Biology subjects

Iram, D.

Publications and source records attributed to Iram, D..

4 recordsLinked to original sources

bioRxiv2025

Genome based analysis of Antibacterial Biosynthetic Clusters in Lactiplantibacillus plantarum C6 and Exploration of their Natural Small Molecules as anti-biofilm in Methicillin-Resistant Staphylococcus aureus

This study presents the complete genome characterization of Lactiplantibacillus plantarum C6, a strain isolated from Indian dairy cheese, using Illumina NovaSeq sequencing. The assembled genome (3.22 Mb, 44.5% GC) comprised 3,076 coding sequences, 59 tRNAs, 10 rRNAs, and 2 CRISPR arrays. Phylogenomic and ANI analyses confirmed its identity within the L. plantarum clade (>99% similarity with NMGL2 and DMDL 9010). Functional annotation revealed genes enriched in carbohydrate metabolism (10.7%), stress response, and host-adaptation pathways, supporting its probiotic potential. Bacteriocin biosynthetic gene clusters were identified, including those encoding PlnE, PlnF, PlnJ, PlnK, and PlnN, indicating the strains ability to produce class II plantaricins. A RiPP cluster encoding a cyclic uberolysin-like peptide was also detected, with structural similarity to known lanthipeptides such as Streptococcin A, Nisin Q, and Lacticin 3147 (Tanimoto scores 0.93-1.0), suggesting antimicrobial relevance. CAZy analysis revealed 102 carbohydrate-active enzymes (GHs, GTs), highlighting metabolic flexibility. To evaluate the antibiofilm potential of L. plantarum-derived metabolites, 15 small molecules from cell-free supernatants (CFS) were selected through literature mining and subjected to molecular docking against the MRSA biofilm-associated enzyme poly-{beta}-1,6-N-acetyl-D-glucosamine synthase (encoded by icaA). 2,4-Di-tert-butylphenol (-7.2 kcal/mol) and Indole-3-lactic acid (-7.1 kcal/mol) showed the strongest binding, followed by Cyclo (L-propyl-L-valine) (-6.8 kcal/mol) and DL-4-Hydroxyphenyllactic acid (-6.4 kcal/mol), indicating promising inhibition of MRSA biofilm synthesis. Organic acids like acetic and lactic acid showed weaker interactions but may contribute synergistically through acidification. Overall, L. plantarum C6 combines robust probiotic features, genomic safety, and antimicrobial potential, supported by bacteriocin gene clusters and effective antibiofilm metabolites, highlighting its application in functional foods and novel antimicrobial development.

genomics↗

bioRxiv2025

Designing Functional Dairy Food Products: Peptide-Fortification Approaches to Improve Safety, Quality, and Consumer Acceptance

This study focused on the development of functional dairy products fortified with bioactive peptides derived from Lactobacillus rhamnosus C25-fermented sheep milk and their evaluation during storage. Microencapsulated peptides were incorporated into flavoured milk and srikhand, and their antimicrobial, antioxidant, and sensory properties were monitored over refrigerated storage. Flavoured milk supplemented with free peptides exhibited strong antimicrobial activity, while encapsulated peptides provided a controlled and sustained release, maintaining functionality over six days. In srikhand, both plain and mango-flavoured formulations demonstrated enhanced biofunctional properties, with encapsulated peptides showing gradual peptide release, higher antioxidant activity, and better preservation of sensory quality over 15 days. Sheep milk used for fermentation showed good microbial quality, supporting safe peptide production. Fermentation yielded peptide fractions (<3, <5, and <10 kDa), which were analyzed using RP-HPLC and LC-MS/MS, identifying over 3,100 peptides. In silico screening predicted 34 peptides with antimicrobial potential, including cationic and amphipathic -helical peptides primarily derived from {beta}-casein and {kappa}-casein. Functional assays demonstrated potent antimicrobial activity against Gram-positive and Gram-negative pathogens, particularly in the 5-10 kDa fractions. Antioxidant activity was highest in the 5 kDa retentate, indicating that medium-sized peptides contributed most to radical scavenging. Microencapsulation using sodium alginate improved peptide stability and controlled release, mitigating bitterness and preserving product acceptability. Overall, the study highlights the potential of L. rhamnosus C25-fermented sheep milk peptides as natural bioactive ingredients for functional dairy products with enhanced shelf life, antimicrobial efficacy, and antioxidant capacity. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/673363v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1c368bdorg.highwire.dtl.DTLVardef@118db8org.highwire.dtl.DTLVardef@6f4addorg.highwire.dtl.DTLVardef@9c2ddc_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

