Article Figures & Data
- FIG 1
Comparisons of regions 1 to 5 in the three or four genomes containing these MGEs. Differences between strains for each region following sequencing to resolve Ns are shown. The remaining SNPs displayed were not tested by sequencing and represent the original genome sequence for each isolate. The positions of IS and RE in regions 1 and 2 are shown with the corresponding sizes of these elements.
- FIG 2
Open reading frame (ORF) maps of regions 1 to 5. Regions are oriented so that the majority of the tra genes (red) read left to right. The letter above the red genes indicates the particular tra gene. An open reading frame map, excluding variable IS and RE, is shown for each region, with the locations of IS and RE indicated. Genes encoding selective orthologous proteins present in each region are color coded as indicated above. Genes comprising the type VI secretion system (T6SS) of region 2 are shown (blue). The 24,866-bp region 1 (boxed) and the 17,607-bp region 3 (boxed) are extended to show the likely extent of the MGEs that were transferred between strains.
- FIG 3
Likely extent of the MGEs containing regions 1 and 3. Boxed regions are the extent of regions 1 and 3 identified by the indicated BLAST criteria. (A) Expansion of region 1 in two of the three genomes. (B) Expansion of region 3 based on smaller matching scaffolds in each of the two genomes that are noncontiguous with the region from P. merdae.
- FIG 4
ORF map of portion of region 2, encoding a putative T6SS. Genes encoding proteins characteristic of or commonly associated with T6SS are color coded as indicated below. These designations are based on the analyses as outlined in Table S6 in the supplemental material. The putative functions of all gene products encoded by the genes shown here are included in Table S6.
- TABLE 1
Composition of natural Bacteroidales communities and identification of highly similar regions in strains coresident in a gut microbial ecosystem
Microbial ecosystem, organisma No. of contigs Genome size (bp) CL02 region (size [bp])b: CL03 region (size [bp])b: CRISPR/Cas systemc 1 (24,866) 2 (116,095) 3 (17,607) 4 (60,734) 5 (42,545) 6 (44,124) CL02 B. cellulosilyticus CL02T12C19 25 7,678,000 ✓ ✓ Type I B. dorei CL02T12C06 21 5,997,310 ✓ ✓ Type I B. nordii CL02T12C05 10 5,707,590 None B. ovatus CL02T12C04 15 7,880,760 None B. salyersiae CL02T12C01 7 5,781,840 ✓ ✓ Type I, III P. goldsteinii CL02T12C30 14 6,690,360 Type I P. johnsonii CL02T12C29 6 4,613,500 ✓ None CL03 B. caccae CL03T12C61 6 5,479,120 ✓ None B. dorei CL03T12C01 20 5,387,250 Type I B. fragilis CL03T12C07 7 5,214,030 ✓ ✓ Type II, III B. ovatus CL03T12C18 19 6,972,150 +/− +/− ✓ None B. uniformis CL03T12C37 14 4,890,740 ✓ ✓ Type II B. xylanisolvens CL03T12C04 13 6,056,100 ✓ ✓ ✓ None P. distasonis CL03T12C09 5 5,055,860 ✓ Type I, II P. merdae CL03T12C32 13 4,918,050 ✓ ✓ None - TABLE 2
BLAST output of regions 1 to 6 against the databasea
