Cryptosporidium parvum-Infected Neonatal Mice Show Gut Microbiota Remodelling Using High-Throughput Sequencing Analysis: Preliminary Results

Cryptosporidium and irritable bowel syndrome

Cryptosporidium is an apicomplexan parasite that causes gastrointestinal disease in a wide variety of hosts and is associated with waterborne outbreaks. Nonetheless, the parasite is underdiagnosed. Cryptosporidium has been proposed as an etiological cause of irritable bowel syndrome (IBS) in several studies. However, the exact mechanism of pathogenesis is unknown, and no direct link has been discovered. This review will discuss several parasite-induced modifications, such as immunological, microbiome, and metabolite modifications, as well as their interactions. To summarize, Cryptosporidium causes low inflammation, dysbiosis, and unbalanced metabolism, which leads to a lack of homeostasis in the intestine in a comparable pattern to postinfectious IBS.

Microbiome diversity is a modifiable virulence factor for cryptosporidiosis

Cryptosporidium spp. infection causes significant disease in immunosuppressed individuals and children under the age of 5 years. The severity of the pathological presentation of cryptosporidiosis is a function of the host and parasite genotypes, host immune status, and the enteric environment or microbiome of the host. Cryptosporidiosis often presents with abdominal pain and severe diarrhoea and is associated with intestinal dysbiosis and inflammation. Our systematic analysis of the available literature revealed that bacterial diversity is reduced during infection in larger animal models, lending support to recent studies which indicate that the use of probiotics or the presence of a naturally diverse gut microbiome can prevent or minimise pathology caused by gastrointestinal pathogens. In summary, we present evidence that the presence of a diverse gut microbiome, natural or induced, reduces both symptomatic pathology and oocyst output.

Therapeutic efficacy of proton pump inhibitor (omeprazole) on cryptosporidiosis parvum in immunosuppressed experimental mice

Cryptosporidiosis is one of the most frequent food and water-borne diseases. The disease might be life-threatening in immunosuppressed patients. Unfortunately, the only approved drug, nitazoxanide, is with variable efficacies, particularly in malnourished children and immunocompromised patients. Therefore, there is a need to discover an alternative treatment that could be achieved by targeting the metabolic pathways. One of the important enzymes in the glycolysis pathway of C. parvum is triosephosphate isomerase, which could be hindered by the proton pump inhibitor (PPI) omeprazole. In this study, omeprazole was repurposed against C. parvum infection in experimentally immunosuppressed mice. This study was conducted on five mice groups (n = 10). Group I (Normal Control), group II (Infected Control): Mice were infected orally with 1 × 105 C. parvum oocysts on the 15th day of DEX induced immunosuppression. Group III (NTZ-treated): infected and treated by NTZ. Group IV (Omeprazole-treated), and lastly, Group V (NTZ + Omeprazole-treated). The result obtained with omeprazole alone was better than nitazoxanide regarding oocyst shedding reduction percentages (84.9% & 56.1%, respectively). Also, it was better regarding restoration of histopathological and ultrastructural architectures, improvement of liver enzymes (alanine aminotransferase and aspartate aminotransferase) and renal functions (urea and creatinine), and the reduction of C. parvum triosephosphate isomerase (TIM) gene expression by RT-PCR. However, the best results were obtained with the combined treatment. Hence, omeprazole could be considered a novel drug option to treat this life-threatening parasitic infection either alone or combined with NTZ, especially in immunosuppressed patients.

Dendritic Cells and Cryptosporidium: From Recognition to Restriction

Host immune responses are required for the efficient control of cryptosporidiosis. Immunity against Cryptosporidium infection has been best studied in mice, where it is mediated by both innate and adaptive immune responses. Dendritic cells are the key link between innate and adaptive immunity and participate in the defense against Cryptosporidium infection. While the effector mechanism varies, both humans and mice rely on dendritic cells for sensing parasites and restricting infection. Recently, the use of mouse-adapted strains C. parvum and mouse-specific strain C. tyzzeri have provided tractable systems to study the role of dendritic cells in mice against this parasite. In this review, we provide an overview of recent advances in innate immunity acting during infection with Cryptosporidium with a major focus on the role of dendritic cells in the intestinal mucosa. Further work is required to understand the role of dendritic cells in the activation of T cells and to explore associated molecular mechanisms. The identification of Cryptosporidium antigen involved in the activation of Toll-like receptor signaling in dendritic cells during infection is also a matter of future study. The in-depth knowledge of immune responses in cryptosporidiosis will help develop targeted prophylactic and therapeutic interventions.

