Interactions Between Parasites and the Bacterial Microbiota of Chickens

Increasing digesta viscosity altered nutrient transporter gene expression and decreased nutrient utilisation in Eimeria-challenged birds

1. Two experiments were conducted, the first was to investigate the effect of increasing digesta viscosity by dietary carboxymethyl cellulose (CMC) on the growth performance and intestinal morphology and characteristics of healthy birds. The second experiment evaluated the impact of increased digesta viscosity in birds during an Eimeria spp. challenge.2. In experiment 1, a corn-soybean meal-based basal diet was supplemented with 0, 10 or 20 g/kg CMC at the expense of cornstarch and offered to seven birds in each of eight replicate cages per diet from d 8 to 22 post hatching.3. Increasing digesta viscosity due to dietary CMC linearly reduced (p < 0.05) body weight (BW) gain and the apparent ileal digestibility of nutrients. The relative lengths of the duodenum, jejunum and ileum linearly increased (p < 0.01) with dietary CMC inclusion.4. In experiment 2, on d 14, 256 broiler chickens were randomly assigned to eight replicate cages in a 2 × 2 factorial arrangement of treatments with two CMC concentrations (0 or 10 g CMC/kg of diet), with or without an Eimeria challenge. On d 15, birds in the challenge groups were orally gavaged with a 1 ml solution containing 25,000, 25,000 or 125,000 oocysts of E. maxima, E. tenella and E. acervulina; or 1% PBS, respectively.5. Increasing digesta viscosity in Eimeria-challenged birds decreased the total tract digestibility of dry matter and gross energy (p < 0.05). The ileal gene expression of glucose transporters was upregulated (p < 0.05) in challenged birds that received the CMC-supplemented diet.6. In summary, increased digesta viscosity induced changes in the expression of nutrient transporter genes and decreased nutrient utilisation in Eimeria-challenged birds.

Acanthocephaliasis by Plagiorhynchus sp. (Acanthocephala:Plagiorhynchidae) associated with necrotic enteritis in quetzals (Pharomachrus mocinno) maintained in captivity

The present report describes a case of acanthocephaliasis associated with necrotic enteritis in quetzals (Pharomachrus mocinno). Three juvenile quetzals exhibited depression, anorexia, ruffled feathers, and sudden death. They were submitted to the laboratory for examination. The birds had hatched and lived in captivity in an aviary in Mexico. Gross lesions observed were hemorrhagic, fibrinoid necrotic enteritis, with acanthocephalans adhered to the intestinal mucosa. The specimens were identified by parasitology, electronic microscopy, and molecular biology as Plagiorhynchus (Prosthorhynchus) sp. Lesions compatible with necrotic enteritis were also confirmed by isolation and genotyping of Clostridium perfringens type E. This is the first report of Plagiorhynchus (Prosthorhynchus) sp. in quetzals in captivity in Mexico. The findings in this manuscript suggest that this parasite could be a predisposing factor for necrotic enteritis as well as a risk component in the breeding programs and survival of this avian species in captivity.

Dynamic response of the intestinal microbiome to Eimeria maxima-induced coccidiosis in chickens

Eimeria maxima is a major cause of coccidiosis in chickens and a key predisposing factor for other economically significant diseases such as necrotic enteritis. However, a detailed understanding of the intestinal microbiome response to E. maxima infection is still lacking. This study aimed to comprehensively investigate the dynamic changes of the intestinal microbiome for 14 days post-infection (dpi) with E. maxima. Bacterial 16S rRNA gene sequencing was performed with the ileal and cecal digesta collected from mock and E. maxima-infected chickens at the prepatent (3 dpi), acute (5 and 7 dpi), and recovery phases (10 and 14 dpi) of infection. Although no notable changes were observed at 3 dpi, significant alterations of the microbiota occurred in both the ileum and cecum at 5 and 7 dpi. By 14 dpi, the intestinal microbiota tended to return to a healthy state. Notably, Lactobacillus was enriched in response to E. maxima infection in both the ileum and cecum, although individual Lactobacillus, Ligilactobacillus, and Limosilactobacillus species varied in the temporal pattern of response. Concurrently, major short-chain fatty acid-producing bacteria, such as Faecalibacterium, were progressively suppressed by E. maxima in the cecum. On the other hand, opportunistic pathogens such as Escherichia, Enterococcus, and Staphylococcus were significantly enriched in the ileum during acute infection.

IMPORTANCE

We have observed for the first time the dynamic response of the intestinal microbiota to Eimeria maxima infection, synchronized with its life cycle. Minimal changes occur in both the ileal and cecal microbiota during early infection, while significant alterations coincide with acute infection and disruption of the intestinal mucosal lining. As animals recover from coccidiosis, the intestinal microbiota largely returns to normal. E. maxima-induced intestinal inflammation likely creates an environment conducive to the growth of aerotolerant anaerobes such as Lactobacillus, as well as facultative anaerobes such as Escherichia, Enterococcus, and Staphylococcus, while suppressing the growth of obligate anaerobes such as short-chain fatty acid-producing bacteria. These findings expand our understanding of the temporal dynamics of the microbiota structure during Eimeria infection and offer insights into the pathogenesis of coccidiosis, supporting the rationale for microbiome-based strategies in the control and prevention of this condition.

