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Table 4 Phylogenetic relationships of Clostridium spp. (low frequency) with Frame work organisms supported by RE patterns and signaturesa

From: Analysis of the unexplored features of rrs (16S rDNA) of the Genus Clostridium

Clostridium spp. Ribosomal Database Acc. No. REb Nucleotide signatures (Motif, M)
    1 2 3 4 5 6 7 8 9 10
Clostridium sp. close to Framework sequences of C. subterminale
C. thiosulfatireducens S000804481, S000434520, S000391440 DpnII +c + + + + Ud + + + +
  S001169692 DpnII + + + + + U + + + - c
C. argentiense S000260680 DpnII + + + + + U + + + +
C. schirmacherense S000608913 DpnII + + + + + - + + + +
C. proteolyticus S000539419 DpnII + + - + + - + + + +
C. tunisiense S000400761 DpnII + + + + + - + - + +
C. sulfidigens S000805548 DpnII + + + + + U + + + +
swine manure bacterium S000356150 DpnII + + - + + U + + + +
red sea bacterium S000130297 DpnII + + + + + - + + + +
bacterium S000362562 DpnII + + + + + U + + + -
  S000362543 No Match + + + + + U + + + -
C. estertheticum S000380961, S000137876, S000013400 No Match + + - - + - + + + +
Clostridium sp. close to Framework sequences of C. beijerinckii
C. diolis S000116547, S000116809, S000115736 Tru9I + + + + + + + + + -
  S000722359 Tru9I + + + + + - + + + -
C. saccharoperbutylacetonicum S000437203 Tru9I + + + + + - + + + -
C. roseum S000022312 Tru9I + + + + + + + + + -
C. corinoforum S000260488 Tru9I + + + + + + + + + -
C. chromoreductans S000403224 Tru9I + + + + + - + + + -
C. favososporum S000260731 Tru9I + + + + + - + + + -
C. puniceum S000259939 No Match + + + + - - + + + -
  S000021696 No Match + + + + + - + + + -
Clostridium sp. close to Framework sequences of C. kluyveri
C. tyrobutyricum S001795516, S000414327 BfaI + - + - - - + + - +
  S001795519, S000436476 BfaI - - + - - - - - - -
C. ljungdahlii S001746374, S001746375, S001746376 BfaI + - + - - + + + - -
Clostridium sp. close to Framework sequences of C. tetani
C. tetanomorphum S000620000, S000380964, S000004728 HaeIII - - - - - - - - - +
C. cochlearium S000436458, S001792987 HaeIII U - - U U U - U U -
Clostridium sp. close to Framework sequences of C. chauvoei
C. septicum S000437948, S001241604 AluI + + U - - + + - U +
  S000859058 AluI - + U - - + + - U +
C. carnis S000436456 AluI U + U U - + - - U +
Clostridium sp. close to Framework sequences of C. perfringens
swine manure bacterium S000356165, S000356166 BfaI, HaeIII U U U U - + + + + +
bacterium S000465625 BfaI, HaeIII U U U U U + - + + +
intestinal bacterium S001612241 BfaI, HaeIII U U U U U + + + + +
Clostridium sp. close to Framework sequences of C. butyricum
rumen bacterium S000927678   + + + + + + + + + +
Clostridium sp. close to Framework sequences of C. pasteurianum
C. acidisoli S000130726 BfaI - - U + U - U U + +
C. akagii S000127491 BfaI - - - + - - U U + +
Clostridiales bacterium S000824422 BfaI - - - - - - - - + +
Clostridium sp. close to Framework sequences of C. novyi/C. botulinum
C. haemolyticum S000004827, S000009602 Tru9I U + U + + U + + + U
Clostridium sp. close to Framework sequences of C. baratii
Eubacterium monoliforme S000414611 No Match + - U + + - + - + +
Eubacterium multiforme S000001853 No Match - - - + + - + + + +
Clostridium sp. close to Framework sequences of C. sporogenes/C. botulinum
rumen bacterium S001611925, S00927677 BfaI, Tru9I - - + - + + + + - -
Clostridium sp. close to Framework sequences of C. sardiniense
Eubacterium budayi S000775713 Tru9I - U + U - - - - - -
Clostridium sp. close to Framework sequences of C. botulinum
C. neonatale S001155546, S001155556, S000390501 Tru9I, BfaI + + + + + + + + + +
Eubacterium combesii S000435788 Tru9I, BfaI + + + + + + + + + +
rumen bacterium S001611929 Tru9I, BfaI + + + + + + + - + +
Clostridium sp. close to Framework sequences of C. acetobutylicum
C. roseum S000010371 AluI + + + + + + + + + +
C. felsineum S000390414, S000390415 AluI + + + + + + + + + +
C. aurantibutyricum S001199386 AluI + + + + + + + + + +
C. collagenovorans S000260454 AluI + + + + + + + + + +
  1. a,b,dClostridium spp. known to occur with low frequency were found to be phylogentically close to Clostridium spp. used for developing Framework (Table 2) were also similar with respect to their in silico REb digestion pattern and uniquec nucleotide signatures (30 nts in lengths) (Table 6) c+/- denotes presence/absence of a nucleotide signature also found in the respective species represented in the phylogenetic framework.