TABLE 2.
Classification of bacteria in the B. cereus group according to 16S rRNA sequences
| Subgroup name | Subgroup-specific signature(s) (position)a | Start and end of sequence | Organismr | GenBank accession no. | Position(s) of strain-specific variations |
|---|---|---|---|---|---|
| Anthracis | Consensusa | 11-1554 | B. anthracis Sterneb | AF176321 | —s |
| 1-1451 | B. anthracis Sternec | X55059 | — | ||
| 18-1499 | B. anthracis Sterne | AF290552 | A/W(1147) | ||
| 11-1554 | B. anthracis Ames ANRb | AF155950 | — | ||
| 1-1554 | B. anthracis Ames (TIGR)d | AE017024-26, AE017039 | A/W(1146) | ||
| 11-1554 | B. anthracis Delta Ames-1b | AF155951 | — | ||
| 33-1517 | B. anthracis (wastewater isolate)e | AY043083 | A/T(1146) | ||
| 18-1499 | B. anthracis Vollum | AF290553 | A/W(1147) | ||
| 12-1424 | B. anthracis W21 | AF390088 | C/A(19), T/A(967), A/T(969), TT/GA(1095,1096), T/G(1100), C/A(1113), ins A(1123-1124), A/T(1146), C/T(1200), A/T(1207), C/A(1209), T/C(1220) | ||
| 61-528, 815-1501 | B. anthracis 1b | J. Jackmanf | — | ||
| 61-528, 815-1501 | B. anthracis 2b | J. Jackmanf | — | ||
| Cereus A | Consensusa | 1-1451 | B. cereus NCTC 11143c | X55063 | — |
| 49-1522 | B. cereus WSBC 10037g | Z84576 | A/G(178), G/T(1518) | ||
| 49-1522 | B. cereus WSBC 10030g | Z84575 | C/T(353), T/C(600), T/C(864), A/C(1146), G/T(1518) | ||
| 49-1489 | B. cereus S-5g | AF390086 | C/T(353), A/C(1146) | ||
| 28-1517 | B. cereus AL1g | AY129651 | A/T(1146), del(1459) | ||
| 28-1513 | B. cereus (bovine serum isolate)g | AF206326 | A/G(181), C/T(285), C/T(467), C/T(480), G/A(482), T/C(600), C/T(995), A/C(1146), T/C(1244), T/C(1345), delT(1459) | ||
| 105-1277 | B. cereus ATCC 10702g | AF363440 | — | ||
| 105-1277 | B. cereus DL5g | AF363441 | C/T(906), C/T(1035), G/A(1046), T/G(1141), T/A(1256), A/G(1263) | ||
| 105-1277 | B. cereus DL115g | AF363442 | A/C(462), ins A(471-472), A/C(623), T/C(746), C/A(771), T/C(872), C/T(906), C/T(1035), T/A(1256) | ||
| 1-1554 | B. cereus ATCC 10987d | AE017264-66AE017280 | — | ||
| B. cereus HFR1414h | ? | ||||
| 31-1462 | Bacillus sp. strain JJ-1g | Y15466 | — | ||
| 28-1534 | Bacillus sp. strain BSID723g | AF027659 | C/A(1232) | ||
| 18-1499 | Bacillus sp. strain AH526g | AF290562 | — | ||
| 52-1517 | Bacillus sp. strain YSS/2001-3g | AF417847 | A/T(1146), A/T(1155), T/G(1402), G/C(1426), ins G(1454-1455) | ||
| 228-1437 | Bacillus sp. strain FO-011g | AF234842 | ins T (276-277), ins C (280-281), C/T(293), C/A(303), A/T(323), C/T(350), G/T(416), C/T(498), C/A(520), A/T(568), G/A(1190), A/T(1205), ins T(1219-1220) | ||
| 11-1554 | B. thuringiensis B8b | AF155955 | — | ||
| Cereus B | C/A(1015)q | 11-1554 | B. cereus NCTC 9620b | AF155952 | — |
| 11-1554 | B. cereus Tb | AF176322 | — | ||
