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Supplementary Table 1. Comparison of representative sequences from predominant Prevotella OTUs to Ribosomal Database Project Release 10.32. The relative abundance of sequences from each Prevotella-affiliated OTU in the enrichment dataset is listed in parentheses next to the OTU identifier. The reported similarity score represents the % identity over all pairwise comparable positions in aligned sequences. The closest matching sequence from an isolate described in a published paper is provided.

OTU ID / Nearest isolate (GenBank sequence ID) / Similarity Score / Reference
5 (10.2%) / Prevotella ruminicola 23 (CP002006) / 0.998 / 1
69 (7.1%) / Prevotella bryantii B14 (AJ006457) / 1.000 / 1
29 (2.4%) / Prevotella sp. RM15 (AB730678) / 0.992 / 2
91 (2.3%) / Prevotella sp. NK4A111 (GU324376) / 0.970 / 3
51 (1.8%) / Prevotella sp. RM15 (AB730678) / 0.968 / 2
53 (1.5%) / Prevotella sp. TC2-28 (AF218619) / 0.951 / 4
132 (1.3%) / Prevotella sp. RM17 (AB730679) / 0.971 / 2
220 (1.2%) / Prevotella sp. RM15 (AM730678) / 1.000 / 2
60 (1.2%) / Prevotella sp. R79 (AB730668) / 0.998 / 2
120 (1.1%) / Prevotella sp. C21a (AF396925) / 0.956 / 5

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Supplementary Table 2. Nucleotide BLAST comparison of selected genomic regions of fosmid clones generated from a bovine rumen enrichment culture

Table S2a. Nucleotide BLAST comparison of contig00026c (JX424618) against P. bryantii B14 (contig_114: NZ_ADWO01000019; contig_020: NZADWO0100066)

contig00026c start / contig00026c finish / P. bryantii start / P. bryantii finish / % ID / length
1 / 4339 / contig_114; 26850 / contig_114; 31187 / 99 / 4340
4492 / 9653 / contig_020; 80038 / contig_020; 74875 / 97 / 5166
9712 / 22603 / contig_020; 74816 / contig_020; 61925 / 99 / 12893
22611 / 27235 / contig_020; 60597 / contig_020; 55973 / 99 / 4625
27283 / 37675 / contig_020; 55925 / contig_020; 45532 / 98 / 10394

Average %: 98.4; Coverage %: 99.3; match: 37,418 / 37675

Table S2b. Nucleotide BLAST comparison of contig00028b (JX424621) against P. ruminicola 23 (CP002006)

contig00028b start / contig00028b finish / P.ruminicola start / P. ruminicola finish / % ID / length
1 / 6883 / 2698231 / 2691339 / 83 / 6917
19127 / 21401 / 2670150 / 2667876 / 81 / 2275
21497 / 22618 / 2657978 / 2656857 / 84 / 1125
22646 / 24079 / 2655873 / 2654443 / 81 / 1434
26671 / 28546 / 2652489 / 2654364 / 78 / 1878
28582 / 37939 / 2652385 / 2643094 / 81 / 9392

Average %: 81.3; Coverage %: 60.6; match: 23021 / 37939

Table S2c. Nucleotide BLAST comparison of scaffold00033 (JX424622) against P. ruminicola 23 (CP002006)

scaffold00033 start / Scaffold00033 finish / P.ruminicola start / P. ruminicola finish / % ID / length
1 / 5871 / 3112394 / 3106517 / 91 / 5887
7346 / 29212 / 3048514 / 3026649 / 86 / 21901
29443 / 30896 / 3106153 / 3104700 / 83 / 1457
30912 / 37916 / 3103015 / 3096008 / 83 / 7074
39035 / 41367 / 3094905 / 3092303 / 86 / 2603
41701 / 43297 / 3092239 / 3090643 / 83 / 1598
43336 / 44772 / 3085363 / 3083991 / 80 / 1377
47237 / 49907 / 3085373 / 3088059 / 80 / 2691

