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Fungal spores are unique cells that mediate dispersal and survival in the environment. For pathogenic fungi encountering a susceptible host, these specialised structures may serve as infectious particles. The main causative agent of the opportunistic disease aspergillosis, Aspergillus fumigatus, produces asexual spores, the conidia, that become dissipated by air flows or water currents but also serve as propagules to infect a susceptible host. We demonstrate that the defX gene of this mould encodes putative antimicrobial peptides resembling cysteine‐stabilised (CS)αβ defensins that are expressed in a specific spatial and temporal manner in the course of asexual spore formation. Localisation studies on strains expressing a fluorescent proxy or tagged defX alleles expose that these antimicrobial peptides are secreted to coat the conidial surface. Deletion mutants reveal that the spore‐associated defX gene products delay the growth of Gram‐positive Staphylococcus aureus and demonstrate that the defX gene and presumably its encoded spore‐associated defensins confer a growth advantage to the fungal opponent over bacterial competitors. These findings have implications with respect to the ecological niche of A. fumigatus that serves as a ‘virulence school’ for this human pathogenic mould; further relevance is given for the infectious process resulting in aspergillosis, considering competition with the host microbiome or co‐infecting microorganisms to break colonisation resistance at host surfaces., Cellular Microbiology, 23 (3), ISSN:1462-5814, ISSN:1462-5822

SRA Dose-Response and Microbial Risk Analysis Specialty Groups jointly sponsored symposia that addressed the intersections between the "microbiome revolution" and dose response. Invited speakers presented on innovations and advances in gut and nasal microbiota (normal microbial communities) in the first decade after the Human Microbiome Project began. The microbiota and their metabolites are now known to influence health and disease directly and indirectly, through modulation of innate and adaptive immune systems and barrier function. Disruption of healthy microbiota is often associated with changes in abundance and diversity of core microbial species (dysbiosis), caused by stressors including antibiotics, chemotherapy, and disease. Nucleic-acid-based metagenomic methods demonstrated that the dysbiotic host microbiota no longer provide normal colonization resistance to pathogens, a critical component of innate immunity of the superorganism. Diverse pathogens, probiotics, and prebiotics were considered in human and animal models (in vivo and in vitro). Discussion included approaches for design of future microbial dose-response studies to account for the presence of the indigenous microbiota that provide normal colonization resistance, and the absence of the protective microbiota in dysbiosis. As NextGen risk analysis methodology advances with the "microbiome revolution," a proposed new framework, the Health Triangle, may replace the old paradigm based on the Disease Triangle (focused on host, pathogen, and environment) and germophobia. Collaborative experimental designs are needed for testing hypotheses about causality in dose-response relationships for pathogens present in our environments that clearly compete in complex ecosystems with thousands of bacterial species dominating the healthy superorganism.

SCOPE The transgenerational impact of dietary fat remains unclear. Here, the role of maternal fat consumption as a modulator of gut microbial communities and infectious disease outcomes in their offspring is explored. METHODS AND RESULTS C57BL/6 mice are fed isocaloric high-fat diets throughout breeding, gestation and lactation. Diets contained either milk fat (MF), olive oil (OO) or corn oil (CO), with or without fish oil. The pups born to maternally exposed mice are weaned on to chow and raised into adulthood. At 8 weeks, the offsprings are either euthanized for colonic 16S rRNA analysis or challenged with the enteric pathogen, Citrobacter rodentium. Maternal CO exposure resulted in unique clustering of bacterial communities in offspring compared with MF and OO. Diets rich in CO reduced survival in offspring challenged with C. rodentium. The addition of fish oil did not improve mortality caused by CO and worsened disease outcomes when combined with OO. Unlike the unsaturated diets, MF is protective with and without fish oil. CONCLUSIONS Overall, these data reveal that maternal intake of fatty acids do have transgenerational impacts on their offspring's bacteriome and enteric infection risk. Based on this study, saturated fats should be included in maternal diets.