BLAST targetb % Identityc Alignment length No. of: Query Target Accession no. MMd Gaps Start End Start End Query—CL02 region 1 B. salyersiae CL02T12C01 100.00 22,005 0 0 1,234 23,238 1,381,606 1,403,610 NZ_JH724307.1 B. cellulosilyticus CL02T12C19 100.00 22,005 0 0 1,234 23,238 5,321 27,325 NZ_JH724088.1 B. dorei CL02T12C06 99.99 17,671 1 0 7,196 24,866 530,799 548,469 NZ_JH724135.1 B. eggerthii DSM 20697 99.78 24,878 25 10 1 24,866 622,697 647,557 NZ_DS995509.1 B. plebeius DSM 17135 97.99 10,412 200 9 10,543 20,946 174,332 184,742 NZ_DS990131.1 B. fragilis 3_1_12 95.05 13,605 615 45 11,286 24,866 1,817,695 1,804,125 NZ_EQ973213.1 Query—CL02 region 2 B. dorei CL02T12C06 100.00 109,844 2 1 6,257 116,095 1,017,432 907,589 NZ_JH724134.1 B. salyersiae CL02T12C01 100.00 109,844 4 1 6,257 116,095 567,507 677,350 NZ_JH724309.1 P. johnsonii CL02T12C29 100.00 55,262 0 2 1 55,262 109,000 164,259 NZ_JH976468.1 100.00 53,650 2 1 62,451 116,095 178,109 231,758 NZ_JH976468.1 B. cellulosilyticus CL02T12C19 100.00 59,402 2 0 1 59,042 290,506 231,465 NZ_JH724088.1 99.99 13,339 1 0 59,002 72,340 231,364 218,026 NZ_JH724088.1 100.00 12,303 0 0 75,233 87,535 214,881 202,579 NZ_JH724088.1 100.00 28,560 1 0 87,536 116,095 202,478 173,919 NZ_JH724088.1 B. ovatus CL02T12C04 99.55 58,086 263 27 58,035 116,095 5,697 63,752 NZ_JH724231.1 Bacteroides sp. strain 3_2_5 98.71 33,023 426 41 2 33,010 2,030,884 2,063,856 NZ_JH636044.1 97.79 24,597 543 9 34,628 59,221 2,065,264 2,089,854 NZ_JH636044.1 Query—CL03 region 3 B. uniformis CL03T12C37 100.00 17,607 0 0 1 17,607 96 17,702 NZ_JH724271.1 P. merdae CL03T12C32 100.00 17,607 0 0 1 17,607 142,174 159,780 NZ_JH976456.1 B. dorei CL03T12C01 100.00 17,607 0 0 1 17,607 17,607 1 NZ_JH724164.1 B. eggerthii 1_2_48FAA 98.53 17,614 245 7 1 17,607 30,388 47,994 NZ_AKBX01000010.1 B. plebeius DSM 17135 98.48 17,615 250 13 2 17,607 30,516 48,121 NZ_DS990120.2 B. intestinalis DSM 17393 98.50 16,772 236 12 2 16,766 17,245 34,007 NZ_ABJL02000003.1 Query—CL03 region 4 B. fragilis CL03T12C07 100.00 60,734 0 0 1 60,734 285,831 346,564 NZ_JH724182.1 P. distasonis CL03T12C09 100.00 60,734 0 0 1 60,734 2,432,090 2,492,823 NZ_JH976495.1 B. xylanisolvens CL03T12C04 100.00 60,734 2 0 1 60,734 2,000,696 1,939,963 NZ_JH724294.1 B. ovatus CL03T12C18 100.00 44,008 2 0 1 44,008 31,399 75,406 NZ_JH724250.1 100.00 16,726 0 0 44,008 60,733 215,190 231,915 NZ_JH724243.1 B. fragilis NCTC 9343 99.20 38,365 289 17 22,378 60,733 2,040,415 2,078,771 NC_003228.3 99.63 15,410 55 2 1,801 17,209 2,017,133 2,032,541 NC_003228.3 B. helcogenes P 36-108 99.60 15,423 58 3 1,801 17,221 230,238 245,659 NC_014933.1 B. uniformis ATCC 8492 95.50 16,906 652 53 30,502 47,366 215,548 198,710 NZ_DS362247.1 Query—CL03 region 5 B. xylanisolvens CL03T12C04 100.00 42,545 0 0 1 42,545 1,171,697 1,214,241 NZ_JH724294.1 B. fragilis CL03T12C07 100.00 42,545 0 0 1 42,545 457,382 414,838 NZ_JH724184.1 B. uniformis CL03T12C37 100.00 42,545 2 0 1 42,545 725,544 768,088 NZ_JH724268.1 B. ovatus CL03T12C18 100.00 28,967 1 0 13,578 42,544 205,601 176,635 NZ_JH724243.1 Bacteroides sp. strain 3_1_23 96.50 18,468 561 50 16,314 34,740 2,449,865 2,431,442 NZ_GG774949.1 B. finegoldii DSM 17565 96.60 17,611 497 57 17,192 34,740 29,060 46,630 NZ_GG688325.1 B. salyersiae DSM 18765 97.03 16,978 442 35 17,790 34,740 554,600 537,659 NZ_KB905466.1 Query—CL03 region 6 B. xylanisolvens CL03T12C04 100.00 44,124 0 0 1 44,124 388,361 344,238 