16s Rrna Based Metagenomics Analysis of Uterine Microbiota in Cattle

Abstract

Metritis severely affects the economy of by reducing productivity and hampering reproductive cycle of the animals. This acts like two-sided sword to damage dairy economy. For prevention and control of metritis, it is essential to understand the dynamics of the uterine microbiota at parturition. Keeping these aspects in mind the present study was planned to establish cattle uterine microbiota at and immediate after parturition; to identify the major bacterial pathogens involved in the cattle metritis and also to suggest the prevention and control strategies to avoid post parturient metritis in cattle. The present study included 24 cattle including 11 showing the clinical signs of metritis where as 13 with regular estrous cycle. Out of them 7 and 3 regular isolates of E. coli were recovered from metritic and apparently healthy cattle. All the presumptive isolates of E. coli were confirmed by the amplification species specific of 556 base pair uidA genes. Four animals also revealed presence of Staphylococcus spp. in metritis cases with the prevalence of 36.6 %. All the bacterial isolates were subjected to antibiotic sensitivity test against 14 antibacterial drugs like Ciprofloxacin, Levofloxacin, Enrofloxacin, Gentamicin, Amikacin, Streptomycin, Cloxacillin, Penicillin G, Cefoperazone, Cephalexin and Ceftriaxone, Metronidazole, Amoxicillin Clavulanic Acid and Oxytetracycline. E. coli isolates revealed 100% resistance against Cloxacillin, Penicillin G, Metronidazole, Levofloxacin and Oxytetracycline, 90% against Enrofloxacin and Streptomycin, 70% against Amikacin and 60% against Amoxyclav. Staphylococcus isolates revealed 100% resistance against Cefoperazone, Cloxacillin, Penicillin G, Streptomycin, Metronidazole, Levofloxacin and Oxytetracycline and 75% against Gentamicin and Ciprofloxacin. When all the isolates were classified for antibiotyping, study revealed eight biotypes of E. coli and four biotypes in Staphylococcus spp. The uterine discharges of both healthy cyclic and metritic cows were subjected for metagenomic analysis to compare the changes in uterine microbiota. The pooled samples of five healthy and five metritic cows of Sahiwal breeds were subjected for NGS and MG-RAST based analysis. The NGS revealed the presence of 4 domain of microbes in metritic animals as compared to two domains in healthy animals. The healthy animals have almost 100% population of archaea with only 29 domains of bacteria. While in contrast to it, metritic animals revealed 87 % bacteria and 12 % archaea. Similarly, studies of Phylum revealed 6 and 19 phyla in healthy and metritic samples. The results of classes revealed 8 and 32 classes in healthy and metritic samples. The samples from metritic cows revealed 108 families in comparison to 17 families in samples of healthy animals. Similarly, samples from metritic cows revealed 235 genera in comparison to 22 genera in samples of healthy animals.