Providencia rettgeri – 3A

PROJECT REPORT

NAME OF SCIENTIST:
Mahendra Trivedi
SERVICE:
Bacterial Identification: 3A
SERVICE NO.:
BIS-119
Project Title Bacterial Identification Service based on 16S rDNA data
Cat#: CSER 47
Name of Scientist: Mahendra Trivedi
Institute: The Life Energy, Mumbai
Sample name: (Providencia rettgeri) 3A
Steps Involved: 1. Genomic DNA was isolated from the pure culture pellet provided by the P.D. Hinduja National Hospital & Medical Research Centre- (Mumbai), on behalf of Mahendra Trivedi
2. Using consensus primers, the ~1.5 kb 16S rDNA fragment was amplified using high-fidelity PCR Polymerase.
3. The PCR product was bi-directionally sequenced using the forward, reverse and an internal primer.
4. Sequence data was aligned and analyzed for finding the closest homologs for the microbe.

Result:

  1. Based on nucleotides homology and phylogenetic analysis the Microbe (Sample: 3A) was detected to be Proteus mirabilis (GenBank Accession Number: AY820623)
  2. Nearest homolog species was found to be Proteus vulgaris (Accession No. DQ499636).
  3. Information about other close homologs for the microbe can be found from the Alignment View table.

Materials Provided to the Scientist:

1. Final Report

Date: 29.03.2008

*The sample has been indicated as 3A

Aligned Sequence Data:(1495 bp)

TGATCCTGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGGTAACAGGAGAAAGCTTGCTTT
CTTGCTGACGAGCGGCGGACGGGTGAGTAATGTATGGGGATCTGCCCGATAGAGGGGGATAACTACTGGAAACGGTG
GCTAATACCGCATAATGTCTACGGACCAAAGCAGGGGCTCTTCGGACCTTGCACTATCGGATGAACCCATATGGGAT
TAGCTAGTAGGTGGGGTAAAGGCTCACCTAGGCGACGATCTCTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGA
CTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCAT
GCCGCGTGTATGAAGAAGGCCTTAGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGATAAGGTTAATACCCTTGT
CAATTGACGTTACCCGCAGAGGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGCT
AATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCAATTAAGTCAGATGTGAAAGCCCCGAGCTTAACTTGGGA
ATTGCATCTGAAACTGGTTGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCATGTGTAGCGGTGAAATGCGTAGAGA
TGTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAAC
AGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGTCGATTTAGAGGTTGTGGTCTTGAACCGTGGCTTCTGGA
GCTAACGCGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACA
AGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTACTCTTGACATCCAGCGAATCCTTTAGA
GATAGAGGAGTGCCTTCGGGAACGCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTT
AAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCACGTAATGGTGGGAACTCAAAGGAGACTGCCGGTGA
TAAACCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGAGTAGGGCTACACACGTGCTACAATGGCA
GATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGAACTCATAAAGTCTGTCGTAGTCCGGATTGGAGTCTGCAACT
CGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTACGGTGAATACGTTCCCGGGCCTTGTACACA
CCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTG
ATTCATGACTGGGGTGAAGTCGTAACAAGGTA

Alignment View using combination of NCBI GenBank and RDP database:

Alignment View
ID
Alignment results
Sequence description
3A
0.93
Sample studied
AY820623
0.93
Proteus mirabilis
AF008582
0.94
Proteus mirabilis
DQ499636
0.94
Proteus vulgaris
DQ885262
0.98
Proteus hauseri strain NCTC 4175
DQ885257
0.98
Proteus vulgaris strain ATCC 29905
DQ885259
0.92
Proteus myxofaciens strain NCIMB 13273
DQ205449
0.90
Xenorhabdus hominickii strain KR05
DQ205448
0.89
Xenorhabdus hominickii strain KR01
AM040489
0.93
Providencia rustigianii type strain DSM 4541
AM040490
0.88
Providencia heimbachae   type strain DSM 3591

Distance Matrix based on Nucleotide Sequence Homology (Using Kimura-2 Parameter):

Distance Matrix
 
 
1
2
3
4
5
6
7
8
9
10
11

DQ499636

 1 
 — 
 0.981 
 0.993 
 0.964 
 0.992 
 0.963 
 0.991 
 0.951 
 0.948 
 0.992 
 0.991 

DQ885259

 2 
 0.019 
 — 
 0.983 
 0.963 
 0.983 
 0.962 
 0.982 
 0.957 
 0.953 
 0.985 
 0.982 

AF008582

 3 
 0.007 
 0.017 
 — 
 0.962 
 0.992 
 0.960 
 0.998 
 0.954 
 0.951 
 0.992 
 0.998 

DQ205449

 4 
 0.036 
 0.037 
 0.038 
 — 
 0.961 
 0.999 
 0.960 
 0.949 
 0.947 
 0.962 
 0.960 

DQ885262

 5 
 0.008 
 0.017 
 0.008 
 0.039 
 — 
 0.960 
 0.990 
 0.951 
 0.948 
 0.999 
 0.990 

DQ205448

 6 
 0.037 
 0.038 
 0.040 
 0.001 
 0.040 
 — 
 0.959 
 0.948 
 0.945 
 0.960 
 0.959 

AY820623

 7 
 0.009 
 0.018 
 0.002 
 0.040 
 0.010 
 0.041 
 — 
 0.952 
 0.948 
 0.991 
 1 

AM040489

 8 
 0.049 
 0.043 
 0.046 
 0.051 
 0.050 
 0.052 
 0.048 
 — 
 0.988 
 0.951 
 0.952 

AM040490

 9 
 0.052 
 0.047 
 0.050 
 0.053 
 0.052 
 0.055 
 0.052 
 0.013 
 — 
 0.948 
 0.948 

DQ885257

 10 
 0.008 
 0.015 
 0.008 
 0.038 
 0.001 
 0.040 
 0.009 
 0.050 
 0.052 
 — 
 0.991 

3A

 11 
 0.009 
 0.018 
 0.002 
 0.040 
 0.010 
 0.041 
 0.000 
 0.048 
 0.052 
 0.009 
 — 

Table indicates nucleotide similarity (above diagonal) and distance (below diagonal) identities between the studied sample ’3A’ and ten other closest homologs microbe.

Phylogenetic Tree made in MEGA 3.1 software using Neighbor Joining method:

 

Approved by: Dr. Avijit Roy

Manager R & D
Bangalore Genei

 

RELATED REPORTS :

ANTIBIOTIC SENSITIVITY/BIOCHEMICAL REACTIONS REPORT