Unveiling the probiotic potential of <i>L. rhamnosus</i> strain 044AE by genomic and phenotypic characterization

Aruna Inamdar; Vikash Kumar; Akanksha Chauhan; Yogini Dixit; Namrata Bhingardeve; Kunali Ambavale; Dina Saroj; Aruna Inamdar; Vikash Kumar; Akanksha Chauhan; Yogini Dixit; Namrata Bhingardeve; Kunali Ambavale; Dina Saroj

doi:10.3934/microbiol.2026007

AIMS Microbiology

2026, Volume 12, Issue 2: 173-191. doi: 10.3934/microbiol.2026007

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Research article

Unveiling the probiotic potential of L. rhamnosus strain 044AE by genomic and phenotypic characterization

Advanced Enzyme Technologies Limited, Sun Magnetica, Louiswadi, Thane-West, Maharashtra 400 604, India

Received: 05 December 2025 Revised: 16 March 2026 Accepted: 25 March 2026 Published: 08 April 2026

Probiotics are living microorganisms that improve overall human health by modulating the gut microbiota and enhancing absorption of nutrients and host immunity. Due to the growing demand for probiotics, efforts are being made to search for and characterize new probiotics. Whole genome sequencing has played a significant role in the identification and characterization of many probiotic candidates. In the present study, hybrid assembly (Illumina and Nanopore-based), genomic analyses, and phenotypic evaluations of Lactobacillus rhamnosus 044AE isolated from a dairy sample were carried out to investigate its probiotic potential. The assembled genome of L. rhamnosus 044AE showed maximum homology with L. rhamnosus BIO5326. Downstream analysis of the genome revealed safety, stability, and gut survival features. In the phenotypic assays, L. rhamnosus 044AE exhibited favorable adhesion, aggregation, gut stability (88.96% viability under fasting conditions; 92%–96% viability under fed conditions), antimicrobial, antioxidant, and enzyme activities. Therefore, L. rhamnosus 044AE appears as a potential probiotic candidate for applications in the food, pharmaceutical, and nutraceutical industries.
- L. rhamnosus 044AE,
- probiotics,
- phenotypic assays,
- safety,
- whole genome sequencing
Citation: Aruna Inamdar, Vikash Kumar, Akanksha Chauhan, Yogini Dixit, Namrata Bhingardeve, Kunali Ambavale, Dina Saroj. Unveiling the probiotic potential of L. rhamnosus strain 044AE by genomic and phenotypic characterization[J]. AIMS Microbiology, 2026, 12(2): 173-191. doi: 10.3934/microbiol.2026007

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Abstract

Probiotics are living microorganisms that improve overall human health by modulating the gut microbiota and enhancing absorption of nutrients and host immunity. Due to the growing demand for probiotics, efforts are being made to search for and characterize new probiotics. Whole genome sequencing has played a significant role in the identification and characterization of many probiotic candidates. In the present study, hybrid assembly (Illumina and Nanopore-based), genomic analyses, and phenotypic evaluations of Lactobacillus rhamnosus 044AE isolated from a dairy sample were carried out to investigate its probiotic potential. The assembled genome of L. rhamnosus 044AE showed maximum homology with L. rhamnosus BIO5326. Downstream analysis of the genome revealed safety, stability, and gut survival features. In the phenotypic assays, L. rhamnosus 044AE exhibited favorable adhesion, aggregation, gut stability (88.96% viability under fasting conditions; 92%–96% viability under fed conditions), antimicrobial, antioxidant, and enzyme activities. Therefore, L. rhamnosus 044AE appears as a potential probiotic candidate for applications in the food, pharmaceutical, and nutraceutical industries.

Acknowledgments

The authors would like to thank Mr. VL Rathi, and Mr. MM Kabra, Advanced Enzyme Technologies Limited for providing the laboratory facilities.

Conflict of interests

Authors declare no competing interests.

Author Contributions

Dr Vikash Kumar—Compilation, Preparation of first draft, Editing; Dr Akanksha Chauhan—Compilation, Preparation of first draft; Dr Yogini Dixit—Investigation; Namrata Bhingardeve—Investigation; Kunali Ambavale—Investigation; Dr Aruna Inamdar- Corresponding—Supervision; Compilation, Preparation of first draft, Editing; Dr Dina Saroj—Conceptualization, Reviewing.

Funding

This study was funded by Advanced Enzyme Technologies, Limited, Thane, India.

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