Shikha Koul

Potential Emergence of Multi-quorum Sensing Inhibitor Resistant (MQSIR) Bacteria

Expression of certain bacterial genes only at a high bacterial cell density is termed as quorum-sensing (QS). Here bacteria use signaling molecules to communicate among themselves. QS mediated genes are generally involved in the expression of phenotypes such as bioluminescence, biofilm formation, competence, nodulation, and virulence. QS systems (QSS) vary from a single in Vibrio spp. to multiple in Pseudomonas and Sinorhizobium species. The complexity of QSS is further enhanced by the multiplicity of signals: (1) peptides, (2) acyl-homoserine lactones, (3) diketopiperazines. To counteract this pathogenic behaviour, a wide range of bioactive molecules acting as QS inhibitors (QSIs) have been elucidated. Unlike antibiotics, QSIs don’t kill bacteria and act at much lower concentration than those of antibiotics. Bacterial ability to evolve resistance against multiple drugs has cautioned researchers to develop QSIs which may not generate undue pressure on bacteria to develop resistance against them. In this paper, we have discussed the implications of the diversity and multiplicity of QSS, in acting as an arsenal to withstand attack from QSIs and may use these as reservoirs to develop multi-QSI resistance.

Multiplicity of Quorum Quenching Enzymes: A Potential Mechanism to Limit Quorum Sensing Bacterial Population

Bacteria express certain of their characteristics especially, pathogenicity factors at high cell densities. The process is termed as quorum sensing (QS). QS operates via signal molecules such as acylhomoserine lactones (AHLs). Other bacteria inhibit QS through the inactivation of AHL signals by producing enzymes like AHL-lactonases and -acylases. Comparative genomic analysis has revealed the multiplicity of genes for AHL lactonases (up to 12 copies per genome) among Bacillus spp. and that of AHL-acylases (up to 5 copies per genome) among Pseudomonas spp. This genetic evolution can be envisaged to enable host to withstand the attacks from bacterial population, which regulates its functioning through QS.

Simple and Rapid Method for Detecting Biofilm Forming Bacteria

Biofilm forming bacteria play a vital role in causing infectious diseases and for enhancing the efficiency of the bioremediation process through immobilization. Different media and conditions have been reported for detecting biofilm forming bacteria, however, they are not quite rapid. Here, we propose the use of a simple medium which can be used for detecting biofilm former, and also provide a mechanism to regulate the expression of biofilm formation process.

A Genome-Wide Profiling Strategy as an Aid for Searching Unique Identification Biomarkers for Streptococcus

The use of rrs (16S rRNA) gene is widely regarded as the “gold standard” for identifying bacteria and determining their phylogenetic relationships. Nevertheless, multiple copies of this gene in a genome is likely to give an overestimation of the bacterial diversity. In each of the 50 Streptococcus genomes (16 species, 50 strains), 4–7 copies of rrs are present. The nucleotide sequences of these rrs genes show high similarity within and among genomes, which did not allow unambiguous identification. A genome-wide search revealed the presence of 27 gene sequences common to all the Streptococcus species. Digestion of these 27 gene sequences with 10 type II restriction endonucleases (REs) showed that unique RE digestion in purH gene is sufficient for clear cut identification of 30 genomes belonging to 16 species. Additional gene-RE combinations allowed identification of another 15 strains belonging to S. pneumoniae, S. pyogenes, and S. suis. For the rest 5 strains, a combination of 2 genes was required for identifying them. The proposed strategy is likely to prove helpful in proper detection of pathogens like Streptococcus.

A Unique Genome Wide Approach to Search Novel Markers for Rapid Identification of Bacterial Pathogens

Shikha Koul1,2, Prasun Kumar1 and Vipin Chandra Kalia1,2* 1Microbial Biotechnology and Genomics, CSIR Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, New Delhi, India 2Academy for Scientific and Innovative Research (AcSIR), New Delhi, India *Corresponding author: Vipin Chandra Kalia, Microbial Biotechnology and Genomics, CSIR-Institute of Genomics and Integrative Biology, Delhi University Campus, New Delhi, India, Tel: 0911127666156; Fax: 0911127667471; E-mail: vckalia@igib.res.in

Searching Biomarkers in the Sequenced Genomes of Staphylococcus for their Rapid Identification

Abstract Bacterial identification using rrs (16S rRNA) gene is widely reported. Bacteria possessing multiple copies of rrs lead to overestimation of its diversity. Staphylococcus genomes carries 5–6 copies of rrs showing high similarity in their nucleotide sequences, which lead to ambiguous results. The genomes of 31 strains of Staphylococcus representing 7 species were searched for the presence of common genes. In silico digestion of 34 common genes using 10 restriction endonucleases (REs) lead to select gene-RE combinations, which could be used as biomarkers. RE digestion of recA allowed unambiguous identification of 13 genomes representing all the 7 species. In addition, a few more genes (argH, argR, cysS, gyrB, purH, and pyrE) and RE combinations permitted further identification of 12 strains. By employing additional RE and genes unique to a particular strain, it was possible to identify the rest 6 Staphylococcus aureus strains. This approach has the potential to be utilized for rapid detection of Staphylococcus strains.

