Insights into the genomic and phenotypic characteristics of Bacillus spp. strains isolated from biofilms in broiler farms.

The characterization of surface microbiota living in biofilms within livestock buildings has been relatively unexplored, despite its potential impact on animal health. To enhance our understanding of these microbial communities, we characterized 11 spore-forming strains isolated from two commercial broiler chicken farms. Sequencing of the strains revealed them to belong to three species Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis. Genomic analysis revealed the presence of antimicrobial resistance genes and genes associated with antimicrobial secretion specific to each species. We conducted a comprehensive characterization of the biofilm formed by these strains under various conditions, and we revealed significant structural heterogeneity across the different strains. A macro-colony interaction model was employed to assess the compatibility of these strains to coexist in mixed biofilms. We identified highly competitive B. velezensis strains, which cannot coexist with other Bacillus spp. Using confocal laser scanning microscopy along with a specific dye for extracellular DNA, we uncovered the importance of extracellular DNA for the formation of B. licheniformis biofilms. Altogether, the results highlight the heterogeneity in both genome and biofilm structure among Bacillus spp. isolated from biofilms present within livestock buildings.IMPORTANCELittle is known about the microbial communities that develop on farms in direct contact with animals. Nonpathogenic strains of Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis were found in biofilm samples collected from surfaces in contact with animals. Significant genetic and phenotypic diversity was described among these Bacillus strains. The strains do not possess mobile antibiotic resistance genes in their genomes and have a strong capacity to form structured biofilms. Among these species, B. velezensis was noted for its high competitiveness compared with the other Bacillus spp. Additionally, the importance of extracellular DNA in the formation of B. licheniformis biofilms was observed. These findings provide insights for the management of these surface microbiota that can influence animal health, such as the use of competitive strains to minimize the establishment of undesirable bacteria or enzymes capable of specifically deconstructing biofilms.

Genome sequences of four colistin-resistant ESKAPE bacterial strains isolated from patients within the same hospital.

The genomes of four clinical Gram-negative ESKAPE bacterial strains highly resistant to the last-resort antibiotic colistin were sequenced and analyzed. The strains were found to carry multidrug-resistant genes besides colistin-resistant genes.

Positive biofilms to guide surface microbial ecology in livestock buildings.

The increase in human consumption of animal proteins implies changes in the management of meat production. This is followed by increasingly restrictive regulations on antimicrobial products such as chemical biocides and antibiotics, used in particular to control pathogens that can spread zoonotic diseases. Aligned with the One Health concept, alternative biological solutions are under development and are starting to be used in animal production. Beneficial bacteria able to form positive biofilms and guide surface microbial ecology to limit microbial pathogen settlement are promising tools that could complement existing biosecurity practices to maintain the hygiene of livestock buildings. Although the benefits of positive biofilms have already been documented, the associated fundamental mechanisms and the rationale of the microbial composition of these new products are still sparce. This review provides an overview of the envisioned modes of action of positive biofilms used on livestock building surfaces and the resulting criteria for the selection of the appropriate microorganisms for this specific application. Limits and advantages of this biosecurity approach are discussed as well as the impact of such practices along the food chain, from farm to fork.

Positive biofilms to control surface-associated microbial communities in a broiler chicken production system - a field study.

In the One Health concept, the use of beneficial bacteria to form positive biofilms that prevent the settlement of undesirable bacteria is a promising solution to limit the use of antimicrobials on farms. However, there is a lack of field studies reporting the onset of these beneficial bacteria after application and the effects on autochthonous surface microbiota. In the study reported here, the inner surfaces of commercial broiler chicken houses were treated or not with a bacterial consortium composed of Bacillus spp. and Pediococcus spp. strains, able to form covering biofilms in different laboratory models. Preinstalled coupons were sampled over time to capture microbial biofilm dynamics on-farm surfaces. The results showed that the bacterial consortium can establish on the farm surfaces, modulate microbial communities, and limit the implantation of Enterobacteriaceae and Enterococcaceae, two families containing potential pathogens.

Genome Sequence of Bacillus velezensis P1, a Strain Isolated from a Biofilm Captured on a Pig Farm Building.

The genome of the Bacillus velezensis P1 strain isolated from a biofilm on the wall of a pig farm was sequenced. The strain harbors many surface colonization genes involved in surfactant, matrix, and antibacterial synthesis.

Capture and Ex-Situ Analysis of Environmental Biofilms in Livestock Buildings.

Little information about biofilm microbial communities on the surface of livestock buildings is available yet. While these spatially organized communities proliferate in close contact with animals and can harbor undesirable microorganisms, no standardized methods have been described to sample them non-destructively. We propose a reproducible coupon-based capture method associated with a set of complementary ex-situ analysis tools to describe the major features of those communities. To demonstrate the biofilm dynamics in a pig farm building, we analyzed the coupons on polymeric and metallic materials, as representative of these environments, over 4 weeks. Confocal laser scanning microscopy (CLSM) revealed a rapid coverage of the coupons with a thick layer of biological material and the existence of dispersed clusters of active metabolic microorganisms. After detaching the cells from the coupons, counts to quantify the CFU/cm2 were done with high reproducibility. High-throughput sequencing of the 16S rRNA V3-V4 region shows bacterial diversity profiles in accordance with reported bacteria diversity in pig intestinal ecosystems and reveals differences between materials. The coupon-based methodology allows us to deepen our knowledge on biofilm structure and composition on the surface of a pig farm and opens the door for application in different types of livestock buildings.

Evaluation of the Probiotic Properties and the Capacity to Form Biofilms of Various Lactobacillus Strains.

Over the last 20 years, Lactobacillus species inhabiting the gastrointestinal tract (GIT) have received much attention, and their health-promoting properties are now well-described. Probiotic effects cannot be generalized, and their uses cover a wide range of applications. It is thus important to proceed to an accurate selection and evaluation of probiotic candidates. We evaluate the probiotic potential of six strains of Lactobacillus in different in vitro models representing critical factors of either survival, efficacy, or both. We characterized the strains for their ability to (i) modulate intestinal permeability using transepithelial electrical resistance (TEER), (ii) form biofilms and resist stressful conditions, and (iii) produce beneficial host and/or bacteria metabolites. Our data reveal the specificity of Lactobacillus strains to modulate intestinal permeability depending on the cell type. The six isolates were able to form spatially organized biofilms, and we provide evidence that the biofilm form is beneficial in a strongly acidic environment. Finally, we demonstrated the ability of the strains to produce γ-aminobutyric acid (GABA) that is involved in the gut-brain axis and beneficial enzymes that promote the bacterial tolerance to bile salts. Overall, our study highlights the specific properties of Lactobacillus strains and their possible applications as biofilms.