Average %: 84; Coverage %: 89.3; match: 44588 / 49907

Table S2d. Nucleotide BLAST comparison of contig00044e (JX424627) against P. ruminicola 23 (CP002006)

contig00044e start / contig00044e finish / P.ruminicola start / P. ruminicola finish / % ID / length
3 / 6804 / 2698135 / 2691339 / 90 / 6834
6977 / 7990 / 2689641 / 2690690 / 70 / 1057
19316 / 22714 / 2677057 / 2673558 / 85 / 3406

Average %: 81.6; Coverage %: 49.5; match: 11297 / 22810

Table S2e. Nucleotide BLAST comparison of scaffold00066 (JX424628) against P. ruminicola 23 (CP002006)

scaffold00066 start / Scaffold00066 finish / P.ruminicola start / P. ruminicola finish / % ID / length
3518 / 5181 / 2959503 / 2961119 / 73 / 1679
5306 / 7379 / 3401114 / 3399071 / 71 / 2089
9081 / 11609 / 3101052 / 3098543 / 79 / 2547
11846 / 12991 / 194749 / 193613 / 69 / 1160
13560 / 16235 / 3038157 / 3040856 / 67 / 2725
16412 / 17514 / 3040979 / 3042081 / 76 / 1103
17687 / 18721 / 2236171 / 2237206 / 75 / 1043
18846 / 21184 / 188440 / 186207 / 73 / 2354
21360 / 22549 / 2079599 / 2078411 / 77 / 1191
22748 / 28835 / 3042129 / 3048210 / 76 / 6138
30702 / 32078 / 3036294 / 3037612 / 65 / 1399

Average %: 72.8; Coverage %: 72.5; match: 23428 / 32307

Supplementary Table 3. Description of putative Sus-like PULs identified in P. bryantii B14, P. ruminicola 23 and five reconstructed rumen Bacteroidales genomes. Protein sequences were analysed using dbCAN and pfam. TonB indicates members of the TonB dependent receptor family of proteins that are predicted to transport solutes and macromolecules. Designation of putative targets is based on functional activities of related CAZymes

Table S3a. P. bryantii B14 (refer to [1] for genome information)

Locus tag / Gene product
PBR_0729
PBR_0730
PBR_0731
PBR_0732
PBR_0733
PBR_0734
PBR_0735 / PL1
hypothetical protein
SusD
SusC (TonB)
CE8
SpoT
GH23/CBM50
PBR_1564 *1
PBR_1565
PRB_1566
PBR_1567
PBR_1568 / SusD
SusC
CE7
hypothetical protein
PL1/CE8
PBR_0377
PBR_0378
PBR_0379
PBR_0380
PBR_0381 *2
PBR_0390 *3
PBR_0391
PBR_0392
PBR_0393
PBR_0394
PBR_0395
PBR_0396
PBR_0397
PBR_0398 / GH10
hypothetical protein
SusD
SusC(TonB)
SusD
SusD
SusC (TonB)
GH43/CE6
AraC
GH43
GH10
sugar transporter
CE12
GH67
This locus corresponds to the major xylanolytic gene cluster described in Figure 2 of the paper published in [6]. Their evidence suggests that PBR_0381 and PBR_0390 make up a single gene split across two contigs of the sequence generated in [1]
PBR_2399
PBR_2400
PBR_2401
PBR_2402
PBR_2403
PBR_2404
PBR_2405
PBR_2406 / AraC
SusC (TonB)
SusD
hypothetical protein
GH32
GH32
sugar transporter
fructokinase
PBR_0281
PBR_0282
PBR_0283
PBR_0284
PBR_0285
PBR_0286
PBR_0287 / AraC
hypothetical protein
SusC (TonB)
SusD
GH30
GH30
GH35/CBM32
PBR_0326
PBR_0327
PBR_0328
PBR_0329
PBR_0330
PBR_0331
PBR_0332
PBR_0333
PBR_0334
PBR_0335
PBR_0336
PBR_0337
PBR_0338
PBR_0339
PBR_0340
PBR_0341
PBR_0342
PBR_0343
PBR_0344
PBR_0345 / GH53
GH53
GH13/CBM26
hypothetical protein
SusE
SusD
SusC (TonB)
LacI
sugar transporter
GH77/CBM20
GH97
GH13
GH13
AraC
SusC (TonB)
SusD
hypothetical protein
GH43
AraC
GH43
PBR_0351 to PBR_0369
(also see Genbank
accession U96771) / function of genes PBR_0363 to PBR_0369 determined in [7];
c.f. Sc00026 in main text
PBR_0601
PBR_0602
PBR_0603
PBR_0604
PBR_0605
PBR_0606
PBR_0607
PBR_0608
PBR_0609 / glycogen debranching enzyme
GT4/GT5
GH57
hypothetical protein
SusD
SusC (TonB)
CE8
PL1
GH28/GH105
PBR_1231
PBR_1232
PBR_1233
PBR_1234
PBR_1235 *4 / PL11
PL11
CE3/CE10
SusC (TonB)
SusD
PBR_0315
PBR_0316
PBR_0317
PBR_0318
PBR_0319
PBR_0320 *5 / GH28
CE12
hypothetical protein
SusC (TonB)
SusD
SusC (TonB)
PBR_0843
PBR_0845
PBR_0846
PBR_0847
PBR_0848 / GH97
GH66
SusE
SusD
SusC (TonB)