Microbiome-Metabolomics Analysis of the Impacts of Cryptosporidium muris Infection in BALB/C Mice

Cryptosporidium is a leading cause of diarrheal disease and mortality in young children worldwide. Cryptosporidium invades small intestinal epithelial cells and forms a unique intracellular niche, a process that may alter gut microbes and their production metabolites. However, the mechanism of interactions between gut microbes, metabolites, and parasites is poorly understood. Here, we first characterized the impacts of Cryptosporidium infection on gut microbiota using a microbiome-to-metabolome association study. BALB/c mice were gavaged with Cryptosporidium muris, and fecal samples were collected at 0, 7, 14, 21, and 28 days postinfection (dpi) to observe changes in the intestinal microbes of the body during parasite infection. The infected group had a significantly increased relative abundance of bacterial taxa, such as Lachnospiraceae and Prevotella (P < 0.05), associated with the biosynthesis of short-chain fatty acids (SCFAs). Metabolites related to the metabolic pathways, steroid hormone biosynthesis, and biosynthesis of unsaturated fatty acids pathway were upregulated at 7 dpi, indicating that related metabolites in the biosynthesis of unsaturated fatty acids may be essential for C. muris reproduction in vivo. The metabolites involved in metabolic pathways, bile secretion, and primary bile acid biosynthesis were upregulated at 14 dpi, and we speculate that these metabolites may be critical to the growth and development of Cryptosporidium oocysts in the host. Correlation analysis revealed that Firmicutes bacteria are significantly associated with α-linolenic acid metabolism pathways (P< 0.05). The gut microbiota changes dynamically, and the metabolites involved in fatty acid and bile acid biosynthesis may play important roles during cryptosporidiosis. Details of the gut microbiota and the metabolome after infection with Cryptosporidium may aid in the discovery of specific diagnostic markers and help us understand the changes in parasite metabolic pathways. IMPORTANCE Cryptosporidiosis is a gastrointestinal disease in humans and animals caused by the protozoan parasite Cryptosporidium. Control and treatment of the disease is challenging due to the lack of sensitive diagnostic tools and effective chemotherapy. The dynamics of gut microbiota and metabolites during Cryptosporidium infection may be the key to finding drugs and targets for parasite infection control. Our results indicate that C. muris infection can disrupt gut microbiota and metabolites, resulting in decreased bacterial abundance at the parasitic site. Unsaturated fatty acid pathway biosynthesis-related metabolites are significantly elevated at the patent period. Interestingly, the metabolite pathway that significantly elevated during peak parasite growth was bile acid, the metabolites of which may be important for the circulation of infection of Cryptosporidium oocysts in the host. The enhancing effects of short-chain fatty acid and bile acid metabolism on the growth and development of Cryptosporidium proposed in this study may provide a theoretical basis for future research on novel drugs and vaccines against this intestinal parasite.

Host innate immune responses and microbiome profile of neonatal calves challenged with Cryptosporidium parvum and the effect of bovine colostrum supplementation

Introduction

Calves are highly susceptible to gastrointestinal infection with Cryptosporidium parvum (C. parvum), which can result in watery diarrhea and eventually death or impaired development. With little to no effective therapeutics, understanding the host's microbiota and pathogen interaction at the mucosal immune system has been critical to identify and test novel control strategies.

Methods

Herein, we used an experimental model of C. parvum challenge in neonatal calves to describe the clinical signs and histological and proteomic profiling of the mucosal innate immunity and microbiota shifts by metagenomics in the ileum and colon during cryptosporidiosis. Also, we investigated the impact of supplemental colostrum feeding on C. parvum infection.

Results

We showed that C. parvum challenged calves experienced clinical signs including pyrexia and diarrhea 5 days post challenge. These calves showed ulcerative neutrophil ileitis with a proteomic signature driven by inflammatory effectors, including reactive oxygen species and myeloperoxidases. Colitis was also noticed with an aggravated mucin barrier depletion and incompletely filled goblet cells. The C. parvum challenged calves also displayed a pronounced dysbiosis with a high prevalence of Clostridium species (spp.) and number of exotoxins, adherence factors, and secretion systems related to Clostridium spp. and other enteropathogens, including Campylobacter spp., Escherichia sp., Shigella spp., and Listeria spp. Daily supplementation with a high-quality bovine colostrum product mitigated some of the clinical signs and modulated the gut immune response and concomitant microbiota to a pattern more similar to that of healthy unchallenged calves.

