[Show abstract][Hide abstract] ABSTRACT: Bacillus represents microbes of high economic, medical and biodefense importance. Bacillus strain identification based on 16S rRNA sequence analyses is invariably limited to species level. Secondly, certain discrepancies exist in the segregation of Bacillus subtilis strains. In the RDP/NCBI databases, out of a total of 2611 individual 16S rDNA sequences belonging to the 175 different species of the genus Bacillus, only 1586 have been identified up to species level. 16S rRNA sequences of Bacillus anthracis (153 strains), B. cereus (211 strains), B. thuringiensis (108 strains), B. subtilis (271 strains), B. licheniformis (131 strains), B. pumilus (83 strains), B. megaterium (47 strains), B. sphaericus (42 strains), B. clausii (39 strains) and B. halodurans (36 strains) were considered for generating species-specific framework and probes as tools for their rapid identification. Phylogenetic segregation of 1121, 16S rDNA sequences of 10 different Bacillus species in to 89 clusters enabled us to develop a phylogenetic frame work of 34 representative sequences. Using this phylogenetic framework, 305 out of 1025, 16S rDNA sequences presently classified as Bacillus sp. could be identified up to species level. This identification was supported by 20 to 30 nucleotides long signature sequences and in silico restriction enzyme analysis specific to the 10 Bacillus species. This integrated approach resulted in identifying around 30% of Bacillus sp. up to species level and revealed that B. subtilis strains can be segregated into two phylogenetically distinct groups, such that one of them may be renamed.
PLoS ONE 02/2009; 4(2):e4438. DOI:10.1371/journal.pone.0004438 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Thirty five bacterial isolates from diverse environmental sources such as contaminated food, nitrogen rich soil, activated sludges from pesticide and oil refineries effluent treatment plants were found to belong to Bacillus, Bordetella, Enterobacter, Proteus, and Pseudomonas sp. on the basis of 16S rRNA gene sequence analysis. Under dark fermentative conditions, maximum hydrogen (H(2)) yields (mol/mol of glucose added) were recorded to be 0.68 with Enterobacter aerogenes EGU16 followed by 0.63 with Bacillus cereus EGU43 and Bacillus thuringiensis EGU45. H(2) constituted 63-69% of the total biogas evolved. Out of these 35 microbes, 18 isolates had the ability to produce polyhydroxybutyrate (PHB), which varied up to 500 mg/l of medium, equivalent to a yield of 66.6%. The highest PHB yield was recorded with B. cereus strain EGU3. Nine strains had high hydrolytic activities (zone of hydrolysis): lipase (34-38 mm) -Bacillus sphaericus strains EGU385, EGU399 and EGU542; protease (56-62 mm) -Bacillus sp. strains EGU444, EGU447 and EGU445; amylase (23 mm) -B. thuringiensis EGU378, marine bacterium strain EGU409 and Pseudomonas sp. strain EGU448. These strains with high hydrolytic activities had relatively low H(2) producing abilities in the range of 0.26-0.42 mol/mol of glucose added and only B. thuringiensis strain EGU378 had the ability to produce PHB. This is the first report among the non-photosynthetic microbes, where the same organism(s) -B. cereus strain EGU43 and B. thuringiensis strain EGU45, have been shown to produce H(2) - 0.63 mol/mol of glucose added and PHB - 420-435 mg/l medium.
[Show abstract][Hide abstract] ABSTRACT: The evolutionary events in organisms can be tracked to the transfer of genetic material. The inheritance of genetic material among closely related organisms is a slow evolutionary process. On the other hand, the movement of genes among distantly related species can account for rapid evolution. The later process has been quite evident in the appearance of antibiotic resistance genes among human and animal pathogens. Phylogenetic trees based on such genes and those involved in metabolic activities reflect the incongruencies in comparison to the 16S rDNA gene, generally used for taxonomic relationships. Such discrepancies in gene inheritance have been termed as horizontal gene transfer (HGT) events. In the post-genomic era, the explosion of known sequences through large-scale sequencing projects has unraveled the weakness of traditional 16S rDNA gene tree based evolutionary model. Various methods to scrutinize HGT events include atypical composition, abnormal sequence similarity, anomalous phylogenetic distribution, unusual phyletic patterns, etc. Since HGT generates greater genetic diversity, it is likely to increase resource use and ecosystem resilience.
