Metagenomic bacterial community profiles of chicken embryo gastrointestinal tract by using T-RFLP analysis

Impacts of coprophagic foraging behaviour on the avian gut microbiome

Avian gut microbial communities are complex and play a fundamental role in regulating biological functions within an individual. Although it is well established that diet can influence the structure and composition of the gut microbiota, foraging behaviour may also play a critical, yet unexplored role in shaping the composition, dynamics, and adaptive potential of avian gut microbiota. In this review, we examine the potential influence of coprophagic foraging behaviour on the establishment and adaptability of wild avian gut microbiomes. Coprophagy involves the ingestion of faeces, sourced from either self (autocoprophagy), conspecific animals (allocoprophagy), or heterospecific animals. Much like faecal transplant therapy, coprophagy may (i) support the establishment of the gut microbiota of young precocial species, (ii) directly and indirectly provide nutritional and energetic requirements, and (iii) represent a mechanism by which birds can rapidly adapt the microbiota to changing environments and diets. However, in certain contexts, coprophagy may also pose risks to wild birds, and their microbiomes, through increased exposure to chemical pollutants, pathogenic microbes, and antibiotic-resistant microbes, with deleterious effects on host health and performance. Given the potentially far-reaching consequences of coprophagy for avian microbiomes, and the dearth of literature directly investigating these links, we have developed a predictive framework for directing future research to understand better when and why wild birds engage in distinct types of coprophagy, and the consequences of this foraging behaviour. There is a need for comprehensive investigation into the influence of coprophagy on avian gut microbiotas and its effects on host health and performance throughout ontogeny and across a range of environmental perturbations. Future behavioural studies combined with metagenomic approaches are needed to provide insights into the function of this poorly understood behaviour.

Interaction Between Cecal Metabolites and Liver Lipid Metabolism Pathways During Induced Molting in Laying Hens

Moult is a normal physiological phenomenon in poultry. Induced molting (IM) is the most widely used and economical molting technique. By inducing moult, the laying hens can grow new feathers during the next laying cycle and improve laying performance. However, the lack of energy supply has a huge impact on both the liver and intestines and acts on the intestines and liver through the “gut-liver axis”. More importantly, lipid metabolism in the liver is closely related to the laying performance of laying hens. Therefore, in this study, cecal metabolites and liver transcriptome data during IM of laying hens at the late stage of laying (stop feeding method) were analyzed together to reveal the regulatory mechanism of “gut-liver axis” affecting the laying performance of laying hens from the perspective of lipid metabolism. Transcriptome analysis revealed that 4,796 genes were obtained, among which 2,784 genes had significant differences (p < 0.05). Forty-nine genes were associated with lipid metabolism, and five core genes (AGPAT2, SGPL1, SPTLC1, PISD, and CYP51A1) were identified by WGCNA. Most of these differential genes are enriched in steroid biosynthesis, cholesterol metabolism, drug metabolism—cytochrome P450, synthesis and degradation of ketone bodies, PPAR signaling pathway, and bile secretion. A total of 96 differential metabolites were obtained by correlating them with metabolome data. Induced moult affects laying performance by regulating genes related to lipid metabolism, and the cecal metabolites associated with these genes are likely to regulate the expression of these genes through the “enterohepatic circulation”. This experiment enriched the theoretical basis of induced moult and provided the basis for prolonging the feeding cycle of laying hens.

