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. 2022 Jan 20;11(1):e01142-21. doi: 10.1128/mra.01142-21

Archaeal and Bacterial Metagenome-Assembled Genome Sequences Derived from Pig Feces

Matthew Crossfield a,b,#, Rachel Gilroy b,#, Anuradha Ravi b, David Baker b, Roberto M La Ragione c,d, Mark J Pallen b,c,e,✉
Editor: Kenneth M Stedmanf
PMCID: PMC8772591  PMID: 35049348

ABSTRACT

We report the recovery of metagenome-assembled genomes (MAGs) from fecal samples collected in 2018 from five healthy adult female pigs in southeast England. The resulting nonredundant catalog of 192 MAGs encompasses 102 metagenomic species, 41 of them novel, spanning 10 bacterial and 2 archaeal phyla.

ANNOUNCEMENT

The domestic pig is one of the most common livestock animals in the world. However, taxonomic and genomic diversity within the pig gut microbiome remains largely unexplored. We therefore applied metagenomic sequencing and analysis to five fecal samples from pigs raised on a commercial livestock farm in Surrey, UK, without the use of antibiotic supplements.

Ethical approval was obtained from the University of Surrey’s Animal Welfare and Ethical Review Body under agreement NERA-2018-011. DNA was extracted from five freshly voided fecal samples using the PowerSoil DNA isolation kit (MoBio Laboratories, Inc., CA, USA) before library construction using the Nextera XT library preparation kit according to the manufacturer’s recommendations. The final pool quality was assessed using the Agilent 2200 TapeStation system and the concentration quantified using Qubit v4. A total of 243,575,779 paired-end reads (2 × 150 bp) were generated on the Illumina NextSeq platform. All subsequent bioinformatics tools were run with default parameters unless otherwise specified. The read quality was assessed using FastQC v0.11.8, before mapping to the host genome (GenBank accession no. GCF_000003025.6) for depletion of the host reads using Bowtie2 v2.3.4 and SAMtools v1.9.0 (1–5) (https://doi.org/10.6084/m9.figshare.16896877.v3).

Sample-specific assemblies were generated using MegaHIT v1.0.6 (6), and the host-depleted reads were mapped back to the assemblies using Bowtie2 and SAMtools to determine the coverage. Contigs were binned using MetaBAT 2 v2.12.1 (7) (contig length, ≥2.5 kb), CONCOCT v1.1.0 (8), and MaxBin 2 v2.2.7 (9) (contig length, ≥1 kb). DAS Tool v1.1.2 was used to integrate the bin predictions and create five sets of optimized, nonredundant metagenome-assembled genomes (MAGs) (10). CheckM v1.0.13 (11) was used to obtain estimates of the completion and contamination, and bins with ≥70% completion, ≤10% contamination, and/or a quality score (completeness minus 5× contamination) of >50 were followed up as “medium- or high-quality MAGs.” MAGs were dereplicated using dRep v2.6.2 (12) at 95% and 99% average nucleotide identity (ANI) (for species and strains, respectively). Taxonomic assignments were made using the Genome Taxonomy Database Toolkit v1.5 (GTDB-tk) with the release 202 database (13). Proteomes were predicted using Prodigal v2.6.1 (14) before comparison against 400 universal marker proteins using PhyloPhlAn v3.0.58 (15) in accordance with DIAMOND v0.9.34 (16) and using the supermatrix configuration at a high diversity scale. Multiple sequence alignment and subsequent refinement were performed using MAFFT v7.271 and trimAl v1.4 (17, 18), before tree construction and refinement using FastTree v2.1.10 (19) and RAxML v8.2.12 (20), respectively. All trees were visualized and annotated using iTol v5.7 (21).

This workflow resulted in a nonredundant catalogue of 192 MAGs, representing 102 metagenomic species spanning 12 phyla. Forty-one of the species are considered novel, showing no classification within currently available databases, including a representative of a new family within the order Christensenellales (Fig. 1; Table 1).

FIG 1.

FIG 1

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Phylogeny of 114 metagenome-assembled genomes from five pig fecal samples. Computed using PhyloPhlAn with the supermatrix configuration on 400 universal merger genes at high diversity scale; visualized and annotated using iTOLv5.7, with the scale bar depicting internal branch lengths. The phyla assigned by GTDB are shown by color. Branch point colors subdivide the traditional phylum Firmicutes into the three phyla assigned by GTDB. Blue filled rectangles represent known species within GTDB, with unfilled shapes representing novel species. The asterisk denotes the placement of the representative of a new family within the order Christensenellales.

TABLE 1.