Interplay of poultry-microbiome interactions - influencing factors and microbes in poultry infections and metabolic disorders

1. The poultry microbiome and its stability at every point in time, either free range or reared under different farming systems, is affected by several environmental and innate factors. The interaction of the poultry birds with their microbiome, as well as several inherent and extraneous factors contribute to the microbiome dynamics. A poor understanding of this could worsen poultry heath and result in disease/metabolic disorders.2. Many diseased states associated with poultry have been linked to dysbiosis state, where the microbiome experiences some perturbation. Dysbiosis itself is too often downplayed; however, it is considered a disease which could lead to more serious conditions in poultry. The management of interconnected factors by conventional and emerging technologies (sequencing, nanotechnology, robotics, 3D mini-guts) could prove to be indispensable in ensuring poultry health and welfare.3. Findings showed that high-throughput technological advancements enhanced scientific insights into emerging trends surrounding the poultry gut microbiome and ecosystem, the dysbiotic condition, and the dynamic roles of intrinsic and exogenous factors in determining poultry health. Yet, a combination of conventional, -omics based and other techniques further enhance characterisation of key poultry microbiome actors, their mechanisms of action, and roles in maintaining gut homoeostasis and health, in a bid to avert metabolic disorders and infections.4. In conclusion, there is an important interplay of innate, environmental, abiotic and biotic factors impacting on poultry gut microbiome homoeostasis, dysbiosis, and overall health. Associated infections and metabolic disorders can result from the interconnected nature of these factors. Emerging concepts (interkingdom or network signalling and neurotransmitter), and future technologies (mini-gut models, cobots) need to include these interactions to ensure accurate control and outcomes.

Eimeria infections of plateau pika altered the patterns of temporal alterations in gut bacterial communities

Intestinal parasites, such as Eimeria, are common among plateau pika (Ochotona curzoniae). The gut microbiome is an essential driver of the host response to gastrointestinal parasites. However, the effects of intestinal protozoal parasites on the temporal variations in the gut microbiome and behavioral and physiological activities remain unknown. Our study conducted treatments involving experimental feeding of pika with Eimeria oocysts or anticoccidia under laboratory conditions to focus on the parasite-associated alterations in gut bacterial communities, host behavioral activity, physiology, and host-bacteria relationships. The results showed insignificant differences in bacterial community structures among treatments on the basis of Bray-Curtis distance metrics, whereas the patterns of temporal alterations in the bacterial communities were changed by the treatments. Bacterial alpha diversities did not vary with the treatments, and experimental feeding with Eimeria slowed down the decrement rate of alpha diversity. Furthermore, few bacterial members were significantly changed by the treatments-only the genus Ruminococcus and the species Ruminococcus flavefaciens, which were associated with energy metabolism. Experimental feeding with Eimeria modified the temporal variations in the bacterial members, including a lower loss rate of the relative abundance of the dominant families Muribaculaceae and Ruminococcaceae in the group with Eimeria experimental feeding. Moreover, a shifting energy trade-off was suggested by the parasite-induced increments in thyroid hormones (triiodothyronine and tetraiodothyronine) and decrements in exploration behavior in the group with Eimeria feeding. However, we did not detect specific connections between gut bacterial communities and pika behaviors and physiology in terms of energy trade-offs. Further in-depth research is needed to examine the role of Eimeria-modified differences in the gut bacteria of plateau pika.

Interactions between the helminth and intestinal microbiome in smallholder chicken farming systems

Helminth parasite infections are widespread in smallholder farming systems affecting farmers and livestock animals. There are pathogenic parasites that populate the gut of their host and coexist closely with the gut microbiota. The physical and immunological environment of the gut can be modified by parasites and microbiota creating a wide range of interactions. These interactions modify the development of infection, affects overall host health, and can modify the way a host interacts with its bacterial microbiota. In addition, where there is a high worm burden parasites will affect the health of the host and intestinal tract colonization. This review highlights key studies on the interaction between helminth parasites and the intestinal microbiome to understand the relationship between parasitic worm infections and gut microbiome health in chickens. Finally, the review discusses modulations, molecular changes, and the importance of helminth-microbiome interactions for the host.

Eimeria maxima infection impacts the protein utilisation of broiler chicks from 14 to 28 days of age

In floor-raised broilers, coccidiosis is responsible for reducing the use of nutrients, mainly by impairing intestinal tissue function and activating the immune system. Understanding and quantifying how balanced dietary protein (BP) is used when birds are challenged will allow nutritionists to make decisions regarding challenged flocks. This study aimed to determine the effects of Eimeria maxima on broiler performance and body composition, and to calculate changes in the maintenance and efficiency of protein utilisation (Ep). A total of 2 400 male 14-day-old Cobb500 broiler chickens were randomly allotted to ten groups with six replications of 40 birds each, with a 5 × 2 factorial arrangement of treatments. Five levels of BP in reference to digestible lysine (3.6, 7.2, 10.8, 14.4, and 18.0 g/kg) were fed to unchallenged (NCH) and challenged (CH) broilers with 7 × 103E. maxima sporulated oocysts from 14 to 28 days of age. Performance and body deposition were measured using a comparative slaughter technique to compare BP maintenance requirements and Ep. ANOVA followed by a posthoc test was performed to compare the effects of BP levels, challenge, and their interactions. A monomolecular model describing the responses of NCH and CH broilers to BP intake, maintenance, and maximum protein deposition was compared. There were significant interactions between body weight gain and digestible lysine intake among the factors studied. Infection had a negative impact on all variables analysed, proving the efficacy of the challenge. The maintenance did not differ between the CH and NCH groups. Increased levels of dietary BP did not recover the maximum protein deposition in CH broilers. Eimeria maxima significantly reduced Ep by a factor of 0.09 times on Ep compared to the control group. The Eimeria maxima challenge was responsible to modify the use of BP altering the body composition and impairing broilers performance.

Interplay between Eimeria acervulina and Cryptosporidium parvum during In Vitro Infection of a Chicken Macrophage Cell Line (HD11)

BACKGROUND

Eimeria acervulina is a frequent intestinal pathogen of chickens, causing economic impact on the poultry industry. Cryptosporidium parvum is a neglected parasite in chickens. However, because of its zoonotic potential, poultry cryptosporidiosis may pose a risk to public health. Little is known about the parasite-host interactions during coinfection with both parasites. In this study, we investigated the possible interactions during in vitro coinfection of E. acervulina and C. parvum in a chicken macrophage cell line (HD11).