Microbiota Analysis of Chickens Raised Under Stressed Conditions

A substantial progress has been made toward understanding stress-associated gut and extraintestinal microbiota. However, a comprehensive understanding of the extraintestinal microbiota of chickens raised under stressed conditions is lacking. In this study, chickens were raised on a wire-floor model to induce stress, and the microbiota in the gut (ceca) and extraintestinal sites (blood, femur, and tibia) were characterized at different ages (1, 17, and 56 days) using 16S rRNA gene microbiota profiling. Open reference OTU picking showed extraintestinal sites had a significantly higher number of unassigned OTUs compared to ceca across all ages of chickens. Extraintestinal sites of all ages, irrespective of body sites, as well as ceca of 1 day-old chickens had significantly lower alpha diversity than ceca of older chickens. Intriguingly, bacterial diversity (alpha and beta) and OTU interaction network analysis showed relatively stable bacterial composition within the extraintestinal sites of chickens regardless of age and sites compared to ceca. Furthermore, assessment using UniFrac distance suggested the gut as a possible source of extraintestinal bacteria. Lastly, LEfSe analysis showed that both commensal and pathogenic bacteria were translocated into the extraintestinal tissues and organs under the stress. Extraintestinal sites have highly abundant novel taxa that need to be further explored. In ovo microbiota colonization and/or translocation of circulating maternal blood microbiota into ovarian follicles might be the source of intestinal and extraintestinal microbiota in 1 day-old chickens. Our comprehensive microbiota data including extraintestinal sites in reference to gut provide unique insights into microbiota of chickens raised under stressed conditions, which may be relevant in other animal species as well.

Topical Application of Adult Cecal Contents to Eggs Transplants Spore-Forming Microbiota but Not Other Members of the Microbiota to Chicks

The intestinal microbiota plays an essential role in the metabolism and immune competence of chickens from the first day after hatching. In modern production systems, chicks are isolated from adult chickens, instead hatching in a clean environment. As a result, chicks are colonized by environmental bacteria, including potential pathogens. There is a need to investigate methods by which chicks can be exposed to a more appropriate microbial community at hatching. Such methods must be easy to apply in a hatchery and produce consistent results. The development of the intestinal microbiota of chicks hatched from eggs sprayed with dilute adult cecal content during incubation was observed at 0, 3, 7, and 14 days posthatching (dph) across two experiments. High-throughput Illumina sequencing was performed for the V4 hypervariable region of the 16S rRNA gene. A topical treatment of dilute adult cecal content was sufficient to transplant spore-forming bacteria such as Lachnospiraceae and Ruminococcaceae However, this treatment was not able to transplant other taxa that are considered to be core elements of the chicken cecal microbiota, such as Bacteroidaceae, Lactobacillaceae, Bifidobacteriaceae, and Burkholderiaceae The topical treatment significantly altered the microbiota of chicks immediately posthatching and accelerated the normal development of the microbiota with earlier colonization by Ruminococcaceae in the cecum and "Candidatus Arthromitus" in the ileum. The effect of the treatment on the cecal microbiota was maximal at 3 dph but diminished over time.IMPORTANCE Over the last 60 years poultry production has intensified in response to increased demand for meat. In modern systems, chicks hatch without contacting chickens and their gut bacteria. Consequently, they are colonized by environmental bacteria that may cause disease. The normal bacteria that live in the gut, or intestinal microbiota, play an important role in the development of the immune system. Therefore, it is essential to find easy ways to expose chicks to the more appropriate bacteria at hatching. This experiment investigated whether spraying eggs with adult cecal contents was sufficient to transfer an adult microbiota to chicks. Our findings show that spore-forming bacteria were transplanted, but other members of the microbiota were not. In this respect, the spray application was partially successful, but the timing of the spray needs to be modified to ensure that more bacteria are transferred.

Early life microbial exposure shapes subsequent animal health

Biosecurity standards and farming practices have profoundly changed the way domestic animals interact with the environment and themselves. Farm intensification processes resemble the lifestyle changes that humans underwent post industrialization, which have been linked to the occurrence of immune-mediated and metabolic disorders. Modern rearing practices reduce maternal and offspring interactions, promote changes in diet, restrict animals indoors, and rely on the use of antibiotics and vaccines to maintain animal health. These practices may hinder the proper colonization of the gastrointestinal tract with commensal organisms that co-evolved with livestock species. The gut microbiota aids nutrient digestion, stimulates immune and intestinal development and maturation, and promotes the competitive exclusion of pathogens. Microbial colonization in early life is critical for host metabolic and immune programming, and disruptions of gut microbial community stability can lead to development of metabolic and immune disorders seen at later stages of life. Identifying how farming practices influence microbial composition and the potential effects on host physiology, metabolism, and disease resistance is necessary to guide intervention strategies to promote beneficial microbial–host interactions, and improve animal health and performance.

Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan

The transgenerational maintenance of symbiotic microbes that benefit host nutrition and health is evolutionarily advantageous. In some vertebrate lineages, coprophagy is used as a strategy for effectively transmitting microbes across generations. However, this strategy has still not been studied in birds. Accordingly, the aim of the present study was to evaluate the role of maternal cecal feces consumption by Japanese rock ptarmigan (Lagopus muta japonica) chicks as a strategy for acquiring essential gut microbes. Both the duration of coprophagy behavior by the chicks and the development process of the chick cecal microbiome (n=20 one- to three-week-old chicks, from three broods) were investigated. In all three broods, coprophagy behavior was only observed from 3 to 18 days of age. Furthermore, there was no significant difference in the number of bacterial operational taxonomic units (OTUs) in 1-week-old chicks (n=651) and adults (n=609), and most of the main OTUs observed in the adults were already present in the 1-week-old chicks. These results indicate that, in this precocial bird species, coprophagy may contribute to the early establishment of cecal bacteria that are essential for food digestion and, thus, chick survival. In fact, Japanese rock ptarmigan chicks consume the same food as their hens from the time of hatching. This behavior may have applications to ex-situ conservation.

Examination of the Expression of Immunity Genes and Bacterial Profiles in the Caecum of Growing Chickens Infected with Salmonella Enteritidis and Fed a Phytobiotic

Simple Summary

Salmonellosis is among the most common infectious poultry diseases that also represent a high risk to human health. The pathological process caused by Salmonella enterica serovar Enteritidis (SE) triggers in the caecum the expression of certain genes, e.g., avian β-defensins (gallinacins), cytokines (interleukins), etc. On the other hand, gut microbiota influences the infection potential of pathogens. The present study aimed at revealing the differential expression of genes associated with the immune system and changes in the bacterial communities in the intestine of growing chickens in response to SE infection. We also tested a feed additive, essential oils-based phytobiotic Intebio, as a potential alternative to antibiotics and showed effects of its administration on the caecal microbiome composition and the expression of some genes related to immunity. The phytobiotic showed its efficiency for application in poultry rearing and production.

Abstract

This study was performed to investigate the differential expression of eight immunity genes and the bacterial profiles in the caecum of growing chickens challenged with Salmonella enterica serovar Enteritidis (SE) at 1 and 23 days post inoculation (dpi) in response to SE infection at 19 days of age and administration of the phytobiotic Intebio. Following infection, the genes CASP6 and IRF7 were upregulated by greater than twofold. Chicks fed Intebio showed at 1 dpi upregulation of AvBD10, IL6, IL8L2, CASP6 and IRF7. At 23 dpi, expression of AvBD11, IL6, IL8L2, CASP6 and IRF7 lowered in the experiment subgroups as compared with the control. Examination of the caecal contents at 1 dpi demonstrated a significant decrease in the microbial biodiversity in the infected subgroup fed normal diet. Bacterial content of Lactobacillus and Bacillus declined, while that of Enterobacteriaceae rose. In the infected subgroup fed Intebio, a pronounced change in composition of the microflora was not observed. In the early infection stages, the phytobiotic seemed to promote response to infection. Subsequently, an earlier suppression of the inflammatory reaction took place in chickens fed Intebio. Thus, use of Intebio as a drug with phytobiotic activity in chickens, including those infected with Salmonella, proved to be promising.

