• Nur Aisyah Atikah Bt Alizan Universiti Teknologi MARA
  • Sarah Shazwani Zakaria


Bacteria of the genus Komagataeibacter are described to be the most noteworthy for having several of its species being efficient and strong cellulose producers. The 16S ribosomal RNA (rRNA) gene analysis is often used for the identification and taxonomic classification of these bacteria species. In order to observe the phylogenetic relationship among Komagataeibacter sp., twelve sequences of the 16S rRNA gene with three sequences each for species namely Komagataeibacter europaeus, Komagataeibacter hansenii, Komagataeibacter intermedius and Komagataeibacter xylinus were retrieved from NCBI GenBank database. The sequences were aligned and analysed using PAUP, OrthoANI and BLAST, followed by the phylogenetic tree construction using a Maximum Likelihood method. The parsimony character diagnostic analysis showed very few numbers of parsimony-informative characters present in the aligned sequences which is only 1.5% of the total characters. The inferred phylogenetic relationships demonstrated the unexpected positioning of K. xylinus (GQ240638: Gluconacetobacter xylinus strain) and K. xylinus (KC11853: G. xylinus strain) into the clades of K. europaeus and K. hansenii respectively. The also very low bootstrap values of the branch points linking the K. europaeus species indicated low support for the produced topologies. The findings of this study indicate that more phylogenies information can be attained by increasing the taxon sampling. In addition, more robust molecular data are needed to infer the phylogenetic relationships between the Komagataeibacter species more accurately.