METHODS

HD11 cells were inoculated with E. acervulina and C. parvum sporozoites and incubated 2, 6, 12, 24, and 48 h post infection (hpi). Mono-infections for each parasite were also investigated. Real-time PCR was used to quantify parasite replication. Additionally, macrophage mRNA expression levels of IFN-γ, TNF-α, iNOS, and IL-10 were measured.

RESULTS

For both parasites, multiplication was, in most groups, lower in the coinfection group (COIG) compared with mono-infections. However, at 6 hpi, the number of C. parvum copies was higher in co-infections. Intracellular replication started to decrease from 12 hpi onward, and it was almost undetectable by 48 hpi in all groups. Infections resulted in low expression of all cytokines, except at 48 hpi.

CONCLUSIONS

Infection of avian macrophages with both E. acervulina and C. parvum seemed to hinder intracellular replication for both parasites in comparison to mono-infection. A clear reduction in intracellular parasites from 12 hpi onward details the important role potentially played by macrophages in host control of these parasites.

A meta-analysis of the effect of Eimeria spp. and/or Clostridium perfringens infection on the microbiota of broiler chickens

Coccidiosis in chickens is caused by Eimeria spp. The infection provides a growth advantage to Clostridium perfringens (CP), frequently leading to necrotic enteritis. One approach to alleviate the negative impacts of the diseases is to improve the bacterial composition in chickens, and many experiments investigating chicken enteric health in recent years include the characterization of the bacterial microbiota. This meta-analysis synthesized the data of studies investigating the intestinal microbiota after infection with coccidia and/or CP to provide a basis for future research. Inclusion criteria were that experiments contained a group infected with one or both pathogens and an uninfected control group, the use of 16SrRNA Illumina sequencing and the availability of raw data. A total of 17 studies could be included. Meta-analyses of 3 different data sets were performed: 1 on data of 9 experiments on chickens infected with coccidia only; the second on data of 4 studies on chickens infected with CP only; the third on raw data of 8 experiments with chickens infected with coccidia and CP. The meta-analysis of relative abundance and alpha diversity of the data sets was performed in R using the SIAMCAT and metafor packages. The number of families of interest identified by the analyses of experiments with infection with coccidia only, CP only and the combined infection were 23, 2, and 29, respectively. There was an overlap of 13 families identified by analyses of experiments with infection with coccidia only and of experiments with the combined infections. Machine learning was not able to find a model to predict changes of the microbiota in either 1 of the 3 analyses. Meta-analyses of functional profiles showed a more uniform reaction to the infections with the relative abundance of many pathways significantly altered. Alpha diversity was not affected by infection with either pathogen or the combination. In conclusion, the heterogeneity of these microbiota studies makes recognizing common trends difficult, although it seems that coccidia infection affects the microbiota more than an infection with CP. Future studies should focus on the bacterial functions that are changed due to these infections using metagenome techniques.

Characterization of the eukaryotic microbial communities in the chicken ileum in cage-free and conventional commercial housing systems

The current shift from conventional cage (CC) hen housing facilities towards cage-free (CF) hen housing in the egg industry has left many questions regarding how level of fecal exposure and exposure to other hens may influence the hen intestinal microbiota. In a previous publication we reported differences in the bacterial ileal communities and ileal morphology between hens in CC and CF production environments at a single commercial site. Here, we present the first 18S rRNA gene amplicon sequencing-based characterization of the eukaryotic ileal microbiota of adult layer hens, and their associations with intestinal health parameters and the bacterial microbiota. DNA was extracted from the ileal digesta of hens (n = 32 CC, n = 48 CF) using the Qiagen Powerlyzer Powersoil kit, followed by amplification of the V9 region of the 18S rRNA gene. Paired end sequencing was performed with the Illumina MiSeq platform, and the resulting reads were processed according to the Mothur MiSeq protocol in Mothur v1.43.0. De novo operational taxonomic unit (OTU) clustering was performed in mothur with a 99% similarity threshold, and OTUs were taxonomically classified with the SILVA SSU v138 reference database. OTUs classified as vertebrate, plant, or arthropod were removed, resulting in 3,136,400 high quality reads and 1,370 OTUs. Associations between OTUs and intestinal parameters were calculated using PROC GLIMMIX. PERMANOVA over Bray-Curtis distances revealed differences between CC and CF eukaryotic ileal microbiota at the whole community level, but no OTUs were differentially abundant after correcting for false discovery (P > 0.05; q > 0.1). Kazachstania and Saccharomyces, closely related genera of yeast, represented 77.1% and 9.7% of sequences respectively. Two Kazachstania OTUs and 1 Saccharomycetaceae OTU were positively correlated with intestinal permeability (r² ≥ 0.35). Eimeria accounted for 7.6% of sequences across all samples. Intriguingly, 15 OTUs classified as Eimeria were inversely associated with intestinal permeability (r² ≤ -0.35), suggesting Eimeria may play a more complex role in the microbiota of healthy birds than has been observed in disease challenges.