Large communities of microorganisms, collectively termed the microbiome, inhabit our body surfaces. With the advent of next-generation sequencing, the diversity and abundance of these communities are being unravelled. Besides an imporant role in metabolic processes, the microbiome is essential for proper functioning of our immune system, including the defense against fungi. Despite the progress of the past years, studies aimed at characterizing our fungal colonizers (the mycobiome) are limited; nevertheless fungi are important players of the microbiome, either as a cofactor in disease or as potential pathogens. In this review, we describe the role of the bacterial microbiome in antifungal host defense. On the one hand, bacteria provide colonization resistance to fungi, inhibit Candida virulence by preventing yeast-hyphal transition and contribute to epithelial integrity, all factors are important for the pathogenesis of invasive fungal disease. On the other hand, several bacterial species modulate mucosal (antifungal) immune responses. Murine studies demonstrate important effects of the microbiome on the antifungal responses of T-helper 17 cells, regulatory T cells and innate lymphoid cells. Inferred from these studies, perturbation of the healthy microbiome should be avoided and microbiome manipulation and interventions based on bacteria-derived pathways involved in immunomodulation are attractive options for modulating antifungal host defense.

The gastrointestinal microbiota is extremely important for human and animal health. Investigations into the composition of the microbiota and its therapeutic modification have received increasing interest in human and veterinary medicine. Probiotics are a way of modifying the microbiota and have been tested to prevent and treat diseases. Probiotics are proposed to exert their beneficial effects through various pathways. Production of antimicrobial compounds targeting intestinal pathogens, general immune stimulation, and colonization resistance are among these mechanisms. Despite widespread availability and use, scientific, peer-reviewed evidence behind commercial probiotic formulations in horses is limited. Additionally, quality control of commercial over-the-counter products is not tightly regulated. Although promising in vitro results have been achieved, in vivo health benefits have been more difficult to prove. Whether the ambiguous results are caused by strain selection, dosage selection or true lack of efficacy remains to be answered. Although these limitations exist, probiotics are increasingly used because of their lack of severe adverse effects, ease of administration, and low cost. This review summarizes the current evidence for probiotic use in equine medicine. It aims to provide veterinarians with evidence-based information on when and why probiotics are indicated for prevention or treatment of gastrointestinal disease in horses. The review also outlines the current state of knowledge on the equine microbiota and the potential of fecal microbial transplantation, as they relate to the topic of probiotics.

Summary Antibiotic therapies are important in combating disease-causing microorganisms and maintaining host health. It is widely accepted that exposure of the gut microbiota to antibiotics can lead to decreased susceptibility and the development of multi-drug-resistant disease-causing organisms, which can be a major clinical problem. It is also important to consider that antibiotics not only target pathogenic bacteria in the gut, but also can have damaging effects on the ecology of commensal species. This can reduce intrinsic colonization resistance and contribute to problems with antibiotic resistance, including lateral transfer of resistance genes. Our knowledge of the impact of antibiotic treatment on the ecology of the normal microbiota has been increased by recent advances in molecular methods and use of in vitro model systems to investigate the impact of antibiotics on the biodiversity of gut populations and the spread of antibiotic resistance. These highlight the need for more detailed structural and functional information on the long-term antibiotic-associated alterations in the gut microbiome, and spread of antibiotic resistance genes. This will be crucial for the development of strategies, such as targeted therapeutics, probiotics, prebiotics and synbiotics, to prevent perturbations in the gut microbiota, the restoration of beneficial species and improvements in host health.

Dense, complex microbial communities, collectively termed the microbiota, occupy a diverse array of niches along the length of the mammalian intestinal tract. During health and in the absence of antibiotic exposure the microbiota can effectively inhibit colonization and overgrowth by invading microbes such as pathogens. This phenomenon is called ‘colonization resistance’ and is associated with a stable and diverse microbiota in tandem with a controlled lack of inflammation, and involves specific interactions between the mucosal immune system and the microbiota. Here we overview the microbial ecology of the healthy mammalian intestinal tract and highlight the microbe–microbe and microbe–host interactions that promote colonization resistance. Emerging themes highlight immunological (T helper type 17/regulatory T-cell balance), microbiota (diverse and abundant) and metabolic (short-chain fatty acid) signatures of intestinal health and colonization resistance. Intestinal pathogens use specific virulence factors or exploit antibiotic use to subvert colonization resistance for their own benefit by triggering inflammation to disrupt the harmony of the intestinal ecosystem. A holistic view that incorporates immunological and microbiological facets of the intestinal ecosystem should facilitate the development of immunomodulatory and microbe-modulatory therapies that promote intestinal homeostasis and colonization resistance.

