Mechanisms of microbial co-aggregation in mixed anaerobic cultures

Co-aggregation of anaerobic microorganisms into suspended microbial biofilms (aggregates) serves ecological and biotechnological functions. Tightly packed aggregates of metabolically interdependent bacteria and archaea play key roles in cycling of carbon and nitrogen. Additionally, in biotechnological applications, such as wastewater treatment, microbial aggregates provide a complete metabolic network to convert complex organic material. Currently, experimental data explaining the mechanisms behind microbial co-aggregation in anoxic environments is scarce and scattered across the literature. To what extent does this process resemble co-aggregation in aerobic environments? Does the limited availability of terminal electron acceptors drive mutualistic microbial relationships, contrary to the commensal relationships observed in oxygen-rich environments? And do co-aggregating bacteria and archaea, which depend on each other to harvest the bare minimum Gibbs energy from energy-poor substrates, use similar cellular mechanisms as those used by pathogenic bacteria that form biofilms? Here, we provide an overview of the current understanding of why and how mixed anaerobic microbial communities co-aggregate and discuss potential future scientific advancements that could improve the study of anaerobic suspended aggregates. KEY POINTS: • Metabolic dependency promotes aggregation of anaerobic bacteria and archaea • Flagella, pili, and adhesins play a role in the formation of anaerobic aggregates • Cyclic di-GMP/AMP signaling may trigger the polysaccharides production in anaerobes.

Exploring coaggregation mechanisms involved in biofilm formation in drinking water through a proteomic-based approach

AIM

Coaggregation, a highly specific cell-cell interaction mechanism, plays a pivotal role in multispecies biofilm formation. While it has been mostly studied in oral environments, its occurrence in aquatic systems is also acknowledged. Considering biofilm formation's economic and health-related implications in engineered water systems, it is crucial to understand its mechanisms. Here, we hypothesized that traceable differences at the proteome level might determine coaggregation ability.

METHODS AND RESULTS

Two strains of Delftia acidovorans, isolated from drinking water were studied. First, in vitro motility assays indicated more swarming and twitching motility for the coaggregating strain (C+) than non-coaggregating strain (C-). By transmission electronic microscopy, we confirmed the presence of flagella for both strains. By proteomics, we detected a significantly higher expression of type IV pilus twitching motility proteins in C+, in line with the motility assays. Moreover, flagellum ring proteins were more abundant in C+, while those involved in the formation of the flagellar hook (FlE and FilG) were only detected in C-. All the results combined suggested structural and conformational differences between stains in their cell appendages.

CONCLUSION

This study presents an alternative approach for identifying protein biomarkers to detect coaggregation abilities in uncharacterized strains.

Transcriptomic and metabolomic analyses to study the key role by which Ralstonia insidiosa induces Listeria monocytogenes to form suspended aggregates

Ralstonia insidiosa can survive in a wide range of aqueous environments, including food processing areas, and is harmful to humans. It can induce Listeria monocytogenes to form suspended aggregates, resulting from the co-aggregation of two bacteria, which allows for more persistent survival and increases the risk of L. monocytogenes contamination. In our study, different groups of aggregates were analyzed and compared using Illumina RNA sequencing technology. These included R. insidiosa under normal and barren nutrient conditions and in the presence or absence of L. monocytogenes as a way to screen for differentially expressed genes (DEGs) in the process of aggregate formation. In addition, sterile supernatants of R. insidiosa were analyzed under different nutrient conditions using metabolomics to investigate the effect of nutrient-poor conditions on metabolite production by R. insidiosa. We also undertook a combined analysis of transcriptome and metabolome data to further investigate the induction effect of R. insidiosa on L. monocytogenes in a barren environment. The results of the functional annotation analysis on the surface of DEGs and qPCR showed that under nutrient-poor conditions, the acdx, puuE, and acs genes of R. insidiosa were significantly upregulated in biosynthetic processes such as carbon metabolism, metabolic pathways, and biosynthesis of secondary metabolites, with Log2FC reaching 4.39, 3.96, and 3.95 respectively. In contrast, the Log2FC of cydA, cyoB, and rpsJ in oxidative phosphorylation and ribosomal pathways reached 3.74, 3.87, and 4.25, respectively. Thirty-one key components were identified while screening for differential metabolites, which mainly included amino acids and their metabolites, enriched to the pathways of biosynthesis of amino acids, phenylalanine metabolism, and methionine metabolism. Of these, aminomalonic acid and Proximicin B were the special components of R. insidiosa that were metabolized under nutrient-poor conditions.