Meta-Analysis of the Use of Eimeria Lesion Scores and Oocyst Counts in Floor-Pen Studies

The success of treatments for, or prophylaxis of, coccidiosis with classical anticoccidial feed additives or alternative treatments can be measured with a variety of metrics. Three important metrics are body weight or body weight gain (BW or BWG), lesion scores (LS), and oocyst shedding (OS). A meta-analysis of floor-pen experiments was performed to determine if using LS and OS would lead to systematically different assessments compared to the use of BW at the end of the experiment, and to what degree changes in LS and OS are correlated with BW. We also investigated if there were days postinfection on which one could expect larger ratios between untreated control groups and treated groups for LS and OS as an aid to selecting sampling days. A total of 38 experiments from 37 articles in peer-reviewed journals were included. Data sets containing experiments that investigated LS or OS in addition to BW or BWG to assess anticoccidial feed additives or alternative treatment were tested for the effectiveness of the intervention either by univariate meta-analyses for each metric or by robust variance estimation multivariate meta-analysis combining BW with LS or BW with OS. The results did not show evidence that the inclusion of LS and OS in experimental designs to assess the effect of conventional and alternative feed additives with assumed anticoccidial activity systematically changed the conclusions drawn from an experiment, but there was no significant correlation between the LS and OS ratios of untreated and treated groups determined during the experiments with the ratios of the BW at the end of the experiment for each experiment. There was also no discernible relationship between LS or OS ratios and days postinfection.

Influence of Eimeria maxima coccidia infection on gut microbiome diversity and composition of the jejunum and cecum of indigenous chicken

Coccidiosis is an economically significant protozoan disease and an intracellular parasite that significantly impacts poultry production. The gastrointestinal tract microbiota plays a central role in host health and metabolism, and these microbes enhance chickens’ immune systems and nutrient absorption. In this study, we analyzed the abundance and diversity of microbiota of the jejunum and cecum of a dual-purpose indigenous Horro chicken following Eimeria maxima infection. We compared microbial abundance, composition, and diversity at the 4- and 7- days post-infection using 16S rRNA gene sequencing. We obtained, on average, 147,742 and 132,986 high-quality sequences per sample for jejunum and cecum content, respectively. Firmicutes, Proteobacteria, Campilobacterota and Bacteroidota were the major microbial phylum detected in the jejunum content. Firmicutes were the dominant phylum for 4- and 7-days jejunum control groups accounting for (>60% of the sequences). In the infected group Campilobacterota was the dominant phylum in the jejunum (> 24% of sequences) at 4-and 7-days post-infection groups, while Proteobacteria was predominant at 4- and 7-days post-infection of the cecum (> 40% of the sequences). The microbial genus Lactobacillus and Helicobacter were found in the jejunum, while Alistipes, Barnesiella and Faecalibacterium were detected in the cecum. In the jejunum, Helicobacter was dominant at 4 -and-7 days post-infection (≥24%), and Lactobacillus was dominant at 4 -and 7- days in the control group (> 50%). In 4- and 7-days post-infection, Alistipes genus was the more prevalent (> 38%) in the cecum. Thus, clear differences were observed in the bacterial microbiota distribution and abundance between the jejunum and cecum, as well as between infected and control groups for both tissues. The results indicate that chicken intestinal microbial imbalance (dysbiosis) is associated with Eimeria parasite infection and will likely affect the host-microbial non-pathogenic and pathogenic molecular interactions.

Infection with Ascaridia galli Does Not Significantly Alter Intestinal Microbiota and Is Cleared After Changes in the Expression of Cytokines

Because of the trend of cage-free egg production, infections with the nematode Ascaridia galli are receiving increased attention. The aim of this study was to establish a timeline for the influence of A. galli on the expression of key cytokines related to a parasitic immune response, and on the composition of the jejunal microbiota. Twenty-eight male layer-type birds were challenged at 24, 25, and 26 days of age. An additional 28 birds were kept as uninfected controls. Starting on Day 31, three birds of each group were euthanized every week until 8 wk postinfection (PI). The number of larvae isolated from the intestinal wall decreased over time, until no larvae were seen at 7 and 8 wk PI. At 5 wk PI, there was a numerical upregulation of all cytokines (TGF-β, IFN-γ, IL-4, IL-8, IL-10, IL-13) in the infected group, but this change was only statistically significant for IL-13. At this time point, larvae were expected to have developed into adults that would have shed eggs in the feces. However, no adult worms were seen and there was no egg shedding. For the microbiota analysis, there were significant differences in the alpha diversity (Faith's phylogenetic diversity) between challenge and control groups, and the beta diversity analysis showed slight differences between samples, suggesting that the age of the birds was the main reason for the separation of groups. These findings suggest that the upregulation of all cytokines evaluated in Week 5 might be the reason for resolution of the infection. Possible explanations are that a high infection dose and the fact that birds were fed with a more nutritionally dense feed might have contributed to the birds' immune system clearing the infection before the worms were able to reach maturity.

Alleviating effect of dietary supplementation of benzoic acid, Enterococcus faecium and essential oil complex on coccidia and Clostridium perfringens challenge in laying hens

The purpose of this experiment is to explore the effects of dietary supplementation of benzoic acid, Enterococcus faecium, and essential oil complex (BEC) on coccidia and Clostridium perfringens challenge in laying hens. A total of 80 Lohmann gray laying hens (35 wk old) were allocated to 4 treatments in a 2 × 2 factorial arrangement with the main effects of Clostridium perfringens type A (CP) and coccidia challenge (with or without challenge) and 2 BEC levels (0 and 1,000 mg/kg). The total experimental period was 6 wk. The results showed that: the challenge group significantly decreased the laying rate and average daily feed intake (ADFI) of laying hens (P_Challenge < 0.01). The BEC + challenge group significantly increased the laying rate and decreased the feed conversion ratio (FCR) of laying hens (P_BEC < 0.05). The challenge significantly decreased the thickness, strength, and relative weight of eggshell (P_Challenge < 0.05). The BCE + challenge group significantly increased the relative weight and strength of the eggshell (P_BEC < 0.05). The challenge significantly increased the crypt depth of the duodenum, jejunum and ileum, and decreased the villus-to-crypt ratio (V/C) (P_Challenge < 0.01). The BEC + challenge group decreased the crypt depth of the duodenum and jejunum, and increased the V/C of the duodenum (P_BEC < 0.01). The pathological scores of duodenum and jejunum of the challenge group were significantly higher than other groups (P_Challenge < 0.01), while the BEC + challenge group had lower pathological scores of jejunum (P_BEC < 0.01). The challenge significantly decreased the mRNA expression of Occludin, Mucin-2, Zonula occluden-1 (ZO-1) (P_challenge < 0.05); whereas the BEC group significantly increased the expression of Occludin, Mucin-2, and Claudin-1 mRNA (P_BEC < 0.05). The challenge significantly increased the level of interleukin 1β (IL-1β) in the jejunum (P_Challenge < 0.05). Taken together, adding BEC to the diet can improved production performance and egg quality of layers, by protecting intestinal health against Clostridium perfringens type A (CP) and coccidia challenge.