*1 This gene is located at the beginning of contig_099 and represents an incomplete ORF with homology to PF14322.1

*2This gene is located at the end of contig_021 and represents an incomplete ORF with homology to PF14322.1

*3 This gene is located at the beginning of contig_025 and represents an incomplete ORF with homology to PF14322.1

*4 This gene is located at the end of contig_080 and represents an incomplete ORF with homology to PF14322.1

*5 This gene is located at the end of contig_018 and represents an incomplete ORF with homology to PF07715.10

Table S3b. P. ruminicola 23 (refer to [1] for genome information)

Locus tag / Gene product
PRU_0153
PRU_0154
PRU_0155 / GH94
SusC (TonB)
SusD
PRU_0268
PRU_0269
PRU_0270
PRU_0271
PRU_0272
PRU_0273 / GH127
GH43/CBM32
GH97
GH127
SusC (TonB)
SusD
PRU_1155
PRU_1156
PRU_1157
PRU_1158
PRU_1159
PRU_1160
PRU_1161
PRU_1162
PRU_1163
PRU_1164
PRU_1165
PRU_1166
PRU_1167
PRU_1168 / CE14
GH20
GH20
GH125
GH92
SusC (TonB)
SusD
GH18/GH78
GH2/CBM32
GH29
GH92
GH29/CBM32
GH3
GH92
PRU_1461
PRU_1462
PRU_1463
PRU_1464
PRU_1465
PRU_1466
PRU_1467
PRU_1468
PRU_1469
PRU_1470
PRU_1471
PRU_1472 / GH28/GH105
SusC (TonB)
SusD
hypothetical protein
rhamnulose-1-P aldolase
sugar transporter
L-rhamnose isomerase
rhamnulokinase
GH28
GH2
hypothetical protein
CE12
PRU_1568
PRU_1569
PRU_1570
PRU_1571
PRU_1572 / GH35
SusD
SusC (TonB)
PL11
AraC
PRU_1590
PRU_1591
PRU_1592
PRU_1593
PRU_1595
PRU_1596
PRU_1597 / SusD
SusC (TonB)
CE12
GH2
GH106
SusD
SusC
PRU_1883
PRU_1884
PRU_1885
PRU_1886
PRU_1887
PRU_1888
PRU_1889 / GH24
hypothetical protein
hypothetical protein
SusC (tonB)
SusD
SusC (tonB)
SusD
PRU_1950
PRU_1951
PRU_1952
PRU_1953
PRU_1954
PRU_1956 / SusC (tonB)
SusD
hypothetical protein
GH16
CotH
GH3
PRU_2072
PRU_2073
PRU_2074
PRU_2075
PRU_2076
PRU_2077 / GH43
SusD
SusC (TonB)
hypothetical protein
GH43
AraC
PRU_2181
PRU_2182
PRU_2183
PRU_2184
PRU_2185
PRU_2186
PRU_2187
PRU_2188 / GH38/CBM32
GH31
hypothetical protein
GH31
hypothetical protein
SusE
SusD
SusC (TonB)
PRU_2222 to PRU_2232 / Refer to Figure 1
PRU_2271
PRU_2272
PRU_2273
PRU_2274
PRU_2275
PRU_2276
PRU_2277
PRU_2278
PRU_2279 / AraC
SusC (TonB)
SusD
hypothetical protein
GH32
GH32
sugar transporter
fructokinase
PEP carboxykinase
PRU_2307
PRU_2308
PRU_2309
PRU_2310
PRU_2311
PRU_2312
PRU_2313
PRU_2314
PRU_2315
