Microcin diversity and role in competitive interactions in poultry microbiota
Ramzi Guerbaa1,2, Stevensia Beaulière3,4, Angélique Salandre2,3, Manon Vandervennet3, Yossi Ekouya-Gandoua3, Baptiste Gregorutti4, Houssem Ben Yahia1, Rabeb Issaoui1, Evelyne Duvernois-Berthet3, Delphine Gey3, Sylvie Rebuffat3, Ismail Fliss2, Karim Ben Slama1, Séverine Zirah3
1 Laboratoire Bioressources, Environnement et Biotechnologie, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis, Tunisia.
² Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada.
3 Unité Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche scientifique, Paris, France.
4 Sorbonne Center for Artificial Intelligence (SCAI), Sorbonne University, Paris, France.
Microcins are bacteriocins produced by Enterobacteriaceae. They contribute to shaping the gut microbiome and constitute an attractive alternative to antibiotics, due to their narrow spectrum of activity and ability to target multidrug-resistant (MDR) bacteria1,2. Genome mining suggests that this diverse and heterogeneous family is still under-explored, and that poultry is enriched in microcin-producing strains3. The objectives of this study were to characterize the diversity and distribution of microcins in a collection of Escherichia coli strains isolated from broiler chickens and to identify potentially novel microcins. We further aimed to investigate the role of microcins in intra-species competitions and their association with virulence and antibiotic resistance factors.
E. coli isolates (40 strains) were individually tested for activity against MDR E. coli strains and subsequently pairwise tested against each other. Their genome was sequenced and analyzed for the presence of biosynthetic gene clusters (BGCs), antimicrobial resistance genes and virulence genes. Culture supernatant extracts were submitted to peptidomics to detect the genome-based predicted microcins. The correlations between microcin biosynthesis, virulence and antibiotic resistance factors were assessed from genomic data. In addition, a binary classification model was developed to predict activities in cross-strain interaction assays.
Genome analysis revealed BGCs for the production of up to three microcins per strain, belonging to class I (Mw ≤ 5 kDa, post-translationally modified) and class II (5 kDa < Mw < 10 kDa, unmodified peptides or siderophore peptides). BGCs for the production of microcin V were the most represented, and variations in the predicted precursor sequence suggested potential novel variants. One genome harbored the MccJ25 BGC and a BGC corresponding to a new class II microcin. Microcin and virulence factors shared a similar distribution pattern, while antibiotic resistance genes showed no significant association with microcin biosynthesis genes. Peptidomic analysis of supernatant extracts permitted to confirm the production of all the class I microcins predicted, while detection of class II microcins was more difficult and required optimizations. Antibacterial activity against at least one MDR strain was observed for 21 strains. Pairwise antimicrobial assays revealed complex intra-species interactions, mainly driven by the production of microcins and siderophores.
Therefore, E. coli strains isolated from poultry display attractive activities against MDR strains and constitute a source to discover novel microcins. Microcin biosynthetic machineries can be accumulated in one strain, subtend complex intra-species interactions and can be associated with virulence factors.
References
Telhig, S., Ben Said, L., Zirah, S., Fliss, I., Rebuffat, S. Front. Microbiol. 11:586433, 2020.
Telhig, S., Ben Said, L., Torres, C., Rebuffat, S., Zirah, S., Fliss, I. Microbiol. Spectr. 10:e02752-21, 2022.
Cole, T.J., Parker, J.K., Feller, A.L., Wilke, C.O., Davies, B.W. Appl. Environ. Microbiol. 88:e01486-22, 2022.