| 28-1513 | B. cereus IAM 12605i | D16266 | — | ||
| 1-1451 | B. cereus NCDO 1771ci | X55060 | — | ||
| 17-1499 | B. cereus ATCC 1778i | AF290546 | — | ||
| 17-1499 | B. cereus ATCC 4579i | AF290547 | — | ||
| 49-1522 | B. cereus ATCC 27877 | Z84581 | A/T(828), G/T(1518) | ||
| 28-1183 | B. cereus (ocular isolate) | AF076031 | C/T(498), del C(520), del (523), T/A(829), C/G(1167) | ||
| 17-1499 | B. cereus ATCG 31293 | AF290548 | — | ||
| 1-1554 | B. cereus BGSC 6A5d | AY224379-88 | — | ||
| 8-1523 | B. cereus SH 01e | AF522353 | A/T(171) | ||
| 11-1249 | B. cereus Tim-r01 | AB050630 | C/T(182) | ||
| 105-1277 | B. cereus DL137 | AF363444 | A/T(170), G/C(407), A/C(623) | ||
| 105-1277 | B. cereus DL122 | AF363443 | A/T(170), G/C(345), A/T(496), A/C(623) | ||
| 20-1534 | Bacillus sp. strain P16 | AY048782 | G/A(28), T/C(30) | ||
| 11-1515 | Bacillus sp. strain 82344 | AF227848 | — | ||
| 45-1513 | Bacillus sp. strain F26 | AF385082 | T/C(49), G/C(530) | ||
| 30-1484 | Glacial ice bacterium SB-12K-9-4 | AF479367 | — | ||
| 30-1481 | Glacial ice bacterium G500K-2 | AF479333 | — | ||
| 30-1475 | Glacial ice bacterium G50-TS3 | AF479356 | — | ||
| 47-1470 | Bacillaceae bacterium PH27B | AF513473 | ins GT(1379-1380) | ||
| 49-1517 | Unident. HTA484 (Mariana Trench isol.) | AB002640 | G/C(72), GC/CG(297,298), del (946), ins C(1111-1112), del (1279) | ||
| 49-1522 | B. thuringiensis WS2614 | Z84584 | A/C(128), G/T(1518) | ||
| 49-1522 | B. thuringiensis WS2617 | Z84585 | G/A(1153), G/T(1518) | ||
| 49-1522 | B. thuringiensis WS2618 | Z84586 | A/G(725), G/T(1518) | ||
| 49-1522 | B. thuringiensis WS2626 | Z84588 | G/T(1518) | ||
| Thuringiensis A | C/A(1015), C/T(192) | 49-1522 | B. thuringiensis WS2623 | Y18473 | G/T(109), A/G(679), T/C(1228), A/G(1503) |
| 49-1522 | B. thuringiensis WS2625 | Z84587 | C/T(565), G/T(1183), G/T(1518) | ||
| 18-1479 | B. thuringiensis ATCC 33679 | AF290549 | C/Y(192) | ||
| B. thuringiensis 4R1,j 4D1,j 4F1,j 4S2,j 4T1, 4W1,j and 4J4j | ? | ||||
| 22-1502 | Bacillus sp. strain FPI/2002 | AY124766 | — | ||
| 8-1514 | Bacillus sp. strain KPU-0013 | AB067810 | C/G(131), C/T(182), G/A(202), del (298), C/T(444), T/G(781), A/C(796), G/A(952), TC/CT(1036,1037), G/T(1313) | ||
| 55-1510 | Unident. sp6 (bovine rumen isolate) | AB003391 | C/T(63), del(108), C/T(182), C/G(227), GC/CG(297,298), del(565), del(1038) | ||
| 20-1530 | Bacillus sp. strain CMB03 | AF406633 | G/A(28), T/C(30), ins C(730-731), A/T(1146), G/A(1254), T/A(1256), A/G(1263), G/A(1266), A/G(1269), G/A(1271), GG/TA(1282,1283), T/C(1287), T/C(1292), A/T(1299), C/T(1301), T/C(1317), T/C(1319), G/T(1322), C/A(1333), A/G(1336), A/G(1338), G/A(1451), T/A(1463), T/G(1477) | ||
| 18-1499 | B. cereus ATCC 43881 | AF290550 | C/Y (182) | ||
| Thuringiensis B | C/A(1015), C/T(192), A/G(77), T/C(90), T/A(92) | ||||