Drinking-water isolated Delftia acidovorans selectively coaggregates with partner bacteria and facilitates multispecies biofilm development

Coaggregation plays an important role in the development of multispecies biofilms in different environments, often serving as an active bridge between biofilm members and other organisms that, in their absence, would not integrate the sessile structure. The ability of bacteria to coaggregate has been reported for a limited number of species and strains. In this study, 38 bacterial strains isolated from drinking water (DW) were investigated for their ability to coaggregate, in a total of 115 pairs of combinations. Among these isolates, only Delftia acidovorans (strain 005P) showed coaggregating ability. Coaggregation inhibition studies have shown that the interactions mediating D. acidovorans 005P coaggregation were both polysaccharide-protein and protein-protein, depending on the interacting partner bacteria. Dual-species biofilms of D. acidovorans 005P and other DW bacteria were developed to understand the role of coaggregation on biofilm formation. Biofilm formation by Citrobacter freundii and Pseudomonas putida strains highly benefited from the presence of D. acidovorans 005P, apparently due to the production of extracellular molecules/public goods favouring microbial cooperation. This was the first time that the coaggregation capacity of D. acidovorans was demonstrated, highlighting its role in providing a metabolic opportunity for partner bacteria.

Characterization of Cellulomonas sp. HM71 as potential probiotic strain for human health

Cellulomonas sp. HM71, a human gut microbe possesses metabolic machinery to catabolize antigenic gluten, hence, holds promises as microbial therapy to treat gluten-derived celiac disease. However, its efficacy, safety, and survivability in the gastrointestinal ecosystem await functional elucidation. The current study is designed to characterize Cellulomonas sp. HM71 for its physiological, genomic, and probiotic properties. The morphological and physiological assessment indicates it as a coccus-shaped gram-positive bacterium growing optimally at 30°C in a neutral environment (pH 7.0). Cellulomonas sp. HM71 showed continuous growth even in stressful environments (salinity up to 3% NaCl and 6% KCl), variable temperature (25°C to 35°C) and pH (5-9), antibiotics, and gastric and intestinal conditions. The Cellulomonas sp. HM71 genome harbors diversified genetic machinery to modulate humongous metabolic potential for the host. This was substantiated by the hemolytic and CaCo-2 cell line assay which confirms its cellular adherence and biosafety. Notably, genome analysis did not identify any pathogenic islands. Probiotic characterization indicates its potential to overcome waterborne infections and digestion-related disorders. Cumulatively, Cellulomonas sp. HM71 can be considered a probiotic strain for improving human health because of the highlighted functions.

Bioprospecting of the probiotic potential of yeasts isolated from a wine environment

Autochthonous yeasts of oenological origin are adapted to highly stressful and selective environments, which makes them potential candidates for probiotics. The objective of the present study was to explore the probiotic potential of 96 native yeasts of oenological origin, their biosafety, resistance to gastrointestinal tract conditions and adhesion properties. Regarding biosafety, 66 isolates shown negative hemolytic activity, negative urease activity and susceptibility to 3 or more antifungals. After the gastrointestinal resistance test, 15 isolates were selected that showed growth at different temperatures, tolerance to low pH and the presence of bile salts in in vitro tests. In general, survival after simulated conditions of the gastrointestinal tract was high and more restrictive was the duodenal. The results of the adhesion properties showed highly variable hydrophobicity and a high percentage of autoaggregation at 24 h. The maximum production of biofilm was detected in the Pichia strains. Of a total of 96 yeast strains, 15 non-Saccharomyces yeasts presented suitable properties as probiotic candidates. The native winemaking strains performed better than the reference probiotic strain, Saccharomyces cerevisiae var. boulardii CNCM I-745, which reaffirms that these strains are promising probiotic candidates and further studies are necessary to confirm their probiosis.

