Microbial ecology shifts in the ileum of broilers during feed withdrawal and dietary manipulations

Effect of dietary supplementation with algae extracts on growth performance and caecal microbiota of broiler chickens

1. The objective of this study was to test the dose response of dietary supplementation with algae extracts rich in marine-sulphated polysaccharides (MSP1 and MSP2) on the growing performance, body composition at slaughter and caecal microbiota of broiler chickens.2. Male broiler Ross 308 chicks 1-d-old were distributed into eight groups, a control group (unsupplemented), four groups supplemented with increasing doses of algae extract MSP1 (40, 81, 121 and 162 g/ton feed) and three groups supplemented with increasing doses of algae extract MSP2 (40, 81 and 162 g/ton feed). Each group comprised six pens of 56 chickens.3. All chickens were reared under challenging conditions, i.e. high rearing density of 42 kg/m2, fed growing and finishing diets containing, palm oil, rye and high levels of wheat and subjected to short daily fasting periods. The growth performance was recorded during rearing. At 10, 22 and 31 d of age, 12 chickens per group were euthanised to collect the caecal contents and determine microbiota composition and short-chain fatty acid levels. At d 35, the quality of litter and the condition of feathers, footpads and tarsals were scored. At d 36, 7 chickens per pen were slaughtered under commercial conditions to determine carcass composition and breast meat quality (ultimate pH and colour).4. Algal extract MSP1 increased the weight of the caeca and butyrate concentration in the caeca at d 22 (p ≤ 0.05). It increased the ultimate pH of breast fillet measured after slaughter at d 36 (p ≤ 0.05). Moreover, the group receiving 162 g/t MSP1 had a more diverse microbiota at d22. However, algal extract MSP2 had negligible effect on the different measured parameters.

Phytogenic Blend Improves Intestinal Health and Reduces Obesity, Diabetes, Cholesterol and Cancers: A Path toward Customised Supplementation

Poultry production is among the most challenging industries for pathogen control. High animal density and abundance of faecal material demand strict biosecurity measures and continual vigilance in monitoring animal health parameters. Despite this vigilance, dealing with disease outbreaks is a part of farmers’ routines. Phytogenic feed additives comprised of herbs, spices, essential oils, and oleoresins have potent antimicrobial and anti-inflammatory actions. Related studies are gaining substantial interest in human and animal health worldwide. In this study, a commercial blend phytogenic feed additive was supplemented to layers in an industrial free-range production system with 20,000 birds in both control and treatment groups. At the end of the trial, the ileum tissue was sampled for RNAseq transcriptomic analysis to study the host reaction to the supplement. Phytogenic supplement significantly inhibited four cholesterol-related pathways and reduced the Arteriosclerosis disease category towards improved cardiovascular health. The supplemented birds exhibited reduced disease susceptibility for 26 cancer categories with p-values in the range from 5.23 × 10⁻⁴ to 1.02 × 10⁻²⁵. Major metabolic shifts in Lipid metabolism in combination with Carbohydrate metabolism have resulted in a decrease in the Obesity category, altering the ratio of fat and carbohydrate metabolism toward lower fat storage.

Microbiota and Transcriptomic Effects of an Essential Oil Blend and Its Delivery Route Compared to an Antibiotic Growth Promoter in Broiler Chickens

This study evaluated the effect of the delivery of a commercial essential oil blend containing the phytonutrients star anise, cinnamon, rosemary, and thyme oil (via different routes) on broiler chickens’ ileal and ceca microbiota and liver transcriptome compared to an antibiotic growth promoter. Eggs were incubated and allocated into three groups: non-injected, in ovo saline, and in ovo essential oil. On day 18 of incubation, 0.2 mL of essential oil in saline (dilution ratio of 2:1) or saline alone was injected into the amnion. At hatch, chicks were assigned to post-hatch treatment combinations: (A) a negative control (corn-wheat-soybean diet), (B) in-feed antibiotics, (C) in-water essential oil (250 mL/1000 L of drinking water), (D) in ovo saline, (E) in ovo essential oil, and (F) in ovo essential oil plus in-water essential oil in eight replicate cages (six birds/cage) and raised for 28 days. On days 21 and 28, one and two birds per cage were slaughtered, respectively, to collect gut content and liver tissues for further analysis. Alpha and beta diversity differed significantly between ileal and ceca samples but not between treatment groups. In-feed antibiotic treatment significantly increased the proportion of specific bacteria in the family Lachnospiraceae while reducing the proportion of bacteria in the genus Christensenellaceae in the ceca, compared to other treatments. Sex-controlled differential expression of genes related to cell signaling and tight junctions were recorded. This study provides data that could guide the use of these feed additives and a foundation for further research.

Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance

Maintenance of "gut health" is considered a priority in commercial chicken farms, although a precise definition of what constitutes gut health and how to evaluate it is still lacking. In research settings, monitoring of gut microbiota has gained great attention as shifts in microbial community composition have been associated with gut health and productive performance. However, microbial signatures associated with productivity remain elusive because of the high variability of the microbiota of individual birds resulting in multiple and sometimes contradictory profiles associated with poor or high performance. The high costs associated with the testing and the need for the terminal sampling of a large number of birds for the collection of gut contents also make this tool of limited use in commercial settings. This review highlights the existing literature on the chicken digestive system and associated microbiota; factors affecting the gut microbiota and emergence of the major chicken enteric diseases coccidiosis and necrotic enteritis; methods to evaluate gut health and their association with performance; main issues in investigating chicken microbial populations; and the relationship of microbial profiles and production outcomes. Emphasis is given to emerging noninvasive and easy-to-collect sampling methods that could be used to monitor gut health and microbiological changes in commercial flocks.

The Microbiota-Gut-Brain Axis During Heat Stress in Chickens: A Review

Heat stress is a global issue for the poultry industries with substantial annual economic losses and threats to bird health and welfare. When chickens are exposed to high ambient temperatures, like other species they undergo multiple physiological alterations, including behavioral changes, such as cessation of feeding, initiation of a stress signaling cascade, and intestinal immune, and inflammatory responses. The brain and gut are connected and participate in bidirectional communication via the nervous and humoral systems, this network collectively known as the gut-brain axis. Moreover, heat stress not only induces hyperthermia and oxidative stress at the gut epithelium, leading to impaired permeability and then susceptibility to infection and inflammation, but also alters the composition and abundance of the microbiome. The gut microflora, primarily via bacterially derived metabolites and hormones and neurotransmitters, also communicate via similar pathways to regulate host metabolic homeostasis, health, and behavior. Thus, it stands to reason that reshaping the composition of the gut microbiota will impact intestinal health and modulate host brain circuits via multiple reinforcing and complementary mechanisms. In this review, we describe the structure and function of the microbiota-gut-brain axis, with an emphasis on physiological changes that occur in heat-stressed poultry.

Recent Advances in Understanding the Influence of Zinc, Copper, and Manganese on the Gastrointestinal Environment of Pigs and Poultry

Simple Summary

Pigs and poultry, similar to humans, need regular consumption of zinc, copper, and manganese for normal functioning. To ensure adequate dietary intake, and prevent deficiency, their diets are supplemented with sufficient, often excessive, levels of these minerals or even at higher levels, which have been associated with improvements in their health and/or growth. However, if provided in excess, mineral quantities beyond those required are simply excreted from the animal, which is associated with negative consequences for the environment and even the development of antimicrobial resistance. Therefore, it is of great interest to better understand the dynamics of zinc, copper, and manganese in the intestine of pigs and poultry following consumption of supplemented diets, and how the requirements and benefits related to these minerals can be optimized and negative impacts minimized. The intestine of pigs and poultry contains vast numbers of microorganisms, notably bacteria, that continually interact with, and influence, their host. This review explores the influence of zinc, copper, and manganese on these interactions and how novel forms of these minerals have the potential to maximize their delivery and benefits, while limiting any negative consequences.

Abstract

Zinc, copper, and manganese are prominent essential trace (or micro) minerals, being required in small, but adequate, amounts by pigs and poultry for normal biological functioning. Feed is a source of trace minerals for pigs and poultry but variable bioavailability in typical feed ingredients means that supplementation with low-cost oxides and sulphates has become common practice. Such trace mineral supplementation often provides significant ‘safety margins’, while copper and zinc have been supplemented at supra-nutritional (or pharmacological) levels to improve health and/or growth performance. Regulatory mechanisms ensure that much of this oversupply is excreted by the host into the environment, which can be toxic to plants and microorganisms or promote antimicrobial resistance in microbes, and thus supplying trace minerals more precisely to pigs and poultry is necessary. The gastrointestinal tract is thus central to the maintenance of trace mineral homeostasis and the provision of supra-nutritional or pharmacological levels is associated with modification of the gut environment, such as the microbiome. This review, therefore, considers recent advances in understanding the influence of zinc, copper, and manganese on the gastrointestinal environment of pigs and poultry, including more novel, alternative sources seeking to maintain supra-nutritional benefits with minimal environmental impact.