PRU_2316 / GH28/GH43
GH43/CBM6
aminotransferase
GH28
hypothetical protein
GH3
GH2
GH97
hypothetical protein
SusC (TonB)
PRU_2436
PRU_2437
PRU_2438
PRU_2439
PRU_2440
PRU_2441
PRU_2442
PRU_2443
PRU_2444
PRU_2445
PRU_2246 / AraC
GH43
SusC (TonB)
SusD
GH105
PL12
hypothetical protein
hypothetical protein
SusD
SusC (TonB)
AraC
PRU_2514 to PRU_2519 / Refer to Figure 1
PRU_2609
PRU_2610
PRU_2611 / GH28
SusC (TonB)
SusD
PRU_2666
PRU_2667
PRU_2668
PRU_2669
PRU_2670
PRU_2671
PRU_2672
PRU_2673
PRU_2674
PRU_2675
PRU_2676
PRU_2677
PRU_2678
PRU_2679
PRU_2680
PRU_2681
PRU_2682
PRU_2683
PRU_2684
PRU_2685
PRU_2686
PRU_2687
PRU_2688
PRU_2689
PRU_2690
PRU_2691
PRU_2692
PRU_2693
PRU_2694
PRU_2695
PRU_2696
PRU_2697
PRU_2698
PRU_2699
PRU_2700
PRU_2701
PRU_2702
PRU_2703
PRU_2704
PRU_2705
PRU_2706
PRU_2707
PRU_2708
PRU_2709
PRU_2710
PRU_2711
PRU_2712
PRU_2713
PRU_2714
PRU_2715
PRU_2716 / LacI
sugar transporter
AraC
SusC (TonB)
SusD
hypothetical protein
GH43
GH43
GH43
hypothetical protein
GH53
GH33
CE7
CE7
GH43
SusC (TonB)
SusD
CBM48
hypothetical protein
GH13
GT2
serine-O-acetyltransferase
GT4
YgbB
hypothetical protein
hypothetical protein
fumarylacetoacetase
GH3
CE1/CBM48
hypothetical protein
SusD
SusC (TonB)
acid phosphatase
AraC
GH13
GH43/CBM13
GH43/CBM6
SusD
SusC (TonB)
SpoIIE
GH5
CE1/CE6
SusC (TonB)
SusD
GH125
GH92
SusC (TonB)
SusD
SusE
GH97
AraC
PRU_2728 to PRU_2739 / xylan utilization locus
(described in [6])

Table S3c. Bacteroidales genome AC2a (refer to [8])

Locus tag / Gene product
AC2a_41 to AC2a_54 / Refer to Figure 1
(AC2a_PUL3)
AC2a_118 to AC2a_125 / Refer to Figure 1
(AC2a_PUL1)
AC2a_153
AC2a_154
AC2a_155
AC2a_156
AC2a_157
AC2a_158
AC2a_159
AC2a_160 / SusD
SusC (TonB)
MFS family transporter
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
GH13
AC2a_857 to AC2a_873 / Refer to Figure 1
(AC2a_PUL2)
AC2a_887
AC2a_888
AC2a_889
AC2a_890
AC2a_891
AC2a_892
AC2a_893
AC2a_894 / SusC (TonB)
SusD
hypothetical protein
GH30
hypothetical protein
hypothetical protein
hypothetical protein
GH30
AC2a_985
AC2a_986
AC2a_987
AC2a_988 / SusC (TonB)
SusD
hypothetical protein
PL6/CBM16
AC2a_1050
AC2a_1051
AC2a_1052
AC2a_1053
AC2a_1054 / SusC (TonB)
SusD
putative glucoamylase (pfam)
GH3
GH20
AC2a_1620
AC2a_1621
AC2a_1622
AC2a_1623
AC2a_1624
AC2a_1625 / PL6/CBM26
DeoR
Amidohydrolase
GH36
SusC (TonB)
SusD

