TABLE 1.

Number of operons, heterogeneity and redundancy of 16S rRNA genes within bacterial and archaeal genomes with multiple operonsa

Domain or microorganismPhylogenetic affiliationNo. of operonsNo. of identical operonsbNo. of different ribotypescNucleotide divergence (% 16S)dNo. of poly- morph- ismseSource or referencef
Bacteria (76 genomes)
    Aquifex aeolicus VF5Aquificales22100rrndb
    Chlorobium tepidum TLSChlorobiales22100This paper
    Synechocystis sp. PCC 6803Cyanobacteria22100This paper
    Treponema pallidum ATCC 25870Spirochaetales22100rrndb
    Leptospira interrogans serovar Lai 56601Spirochaetales22100This paper
    Caulobacter crecentus CB15Alpha proteobacteria22100This paper
    Xanthomonas axonopodis pv. citri 306Gamma proteobacteria22100This paper
    Xylella fastidiosa 9a5cGamma proteobacteria22100rrndb
    Xanthomonas campestris ATCC 33913Gamma proteobacteria22100This paper
    Helicobacter pylori 26695Epsilon proteobacteria22100rrndb
    Helicobacter pylori J99Epsilon proteobacteria202NDND27
    Ureaplasma urealyticum serovar 3Mycoplasmatales2020.071rrndb
    Mycobacterium celatumActinomycetales202ND4/534
    Mycobacterium strain “X"Actinomycetales2021.201830
    Desulfotomaculum kuznestoviiClostridales2028.3ND40
    Chlamydia trachomatisChlamydiae2210027
    Geobacter sulfurreducensDelta proteobacteria20/21/20/0.20/3This paper
    Deincoccus radiodurans ATCC 13939Deinococcales3220.132rrndb
    Rhodobacter sphaeroidesAlpha proteobacteria3310010
    Brucella suis 1330, biovar 1Alpha proteobacteria33100This paper
    Brucella melitensis 16MAlpha proteobacteria33100This paper
    Sinorhizobium melilotiAlpha proteobacteria33100This paper
    Ralstonia solanacearumBeta proteobacteria33100This paper
    Campylobacter jenuni ATCC 700819Epsilon proteobacteria33100rrndb
    Nostoc sp. PCC 7120Cyanobacteria4320.071This paper
    Agrobacterium tumefaciens C58Alpha proteobacteria44100This paper
    Neisseria meningitidis MC58Alpha proteobacteria44100rrndb
    Pseudomonas aeruginosa PAO1Gamma proteobacteria42 + 220.071This paper
    Enterococcus faecalis V583Firmicutes43 + 120.071This paper
    Streptococcus pneumoniae R6Firmicutes44100This paper
    Streptococcus pneumoniae TIGR4Firmicutes44100This paper
    Thermobispora bispora R51Actinomycetales4046.49841
    Thermoanaerobacter tengcongensisThermoanaerobacteriales4046.5/11.699/188This paper
    Pseudomonas syringae pv tomato DC3000Gamma proteobacteria55100This paper
    Fusobacterium nucleatum subsp. nucleatumFusobacteria52 + 1 + 1 + 140.203This paper
    Corynebacterium efficiens YS-314Actinomycetales54 + 120.21/0.423/6This paper
    Staphylococcus epidermidis ATCC 12228Firmicutes5050.8413This paper
    Staphylococcus aureus N315Firmicutes52 + 1 + 1 + 140.254This paper
    Staphylococcus aureus Mu50Firmicutes5050.386This paper
    Lactobacillus plantarum WCFS1Firmicutes52 + 2 + 130.132This paper
    Streptococcus mutans UA159Firmicutes53 + 220.193This paper
    Streptococcus pyogenes SSI-1Firmicutes55100This paper
    Clostridium tetani E88Clostridiales52 + 1 + 1 + 140.396This paper
    Desulfovibrio vulgarisDelta proteobacteria52 + 1 + 1 + 140.264This paper
    Bacteroides thetaiotaomicron VPI-5482Bacteroidales52 + 2 + 131.23/1.317/18This paper
    Haemophilus influenzae Rd (ATCC 51907)Gamma proteobacteria66100rrndb
    Yersina pestis CO92Gamma proteobacteria62 + 1 + 1 + 1 + 150.274This paper
    Corynebacterium glutamicum ATCC 13032Actinomycetales62 + 1 + 1 + 1 + 150.33/0.396This paper
    Thermomonospora chromogenaActinomycetales6066ND43
    Staphylococcus aureus MW2Firmicutes63 + 1 + 1 + 140.325This paper