Designing multiepitope-based vaccine against Eimeria from immune mapped protein 1 (IMP-1) antigen using immunoinformatic approach

Drug resistance against coccidiosis has posed a significant threat to chicken welfare and productivity worldwide, putting daunting pressure on the poultry industry to reduce the use of chemoprophylactic drugs and live vaccines in poultry to treat intestinal diseases. Chicken coccidiosis, caused by an apicomplexan parasite of Eimeria spp., is a significant challenge worldwide. Due to the experience of economic loss in production and prevention of the disease, development of cost-effective vaccines or drugs that can stimulate defence against multiple Eimeria species is imperative to control coccidiosis. This study explored Eimeria immune mapped protein-1 (IMP-1) to develop a multiepitope-based vaccine against coccidiosis by identifying antigenic T-cell and B-cell epitope candidates through immunoinformatic techniques. This resulted in the design of 7 CD8⁺, 21 CD4⁺ T-cell epitopes and 6 B-cell epitopes, connected using AAY, GPGPG and KK linkers to form a vaccine construct. A Cholera Toxin B (CTB) adjuvant was attached to the N-terminal of the multiepitope construct to improve the immunogenicity of the vaccine. The designed vaccine was assessed for immunogenicity (8.59968), allergenicity and physiochemical parameters, which revealed the construct molecular weight of 73.25 kDa, theoretical pI of 8.23 and instability index of 33.40. Molecular docking simulation of vaccine with TLR-5 with binding affinity of - 151.893 kcal/mol revealed good structural interaction and stability of protein structure of vaccine construct. The designed vaccine predicts the induction of immunity and boosted host's immune system through production of antibodies and cytokines, vital in hindering surface entry of parasites into host. This is a very important step in vaccine development though further experimental study is still required to validate these results.

Metabarcoding options to study eukaryotic endoparasites of birds

There is growing interest in the study of avian endoparasite communities, and metabarcoding is a promising approach to complement more conventional or targeted methods. In the case of eukaryotic endoparasites, phylogenetic diversity is extreme, with parasites from 4 kingdoms and 11 phyla documented in birds. We addressed this challenge by comparing different primer sets across 16 samples from 5 bird species. Samples consisted of blood, feces, and controlled mixes with known proportions of bird and nematode DNA. Illumina sequencing revealed that a 28S primer set used in combination with a custom blocking primer allowed detection of various plasmodiid parasites and filarioid nematodes in the blood, coccidia in the feces, as well as two potentially pathogenic fungal groups. When tested on the controlled DNA mixes, these primers also increased the proportion of nematode DNA by over an order of magnitude. An 18S primer set, originally designed to exclude metazoan sequences, was the most effective at reducing the relative number of avian DNA sequences and was the only one to detect Trypanosoma in the blood. Expectedly, however, it did not allow nematode detection and also failed to detect avian malaria parasites. This study shows that a 28S set including a blocking primer allows detection of several major and very diverse bird parasite clades, while reliable amplification of all major parasite groups may require a combination of markers. It helps clarify options for bird parasite metabarcoding, according to priorities in terms of the endoparasite clades and the ecological questions researchers wish to focus on.

Understanding the interactions between Eimeria infection and gut microbiota, towards the control of chicken coccidiosis: a review

The gastrointestinal tract in poultry harbours a diverse microbial community that serves a crucial role in digestion and protection. Disruption of the gut environment due to Eimeria spp. parasite infection causes an imbalance in intestinal homeostasis, driving the increment of pathogens such as Clostridium species. Coccidiosis infection affects the composition and integrity of gut microbiota, resulting in elevated susceptibility to diseases that pose a serious threat to the overall health and productivity of chickens. Anticoccidial drugs have proven effective in curbing coccidiosis but with concerning drawbacks like drug resistance and drug residues in meat. The exploration of natural alternative strategies such as probiotics and phytochemicals is significant in controlling coccidiosis through modification and restoration of gut microbiota, without inducing drug resistance. Understanding the interaction between Eimeria parasites and gut microbiota is crucial for the control and prevention of coccidiosis, and the development of novel alternative treatments.

