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Genome of Bifidobacterium longum NCIM 5672 provides insights into its acid-tolerance mechanism and probiotic properties

Abstract

Bifidobacterium longum NCIM 5672 is a probiotic strain isolated from the Indian infant feces. The probiotic efficacy of Bifidobacteria is majorly affected by its acid tolerance. This study determined the probiotic properties and acid-tolerance mechanism of B. longum NCIM 5672 using whole-genome sequencing. The genome annotation is carried out using the RAST web server and NCBI PGAAP. The draft genome sequence of this strain, assembled in 63 contigs, consists of 22,46,978 base pairs, 1900 coding sequences and a GC content of 59.6%. The genome annotation revealed that seven candidate genes might be involved in regulating the acid tolerance of B. longum NCIM 5672. Furthermore, the presence of genes associated with immunomodulation and cell adhesion support the probiotic background of the strain. The analysis of candidate acid- tolerance-associated genes revealed three genes, argC, argH, and dapA, may play an essential role in high acid tolerance in B. longum NCIM 5672. The results of RT-qPCR supported this conclusion. Altogether, the results presented here supply an effective way to select acid-resistant strains for the food industry and provide new strategies to enhance this species' industrial applications and health-promoting properties.

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Data availability and material

B. longum NCIM 5672 is patently stored in the National Collection of Industrial Microorganism, Pune, India. The datasets supporting the results of this article are included in the article. The whole-genome sequence of the strain is submitted to Genbank with (primary) accession ‘VICA00000000’. Requests to access strains shown in this manuscript should be directed to Dr. Prakash Halami (prakashalami@cftri.res.in).

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Acknowledgements

The author is thankful to The Director, CSIR- CFTRI for providing facilities and infrastructure at the institute. AS acknowledges CSIR for the award of Nehru Post-Doctoral fellowship. PBP acknowledge CSIR-IMTECH project on High-throughput and integrative genomics approaches to understand adaptation of probiotic and pathogenic bacteria (OLP-148).

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Contributions

AS and PH conceived and designed the experiments. AS, KB and JS performed the experiments. PP and PH provided facilities, supervised the work flow and validated the results. AS wrote the manuscript. All authors read and approved the manuscript.

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Correspondence to Prabhu Patil or Prakash M. Halami.

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Communicated by Erko Stackebrandt.

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Sundararaman, A., Bansal, K., Sidhic, J. et al. Genome of Bifidobacterium longum NCIM 5672 provides insights into its acid-tolerance mechanism and probiotic properties. Arch Microbiol 203, 6109–6118 (2021). https://doi.org/10.1007/s00203-021-02573-3

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Keywords

  • Bifidobacterium longum
  • Whole-genome sequencing
  • Health benefits
  • Probiotic marker genes