Metagenome-assembled genomes from five pig fecal samplesa

MAG_IDb Species/strain Taxonomic assignmentc Coverage (×) FastANI (%) Genome size (bp) No. of contigs N50 (bp) GC content (%) Completeness (%) Contamination (%) BioSample accession no. GenBank accession no. or Figshare link
108d 1_1 Megasphaera elsdenii 14.6 98.92 2,081,739 458 7,910 54.14 91.38 2.59 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
51 1_1 Megasphaera elsdenii NA 98.92 1,893,361 591 4,166 54.59 93.03 1.88 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
12 1_1 Megasphaera elsdenii NA 98.92 1,898,913 543 4,510 54.53 98.12 1.72 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
54d 10_1 Novel species 10 within the genus W2P13-069 4.4 NA 1,281,580 645 2,152 65.25 79.67 3.61 SAMN16580179 GCA_018383355.1
157_3 10_1 Novel species 10 within the genus W2P13-070 NA NA 1,364,454 735 1,906 64.84 87.15 6.37 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
119d 10_2 Novel species 10 within the genus W2P13-071 NA NA 1,502,460 617 2,855 65.19 80.17 4.31 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
164d 100_0 UBA4248 sp004554395 7.3 98.92 3,068,288 706 5,709 52.11 91.38 0 SAMN16580178 GCA_018384915.1
192_2d 101_0 Novel species 101 within the genus RZZT01 7.1 NA 627,079 166 5,146 42.04 80.56 0 SAMN16580181 GCA_018384895.1
222d 102_0 RUG369 sp004556055 6.3 98.87 2,737,201 738 4,630 51.12 84.33 1.02 SAMN16580181 GCA_018384795.1
142_2d 11_1 F23-B02 sp004556755 8.5 99.02 1,554,224 231 9,615 54.92 97.65 6.35 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
161 11_1 F23-B02 sp004556755 6.2 99.02 1,455,046 274 6,763 55.2 94.89 0 SAMN16580179 GCA_018385075.1
MB2.57d 12_0 SFMI01 sp004556155 8.3 99.25 2,129,070 271 9,714 59.08 85.34 2.59 SAMN16580178 GCA_018384115.1
MB2.59d 13_0 PeH17 sp004556165 121.7 98.31 1,330,707 69 30,851 50.07 86.21 0 SAMN16580179 GCA_018384005.1
MBin.060d 14_0 PeH17 sp000435055 14.2 98.89 1,884,822 135 24,258 49.6 96.55 2.59 SAMN16580178 GCA_018384705.1
159_2d 15_0 Phascolarctobacterium_A succinatutens 24.8 99.42 1,935,117 339 8,719 48.28 89.34 5.17 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
MBin.031d 16_0 Ruminococcus flavefaciens_G 30.8 97.45 2,560,973 95 43,414 51.35 100 0 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
123d 17_0 CAG-180 sp004556705 8.4 98.07 1,673,664 349 6,771 43.71 90.34 6.19 SAMN16580179 GCA_018384955.1
64d 18_0 Novel species 18 within the genus DTU089 8.1 NA 1,810,698 519 4,294 38.78 98.28 1.88 SAMN16580181 GCA_018384655.1
MB2.42d 19_0 Novel species 19 within the genus HGM11525 18.0 NA 1,976,368 150 19,416 39.82 93.1 3.45 SAMN16580178 GCA_018384175.1
MBin.003_2 2_1 Novel species 2 within the genus Comamonas NA NA 2,733,925 206 20,654 60.62 97.93 0 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.19d 2_1 Novel species 2 within the genus Comamonas 28.8 NA 2,672,762 99 45,383 60.77 98.28 0 SAMN16580182 GCA_018384445.1
192d 20_1 CAG-115 sp004555635 7.0 98.06 2,141,678 498 5,642 52.02 93.5 5.04 SAMN16580178 GCA_018384805.1
87 20_1 CAG-115 sp004555635 NA 98.06 1,969,602 530 4,700 52.29 88.48 1.88 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
126d 21_1 Novel species 21 within the genus Ruminiclostridium_E 11.0 NA 1,651,903 724 2,519 44.73 92.79 1.88 SAMN16580182 GCA_018385035.1
46d 21_2 Novel species 21 within the genus Ruminiclostridium_E NA NA 1,679,956 712 2,527 45.05 91.22 4.08 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
164_2d 21_3 Novel species 21 within the genus Ruminiclostridium_E NA NA 1,717,232 858 2,149 44.83 88.32 5.49 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
4_3d 21_4 Novel species 21 within the genus Ruminiclostridium_E NA NA 1,839,562 671 3,102 44.9 91.22 3.76 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.83d 22_1 Novel species 22 within the order Christensenellales 11.5 NA 1,636,615 80 32,741 57.98 89.66 0 SAMN16580178 GCA_018385275.1
