In vitro and in silico analysis of bifidobacterium spp.

Figo, Figo (2024) In vitro and in silico analysis of bifidobacterium spp. Bachelor thesis, Universitas Pelita Harapan.

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Abstract

Prebiotics are human non-digestible nutrients that selectively promote the growth of probiotics in a strain-specific manner, especially in the Bifidobacterium sp.. The combination of probiotics and prebiotics (termed ‘synbiotics’) poses beneficial health impacts in human. Given its impact on human health, assessing the capabilities of bifidobacteria species and strains in utilizing prebiotics become crucial. This study aimed to adopt two different approaches, both in vitro and in silico analyses, to reveal prebiotic-utilization capabilities (L-arabinose, maltodextrin and XOS) in B. breve BS2-PS1, BS2-PS2, BS2-PB3, and B. animalis BR2-5. In vitro analyses include fermentation activity assay, which evaluated the capability of four Bifidobacteria strains in fermenting L-arabinose, maltodextrin, and XOS, and colony enumeration, which quantitatively measured the growth of these strains in prebiotics-supplemented media. In silico analyses predicted the presence of prebiotics-utilizing genes in the whole genome sequences of the isolates. In vitro findings revealed that among three prebiotics, all strains of B. breve can only utilize maltodextrin, indicated by significantly lower pH (5.34 ± 0.06, 5.95 ± 0.19, and 4.89 ± 0.34 in B. breve BS2-PS1, BS2-PS2, and BS2-PB3, respectively) and higher growth (8.943, 10.857, and 6.637 × 108 CFU/mL in B. breve BS2-PS1, BS2-PS2, and BS2-PB3) in maltodextrin-supplemented media. In contrast, B. animalis BR2-5 was found to be able to utilize L-arabinose, maltodextrin and XOS by significantly lowered the pH (4.78 ± 0.15, 4.83 ± 0.03, and 4.63 ± 0.08, respectively) and increased the growth (14.537, 15.840, and 17.727 × 108 CFU/mL in maltodextrin-, L-arabinose-, and XOS-supplemented media, respectively). In silico results revealed that prebiotics-utilizing gene profile is identical across all strains of B. breve. The absence of xylose isomerase, L-ribulokinase, and L-arabinose isomerase might explain the inability of B. breve in utilizing L-arabinose and XOS. On the other hand, the prebiotics-utilizing genes predicted in B. animalis BR2-5 are complete and might explain the ability of B. animalis BR2-5 in utilizing all prebiotics used in this study. The findings from both in vitro and in silico analyses of three B. breve strains and B. animalis BR2-5 were consistent.

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