Probiotic Properties of Chicken-Derived Highly Adherent Lactic Acid Bacteria and Inhibition of Enteropathogenic Bacteria in Caco-2 Cells

Lactic acid bacteria (LAB) as probiotic candidates have various beneficial functions, such as regulating gut microbiota, inhibiting intestinal pathogens, and improving gut immunity. The colonization of the intestine is a prerequisite for probiotic function. Therefore, it is necessary to screen the highly adherent LAB. In this study, the cell surface properties, such as hydrophobicity, auto-aggregation, co-aggregation, and adhesion abilities of the six chicken-derived LAB to Caco-2 cells were investigated. All six strains showed different hydrophobicity (21.18-95.27%), auto-aggregation (13.61-30.17%), co-aggregation with Escherichia coli ATCC 25922 (10.23-36.23%), and Salmonella enterica subsp. enterica serovar Typhimurium ATCC 13311 (11.71-39.35%), and adhesion to Caco-2 cells (8.57-26.37%). Pediococcus pentosaceus 2-5 and Lactobacillus reuteri L-3 were identified as the strains with strong adhesion abilities (26.37% and 21.57%, respectively). Moreover, these strains could survive in a gastric acid environment at pH 2, 3, and 4 for 3 h and in a bile salt environment at 0.1%, 0.2%, and 0.3% (w/v) concentration for 6 h. Furthermore, the cell-free supernatant of P. pentosaceus 2-5 and L. reuteri L-3 inhibited the growth of enteropathogenic bacteria and the strains inhibited the adhesion of these pathogens to Caco-2 cells. In this study, these results suggested that P. pentosaceus 2-5 and L. reuteri L-3, isolated from chicken intestines might be good probiotic candidates to be used as feed additives or delivery vehicles of biologically active substances.

Towards understanding mechanisms and functional consequences of bacterial interactions with members of various kingdoms in complex biofilms that abound in nature

The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonise a surface develop architecturally complex surface-adhered communities which we refer to as biofilms. They are embedded in polymeric structural scaffolds serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed co-existence of microorganisms from all domains of life, including Bacteria, Archaea and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.

Intimate relationships among actinomycetes and mycolic acid-containing bacteria

Co-culture is an efficient strategy for natural product discovery. We have used mycolic acid-containing bacteria (MACB) Tsukamurella pumonis TP-B0596 to induce secondary metabolism by actinomycetes and have found several natural products. We also observed that MACB attached to the mycelium of Streptomyces lividans forming coaggregates during combined-culture. This stimulated interest in the interactions among actinomycetes and MACB, and we found that soil isolated cultures contained a mixture of actinomycetes and MACB. Our previously observed interactions were the result of selective screening and combination of bacteria in the lab, which warranted investigation of the existence of these interactions in the natural soil environment. Therefore, in this paper, we report the interaction between a co-isolated natural pair of actinomycetes and MACB in terms of morphology and metabolic changes. A natural pair of actinomycetes and MACB co-aggregated in liquid culture and showed metabolic changes. Interestingly, co-aggregated actinomycetes and MACB were re-isolated from soil with no obvious morphological colony differences from the colony of a single strain. The results demonstrate that there is a stochastic chance of picking colonies containing co-aggregated actinomycetes and MACB, which suggests that the pair can exist in co-aggregate form in the soil environment and interact with each other.

Polymicrobial Interactions of Oral Microbiota: a Historical Review and Current Perspective

The oral microbiota is enormously diverse, with over 700 microbial species identified across individuals that play a vital role in the health of our mouth and our overall well-being. In addition, as oral diseases such as caries (cavities) and periodontitis (gum disease) are mediated through interspecies microbial interactions, this community serves as an important model system to study the complexity and dynamics of polymicrobial interactions. Here, we review historical and recent progress in our understanding of the oral microbiome, highlighting how oral microbiome research has significantly contributed to our understanding of microbial communities, with broad implications in polymicrobial diseases and across microbial community ecology. Further, we explore innovations and challenges associated with analyzing polymicrobial systems and suggest future directions of study. Finally, we provide a conceptual framework to systematically study microbial interactions within complex communities, not limited to the oral microbiota.

Probiotics: Symbiotic Relationship with the Animal Host

Antibiotic growth-promoters in animal feeding are known to generate bacterial resistance on commercial farms and have proven deleterious effects on human health. This review addresses the effects of probiotics and their symbiotic relationship with the animal host as a viable alternative for producing healthy meat, eggs, and milk at present and in the future. Probiotics can tolerate the conditions of the gastrointestinal tract, such as the gastric acid, pH and bile salts, to exert beneficial effects on the host. They (probiotics) may also have a beneficial effect on productivity, health and wellbeing in different parameters of animal performance. Probiotics stimulate the native microbiota (microbes that are present in their place of origin) and production of short-chain fatty acids, with proven effects such as antimicrobial, hypocholesterolemic and immunomodulatory effects, resulting in better intestinal health, nutrient absorption capacity and productive responses in ruminant and non-ruminant animals. These beneficial effects of probiotics are specific to each microbial strain; therefore, the isolation and identification of beneficial microorganisms, as well as in vitro and in vivo testing in different categories of farm animals, will guarantee their efficacy, replicability and sustainability in the current production systems.