Alkindy, B., Al-Nuaimi, B., Guyeux, C., Couchot, J.-F., Salomon, M., Alsrraj, R., & Philippe, L. (2015). Binary particle swarm optimization versus hybrid genetic algorithm for inferring well supported phylogenetic trees. Paper presented at the International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics.
Barja, F., Andrés-Barrao, C., Pérez, R. O., Cabello, E. M., & Chappuis, M.-L. (2016). Physiology of Komagataeibacter spp. during acetic acid fermentation. In Acetic Acid Bacteria (pp. 201-221): Springer.
Bybee, S. (2008). Phylogenetics. In J. L. Capinera (Ed.), Encyclopedia of Entomology (pp. 2863-2868). Dordrecht: Springer Netherlands.
Cheng, K.-C., Catchmark, J. M., & Demirci, A. (2009). Effect of different additives on bacterial cellulose production by Acetobacter xylinum and analysis of material property. Cellulose, 16(6), 1033-1045.
Clarridge, J. E. (2004). Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clinical microbiology reviews, 17(4), 840-862.
Dewhirst, F. E., Shen, Z., Scimeca, M. S., Stokes, L. N., Boumenna, T., Chen, T., . . . Fox, J. G. (2005). Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics. Journal of bacteriology, 187(17), 6106-6118.
Fitch, W. M. (1977). On the problem of discovering the most parsimonious tree. The American Naturalist, 111(978), 223-257.
Ibrahim, K. S., Gurusubramanian, G., Yadav, R. P., Kumar, N. S., Pandian, S. K., Borah, P., & Mohan, S. (2017). Nucleotide Analysis. In Bioinformatics-A Student's Companion (pp. 1-116): Springer.
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T., & Aluru, S. (2018). High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature communications, 9(1), 1-8.
Jill Harrison, C., & Langdale, J. A. (2006). A step by step guide to phylogeny reconstruction. The Plant Journal, 45(4), 561-572.
Kitahara, K., Yasutake, Y., & Miyazaki, K. (2012). Mutational robustness of 16S ribosomal RNA, shown by experimental horizontal gene transfer in Escherichia coli. Proceedings of the National Academy of Sciences, 109(47), 19220-19225.
Kitching, I. J., Forey, P., Forey, P. L., Humphries, C., & Williams, D. (1998). Cladistics: the theory and practice of parsimony analysis: Oxford University Press, USA.
Konstantinidis, K. T., & Tiedje, J. M. (2005). Genomic insights that advance the species definition for prokaryotes. Proceedings of the National Academy of Sciences, 102(7), 2567-2572.
Laios, E., Waddington, M., Saraiya, A. A., Baker, K. A., O'Connor, E., Pamarathy, D., & Cunningham, P. R. (2004). Combinatorial genetic technology for the development of new anti-infectives. Archives of pathology & laboratory medicine, 128(12), 1351-1359.
Lee, I., Kim, Y. O., Park, S.-C., & Chun, J. (2016). OrthoANI: an improved algorithm and software for calculating average nucleotide identity. International journal of systematic and evolutionary microbiology, 66(2), 1100-1103.
Li, L., Cleenwerck, I., De Vuyst, L., & Vandamme, P. (2017). Identification of acetic acid bacteria through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and report of Gluconobacter nephelii Kommanee et al. 2011 and Gluconobacter uchimurae Tanasupawat et al. 2012 as later heterotypic synonyms of Gluconobacter japonicus Malimas et al. 2009 and Gluconobacter oxydans (Henneberg 1897) De Ley 1961 (Approved Lists 1980) emend. Gosselé et al. 1983, respectively. Systematic and applied microbiology, 40(3), 123-134.
Mariadassou, M., Bar-Hen, A., & Kishino, H. (2012). Taxon Influence Index: Assessing Taxon-Induced Incongruities in Phylogenetic Inference. Systematic Biology, 61(2), 337-345. doi:10.1093/sysbio/syr129
Matsutani, M., Ito, K., Azuma, Y., Ogino, H., Shirai, M., Yakushi, T., & Matsushita, K. (2015). Adaptive mutation related to cellulose producibility in Komagataeibacter medellinensis (Gluconacetobacter xylinus) NBRC 3288. Applied microbiology and biotechnology, 99(17), 7229-7240.
Morrison, D. A. (2006). Phylogenetic analyses of parasites in the new millennium. Advances in Parasitology, 63, 1-124.
Naloka, K., Yukphan, P., Matsushita, K., & Theeragool, G. (2018). Molecular taxonomy and characterization of thermotolerant Komagataeibacter species for bacterial nanocellulose production at high temperatures. Chiang Mai Journal of Science, 45(4), 1610-1622.
Papathanassopoulou, A., & Lorentzos, N. A. (2014). Parsimony-Informative Characters. Paper presented at the 9th Conf. Hellenic Society for Computational Biology and Bioinformatics.
Rashid, M. H.-o., Young, J. P. W., Everall, I., Clercx, P., Willems, A., Braun, M. S., & Wink, M. (2015). Average nucleotide identity of genome sequences supports the description of Rhizobium lentis sp. nov., Rhizobium bangladeshense sp. nov. and Rhizobium binae sp. nov. from lentil (Lens culinaris) nodules. International journal of systematic and evolutionary microbiology, 65(9), 3037-3045.
Rastogi, A., Gautam, S., Kumar, M., & Tomar, R. S. (2019). RIBOSOMAL GENE BASED COMPARATIVE PHYLOGENIES FOR THE GENUS MYCOBACTERIUM: AN IN-SILICOAPPROACH. Journal of Scientific Research, 63, 89-103.
Rehm, B. H. (2010). Bacterial polymers: biosynthesis, modifications and applications. Nature Reviews Microbiology, 8(8), 578.
Reiniati, I., Hrymak, A. N., & Margaritis, A. (2017). Recent developments in the production and applications of bacterial cellulose fibers and nanocrystals. Critical reviews in biotechnology, 37(4), 510-524.
Ribeiro, P. L., Rapini, A., e Silva, U. C. S., & van den Berg, C. (2012). Using multiple analytical methods to improve phylogenetic hypotheses in Minaria (Apocynaceae). Molecular phylogenetics and evolution, 65(3), 915-925.
Ryngajłło, M., Jacek, P., Cielecka, I., Kalinowska, H., & Bielecki, S. (2019). Effect of ethanol supplementation on the transcriptional landscape of bionanocellulose producer Komagataeibacter xylinus E25. Applied microbiology and biotechnology, 1-16.
Sato, M., & Miyazaki, K. (2017). Phylogenetic network analysis revealed the occurrence of horizontal gene transfer of 16S rRNA in the genus Enterobacter. Frontiers in microbiology, 8, 2225.
Simpson, M. (2010). Plant Systematics. Second. In: San Diego, CA, USA: Elsevier Inc.
Škraban, J., Cleenwerck, I., Vandamme, P., Fanedl, L., & Trček, J. (2018). Genome sequences and description of novel exopolysaccharides producing species Komagataeibacter pomaceti sp. nov. and reclassification of Komagataeibacter kombuchae (Dutta and Gachhui 2007) Yamada et al., 2013 as a later heterotypic synonym of Komagataeibacter hansenii (Gosselé et al. 1983) Yamada et al., 2013. Systematic and applied microbiology, 41(6), 581-592.
Soltis, P., & Doyle, J. J. (2012). Molecular systematics of plants II: DNA sequencing: Springer Science & Business Media.
Swofford, D. L., & Sullivan, J. (2003). Phylogeny inference based on parsimony and other methods using PAUP*. The phylogenetic handbook: a practical approach to DNA and protein phylogeny, 7, 160-206.
Tian, R.-M., Cai, L., Zhang, W.-P., Cao, H.-L., & Qian, P.-Y. (2015). Rare Events of Intragenus and Intraspecies Horizontal Transfer of the 16S rRNA Gene. Genome biology and evolution, 7(8), 2310-2320. doi:10.1093/gbe/evv143
Wilgenbusch, J. C., & Swofford, D. (2003). Inferring evolutionary trees with PAUP. Current protocols in bioinformatics(1), 6.4. 1-6.4. 28.
Yang, B., Wang, Y., & Qian, P.-Y. (2016). Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis. BMC bioinformatics, 17(1), 135.
How to Cite
BT ALIZAN, Nur Aisyah Atikah; ZAKARIA, Sarah Shazwani. PHYLOGENETIC ANALYSIS OF Komagataeibacter sp.: A CELLULOSE-PRODUCER BACTERIA BASED ON 16S rRNA GENE SEQUENCES. Journal of Academia, [S.l.], v. 9, n. 1, p. 97-105, apr. 2021. ISSN 2289-6368. Available at: <>. Date accessed: 20 may 2024.

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