| 11-1554 | B. thuringiensis 4Q281b | AF155954 | — | ||
| 28-1513 | B. thuringiensis IAM 12077k | D16281 | — | ||
| 1-1451 | B. thuringiensis NCIMB 9134ck | X55062 | — | ||
| 18-1499 | B. thuringiensis ATCC 10792k | AF290545 | — | ||
| 37-1491 | B. thuringiensis 82347 | AF157112 | C/Y(182), del C(303), del C(347), ins T(395-396), G/A(1029), C/T(1111), del G(1148), del G(1240), del C(1246), del G(1262), GG/AS(1321,1322), del G(1492) | ||
| 49-1522 | B. thuringiensis (Pieris brassicae isolate) | AF160221 | A/C(161), A/T(183), no C/T(192), G/T(1518) | ||
| 50-1513 | B. thuringiensis Bactisubtil | AF172711 | G/A(733), G/A(778), C/A(857) | ||
| 11-1052 | B. thuringiensis HMB12389 | AF501348 | G/C(39) | ||
| B. thuringiensis 9308,l 20,l Lb5,l 1230,l and L3l | ? | ||||
| B. thuringiensis 4A1,j 4A7,j 4Q1,j 4Q2,j and 4M1j | ? | ||||
| B. cereus Nagoya 126m and 127m | ? | ||||
| 11-1554 | B. medusa ATCC 25621bn | AF155958 | No C/T (192) | ||
| 7-1440 | B. medusa NCIMB10437cn | X60628 | del C(1038), A/G (1383) | ||
| 18-1499 | Bacillus sp. strain AH540 | AF290557 | A/R(77), T/Y(90), T/W(92), T/A(1462) | ||
| 8-1497 | Bacillus sp. strain Fa7 | AY131217 | C/A(19), del (28), no C/T(192) | ||
| 20-1499 | Bacillus sp. strain SVM | AF503203 | C/Y(192) | ||
| 8-1554 | Bacillus sp. strain Kaza-37 | AF441732 | del (25), G/C(634), A/G(828), G/C(949), ins (955-956), del (963), del (982), G/A(983), ins T(990-991), ins T(1000-1001), ins AG(1048-1049), G/A(1049), G/A(1089) | ||
| 8-1554 | Bacillus sp. strain Kaza-31 | AF441728 | no C/T(192), GGG/CCC(309-311), ins C(496-497), ins T(516-517), ins G(523-524), G/A(526), G/C(712), G/C(949), ins A(973-974), ins C(979-980), ins C(988-989), ins T(1009-1010), del G(1029), ins A(1055-1056), G/A(1098), delA(1269) | ||
| 28-1403 | Bacillus sp. strain A23 | AF397398 | No T/A (92) | ||
| 26-1401 | Bacillus sp. strain A24 | AF397399 | — | ||
| 18-1499 | Bacillus sp. strain AH533 | AF290556 | C/Y(182) | ||
| 7-1551 | Bacillus sp. strain Termite isolate bac | X81132 | C/T(182), TT/GG(186,187), G/C(769), TA/CT(822,823), del A(875), G/C(897), TGG/CTA(1281-1283), del C(1301), ins GG(1428-1429), T/A(1461), del T(1463), CG/GT(1473,1474), del CT(1475,1476) | ||
| 28-1513 | Bromate-reducing bacterium B6e | AF442522 | G/K(61), G/S(66), G/R(93), G/S(100), G/R(141), C/T(182), G/C(255), T/K(264), G/S(297), G/A(307), G/R(334), C/A(1130), T/A(1462) | ||
| 30-1489 | Glacial ice bacterium SB100-8-1 | AF479369 | C/T(182), T/A(1462) | ||
| 33-1485 | Unident. bacterium V | AB004761 | No T/A(92), G/C(667), T/A(1462) | ||
| 18-1499 | B. cereus ATCC 53522 | AF290551 | CG/AM(1423,1424) | ||
| 18-1499 | B. cereus AH527 | AF290555 | C/Y(182) | ||
| 29-1532 | B. cereus ATCC 14893 | AJ310098 | CG/AY(43,44) | ||
