Next-generation sequencing analysis reveals high bacterial diversity in wild venomous and non-venomous snakes from India

 

Sajesh Puthenpurackal Krishnankutty^1 3, Megha Muraleedharan¹, Rajadurai Chinnasamy Perumal¹, Saju Michael¹, Jubina Benny¹, Bipin Balan¹, Pramod Kumar¹, Jishnu Manazhi², Bangaruswamy Dhinoth Kumar¹, Sam Santhosh¹, George Thomas³, Ravi Gupta⁴, Arun Zachariah²

 

1 AgriGenome Labs Pvt. Ltd., SmartCity Kochi, Kakkanad, Kerala 682042, India

2 Department of Forests and Wildlife, Sulthan Batheri, Wayanad District, Kerala 673592, India

3 SciGenom Research Foundation, Cheruthuruthy, Kerala 679531, India

4 Medgenome Labs Pvt. Ltd., Narayana Health City, Bommasandra, Bengaluru, Karnataka 560099, India

 

ABSTRACT

Background:

The oral cavities of snakes are replete with various types of bacterial flora. Culture-dependent studies suggest that some of the bacterial species are responsible for secondary bacterial infection associated with snakebite. A complete profile of the ophidian oral bacterial community has been unreported until now. Therefore, in the present study, we determined the complete bacterial compositions in the oral cavity of some snakes from India.

 

Methods:

Total DNA was isolated from oral swabs collected from three wild snake species (Indian Cobra, King Cobra and Indian Python). Next, the DNA was subjected to PCR amplification of microbial 16S rRNA gene using V3-region-specific primers. The amplicons were used for preparation of DNA libraries that were sequenced on an Illumina MiSeq platform.

 

Results:

The cluster-based taxonomy analysis revealed that Proteobacteria and Actinobacteria were the most predominant phyla present in the oral cavities of snakes. This result indicates that snakes show more similarities to birds than mammals as to their oral bacterial communities. Furthermore, our study reports all the unique and common bacterial species (total: 147) found among the oral microbes of snakes studied, while the majority of commonly abundant species were pathogens or opportunistic pathogens to humans. A wide difference in ophidian oral bacterial flora suggests variation by individual, species and geographical region.

 

Conclusion:

The present study would provide a foundation for further research on snakes to recognize the potential drugs/antibiotics for the different infectious diseases.

 

Keywords: Microbial community; Next-generation sequencing; Venomous snake; Hypervariable region.

 

Received: June 21, 2018.

Accepted: December 06, 2018.

Published: December 22, 2018.

 

Correspondence: zacharun@gmail.com

 

Authors’ contributions

SPK was responsible for sample collection and played a major contributor in preparation of the manuscript. SM performed DNA isolation and quality check of the samples. MM carried out library preparation based on Illumina protocol and carried out the sequencing run. RCP was responsible for setting up and performing bioinformatics analysis pipeline. JB was involved in testing, validating and running bioinformatics tools. BP was responsible for writing scripts and parsing the generated results from the pipeline. PK supported in manuscript write up and interpreting the results. JM contributed in data deposition and assisted in data analysis. BDK assisted in sample collection and sequencing. SS & GT supported in framing the whole experimental design. RG contributed in manuscript preparation and provided technical guidance for the bioinformatics team. AZ coordinated the whole team and provided all the technical support. All authors read and approved the final manuscript.

 

Competing interests

The authors declare that they have no competing interests.