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. 2024 Sep 20;25(1):884.
doi: 10.1186/s12864-024-10695-3.

Unveiling the Brazilian kefir microbiome: discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties

Matheus H Silva  1 , Letícia L Batista  2 , Serena M Malta  3 , Ana C C Santos  3 , Ana P Mendes-Silva  4 , Ana M Bonetti  3 , Carlos Ueira-Vieira  5 , Anderson R Dos Santos  6
Affiliations

Unveiling the Brazilian kefir microbiome: discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties

Matheus H Silva et al. BMC Genomics. .

Abstract

Background: Kefir is a complex microbial community that plays a critical role in the fermentation and production of bioactive peptides, and has health-improving properties. The composition of kefir can vary by geographic localization and weather, and this paper focuses on a Brazilian sample and continues previous work that has successful anti-Alzheimer properties. In this study, we employed shotgun metagenomics and peptidomics approaches to characterize Brazilian kefir further.

Results: We successfully assembled the novel genome of Lactobacillus kefiranofaciens (LkefirU) and conducted a comprehensive pangenome analysis to compare it with other strains. Furthermore, we performed a peptidome analysis, revealing the presence of bioactive peptides encrypted by L. kefiranofaciens in the Brazilian kefir sample, and utilized in silico prospecting and molecular docking techniques to identify potential anti-Alzheimer peptides, targeting β-amyloid (fibril and plaque), BACE, and acetylcholinesterase. Through this analysis, we identified two peptides that show promise as compounds with anti-Alzheimer properties.

Conclusions: These findings not only provide insights into the genome of L. kefiranofaciens but also serve as a promising prototype for the development of novel anti-Alzheimer compounds derived from Brazilian kefir.

Keywords: Lactobacillus kefiranofaciens; Alzheimer’s disease; Kefir; Metagenome; Next Generation DNA Sequencing; Peptidome.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The initial region of the LkefirU genome displaying regions with absent coding sequences (CDS) in the reference genome of Lactobacillus kefiranofaciens ASM1465658v1 (CP061341) is highlighted in red. Notice the distinctive change in GC content pattern on the flanks of the region lacking CDSs in the reference genome, indicating a potential gene transfer phenomenon in LkefirU
Fig. 2
Fig. 2
The LKefirU interaction network depicting. the colors white, green, red, and blue represents cytoplasmic, membrane, surface exposed, and secreted proteins, respectively. These figure show that LkefirU have a solide network and preserve some philogenetics characteristics
Fig. 3
Fig. 3
Molecular docking of Aβ monomer and peptides KSPCVFILDQKKRL and VPGYPFLPI. A Molecular docking analysis of the KSPCVFILDQKKRL peptide (indicated in red) and their interaction with Aβ monomer (indicated in blue). Zoomed-in image of the panel of amino acids residues (aa) interactions in the left. B Molecular docking analysis of the VPGYPFLPI peptide (indicated in red) and their interaction with Aβ monomer (indicated in blue) and zoomed-in image of a panel of aa interactions in the left. The yellow color is interactions between the aa of both peptides
Fig. 4
Fig. 4
Molecular docking of Aβ plate and peptides KSPCVFILDQKKRL and VPGYPFLPI. The plate has twelve chains of β-amyloid peptide named by letters A to L. (A) Molecular docking analysis of the KSPCVFILDQKKRL peptide (indicated in red) and their interaction with Aβ plate (indicated in blue) and zoomed-in image of the panel of aa interactions on left (B) Molecular docking analysis of the VPGYPFLPI peptide (indicated in red) and their interaction with Aβ plate (indicated in blue), and zoomed-in image of the panel of aa interactions on left. The yellow color is interactions between the aa of both peptides
Fig. 5
Fig. 5
Molecular docking of BACE1 and peptides KSPCVFILDQKKRL and VPGYPFLPI. The color yellow represents the active site and green represents the flap of BACE1 (A)- Molecular docking analysis of the KSPCVFILDQKKRL peptide (indicated in red) and their interaction with BACE enzyme and zoomed-in image of the panel of aa interactions on left. (B) Molecular docking analysis of the VPGYPFLPI peptide (indicated in red) with the BACE enzyme and zoomed-in image of the panel of aa interactions on left
Fig. 6
Fig. 6
Molecular docking of AChE and peptides KSPCVFILDQKKRL and VPGYPFLPI. The yellow represents catalytical active site (CAS) and green represents the peripheral anionic site (PAS) of AchE (A) Molecular docking analysis of the KSPCVFILDQKKRL peptide (indicated in red) and their interaction with acetylcholinesterase enzyme and zoomed in the image of the panel of aa interactions on left. B Molecular docking analysis of the VPGYPFLPI peptide (indicated in red) with acetylcholinesterase enzyme and zoomed-in image of the panel of aa interactions. The yellow color is interactions between the aa of both peptides on left
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