Discussion

C. parvum infection in neonatal calves provoked severe diarrheic neutrophilic enterocolitis, perhaps augmented due to the lack of fully developed innate gut defenses. Colostrum supplementation showed limited effect mitigating diarrhea but demonstrated some clinical alleviation and specific modulatory influence on host gut immune responses and concomitant microbiota.

Cryptosporidium infection induced the dropping of SCFAS and dysbiosis in intestinal microbiome of Tibetan pigs

The infection of Cryptosporidium in pigs causes digestive system ailments, diarrhea and weight loss serving as an economic burden, especially in newborn animals. The bacterial fermentation products of short-chain fatty acids have important roles in immune function, microbiota regulation, osmotic balance and metabolism. However, till now little knowledge is available about the effect of Cryptosporidium infection on microbiota and SCFAs in plateau pigs. Hence, we performed this study to explore the response of microbiota and SCFAs in the natural infection of Cryptosporidium in Tibetan pigs. Cryptosporidium positive (infected, G) and negative samples (healthy, J) in our previous study were used for high throughputsequencing and Gas Chromatography-Mass Spectrometer analysis. Over 81 000 and 74 000 filtered sequences were detected in healthy and infected Tibetan pigs, respectively. Lower sample richness and evenness were observed in Cryptosporidium infection, as alpha diversity analysis found that chao1 (p < 0.05), faith_pd (p < 0.05), and observed_features in group G were significantly lower than pigs in group J. A total of 4 and 27 significant different phyla and genera were found between group G and J. The changed genera were Psychrobacter, Desemzia, Succiniclasticum, Treponema, Campylobacter, Atopobium, Olsenella, Pediococcus, Peptococcus, Sharpea, Desulfovibrio, Acinetobacter, Rhodococcus, Anaerostipes, Turicibacter, Lactobacillus, RFN20, Phascolarctobacterium, Roseburia, Megasphaera, Streptococcus, Blautia, Lachnospira, rc4_4, Gemmiger, Dorea, Oribacterium and Prevotella, which affected the microbiota functions with 360 abundance changed enzymes, and pathways in L1, L2 and L3 levels of KEGG. The concentration of acetic acid (p < 0.01), butyric acid (p < 0.05) and caproic acid (p < 0.01) were lower in group G. In conclusion, the present study herein uncovered that the host responses to Cryptosporidium infection in Tibetan pigs with 27 of significantly changed genera decreased SCFAs in pigs, which may provide insights in further developing novel therapy against this protozoan.

Intestinal immune responses to commensal and pathogenic protozoa

The physical barrier of the intestine and associated mucosal immunity maintains a delicate homeostatic balance between the host and the external environment by regulating immune responses to commensals, as well as functioning as the first line of defense against pathogenic microorganisms. Understanding the orchestration and characteristics of the intestinal mucosal immune response during commensal or pathological conditions may provide novel insights into the mechanisms underlying microbe-induced immunological tolerance, protection, and/or pathogenesis. Over the last decade, our knowledge about the interface between the host intestinal mucosa and the gut microbiome has been dominated by studies focused on bacterial communities, helminth parasites, and intestinal viruses. In contrast, specifically how commensal and pathogenic protozoa regulate intestinal immunity is less well studied. In this review, we provide an overview of mucosal immune responses induced by intestinal protozoa, with a major focus on the role of different cell types and immune mediators triggered by commensal (Blastocystis spp. and Tritrichomonas spp.) and pathogenic (Toxoplasma gondii, Giardia intestinalis, Cryptosporidium parvum) protozoa. We will discuss how these various protozoa modulate innate and adaptive immune responses induced in experimental models of infection that benefit or harm the host.