| 28-1530 | B. cereus biovar toyoi CNCM I-1012/NCIB 40112 | AJ310100 | — | ||
| 62-1511 | B. cereus Biosubtil-Dalat | AJ277907 | del T(76), G/A(388), G/A(402), del G(407), del G(425), G/T(436), G/A(769), G/C(772), G/A(787), ins C(788-789), C/T(1073) | ||
| 62-1511 | B. cereus Bactisubtil | AJ277908 | del A(70), del T(76), G/A(424), G/C(431), G/T(436), del G(680), G/A(769), G/C(772), C/T(1037), T/C(1039), C/T(1041), del AGCA(1045-1048), del A(1048), T/A(1052), AC/GA(1054,1055), del T(1072), C/T(1073), ins A(1103-1104), C/G(1113), ins A(1121-1122) | ||
| B. thuringiensis BT3,ko BT13,o BT15,o BT16,o BTT6,o and BTT8o | ? | ||||
| Mycoides A | C/A(1015), C/T(192), G/A(133), C/T(182), G/A(197), A/G(286), C/T(1029), G/A(1030), T/A(1464) | 1-1451 | B. mycoides DSM2048Tp | X55061 | — |
| 49-1551 | B. mycoides MWS5303-1-4 | Z84591 | T/C(1454), G/T(1518) | ||
| 49-1523 | B. mycoides DRC1 | AF144645 | C/G(63), G/A(1279), TAG/GTA(1319-1321), C/G(1398), A/C(1437), G/T(1441), G/T(1471), T/A(1477), G/A(1492) | ||
| 49-1522 | B. mycoides MWS5303-2-51 | Z84583 | A/G(180), G/T(1518) | ||
| 32-1544 | B. mycoides ATCC 6462p | AB021192 | — | ||
| 228-1415 | B. mycoides FO-080 | AF234860 | G/T(289), G/C(297), del G(311), C/G(387), G/T(392), C/T(520), ins A(532-533), ins G(827-828), A/T(1112), C/T(1117), G/A(1134), G/C(1148), del G(1162), del G(1202) | ||
| 32-574 | B. mycoides B10 | BMY491827 | ins G(111) | ||
| 16-340 | B. mycoides SFLB6 | BMY344516 | A/T(50), A/G(69) | ||
| 14-1544 | B. weihenstephanensis DSM11821 | AB021199 | — | ||
| 49-1522 | B. cereus WSBC10201 | Z84577 | A/G(203), no A/G(286), A/G(1513), G/T(1518) | ||
| 49-1522 | B. cereus WSBC10204 | Z84578 | A/G(128), G/T(1518) | ||
| 49-1554 | B. cereus WSBC10206 | Z84579 | G/C(225), AG/GT(1517,1518) | ||
| 49-1522 | B. cereus WSBC10210 | Z84580 | A/G(60), T/C(375), A/G(1298), G/T(1518) | ||
| 18-1499 | B. cereus AH521 | AF290554 | — | ||
| 18-1499 | Bacillus sp. strain AH628 | AF290558 | — | ||
| 18-1499 | Bacillus sp. strain AH648 | AF290559 | — | ||
| 18-1499 | Bacillus sp. strain AH665 | AF290560 | — | ||
| 18-1499 | Bacillus sp. strain AH678 | AF290561 | — | ||
| 28-1517 | Bacillus sp. strain Fa25 | AY131220 | — | ||
| Mycoides B | A/C(189), T/G(200), G/C(208), T/C(1036), A/G(1045) | 11-1554 | B. mycoides ATCC 6462mb | AF155956 | — |
| 11-1554 | B. mycoides ATCC 10206b | AF155957 | — | ||
| 117-423 | B. mycoides jshs5 | AY039819 | T/G(132), T/A(185), ins C(185-186), ins G(202-203), T/G(206), C/G(411) | ||
| 7-1520 | B. pseudomycoides sp. nov. | AF013121 | A/T(55), C/A(341), T/C(495), C/T(516), G/C(566), A/T(929), C/A(958), A/C(1017), T/C(1034), T/G(1040), G/C(1104), C/A(1110), A/C(1121), A/T(1128), C/G(1138), C/A(1232), C/A(1276), T/A(1281), T/A(1390), G/A(1441), G/A(1485), T/A(1508) | ||