NZ_JH724296.1 P. merdae CL03T12C32 100.00 26,817 0 0 1 26,817 204,214 231,030 NZ_JH976457.1 100.00 16,701 0 0 27,424 44,124 236,576 253,276 NZ_JH976457.1 B. ovatus CL03T12C18 100.00 12,583 0 0 1 12,583 530,345 542,927 NZ_JH724241.1 100.00 23,711 1 0 12,584 36,294 545,391 569,101 NZ_JH724241.1 B. eggerthii DSM 20697 100.00 44,124 0 0 1 44,124 159,910 204,033 NZ_DS995511.1 P. merdae CL09T00C40 100.00 44,124 0 0 1 44,124 372,514 416,637 NZ_JH976526.1 Bacteroides sp. strain 3_1_19 100.00 44,124 0 0 1 44,124 180,923 225,046 NZ_GG774763.1 Bacteroides sp. strain D22 100.00 44,124 0 0 1 44,124 56,078 100,201 NZ_GG774819.1 Alistipes sp. strain HGB5 100.00 44,124 0 0 1 44,124 66,384 110,507 NZ_AENZ01000040.1 Alistipes onderdonkii DSM 19147 100.00 44,124 1 0 1 44,124 55,386 11,263 NZ_KB894552.1 B. intestinalis DSM 17393 100.00 44,124 0 1 1 44,124 456,857 412,735 NZ_ABJL02000006.1 B. stercoris ATCC 43183 100.00 44,124 2 0 1 44,124 103,168 59,045 NZ_DS499672.1 P. merdae ATCC 43184 100.00 44,124 1 1 1 44,124 73,390 117,512 NZ_DS264518.1 B. fragilis YCH46 DNA 100.00 44,124 1 1 1 44,124 163,822 119,700 NC_006347.1 - TABLE 3
BLAST output of three unique regions from the mock communities against the databasea
BLAST query (accession no.:position), targetb % Identityc Alignment length No. of: Query Target Accession no. MMd Gaps Start End Start End Query—B. stercoris ATCC 43183 (NZ_DS499676.1:176961–207558) B. stercoris ATCC 43183 100.00 30,598 0 0 1 30,598 176,961 207,558 NZ_DS499676.1 B. vulgatus PC510 99.96 30,599 10 2 1 30,598 30,597 1 NZ_ADKO01000036.1 B. uniformis ATCC 8492 99.95 30,602 9 3 1 30,598 176,746 207,345 NZ_DS362245.1 B. cellulosilyticus CL02T12C19 99.80 13,767 23 3 1 13,764 624,314 610,549 NZ_JH724089.1 B. vulgatus ATCC 8482 99.66 25,496 76 10 1 25,491 2,046,625 2,021,136 NC_009614.1 P. merdae ATCC 43184 99.61 25,500 83 12 1 25,491 117,639 92,147 NZ_DS264524.1 Query—B. fragilis HMW 616 (NZ_JH815527.1:1–13248) B. fragilis HMW 616 100.00 13,248 0 0 1 13,248 1 13,248 NZ_JH815527.1 100.00 13,248 0 0 1 13,248 80,750 67,503 NZ_JH815526.1 P. merdae ATCC 43184 99.99 13,248 1 0 1 13,248 356,073 342,826 NZ_DS264540.1 Bacteroides sp. strain 4_3_47FAA 99.99 13,248 1 0 1 13,248 561,549 548,302 NZ_JH114362.1 B. coprocola DSM 17136 89.09 8,440 800 87 4,875 13,248 8,644 17,028 NZ_DS981488.1 B. plebeius DSM 17135 89.09 8,440 800 87 4,875 13,248 241,574 249,958 NZ_DS990119.1 B. finegoldii CL09T03C10 86.88 5,349 638 46 7,935 13,248 82,421 77,102 NZ_JH951901.1 Query—B. faecis MAJ27 (NZ_AGDG01000049.1:1–12502) B. faecis MAJ27 100.00 12,502 0 0 1 12,502 1 12,502 NZ_AGDG01000049.1 B. plebeius DSM 17135 99.98 12,502 2 0 1 12,502 28,019 15,518 NZ_DS990120.2 B. intestinalis DSM 17393 99.98 12,502 2 1 1 12,502 14,748 2,248 NZ_ABJL02000003.1 Bacteroides sp. strain D22 99.87 12,502 0 4 1 12,502 35,210 22,725 NZ_GG774809.1 P. merdae CL03T12C32 98.71 8,731 112 1 603 9,333 139,124 130,395 NZ_JH976456.1 Bacteroides sp. strain 9_1_42FAA 98.67 9,241 120 1 2,512 11,752 25,552 34,789 NZ_EQ973174.1 - TABLE 4
Numbers of various products encoded by the five intracommunity-transferred regions