Influence of culture conditions on co-aggregation of probiotic yeast Saccharomyces boulardii with Candida spp. and their auto-aggregation

Systemic infections caused by pathogenic Candida species pose a significant threat to public health in the past decades due to increasing resistance to existing antifungal drugs. Given this scenario, probiotics have been suggested as an alternative approach for managing Candida infections. Hence, the purpose of this study was to evaluate whether probiotic yeast Saccharomyces boulardii co-aggregate with Candida spp. as well as to determine their auto-aggregation ability in dependence on temperature (28 °C, 37 °C, 42 °C) and pH (4.5, 7.0, 8.5) after 5 h and 24 h. Our results revealed that the aggregation of tested yeasts was lower in the first 5 h but increased significantly after 24 h. All strains were able to auto-aggregate in different degrees ranging from 47.46 to 95.95% assessed at 24 h of incubation. Among them the highest auto-aggregation values had C. albicans and C. krusei strains followed by probiotic strain S. boulardii, while the less were observed in C. glabrata strains. In addition, co-aggregation between probiotic and Candida strains was strain-specific. It was evident that S. boulardii significantly inhibited the aggregation of C. albicans ATCC 10261, C. krusei ATCC 6258, and C. glabrata ZIM 2369. However, in C. glabrata ZIM 2382, the aggregation was even enhanced. Temperature and pH also affected the ability to aggregate in a different way only after 5 h of incubation, with the highest cell aggregation evidenced at temperature 37 °C in most cases and pH 4.5. These findings may be of importance when trying to establish probiotic use against pathogenic Candida species.

Inhibitory effect of d-arabinose on oral bacteria biofilm formation on titanium discs

OBJECTIVES

Biofilm formation on dental implant surfaces can cause peri-implant mucositis and peri-implantitis. Lectins are involved in interactions between bacteria or between bacteria and their hosts. Disrupting these interactions via specific sugars can result in reduced adhesion and biofilm formation. The purpose of this study was to identify sugars that function as antiadhesion or antibiofilm agents on titanium discs.

METHODS

Of the sugars tested, the sugars that did not affect the planktonic growth of Streptococcus oralis, Fusobacterium nucleatum, and Porphyromonas gingivalis were selected. The selected sugars were assessed for their ability to inhibit biofilm formation of bacteria in single and consortium species by crystal violet staining, confocal laser scanning microscopy after live/dead staining, and scanning electron microscopy. The sugars were evaluated for their ability to inhibit activity of the quorum sensing molecule autoinducer 2 (AI-2) by bioluminescence assay.

RESULTS

Biofilm formation of single bacteria or consortia of S. oralis, F. nucleatum, and P. gingivalis on titanium discs was significantly inhibited in the presence of d-arabinose. Pretreating titanium discs with d-arabinose for 3 min inhibited biofilm formation at a level comparable to that observed when d-arabinose was present over the entire period, suggesting that d-arabinose had initial anti-adhesive activity. In addition, d-arabinose inhibited the activity of AI-2.

CONCLUSIONS

d-Arabinose may be a good candidate for application as an antibiofilm agent and AI-2 inhibitor.

Formation, Development, and Cross-Species Interactions in Biofilms

Biofilms, which are essential vectors of bacterial survival, protect microbes from antibiotics and host immune attack and are one of the leading causes that maintain drug-resistant chronic infections. In nature, compared with monomicrobial biofilms, polymicrobial biofilms composed of multispecies bacteria predominate, which means that it is significant to explore the interactions between microorganisms from different kingdoms, species, and strains. Cross-microbial interactions exist during biofilm development, either synergistically or antagonistically. Although research into cross-species biofilms remains at an early stage, in this review, the important mechanisms that are involved in biofilm formation are delineated. Then, recent studies that investigated cross-species cooperation or synergy, competition or antagonism in biofilms, and various components that mediate those interactions will be elaborated. To determine approaches that minimize the harmful effects of biofilms, it is important to understand the interactions between microbial species. The knowledge gained from these investigations has the potential to guide studies into microbial sociality in natural settings and to help in the design of new medicines and therapies to treat bacterial infections.