    Listeria monocytogenes EGD-eFirmicutes62 + 2 + 1 + 140.325This paper
    Listeria innocua Clip 11262Firmicutes65 + 120.254This paper
    Lactococcus lactis subsp. lactisFirmicutes65 + 120.061This paper
    Streptococcus pyogenes MGAS315Firmicutes66100This paper
    Streptococcus pyogenes M1 GAS (SF370)Firmicutes63 + 2 + 130.075/0.151/2This paper
    Streptococcus pyogenes MGAS8232Firmicutes66100This paper
    Pseudomonas putida KT2440Gamma proteobacteria72 + 2 + 2 + 140.193This paper
    Shigella flexneri 2a 301Gamma proteobacteria74 + 2 + 130.51/0.588/9This paper
    Escherichia coli K-12Gamma proteobacteria73 + 1 + 1 + 1 + 151.23/1.3618/21This paper
    Escherichia coli EDL933 (O157:H7)Gamma proteobacteria72 + 1 + 1 + 1 + 1 + 160.45/0.977/15This paper
    Escherichia coli Sakai (O157:H7)Gamma proteobacteria73 + 2 + 1 + 140.45/0.587/9This paper
    Escherichia coli ATCC 10798Gamma proteobacteria73 + 1 + 1 + 1 + 151.2319rrndb
    Salmonella entercia serovar Typhimurium LT2Gamma proteobacteria73 + 1 + 1 + 1 + 150.64/0.589/10This paper
    Salmonella enterica subs P. enterica serovar TyphiGamma proteobacteria73 + 2 + 1 + 140.13/0.192/3This paper
    Salmonella enterica subs P. enterica serovar Typhi Ty2Gamma proteobacteria73 + 3 + 130.13/0.192/3This paper
    Yersina pestis KIM10+Gamma proteobacteria75 + 220.061This paper
    Oceanobacillus iheyensis HTE831Firmicutes73 + 1 + 1 + 1 + 150.96/1.0215/16This paper
    Streptococcus agalactiae NEM316Firmicutes76 + 120.071This paper
    Streptococcus agalactiae 2603 V/RFirmicutes77100This paper
    Vibrio cholerae El Tor N16961Gamma proteobacteria8080.91/1.0412/14This paper
    Shewanella oneidensis MR-1Gamma proteobacteria94 + 3 + 1 + 140.325This paper
    Bacillus subtilis 168Firmicutes100101.48/2.1823/34This paper
    Clostridium perfringens 13Clostridiales100100.93/1.1814/1837; this paper
    Vibrio parahaemolyticus (RIMB22106633)Gamma proteobacteria112 + 2 + 2 + 1 + 1 + 1 + 1 + 180.619This paper
    Clostridium acetobutylicumClostridiales117 + 1 + 1 + 1 +150.26/0.924/14This paper
    Bacillus cereus ATCC 14579Firmicutes137 + 1 + 1 + 1 + 1 + 1 + 170.467This paper
Archaea (5 genomes)
    Methanocaldococcus jannaschiiMethanococcales (Euryarchaeota)2020.07/0.271/4rrndb; this paper
    Methanothermobacter thermoauto- trophicusMethanobacteriales (Euryarchaeota)2020.142rrndb
    Haloarcula marismortuiHalobacteriales (Euryarchaeota)20257428
    Methanosarcina acetivorans C2AMethanosarcinales (Euryarchaeota)32 + 120.071This paper
    Methanosarcina mazei Goe1Methanosarcinales (Euryarchaeota)33100This paper
  • a Data were obtained from the NCBI (www.ncbi.nlm.nih.gov/PMGifs/Genomes/micr.html) and TIGR (www.tigr.org/tdb/mdbcomplete.html) genome databases, the rrndb (http://rrndb.cme.msu.edu) (22), and multiple literature sources.

  • b Different numbers indicate identical 16S rRNA gene sequences in genomes with multiple operons.

  • c Ribotypes are defined as identical 16S rRNA sequences.

  • d Divergence is represented by pairwise distances calculated from alignments of all 16S rRNA sequences for each genome. Single values indicate that there are no insertions or deletions (I/D). When two values are given, left values represent no I/D and right values are with I/D.

  • e The numbers of polymorphisms represent the cumulative numbers of sequence positions in which the aligned sequences differed. Single values indicate that there are no insertions or deletions (I/D). When two values are given, left values represent no I/D and right values are with I/D.

  • f ND, not determined. Analyses were performed on alignments generated for this paper unless other sources are listed.