Metagenomic Analysis of the Faecal Microbiome of Rats with 1, 2-Dimethylhydrazine Induced Colon Cancer and Prophylactic
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ORIGINAL RESEARCH ARTICLE
Metagenomic Analysis of the Faecal Microbiome of Rats with 1, 2-Dimethylhydrazine Induced Colon Cancer and Prophylactic Whole-Cell Carotenoid Intervention Sankaranarayanan Gomathinayagam1
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Gothandam Kodiveri Muthukaliannan1
Received: 19 May 2020 / Accepted: 30 September 2020 Ó Association of Microbiologists of India 2020
Abstract Rapidly evolving sequencing technologies have enabled efficient sequencing of complex genomes and metagenomes. Here, we have presented our metagenomic analysis of rat faeces isolated DNA, sequenced using longread sequencing technology. The microbiome changes in the rat faeces after sixteen weeks of prolonged administration of subcutaneous 1,2 dimethylhydrazine to induce colon carcinogenesis and oral carotenoid-rich whole-cell lyophilised Dunaliella salina supplement. The faecal pellets were aseptically collected, and DNA was isolated and sequenced subsequently. The post-sequencing analysis revealed that the rat gut microbiome is highly complex and diverse. There was a significant difference between the microbiome of rats that received Dunaliella salina supplement in comparison with rats treated with 1,2 dimethylhydrazine and control rats. We observed the dominance of Bacteroidetes over Firmicutes in both cases of administration. The dominance was notably contributed by individuals like B. vulgatus, B. dorei, B. fragilis, P. ruminicola, and P. copri. The presence of protozoans like Trypanosoma, Trichomonas, and Leishmania was also identified among other commensal eukaryotes. Moreover, there was an abundant presence of bacteriophages targeting probiotic organisms like Lactobacillus among the identified DNA viruses.
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12088-020-00909-z) contains supplementary material, which is available to authorized users. & Gothandam Kodiveri Muthukaliannan [email protected] 1
School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu 632014, India
Keywords Metagenomics Colon cancer Carotenoid Dunaliella salina Gut dysbiosis Rat faeces Abbreviations DSLP Dunaliella salina Lyophilised powder DMH Dimethyl hydrazine MG Metagenomics rapid annotation based on RAST subsystems technology GUS Glucuronidase
Introduction The gut microbiome is one of the most complex microbiomes ever studied. They outnumber even their hosts’ total unit cell count. It is both vulnerable and indicative of almost all changes in the physiology of an individual [1, 2]. The implications of this gut microbiota in several diseases are well known and are increasingly studied in depth. Dysbiosis of the gut microbiota is associated with inflammatory disorders, metabolic syndromes, irritable bowel syndrome, and even colorectal cancer [3]. There is a growing interest now among individuals to know their gut microbiome, and many commercial sequencing service providers are offering the same along with personalised dietary recommendations to tune the gut health. Already there a
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