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The Influence of Protein Secretomes of Enterococcus durans on ex vivo Human Gut Microbiome

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Abstract

The gut microbiome plays a critical role to all animals and humans health. Methods based on ex vivo cultures are time and cost-effective solutions for rapid evaluation of probiotic effects on microbiomes. In this study, we assessed whether the protein secretome from the potential probiotic Enterococcus durans LAB18S grown on fructoligosaccharides (FOS) and galactoligosaccharides (GOS) had specific effects on ex vivo cultured intestinal microbiome obtained from a healthy individual. Metaproteomics was used to evaluate changes in microbial communities of the human intestinal microbiome. Hierarchical clustering analysis revealed 654 differentially abundant proteins from the metaproteome samples, showing that gut microbial protein expression varied on the presence of different E. durans secretomes. Increased amount of Bacteroidetes phylum was observed in treatments with secretomes from E. durans cultures on FOS, GOS and albumin, resulting in a decrease of the Firmicutes to Bacteroidetes (F/B) ratio. The most functionally abundant bacterial taxa were Roseburia, Bacteroides, Alistipes and Faecalibacterium. The results suggest that the secretome of E. durans may have favorable effects on the intestinal microbial composition, stimulating growth and different protein expression of beneficial bacteria. These findings suggest that proteins secreted by E. durans growing on FOS and GOS have different effects on the modulation of gut microbiota functional activities during cultivation.

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Availability of Data and Material

The proteomics mass spectrometry data are available via ProteomicXchange under the identifier PXD040751 (Username: reviewer_pxd040751@ebi.ac.uk; Password: glc8SRky).

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Funding

This work received financial support from Conselho Nacional de Desenvolvimento Científico e Tecnológico of Brazil (CNPq, grant 308880/2021–8) and the Emerging Leaders in the Americas Program (ELAP, Canada). This work was also supported by the Government of Canada through the Natural Sciences and Engineering Research Council of Canada (NSERC, grant no. 210034). CBC was a former recipient of a PhD fellowship from CAPES.

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Authors and Affiliations

  1. Laboratório de Bioquímica e Microbiologia Aplicada, Instituto de Ciência e Tecnologia de Alimentos, Universidade Federal do Rio Grande do Sul, 91510-970, Porto Alegre, Brazil

    Carolina Baldisserotto Comerlato & Adriano Brandelli

  2. School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada

    Xu Zhang, Krystal Walker, Janice Mayne & Daniel Figeys

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  1. Carolina Baldisserotto Comerlato
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  2. Xu Zhang
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  4. Janice Mayne
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  5. Daniel Figeys
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  6. Adriano Brandelli
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Contributions

CBC, XZ, JM, AB and DF contributed to the study conception and design. Material preparation, data collection, CBC and KW; data analysis and statistical analysis were performed by CBC, XZ, JM. The manuscript was written by CBC, and critically revised by AB. All the authors read and approved the final manuscript.

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Correspondence to Daniel Figeys or Adriano Brandelli.

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The protocol for stool sample collection was approved by the Ottawa Health Science Network Research Ethics Board at the Ottawa Hospital (Ottawa, Canada).

Competing Interests

DF is a co-founder of MedBiome Inc., a personalized microbiome therapeutic company. The other Authors declare no conflicts of interest.

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Comerlato, C.B., Zhang, X., Walker, K. et al. The Influence of Protein Secretomes of Enterococcus durans on ex vivo Human Gut Microbiome. Probiotics & Antimicro. Prot. (2023). https://doi.org/10.1007/s12602-023-10136-9

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