Heterologous Expression of Quorum Sensing Inhibitory Genes in Diverse Organisms

The discovery of antibiotics was a wonderful solution to provide relief to human beings from infectious diseases. However, indiscriminate usage of antibiotics turned out to be counterproductive. It was observed that patients were not getting cured in spite of the systematic use of antibiotics. In fact, microbes had developed resistance to antibiotics. This perturbation has been in operation even with antibiotics subsequently developed during the next 6–7 decades (D’Costa et al. 2006). Pharmaceutical companies are no longer interested in investing money into this business (Spellberg et al. 2004; Courvalin 2008). It obliged scientists to look for alternative drugs and new drug targets. It was realised that more than 80 % of the infectious diseases are caused by microbial pathogens, through specialised structures – biofilms. It enables bacteria to survive the lethal effect of drugs, as they “become” up to 1,000 times more resistant to antibiotics (Kalia 2013; Gui et al. 2014; Kalia et al. 2014a, b). These biofilms are developed by bacteria in a population density-dependent process called quorum sensing (QS) (Dong and Zhang 2005). Most Gram-negative bacteria operate through a QS system termed as LuxR/I-type, where acylated homoserine lactones (AHLs) acts as signals. QS signals consist of the lactone ring with varying acyl chains (Yang et al. 2012; Shang et al. 2014). QS regulates the expression of virulence factors, antibiotic production, nitrogen fixation, sporulation, conjugation, swarming, etc. (Borlee et al. 2008; Kalia and Purohit 2011; Kalia 2013; Wang et al. 2013; Zhang et al. 2013; Kalia et al. 2014a, b). These properties allow such bacteria to dominate the community structure. It is thus no surprise that the competing organisms have also developed mechanisms to interfere with the QSS and degrade these signals – a phenomenon termed as quorum quenching (QQ) (Kalia and Purohit 2011; Annapoorani et al. 2012; Bakkiyaraj et al. 2013; Kalia 2013; Agarwala et al. 2014).

Wastewater: A Potential Bioenergy Resource

Wastewaters are a rich source of nutrients for microorganisms. However, if left unattended the biodegradation may lead to severe environmental hazards. The wastewaters can thus be utilized for the production of various value added products including bioenergy (H2 and CH4). A number of studies have reported utilization of various wastewaters for energy production. Depending on the nature of the wastewater, different reactor configurations, wastewater and inoculum pretreatments, co-substrate utilizations along with other process parameters have been studied for efficient product formation. Only a few studies have reported sequential utilization of wastewaters for H2 and CH4 production despite its huge potential for complete waste degradation.

In Silico Analytical Tools for Phylogenetic and Functional Bacterial Genomics

Microbial significance in human lives has been gaining importance due to their biotechnological applications and ability to cause diseases. The use of antibiotics to kill them has proved counterproductive. Bacterial resistance to antibiotics has caused huge economic losses. Many bacteria have turned highly drug resistant due to modifications in their genetic reservoirs. It has been recognized that bacteria had another mechanism to circumvent the impact of antibiotics. Bacteria causing infectious diseases form biofilm at high cell density. Biofilm protects bacteria from even extremely high dosages of antibiotics. Under all these conditions, the most important aspect to initiate treatment is to diagnose the organism responsible for the disease. Bacterial identification through the rrs gene sequence has been the most prevalent and effective approach. The trouble arises in two main situations: (1) high similarity among gene sequences and (2) the presence of multiple copies of rrs gene within a genome. An obvious solution is to employ other highly conserved genes (housekeeping genes), which is uneconomical in terms of time and money. However, a few studies have revealed the presence of latent features within rrs. A set of genomic tools allowed identification of organisms up to the species level from their previous status of genus level identity. The most interesting aspect is that the strategy can be extended to all genes from all kinds of organisms.

Exploiting Bacterial Genomes to Develop Biomarkers for Identification

Bacteria have unique abilities to adjust itself to diverse environmental conditions. Under adverse conditions, their genetic reservoir provides necessary help. Although bacteria have been perceived as pathogens to most living beings, the most critical are the ones which infect human being. Bacteria also harbour the human gut and skin and have been shown to be helpful. The pathogenic bacteria cause diseases and contribute to ill health. The need is to identify them rapidly, diagnose the disease and initiate the treatment. Most bacteria can be easily identified on the basis of their 16S rRNA (rrs) gene. However, in case where multiple copies of rrs are present within a bacterial genome, it is difficult to identify them, since they show great homology with other species of a genus. Here, novel approaches have been reviewed, which rely upon certain genes which are common to a large number of species of Clostridium, Lactobacillus, Staphylococcus, Streptococcus, Vibrio and Yersinia and show unique digestion patterns on treatment with restriction endonucleases.