DC13: Gaurav Adhikari

About Gaurav and His Academic Background

Gaurav Adhikari is a Nepalese researcher with an academic background in zoology, biotechnology, molecular biology, and bacteriophage research.

He obtained a bachelor’s degree in Zoology before completing a master’s degree in Biotechnology at Tribhuvan University in Nepal.

During his master’s studies, he worked at the molecular level on bacteriophages and their endolysins. His research focused on the molecular analysis of bacteriophage-derived endolysins against multidrug-resistant Escherichia coli associated with urinary tract infections.

This previous experience introduced him to the potential of bacteriophages and their enzymes as targeted antimicrobial tools and provided a strong foundation for his current doctoral research.

About His Research

Gaurav’s PhD research is part of the SpoilControl project, an international doctoral network funded by the Horizon Europe Marie Skłodowska-Curie Actions.

As Doctoral Candidate 13, he is based primarily at University College Cork in Ireland and will also conduct part of his research at the University of Bordeaux in France.

His project focuses on controlling lactic acid bacteria responsible for microbial spoilage in wine and cider. Although lactic acid bacteria can play beneficial roles during fermentation, some species or strains may produce undesirable compounds and negatively affect the aroma, taste, stability, and overall quality of beverages.

Gaurav is investigating the use of bacteriophages and their derived enzymes as targeted biological solutions against these spoilage microorganisms. Bacteriophages are viruses that specifically infect bacteria. Their high specificity makes them promising alternatives to conventional chemical treatments, as they can target unwanted bacteria while limiting their effects on other microorganisms involved in fermentation.

His first objective is to isolate lactic acid bacteria from wine and cider samples and establish a biobank representing the diversity of spoilage bacteria found in these beverages. The bacterial isolates are identified using 16S ribosomal RNA gene sequencing and Sanger sequencing. Whole-genome sequencing will then provide a more detailed confirmation and characterisation of selected strains.

The next stage involves isolating bacteriophages capable of infecting the identified spoilage bacteria. These phages will be characterised to determine their host range, activity, and potential use as biological control agents.

Gaurav is also studying endolysins, enzymes naturally produced by bacteriophages to break down bacterial cell walls. These enzymes can potentially be isolated and applied directly against spoilage bacteria without using the complete bacteriophage.

His research specifically focuses on:

• Isolating lactic acid bacteria responsible for spoilage in wine and cider.
• Establishing a biobank of representative spoilage strains.
• Identifying bacterial isolates using 16S rRNA and Sanger sequencing.
• Confirming selected strains through whole-genome sequencing.
• Isolating bacteriophages that infect lactic acid bacteria.
• Characterising the activity and host range of the isolated bacteriophages.
• Identifying and producing bacteriophage-derived endolysins.
• Purifying endolysin proteins and evaluating their antimicrobial activity.
• Determining the concentrations required to lyse spoilage bacteria.
• Investigating the microbial and viral communities of wine and cider using metagenomic and viromic approaches.
• Assessing the potential of phages and endolysins as natural preservation treatments.

In his current laboratory work, Gaurav is optimising the production and purification of endolysin proteins. He tests different induction conditions and concentrations to improve protein production.

The proteins are purified using column chromatography, while sodium dodecyl sulfate–polyacrylamide gel electrophoresis, commonly known as SDS-PAGE, is used to verify their size and assess the quality of the purification.

The purified endolysins are then tested against their corresponding bacterial strains. These experiments will help determine whether the enzymes can effectively lyse lactic acid bacteria and identify the concentration required to achieve an antimicrobial effect.

As part of the project, Gaurav will complete a six-month secondment at the University of Bordeaux. During this period, he will isolate lactic acid bacteria and bacteriophages from French wine and cider samples. A short stay at the French Institute of Vine and Wine is also planned to support sample collection.

Ultimately, his research aims to identify bacteriophages and endolysins with effective protective properties against lactic acid bacteria responsible for spoilage. These biological agents could contribute to the development of more targeted and sustainable preservation strategies for wine, cider, and other fermented beverages.