Microbial fuel cells and their electrified biofilms

Bioelectrochemical systems (BES) represent a wide range of different biofilm-based bioreactors that includes microbial fuel cells (MFCs), microbial electrolysis cells (MECs) and microbial desalination cells (MDCs). The first described bioelectrical bioreactor is the Microbial Fuel Cell and with the exception of MDCs, it is the only type of BES that actually produces harvestable amounts of electricity, rather than requiring an electrical input to function. For these reasons, this review article, with previously unpublished supporting data, focusses primarily on MFCs. Of relevance is the architecture of these bioreactors, the type of membrane they employ (if any) for separating the chambers along with the size, as well as the geometry and material composition of the electrodes which support biofilms. Finally, the structure, properties and growth rate of the microbial biofilms colonising anodic electrodes, are of critical importance for rendering these devices, functional living 'engines' for a wide range of applications.

Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions

Microorganisms are a fundamental part of virtually every ecosystem on earth. Understanding how collectively they interact, assemble, and function as communities has become a prevalent topic both in fundamental and applied research. Owing to multiple advances in technology, answering questions at the microbial system or network level is now within our grasp. To map and characterize microbial interaction networks, numerous computational approaches have been developed; however, experimentally validating microbial interactions is no trivial task. Microbial interactions are context-dependent, and their complex nature can result in an array of outcomes, not only in terms of fitness or growth, but also in other relevant functions and phenotypes. Thus, approaches to experimentally capture microbial interactions involve a combination of culture methods and phenotypic or functional characterization methods. Here, through our perspective of food microbiologists, we highlight the breadth of innovative and promising experimental strategies for their potential to capture the different dimensions of microbial interactions and their high-throughput application to answer the question; are microbial interaction patterns or network architecture similar along different contextual scales? We further discuss the experimental approaches used to build various types of networks and study their architecture in the context of cell biology and how they translate at the level of microbial ecosystem.

Bacterial coaggregation in aquatic systems

The establishment of a sessile community is believed to occur in a sequence of steps where genetically distinct bacteria can become attached to partner cells via specific molecules, in a process known as coaggregation. The presence of bacteria with the ability to autoaggregate and coaggregate has been described for diverse aquatic systems, particularly freshwater, drinking water, wastewater, and marine water. In these aquatic systems, coaggregation already demonstrated a role in the development of complex multispecies sessile communities, including biofilms. While specific molecular aspects on coaggregation in aquatic systems remain to be understood, clear evidence exist on the impact of this mechanism in multispecies biofilm resilience and homeostasis. The identification of bridging bacteria among coaggregating consortia has potential to improve the performance of wastewater treatment plants and/or to contribute for the development of strategies to control undesirable biofilms. This study provides a comprehensive analysis on the occurrence and role of bacterial coaggregation in diverse aquatic systems. The potential of this mechanism in water-related biotechnology is further described, with particular emphasis on the role of bridging bacteria.

Role of coaggregation in the pathogenicity and prolonged colonisation of Vibrio cholerae

Cholera is an acute diarrheal illness caused by the Gram-negative bacterium Vibrio cholerae. The pathogen is known for its ability to form biofilm that confers protection against harsh environmental condition and as part of the colonisation process during infection. Coaggregation is a process that facilitates the formation of biofilm. In a preliminary in vitro study, high coaggregation index and biofilm production were found between V. cholerae with human commensals namely Escherichia coli and Enterobacter cloacae. Building upon these results, the effects of coaggregation were further evaluated using adult BALB/c mouse model. The animal study showed no significant differences in mortality and fluid accumulation ratio between treatment groups infected with V. cholerae alone and those infected with coaggregation partnership (V. cholerae with E. coli or V. cholerae with E. cloacae). However, mild inflammation was detected in both partnering pairs. Higher density of V. cholerae was recovered from faecal samples of mice co-infected with E. coli and V. cholerae in comparison with other groups at 24 h post-infection. This partnership also elicited slightly higher levels of interleukin-5 (IL-5) and interleukin-10 (IL-10). Nonetheless, the involvement of autoinducer-2 (AI-2) as the signalling molecules in quorum sensing system is not evident in this study. Since E. coli is one of the common commensals, our result may suggest the involvement of commensals in cholera development.