"Decoding Mobile Genetic Elements, Virulence Factors, and Antibiotic Resistance Genes Driving Biofilm Formation in MRSA via Network Analysis"

This study aimed to analyze the genome of the Methicillin-resistant Staphylococcus aureus (MRSA) strain d1418m22 through whole-genome sequencing (WGS) and comprehensive bioinformatics analysis with six references strains. De novo assembly resulted in 61 scaffolds with a total genome size of 2.78 Mb. Functional annotation revealed 2,625 predicted genes, including those involved in metabolism, cellular processes, and virulence. Comparative genomic analysis identified 20 antibiotic resistance genes, including those conferring resistance to beta-lactams, fluoroquinolones, and aminoglycosides. In addition, 21 virulence factors (VFs) were identified, including Panton-Valentine leukocidin (PVL) and various enterotoxins. The presence of staphylococcal cassette chromosome mec (SCCmec) type IVa and mobile genetic elements (MGEs), such as prophages and transposons, underscored the role of horizontal gene transfer (HGT) in the evolution and transmission of resistance and virulence factors. Interaction network analysis identified key hub genes involved in various cellular processes, including biofilm formation. This comprehensive genomic analysis provides valuable insights into the genetic makeup of MRSA strain d1418m22, contributing to a better understanding of its pathogenicity and potential public health implications. Six reference MRSA strains were isolated from (MRSA-AMRF4 and MRSA-AMRF5) eye infections, (MRSA and MRSA-15) wound pus, (VMRSA-WC071, and VMRSA-WC081) urine samples. The analysis identified resistance genes, virulence factors, GC content, ANI values, and SCCmec elements, which were found to be similar to those present in the resistant MRSA d1418m22 strain genome.

genomics↗

bioRxiv2024

Proteomic Characterization and Molecular Mechanism of Goat Whey Protein-Derived Bioactive Peptides as Pancreatic Lipase and alpha-Amylase Inhibitors

Goat whey protein (GWP) is recognized as a valuable source of bioactive peptides with significant health-promoting properties. In this study, GWP was enzymatically hydrolyzed using a combination of gastrointestinal enzymes-- pepsin, trypsin, and chymotrypsin--to generate peptides. These peptides were identified through high-resolution liquid chromatography-mass spectrometry (HR-LC/MS), resulting in library of 2,883 peptides with lengths ranging from 6 to 44 amino acids. Among them, 40 peptides were predicted to exhibit high bioactivity scores (0.90-1) based on PeptideRanker analysis, with 28 of these being classified as nontoxic. Molecular docking simulations were employed to investigate the interactions of these peptides with pancreatic lipase and -amylase to screening of inhibitors, these two enzymes critical in lipid and carbohydrate metabolism. Several peptides demonstrated strong binding affinities, suggesting their potential as enzyme inhibitors. Notably, peptides WPGIMR and WQDGSWQF showed the highest binding affinity for pancreatic lipase, while AAPFIWL and WQDGSWQF exhibited significant interactions with -amylase. These results shed light on the molecular mechanisms underlying the inhibitory activities of whey protein-derived peptides. They highlight their potential applications as functional food ingredients or natural therapeutic agents for managing metabolic disorders such as obesity and diabetes, advancing the understanding of whey protein hydrolysates in modulating key metabolic enzymes.

bioinformatics↗