Abstract
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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Agarwala M, Choudhury B, Yadav RNS (2014) Comparative study of antibiofilm activity of copper oxide and iron oxide nanoparticles against multidrug resistant biofilm forming uropathogens. Indian J Microbiol 54:365–368. doi:10.1007/s12088-014-0462-z
Alipiah NM, Shamsudin MN, Yusoff FM, Arshad A (2015) Membrane biosynthesis gene disruption in methicillin-resistant Staphylococcus aureus (MRSA) as potential mechanism for reducing antibiotic resistance. Indian J Microbiol 54:41–49. doi:10.1007/s12088-014-0488-2
Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H (2000) Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50:1563–1589. doi:10.1099/00207713-50-4-1563
Arasu MV, Al-Dhabi NA, Rejiniemon TS, Lee KD, Huxley VAJ, Kim DH, Duraipandiyan V, Karuppiah P, Choi KC (2015) Identification and characterization of Lactobacillus brevis P68 with antifungal, antioxidant and probiotic functional properties. Indian J Microbiol 55:19–28. doi:10.1007/s12088-014-0495-3
Aremu BR, Babalola OO (2015) Classification and taxonomy of vegetable macergens. Front Microbiol 6:1361. doi:10.3389/fmicb.01361
Arya R, Princy SA (2016) Exploration of modulated genetic circuits governing virulence determinants in Staphylococcus aureus. Indian J Microbiol 56:19–27. doi:10.1007/s12088-015-0555-3
Bhushan A, Joshi J, Shankar P, Kushwah J, Raju SC, Purohit HJ, Kalia VC (2013) Development of genomic tools for the identification of certain Pseudomonas up to species level. Indian J Microbiol 53:253–263. doi:10.1007/s12088-013-0412-1
Bhushan A, Mukherjee T, Joshi J, Shankar P, Kalia VC (2015) Insights into the origin of Clostridium botulinum strains: evolution of distinct restriction endonuclease sites in rrs (16S rRNA gene). Indian J Microbiol 55:140–150. doi:10.1007/s12088-015-0514-z
Carere CR, Kalia VC, Sparling R, Cicek N, Levin DB (2008) Pyruvate catabolism and hydrogen synthesis pathway genes of Clostridium thermocellum ATCC 27405. Indian J Microbiol 48:252–266. doi:10.1007/s12088-008-0036-z
Goodwin CS, Armstrong JA, Chilvers T, Peters M, Collins MD, Sly L, McConnell W, Harper WES (1989) Transfer of Campylobacter pylori and Campylobacter mustelae to Helicobacter gen. nov. as Helicobacter pylori comb. nov. and Helicobacter mustelae comb. nov. respectively. Int J Syst Bacteriol 39:397–405. doi:10.1099/00207713-39-4-397
Gui Z, Wang H, Ding T, Zhu W, Zhuang X, Chu W (2014) Azithromycin reduces the production of α-hemolysin and biofilm formation in Staphylococcus aureus. Indian J Microbiol 54:114–117. doi:10.1007/s12088-013-0438-4
Hema M, Balasubramanian S, Princy SA (2015) Meddling Vibrio cholerae murmurs: a neoteric advancement in cholera research. Indian J Microbiol 55:121–130. doi:10.1007/s12088-015-0520-1
Heyndrickx M, Lebbe L, Kersters K, Hoste B, De Wachter R, De Vos P, Forsyth G, Logan NA (1999) Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998. Int J Syst Bacteriol 49:1083–1090
Hilario E, Buckley TR, Young JM (2004) Improved resolution on the phylogenetic relationships among Pseudomonas by combined analysis of atpD, carA, recA and 16S rDNA. Antonie Van Leeuwenhoek 86:51–64. doi:10.1023/B:ANTO.0000024910.57117.16
Huma N, Shankar P, Kushwah J, Bhushan A, Joshi J, Mukherjee T, Raju S, Purohit HJ, Kalia VC (2011) Diversity and polymorphism in AHL-lactonase gene (aiiA) of Bacillus. J Microbiol Biotechnol 21:1001–1011. doi:10.4014/jmb.1105.05056
Kalia VC (2013a) Quorum sensing inhibitors: an overview. Biotechnol Adv 31:224–245. doi:10.1016/j.biotechadv.2012.10.004
Kalia VC (2013b) The visionary: Prof. Carl R. Woese. Indian J Microbiol 53:245–246. doi:10.1007/s12088-013-0417-9
Kalia VC (2014a) In search of versatile organisms for quorum-sensing inhibitors: acyl homoserine lactones (AHL)-acylase and AHL-lactonase. FEMS Microbiol Lett 359:143. doi:10.1111/1574-6968.12585
Kalia VC (2014b) Microbes, antimicrobials and resistance: the battle goes on. Indian J Microbiol 54:1–2. doi:10.1007/s12088-013-0443-7
Kalia VC (2015a) Let’s explore the latent features of genes to identify bacteria. J Mol Genet Med 9, e105. doi:10.4172/1747-0862.1000E105
Kalia VC (2015b) Microbes: the most friendly beings? In: Kalia VC (ed) Quorum sensing vs quorum quenching: a battle with no end in sight. Springer, New Delhi, pp 1–5. doi:10.1007/978-81-322-1982-8_1. ISBN 978-81-322-1981-1
Kalia VC, Kumar P (2015) Genome wide search for biomarkers to diagnose Yersinia infections. Indian J Microbiol 55:366–374. doi:10.1007/s12088-015-0552-6
Kalia VC, Purohit HJ (2011) Quenching the quorum sensing system: potential antibacterial drug targets. Crit Rev Microbiol 37:121–140. doi:10.3109/1040841X.2010.532479
Kalia VC, Mukherjee T, Bhushan A, Joshi J, Shankar P, Huma N (2011a) Analysis of the unexplored features of rrs (16S rDNA) of the genus Clostridium. BMC Genomics 12:18. doi:10.1186/1471-2164-12-18
Kalia VC, Raju SC, Purohit HJ (2011b) Genomic analysis reveals versatile organisms for quorum quenching enzymes: acyl-homoserine lactone-acylase and -lactonase. Open Microbiol J 5:1–13. doi:10.2174/187428580110501000
Kalia VC, Kumar P, Kumar R, Mishra A, Koul S (2015) Genome wide analysis for rapid identification of Vibrio species. Indian J Microbiol 55:375–383. doi:10.1007/s12088-015-0553-5
Kalia VC, Kumar R, Kumar P, Koul S (2016) A genome-wide profiling strategy as an aid for searching unique identification biomarkers for Streptococcus. Indian J Microbiol 56:46–58. doi:10.1007/s12088-015-0561-5
Kapley A, Purohit HJ (2009) Genomic tools in bioremediation. Indian J Microbiol 49:108–113. doi:10.1007/s12088-009-0012-2
Kaur G, Rajesh S, Princy SA (2015) Plausible drug targets in the Streptococcus mutans quorum sensing pathways to combat dental biofilms and associated risks. Indian J Microbiol 55:349–357. doi:10.1007/s12088-015-0534-8
Kekre A, Bhushan A, Kumar P, Kalia VC (2015) Genome wide analysis for searching novel markers to rapidly identify Clostridium strains. Indian J Microbiol 55:250–257. doi:10.1007/s12088-015-0535-7
Koul S, Kalia VC (2016) Comparative genomics reveals biomarkers to identify Lactobacillus species. Indian J Microbiol 56:253–263. doi:10.1007/s12088-016-0605-5
Koul S, Kumar P, Kalia VC (2015a) A unique genome wide approach to search novel markers for rapid identification of bacterial pathogens. J Mol Genet Med 9:194. doi:10.4172/1747-0862.1000194
Koul S, Prakash J, Mishra A, Kalia VC (2015b) Potential emergence of multi-quorum sensing inhibitor resistant (MQSIR) bacteria. Indian J Microbiol 56:1–18. doi:10.1007/s12088-015-0558-0
Kumar R, Koul S, Kumar P, Kalia VC (2016) Searching biomarkers in the sequenced genomes of Staphylococcus for their rapid identification. Indian J Microbiol 56:64–71. doi:10.1007/s12088-016-0565-9
Lal D, Verma M, Lal R (2011) Exploring internal features of 16S rRNA gene for identification of clinically relevant species of the genus Streptococcus. Ann Clin Microbiol Antimicrob 10:28. doi:10.1186/1476-0711-10-28
Lalucat J, Bennasar A, Bosch R, Garcia-Valdés E, Palleroni NJ (2006) Biology of Pseudomonas stutzeri. Microbiol Mol Biol Rev 70:510–547. doi:10.1128/MMBR.00047-05
Mahale KN, Paranjape PS, Marathe NP, Dhotre DP, Chowdhury S, Shetty SA, Sharma A, Sharma K, Tuteja U, Batra HV, Shouche YS (2014) Draft genome sequences of Yersinia pestis strains from the 1994 plague epidemic of Surat and 2002 Shimla outbreak in India. Indian J Microbiol 54:480–482. doi:10.1007/s12088-014-0475-7
Meza-Lucas A, Pérez-Villagómez M, Martínez-López JP, García-Rodea R, Martínez-Castelán MG, Escobar-Gutiérrez A, de-la-Rosa-Arana JL, Villanueva-Zamudio A (2016) Comparison of DOT-ELISA and Standard-ELISA for detection of the Vibrio cholerae toxin in culture supernatants of bacteria isolated from human and environmental samples. Indian J Microbiol 56:379–382. doi:10.1007/s12088-016-0596-2
Moroeanu VI, Vamanu E, Paun G, Neagu E, Ungureanu OR, Eremia SAV, Radu GL, Ionescu R, Pelinescu DR (2015) Probiotic strains influence on infant microbiota in the in vitro colonic fermentation model GIS1. Indian J Microbiol 55:423–429. doi:10.1007/s12088-015-0542-8
Nakamura LK, Roberts MS, Cohan FM (1999) Relationship of Bacillus subtilis clades associated with strains 168 and W23: a proposal for Bacillus subtilis subsp. subtilis subsp. nov. and Bacillus subtilis subsp. spizizenii subsp. nov. Int J Syst Bacteriol 49:1211–1215
Nazina TN, Tourova TP, Poltaraus AB, Novikova EV, Grigoryan AA, Ivanova AE, Lysenko AM, Petrunyaka VV, Osipov GA, Belyaev SS, Ivanov MV (2001) Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp nov and Geobacillus uzenensis sp nov from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. thermocatenulatus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans. Int J Syst Evol Microbiol 51:433–446. doi:10.1099/00207713-51-2-433
Nguyen THK, Doan VTT, Ha LD, Nguyen HN (2013) Molecular cloning, expression of minD gene from Lactobacillus acidophilus VTCC-B-871 and analyses to identify Lactobacillus rhamnosus PN04 from Vietnam Hottuyniacordata Thunb. Indian J Microbiol 53:385–390. doi:10.1007/s12088-013-0384-1
Peix A, Valverde A, Rivas R, Igual JM, Ramírez-Bahena MH, Mateos PF, Santa-Regina I, Rodríguez-Barrueco C, Martínez-Molina E, Velázquez E (2007) Reclassification of Pseudomonas aurantiaca as a synonym of Pseudomonas chlororaphis and proposal of three subspecies, P. chlororaphis subsp. chlororaphis subsp. nov., P. chlororaphis subsp. aureofaciens subsp. nov., comb. nov. and P. chlororaphis subsp. aurantiaca subsp. nov., comb. nov. Int J Syst Evol Microbiol 57:1286–1290. doi:10.1099/ijs.0.000164
Peix A, Ramírez-Bahena MH, Velázquez E (2009) Historical evolution and current status of the taxonomy of genus Pseudomonas. Infect Genet Evol 9:1132–1147. doi:10.1016/j.meegid.2009.08.001
Porwal S, Lal S, Cheema S, Kalia VC (2009) Phylogeny in aid of the present and novel microbial lineages: diversity in Bacillus. PLoS One 4, e4438. doi:10.1371/journal.pone.0004438
Prakash O, Jangid K, Shouche YS (2013) Carl Woese: from biophysics to evolutionary microbiology. Indian J Microbiol 53:247–252. doi:10.1007/s12088-013-0401-4
Prakash O, Pandey PK, Kulkarni GJ, Mahale KN, Shouche YS (2014) Technicalities and glitches of terminal restriction fragment length polymorphism (T-RFLP). Indian J Microbiol 54:255–261. doi:10.1007/s12088-014-0461-0
Prakasham RS, Kumar BS, Kumar YS, Kumar KP (2014) Production and characterization of protein encapsulated silver nanoparticles by marine isolate Streptomyces parvulus SSNP11. Indian J Microbiol 54:329–336. doi:10.1007/s12088-014-0452-1
Puri A, Rai A, Dhanaraj PS, Lal R, Patel DD, Kaicker A, Verma M (2016) An in silico approach for identification of the pathogenic species, Helicobacter pylori and its relatives. Indian J Microbiol 56:277–286. doi:10.1007/s12088-016-0575-7
Saxena A, Mukherjee M, Kumari R, Singh P, Lal R (2014) Synthetic biology in action: developing a drug against MDR-TB. Indian J Microbiol 54:369–375. doi:10.1007/s12088-014-0498-0
Selvakumaran S, Kapley A, Kashyap SM, Daginawala HF, Kalia VC, Purohit HJ (2011) Diversity of aromatic ring-hydroxylating dioxygenase gene in Citrobacter. Bioresour Technol 101:4600–4609. doi:10.1016/j.biortech.2011.01.011
Shang Z, Wang H, Zhou S, Chu W (2014) Characterization of N-acyl-homoserine lactones (AHLs)-deficient clinical isolates of Pseudomonas aeruginosa. Indian J Microbiol 54:158–162. doi:10.1007/s12088-014-0449-9
Sharma P, Kumari H, Kumar M, Verma M, Malhotra S, Khurana J, Lal R (2008) From bacterial genomics to metagenomics: concepts, tools and recent advances. Indian J Microbiol 48:173–194. doi:10.1007/s12088-008-0031-4
Spiers AJ, Buckling A, Rainey PB (2000) The causes of Pseudomonas diversity. Microbiology 146:2345–2350. doi:10.1099/00221287-146-10-2345
Suerbaum S, Michetti P (2002) Helicobacter pylori infection. N Engl J Med 347:1175–1186. doi:10.1056/NEJMra020542
Tourkya B, Boubellouta T, Dufour E, Leriche F (2009) Fluorescence spectroscopy as a promising tool for a polyphasic approach to pseudomonad taxonomy. Curr Microbiol 58:39–46. doi:10.1007/s00284-008-9263-0
Verma V, Raju SC, Kapley A, Kalia VC, Daginawala HF, Purohit HJ (2010) Evaluation of genetic and functional diversity of Stenotrophomonas isolates from diverse effluent treatment plants. Bioresour Technol 101:7744–7753. doi:10.1016/j.biortech.2010.05.014
Verma V, Raju SC, Kapley A, Kalia VC, Kanade GS, Daginawala HF, Purohit HJ (2011) Degradative potential of Stenotrophomonas strain HPC383 having genes homologous to dmp operon. Bioresour Technol 102:3227–3233. doi:10.1016/j.biortech.2010.11.016
Wang R, Fang S, Xiang S, Ling S, Yuan J, Wang S (2014) Generation and characterization of a scFv antibody against T3SS needle of Vibrio parahaemolyticus. Indian J Microbiol 54:143–150. doi:10.1007/s12088-013-0428-6
Yagnik B, Patel S, Dave M, Sharma D, Padh H, Desai P (2016) Factors affecting inducible expression of outer membrane protein A (OmpA) of Shigella dysenteriae Type-1 in Lactococcus lactis using nisin inducible controlled expression (NICE). Indian J Microbiol 56:80–87. doi:10.1007/s12088-015-0556-2
Yoon JH, Weiss N, Lee KC, Lee IS, Kang KH, Park YH (2001) Jeotgalibacillus alimentarius gen. nov., sp. nov., a novel bacterium isolated from jeotgal with L-lysine in the cell wall, and reclassification of Bacillus marinus Ruger 1983 as Marinibacillus marinus gen. nov., comb. nov. Int J Syst Evol Microbiol 51:2087–2093. doi:10.1016/j.biortech.2010.11.016
Yu S, Peng Y, Chen W, Deng Y, Zheng Y (2014) Comparative genomic analysis of two-component signal transduction systems in probiotic Lactobacillus casei. Indian J Microbiol 54:293–301. doi:10.1007/s12088-014-0456-x
Yu S, Peng Y, Zheng Y, Chen W (2015) Comparative genome analysis of Lactobacillus casei: insights into genomic diversification for niche expansion. Indian J Microbiol 55:102–107. doi:10.1007/s12088-014-0496-2
Acknowledgments
We are thankful to the Director of CSIR-Institute of Genomics and Integrative Biology (IGIB) and CSIR project GENESIS (BSC0121) for providing the necessary funds, facilities, and moral support. Authors are also thankful to the Academy of Scientific and Innovative Research (AcSIR), New Delhi.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Kalia, V.C., Kumar, R., Koul, S. (2017). In Silico Analytical Tools for Phylogenetic and Functional Bacterial Genomics. In: Arora, G., Sajid, A., Kalia, V. (eds) Drug Resistance in Bacteria, Fungi, Malaria, and Cancer. Springer, Cham. https://doi.org/10.1007/978-3-319-48683-3_15
Download citation
DOI: https://doi.org/10.1007/978-3-319-48683-3_15
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-48682-6
Online ISBN: 978-3-319-48683-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)