Biology subjects

Istiaq, A.

Publications and source records attributed to Istiaq, A..

3 recordsLinked to original sources

bioRxiv2020

Microbiome Dynamics of Bovine Mastitis Progression and Genomic Determinants

The milk of lactating cows presents a complex ecosystem of interconnected microbial communities which can impose a significant influence on the pathophysiology of mastitis. Previously, we reported the alteration of microbiome (bacteria, archaea, virus) composition between clinical mastitis (CM) and healthy (H) milk. We hypothesized possible dynamic shifts of microbiome compositions with the progress of different pathological states of mastitis (CM, Recurrent CM; RCM, Subclinical Mastitis; SCM) determined by its favoring genomic potentials. To evaluate this hypothesis, we employed whole metagenome sequencing (WMS) in 20 milk samples (CM = 5, RCM = 6, SCM = 4, H = 5) to unravel the microbiome dynamics, interrelation, and relevant metabolic functions. PathoScope (PS) and MG-RAST (MR) analyses mapped the WMS data to 442 bacterial, 58 archaeal and 48 viral genomes with distinct variation in microbiome composition and abundances across these metagenomes (CM>H>RCM>SCM). PS analysis identified 385, 65, 80 and 144 bacterial strains in CM, RCM, SCM, and H milk, respectively, with an inclusion of 67.19% previously unreported opportunistic strains in mastitis metagenomes. Moreover, MR detected 56, 13, 9 and 46 archaeal, and 40, 24, 11 and 37 viral genera in CM, RCM, SCM and H-milk metagenomes, respectively. The CM-microbiomes had closest association with RCM-microbiomes followed by SCM, and H-microbiomes. Furthermore, we identified 333, 304, 183 and 50 virulence factors-associated genes (VFGs), and 48, 31, 11 and 6 antibiotic resistance genes (AGRs) in CM, RCM, SCM, and H-microbiomes, respectively, showing a significant correlation between the relative abundances of VFGs (p = 0.001), ARGs (p = 0.0001), and associated bacterial taxa. We also detected correlated variations in the presence and abundance of several metabolic functional genes related to bacterial colonization, proliferation, chemotaxis, motility and invasion, oxidative stress, virulence and pathogenicity, phage integration and excision, biofilm-formation, and quorum-sensing to be associated with different episodes of mastitis. Therefore, profiling the dynamics of microbiome in different states of mastitis, concurrent VFGs, ARGs, and genomic functional correlations will contribute to developing microbiome-based diagnostics and therapeutics for bovine mastitis, and carries significant implications on curtailing the economic fallout from this disease.

microbiology↗

bioRxiv2019

Resistome diversity in bovine clinical mastitis microbiome, a signature concurrence

The bovine clinical mastitis (CM) milk is a large reservoir for diverse groups of resistomes, which play important roles in the pathogenesis of mastitis, but little is known about the concurrence of CM microbiome signature and its associated resistomes. Here we deciphered the total resistance (antibiotics and metals resistance, biofilm formation, quorum sensing) present in CM microbiome using whole metagenome sequencing (WMS) and in vitro cultural approaches. Significant correlation (p=0.001) was found between the resistome diversity and microbiome signature. We identified the strain-level microbiome diversity in four cattle breeds, with microbiome composition represented by the phyla Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Fusobacteria (contributing to >95.0% of total strains). However, the resistome diversity did not vary significantly (p=0.692) across the microbiomes of cattle breeds. The in vitro investigation showed that biofilm producing CM pathogens were resistant to most of the conventional antibiotics used for CM treatment, whereas these pathogens remained sensitive to five heavy metals (Cr, Co, Ni, Cu, Zn) at varying concentrations. We also found association of some genomic functional potentials such as bacterial flagellar movement and chemotaxis, regulation and cell signaling, phages-prophages, transposable elements, plasmids and oxidative stress in the pathophysiology of bovine CM. These findings of rapid and reliable identification of CM microbiomes and associated resistomes will help improve the optimization of therapeutic schemes involving antibiotics and metals usage in the prevention and control programs of bovine CM.

microbiology↗

bioRxiv2019

Association of milk microbiome in bovine clinical mastitis and their functional implications in cows in Bangladesh

Milk microbiomes impose a significant influence on the pathophysiology of bovine mastitis. To assess the association, we compared the microbiome of clinical mastitis (CM) and healthy (H) milk samples through whole metagenomic deep sequencing. A total of 483.38 million reads generated from both metagenomes were analyzed through PathoScope and MG-RAST, and mapped to 380 bacterial, 56 archaeal, and 39 viral genomes. We observed distinct shifts and differences in abundance between the microbiome of CM and H milk in phyla Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria with an inclusion of 68.04% unreported and/or opportunistic species in CM milk. Additionally, 14 archaeal and 14 viral genera were found to be solely associated with CM. The functional metagenomics identified several pathways related to bacterial proliferation and colonization such as metabolism, chemotaxis and invasion, immune-diseases, oxidative stress, regulation and cell signaling, phage and prophases, antibiotic and heavy metal resistance to be associated with CM. Therefore, the present study provides conclusive data on milk microbiome diversity associated with bovine CM and its role in udder health.

molecular biology↗