AFLP fingerprinting of Colombian Clostridium spp strains, multivariate data analysis and its taxonomical implications Claudia P. Jaimes a , Fabio A. Aristizábal G. b , Mauricio Bernal M. a , Zulma R. Suárez a , Dolly Montoya a, ⁎ a Instituto de Biotecnología, Universidad Nacional de Colombia A.A. 14490, Colombia b Departamento de Farmacia, Universidad Nacional de Colombia A.A. 14490, Colombia Received 27 July 2005; received in revised form 26 December 2005; accepted 2 March 2006 Available online 19 April 2006 Abstract Amplified Fragment Length Polymorphism (AFLP) analysis was used for characterising 13 native Colombian Clostridium spp strains. The DNA extraction method was optimised and the use of cetyl trimethyl ammonium bromide (CTAB) and sodium chloride (NaCl) was incorporated. All strains could be typed in these conditions. The AFLP profiles obtained were submitted to multivariate analysis and compared with previous pulsed field gel electrophoresis (PFGE) results. The results suggested that the set of native strains could correspond to two new species different to those having been described to date. It is proposed that DNA– DNA hybridisation analysis should be done to produce complementary information for describing the new species. © 2006 Elsevier B.V. All rights reserved. Keywords: AFLP; PFGE; Bioprospecting; Fingerprinting; Taxonomic classification; Biodiversity 1. Introduction Knowledge of prokaryote species' biological diver- sity remains incomplete in terms of their richness, overall distribution and function within Colombian ecosystems. Bioprospecting strategies have thus been implemented for exploring bacterial biodiversity, accompanied by molecular techniques for identifying promising micro- organisms and their taxonomic classification. Amplified fragment length polymorphism (AFLP) represents one of the molecular characterisation techni- ques used in taxonomic classification, based on detecting DNA restriction fragments for polymerase chain reaction (PCR) amplification (Zabeau and Vos, 1993). AFLP has been applied to studying different bacterial genera for both taxonomic ends and epidemi- ological typing, showing it to be a useful molecular tool because it allows genera, species and even strains to be differentiated (Blears et al., 1998; Gaafar et al., 2003; Moreno et al., 2003; Rademaker et al., 2003;Vos et al., 1995; Savelkoul et al., 1999). AFLP fingerprinting studies have been done recently on Clostridium novyi, Clostridium perfringens, Clostridium botulinum and Journal of Microbiological Methods 67 (2006) 64 – 69 www.elsevier.com/locate/jmicmeth Abbreviations: AFLP, amplified fragment length polymorphism; PCR, polymerase chain reaction; OD, optical density; PFGE, pulsed field gel electrophoresis; CTAB, cetyl trimethyl ammonium bromide; DNA, deoxyribonucleic acid; NaCl, sodium chloride. ⁎ Corresponding author. Tel.: +57 1 3165000 16954; fax: +57 1 3165415. E-mail addresses: cpjaimes@uniboyaca.edu.co (C.P. Jaimes), faaristizabalg@unal.edu.co (F.A. Aristizábal G.), jmbernalmo@unal.edu.co (M. Bernal M.), zrsuarezm@unal.edu.co (Z.R. Suárez), dmontoyac@unal.edu.co (D. Montoya). URL: http://www.ibun.unal.edu.co (D. Montoya). 0167-7012/$ - see front matter © 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.mimet.2006.03.002