Table S3c. Bacteroidales genome AH (refer to [8])

Locus tag / Gene product
AH_888 to AH_895 / Refer to Figure 1
AH_967
AH_968
AH_969
AH_970
AH_971 / GH43
SusD
SusC (TonB)
GH43
Response regulator

Table S3d. Bacteroidales genome AJ (refer to [8])

Locus tag / Gene product
AJ_289
AJ_290
AJ_291
AJ_292
AJ_293
AJ_294
AJ_295
AJ_296
AJ_297
AJ_298
AJ_299
AJ_300
AJ_301
AJ_302 / CE1
GH9
hypothetical protein
hypothetical protein
GH2
CE3
hypothetical protein
hypothetical protein
ECF (sigma 70)
TIG domain
SusC (TonB)
SusD
hypothetical protein
GH43
AJ_376 to AJ_383 / Refer to Figure 1
AJ_617
AJ_618
AJ_619
AJ_620 / GH13
hypothetical protein
SusC (TonB)
SusD
AJ_902
AJ_903
AJ_904
AJ_905
AJ_906
AJ_907
AJ_908
AJ_909
AJ_910
AJ_911
AJ_912
AJ_913
AJ_914
AJ_915
AJ_916
AJ_917
AJ_918 / GH26
hypothetical protein
GH128
2 x CBM61
GH109
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
SusC (TonB)
SusD
Fas domain
Fas domain
Fas domain
Fas domain
SusC (TonB)
SusD
AJ_1121
AJ_1122
AJ_1123
AJ_1124
AJ_1125
AJ_1126
AJ_1127
AJ_1128 / GH106
GH76
GH92
hypothetical protein
SusD
SusC (TonB)
TIG domain
CBM67
AJ_1486
AJ_1487
AJ_1488
AJ_1489
AJ_1490
AJ_1491
AJ_1492
AJ_1493
AJ_1494
AJ_1495
AJ_1496
AJ_1497
AJ_1498 / GH13
GH53
GH13
hypothetical protein
hypothetical protein
putative metallopeptidase
hypothetical protein
hypothetical protein
hypothetical protein
SusE
SusD
SusC (TonB)
MFS family transporter

References for Supplementary Materials

1. Purushe J, Fouts DE, Morrison M, White BA, Mackie RI, Coutinho PMet al(2010) Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. Microb Ecol 60: 721-729

2. Nyonyo T, Shinkai T, Tajima A, Mitsumori M (2013) Effect of media composition, including gelling agents, on isolation of previously uncultured rumen bacteria. Lett Appl Microbiol 56(1): 63-70

3. Kenters N, Henderson G, Jeyanathan J, Kittelmann S, Janssen PH (2011) Isolation of previously uncultured rumen bacteria by dilution to extinction using a new liquid culture medium. J Microbiol Methods 84(1):52-60

4. Ramsak A, Peterka M, Tajima K, Martin JC, Wood J, Johnston MEA et al(2000) Unraveling genetic diversity of ruminal bacteria belonging to the CFB phylum. FEMS Microbiol Ecol 33(1):69-79

5. Reilly K, Carruthers VR, Attwood GT (2002) Design and use of 16S ribosomal DNA-directed primers in competitive PCRs to enumerate proteolytic bacteria in the rumen. Microb Ecol 43(2): 259-270

6. Dodd D, Moon Y-H, Swaminathan K, Mackie RI, Cann IKO (2010) Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic Bacteroidetes. J Biol Chem 285: 30261-30273

7. Gardner RG, Wells JE, Fields MW, Wilson DB, Russell JB (1997) A Prevotella ruminicola B14 operon encoding extracellular polysaccharide hydrolases. Curr Microbiol 35: 274-277.

8. Hess M, Sczyrba A, Egan R, KimT-W, Chokhawala H, Schroth G et al (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331: 463-467