Computer-assisted numerical analysis of colour-group data for dereplication of streptomycetes for bioprospecting and ecological purposes.
Large numbers of alkaliphilic streptomycetes isolated from a beach and dune sand system were dereplicated manually based on aerial spore mass, colony reverse and diffusible pigment colours formed on oatmeal agar, and on their capacity to produce melanin pigments on peptone-yeast extract-iron agar. The resultant data were converted to their respective red, blue and green shade intensities. The Euclidean distances between each of the colours were calculated by considering red, green and blue shade intensity values as X, Y and Z coordinates in three dimensional space. The clusters of isolates delineated in the dendrogram generated using the distances were found to match those obtained by manual colour-grouping of the isolates. A reasonable linear correlation was found between the colour-group and corresponding rep-PCR data. The implications of the computer-assisted colour-grouping method for bioprospecting and ecological studies are discussed.
Antony-Babu
Sanjay
S
Microbial Resources Laboratory, School of Biology, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK. Sanjay.Antony-Babu@ncl.ac.uk
Stach
James E M
JE
Goodfellow
Michael
M
D015373:Bacterial Typing Techniques; D016000:Cluster Analysis; D016172:DNA Fingerprinting / Q000379:methods; D004269:DNA, Bacterial / Q000235:genetics; D004783:Environmental Microbiology; D019015:Geologic Sediments / Q000382:microbiology*; D009716:Numerical Analysis, Computer-Assisted; D010860:Pigments, Biological / Q000378:metabolism*; D016133:Polymerase Chain Reaction / Q000379:methods; D013302:Streptomyces / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*
D004269:DNA, Bacterial; D010860:Pigments, Biological