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Biodiversity and Phylogenetic Relationships of Novel Bacteriocinogenic Strains Isolated from Animal’s Droppings at the Zoological Garden of Lille, France

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Abstract

This study aimed at exploring droppings of animals living in captivity in the zoological garden (Zoo) of Lille (France), as novel sources of bacteriocinogenic strains. A collection of 295 bacterial isolates was constituted from droppings of capybara, alpaca, muntjac, zebra, tapir, rhinoceros, binturong, armadillo, saki monkey and cockatoo. Of 295 isolates, 51 exhibited antagonism against a panel of pathogenic target bacteria like Escherichia coli MC4100, Clostridium perfringens DSM 756 and Salmonella enterica subsp. enterica Newport ATCC6962. Remarkably, within this collection, only 2 Gram-negative bacilli exhibited activity against E. coli MC4100 strain used as target organism. Then, the 16S rDNA sequencing revealed these thereafter cited species, Pediococcus pentosaceus, Weissella cibaria, E. coli, Lactobacillus reuteri, Enterococcus hirae and Enterococcus faecalis. Characterization of this antagonism has revealed 11 strains able producing extracellular protease-sensitive inhibitory compounds. These strains included E. coli ICVB442 and ICVB443, Ent. faecalis ICVB472, ICVB474, ICVB477 ICVB479, ICVB481, ICVB497 and ICVB501 and Ped. pentosaceus ICVB491 and ICVB492. The genomes of the 5 most promising bacteriocinogenic strains were sequenced and analysed with Bagel4 software. Afterwards, this bioinformatics analysis permitted to locate genes encoding bacteriocins like colicin Y (E. coli), enterocin 1071A, enterocin 107 B (Ent. faecalis) and penocin A (Ped. pentosaceus), associating the above-mentioned antibacterial activity of proteinaceous nature to possible production of bacteriocins. All these results enabled us to select different bacteriocinogenic strains for a further characterization in terms of beneficial traits.

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Acknowledgements

Mégane Eveno was a recipient of PhD from Lille University (France) and Laval University (Québec, Canada) through METABIOLAC Industrial Research Chair and CRSNG Industrial Research Chair awarded for Prof. Fliss and Prof. L. Bazinet. Research at Lille University was supported by CPER/FEDER Alibiotech programme (2016-2021).

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  1. UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV – Institut Charles Viollette, F-59000, Lille, France

    Mégane Eveno, Amine Salouhi, Yanath Belguesmia & Frédérique Gancel

  2. Pavillon Paul-Comtois, Université Laval, 2425 Rue de l’Agriculture, Local 1413, Québec, Canada

    Mégane Eveno, Laurent Bazinet, Ismail Fliss & Djamel Drider

  3. Université de Lille, Cité Scientifique/Avenue Paul Langevin, Polytech-Lille, Bureau C315, 59655, Villeneuve d’Ascq, France

    Djamel Drider

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Eveno, M., Salouhi, A., Belguesmia, Y. et al. Biodiversity and Phylogenetic Relationships of Novel Bacteriocinogenic Strains Isolated from Animal’s Droppings at the Zoological Garden of Lille, France. Probiotics & Antimicro. Prot. 13, 218–228 (2021). https://doi.org/10.1007/s12602-020-09657-4

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