Biofilms in Food Processing Environments: Challenges and Opportunities

This review examines the impact of microbial communities colonizing food processing environments in the form of biofilms on food safety and food quality. The focus is both on biofilms formed by pathogenic and spoilage microorganisms and on those formed by harmless or beneficial microbes, which are of particular relevance in the processing of fermented foods. Information is presented on intraspecies variability in biofilm formation, interspecies relationships of cooperativism or competition within biofilms, the factors influencing biofilm ecology and architecture, and how these factors may influence removal. The effect on the biofilm formation ability of particular food components and different environmental conditions that commonly prevail during food processing is discussed. Available tools for the in situ monitoring and characterization of wild microbial biofilms in food processing facilities are explored. Finally, research on novel agents or strategies for the control of biofilm formation or removal is summarized.

Highly efficient phenol degradation in a batch moving bed biofilm reactor: benefiting from biofilm-enhancing bacteria

In this study, the efficiency improvement of three moving bed biofilm reactors (MBBRs) was investigated by inoculation of activated sludge cells (R1), mixed culture of eight strong phenol-degrading bacteria consisted of Pseudomonas spp. and Acinetobacter spp. (R2) and the combination of both (R3). Biofilm formation ability of eight bacteria was assessed initially using different methods and media. Maximum degradation of phenol, COD, biomass growth and also changes in organic loading shock were used as parameters to measure the performance of reactors. According to the results, all eight strains were determined as enhanced biofilm forming bacteria (EBFB). Under optimum operating conditions, more than 90% of initial COD load of 2795 mg L^-1 was reduced at 24 HRT in R3 while this reduction efficiency was observed in concentrations of 1290 mg L^-1 and 1935 mg L^-1, in R1 and R2, respectively. When encountering phenol loading shock-twice greater than optimum amount-R1, R2 and R3 managed to return to the steady-state condition within 32, 24 and 18 days, respectively. SEM microscopy and biomass growth measurements confirmed the contribution of more cells to biofilm formation in R3 followed by R2. Additionally, established biofilm in R3 was more resistant to phenol loading shock which can be attributed to the enhancer role of EBFB strains in this reactor. It has been demonstrated that the bacteria with both biofilm-forming and contaminant-degrading abilities are not only able to promote the immobilization of other favorable activated sludge cells in biofilm structure, but also cooperate in contaminant degradation which all consequently lead to improvement of treatment efficiency.

Protective Yeasts Control V. anguillarum Pathogenicity and Modulate the Innate Immune Response of Challenged Zebrafish (Danio rerio) Larvae

We investigated mechanisms involved in the protection of zebrafish (Danio rerio) larvae by two probiotic candidate yeasts, Debaryomyces hansenii 97 (Dh97) and Yarrowia lypolitica 242 (Yl242), against a Vibrio anguillarum challenge. We determined the effect of different yeast concentrations (104-107 CFU/mL) to: (i) protect larvae from the challenge, (ii) reduce the in vivo pathogen concentration and (iii) modulate the innate immune response of the host. To evaluate the role of zebrafish microbiota in protection, the experiments were performed in conventionally raised and germ-free larvae. In vitro co-aggregation assays were performed to determine a direct yeast-pathogen interaction. Results showed that both yeasts significantly increased the survival rate of conventionally raised larvae challenged with V. anguillarum. The concentration of yeasts in larvae tended to increase with yeast inoculum, which was more pronounced for Dh97. Better protection was observed with Dh97 at a concentration of 106 CFU/mL compared to 104 CFU/mL. In germ-free conditions V. anguillarum reached higher concentrations in larvae and provoked significantly more mortality than in conventional conditions, revealing the protective role of the host microbiota. Interestingly, yeasts were equally (Dh97) or more effective (Yl242) in protecting germ-free than conventionally-raised larvae, showing that protection can be exerted only by yeasts and is not necessarily related to modulation of the host microbiota. Although none of the yeasts co-aggregated with V. anguillarum, they were able to reduce its proliferation in conventionally raised larvae, reduce initial pathogen concentration in germ-free larvae and prevent the upregulation of key components of the inflammatory/anti-inflammatory response (il1b, tnfa, c3, mpx, and il10, respectively). These results show that protection by yeasts of zebrafish larvae challenged with V. anguillarum relates to an in vivo anti-pathogen effect, the modulation of the innate immune system, and suggests that yeasts avoid the host-pathogen interaction through mechanisms independent of co-aggregation. This study shows, for the first time, the protective role of zebrafish microbiota against V. anguillarum infection, and reveals mechanisms involved in protection by two non-Saccharomyces yeasts against this pathogen.