The mammalian intestine is colonized by a dense microbial community, the microbiota. Homeostatic and symbiotic interactions facilitate the peaceful co-existence between the microbiota and the host, and inhibit colonization by most incoming pathogens ('colonization resistance'). However, if pathogenic intruders overcome colonization resistance, a fierce, innate inflammatory defense can be mounted within hours, the adaptive arm of the immune system is initiated, and the pathogen is fought back. The molecular nature of the homeostatic interactions, the pathogen's ability to overcome colonization resistance, and the triggering of native and adaptive mucosal immune responses are still poorly understood. To study these mechanisms, the streptomycin mouse model for Salmonella diarrhea is of great value. Here, we review how S. Typhimurium triggers mucosal immune responses by active (virulence factor elicited) and passive (MyD88-dependent) mechanisms and introduce the S. Typhimurium mutants available for focusing on either response. Interestingly, mucosal defense turns out to be a double-edged sword, limiting pathogen burdens in the gut tissue but enhancing pathogen growth in the gut lumen. This model allows not only studying the molecular pathogenesis of Salmonella diarrhea but also is ideally suited for analyzing innate defenses, microbe handling by mucosal phagocytes, adaptive secretory immunoglobulin A responses, probing microbiota function, and homeostatic microbiota-host interactions. Finally, we discuss the general need for defined assay conditions when using animal models for enteric infections and the central importance of littermate controls.

The consortia of microorganisms inhabiting the length of the gastrointestinal tract, the gastrointestinal microbiota, are vital to many aspects of normal host physiology. In addition, they are an active participant in the progression of many diseases, among them enteric infections. Healthy intestinal microbiota contribute to host resistance to infection through their involvement in the development of the host immune system and provision of colonization resistance. It is not surprising then that disruptions of the microbial community translate into alterations of host susceptibility to infection. Additionally, the process of the infection itself results in a disturbance to the microbiota. This disturbance is often mediated by the host inflammatory response, allowing the pathogen to benefit from the inflammation at the intestinal mucosa. Uncovering the mechanisms underlying the host–pathogen-microbiota interactions will facilitate our understanding of the infection process and promote design of more effective and focused prophylactic and therapeutic strategies.

Escherichia coli is the predominant facultative anaerobe in the gastrointestinal tracts of mammals. A large and growing body of evidence indicates that commensal E. coli strains grow in the intestine on nutrients acquired from mucus. Fluorescence in situ hybridization analysis of mouse intestinal thin slices showed that E. coli BJ4, a rat commensal isolate, is dispersed in the mucus layer but is not associated with the epithelium. Colonization resistance is the ability of a complete intestinal microflora to resist colonization by an invading bacterium. When E. coli and serovar Typhimurium enter the mouse cecum, they initially encounter cecal contents. Since E. coli and serovar Typhimurium fail to grow in cecal contents but grow rapidly in cecal mucus, they must be able to enter the mucus layer and grow by using available nutrients. Genetic screens based on signature-tagged mutagenesis identify individual mutants that are lost from pools of mutants used to infect suitable animals. It is becoming increasingly clear that once E. coli strains reach the large intestine, in order to colonize, they must enter the mucus layer and utilize nutrients there for growth.

Diversity-invasibility relationships were explored in the novel context of the colonization resistance provided by gut bacteria of the desert locust Schistocerca gregaria against pathogenic bacteria. Germ-free insects were associated with various combinations of one to three species of locust gut bacteria and then fed an inoculum of the pathogenic bacterium Serratia marcescens. There was a significant negative relationship between the resulting density of Serratia marcescens and the number of symbiotic gut bacterial species present. Likewise there was a significant inverse relationship between community diversity and the proportion of locusts that harboured Serratia. Host mortality was not negatively correlated with resistance to gut-invasion by Serratia marcescens, although there were significantly more deaths among pathogen fed germ-free insects than tri-associated gnotobiotes. The outcome is consistent with the predictions of community ecology theory that species-rich communities are more resistant to invasion than species-poor communities.

An important component of a Hazard Analysis Critical Control Point (HACCP) approach applied to animal production is reducing the carriage of food-associated pathogens by animals. Two approaches that have both great potential for reducing pathogen colonization of animals and merit for practical application include (1) vaccination and (2) competitive exclusion. Vaccination involves acquisition of immunity in an animal following exposure to an attenuated pathogen or an antigen of a virulent microorganism. Adherence factors that influence bacterial colonization of animals are useful antigens for vaccines. A strategy to developing a vaccine to reduce carriage of pathogens includes (1) identifying sites of colonization by the pathogen in the animal, (2) defining the mechanism of colonization, (3) characterizing genes that encode colonization factors, (4) transforming the colonization factor antigen genes into a suitable nonpathogenic vector, and (5) determining the optimal methods of immunization. Studies are underway to identify colonization factors of Escherichia coli O157:H7 for use in vaccine development to protect cattle from colonization by this pathogen. Competitive exclusion involves the use of microbial cultures that out-compete pathogens from colonizing specific niches. A science-based approach to identifying/developing useful competitive exclusion cultures is to: (1) define how a pathogen colonizes the site of interest, (2) isolate microbes that colonize the same site and produce metabolites that inhibit or kill the pathogen, and (3) verify that the inhibitory microbes, when introduced into pathogen-free animals, can reduce or prevent colonization by the pathogen. This approach has been used successfully to identify defined bacterial cultures that can greatly reduce colonization of Campylobacter jejuni in poultry. Commercial implementation of techniques of these types is an essential part of the overall HACCP approach to reducing the prevalence of foodborne pathogens from farm to fork.