Effects of heat stress on the gut health of poultry

Stress is a biological adaptive response to restore homeostasis, and occurs in every animal production system, due to the multitude of stressors present in every farm. Heat stress is one of the most common environmental challenges to poultry worldwide. It has been extensively demonstrated that heat stress negatively impacts the health, welfare, and productivity of broilers and laying hens. However, basic mechanisms associated with the reported effects of heat stress are still not fully understood. The adaptive response of poultry to a heat stress situation is complex and intricate in nature, and it includes effects on the intestinal tract. This review offers an objective overview of the scientific evidence available on the effects of the heat stress response on different facets of the intestinal tract of poultry, including its physiology, integrity, immunology, and microbiota. Although a lot of knowledge has been generated, many gaps persist. The development of standardized models is crucial to be able to better compare and extrapolate results. By better understanding how the intestinal tract is affected in birds subjected to heat stress conditions, more targeted interventions can be developed and applied.

Effects of Bacillus subtilis and coccidial vaccination on cecal microbial diversity and composition of Eimeria-challenged male broilers

In a companion study, the effects of dietary antibiotic alternative and coccidial vaccination on the growth performance of male broilers have been reported. In this paper, the effects of dietary probiotics and coccidial vaccination on diversity and composition of cecal microbiota were investigated using a 3 (diets) × 2 (vaccinated or non-vaccinated) factorial setting of treatments. Three diets, including a corn and soybean-meal control diet, an antibiotic diet (a control diet supplemented with bacitracin and salinomycin), and a probiotic diet (a control diet supplemented with Bacillus subtilis) were provided to broiler chicken from day 0 to 42. To simulate an Eimeria challenge in the field, all chicks were gavaged with a 20× dose of commercial coccidial vaccine containing live Eimeria oocysts on day 14. Cecal contents were collected on day 42. High-throughput sequencing of the 16S rRNA gene was used to determine microbial diversity and composition. Coccidial vaccination to broilers reduced bacterial diversity (Shannon index) of the cecal microbiota. There was a significant interaction between the dietary additive and coccidial vaccination on the observed bacterial species number. Diets supplemented with B. subtilis increased bacterial species of non-vaccinated broilers but decreased bacterial species of vaccinated broilers. In contrast, diets supplemented with antibiotics reduced bacterial species of broilers from both groups. Interactions between dietary additive and coccidial vaccination were also observed on microbial composition. Vaccinated broilers fed the B. subtilis diet exhibited the lowest Firmicutes percentage and highest Bacteroidetes percentage within the microbial community. In addition, vaccinated broilers fed the B. subtilis diet exhibited the highest Rikenella microfusus percentage. From this study, the coccidial vaccination on the day of hatch reduced the microbial diversity of broilers at a later age. The inclusion of B. subtilis-probiotics in the feed of vaccinated broilers may reduce microbial diversity in cecal content by increasing the proportion of a predominant bacterial species, R. microfusus, in the microbial community.

Host and Environmental Factors Affecting the Intestinal Microbiota in Chickens

The initial development of intestinal microbiota in poultry plays an important role in production performance, overall health and resistance against microbial infections. Multiplexed sequencing of 16S ribosomal RNA gene amplicons is often used in studies, such as feed intervention or antimicrobial drug trials, to determine corresponding effects on the composition of intestinal microbiota. However, considerable variation of intestinal microbiota composition has been observed both within and across studies. Such variation may in part be attributed to technical factors, such as sampling procedures, sample storage, DNA extraction, the choice of PCR primers and corresponding region to be sequenced, and the sequencing platforms used. Furthermore, part of this variation in microbiota composition may also be explained by different host characteristics and environmental factors. To facilitate the improvement of design, reproducibility and interpretation of poultry microbiota studies, we have reviewed the literature on confounding factors influencing the observed intestinal microbiota in chickens. First, it has been identified that host-related factors, such as age, sex, and breed, have a large effect on intestinal microbiota. The diversity of chicken intestinal microbiota tends to increase most during the first weeks of life, and corresponding colonization patterns seem to differ between layer- and meat-type chickens. Second, it has been found that environmental factors, such as biosecurity level, housing, litter, feed access and climate also have an effect on the composition of the intestinal microbiota. As microbiota studies have to deal with many of these unknown or hidden host and environmental variables, the choice of study designs can have a great impact on study outcomes and interpretation of the data. Providing details on a broad range of host and environmental factors in articles and sequence data repositories is highly recommended. This creates opportunities to combine data from different studies for meta-analysis, which will facilitate scientific breakthroughs toward nutritional and husbandry associated strategies to improve animal health and performance.

Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment

Gut health is paramount for commercial poultry production, and improved methods to assess gut health are critically needed to better understand how the avian gastrointestinal tract matures over time. One important aspect of gut health is the totality of bacterial populations inhabiting different sites of the avian gastrointestinal tract, and associations of these populations with the poultry farm environment, since these bacteria are thought to drive metabolism and prime the developing host immune system. In this study, a single flock of commercial turkeys was followed over the course of 12 weeks to examine bacterial microbiome inhabiting the ceca, ileum, and corresponding poultry litter. Furthermore, the effects of low-dose, growth-promoting penicillin treatment (50 g/ton) in feed on the ileum bacterial microbiome were also examined during the early brood period. The cecum and ileum bacterial communities of turkeys were distinct, yet shifted in parallel to one another over time during bird maturation. Corresponding poultry litter was also distinct yet more closely represented the ileal bacterial populations than cecal bacterial populations, and also changed parallel to ileum bacterial populations over time. Penicillin applied at low dose in feed significantly enhanced early weight gain in commercial poults, and this correlated with predictable shifts in the ileum bacterial populations in control versus treatment groups. Overall, this study identified the dynamics of the turkey gastrointestinal microbiome during development, correlations between bacterial populations in the gastrointestinal tract and the litter environment, and the impact of low-dose penicillin on modulation of bacterial communities in the ileum. Such modulations provide a target for alternatives to low-dose antibiotics.

The functionality of the gastrointestinal microbiome in non-human animals

Due to the significance of the microbiome on human health, much of the current data available regarding microbiome functionality is centered on human medicine. For agriculturally important taxa, the functionality of gastrointestinal bacteria has been studied with the primary goals of improving animal health and production performance. With respect to cattle, the digestive functions of bacteria in cattle are unarguably critical to digestion and positively impact production performance. Conversely, some research suggests that the gastrointestinal microbiome in chickens competes with the host for nutrients and produces toxins that can harm the host resulting in decreased growth efficiency. Concerning many other species including reptiles and cetaceans, some cataloging of fecal bacteria has been conducted, but the functionality within the host remains ambiguous. These taxa could provide interesting gastrointestinal insight into functionality and symbiosis considering the extreme feeding regimes (snakes), highly specialized diets (vampire bats), and living environments (polar bears), which warrants further exploration.

Temporary feed restriction partially protects broilers from necrotic enteritis

The objective of this study was to investigate the effect of feed restriction on the intestinal ecosystem and on the pathogenesis of experimental necrotic enteritis in broiler chicks. To induce subclinical necrotic enteritis, an experimental challenge model using a specific diet formulation, Gumboro vaccination, oral inoculation of broilers with a 10-fold dose of attenuated anticoccidial vaccine and multiple oral inoculations with a specific strain of Clostridium perfringens was adopted. Two hundred and forty 1-day-old Cobb 500 broilers were randomly allocated to four groups: feed restricted, challenged, both feed restricted and challenged, and negative control. At 21, 22, 23 and 24 days of age, the intestines, gizzard and liver were collected from 15 birds in each group and scored for gross lesions. The intestinal digesta was collected for pH and viscosity determination. One caecum from each bird was taken for microbiological analysis. The application of feed restriction in birds challenged with C. perfringens reduced the necrotic enteritis lesion score significantly (P ≤ 0.05) and feed restriction significantly reduced (P ≤ 0.05) pH in the small intestine, the viscosity of the jejunum digesta as well as the C. perfringens counts in the caeca compared with the controls. In conclusion, feed restriction of broilers has a positive effect on the intestinal ecosystem and a significant protective effect against necrotic enteritis in the subclinical experimental model.