Faecal microbiota in two-week-old female dairy calves during acute cryptosporidiosis outbreak - Association with systemic inflammatory response

In the present study, relationships between the intestinal microbiota and innate immunity response, acute cryptosporidiosis, and weight gain in female dairy calves were investigated. A total of 112 calves born during a natural outbreak of cryptosporidiosis on one dairy farm was included in the study. Microbiota composition was analysed by means of 16S ribosomal RNA gene amplicon sequencing from faecal samples collected during the second week of life, while the status of Cryptosporidium spp. infection was determined using immunofluorescence. Serum samples from the second week of life were colourimetrically analysed for the following markers of acute inflammation: acute-phase proteins (serum amyloid A and haptoglobin) and pro-inflammatory cytokines (interleukin-1 beta, interleukin-6, and tumour necrosis factor-alpha). Statistical analyses were performed using random forest analysis, variance-partitioning, and negative binomial regression. The faecal microbiota of the two-week old calves was composed of the phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, and Actinobacteria (in order of decreasing abundance). Microbial diversity, measured in terms of the Shannon index, increased with the age of the calves and decreased if a high count of Cryptosporidium spp. oocysts was found in the faeces. Fusobacterium was positively associated with Cryptosporidium spp. oocyst count and serum amyloid A concentration. Peptostreptococcus was positively associated with haptoglobin and serum amyloid A concentrations, and negatively associated with average daily weight gain at 9 months of age. The markers of innate immunity, in combination with age, explained 6% of the microbial variation. These results suggest that some components of the intestinal microbiota may have a long-lasting negative effect on animal growth through the stimulation of the systemic innate immune response.

Effect of Caging on Cryptosporidium parvum Proliferation in Mice

Cryptosporidiosis is an enteric infection caused by several protozoan species in the genus Cryptosporidium (phylum Apicomplexa). Immunosuppressed mice are commonly used to model this infection. Surprisingly, for a pathogen like Cryptosporidium parvum, which is readily transmitted fecal-orally, mice housed in the same cage can develop vastly different levels of infection, ranging from undetectable to lethal. The motivation for this study was to investigate this phenomenon and assess the association between the severity of cryptosporidiosis and the fecal microbiota. To this aim, the association between severity of cryptosporidiosis and caging (group caged vs. individually caged) and between the microbiota taxonomy and the course of the infection was examined. In contrast to mice caged in groups of four, a majority of mice caged individually did not excrete a detectable level of oocysts. Microbiota α diversity in samples collected between three days prior to infection and one day post-infection was negatively correlated with the severity of cryptosporidiosis, suggesting a causal negative relationship between microbiota diversity and susceptibility to C. parvum.

The interaction of gut microbiota with parasitic protozoa

The human intestinal microbiota is composed of a complex combination of microorganisms including bacteria, virus, and eukaryotes. The microbiota plays a critical role in homeostasis through creating a mucosal barrier, providing protective responses to pathogens, and affecting the immune system and metabolism of the host. Molecules secreted by parasites can alter composition of microbiota both by acting directly on the microbial community and indirectly by affecting the host physiology. On the other hand, the microbiota composition can affect the survival, physiology, and virulence of many parasitic protozoa. Explanation of possible interactions between the microbiota, immune response, and protozoa may further clarify the underlying mechanisms of infectivity, clinical variations, and life-cycle of protozoa.

Curcumin mitigates Cryptosporidium parvum infection through modulation of gut microbiota and innate immune-related genes in immunosuppressed neonatal mice

Cryptosporidium parvum is a major cause of diarrheal disease in immature or weakened immune systems, mainly in infants and young children in resource-poor settings. Despite its high prevalence, fully effective and safe drugs for the treatment of C. parvum infections remain scarce, and there is no vaccine. Meanwhile, curcumin has shown protective effects against C. parvum infections. However, the mechanisms of action and relationship to the gut microbiota and innate immune responses are unclear. Immunosuppressed neonatal mice were infected with oocysts of C. parvum and either untreated or treated with a normal diet, curcumin or paromomycin. We found that curcumin stopped C. parvum oocysts shedding in the feces of infected immunosuppressed neonatal mice, prevented epithelial damage, and villi degeneration, as well as prevented recurrence of infection. Curcumin supplementation increased the relative abundance of Bacteroidetes and decreased the relative abundance of Firmicutes and Proteobacteria in mice infected with C. parvum as shown by 16S rRNA gene sequencing analysis. The relative abundance of Lactobacillus, Bacteroides, Akkermansia, Desulfovibrio, Prevotella, and Helicobacter was significantly associated with C. parvum infection inhibited by curcumin. Curcumin significantly (P < 0.01) suppressed IFN-γ and IL -18 gene expression levels in immunosuppressed neonatal C. parvum-infected mice. We demonstrate that the therapeutic effects curcumin are associated with alterations in the gut microbiota and innate immune-related genes, which may be linked to the anti-Cryptosporidium mechanisms of curcumin.