Bacteria and fungi in day-old turkeys vary among companies, collection periods, and breeder flocks

Microbial colonization of the intestinal tract of commercial poultry is highly variable, likely due to the fact that poults and chicks are hatched and raised without exposure to adult birds and their microbiota. In industrial poultry production, it is hypothesized that most of the microbiota is obtained through horizontal transmission from the environment and very little by maternal transmission. The initial gut microbiota will therefore differ between flocks and companies based on environmental conditions at the hatchery. Day-old poults were collected from the hatchery of 2 companies at 3 different time points to monitor the initial colonizing microbiota by sequencing amplicons of marker genes for bacteria, lactic acid bacteria (LAB), fungi, and archaea. Bacterial colonizers were distinct by company (pseudo-F 38.7, P ≤ 0.05) with the predominant bacteria at Company A being clostridia, specifically Clostridium celatum group, C. paraputrificum, and C. tertium. Predominant bacteria at Company B were Enterobacteriaceae, belonging to 2 different groups, one that included Escherichia; Shigella and Salmonella and the other Klebsiella; Enterobacter; and others. The predominant LAB at both companies were Enterococcus faecalis and E. gallinarum, confirmed by sequencing the 16S ribosomal RNA (rRNA) gene of colonies picked from lactobacilli agar plate counts. The predominant fungi were Aspergillus niger and Saccharomyces cerevisiae, with Candida sake or Alterneria sp. in some samples of Company A. Archaeal sequences were detected only in a single poult from Company B. The initial gastrointestinal colonizers of poults vary across company and time, signifying a strong environmental effect on microbiota acquisition. There was an indication of maternal effects in certain breeder flocks from Company B. Further work is necessary to determine how this variability affects microbiota succession and impacts growth and production of the birds.

Performance, gut morphology and microbiology effects of a Bacillus probiotic, avilamycin and their combination in mixed grain broiler diets

1. This study aimed to determine the effect of avilamycin (AGP) and a multi-strain Bacillus probiotic (DFM) on the performance, gut histology and microbiology of broilers fed on a mixed grain diet. 2. A total of 800 chicks were allocated to four treatments: a control diet, control+AGP, control+DFM, or control+AGP+DFM. Bodyweight, feed intake and FCR were measured at d 0, 21 and 42. Samples were taken at d42 to determine villus height (VH), crypt depth (CD) and ratio (VH:CD). Mucosal E. coli and Lactobacilli counts were measured at d42. 3. At d42, DFM and AGP+DFM significantly increased weight over the control, with AGP returning an intermediate value. FCR followed a similar pattern. DFM and AGP+DFM significantly increased VH and CD in all gut sections compared to the control. 4. DFM and AGP+DFM reduced E. coli counts compared to control, with AGP reducing caecal counts only, while Lactobacilli counts were increased. 5. Divergent histology and microbiology between treatments highlight the different modes of action of AGP and DFM for improving broiler growth and feed efficiency.

Applications of In Ovo Technique for the Optimal Development of the Gastrointestinal Tract and the Potential Influence on the Establishment of Its Microbiome in Poultry

As the current poultry production system stands, there is a period of time when newly hatched chicks are prevented from access to feed for approximately 48-72 h. Research has indicated that this delay in feeding may result in decreased growth performance when compared to chicks that are fed immediately post-hatch. To remedy this issue, in ovo methodology may be applied in order to supply the embryo with additional nutrients prior to hatching and those nutrients will continue to be utilized by the chick post-hatch during the fasting period. Furthermore, in ovo injection of various biologics have been researched based on the ability of not only supplying the chick embryo with additional nutrients that would promote improved growth but also compounds that may benefit the future health of the chicken host. Such compounds include various immunostimulants, live beneficial bacteria, prebiotics, and synbiotics. However, it is important to determine the site and age of the in ovo injection for the most productive effects. The primary focus of the current review is to address these two issues [the most effective site(s) and age(s) of in ovo injection] as well as provide the framework for the development of the gastrointestinal tract (GIT) of the chick embryo. Additionally, recent research suggests the colonization of the microbiota in the developing chick may occur during the late stages of embryogenesis. Therefore, we will also discuss the potentials of the in ovo injection method in establishing a healthy and diverse community of microorganisms to colonize the developing GIT that will provide both protection from pathogen invasion and improvement in growth performance to developing chicks.