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

Kalia, Vipin Chandra; Mukherjee, Tanmoy; Bhushan, Ashish; Joshi, Jayadev; Shankar, Pratap; Huma, Nusrat

doi:10.1186/1471-2164-12-18

BMC Genomics

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

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

Clostridium spp.	Ribosomal Database Acc. No.	RE^b	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	+	+	+	+	U^d	+	+	+	+
	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 RE^b digestion pattern and unique^c 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.

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com