Bioinformatics Tools for Genome Mining of Marine Associated Bacteria

Deepa S, Srikumar M


Many of the novel bioactive compounds reported from marine organisms have originated from their microbial symbionts.  Isolation and taxonomical studies of these symbiotic microbes are essential in different aspects including the mining of novel products. Bacterial differentiation and classification are a prolonged process involving some ambiguous steps for the non-specialist group. In this context, bioinformatics tools have been used for microbial biotechnology in many ways, such as for sequencing and analyzing the genome, identifying coding sequences, computational analysis of the wet-lab data, etc. This paper provides insight into the genomic isolation techniques of microbes from marine organisms and the available bioinformatics tools.


Microbes, Isolation techniques, Microbial taxonomy, genome sequencing, bioinformatics tools.

Full Text:



Alawi, M., Burkhardt, L., Indenbirken, D., Reumann, K.,Christopeit, M., et al. (2019). DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples. Scientific Reports,9:16841 |

Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D. J ( 1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389 –3402.

Ambrosino, L., Tangherlini, M., Colantuono, C., Esposito, A., Sangiovanni, M., Miralto,M., Sansone, M., Chiusano, M.L (20019). Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives .Mar. Drugs, 17, 576; doi:10.3390/md17100576

Arvind K Bansal, A.K (2005). Bioinformatics in microbial biotechnology – a mini review. Microbial Cell Factories , 4:19

Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A and Struhl, K (1994). Current Protocols in Molecular Biology. Greene Publishing Associates and Wiley-Interscience, New York, NY

Azad, R.K. and Borodovsky, M (2004) Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory. Brief Bioinformatics. 5(2):118-30

Bansal, A.K. (2005). Bioinformatics in microbial biotechnology - a mini review. Microbial Cell Factories, 4: 19.

Bengtsson, M.M. Sjøtun, K., Lanzén, A and Ovreas, L. Bacterial diversity in relation to secondary production and succession on surfaces of the kelp Laminaria hyperborean. Isme J. 2012, 6, 2188–2198. [CrossRef] [PubMed]

Brooksbank, C., Bergman, M.T., Apweiler, R., Birney, E., Thornton, J (2014). The European Bioinformatics Institute’s data resources 2014. Nucleic Acids Res 42:D18 –D25.

Dabdoub, S. M. et al. (2016). PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets. Sci. Rep. 6, 29123; doi: 10.1038/srep29123

Delcher, A. L., Harmon, D., Kasif, S., White, O. and Salzberg, S.L (1999) . Improved microbial gene identification with GLIMMER. Nucleic Acids Research , 27(23):4636-41

Devulder, G., Perrie`re, G., Baty, F and Flandrois, J. P. (2003). BIBI, a Bioinformatics Bacterial Identification Tool. Journal of Clinical Microbiology, (41) 1785–1787.No.4 0095-1137/03/$08.000 DOI: 10.1128/JCM.41.4.1785–1787.

Fleischmann, R. D, et al. (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science , 269:496-512

Kennedy, J., Marchesi, J.R. and Dobson, A.D. (2008). Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microbial Cell Factories 7:27 doi:10.1186/1475-2859-7-27

Larkin, M.A., Blackshields, G., Brown, N.P(2007). Clustal W and clustal X version 2.0. Bioinformatics 23, 2947–2948.

Liang, Q., Liu, C., Xu, R., Song, M,, Zhou, Z,, Li, H,, Dai, W., Yang, M., Yu, Y and Chen, H (2021). fIDBAC: A Platform for Fast Bacterial Genome Identification and Typing. Front. Microbiol. 12:723577. doi: 10.3389/fmicb.2021.723577

Maji, P., Chakrabarti, C., Chatterjee, S.N ( 2012). Phenotyping and molecular characterization of Lysinibacillus sp. P-011 (GU288531) and their role in the development of Drosophila melanogaster. Afr. J. Biotechnol. 11, 15967–15974.

Mount, D.W (2000). Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Laboratory Press, Newyork.

Nakashima, N., Mitani, Y., Tamura, T(2005). Actinomycetes as host cells for production of recombinant proteins. Microbial Cell Factories , 4(7):1-5.

Pruitt, K.D., Tatusova ,T., Brown, G.R., Maglott, D.R ( 2012). NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 40:D130 –D135. /gkr1079.

Rekadwad , B.N., Gonzalez, J.M., and Khobragad, C.N (2016). Genomic analysis of a marine bacterium: bioinformatics for comparison, evaluation, and interpretation of DNA sequences. BioMed. Research. Article ID 7215379, 7 pages

Saputra et al. (2015). Reads2Type: a web application for rapid microbial taxonomy identification BMC Bioinformatics .16:398 DOI 10.1186/s12859-015-0829-0

Sigrist, C.J., Cerutti, L., Hulo, N., Gattiker, A., Falquet, L., Pagni, M., Bairoch, A., Bucher, P (2002). PROSITE: a documented database using patterns and profiles as motif descriptors. Briefings in Bioinformatics , 3(3):265-74.

Sonnhammer, E.L., Eddy, S.R., Birney, E., Batman, A., Durbin, R (1998). Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Research . 26:320-322

Suzek, B.E., Ermolaeva, M.D., Schreiber, M., Salzberg, S.L. (2001). A probabilistic method for identifying start codons in bacterial genomes. Bioinformatics, 17(12):1123-30.

Tamura, K., Peterson, D., Peterson, N (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731–2739.

Tawfike, A.F., Attia, E.Z., Desoukey, S.Y., Hajjar, D., Makki, A.A., Schupp, P.J., Edrada-Ebel, R. and Abdelmohsen, U.R. New bioactive metabolites from the elicited marine sponge-derived bacterium Actinokineospora spheciospongiae sp. nov. AMB Express 2019, 9, 1–9. [CrossRef]

Ventosa, A., Nieto, J.J., Oren, A ( 1998) . Biology of moderately halophilic aerobic bacteria. Microbiol. Mol. Biol. Rev. 62, 504–544.

Webster, N.S., Wilson, K.J., Blackall, L.L., Hill, R.T., Toledo-Arana, A., Valle, J., Solano, C.; Arrizubieta, M.J., Cucarella, C., Lamata, M. et al. Phylogenetic Diversity of Bacteria Associated with the Marine Sponge Rhopaloeides odorabile. Appl. Environ. Microbiol. 2001, 67, 4538–4545. [CrossRef]

Whisstock, J.C., and Lesk, A. M (2003).Prediction of protein function from protein sequence and structure. Q Rev Biophysics 36(3):307-340.

Zhulin, I.B (2015). Databases for microbiologists. J Bacteriol 197:2458 –2467. doi:10.1128/JB.00330-15.


  • There are currently no refbacks.

Print Version ISSN: 2320-530X (Application for ISSN Online Version Pending)