Insights into resistome and stress responses genes in Bubalus bubalis rumen through metagenomic analysis
- 485 Downloads
Buffalo rumen microbiota experience variety of diets and represents a huge reservoir of mobilome, resistome and stress responses. However, knowledge of metagenomic responses to such conditions is still rudimentary. We analyzed the metagenomes of buffalo rumen in the liquid and solid phase of the rumen biomaterial from river buffalo adapted to varying proportion of concentrate to green or dry roughages, using high-throughput sequencing to know the occurrence of antibiotics resistance genes, genetic exchange between bacterial population and environmental reservoirs. A total of 3914.94 MB data were generated from all three treatments group. The data were analysed with Metagenome rapid annotation system tools. At phyla level, Bacteroidetes were dominant in all the treatments followed by Firmicutes. Genes coding for functional responses to stress (oxidative stress and heat shock proteins) and resistome genes (resistance to antibiotics and toxic compounds, phages, transposable elements and pathogenicity islands) were prevalent in similar proportion in liquid and solid fraction of rumen metagenomes. The fluoroquinolone resistance, MDR efflux pumps and Methicillin resistance genes were broadly distributed across 11, 9, and 14 bacterial classes, respectively. Bacteria responsible for phages replication and prophages and phage packaging and rlt-like streptococcal phage genes were mostly assigned to phyla Bacteroides, Firmicutes and proteaobacteria. Also, more reads matching the sigma B genes were identified in the buffalo rumen. This study underscores the presence of diverse mechanisms of adaptation to different diet, antibiotics and other stresses in buffalo rumen, reflecting the proportional representation of major bacterial groups.
KeywordsResistome Personal genome machine MG-RAST Virulence genes Stress gene
This research work was supported by Niche area of excellence project funded by Indian Council of Agricultural Research, New Delhi, India.
- 1.Hespell RB, Mackie RI, White BA, Isaacson R (1997) Gastrointestinal microbiology, vol 2. Chapman and Hall, LondonGoogle Scholar
- 7.Bockelmann U, Dorries HH, Ayuso-Gabella MN, Salgot de Marcay M, Tandoi V et al (2009) Quantitative PCR monitoring of antibiotic resistance genes and bacterial pathogens in three European artificial groundwater recharge systems. Appl Environ Microbiol 75:154–163PubMedCentralCrossRefPubMedGoogle Scholar
- 14.Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM et al (2011) Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. ISME J 5:639–649Google Scholar
- 15.Durso LM, Harhay GP, Smith TP, Bono JL, DeSantis TZ et al (2011) Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces. Foodborne Pathog Dis 8:647–649Google Scholar
- 16.Brulc JM, Antonopoulos D, Berg-Miller ME, Wilson KM, Yannarell CA, Dinsdale AE, Edwards ER, Frank ED, Emerson BJ, Wacklin P, Coutinho MP, Henrissat B, Nelson EK, White AB (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci USA 106:1948–1953Google Scholar
- 17.Singh KM, Ahir V, Tripathi AK et al (2012) Metagenomic analysis of Surti buffalo 400 366 (Bubalus bubalis) rumen: a preliminary study. Mol Biol Rep 39(4):4841–4848Google Scholar
- 18.Overbeek R, Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, Crécy-Lagard DV, Diaz N, Disz T, Edwards R et al (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691–5702Google Scholar
- 19.Durso LM, Miller DN, Wienhold B (2012) Distribution and Quantification of Antibiotic Resistant Genes and Bacteria across Agricultural and Non Agricultural Metagenomes. PLoS ONE 7(11):e48325Google Scholar
- 22.Allen HK, Cloud-Hansen KA, Wolinski JM, Guan C, Greene S, Lu S, Boeyink M, Broderick NA, Raffa KF, Handelsman J (2009) Resident microbiota of the gypsy moth midgut harbors antibiotic resistance determinants. DNA Cell Biol 28(3):109–117Google Scholar