Cryptosporidiosis Modulates the Gut Microbiome and Metabolism in a Murine Infection Model

Cryptosporidiosis is a major human health concern globally. Despite well-established methods, misdiagnosis remains common. Our understanding of the cryptosporidiosis biochemical mechanism remains limited, compounding the difficulty of clinical diagnosis. Here, we used a systems biology approach to investigate the underlying biochemical interactions in C57BL/6J mice infected with Cryptosporidium parvum. Faecal samples were collected daily following infection. Blood, liver tissues and luminal contents were collected 10 days post infection. High-resolution liquid chromatography and low-resolution gas chromatography coupled with mass spectrometry were used to analyse the proteomes and metabolomes of these samples. Faeces and luminal contents were additionally subjected to 16S rRNA gene sequencing. Univariate and multivariate statistical analysis of the acquired data illustrated altered host and microbial energy pathways during infection. Glycolysis/citrate cycle metabolites were depleted, while short-chain fatty acids and D-amino acids accumulated. An increased abundance of bacteria associated with a stressed gut environment was seen. Host proteins involved in energy pathways and Lactobacillus glyceraldehyde-3-phosphate dehydrogenase were upregulated during cryptosporidiosis. Liver oxalate also increased during infection. Microbiome–parasite relationships were observed to be more influential than the host–parasite association in mediating major biochemical changes in the mouse gut during cryptosporidiosis. Defining this parasite–microbiome interaction is the first step towards building a comprehensive cryptosporidiosis model towards biomarker discovery, and rapid and accurate diagnostics.

Decreased Ecological Resistance of the Gut Microbiota in Response to Clindamycin Challenge in Mice Colonized with the Fungus Candida albicans

The mammalian gut microbiota is a complex community of microorganisms which typically exhibits remarkable stability. As the gut microbiota has been shown to affect many aspects of host health, the molecular keys to developing and maintaining a "healthy" gut microbiota are highly sought after. Yet, the qualities that define a microbiota as healthy remain elusive. We used the ability to resist change in response to antibiotic disruption, a quality we refer to as ecological resistance, as a metric for the health of the bacterial microbiota. Using a mouse model, we found that colonization with the commensal fungus Candida albicans decreased the ecological resistance of the bacterial microbiota in response to the antibiotic clindamycin such that increased microbiota disruption was observed in C. albicans-colonized mice compared to that in uncolonized mice. C. albicans colonization resulted in decreased alpha diversity and small changes in abundance of bacterial genera prior to clindamycin challenge. Strikingly, co-occurrence network analysis demonstrated that C. albicans colonization resulted in sweeping changes to the co-occurrence network structure, including decreased modularity and centrality and increased density. Thus, C. albicans colonization resulted in changes to the bacterial microbiota community and reduced its ecological resistance.IMPORTANCECandida albicans is the most common fungal member of the human gut microbiota, yet its ability to interact with and affect the bacterial gut microbiota is largely uncharacterized. Previous reports showed limited changes in microbiota composition as defined by bacterial species abundance as a consequence of C. albicans colonization. We also observed only a few bacterial genera that were significantly altered in abundance in C. albicans-colonized mice; however, C. albicans colonization significantly changed the structure of the bacterial microbiota co-occurrence network. Additionally, C. albicans colonization changed the response of the bacterial microbiota ecosystem to a clinically relevant perturbation, challenge with the antibiotic clindamycin.

Neonatal Mouse Gut Metabolites Influence Cryptosporidium parvum Infection in Intestinal Epithelial Cells

Cryptosporidium sp. occupies a unique intracellular niche that exposes the parasite to both host cell contents and the intestinal lumen, including metabolites from the diet and produced by the microbiota. Both dietary and microbial products change over the course of early development and could contribute to the changes seen in susceptibility to cryptosporidiosis in humans and mice.

