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Probing the microbial diversity and probiotic candidates from Pakistani foods: isolation, characterization, and functional profiling

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Abstract

Probiotics represent beneficial living microorganisms that confer physiological, nutritional, and functional advantages to human health, holding significant potential for development of functional foods. This research aimed to isolate, identify, and characterize potential probiotic bacterial strains sourced from fermented and non-fermented foods from Pakistan. A total of 341 bacterial strains were isolated from diverse food samples (81) collected from various regions of Pakistan. Strains were identified using 16S rRNA gene sequencing and phylogenetic analysis. The identified strains belonged to genera Bacillus, Staphylococcus, Microbacterium, Shigella, Micrococcus, Enterococcus, Sporosarcina, Paenibacillus, Limosilactobacillus, Kosakonia, Dietzia, Leclercia, Lacticaseibacillus, Levilactobacillus, Kluyvera, Providencia, Enterobacter, Neisseria, Streptococcus, Acinetobacter, Corynebacterium, Pantoea, Mammaliicoccus, Pseudomonas, Burkholderia, and Alkalihalobacillus. Selected strains were chosen for probiotic assessment, employing existing literature as a guideline. Among these selections, six strains exhibited hemolytic activity, and seven strains displayed resistance to multiple antibiotics, prompting their exclusion from subsequent evaluations. The remaining strains demonstrated auto-aggregation capacities spanning 3.39–79.7%, and displayed coaggregation capabilities with reported food-borne pathogens. Furthermore, nine strains exhibited antimicrobial properties against food-borne pathogens. The assessment encompassed diverse characteristics such as cell surface hydrophobicity, survival rates under varying conditions, cholesterol reduction ability, casein digestion capability, and antioxidant activity. Phylogenomic analysis, digital-DNA DNA hybridization (digi-DDH), and average nucleotide identity (ANI) calculations unveiled novel species potentially belonging to the genera Sporosarcina and Dietzia. Based on these findings, we advocate for the consideration of Staphylococcus cohnii subsp. cohnii NCCP-2414, Lacticaseibacillus rhamnosus NCCP-2569 and Levilactobacillus brevis NCCP-2574 as prime probiotic candidates with the potential for integration into formulation of functional foods.

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Data availability

All the sequence data (16S rRNA gene sequences and Whole Genome sequences) are available online in the NCBI Genebank. The accession numbers are mentioned in Table S3 and Tables 4–6, respectively. The statement may be added at suitable place as per journal policy/guidelines.

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Acknowledgements

This study was financially supported by the Agriculture Linkages Program (ALP) funded Project “Isolation, Identification and Characterization of Probiotic Bacteria from Indigenous Plant based Foods and Food Wastes, CS-016”.

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Authors and Affiliations

  1. Food Science Research Institute (FSRI), National Agricultural Research Centre, Islamabad, 45500, Pakistan

    Amer Mumtaz, Rehana Batool & Nazir Ahmad

  2. National Microbial Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agricultural Research Centre (NARC), Islamabad, 45500, Pakistan

    Amer Mumtaz, Amina F. Mughal, Zainab Batool & Iftikhar Ahmed

  3. National Agricultural Research Centre (NARC), Islamabad, 45500, Pakistan

    Ahmad Ali

  4. Department of Zoology, University of Science and Technology, Bannu, Pakistan

    Saira Abbas

  5. Department of Food Science and Technology, School of Food and Agricultural Sciences, University of Management and Technology, Lahore, 54000, Pakistan

    Nauman Khalid

  6. College of Health Sciences, Abu Dhabi University, Abu Dhabi, 59911, United Arab Emirates

    Nauman Khalid

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  1. Amer Mumtaz
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Contributions

AM, IA and NK contributed to conception and design of the study. AM, RB and AFM collected samples and performed isolation of strains from the samples. AM, AA, AFM, RB, NA, ZB and IA performed the experiments. AM, AA, NZ, SA and IA organized the data and contributed to the statistical data analysis and finalizing the figures. AM, AA, NA and IA wrote the first draft of the manuscript. AM, and IA managed funds for research and supervised the experiments. All authors contributed to manuscript revision, read, and approved the submitted version.

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Correspondence to Iftikhar Ahmed.

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Mumtaz, A., Ali, A., Batool, R. et al. Probing the microbial diversity and probiotic candidates from Pakistani foods: isolation, characterization, and functional profiling. 3 Biotech 14, 60 (2024). https://doi.org/10.1007/s13205-023-03903-6

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