A survey of coccidia and nematodes in pastured poultry in the state of Georgia

The aim of this study was to evaluate and quantify the parasitological challenge in pastured poultry production in the state of Georgia. Over the course of one year, fecal samples from six turkey flocks, ten broiler flocks and 13 layer flocks were collected on a pastured farm in two-week intervals to determine counts of Eimeria oocysts and nematode eggs. Average coccidia counts were 10,198 oocysts per gram of feces (OPG) in broiler flocks, 1,470 OPG in layer flocks and 695 OPG in turkey flocks. The means in broiler and turkey flocks were higher at their first week on pasture. Counts in broilers and layers were significantly higher in spring than in winter and summer. Coccidia counts in broilers were lower than published numbers in conventionally reared poultry, indicating the rotation system of the pastures might effectively reduce the infection pressure. Next-generation sequencing of PCR products showed the presence of most described Eimeria spp. in broilers, layers, and turkeys. In addition, Operational Taxonomic Units (OTUs) x, y and z were found. The frequency of species was similar for broilers and layers, with the exception that Eimeria praecox and OTU z were more common in layers. In layer flocks, the average count of roundworm eggs per gram of feces (EPG) was 509 EPG with 80% of the samples being positive. The mean counts had no clear pattern related to age. There was an increase of EPG with the increase of temperatures during spring and summer with the peak at mid-fall. Worm eggs from laying hens were identified as A. galli. The seasonal differences suggest that higher temperatures might result in an increase of egg survival and sporulation in the environment.

Challenges in Vaccinating Layer Hens against Salmonella Typhimurium

Salmonella Typhimurium is among the most common causes of bacterial foodborne gastrointestinal disease in humans. Food items containing raw or undercooked eggs are frequently identified during traceback investigation as the source of the bacteria. Layer hens can become persistently infected with Salmonella Typhimurium and intermittently shed the bacteria over the course of their productive lifetime. Eggs laid in a contaminated environment are at risk of potential exposure to bacteria. Thus, mitigating the bacterial load on farms aids in the protection of the food supply chain. Layer hen producers use a multifaceted approach for reducing Salmonella on farms, including the all-in-all-out management strategy, strict biosecurity, sanitization, and vaccination. The use of live attenuated Salmonella vaccines is favored because they elicit a broader host immune response than killed or inactivated vaccines that have been demonstrated to provide cross-protection against multiple serovars. Depending on the vaccine, two to three doses of Salmonella Typhimurium vaccines are generally administered to layer hens within the first few weeks. The productive life of a layer hen, however, can exceed 70 weeks and it is unclear whether current vaccination regimens are effective for that extended period. The objective of this review is to highlight layer hen specific challenges that may affect vaccine efficacy.

Associations between phenotypic characteristics and clinical parameters of broilers and intestinal microbial development throughout a production cycle: A field study

Disturbances in intestinal health are a common problem affecting commercial broiler chickens worldwide. Several studies have revealed associations between health, production performance, and intestinal microbiota. This study aimed to describe the development of the intestinal microbiota of broilers within a production cycle to evaluate to what extent clinical parameters and phenotypic characteristics can explain the intestinal microbiota variation. Of four well-performing flocks within two farms, the cecal content was collected of nine broilers at 0, 2, 4, or 5, 7, 11, or 12, 14, 21, 28, 35, and 40 days of the production cycle. In total, 342 samples were analyzed using 16S ribosomal RNA gene amplicon sequencing. Variables as macroscopic gut abnormalities, gut lesions, age, individual body weight, sex, footpad integrity, the color of ceca, and foam in cecal content were determined. Ileum tissue was collected for histological quantification of villus length and crypt depth. Flock infection levels of the intestinal disease coccidiosis were measured in pooled feces from the poultry house. Increases in phylogenetic diversity were observed from hatch until day 21 of age. Constrained multivariate analysis indicated that age, farm, body weight, ileum crypt depth, cecal color, and the coccidiosis lesion score were important variables to describe the variation in cecal microbiota. These results contribute to determining relevant variables in flocks that may be indicative of the intestinal microbiota composition. Moreover, this knowledge increases the awareness of interactions between the intestinal microbiota and broiler health as well as their relative importance.

Influence of Eimeria spp. Infection on Chicken Jejunal Microbiota and the Efficacy of Two Alternative Products Against the Infection

Eimeria spp. are important intestinal pathogens of chickens (Gallus gallus domesticus). Anticoccidial feed additives, chemicals, and ionophores have traditionally been used to control Eimeria infections in broiler production. Thus, the trend toward antibiotic-free and organic production requires new approaches to coccidiosis prevention. Two not mutually exclusive methods are the use of plant extracts with antiparasitic activity and manipulation of the intestinal microbiota by pre- and probiotics. In the present study, birds were inoculated with a combination of Eimeria acervulina, Eimeria maxima, and Eimeria tenella. We profiled the jejunal microbiome at multiple time points postinfection to investigate the changes in jejunum microbiota and to identify the time point of the maximum difference between infected and noninfected birds. Additionally, we assessed the anticoccidial effects of two anecdotal treatment methods, green tea and apple cider vinegar, as well as amprolium. Green tea and apple cider vinegar had no effect on oocyst shedding, but green tea reduced the mild unspecific lesions in coccidia-infected birds; there was no influence on unspecific lesions in uninfected controls. Jejunal contents were collected on the day of the infection and 1, 2, 4, 6, 10, and 14 days postinfection (dpi) for investigation of the intestinal microbiota by 16S ribosomal (r)RNA gene sequencing. Comparison of the untreated-uninfected and the untreated-infected groups showed a maximum community dissimilarity of 10 dpi. From 4 days after infection, Clostridiales were significantly enriched at the expense of Lactobacillales in infected compared with uninfected birds. Interestingly, treatment with green tea prevented proliferation of Clostridiales induced by the coccidia and increased the relative abundance of Melainabacteria.