MB2.66_2 22_1 Novel species 22 within the order Christensenellales NA NA 1,384,958 239 6,702 58.11 75.86 1.72 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.1_2 23_1 “Angelakisella” sp004554485 NA 98.33 1,156,090 185 7,110 59.74 85.58 0.16 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.042d 23_1 Angelakisella sp004554485 13.1 98.33 1,192,484 181 7,616 59.78 78.06 1.72 SAMN16580181 GCA_018384415.1
MB2.34_2 23_1 Angelakisella sp004554485 NA 98.33 1,112,822 203 6,282 59.61 77.59 0.16 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.127d 24_1 CAG-272 sp000433515 20.8 98.56 2,059,360 75 41,032 53.15 94.83 0 SAMN16580179 GCA_018383935.1
54_2 24_1 CAG-272 sp000433515 NA 98.56 2,148,591 372 8,222 53.33 96.24 9.09 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.120d 25_1 Novel species 25 within the genus CAG-841 15.0 NA 1,476,605 90 24,557 49.07 95.72 0 SAMN16580179 GCA_018383975.1
MB2.51 25_1 Novel species 25 within the genus CAG-841 NA NA 1,345,663 156 10,952 49.1 92.24 0 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.013d 26_0 Novel species 26 within the genus UBA1712 9.4 NA 1,429,645 186 9,637 44.02 79.15 1.72 SAMN16580181 GCA_018384635.1
MB2.132d 27_0 UBA2868 sp004552595 10.0 98.84 1,459,382 226 8,072 38.12 87.93 1.72 SAMN16580178 GCA_018384285.1
MBin.045 28_1 Novel species 28 within the genus Acetatifactor NA NA 2,381,748 366 11,666 50.42 85.52 3.45 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.86d 28_1 Novel species 28 within the genus Acetatifactor 38.3 NA 2,467,536 177 22,051 50.22 94.83 4.48 SAMN16580179 GCA_018385425.1
MB2.96_2 28_1 Novel species 28 within the genus Acetatifactor NA NA 1,898,589 369 5,714 50.24 75.41 1.72 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.1 28_1 Novel species 28 within the genus Acetatifactor NA NA 2,322,269 252 12,308 50.45 83.86 4.31 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MBin.029d 29_0 Novel species 29 within the genus CAG-95 27.9 NA 3,111,859 125 51,022 43.83 95.45 3.45 SAMN16580178 GCA_018384375.1
113 3_1 UBA1723 sp002371265 NA 96.37 3,291,296 456 9,374 41.24 94.83 1.72 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
2d 3_1 UBA1723 sp002371265 15.2 96.37 3,549,890 320 15,986 41.1 98.28 0 SAMN16580181 GCA_018384995.1
MB2.44d 30_0 Novel species 30 within the genus SFDP01 11.6 NA 1,671,723 141 16,841 40.27 83.62 2.59 SAMN16580178 GCA_018385375.1
141d 31_0 Novel species 31 within the genus UBA7642 5.4 NA 816,795 374 2,327 43.69 74.14 3.43 SAMN16580182 GCA_018383255.1
24d 32_0 UBA636 sp002299675 7.0 98.61 1,489,909 499 3,818 38.2 87.77 0 SAMN16580181 GCA_018384855.1
MB2.95_2d 33_1 Novel species 33 within the genus UBA1067 16.3 NA 1,819,028 117 21,057 51.15 92.95 1.38 SAMN16580179 GCA_018384485.1
14 33_1 Novel species 33 within the genus UBA1067 NA NA 1,974,080 586 4,278 51.27 87.3 5.52 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
81d 34_0 UMGS687 sp900544595 6.1 98.42 633,718 271 2,630 36.19 73.79 3.45 SAMN16580178 GCA_018384875.1
MB2.56d 35_0 SFEB01 sp004558105 18.2 98.26 987,321 154 7,610 45 89.83 1.72 SAMN16580178 GCA_018384135.1
157d 36_0 SFEL01 sp004557245 11.9 98.15 1,636,433 430 4,785 53.75 87.93 0.92 SAMN16580179 GCA_018383265.1
MBin.013d 37_0 Phil1 sp004558525 52.0 99.13 1,801,179 77 33,534 51.52 98.28 0 SAMN16580178 GCA_018384765.1
75d 38_0 Phil1 sp001940855 13.7 96.84 2,199,755 128 29,680 52.48 97.36 0.86 SAMN16580178 GCA_018384665.1
MB2.113d 39_1 Novel species 39 within the genus SFDB01 51.6 NA 1,791,970 22 134,508 48.31 98.28 0.86 SAMN16580178 GCA_018384315.1
MB2.89 39_1 Novel species 39 within the genus SFDB01 NA NA 1,547,308 84 25,379 48.55 98.28 2.04 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.92d 4_1 Fibrobacter sp900142475 31.8 95.34 3,169,736 129 38,467 51.4 100 0 SAMN16580178 GCA_018384535.1
176 4_1 Fibrobacter sp900142475 NA 95.34 4,194,492 412 19,093 50.56 96.55 0.34 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.45 4_1 Fibrobacter sp900142475 NA 95.34 2,896,090 206 20,168 51.81 97.41 0 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.048 4_1 Fibrobacter sp900142475 NA 95.34 3,088,752 245 17,992 51.43 99.14 1.72 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.93 4_1 Fibrobacter sp900142475 NA 95.34 2,773,889 143 30,346 51.97 94.83 0 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.100d 40_0 SFDB01 sp004558825 14.5 99.08 1,551,443 95 27,719 51.3 98.28 0 SAMN16580179 GCA_018380645.1
