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An Approach to In Silico Dissection of Bacterial Intelligence Through Selective Genomic Tools

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Abstract

All the genetic potential and the intelligence a bacteria can showcase in a given environment are embedded in its genome. In this study, we have presented systematic guidelines to understand a bacterial genome with the relevant set of in silico tools using a novel bacteria as an example. This study presents a multi-dimensional approach from genome annotation to tracing genes and their network of metabolism operating in an organism. It also shows how the sequence can be used to mine the enzymes and construction of its 3-dimensional structure so that its functional behavior can be predicted and compared. The discriminating algorithm allows analysis of the promoter region and provides the insight in the regulation of genes in spite of the similarity in its sequences. The ecological niche specific bacterial behavior and adapted altered physiology can be understood through the presence of secondary metabolite, antibiotic resistance genes, and viral genes; and it helps in the valorization of genetic information for developing new biological application/processes. This study provides an in silico work plan and necessary steps for genome analysis of novel bacteria without any rigorous wet lab experiments.

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Acknowledgements

Miss Reshma talkal acknowledge DBT for providing stipend and Mr. Hitesh Tikariha acknowledge the Senior Research Fellowship (SRF) from the University Grants Commission (UGC) of India for carrying out the research work. Author also thanks CSIR-NEERI for providing facilty to carry out the research work and KRC for plagiarsim check [KRC No.: CSIR-NEERI/KRC/2018/APRIL/EBGD/1].

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Authors and Affiliations

  1. Environmental Biotechnology and Genomics Division, CSIR-NEERI, National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India

    Reshma Talkal, Hitesh Tikariha & Hemant Purohit

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  1. Reshma Talkal
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  2. Hitesh Tikariha
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  3. Hemant Purohit
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Correspondence to Hemant Purohit.

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Supplementary Table

 1 Table showing the list of all phage genes found to be present in bacterial genome under study. The phage genes were distributed in different contigs. (DOCX 17 kb)

Supplementary Fig.

 1 Subsystem classification of the annotated genome by RAST (JPEG 613 kb)

Supplementary Fig.

 2 Phylogenetic tree of all the vio genes constructed separately using MEGA 6. The gene from P. ferroxidans EGD-HP2 are shown in red box and the nearest member is shown with blue arrow. (JPEG 756 kb)

Supplementary Fig.

 3 Phylogenetic tree of phlD gene generated using MEGA 6. The gene under study is shown in red box. The different cluster that are formed in the tree are grouped as represented with yellow boxes. (JPEG 358 kb)

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Talkal, R., Tikariha, H. & Purohit, H. An Approach to In Silico Dissection of Bacterial Intelligence Through Selective Genomic Tools. Indian J Microbiol 58, 278–286 (2018). https://doi.org/10.1007/s12088-018-0726-0

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