The Absence of Gut Microbiota Alters the Development of the Apicomplexan Parasite Eimeria tenella

Correlation of caecal microbiome endotoxins genes and intestinal immune cells in Eimeria tenella infection based on bioinformatics

Introduction

The infection with Eimeria tenella (ET) can elicit expression of various intestinal immune cells, incite inflammation, disrupt intestinal homeostasis, and facilitate co-infection with diverse bacteria. However, the reciprocal interaction between intestinal immune cells and intestinal flora in the progression of ET-infection remains unclear.

Objective

The aim of this study was to investigate the correlation between cecal microbial endotoxin (CME)-related genes and intestinal immunity in ET-infection, with subsequent identification of hub potential biomarker and immunotherapy target.

Methods

Differential expression genes (DEGs) within ET-infection and hub genes related to CME were identified through GSE39602 dataset based on bioinformatic methods and Protein-protein interaction (PPI) network analysis. Moreover, immune infiltration was analyzed by CIBERSORT method. Subsequently, comprehensive functional enrichment analyses employing Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis along with Gene Ontology (GO), gene set enrichment analysis (GSEA), and gene set variation analysis (GSVA) were performed.

Results

A total of 1089 DEGs and 25 hub genes were identified and CXCR4 was ultimately identified as a essential CME related potential biomarker and immunotherapy target in the ET-infection. Furthermore, activated natural killer cells, M0 macrophages, M2 macrophages, and T regulatory cells were identified as expressed intestinal immune cells. The functional enrichment analysis revealed that both DEGs and hub genes were significantly enriched in immune-related signaling pathways.

Conclusion

CXCR4 was identified as a pivotal CME-related potential biomarker and immunotherapy target for expression of intestinal immune cells during ET-infection. These findings have significant implications in elucidating the intricate interplay among ET-infection, CME, and intestinal immunity.

Phylogenetic analysis of Eimeria tenella isolates from chicken of sub-tropical mountains of Meghalaya, India

BACKGROUND

Coccidiosis is the most common and pathogenic intestinal disease caused by different species of Eimeria is chicken. In this study, we describe the prevalence, molecular diagnosis and evolutionary insight of Eimeria tenella in chicken of Meghalaya's sub-tropical mountainous area.

METHODS AND RESULTS

Faecal samples (337 no.) and dead chicks (298 no.) were collected every month from January to July' 2023 from poultry farms (4nos.) in and around Umiam, Ri-Bhoi, Meghalaya. The chicks were categorized into different age groups viz. < 3, 3-6 and > 6 weeks. Samples were examined by flotation techniques and post-mortem. The oocysts were sporulated in 2.5% potassium dichromate solution. Eimeria tenella's 18 S rRNA gene genomic DNA was extracted, amplified, and sequenced. Fecal sample and postmortem examinations revealed 24.04% and 33.22% infections of Eimeria sp., respectively. Oocyst per gram (OPG) was recorded highest and lowest in July (26,500) and February (9800), respectively. Amplification of the 18 S rRNA small subunit gene (SSU) by Polymerase Chain Reaction (PCR) revealed a 1790 bp band size. The amplicon was sequenced and deposited in the NCBI database. BLAST analyses of the SSU rRNA gene of E. tenella, Umiam, Meghalaya isolate (OR458392.1) revealed sequence similarities of more than 99% with SSU rRNA gene sequences available in the NCBI database. Pair wise alignment exhibited nucleotide homology ranging from 71.59 to 100.0% with the maximum sequence homology (100.0%) shared with the E. tenella isolate from Turkey (HQ680474.1) and the lowest homology of 95.6% with UK (HG994972.1). Umiam isolate were found to have 97.08% and 100.0% nucleotide similarities with E. tenella from both the UK (AF026388.1) and the USA (U40264.1), respectively. However, nucleotide similarities of 98.24%, 85.33%, 84.75% and 81.35% were observed with E. tenella strain Bangalore (JX312808.1), E. tenella isolate Kerala-1 (JX093898.1), E. tenella isolate Kerala-3 (JX093900.1) and E. tenella isolate Kerala-2 (JX093899.1), respectively. Phylogenetic analysis of SSU rRNA sequences of E. tenella Umiam, Meghalaya isolate with cognate sequences throughout the world revealed these sequences are distinct but at the same time share a close phylogenetic relationship with Indian isolates from Bangalore and Andhra Pradesh. In addition, the distant phylogenetic relationship was observed with cognate gene sequences of United States of America, Canada, China.