MB2.73 41_1 Bifidobacterium pseudolongum NA 99.54 1,668,768 92 25,976 63.66 98.28 0 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.115d 41_1 Bifidobacterium pseudolongum 19.7 99.54 1,641,528 98 28,425 63.73 98.28 0 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
33 41_1 Bifidobacterium pseudolongum NA 99.54 1,927,110 344 8,852 63.35 100 2.07 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.005 41_1 Bifidobacterium pseudolongum NA 99.54 1,653,031 115 22,636 63.74 94.83 0 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
MBin.057d 42_1 Novel species 42 within the genus Oxalobacter 15.4 NA 1,932,695 64 65,154 51.73 100 0 SAMN16580178 GCA_018384065.1
MB2.38_2 42_1 Novel species 42 within the genus Oxalobacter NA NA 1,758,046 155 15,110 51.88 94.83 0 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
71d 43_0 Novel species 43 within the genus Oxalobacter 5.1 NA 1,446,023 634 2,598 54.07 82.65 3.76 SAMN16580179 GCA_018383305.1
MB2.8d 44_1 Novel species 44 within the genus Treponema_D 27.0 NA 2,216,246 106 30,570 41.67 90.52 0 SAMN16580178 GCA_018384055.1
160 44_1 Novel species 44 within the genus Treponema_D NA NA 2,060,482 257 10,336 42.01 84.48 0 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.76d 45_0 Novel species 45 within the genus Treponema_D 76.3 NA 2,570,216 223 18,158 33.79 90.52 0.86 SAMN16580178 GCA_018385315.1
MB2.8_2d 46_0 Novel species 46 within the genus Treponema_D 126.9 NA 2,578,587 231 16,947 39.39 85.34 0 SAMN16580179 GCA_018383995.1
MB2.136 47_1 Novel species 47 within the genus Treponema_D NA NA 2,428,835 224 16,313 39.33 90.52 2.59 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.91_2d 47_1 Novel species 47 within the genus Treponema_D 25.0 NA 2,270,652 171 18,281 39.59 87.07 1.72 SAMN16580182 GCA_018385395.1
MB2.38d 48_0 Novel species 48 within the genus Treponema_D 51.9 NA 2,337,410 118 44,527 36.24 93.97 0 SAMN16580178 GCA_018385415.1
MB2.015d 49_0 Novel species 49_0 within the genus Thiopseudomonas 14.5 NA 2,246,815 124 28,600 57.9 87.15 0 SAMN16580181 GCA_018384595.1
107d 5_0 Fibrobacter_A sp002797675 6.1 99.08 2,165,544 690 3,858 49.86 89.66 2.57 SAMN16580182 GCA_018383235.1
226d 50_0 SFTJ01 sp004563195 NA 97.88 2,302,692 804 3,309 48.55 74.45 3.76 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
23d 51_0 CAG-279 sp004555955 15.6 98.07 2,104,689 723 3,468 49.91 86.83 0 SAMN16580180 GCA_018383405.1
102_2d 52_0 CAG-485 sp004553095 17.0 98.46 2,127,132 264 13,188 49.45 96.55 0 SAMN16580181 GCA_018384695.1
137d 53_1 Sodaliphilus sp004559845 7.9 97.27 1,991,868 565 4,337 49 86.05 3.76 SAMN16580179 GCA_018385115.1
59d 53_2 Sodaliphilus sp004559845 NA 98 2,158,008 537 5,560 48.6 82.76 3.45 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
60d 53_3 Sodaliphilus sp004559845 NA 97.66 1,970,221 708 3,237 48.91 74.69 0.16 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
109d 54_1 Sodaliphilus sp004557565 24.9 98.25 2,524,898 545 6,335 48.18 98.28 1.72 SAMN16580178 GCA_018385175.1
MB2.67 54_1 Sodaliphilus sp004557565 NA 98.25 1,797,432 321 6,002 48.53 72.41 0 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
166 54_1 Sodaliphilus sp004557565 NA 98.25 2,459,097 646 4,754 48.18 94.83 1.72 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.57_2 54_1 Sodaliphilus sp004557565 NA 98.25 1,813,601 326 5,991 48.11 84.48 1.72 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
157_2d 55_1 CAG-279 sp004561555 9.8 98.77 2,043,626 310 8,798 45.84 96.55 2.04 SAMN16580181 GCA_018384195.1
29 55_1 CAG-279 sp004561555 NA 98.77 2,007,650 358 7,577 46.49 89.66 6.21 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MBin.037d 56_0 Parabacteroides sp000436495 23.4 96.8 3,220,218 162 30,201 42.39 90.52 0 SAMN16580178 GCA_018384275.1
102d 57_1 “Prevotellamassilia” sp004552865 7.3 97.48 2,025,313 673 3,832 53.09 88.4 4.47 SAMN16580182 GCA_018383295.1