Putative category Putative assignment/function of gene products No. of products in: CL02 region: CL03 region: 1 2 3 4 5 Conjugative transfer machinery TraD (coupling protein) 1 1 1 1 1 TraG 1 1 1 1 TraJ 1 1 1 1 TraK 1 1 1 1 1 TraM 1 1 1 1 1 TraN 1 1 1 1 1 TraO 1 1 Recombinases Serine site-specific recombinases 2 1 1 Tyrosine site-specific recombinases/integrases 1 2 2 Element transfer/partitioning/segregation TOPRIM-like, DUF3991 2 1 1 TOPRIM primase 1 1 1 Excisionase 1 1 Single-stranded-DNA-binding protein family 3 2 ATPases—chromosome partitioning/CobQ/CobB/MinD/ ParA nucleotide binding 1 1 1 1 1 PRTRC system ParB family 1 1 1 Chromosome segregation protein SMC 1 1 Relaxase/mobilization nuclease 1 1 1 Other common proteins/domains RibD C-terminal domain, dihydrofolate reductase 1 1 1 DUF4099 1 1 1 1 1 DUF4133 1 1 1 DUF4134 1 1 1 DUF3408 1 1 1 PH domain protein 1 1 1 Transcriptional regulation/DNA binding RteC family 1 1 TetR family 1 1 1 Other transcriptional regulator 2 1 1 Other helix-turn-helix domain DNA-binding proteins 1 1 4 1 Selfish genes/element survival Putative toxin 1 1 1 2 1 Putative antitoxin /immunity protein 1 2 1 4 1 Anti-restriction protein 1 1 1 1 1 DNA methylase 1 3 Potential fitness genes Fimbria synthesis 2 MACPF domain containing 1 M23 peptidase family 2 3 1 Type VI secretion system (T6SS) ✓a ↵a ✓, the region is present in the organism.
Supplemental Material
Table S1
PCR primers used to elucidate DNA sequences of segments containing Ns. Table S1, DOCX file, 0.1 MB.
Copyright © 2014 Coyne et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Table S2
Characteristics of insertion sequences (IS) and retroelements (RE) present in regions 1 to 5. Each IS or RE element listed is different and shares little if any DNA homology to the other IS or RE listed. A pound sign (#) in a genome refers to additional copies not including the copy in the specified region. Table S2, DOCX file, 0.1 MB.
Copyright © 2014 Coyne et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Table S3
Human gut Bacteroidales strains used to compile the mock communities. Table S3, DOCX file, 0.1 MB.
Copyright © 2014 Coyne et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Table S4
Presence in 1,000 mock Bacteroidales communities of highly similar sequences with no or few other highly similar matches in the database. Table S4, DOCX file, 0.1 MB.
Copyright © 2014 Coyne et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Table S5
Putative annotations and motifs of the proteins encoded within regions 1 to 5. The genes with colored text correspond to the color coding shown in Fig. 2. Table S5, XLSX file, 0.1 MB.
Copyright © 2014 Coyne et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Table S6
Assignments of proteins encoded within a putative type VI secretion system of region 2 based on motif and homology/structure analyses (HHpred). Table S6, XLSX file, 0.1 MB.
Copyright © 2014 Coyne et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Additional Files
Supplementary Data
Supplementary Data
Files in this Data Supplement:
- Table st1, DOCX - Table st1, DOCX
- Table st2, DOCX - Table st2, DOCX
- Table st3, DOCX - Table st3, DOCX
- Table st4, DOCX - Table st4, DOCX
- Table st5, XLSX - Table st5, XLSX
- Table st6, XLSX - Table st6, XLSX