| 34-1373 | B. cereus Ki21 | AJ288157 | A/T(95), no T/G(200), del G(202), A/G(329), T/G(752), G/C(778), A/G(793), no T/C(1036), T/A(1350), T/A(1357) |
For more details, see Fig. 1.
Sequenced in this work.
Sequences need to be reexamined; see also Results.
From sequences of whole genome; data represent average sequence of all available 16S rRNA genes.
Sequence submitted in 3′ to 5′ form.
J. Jackman, unpublished.
Final discrimination from Anthracis subgroup will be done after sequencing of 23S rRNA gene (see Results).
Not sequenced; identified through hybridization analysis (see Results).
These four strains are identical and correspond to B. cereus DSM 31; see 23S rRNA sequence of this strain in Table 3.
Not sequenced; assignment to subgroups Thuringiensis A or B was based on hybridization with subgroup-specific probes (S. Bavykin and J. Jackman, unpublished).
These four strains are identical and correspond to B. thuringiensis DSM2046; see the 23S rRNA sequence of this strain in Table 3.
Not sequenced; subgroup-specific signatures A/G(77), T/C(90), and T/A(92) were identified by hybridization with subgroup-specific probes (18).
Not sequenced; subgroup-specific signatures A/G(77), T/C(90), and T/A(92) were identified by hybridization with subgroup-specific probes (55).
According to Bergey's Manual (45), these two strains of B. medusa should be identical.
Not sequenced; subgroup-specific signatures A/G(77), T/C(90), and T/A(92) were identified by hybridization with subgroup-specific probes (13).
According to Bergey's Manual (45), these two strains of B. mycoides should be identical.
Subgroup-specific mutations, which are highlighted in bold, were identical for two or more subgroups and are shown on separate lines to demonstrate connections between different subgroups.
Selected abbreviations of collections and institutions appearing in titles of listed strains: ATCC, American Type Culture Collection, Rockville, Md; NCTC, National Collection of Type Cultures and Pathogenic Fungi, London, United Kingdom; DSM or DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; HER, Center of Reference bacteria and viruses, Laval University, Department of Microbiology, Quebec, Canada; IAM, Institute of Applied Microbiology, University of Tokyo, Tokyo, Japan; NSDO or NSFB, National Collection of Food Bacteria, c/o NCIMB Ltd., Aberdeen, Scotland, United Kingdom; NCIMB or NCIB, National Collections of Industrial and Marine Bacteria Ltd., Aberdeen, Scotland, United Kingdom; CNCM, National Collection of Microorganisms and Cell Cultures, Pasteur Institute, Paris, France; TIGR, The Institute for Genomic Research, Rockville, Md. W = A or T; Y = C or T; S = C or G; M = A or C. Del, deletion; ins, insertion.
—, no strain-specific variations in this strain.