Abstract
BackgroundBacterial taxonomy and phylogeny based on rrs (16S rDNA) sequencing is being vigorously pursued. In fact, it has been stated that novel biological findings are driven by comparison and integration of massive data sets. In spite of a large reservoir of rrs sequencing data of 1,237,963 entries, this analysis invariably needs supplementation with other genes. The need is to divide the genetic variability within a taxa or genus at their rrs phylogenetic boundaries and to discover those fundamental features, which will enable the bacteria to naturally fall within them. Within the large bacterial community, Clostridium represents a large genus of around 110 species of significant biotechnological and medical importance. Certain Clostridium strains produce some of the deadliest toxins, which cause heavy economic losses. We have targeted this genus because of its high genetic diversity, which does not allow accurate typing with the available molecular methods.ResultsSeven hundred sixty five rrs sequences (> 1200 nucleotides, nts) belonging to 110 Clostridium species were analyzed. On the basis of 404 rrs sequences belonging to 15 Clostridium species, we have developed species specific: (i) phylogenetic framework, (ii) signatures (30 nts) and (iii) in silico restriction enzyme (14 Type II REs) digestion patterns. These tools allowed: (i) species level identification of 95 Clostridium sp. which are presently classified up to genus level, (ii) identification of 84 novel Clostridium spp. and (iii) potential reduction in the number of Clostridium species represented by small populations.ConclusionsThis integrated approach is quite sensitive and can be easily extended as a molecular tool for diagnostic and taxonomic identification of any microbe of importance to food industries and health services. Since rapid and correct identification allows quicker diagnosis and consequently treatment as well, it is likely to lead to reduction in economic losses and mortality rates.
Highlights
Bacterial taxonomy and phylogeny based on rrs (16S rDNA) sequencing is being vigorously pursued
The diversity of its economic importance varies from production of solvents - Clostridium beijerinckii, C. acetobutylicum, C. saccharoperbutylacetonicum and C. sachharobutylicum [5], biofuels such as ethanol and hydrogen - Clostridium thermocellum and C. acetobutylicum [6,7,8,9], indigo dye and flax retting to enzymes as therapeutic and cosmetic agents [10]
The selected 765 rrs sequences (> 1200 nts) belonging to these 110 Clostridium species have been grouped into three categories (Table 1, Additional file 1: Table S1): (i) 15 Clostridium spp. with relatively higher number (8-128) of identified organisms, (ii) 94 Clostridium spp. with relatively low frequency (1-15) of identified organisms and (iii) 179 organisms identified only up to genus level - Clostridium sp
Summary
Bacterial taxonomy and phylogeny based on rrs (16S rDNA) sequencing is being vigorously pursued. In spite of a large reservoir of rrs sequencing data of 1,237,963 entries, this analysis invariably needs supplementation with other genes. Within the large bacterial community, Clostridium represents a large genus of around 110 species of significant biotechnological and medical importance. Certain Clostridium strains produce some of the deadliest toxins, which cause heavy economic losses. We have targeted this genus because of its high genetic diversity, which does not allow accurate typing with the available molecular methods. The key questions which we are addressing: Whether there are certain latent and as yet un-explored features in the nucleotide sequences of the rrs, which can be used to define the phylogenetic limits of a particular genus or species? Clostridium represents a large bacterial genus of significant biotechnological as well as medical importance. Members of the Clostridium spp. are responsible for economic and medical problems [24]
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