Ileal microbiota composition of broilers fed various commercial diet compositions

Microbiota plays a role in the release and absorption of nutrients from feed components, thereby affecting digesta composition and moisture content of the excreta. The objective of the current study was to determine the effects of 5 different diets varying in ingredients (medium-chain fatty acids, nonstarch polysaccharides, and starch) on the microbiota composition of ileal digesta of broiler chickens and excreta DM content. Each treatment was repeated 6 times in cages each containing 18 Ross 308 broilers, with growth performance measured from 0 to 34 d of age and excreta DM and ileal microbiota composition analyzed at 34 d of age. Microbiota composition was evaluated using a novel ribosomal RNA microarray technology containing 370 different probes covering various genera, groups of microbial species, and individual species of the chicken gut microbiota, of which 321 had a signal above the background threshold. Replacing part of the animal fat and soybean oil in the wheat-based diet with medium-chain fatty acids (MCFA; 0.3% C10 and 2.7% C12) improved feed efficiency compared with the other dietary treatments. This coincided with a suppression of gram-positive bacteria belonging to the phylum of the Firmicutes, including Lactobacillus species, and species belonging to the family of the Enterococcaceae and Micrococcaceae, whereas the gram-negative bacteria belonging to the family of the Enterobacteriaceae were promoted. None of the other diets used in the present study notably changed the ileal digesta bacteria composition. Excreta DM content was not affected by dietary treatment. The variation between individual birds per dietary treatment was more pronounced than variation caused by feed composition, with the exception of the digesta microbiota of the birds fed the MCFA diet. It is concluded that a diet with MCFA significantly changes the ileal microbiota composition, whereas the effect of the other diets on the composition of the microbiota and excreta DM content is small in broiler chickens.

Recombinant expression of two bacteriophage proteins that lyse clostridium perfringens and share identical sequences in the C-terminal cell wall binding domain of the molecules but are dissimilar in their N-terminal active domains

Clostridium perfringens is a Gram-positive anaerobic spore-forming bacterium capable of producing four major toxins that are responsible for disease symptoms and pathogenesis in a variety of animals, humans, and poultry. The organism is the third leading cause of human foodborne bacterial disease, and C. perfringens is the presumptive etiologic agent of necrotic enteritis among chickens, which in the acute form can cause increased mortality among broiler flocks. Countries that have complied with the ban on antimicrobial growth promoters (AGP) in feeds have had increased incidences of C. perfringens-associated necrotic enteritis in poultry. To address this issue, new antimicrobial agents, putative lysins from the genomes of bacteriophages, are identified. Two putative phage lysin genes (ply) from the clostridial phages phiCP39O and phiCP26F were cloned and expressed in Escherichia coli , and the resultant proteins were purified to near homogeneity. Gene and protein sequencing revealed that the predicted and chemically determined amino acid sequences of the two recombinant proteins were homologous to N-acetylmuramoyl-l-alanine amidases. The proteins were identical in the C-terminal putative cell-wall binding domain, but only 55% identical to each other in the presumptive N-terminal catalytic domain. Both recombinant lysins were capable of lysing both parental phage host strains of C. perfringens as well as other strains of the bacterium in spot and turbidity reduction assays. The observed reduction in turbidity was correlated with up to a 3 log cfu/mL reduction in viable C. perfringens on brain-heart infusion agar plates. However, other member species of the clostridia were resistant to the lytic activity by both assays.

The influence of copper concentration and source on ileal microbiota

Copper is normally supplemented in poultry diets as a growth promotant and antimicrobial. However, there are conflicting reports about the growth benefits and little information about how Cu affects the microbiota in the intestinal tract of poultry. Therefore, in vitro and in vivo experiments were conducted with broilers to determine the effects of Cu source and supplementation on ileal microbiota. The influence of Cu on growth of lactobacilli and Escherichia coli in media inoculated with ileal contents was determined in the first study. When Cu sulfate pentahydrate was supplemented to the cultures, quadratic increases in lactobacilli to graded concentrations of Cu up to 125 mg/kg and quadratic decreases in E. coli up to 250 mg/kg of Cu were observed after 24 h of incubation at 37 degrees C. However, when tribasic Cu chloride (TBCC) was supplemented, neither linear nor quadratic responses to graded concentrations of dietary Cu were observed on number of lactobacilli or number of E. coli. The effects of Cu and Cu source on ileal microbiota and growth performance in broiler chickens were determined in the second study. Bird performance was not affected by Cu source or concentration. The bacterial culture enumeration results revealed that supplementation with 187.5 mg/kg of Cu from Cu sulfate pentahydrate and TBCC had no effect on number of ileal lactobacilli of birds. The denaturing gradient gel electrophoresis analyses of ileal microbial communities revealed that neither Cu supplementation nor source had effects on the number of bacterial species predominant in the ileal digesta or associated with the ileal mucosa. Supplementation with TBCC supplementation significantly increased the similarity coefficients of microbiota in the ileal mucosa compared with cross-products of all individuals. This suggests that TBCC may alter the intestinal microbiota, yet this shift had no effect on bird performance.