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Sakib, N.

Publications and source records attributed to Sakib, N..

2 recordsLinked to original sources
bioRxiv2025

Dairy manure analysis reveals significant risk of Antibiotic resistance from Extracellular DNA in Manure storage Pit

AbstractDairy manure pit storage systems are significant reservoirs for antimicrobial resistance genes (ARGs). These genes occur in both intracellular DNA (iDNA) and extracellular DNA (exDNA), but their distribution across these categories in fresh (loafing pen surface) and pit-stored dairy manure has not been previously characterized. To address this gap, we quantified the abundance of six ARGs (tetG, tetM, tetX- tetracyline, sul1-sulfonamide, and ermB-macrolide) and three mobile genetic elements (MGEs) (intI1, intI2, and intI3) in iDNA and exDNA extracted from fresh and pit-stored manure collected at a dairy farm in Iowa. While total DNA yields were lower in pit-stored relative to fresh manure samples, exDNA-to-iDNA ratios were significantly elevated across all genes (p<0.001), indicating relative enrichment of exDNA during storage. Notably, tetM exhibited a higher free (unattached) to bound (surface-attached) exDNA ratio in pit samples, which suggested an increased potential for gene transfer in the pit. Correlation network analysis revealed similar numbers of strong ARG-MGE associations in pit and fresh exDNA, but lower interconnectivity in pit exDNA. Merging fresh and pit datasets showed wider ARG-MGE associations: intI1 and intI3 strongly co-occurred with tetracyclines and macrolide resistance in iDNA, while sul1 correlated with MGEs only in the exDNA network. Microbial community profiling showed similar taxa in exDNA across manure types, while iDNA communities diverged significantly. This result could support that exDNA is relatively stable over time and in varying environments, and that iDNA is relatively more reflective of selective pressures. Overall, our results highlight exDNA as a critical but overlooked reservoir of resistance determinants, warranting further investigation and targeted management strategies in dairy systems. ImportanceTo date, extracellular DNA (exDNA) has been shown to contribute to the spread of antibiotic resistance genes (ARGs) in the environment; however, few studies have evaluated its enrichment in dairy pit-stored manure systems. This study demonstrates that dairy manure pits concentrate exDNA during dairy manure storage and serve as a reservoir for ARGs, along with mobile genetic elements that can facilitate subsequent gene transfer. The results of this study are a strong rationale for further investigation and targeted management strategies of exDNA in manure pits.

microbiology↗
bioRxiv2018

A Network based Approach to Identify the Genetic Influence Caused by Associated Factors and Disorders for the Parkinsons Disease Progression

Actual causes of Parkinsons disease (PD) are still unknown. In any case, a better comprehension of genetic and ecological influences to the PD and their interaction will assist physicians and patients to evaluate individual hazard for the PD, and definitely, there will be a possibility to find a way to reduce the progression of the PD. We introduced quantitative frameworks to reveal the complex relationship of various biasing genetic factors for the PD. In this study, we analyzed gene expression microarray data from the PD, ageing (AG), severe alcohol consumption (AC), type II diabetes (T2D), high body fat (HBF), hypercholesterolemia (HC), high dietary fat (HDF), red meat dietary (RMD), sedentary lifestyle (SL), smoking (SM), and control datasets. We have developed genetic associations of various factors with the PD based on the neighborhood-based benchmarking and multilayer network topology.\n\nWe identified 1343 significantly dysregulated genes in the PD patients compared to the healthy control, where we have 779 genes down regulated and 544 genes up regulated. 69 genes were highly expressed in both for the PD and alcohol consumption whereas the number of shared genes for the PD and the type II diabetes is 51. However, the PD shared 45, 43 and 42 significantly expressed genes with the ageing, high dietary fat and high body fat respectively. The PD shared less than 40 significant transcripts with other factors. Ontological and pathway analyses have identified significant gene ontology and molecular pathways that enhance our understanding of the fundamental molecular procedure of the PD progression. Therapeutic targets of the PD could be developed using these identified target genes, ontologies and pathways. Our formulated methodologies demonstrate a network-based approach to understand the disease mechanism and the causative reason of the PD, and the identification for therapeutic targets of the PD.

neuroscience↗