The protozoan parasite Cryptosporidium sp. is a leading cause of diarrheal disease in those with compromised or underdeveloped immune systems, particularly infants and toddlers in resource-poor localities. As an enteric pathogen, Cryptosporidium sp. invades the apical surface of intestinal epithelial cells, where it resides in close proximity to metabolites in the intestinal lumen. However, the effect of gut metabolites on susceptibility to Cryptosporidium infection remains largely unstudied. Here, we first identified which gut metabolites are prevalent in neonatal mice when they are most susceptible to Cryptosporidium parvum infection and then tested the isolated effects of these metabolites on C. parvum invasion and growth in intestinal epithelial cells. Our findings demonstrate that medium or long-chain saturated fatty acids inhibit C. parvum growth, perhaps by negatively affecting the streamlined metabolism in C. parvum, which is unable to synthesize fatty acids. Conversely, long-chain unsaturated fatty acids enhanced C. parvum invasion, possibly by modulating membrane fluidity. Hence, gut metabolites, either from diet or produced by the microbiota, influence C. parvum growth in vitro and may also contribute to the early susceptibility to cryptosporidiosis seen in young animals.

Cryptosporidium parvum Infection Depletes Butyrate Producer Bacteria in Goat Kid Microbiome

Cryptosporidium parvum is an important apicomplexan parasite infecting ruminants and humans. We characterized the impact of C. parvum infection on the goat kid microbiome. C. parvum was orally administered to parasite-naïve goats, and infection was monitored for 26 days in fecal samples using immunofluorescence assay and qPCR tests. Age-matched goats served as uninfected controls. A reduction in body weight gain, diarrhea, and dehydration were observed in infected goats compared to the uninfected controls. Infection decreased the bacterial diversity 5 days post-infection (dpi), but this parameter recovered at 15 dpi. The infection altered the relative abundance of several taxa. A total of 38 taxa displayed significant differences in abundance between control and infected goats at both 5 and 15 dpi. Co-occurrence network analysis revealed that the infection resulted in a differential pattern of taxa interactions and that C. parvum infection increased the relative abundance of specific taxa. The 16S data set was used for metagenome predictions using the software package PICRUSt2. As many as 34 and 40 MetaCyc pathways (from 387 total) were significantly affected by the infection at 5 and 15 dpi, respectively. Notably, C. parvum decreased the abundance of butyrate-producing pathways in bacteria. Low levels of butyrate may increase mucosal inflammation and tissue repair. Our results suggest that the gut inflammation induced by C. parvum infection is associated with the reduction of butyrate-producing bacteria. This insight could be the basis for the development of novel control strategies to improve animal health.

Shifts in the Fecal Microbial Community of Cystoisospora suis Infected Piglets in Response to Toltrazuril

The protozoan parasite Cystoisospora suis causes diarrhea and reduced weight gain in suckling piglets. Infections occur in the first days of life; it is transient but can lead to dysbiosis, exacerbating disease and increasing mortality. Cystoisosporosis is effectively controlled by toltrazuril treatment; however, alterations of the gut microbial composition upon infection and treatment have not been investigated. This study evaluated the development of fecal microbiota of C. suis infected piglets in response to treatment with toltrazuril. Thirty-eight conventional piglets were infected with C. suis on the first day of life (dol 1). Twenty-six of them received either parenteral or oral toltrazuril 2 days later. Fecal samples were collected pre- and post-weaning (dol 1-15 and 31-38) for microbiota analysis using 16S rRNA amplicon sequencing and during dol 5-18 to determine fecal consistency and parasite excretion. All control animals shed parasites at least once and the majority developed diarrhea, while toltrazuril-treated piglets did not excrete parasites and only had low levels of diarrhea. Age-related shifts in the fecal microbiota composition and increase in diversity and species richness were seen until after weaning. Parasite infection disrupted bacterial maturation 2 weeks after infection. Irrespective of the route of administration, fecal communities of piglets in the treated groups clustered separately and were more diverse compared to that of control piglets during the acute phase of infection on dol 11. Control piglet feces showed higher levels of Fusobacteriaceae and Veillonellaceae, while Ruminococcaceae, Lachnospiraceae, S24-7, Clostridiaceae, and Erysipelotrichaceae were more abundant in feces of treated piglets on dol 11. Thereafter, treatment-related effects on the microbial communities were small and mainly detectable on dol 34 (5 days post-weaning), potentially indicating that the oral toltrazuril treatment might have had long-term effects on host physiological responses post-weaning. Irrespective of the administration route, toltrazuril prevented C. suis-related dysbiosis and maintained species richness and diversity on dol 11. In addition to cystoisosporosis prevention, toltrazuril seems to contribute to the stabilization of the gut microbial development during the suckling phase and thus may reduce the need for antibiotics to control infections with secondary bacterial enteropathogens in C. suis-infected suckling piglets.