97d 57_2 Prevotellamassilia sp004552865 NA 97.56 2,308,037 399 8,045 52.53 94.51 0 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.96d 58_0 UBA6398 sp003150315 8.1 98.63 1,741,886 284 7,383 45.21 78.84 3.28 SAMN16580182 GCA_018380595.1
MBin.002d 59_0 Novel species 59 within the genus Caryophanon 223.7 NA 2,149,313 170 25,329 42.61 90.75 1.88 SAMN16580180 GCA_018384745.1
61d 6_1 Novel species 6 within the genus UBA2658 16.5 NA 1,880,025 81 47,276 51.68 98.28 0 SAMN16580178 GCA_018385135.1
22 6_1 Novel species 6 within the genus UBA2658 NA NA 1,744,341 272 8,568 51.82 92.87 0.86 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MBin.007d 60_0 Bacteroides fragilis 98.0 99.03 5,507,632 223 142,876 43.24 100 6.9 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
155d 61_0 “Bacteroides togonis” 53.7 97.13 3,453,740 115 46,600 48.88 95.77 6.03 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.105d 62_0 Phocaeicola plebeius_A 33.1 96.01 3,369,676 79 59,934 44.69 93.03 0 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.88_2 63_1 Prevotella sp002251295 NA 99.34 2,564,796 199 20,555 46.6 90.05 0.69 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.76_3 63_1 Prevotella sp002251295 NA 99.34 2,415,843 137 30,218 46.8 96.55 2.76 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.128d 63_1 Prevotella sp002251295 32.1 99.34 2,299,847 120 30,440 46.82 92.07 1.72 SAMN16580181 GCA_018384355.1
MB2.81d 64_0 Prevotella hominis 48.5 95.41 2,612,864 325 10,261 43.46 79.31 5.5 SAMN16580182 GCA_018383955.1
MB2.133d 65_0 Jeotgalibaca porci 30.4 99.06 1,582,154 195 11,256 40.62 91.38 3.45 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
MBin.003 66_1 UBA4334 sp900316975 NA 97.68 2,468,196 282 15,587 48.26 96.55 3.61 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.31 66_1 UBA4334 sp900316975 NA 97.68 2,219,084 220 12,979 48.35 87.93 0.16 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.082d 66_1 UBA4334 sp900316975 30.8 97.68 2,254,860 180 19,020 48.38 91.03 0 SAMN16580181 GCA_018384255.1
MB2.6_2 66_1 UBA4334 sp900316975 NA 97.68 2,209,849 183 16,499 48.36 91.38 0 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
39d 67_0 Novel species 67 within the genus Prevotellamassilia 12.7 NA 2,200,295 355 9,893 53.4 96.55 3.45 SAMN16580178 GCA_018383375.1
100d 68_0 Prevotella sp002300055 28.1 99.35 2,972,104 166 30,510 53.78 98.28 3.45 SAMN16580179 GCA_018383335.1
122 69_1 UBA3388 sp004551865 NA 98.52 2,167,825 212 20,167 42.02 100 0 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
199_2 69_1 UBA3388 sp004551865 NA 98.52 2,285,050 332 11,249 42.35 98.28 2.04 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MBin.021 69_1 UBA3388 sp004551865 NA 98.52 1,701,589 691 2,829 42.64 92.24 3.45 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.144d 69_1 UBA3388 sp004551865 102.4 98.52 1,912,382 96 30,760 42.28 100 0 SAMN16580181 GCA_018384335.1
MB2.48_2 69_1 UBA3388 sp004551865 NA 98.52 1,758,019 164 14,634 42.5 94.83 0 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
91d 7_1 Novel species 7 within the family UBA1242 17.9 NA 983,269 77 110,292 43.14 87.93 0 SAMN16580179 GCA_018384735.1
197 7_1 Novel species 7 within the family UBA1242 NA NA 870,039 44 47,297 42.99 86.21 0 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
138d 70_1 UBA1232 sp004561775 10.2 97.13 1,592,739 433 5,120 47.32 93.1 0 SAMN16580178 GCA_018385195.1
142d 70_2 UBA1232 sp004561775 NA 96.78 1,360,217 578 2,641 47.6 71.47 0 SAMN16580180 GCA_018385055.1
138_2d 70_3 UBA1232 sp004561775 NA 97.4 1,411,325 552 2,921 47.81 78.45 1.88 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
36d 70_4 UBA1232 sp004561775 NA 96.92 1,601,980 467 4,579 47.58 94.67 4.31 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.79d 71_0 Novel species 71 within the genus RC9 10.2 NA 2,052,541 172 17,023 48.59 90.52 6.9 SAMN16580178 GCA_018384035.1
199d 72_1 Prevotella sp900548195 15.2 96.67 2,626,542 335 10,473 45.48 96.55 1.72 SAMN16580178 GCA_018384615.1
