Table 4

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

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

+

+

+

+

+

+

+

+

+

+


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.

Kalia et al. BMC Genomics 2011 12:18   doi:10.1186/1471-2164-12-18

Open Data