Varying starch to fat ratios in pelleted diets: I. Effects on nutrient digestibility and production performance in Eimeria-challenged broiler chickens

1. The hypothesis was that a diet with a high starch to fat ratio (HS) impairs nutrient digestibility and growth performance, as compared to a diet with a low starch to fat ratio (LS) in Eimeria-challenged broilers. From days 10 to 29, 12 replicate pens of birds were given isocaloric and isonitrogenous steam-pelleted diets with either HS or LS, by replacing the wheat starch in one diet by a mixture of rapeseed oil and inert sand in the other. On d 17, a 10-fold dose of live vaccine strains of Eimeria spp. was administered via drinking water. Ileal samples were collected on days 16 and 29. 2. Starch content in the ileum tended to be higher on d 16 and was significantly higher on d 29 in the HS group. 3. The HS diet did not induce exceedingly high levels of starch in the ileum, suggesting there was no starch overload in the gut. Ileal starch digestibility was improved with increasing dietary starch level from 23% to 45%. This demonstrated the capacity of the broiler chicken to digest high levels of starch regardless of Eimeria spp. infection. Ileal energy digestibility was not affected by the treatments. 4. Weight gain did not differ between treatments; however, birds fed the LS diet were less efficient in feed conversion as compared to those fed the HS diet. 5. The use of isolated starch and the unintended higher extent of starch gelatinisation in the HS diet may have contributed to the higher starch digestibility in birds given the HS diet. Thus, the hypothesis that high ratios of starch to fat in pelleted diets may impair starch digestibility and production performance in Eimeria-challenged broiler chickens was not verified. Further work is required to clarify this research question, taking into consideration the physical form of starch source and the potentially confounding role of feed processing on starch availability.

Modulation of the intestinal microbiota of broilers supplemented with monensin or functional oils in response to challenge by Eimeria spp

The objective of this study was to evaluate the effect of supplementation with 100ppm sodium monensin or 0.15% of a blend of functional oils (cashew nut oil + castor oil) on the intestinal microbiota of broilers challenged with three different Eimeria spp. The challenge was accomplished by inoculating broiler chicks with sporulated oocysts of Eimeria tenella, Eimeria acervulina, and Eimeria maxima via oral gavage. A total of 864, day-old male broiler chicks (Cobb) were randomly assigned to six treatments (eight pens/treatment; 18 broilers/pen) in a 3 × 2 factorial arrangement, composed of three additives (control, monensin or blend), with or without Eimeria challenge. Intestinal contents was collected at 28 days of age for microbiota analysis by sequencing 16s rRNA in V3 and V4 regions using the Illumina MiSeq platform. Taxonomy was assigned through the SILVA database version 132, using the QIIME 2 software version 2019.1. No treatment effects (p > 0.05) were observed in the microbial richness at the family level estimated by Chao1 and the biodiversity assessed by Simpson’s index, except for Shannon's index (p < 0.05). The intestinal microbiota was dominated by members of the order Clostridiales and Lactobacillales, followed by the families Ruminococcaceae, Bacteroidaceae, and Lactobacillaceae, regardless of treatment. When the controls were compared, in the challenged control group there was an increase in Erysipelotrichaceae, Lactobacillaceae, Bacteroidaceae, Streptococcaceae, and Peptostreptococcaceae, and a decrease in Ruminococcaceae. Similar results were found for a challenged group that received monensin, while the blend partially mitigated this variation. Therefore, the blend alleviated the impact of coccidiosis challenge on the microbiome of broilers compared to monensin.

Microbiome and pathogen interaction with the immune system

The intestinal tract harbors a diverse community of microbes that have co-evolved with the host immune system. Although many of these microbes execute functions that are critical for host physiology, the host immune system must control the microbial community so that the dynamics of this interdependent relationship is maintained. To facilitate host homeostasis, the immune system ensures that the microbial load is tolerated, but anatomically contained, while remaining reactive to microbial invasion. Although the microbiota is required for intestinal immune development, immune responses regulate the structure and composition of the intestinal microbiota by evolving unique immune adaptations that manage this high-bacterial load. The immune mechanisms work together to ensure that commensal bacteria rarely breach the intestinal barrier and that any that do invade should be killed rapidly to prevent penetration to systemic sites. The communication between microbiota and the immune system is mediated by the interaction of bacterial components with pattern recognition receptors expressed by intestinal epithelium and various antigen-presenting cells resulting in activation of both innate and adaptive immune responses. Interaction between the microbial community and host plays a crucial role in the mucosal homeostasis and health status of the host. In addition to providing a home to numerous microbial inhabitants, the intestinal tract is an active immunological organ, with more resident immune cells than anywhere else in the body, organized in lymphoid structures called Peyer's patches and isolated lymphoid follicles such as the cecal tonsils. Macrophages, dendritic cells, various subsets of T cells, B cells and the secretory immunoglobulin A (IgA) they produce, all contribute to the generation of a proper immune response to invading pathogens while keeping the resident microbial community in check without generating an overt inflammatory response to it. IgA-producing plasma cells, intraepithelial lymphocytes, and γδT cell receptor-expressing T cells are lymphocytes that are uniquely present in the mucosa. In addition, of the γδT cells in the intestinal lamina propria, there are significant numbers of IL-17-producing T cells and regulatory T cells. The accumulation and function of these mucosal leukocytes are regulated by the presence of intestinal microbiota, which regulate these immune cells and enhance the mucosal barrier function allowing the host to mount robust immune responses against invading pathogens, and simultaneously maintains immune homeostasis.

