26The bovine clinical mastitis (CM) milk is a large reservoir for diverse groups of resistomes, 27 which play important roles in the pathogenesis of mastitis, but little is known about the 28 concurrence of CM microbiome signature and its associated resistomes. Here we deciphered 29 the total resistance (antibiotics and metals resistance, biofilm formation, quorum sensing) 30 present in CM microbiome using whole metagenome sequencing (WMS) and in vitro cultural 31 approaches. Significant correlation (p=0.001) was found between the resistome diversity and 32 microbiome signature. We identified the strain-level microbiome diversity in four cattle 33 breeds, with microbiome composition represented by the phyla Proteobacteria, 34Bacteroidetes, Firmicutes, Actinobacteria and Fusobacteria (contributing to >95.0% of total 35 strains). However, the resistome diversity did not vary significantly (p=0.692) across the 36 microbiomes of cattle breeds. The in vitro investigation showed that biofilm producing CM 37 pathogens were resistant to most of the conventional antibiotics used for CM treatment, 38 whereas these pathogens remained sensitive to five heavy metals (Cr, Co, Ni, Cu, Zn) at 39 varying concentrations. We also found association of some genomic functional potentials 40 such as bacterial flagellar movement and chemotaxis, regulation and cell signaling, phages-41 prophages, transposable elements, plasmids and oxidative stress in the pathophysiology of 42 bovine CM. These findings of rapid and reliable identification of CM microbiomes and 43 associated resistomes will help improve the optimization of therapeutic schemes involving 44 antibiotics and metals usage in the prevention and control programs of bovine CM. 45 46 47 48 Mastitis is the foremost production and major economic burden confronted by the 52 global dairy industry 1-3 . Bovine clinical mastitis (CM) is of special concern for milk 53 producers in developing countries like Bangladesh, where dairying plays a pivotal role in the 54 national economy. The CM milk from dairy animals is now considered to host a complex 55 microbial community with great diversity 2-4 . The most frequently isolated pathogens are 56Staphylococcus aureus, Escherichia coli, Klebsiella spp., Streptococcus spp., Mycoplasma 57 spp., Enterobacter spp., Bacillus spp., Corynebacterium species 5-8 . Therefore, accurate 58 identification of pathogens causing CM enables appropriate choices for antimicrobial 59 treatment and preventive mastitis management [8][9][10] . Over the past two decades, a wide range of 60 phenotyping and genotyping methods have been implemented to study mastitis-causing 61 bacteria 6-9 . Although culture-based techniques are in the forefront of detecting CM bacteria, 62 these methods are time-consuming and have inherent drawback of not being applicable to 63 non-cultivable bacteria 11 . Until recently, 16S rRNA partial gene sequencing remained as the 64 most commonly used genomic survey tool to study bovine mastitis microbiomes 3,4,12 . 65 However, this technique...