CONCLUSION

Phylogenetic analysis of SSU rRNA sequences of E. tenella Umiam, Meghalaya isolate with cognate sequences throughout the world revealed these sequences are distinct but at the same time share a close phylogenetic relationship with Indian isolates from Bangalore and Andhra Pradesh. Distant phylogenetic relationship was observed with cognate gene sequences of United States of America, Canada, China.

Microbiota promotes recruitment and pro-inflammatory response of caecal macrophages during E. tenella infection

BACKGROUND

Eimeria genus belongs to the apicomplexan parasite phylum and is responsible for coccidiosis, an intestinal disease with a major economic impact on poultry production. Eimeria tenella is one of the most virulent species in chickens. In a previous study, we showed a negative impact of caecal microbiota on the physiopathology of this infection. However, the mechanism by which microbiota leads to the physiopathology remained undetermined. Macrophages play a key role in inflammatory processes and their interaction with the microbiota during E. tenella infection have never been investigated. We therefore examined the impact of microbiota on macrophages during E. tenella infection. Macrophages were monitored in caecal tissues by immunofluorescence staining with KUL01 antibody in non-infected and infected germ-free and conventional chickens. Caecal cells were isolated, stained, analyzed and sorted to examine their gene expression using high-throughput qPCR.

RESULTS

We demonstrated that microbiota was essential for caecal macrophage recruitment in E. tenella infection. Furthermore, microbiota promoted a pro-inflammatory transcriptomic profile of macrophages characterized by increased gene expression of NOS2, ACOD1, PTGS2, TNFα, IL1β, IL6, IL8L1, IL8L2 and CCL20 in infected chickens. Administration of caecal microbiota from conventional chickens to germ-free infected chickens partially restored macrophage recruitment and response.

CONCLUSIONS

Taken together, these results suggest that the microbiota enhances the physiopathology of this infection through macrophage recruitment and activation. Consequently, strategies involving modulation of the gut microbiota may lead to attenuation of the macrophage-mediated inflammatory response, thereby limiting the negative clinical outcome of the disease.

The caecal microbiota promotes the acute inflammatory response and the loss of the intestinal barrier integrity during severe Eimeria tenella infection

Introduction

Coccidiosis, a disease caused by intestinal apicomplexan parasites Eimeria, is a threat to poultry production. Eimeria tenella is one of the most pathogenic species, frequently causing a high prevalence of opportunistic infections.

Objective

The objective of this study is to investigate the role of the microbiota in the pathogenesis of severe Eimeria tenella infection.

Methods

We have previously shown that microbiota can promote parasite development. To study the effect of the microbiota on the pathogenesis of this infection, we used an experimental condition (inoculum of 10 000 oocysts E. tenella INRAE) in which the parasite load is similar between germ-free and conventional broilers at 7 days post-infection (pi). Thirteen conventional and 24 germ-free chickens were infected. Among this latter group, 12 remained germ-free and 12 received a microbiota from conventional healthy chickens at 4 days pi. Caeca and spleens were collected at 7 days pi.

Results

Our results demonstrated caecal lesions and epithelium damage in conventional chickens at 7 days pi but not in germ-free infected chickens. Administration of conventional microbiota to germ-free chickens partially restored these deleterious effects. At day 7 pi, both infected conventional and germ-free chickens exhibited increased gene expression of inflammatory mediators, including IL15, IFNγ, TNFα and the anti-inflammatory mediator SOCS1, whereas the inflammatory mediators CXCLi2, CCL20, IL18, CSF1, NOS2, PTGS2, IL1β, IL6, the receptor CCR2, and the anti-inflammatory mediators TGFβ1 and IL10 were upregulated only in infected conventional chickens. Notably, the IL18, PTGS2 gene expression was significantly higher in the infected conventional group. Overall, the inflammatory response enhanced by the microbiota might be in part responsible for higher lesion scores. Epithelial tight junction protein gene expression analysis revealed a significant upregulation of CLDN1 with the infection and microbiota, indicating a potential loss of the intestinal barrier integrity.

Conclusion

These observations imply that, during E. tenella infection, the caecal microbiota could trigger an acute inflammatory response, resulting in a loss of intestinal integrity. Increase in bacterial translocation can then lead to the likelihood of opportunistic infections. Hence, modulating the microbiota may offer a promising strategy for improving poultry gut health and limiting caecal coccidiosis.

Orally delivered Bacillus subtilis expressing chicken NK-2 peptide stabilizes gut microbiota and enhances intestinal health and local immunity in coccidiosis-infected broiler chickens

We recently reported a stable Bacillus subtilis-carrying chicken NK-lysin peptide (B. subtilis-cNK-2) as an effective oral delivery system of an antimicrobial peptide to the gut with therapeutic effect against Eimeria parasites in broiler chickens. To further investigate the effects of a higher dose of an oral B. subtilis-cNK-2 treatment on coccidiosis, intestinal health, and gut microbiota composition, 100 (14-day-old) broiler chickens were allocated into 4 treatment groups in a randomized design: 1) uninfected control (CON), 2) infected control without B. subtilis (NC), 3) B. subtilis with empty vector (EV), and 4) B. subtilis with cNK-2 (NK). All chickens, except the CON group, were infected with 5,000 sporulated Eimeria acervulina (E. acervulina) oocysts on d 15. Chickens given B. subtilis (EV and NK) were orally gavaged (1 × 10¹² cfu/mL) daily from d 14 to 18. Growth performances were measured on d 6, 9, and 13 postinfection (dpi). Spleen and duodenal samples were collected on 6 dpi to assess the gut microbiota, and gene expressions of gut integrity and local inflammation makers. Fecal samples were collected from 6 to 9 dpi to enumerate oocyst shedding. Blood samples were collected on 13 dpi to measure the serum 3-1E antibody levels. Chickens in the NK group showed significantly improved (P < 0.05) growth performance, gut integrity, reduced fecal oocyst shedding and mucosal immunity compared to NC. Interestingly, there was a distinct shift in the gut microbiota profile in the NK group compared to that of NC and EV chickens. Upon challenge with E. acervulina, the percentage of Firmicutes was reduced and that of Cyanobacteria increased. In NK chickens, however, the ratio between Firmicutes and Cyanobacteria was not affected and was similar to that of CON chickens. Taken together, NK treatment restored dysbiosis incurred by E. acervulina infection and showed the general protective effects of orally delivered B. subtilis-cNK-2 on coccidiosis infection. This includes reduction of fecal oocyst shedding, enhancement of local protective immunity, and maintenance of gut microbiota homeostasis in broiler chickens.

Antibiotic Changes Host Susceptibility to Eimeria falciformis Infection Associated with Alteration of Gut Microbiota

Eimeria falciformis is a murine-infecting coccidium that mainly infects the cecum and colon where it coexists with a large number of endogenous bacteria. Here, we found that mice treated with a broad-spectrum antibiotic cocktail including ampicillin, neomycin, metronidazole, and vancomycin had less oocyst production and milder pathological consequences after E. falciformis infection than mice without antibiotics, regardless of the inoculation doses. Furthermore, we showed that antibiotic treatment reduced parasitic invasion and prolonged asexual stage during E. falciformis infection, which may result in alleviating the infection. Interestingly, when further defining different antibiotic combinations for E. falciformis infection, it was shown that mice treated with ampicillin plus vancomycin had substantially attenuated E. falciformis infections as measured by cecal parasite counts and histopathological features. In contrast, treatment with metronidazole plus neomycin was beneficial to E. falciformis infection. Analyses of gut microbiota revealed various changes in bacterial composition and diversity following antibiotic treatments that were associated with host susceptibility to E. falciformis infection. Together, these findings suggest that gut microbiota may regulate the course and pathogenicity of E. falciformis infection, while the mechanisms need to be further investigated, especially for the development of coccidial vaccines for use in farm animals.

Comparative biology of germ-free and conventional poultry

Interaction between the host and the enteric microbiome is highly complex. Microbial involvement in certain pathologies is moderately well established, but the contribution of the microbiome to animal welfare, behavior, sustainability, immune development, nutritional status, physiology, and maturation is less clear. A valuable experimental model to enable scientists to explore the role of the microbiome in various domains is to compare various phenotypes of a conventionally reared (CV) cohort with those in a germ-free (GF) state. A GF animal is one that is devoid of any detectable microbial life including bacteria, viruses, protozoa and parasites. The GF state is different from gnotobiotic animals where the microbiome is fully described, or ‘specific pathogen free’ (SPF) animals where a moderately normal microbiome is present but devoid of pathogenic microorganisms. Pioneering GF research in poultry in the late 1940s and 1950s has its origin in a need understand the mode of action of antibiotics. Early researchers quickly established that GF chicks responded differently to antibiotics than CV counterparts. The GF experimental model has since been exploited in many divergent fields including pathology, immunology, metabolism, anatomy, physiology, and others. The absence of a microbiome presents the host with a range of advantages and disadvantages. For example, GF chicks often grow more quickly and have lower feed conversion ratio (FCR) than their CV counterparts but may be less resilient to external stress and have a compromised immunological maturation rate. This review will summarize the literature on GF animal research with a special emphasis on poultry. The objective of the review is to establish a frame of reference to understand the extent of the role of the microbiome in animal health, welfare, nutrition, and growth, to provide opportunities for targeted modulation of the microbiome to achieve desired phenotypic responses whilst simultaneously minimizing unintended collateral effects.

Comparison of functional-oil blend and anticoccidial antibiotics effects on performance and microbiota of broiler chickens challenged by coccidiosis

This study aimed to compare the effects of different levels of cashew nutshell liquid (CNSL) and castor oil (CNSL-castor oil) with growth-promoting antibiotics associated with anticoccidials in broiler chickens challenged with coccidiosis. In this work, 2520 one-day-old male broiler chicks (Cobb) were randomly assigned to 84 pens, containing 30 birds each. The experimental design was completely randomized, with seven treatments: enramycin (8 ppm), virginiamycin (16.5 ppm), and tylosin (55 ppm); different doses of CNSL-castor oil (0.5, 0.75, and 1.00 kg/t); and a control diet (without additives). All treatments received semduramicin + nicarbazin (500 g/t; Aviax® Plus) from 0 to 28 d and monensin sodium (100 ppm; Elanco) from 29 to 35 days of age, when the feed was without antibiotics. The challenge was introduced at 14 days of age by inoculating broiler chickens with sporulated Eimeria tenella, Eimeria acervulina, and Eimeria maxima oocysts via oral gavage. In addition to performance parameters, intestinal contents were collected at 28 and 42 days of age for microbiota analysis by sequencing the 16s rRNA in V3 and V4 regions using the Illumina MiSeq platform. Taxonomy was assigned using the SILVA database (v. 138) with QIIME2 software (v. 2020.11). After one week of challenge, the broilers that received tylosin had a higher body weight gain (BWG) than those in the control group (p < 0.05), while the other treatments presented intermediate values. At 28 d, the BWG was lower for the control, CNSL-Castor oil 0.5 kg/t, enramycin, and virginiamycin treatments than that in the tylosin treatment. The inclusion of CNSL-Castor oil at concentrations of 0.75 and 1 kg/t acted as an intermediate treatment (p < 0.05). For alpha diversity, using the Shannon index, it was possible to observe the effect of age, with substantial diversity at 42 d. The Firmicutes phylum had the highest abundance, with values between 84.33% and 95.16% at 42 d. Tylosin showed better performance indices than other treatments. CNSL-castor oil treatments with concentrations of 0.75 and 1 kg/t showed similar results to those of enramycin and virginiamycin. Furthermore, CNSL-castor oil acted as a modulator of intestinal microbiota, reducing the abundance of pathogenic bacteria.

Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys

Turkeys (Meleagris gallopavo) provide a globally important source of protein and constitute the second most important source of poultry meat in the world. Bacterial diseases are common in commercial poultry production causing significant production losses for farmers. Due to the increasingly recognized problems associated with large-scale/indiscriminant antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study we compared the cecal microbiota of wild and domestic turkeys, hypothesizing that environmental pressures faced by wild birds may select for a disease-resistant microbial community. Sequence analysis of 16S rRNA genes amplified from cecal samples indicate that free-roaming wild turkeys carry a rich and variable microbiota compared to domestic turkeys raised on large-scale poultry farms. Wild turkeys also had very low levels of Staphylococcus, Salmonella and E. coli when compared to domestic turkeys. E. coli strains isolated from wild or domestic turkey cecal samples also belong to distinct phylogenetic backgrounds and differ in their propensity to carry virulence genes. E. coli strains isolated from factory-raised turkeys were far more likely to carry genes for capsule (kpsII, kpsIII) or siderophore (iroN, fyuA) synthesis than those isolated from wild turkeys. These results suggest that the microbiota of wild turkeys may provide colonization resistance against common poultry pathogens. Importance Due to the increasingly recognized problems associated with antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study we compare the microbiota of wild and domestic turkeys. Results suggest that free ranging wild turkeys carry a distinct microbiome when compared to farm raised turkeys. The microbiome of wild birds contains very low levels of poultry pathogens compared to farm raised birds. The microbiomes of wild turkeys may be used to guide development of new ways to control disease in large scale poultry production.

Managing Gut Microbiota through In Ovo Nutrition Influences Early-Life Programming in Broiler Chickens

The chicken gut is the habitat to trillions of microorganisms that affect physiological functions and immune status through metabolic activities and host interaction. Gut microbiota research previously focused on inflammation; however, it is now clear that these microbial communities play an essential role in maintaining normal homeostatic conditions by regulating the immune system. In addition, the microbiota helps reduce and prevent pathogen colonization of the gut via the mechanism of competitive exclusion and the synthesis of bactericidal molecules. Under commercial conditions, newly hatched chicks have access to feed after 36-72 h of hatching due to the hatch window and routine hatchery practices. This delay adversely affects the potential inoculation of the healthy microbiota and impairs the development and maturation of muscle, the immune system, and the gastrointestinal tract (GIT). Modulating the gut microbiota has been proposed as a potential strategy for improving host health and productivity and avoiding undesirable effects on gut health and the immune system. Using early-life programming via in ovo stimulation with probiotics and prebiotics, it may be possible to avoid selected metabolic disorders, poor immunity, and pathogen resistance, which the broiler industry now faces due to commercial hatching and selection pressures imposed by an increasingly demanding market.

Anticoccidial efficacy of Garcinia kola (Heckel H.) against experimental Eimeria tenella infection in chicks

There is a need to advance commercial poultry production to cater to the essential protein needs of an ever-increasing population, however, the rampant occurrence of coccidiosis infection poses a threat to this achievement. This study evaluated the in vivo anticoccidial activities of the extracts and fractions of Garcinia kola against experimental Eimeria tenella infection using broiler chickens as experimental subjects. A total of 40 broiler chicks were experimentally infected with E. tenella and assigned randomly into five groups consisting of eight chicks each. Three days post experimental infection groups I and II were administered orally with tween 80 (0.8%) and Amprolium (30 mg/kg) and served as untreated and treated control groups, respectively whereas Groups III, IV, and V were administered orally with crude methanol extract (CME) at doses of 200, 400 and 600 mg/kg, respectively, for five consecutive days. Daily weight gains were recorded and faecal oocysts per gram (OPG) counts were made by the McMaster Egg counting technique. Blood samples from each experimental group were collected on days 0, 3, 6, and 8 for haematological examination. In the acute toxicity studies, the CME of G. kola did not produce any toxic effect or mortality at doses between 10 and 5000 mg/kg. The CME G. kola was then considered safe and the LD50 was assumed to be > 5000 mg/kg. Graded doses of CME of G. kola considerably (P < 0.05) improved body weight gain and decreased OPG in a dose-depended manner. There was also significant improvement in the Packed Cell Volume (PCV), Red Blood Cell (RBC) and White Blood Cell (WBC) counts upon treatment with the graded doses of CME of G. kola. Besides, G. kola significantly decreased histopathological lesions in the caecum. The results of this study indicates that G. kola may provide beneficial effects against E. tenella-induced coccidiosis in broiler chickens.

Effects of Eimeria tenella Infection on Key Parameters for Feed Efficiency in Broiler Chickens

The purpose of the study was to investigate effects of different inoculation dosages of E. tenella on growth performance, gastrointestinal permeability, oocyst shedding, intestinal morphology, fecal consistency, ileal apparent digestibility, antioxidant capacity, and cecal VFA profile in broiler chickens. Five different dosages (T0: 0, T1: 6250, T2: 12,500, T3: 25,000, and T4: 50,000) of E. tenella oocysts were inoculated via oral gavage to fourteen-day-old broilers. Inoculation of E. tenella linearly increased FCR (p < 0.05), and feed intake was quadratically increased on 6 days post-infection (dpi; p = 0.08) and 7 dpi (p = 0.09). Cecal lesion score of each treatment was T0: 0; T1: 0.39 ± 0.14; T2: 0.93 ± 0.21; T3: 1.25 ± 0.16; and T4: 1.58 ± 0.2. Cecal total VFA production was linearly reduced due to E. tenella infection on 6 dpi (p < 0.01). E. tenella infection deepened cecal crypts depth on 6 dpi (CD; p < 0.05). Gastrointestinal permeability tended to be linearly increased (p = 0.07). E. tenella infection tended to linearly reduce duodenal VH (p = 0.1) and jejunal VH on 9 dpi (p = 0.09). Different dosages of E. tenella modulated the tendency of fecal moisture content and oocyst shedding. Therefore, E. tenella infection impaired feed efficiency and small intestinal health mainly by reducing cecal VFA production and deepening cecal CD in broilers.

Coccidia-Microbiota Interactions and Their Effects on the Host

As a common parasitic disease in animals, coccidiosis substantially affects the health of the host, even in the absence of clinical symptoms and intestinal tract colonization. Gut microbiota is an important part of organisms and is closely related to the parasite and host. Parasitic infections often have adverse effects on the host, and their pathogenic effects are related to the parasite species, parasitic site and host-parasite interactions. Coccidia-microbiota-host interactions represent a complex network in which changes in one link may affect the other two factors. Furthermore, coccidia-microbiota interactions are not well understood and require further research. Here, we discuss the mechanisms by which coccidia interact directly or indirectly with the gut microbiota and the effects on the host. Understanding the mechanisms underlying coccidia-microbiota-host interactions is important to identify new probiotic strategies for the prevention and control of coccidiosis.

Upregulation of gut cathepsin L during Eimeria tenella infection

Coccidiosis is a disease caused by Eimeria, which represents the first parasitic disease in poultry farming. Among them, E. tenella is a virulent species which specifically colonizes the caecum. The inflammatory response to infection is associated to numerous host proteases including cysteine cathepsins that can be deleterious for tissue and innate immunity integrity. Here, germ-free and conventional chickens were used as models to find out whether the microbiota could modify the intestinal expression of host cysteine cathepsins during coccidiosis. The basal caecal peptidase activity primarily relies on host proteases rather than proteases from the commensal flora. While mRNA levels of E. tenella cathepsins B and L remained unchanged in germ-free and conventional broilers, an overall increase in endopeptidase activity of cysteine cathepsins was found in E. tenella-infected caeca in both experimental models (P < 0.005). A significant decrease in avian cystatin C transcription was also observed in infected conventional, but not in infected germ-free broilers. Despite an unchanged mRNA level of avian cathepsin L (CatL), its protein expression raised following infection, in parallel with an increased transcription of antimicrobial β-defensins (AvBD1, AvBD2, AvBD4, AvBD6, and AvBD7). Taken together, data support that host CatL is post-translationally upregulated during E. tenella infection, and thus may be involved in the alteration of the gut proteolytic balance. Furthermore, CatL may participate to inflammation occurring during coccidiosis through its known ability to proteolytically inactivates up-regulated avian β-defensins that are key molecules of innate immunity.