject accession number PRJNA768492. NCBI genome accession numbers for all 278 MAGs are displayed in Table 1. All information on library construction and sequencing can be found at https://img.jgi.doe.gov using JGI GOLD Study identification number Gs0150020. All custom scripts are available on GitHub (https://github.com/GLBRC/metagenome_analysis).

ACKNOWLEDGMENTS

This work was supported by the Great Lakes Bioenergy Research Center, U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research, under award DE-SC0018409 and by funding from the National Dairy Council under project MSN214606. The work (proposal 10.46936/10.25585/60001333) conducted by the U.S. DOE JGI (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. DOE operated under contract DE-AC02-05CH11231.

We thank collaborators at the Center for Dairy Research for providing the ultrafiltered milk permeate. We also thank Matt Seib and the Madison Metropolitan Sewerage District for providing the inoculum for the bioreactor experiments.

Contributor Information

Daniel R. Noguera, Email: noguera@engr.wisc.edu.

Irene L. G. Newton, Indiana University, Bloomington

REFERENCES

  • 1.Scarborough MJ, Lawson CE, Hamilton JJ, Donohue TJ, Noguera DR. 2018. Metatranscriptomic and thermodynamic insights into medium-chain fatty acid production using an anaerobic microbiome. mSystems 3:e00221-18. doi: 10.1128/mSystems.00221-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Clum A, Huntemann M, Bushnell B, Foster B, Foster B, Roux S, Hajek PP, Varghese N, Mukherjee S, Reddy TBK, Daum C, Yoshinaga Y, O’Malley R, Seshadri R, Kyrpides NC, Eloe-Fadrosh EA, Chen I-MA, Copeland A, Ivanova NN. 2021. DOE JGI Metagenome Workflow. mSystems 6:e00804-20. doi: 10.1128/mSystems.00804-20. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Bushnell B. 2014. BBMap: a fast, accurate, splice-aware aligner. https://sourceforge.net/projects/bbmap.
  • 4.Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. 2017. metaSPAdes: a new versatile metagenomic assembler. Genome Res 27:824–834. doi: 10.1101/gr.213959.116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Kolmogorov M, Bickhart DM, Behsaz B, Gurevich A, Rayko M, Shin SB, Kuhn K, Yuan J, Polevikov E, Smith TPL, Pevzner PA. 2020. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat Methods 17:1103–1110. doi: 10.1038/s41592-020-00971-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094–3100. doi: 10.1093/bioinformatics/bty191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, Wang Z. 2019. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7:e7359. doi: 10.7717/peerj.7359. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Tennessen K, Palaniappan K, Szeto E, Pillay M, Chen IMA, Pati A, Nielsen T, Markowitz VM, Kyrpides NC. 2016. The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4). Stand Genomic Sci 11:17. doi: 10.1186/s40793-016-0138-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Tatusova T, Dicuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. doi: 10.1093/nar/gkw569. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Tennessen K, Andersen E, Clingenpeel S, Rinke C, Lundberg DS, Han J, Dangl JL, Ivanova N, Woyke T, Kyrpides N, Pati A. 2016. ProDeGe: a computational protocol for fully automated decontamination of genomes. ISME J 10:269–272. doi: 10.1038/ismej.2015.100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Olm MR, Brown CT, Brooks B, Banfield JF. 2017. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J 11:2864–2868. doi: 10.1038/ismej.2017.126. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. doi: 10.1101/gr.186072.114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. 2019. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36:1925–1927. doi: 10.1093/bioinformatics/btz848. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. 2019. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35:4453–4455. doi: 10.1093/bioinformatics/btz305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Stamatopoulou P, Malkowski J, Conrado L, Brown K, Scarborough M. 2020. Fermentation of organic residues to beneficial chemicals: a review of medium-chain fatty acid production. Processes 8:1571. doi: 10.3390/pr8121571. [DOI] [Google Scholar]
  • 16.Duber A, Jaroszynski L, Zagrodnik R, Chwialkowska J, Juzwa W, Ciesielski S, Oleskowicz-Popiel P. 2018. Exploiting the real wastewater potential for resource recovery: n-caproate production from acid whey. Green Chem 20:3790–3803. doi: 10.1039/C8GC01759J. [DOI] [Google Scholar]
  • 17.Scarborough MJ, Myers KS, Donohue TJ, Noguera DR. 2020. Medium-chain fatty acid synthesis by “Candidatus Weimeria bifida” gen. nov., sp. nov., and “Candidatus Pseudoramibacter fermentans” sp. nov. Appl Environ Microbiol 86:e02242-19. doi: 10.1128/AEM.02242-19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 18.Fortney NW, Hanson NJ, Rosa PRF, Donohue TJ, Noguera DR. 2021. Diverse profile of fermentation byproducts from thin stillage. Front Bioeng Biotechnol 9:695306. doi: 10.3389/fbioe.2021.695306. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.Ingle AT, Fortney NW, Walters KA, Donohue TJ, Noguera DR. 2021. Mixed acid fermentation of carbohydrate-rich dairy manure hydrolysate. Front Bioeng Biotechnol 9:724304. doi: 10.3389/fbioe.2021.724304. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Hollister EB, Forrest AK, Wilkinson HH, Ebbole DJ, Tringe SG, Malfatti SA, Holtzapple MT, Gentry TJ. 2012. Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion. PLoS One 7:e39689. doi: 10.1371/journal.pone.0039689. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Zhu X, Feng X, Liang C, Li J, Jia J, Feng L, Tao Y, Chen Y. 2021. Microbial ecological mechanism for long-term production of high concentrations of n-caproate via lactate-driven chain elongation. Appl Environ Microbiol 87:e03075-20. doi: 10.1128/AEM.03075-20. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Wu SL, Sun J, Chen X, Wei W, Song L, Dai X, Ni BJ. 2020. Unveiling the mechanisms of medium-chain fatty acid production from waste activated sludge alkaline fermentation liquor through physiological, thermodynamic and metagenomic investigations. Water Res 169:115218. doi: 10.1016/j.watres.2019.115218. [DOI] [PubMed] [Google Scholar]
  • 23.Crognale S, Braguglia CM, Gallipoli A, Gianico A, Rossetti S, Montecchio D. 2021. Direct conversion of food waste extract into caproate: metagenomics assessment of chain elongation process. Microorganisms 9:327. doi: 10.3390/microorganisms9020327. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Han W, He P, Shao L, Lü F. 2018. Metabolic interactions of a chain elongation microbiome. Appl Environ Microbiol 84:e01614-18. doi: 10.1128/AEM.01614-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Carvajal-Arroyo JM, Candry P, Andersen SJ, Props R, Seviour T, Ganigué R, Rabaey K. 2019. Granular fermentation enables high rate caproic acid production from solid-free thin stillage. Green Chem 21:1330–1339. doi: 10.1039/C8GC03648A. [DOI] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

Raw metagenomic sequence data and MAGs for each sample are available at NCBI GenBank under BioProject accession number PRJNA768492. NCBI genome accession numbers for all 278 MAGs are displayed in Table 1. All information on library construction and sequencing can be found at https://img.jgi.doe.gov using JGI GOLD Study identification number Gs0150020. All custom scripts are available on GitHub (https://github.com/GLBRC/metagenome_analysis).

Articles from Microbiology Resource Announcements are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES