Research Focus Key Words

Genomics, Pathogenomics, Horizontal Gene Transfer, Taxonomy, Bacterial Pigments


Prof. Shivakumara obtained his PhD in Biomedical and Veterinary Sciences from Virginia Tech, USA, in 2007.

After two (2007-2011) postdoctoral stints (one at the University of Kansas, and the other at the Los Alamos National Laboratory) he joined IBAB as a Faculty Scientist in February 2012. In addition to genomics research, he is involved in teaching microbiology, cell biology, and lab courses related to these modules to MSc students at IBAB.

Prof. Shivakumara is also the coordinator of the MSc program (since April 2015).


PhD: Virginia Tech, USA, 2007

Postdoctoral Research:

  1. University of Kansas, Lawrence, Kansas, USA
  2. Los Alamos National Laboratory, Los Alamos, New Mexico, USA

Professional Experience

Instructor and Lecturer, University of Agricultural Sciences, Bengaluru, 1999-2001

Research Interest Profile

Welcome to SK’s lab page!

We are interested in the genetics and genomics of prokaryotes.

We are particularly interested in elucidating the mechanisms and roles of gene gain and loss in bacteria of pathogenic and biotechnological importance.

Our current research emphasis is on the application of comparative genomics for understanding horizontal gene transfer and the evolution of bacteria of diverse genera.

Another area of research is genome-based taxonomy of bacteria.


  1. Characterization of C40 carotenoid biosynthesis in Sphingomonas spp.
    Carotenoids possess potent antioxidant and free radical scavenging properties, and are produced by several species of bacteria, including members of the genus Sphingomonas. Sphingomonas. [Pseudomonas] Sphingomonas echinoides was isolated and characterized by Dr. Wolfram Heumann, and is believed to produce nostoxanthin, which is a xanthophyll that imparts yellow colour. The NRRL culture collection contains two strains of Sphingomonas echinoides, one of which (B-3126) forms yellow colonies, while the other (B-3127) forms off-white colonies. We are working on further characterization of these two strains, including the pathways of carotenoid biosynthesis in them as well as other strains of Sphingomonas spp.

  2. Characterization of C50 carotenoid biosynthesis in Kocuria spp.
    Kocuria rosea is the type species of the genus Kocuria, which is named after the Slovakian microbiologist Dr. Miroslav Kocur. Members of this genus are Gram positive, coccoid, NON-MOTILE, and non-encapsulated. Members of Kocuria rosea are known to occur in pairs, tetrads, or clusters. Colonies are pink or red. Our laboratory has isolated a strain of Kocuria spp. that is motile and produces C50 carotenoids and a water-soluble pigment. We are working on further characterization of this strain, using genomic and proteomic approaches.

  3. Characterization of flexirubin biosynthesis in Chryseobacterium spp.
    The genus Chryseobacterium was formally established in 1994 and contains more than 100 species with validly published names. Most of these species are yellow or orange coloured, and contain a flexirubin type pigment. Our laboratory has isolated a strain of Chryseobacterium spp. that appears to represent a novel species within the genus. In addition to the investigation of flexirubin biosynthesis pathways in bacteria, we are working on the taxonomic characterization of novel species of Chryseobacterium.

Lab members:

  1. Vandana Viswanathan – PhD student
  2. Enid Mendonca –Intern (MSc student at VITU, Vellore, TN)


  1. Dr. Sathish B. Shivachandra, Principal Scientist, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, India
  2. Dr. B. E. Pradeep, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, AP, India

Publications and patents:


  1. Siddaramappa S, Pullela K, Thimmappa B, Devkota R, Bajaj R, Manivannan B,Mahalingam N, Pradeep BE.
    Characterization of bla(CTX-M) sequences of Indianorigin and thirteen uropathogenic Escherichia coli isolates resistant to multiple antibiotics. BMC Res Notes. 2018 Aug 31;11(1):630. doi:10.1186/s13104-018-3735-5.
  2. Siddaramappa S, Viswanathan V, Thiyagarajan S, Narjala A.
    Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales. Microb Genom. 2018 Apr 5. doi: 10.1099/mgen.0.000172.
  3. Mahalingam N, Manivannan B, Khamari B, Siddaramappa S, Adak S, Bulagonda EP.
    Detection of Antibiotic Resistance Determinants and Their Transmissibility among Clinically Isolated Carbapenem-Resistant Escherichia coli from South India. MedPrinc Pract. 2018;27(5):428-435. doi: 10.1159/000489885.
  4. Shukla P, Khodade VS, SharathChandra M, Chauhan P, Mishra S, Siddaramappa S,Pradeep BE, Singh A, Chakrapani H.
    “On demand” redox buffering by H(2)S contributes to antibiotic resistance revealed by a bacteria-specific H(2)S donor. Chem Sci. 2017 Jul 1;8(7):4967-4972. doi: 10.1039/c7sc00873b.


  1. Viswanathan V, Narjala A, Ravichandran A, Jayaprasad S, Siddaramappa S.
    Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales.Genome Biol Evol. 2017 Feb 15. doi: 10.1093/gbe/evx024.


  1. Siddaramappa S.
    Histophilus somni Genomics and Genetics.
    Curr Top Microbiol Immunol. 2016;396:49-70. doi: 10.1007/82_2015_5009. Review.


  1. Mukherjee K, Bowman KS, Rainey FA, Siddaramappa S, Challacombe JF, Moe WM.
    Dehalogenimonas lykanthroporepellens BL-DC-9T simultaneously transcribes many rdhA genes during organohalide respiration with 1,2-DCA, 1,2-DCP, and 1,2,3-TCP as electron acceptors. FEMS Microbiol Lett. 2014 May;354(2):111-8. doi:10.1111/1574-6968.
  2. Siddaramappa S, Challacombe JF, Petersen JM, Pillai S, Kuske CR.
    Comparative analyses of a putative Francisella conjugative element. Genome. 2014 Mar;57(3):137-44. doi: 10.1139/gen-2013-0231.


  1. Siddaramappa S, Challacombe JF, Petersen JM, Pillai S, Kuske CR.
    Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources. BMC Genomics. 2012 Aug 24;13:422. doi: 10.1186/1471-2164-13-422.
  2. Siddaramappa S, Challacombe JF, Delano SF, Green LD, Daligault H, Bruce D, Detter C, Tapia R, Han S, Goodwin L, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Land M, Chang YJ, Kyrpides NC, Ovchinnikova G, Hauser L, Lapidus A, Yan J, Bowman KS, da Costa MS, Rainey FA, Moe WM.
    Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to “Dehalococcoides” strains. Stand Genomic Sci. 2012 May 25;6(2):251-64. doi:10.4056/sigs.2806097.
  3. Siddaramappa S, Challacombe JF, Decastro RE, Pfeiffer F, Sastre DE, Giménez MI, Paggi RA, Detter JC, Davenport KW, Goodwin LA, Kyrpides N, Tapia R, Pitluck S, Lucas S, Woyke T, Maupin-Furlow JA.
    A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T. BMC Genomics. 2012 May 4;13:165. doi: 10.1186/1471-2164-13-165.


  1. Siddaramappa S, Challacombe JF, Duncan AJ, Gillaspy AF, Carson M, Gipson J, Orvis J, Zaitshik J, Barnes G, Bruce D, Chertkov O, Detter JC, Han CS, Tapia R, Thompson LS, Dyer DW, Inzana TJ.
    Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses. BMC Genomics. 2011 Nov 23;12:570. doi: 10.1186/1471-2164-12-570.
  2. Siddaramappa S, Challacombe JF, Petersen JM, Pillai S, Hogg G, Kuske CR.
    Common ancestry and novel genetic traits of Francisella novicida-like isolates from North America and Australia as revealed by comparative genomic analyses. Appl Environ Microbiol. 2011 Aug;77(15):5110-22. doi: 10.1128/AEM.00337-11.


  1. McKinlay JB, Laivenieks M, Schindler BD, McKinlay AA, Siddaramappa S,Challacombe JF, Lowry SR, Clum A, Lapidus AL, Burkhart KB, Harkins V, Vieille C.
    A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production. BMC Genomics. 2010 Nov 30;11:680. doi: 10.1186/1471-2164-11-680.


  1. Siddaramappa S, Duncan AJ, Brettin T, Inzana TJ.
    Comparative analyses of two cryptic plasmids from Haemophilus somnus (Histophilus somni). Plasmid. 2006 May;55(3):227-34.


  1. Siddaramppa S, Inzana TJ.
    Haemophilus somnus virulence factors and resistance to host immunity. Anim Health Res Rev. 2004 Jun;5(1):79-93. Review.