MB2.76_2 72_1 Prevotella sp900548195 NA 96.67 2,533,978 321 9,789 45.4 84.95 1.72 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.140 73_1 F082 sp900769945 NA 98.73 1,988,821 209 11,979 45.18 96.55 1.72 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.61 73_1 F082 sp900769945 NA 98.73 1,808,756 248 9,465 45.65 93.5 4.31 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.64_2 73_1 F082 sp900769945 NA 98.73 1,651,934 291 6,081 45.48 86 0 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
10_2d 73_1 F082 sp900769945 43.0 98.73 2,284,399 128 32,074 44.7 98.28 0 SAMN16580181 GCA_018384935.1
MB2.90d 74_0 Novel species 74 within the family Bacteroidaceae 18.2 NA 2,326,429 84 37,962 49.24 99.84 0 SAMN16580178 GCA_018385335.1
MB2.97d 75_1 RC9 sp004554455 17.3 98.49 1,454,040 207 8,934 55.36 81.9 5.17 SAMN16580178 GCA_018385325.1
MB2.52 75_1 RC9 sp004554455 NA 98.49 1,308,014 213 7,254 55.54 74.14 1.72 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.103 75_1 RC9 sp004554455 NA 98.49 1,276,739 206 6,872 55.35 72.41 1.8 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.109_2 75_1 RC9 sp004554455 NA 98.49 1,372,827 223 7,379 55.49 87.93 1.88 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.64d 76_0 RC9 sp000431015 12.6 98.71 2,153,407 220 13,730 53.78 85.34 2.04 SAMN16580178 GCA_018385295.1
MB2.118d 77_1 RC9 sp900546925 25.2 99 1,868,948 111 27,465 47.6 96.55 0 SAMN16580181 GCA_018384095.1
MB2.65 77_1 RC9 sp900546925 NA 99 2,033,531 160 20,061 47.63 98.28 6.9 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
136d 78_0 Novel species 78 within the genus UBA5920 9.5 NA 1,483,767 512 3,683 47.26 79.26 1.72 SAMN16580182 GCA_018385155.1
MB2.54_2d 79_1 RC9 sp004556005 70.3 98.85 1,821,683 170 17,759 51.99 92.24 6.03 SAMN16580179 GCA_018384575.1
MB2.087 79_1 RC9 sp004556005 NA 98.85 1,761,281 146 17,731 51.9 84.48 0.34 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.116 79_1 RC9 sp004556005 NA 98.85 1,674,035 172 15,264 51.82 80.44 1.72 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.54d 8_1 ER4 sp900317525 12.3 97.74 1,406,667 184 9,148 62.39 91.38 0 SAMN16580178 GCA_018384155.1
MB2.32_2 8_1 ER4 sp900317525 NA 97.74 1,436,706 192 8,977 62.3 88.32 1.72 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.101_2 8_1 ER4 sp900317525 NA 97.74 1,410,060 190 8,617 62.41 84.64 4.36 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.6d 80_1 RC9 sp000432655 92.5 97.68 1,524,799 45 52,040 49.03 94.83 0 SAMN16580178 GCA_018385255.1
MB2.35 80_1 RC9 sp000432655 NA 97.68 1,591,216 87 35,010 49.13 86.83 0 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.052 80_1 RC9 sp000432655 NA 97.68 1,493,030 57 48,600 49.11 86.21 4.31 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.5 81_1 RC9 sp004552965 NA 98.74 1,923,243 176 15,583 53.71 91.38 0 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.88d 81_1 RC9 sp004552965 42.0 98.74 1,853,595 164 17,205 53.7 88.79 1.72 SAMN16580179 GCA_018384515.1
MB2.058 81_1 RC9 sp004552965 NA 98.74 1,938,889 163 15,807 53.7 93.97 3.45 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.101 81_1 RC9 sp004552965 NA 98.74 1,930,449 172 15,422 53.8 93.1 1.72 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.9d 82_1 Novel species 82 within the genus RC9 41.5 NA 1,687,862 116 23,135 54.82 93.1 7.37 SAMN16580179 GCA_018384555.1
MB2.83_3 82_1 Novel species 82 within the genus RC9 NA NA 1,802,719 123 19,776 54.82 86.21 1.38 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.26 83_1 Novel species 83 within the genus RC9 NA NA 1,582,938 169 13,745 54.89 73.67 4.39 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.52_2 83_1 Novel species 83 within the genus RC9 NA NA 1,427,062 226 7,651 55.05 70.97 1.25 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.109d 83_1 Novel species 83 within the genus RC9 18.1 NA 1,694,760 169 15,584 54.83 87.93 0.86 SAMN16580181 GCA_018384235.1
MB2.77 83_1 Novel species 83 within the genus RC9 NA NA 1,660,044 174 13,126 54.89 87.07 0.16 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.48d 84_0 Novel species 84 within the genus RC9 6.8 NA 1,027,778 198 5,726 53.89 70.38 3.45 SAMN16580178 GCA_018384215.1
MB2.029d 85_1 Novel species 85 within the genus Myroides 53.3 NA 1,924,990 331 6,245 34.49 76.15 2.04 SAMN16580181 GCA_018384465.1