Indian Journal of Microbiology 06/2008; 48(2):228-42. DOI:10.1007/s12088-008-0034-1 · 0.83 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Mycobacterium tuberculosis is the etiological agent for tuberculosis in humans. The studies related to survival of this pathogen in the human host and development of drugs against reveal that the organism uses a complex physiology to adapt to the host environment. Many studies were targeted to key enzymes that allow this pathogen to either survive or remain latent within the host. Most of the models, which address the survival of pathogen, have evaluated limited dissolved oxygen and prevailing stress conditions. Hence, the truncated citric acid cycle, with the glyoxylate shunt was suggested as an option for survival of the pathogen and pathogenesis. We propose that the precursors to support this pathway could also be generated via enzymatic conversion involving poly-beta-hydroxybutyrate (PHB). We have used available genome sequence data and analyzed for the possible enzymatic conversions that can generate glyoxylate, acetyl CoA, and other enolases that can also be useful for various fatty acid transformations. The enzymes for accumulation and further hydrolysis of PHB were examined in sequence data analysis. The target enzymes were searched for in the genome using identified conserved domains. Using M. tuberculosis H37Rv as a model bacterium a supportive pathway has been envisaged and integrated with glyoxylate cycle to provide a complete option to pathogen for sustainable consumption of available carbon source(s). The study proposes that the enzymes of PHB synthesis and hydrolysis are possible targets for drug design, and that this should be considered when evaluating isocitrate lyase and malate synthase as targets.
Infectious Disorders - Drug Targets(Formerly Current Drug Targets - Infectious Disorders) 10/2007; 7(3):245-50. DOI:10.2174/187152607782110068
[Show abstract][Hide abstract] ABSTRACT: Polyhydroxyalkanoates (PHAs) are gaining more and more importance the world over due to their structural diversity and close analogy to plastics. Their biodegradability makes them extremely desirable substitutes for synthetic plastics. PHAs are produced in organisms under certain stress conditions. Here, we investigated 253 sequenced (completely and unfinished) genomes for the diversity and phylogenetics of the PHA biosynthesis. Discrepancies in the phylogenetic trees for phaA, phaB and phaC genes of the PHA biosynthesis have led to the suggestion that horizontal gene transfer (HGT) may be a major contributor for its evolution. Twenty four organisms belonging to diverse taxa were found to be involved in HGT. Among these, Bacillus cereus ATCC 14579 and Xanthomonas axonopodis pv. citri str. 306 seem to have acquired all the three genes through HGT events and have not been characterized so far as PHA producers. This study also revealed certain potential organisms such as Streptomyces coelicolor A3(2), Staphylococcus epidermidis ATCC 12228, Brucella suis 1330, Burkholderia sp., DSMZ 9242 and Leptospira interrogans serovar lai str. 56601, which can be transformed into novel PHA producers through recombinant DNA technology.
[Show abstract][Hide abstract] ABSTRACT: The large-scale, persistent use of antibiotics has provoked microbes to evolve mechanisms to evade them. Pharmaceutical companies have found this to be counterproductive to their business economics. To maintain company interest to invest in this sector, innovative alternatives are needed. The availability of metabolic and genomic databases has opened up an avenue for such discoveries. Using these databases, potential producers of penicillin and cephalosporin have been traced. In addition, organisms that can be transformed from their present 'non'-producer status to antibacterial producers by supplementing their missing gene(s) by recombinant DNA technology have been revealed.
Expert Opinion on Drug Discovery 02/2007; 2(2):211-24. DOI:10.1517/17460422.214.171.124 · 3.47 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The realization that fossil fuel reserves are limited and their adverse effect on the environment has forced us to look into alternative sources of energy. Hydrogen is a strong contender as a future fuel. Biological hydrogen production ranges from 0.37 to 3.3 moles H(2) per mole of glucose and, considering the high theoretical values of production (4.0 moles H(2) per mole of glucose), it is worth exploring approaches to increase hydrogen yields. Screening the untapped microbial population is a promising possibility. Sequence analysis and pathway alignment of hydrogen metabolism in complete and incomplete genomes has led to the identification of potential hydrogen producers.
Trends in Biotechnology 05/2003; 21(4):152-6. DOI:10.1016/S0167-7799(03)00028-3 · 10.04 Impact Factor