The similarity of the effect of carbohydrase or prebiotic supplementation in broilers aged 21 days, fed mixed cereal diets and challenged with coccidiosis infection

The aim of this study was to investigate the effect on growth performance and nutrient utilisation when supplementing diets deficient in energy and protein with carbohydrase enzymes or xylo-oligosaccharide in broilers challenged with coccidia. 960 Ross 308 broilers were used in this 21-day study. The treatments were arranged into a 2×4 factorial with 2 challenge states (challenged and non-challenged) and 4 different additive types (control, xylanase alone, xylanase and β-glucanase mixture and xylo-oligosaccharide). On day 14, the challenged group received 12× the recommended dose of coccidiosis vaccine while the non-challenged group received a sham treatment of water only. The birds and feed were weighed on days 0, 14 and 21. On day 21, two birds per pen were euthanized, the caeca were removed and the contents collected for short chain fatty acid analysis. Six more birds per pen were euthanized and ileal digesta were collected and pooled per pen for nutrient digestibility analysis. Feed intake was greater (P < 0.05) on days 14 and 21 when xylo-oligosaccharide was included in the diet compared to the xylanase and β-glucanase mixture in birds challenged with coccidiosis. Including xylo-oligosaccharide in the diet improved (P < 0.05) the digestibility of nitrogen and supplementing diets with the xylanase and β-glucanase mixture improved (P < 0.05) the digestibility of several amino acids. The concentration of arabinose and xylose was (P < 0.001) greater when broiler diets were supplemented with carbohydrase enzymes or xylo-oligosaccharide compared to the control. Although there was an increase in short chain fatty acid production due to the addition of carbohydrase enzymes or xylo-oligosaccharide, there was no additive effect on the %G+C profile of caecal bacteria however there was a negative effect of coccidiosis. In conclusion, the similarity in the response to carbohydrase enzymes or xylo-oligosaccharide supplementation illustrates that the hydrolysis products from carbohydrase activity may have prebiotic like effects.

Take care of the environment: housing conditions affect the interplay of nutritional interventions and intestinal microbiota in broiler chickens

Background

The intestinal microbiota is shaped by many interactions between microorganisms, host, diet, and the environment. Exposure to microorganisms present in the environment, and exchange of microorganisms between hosts sharing the same environment, can influence intestinal microbiota of individuals, but how this affects microbiota studies is poorly understood. We investigated the effects of experimental housing circumstances on intestinal microbiota composition in broiler chickens, and how these effects may influence the capacity to determine diet related effects in a nutrition experiment. A cross-sectional experiment was conducted simultaneously in a feed research facility with mesh panels between pens (Housing condition 1, H1), in an extensively cleaned stable with floor pens with solid wooden panels (H2), and in isolators (H3). In H1 and H2 different distances between pens were created to assess gut microbiota exchange between pens. Feed with and without a blend of medium-chain fatty acids (MCFA) was used to create differences in cecal microbiota between pens or isolators within the same housing condition. Male one-day-old Ross broiler chickens (n = 370) were randomly distributed across H1, H2, and H3. After 35 days cecal microbiota composition was assessed by 16S ribosomal RNA gene amplicon sequencing. Metabolic functioning of cecal content was assessed based on high-performance liquid chromatography.

Results

Microbial alpha diversity was not affected in broilers fed +MCFA in H1 but was increased in H2 and H3. Based on weighted UniFrac distances, the nutritional intervention explained 10%, whereas housing condition explained 28% of cecal microbiota variation between all broilers. The effect size of the nutritional intervention varied within housing conditions between 11, 27, and 13% for H1, H2, and H3. Furthermore, performance and metabolic output were significantly different between housing conditions. The distance between pens within H1 and H2 did not influence the percentage of shared genera or operational taxonomic units (OTUs).

Conclusions

The cecal microbiota of broilers was modifiable by a nutritional intervention, but the housing condition affected microbiota composition and functionality stronger than the diet intervention. Consequently, for interpretation of intestinal microbiota studies in poultry it is essential to be aware of the potentially large impact of housing conditions on the obtained results.

Electronic supplementary material

The online version of this article (10.1186/s42523-019-0009-z) contains supplementary material, which is available to authorized users.

Responses of broiler chickens to Eimeria challenge when fed a nucleotide-rich yeast extract

Nucleotide-rich yeast extract (YN) was investigated for effects on growth performance, jejunal physiology, and cecal microbial activity in Eimeria-challenged broiler chickens. A total of 360-day-old male chicks (Ross × Ross 708) were placed on floor pens and provided a corn-soybean meal-based diet without or with YN (500 g/MT; n = 12). On d 10, 6 replicates per diet were orally administered with 1 mL of E. acervulina and E. maxima sporulated oocysts and the rest (non-challenged control) were administered with 1 mL of distilled water. On d 15, 5 birds/pen were then necropsied for intestinal lesion scores, histomorphology and cecal digesta pH, short chain fatty acids (SCFA), and microbial community using Illumina Miseq platform. Supplemental YN improved (P = 0.01) Feed conversion ratio (FCR) during the prechallenge phase (d 0 to 10). In the postchallenge period (d 11 to 15), Eimeria depressed (P < 0.05) Body weight gain (BWG) relative to non-challenged birds, whereas YN-fed birds had a higher (P = 0.05) BWG compared to that of non-YN-fed birds. There was an interaction between YN and Eimeria on jejunal villi height (VH) (P = 0.001) and expression of cationic amino acid transporter 1(CAT1) (P = 0.04). Specifically, in the absence of Eimeria, YN-fed birds had a shorter VH (892 vs. 1,020 μm) relative to that of control but longer VH (533 vs. 447 μm) in the presence of Eimeria. With respect to CAT1, YN-fed birds had a higher (1.65 vs. 0.78) expression when subjected to Eimeria than when not challenged. Independently, Eimeria decreased (P < 0.01) the jejunal expression of maltase, Na glucose transporter 1 and occludin genes, ceca digesta abundance of genus Clostridium cluster XlVa and Oscillibacter but increased (P < 0.01) jejunal proliferating cell nuclear antigen and interleukin 10. Interaction between YN and Eimeria was observed for ceca digesta pH (P = 0.04) and total SCFA (P = 0.01) such that YN increased SCFA in the absence of Eimeria but reduced SCFA and increased pH in the presence of Eimeria. In summary, Eimeria impaired performance and gut function and shifted gut microbiome; YN improved performance independently, attenuated Eimeria damage on indices of gut function, and modulated cecal microbiome.