MB2.8_3 85_1 Novel species 85 within the genus Myroides NA NA 1,391,904 314 4,675 34.89 73.82 3.92 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.020d 86_0 Novel species 86_0 within the genus YIM-102668 49.0 NA 2,770,569 206 20,377 31.23 93.1 2.59 SAMN16580181 GCA_018384435.1
170 87_1 Streptococcus alactolyticus NA 99.2 1,793,166 138 24,966 40.54 98.28 2.59 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.24d 87_1 Streptococcus alactolyticus 259.0 99.2 1,460,880 63 42,702 41.11 93.97 0 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.83_2 87_1 Streptococcus alactolyticus NA 99.2 1,591,166 125 16,988 41.03 97.81 4.47 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.097 87_1 Streptococcus alactolyticus NA 99.2 1,460,509 80 30,127 40.95 87.07 3.45 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.13 87_1 Streptococcus alactolyticus NA 99.2 1,514,600 85 25,521 40.92 96.55 0 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.32d 88_1 Limosilactobacillus reuteri 68.5 96.32 1,596,378 71 39,896 38.8 94.83 0 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.34 88_1 Limosilactobacillus reuteri NA 96.32 1,650,438 151 15,523 38.84 95.61 0.57 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.39 88_1 Limosilactobacillus reuteri NA 96.32 1,480,767 110 19,594 39.07 91.69 0 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MBin.004 89_1 Lactobacillus amylovorus NA 97.64 1,945,777 267 15,066 37.88 89.66 1.72 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.138d 89_1 Lactobacillus amylovorus 26.1 97.64 1,515,149 119 19,534 38.63 98.28 0 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.95d 9_1 Novel species 9 within the genus ER4 21.8 NA 1,237,038 125 12,747 58.23 93.89 0 SAMN16580178 GCA_018380655.1
MB2.84 9_1 Novel species 9 within the genus ER4 NA NA 1,265,700 132 12,202 58.34 94.83 3.03 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.105_2 9_1 Novel species 9 within the genus ER4 NA NA 1,203,093 162 8,475 58.28 88.35 1.02 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.91d 90_0 Methanobrevibacter_A sp900769095 39.3 98.84 2,058,317 258 10,227 32.03 92.52 6.07 SAMN16580178 GCA_018385235.1
9d 91_0 CAG-177 sp900771185 5.8 95.19 1,339,283 491 3,126 49.69 78.84 3.45 SAMN16580179 GCA_018385015.1
MB2.102d 92_0 Novel species 92 within the genus UMGS1384 12.7 NA 2,110,823 63 51,290 54.68 87.93 0 SAMN16580178 GCA_018384365.1
MBin.083 93_1 Acinetobacter pseudolwoffii NA 98.51 3,218,104 880 5,371 44.46 92.71 4.31 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.58d 93_1 Acinetobacter pseudolwoffii 25.6 98.51 2,150,411 294 8,889 44.18 86.13 0 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
MB2.66d 94_1 Escherichia flexneri 35.1 97.97 3,512,380 515 8,317 50.96 86.21 0 SAMN16580178 https://doi.org/10.6084/m9.figshare.16896877.v3
169 94_1 Escherichia flexneri NA 97.97 3,947,168 844 6,167 51.15 94.67 3.45 SAMN16580180 https://doi.org/10.6084/m9.figshare.16896877.v3
15 94_1 Escherichia flexneri NA 97.97 3,212,344 1,334 2,664 51.49 76.77 1.72 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
106 94_1 Escherichia flexneri NA 97.97 2,360,607 1,127 2,237 51.91 79.7 2.85 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
159d 95_0 Novel species 95 within the genus SFVR01 19.9 NA 1,795,205 360 7,175 37.19 98.28 4.31 SAMN16580178 GCA_018385185.1
4d 96_0 Psychrobacter pasteurii 9.7 97.62 2,133,879 600 4,479 43.11 80.25 3.45 SAMN16580181 https://doi.org/10.6084/m9.figshare.16896877.v3
144d 97_1 Novel species 97 within the genus Rs-D84 5.7 NA 734,502 267 3,229 44.87 81.58 0 SAMN16580178 GCA_018383165.1
82d 97_2 Novel species 97 within the genus Rs-D84 NA NA 769,008 165 5,928 44.97 86.05 1.72 SAMN16580182 https://doi.org/10.6084/m9.figshare.16896877.v3
146d 97_3 Novel species 97 within the genus Rs-D84 NA NA 855,668 89 15,967 44.74 91.38 1.72 SAMN16580179 https://doi.org/10.6084/m9.figshare.16896877.v3
10d 98_0 MX-02 sp006954405 9.2 99.14 1,434,374 143 17,966 47.98 97.66 1.4 SAMN16580178 GCA_018384975.1
150d 99_0 UBA4372 sp900766785 14.0 97.69 2,081,807 432 6,161 50.82 77.66 0 SAMN16580182 GCA_018385095.1
Open in a new tab
a

