Exploring the potential for competitive exclusion of commensal probiotic candidates against the insidious swine pathogen Brachyspira hyodysenteriae.

Abstract

Background: Research into animal microbiota reveals the intricate relationships between commensal bacteria and enteric pathogens. Metagenomics and culturomics offer novel opportunities in probiotic research, which is particularly interesting for diseases where treatment alternatives are limited, such as swine dysentery (SD), which is caused by Brachyspira hyodysenteriae (B. hyo). This study evaluates the potential ability of a collection of 28 isolates from species of interest to outcompete the anaerobic pathogen B. hyo by an array of in vitro assays designed to characterize their competitive exclusion capacity in co-cultures, alongside assessing the antimicrobial activity of the isolates cell-free supernatants (CFS) and the mechanisms by which they inhibit B. hyo growth.

Results: 20 of the 28 isolates tested were able to reduce the growth of B. hyo by more than one log10 bacteria/mL after 96 h of co-culture, with different inhibitory dynamics observed. Notably, Intestinibaculum porci (J1/23 CM6), Dorea longicatena (J1/23 YB16), Bifidobacterium thermoacidophilum (J1/23 YB69), Mobilitalea sibirica (J1/23 YB21), Clostridium butyricum (CECT 361), and _Parabacteroides goldsteinii (_DSMZ 29187) reduced B. hyo growth in more than 2 log10 units (bacteria/mL). The anti-B. hyo activity of the tested CFS demonstrated that the mechanisms involved went beyond nutrient competition, with a CFS concentration-dependent reduction. CFS from 11 isolates achieved a reduction of over 2 log10 bacteria/mL, with C. butyricum and Paraprevotella clara (DSMZ 19731) CFS standing out with values of 2–3 log10 bacteria/mL. A pH-dependent effect was disclosed for part of the isolates tested, while C. butyricum, Limosilactobacillus mucosae, B. thermoacidophilum and Lactiplantibacillus plantarum maintained part of their anti-B. hyo activity at fixed pH (7.0). A combined analysis of the short chain fatty acid profile and pH on B. hyo growth inhibition revealed differences between isolates, with similar effect for CFS of isolates with similar production of lactic and acetic acids and no clear effect of the pH.

Conclusions: This study demonstrates the potential of pig gut commensals to outcompete B. hyo and discloses part of the mechanisms involved in the growth inhibition, providing a foundation into future research in competitive exclusion as strategy to control SD.

Supplementary Information: The online version contains supplementary material available at 10.1186/s42523-025-00511-y.

Keywords: Anaerobic; Co-culture; Control.; Microbiota; Supernatant; Swine dysentery.