Many patients with advanced cancer have oral problems, some of which may have a microbiologic basis. The oral flora in such patients has not, however, been characterized. This study has assessed the prevalence of yeasts, coliforms and coagulase positive staphylococci in the oral flora of 197 patients with advanced cancer. Both imprint cultures (n = 197) and oral rinses (n = 161) were collected. Yeasts were isolated from the mouths of 83% of the patients, coliforms from 49.1% and coagulase-positive staphylococci from 28%. All these percentages are considerably in excess of reported levels for healthy individuals. The results indicate a loss of colonization resistance of the oral mucosa in terminal cancer, with potential implications for the development of mouth care regimes for such patients.

Persistent Escherichia coli urinary tract infection (UTI) in dogs is a frustrating clinical problem. Affected dogs often appear to fail to respond to therapy or to reacquire infection shortly after therapy is completed. Urovirulence factors (UVFs) of the infecting E. coli, antibiotic resistance, and tissue colonization may be contributory but have not been evaluated in dogs with persistent E. coli UTI. In this study, the strain types of E. coli in dogs with persistent UTI were evaluated with pulsed-field gel electrophoresis (PFGE) to determine whether persistence was due to acquisition of new isolates or failure to eradicate existing isolates. UVFs in these isolates, assessed by polymerase chain reaction, and antibiograms were correlated with treatment outcome in these dogs. Results documented a mixed pattern: 9 dogs remained chronically infected with 1 or 2 strains, each with distinct reproducible UVFs, but 1 dog was infected with numerous unrelated E. coli strains over time. Two dogs had a mixed pattern, consisting of 1 or more episodes of persistent E. coli infection attributable to a single strain in addition to episodes caused by unrelated strains. Many isolates had no detectable UVFs, highlighting the likely importance of impaired colonization resistance in the affected dogs. Antibiotic resistance was common, often in response to previous treatments, especially with trimethoprim-sulfamethoxazole. Antibiotic resistance patterns differed significantly within PFGE strain types, suggesting lateral acquisition of resistance plasmids or integrons. These results can be used to help guide testing for and management of persistent E. coli UTI in dogs.

Oral challenge with a strain of Salmonella kedougou, resistant to nalidixic acid, gave a time-course for salmonella survival in the alimentary tract of chicks pre-treated with a caecal culture from an eight-week-old bird to increase colonization resistance. In untreated, control chicks, salmonella colonization of the caeca resulted in counts of greater than 10(6)/g within 48 h and a mean generation time of 1.6 h. With treated birds, however, the salmonellas failed to multiply in the caeca and decreased to a low level over a 48-h period, thus suggesting a mainly bacteriostatic effect. Pre-treatment of chicks with the caecal culture also reduced the proportion of salmonella-positive crop samples. Growth of the salmonella in a feed-slurry system resembling moistened crop contents occurred rapidly at 37 degrees C but was prevented by addition of the treatment culture, a decline in numbers coinciding with Lactobacillus populations of ca 10(9)/g and a pH value of 5.5. Incorporation of a feed decontaminant, 1% formic acid (pH 4.0), rapidly eliminated both salmonellas and organisms added from the treatment culture.

Members of at least eight of the 14 general of the Enterobacteriaceae are found associated with animals. A large number of these are present as members of the microbiota of the gut of many animals without causing harmful effects. Indeed, their presence as part of the stable flora contributes to the defences of the animal by excluding enteric pathogens by competitive exclusion which contributes to the phenomenon of [colonization resistance' (van der Waaij 1983). some of these strains can cause disease if they contaminate a normally 'sterile' site such as the body cavities. In contrast, particular strains within each bacterial species are overt pathogens and are regularly associated with disease. Nevertheless, even these may colonize the animal without producing clinical illness. In this paper E. coli and Salmonella spp. have been used to illustrate the various aspect of host-parasite relationships.