Genome statistics were derived using CheckM. NA, not applicable.

b

Species and strain clusters have been numbered according to clustering at 95% and 99% ANI, with the species cluster number followed by an underscore and then the strain designation.

c

The taxonomic assignment represents the species designation given by the GTDB toolkit. For novel species, we have listed our species cluster within the lowest level assigned by GTDB.

d

Strain representative with the best binning statistics.

Data availability.

The shotgun sequence data have been deposited at the NCBI under BioProject accession number PRJNA672868 and BioSample accession numbers SAMN16580178, SAMN16580179, SAMN16580180, SAMN16580181 and SAMN16580182, with supplementary information on Figshare at https://doi.org/10.6084/m9.figshare.16896877.v3. The recovered MAGs dereplicated at 99% ANI can be found on Figshare at https://doi.org/10.6084/m9.figshare.16896877.v3, with the assemblies representing novel species available under NCBI BioProject accession number PRJNA672868 (Table 1).

ACKNOWLEDGMENTS

This research is supported by the Quadram Institute Bioscience BBSRC-funded Strategic Program: Microbes in the Food Chain (project number BB/R012504/1) and its constituent project BBS/E/F/000PR10351 (Theme 3, Microbial Communities in the Food Chain) and by the Medical Research Council CLIMB grant (MR/L015080/1). This project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement number 773830.

We thank the farm involved in the collection of pig fecal samples alongside the QIB bioinformatics team.

Contributor Information

Mark J. Pallen, Email: m.pallen@uea.ac.uk.

Kenneth M. Stedman, Portland State University

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Associated Data

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

Data Availability Statement

The shotgun sequence data have been deposited at the NCBI under BioProject accession number PRJNA672868 and BioSample accession numbers SAMN16580178, SAMN16580179, SAMN16580180, SAMN16580181 and SAMN16580182, with supplementary information on Figshare at https://doi.org/10.6084/m9.figshare.16896877.v3. The recovered MAGs dereplicated at 99% ANI can be found on Figshare at https://doi.org/10.6084/m9.figshare.16896877.v3, with the assemblies representing novel species available under NCBI BioProject accession number PRJNA672868 (Table 1).

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