Intestinal microbiome of poultry and its interaction with host and diet

Biophysiology of in ovo administered bioactive substances to improve gastrointestinal tract development, mucosal immunity, and microbiota in broiler chicks

Early embryonic exogenous feeding of bioactive substances is a topic of interest in poultry production, potentially improving gastrointestinal tract (GIT) development, stimulating immunization, and maximizing the protection capability of newly hatched chicks. However, the biophysiological actions and effects of in ovo administered bioactive substances are inconsistent or not fully understood. Thus, this paper summarizes the functional effects of bioactive substances and their interaction merits to augment GIT development, the immune system, and microbial homeostasis in newly hatched chicks. Prebiotics, probiotics, and synbiotics are potential bioactive substances that have been administered in embryonic eggs. Their biological effects are enhanced by a variety of mechanisms, including the production of antimicrobial peptides and antibiotic responses, regulation of T lymphocyte numbers and immune-related genes in either up- or downregulation fashion, and enhancement of macrophage phagocytic capacity. These actions occur directly through the interaction with immune cell receptors, stimulation of endocytosis, and phagocytosis. The underlying mechanisms of bioactive substance activity are multifaceted, enhancing GIT development, and improving both the innate and adaptive immune systems. Thus summarizing these modes of action of prebiotics, probiotics and synbiotics can result in more informed decisions and also provides baseline for further research.

Effect of Pu-erh tea pomace on the composition and diversity of cecum microflora in Chahua chicken No. 2

Pu-erh tea pomace (PTP), a solid substance after extracting functional substances or steeping tea, is rich in crude protein, and crude fiber, and could be used as considerable bioactive substances in animal production. However, its application as poultry feed and its role in regulating the characteristics of gut microorganisms is unclear. The present study investigated the effects of PTP on growth performance and gut microbes of chicken. A total of 144 Chahua chickens No. 2 were individually housed and divided into three groups which were fed diets containing 0% (CK), 1% PTP (T1), and 2% PTP (T2), respectively. The serum and cecum contents were collected after slaughter for analysis. The results indicated that growth performance and carcass traits were not affected by the PTP content. Serum total triglyceride (TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-C) levels in the T1 and T2 groups were significantly lower than in the CK group (p < 0.05). The gut microbiota α-diversity in the T2 group was significantly lower than in the CK group (p < 0.05). Based on partial least squares-discriminant analysis (PLS-DA), we observed significant segregation in gut bacterial communities among the groups. At the phylum level, Bacteroidetes and Firmicutes were dominant in the cecum, occupying about 85% of the cecum flora. The relative abundance of Bacteroidetes tended to increase. At the genus level, the relative abundance of Bacteroides is the highest in the CK、T1 and T2 groups. The relative abundances of Bacteroides and Prevotellaceae_UCG-001 microorganisms in the T2 group were significantly higher than in the CK group (p < 0.05). However, the relative abundance of CHKCI001 microorganisms in the T2 group was significantly lower compared to the CK group (p < 0.05). TG content was significantly positively correlated with CHKCI001 relative abundance, and significantly negatively correlated with Prevotellaceae_UCG-001 relative abundance (p < 0.05). Moreover, the LDL-C content was significantly positively correlated with CHKCI001 relative abundance (p < 0.05). In conclusion, PTP could decrease the cholesterol levels in the blood by improving the composition of gut microbiota, which provides a reference for the application of PTP in the poultry industry.

Effects of prebiotics and precision biotics on performance, animal welfare and environmental impact. A review

This review aims to analyze the recent studies about prebiotics and precision biotics, as alternatives to animal growth promoters. These substances improve intestinal health, growth performance and poultry environmental impact. Prebiotics are insoluble fibers, that have no nutritive value, but they promote the growth of positive bacteria, increase the nutrients absorption and modulate the immune response. Instead, precision biotics are carbohydrates with glycosidic linkages, which interact with gut bacteria metabolism, reducing the excretion of nitrogen and consequentially, the poultry environmental impact. In the last years, different studies were published in this field, and for this reason, it is necessary to organize the results found. It was shown that mannan-oligosaccharides and β-glucans increase ileal nutrient digestibility, nitrogen retention and antibodies titers. Inulin, arabinoxylans-derived oligosaccharides, and galacto-oligosaccharides improved intestinal morphology, arranging for a larger absorption surface area. It was reported that prebiotics enhance the colonization of positive bacteria and can reduce the count of Campylobacter colonies. Furthermore, xylo-oligosaccharides are often used in animal feed, due to their ability to form organic acids, which decompose noxious substances, improving litter quality, and consequentially, reducing the environmental impact. Litter quality is a relevant aspect for ammonia emissions and for animal welfare. Whether the litter quality is poor, footpad dermatitis increase, worsening animal welfare and increasing nitrogen emissions to air. Precision biotics select metabolic pathways to modulate amino acid degradation, reintegrating the nitrogen discarded, and reducing the ammonia level in litter. It was also reported an improvement of growth performance and a better animal welfare. In conclusion, prebiotics and precision biotics can have positive effects on animal performance and welfare, and they can be a new strategy to reduce the environmental impact of chickens' farms.

Effects of different levels of Citri Sarcodactylis Fructus by-products fermented feed on growth performance, serum biochemical, and intestinal health of cyan-shank partridge birds

This research aimed to investigate the effects of supplements containing fermented feed made from Citri Sarcodactylis Fructus by-products (CSFBP-Fermented feed) on the growth performance, immunological function, and gut health of broilers. 1080 cyan-shank partridge birds aged 47 days were chosen and casually distributed to four groups, each with 6 replicates and 45 birds per replicate. The experimental groups were provided with 1% (group T2), 3% (group T3) and 5% (group T4) of CSFBP-fermented feed in the basic diet, while the control group (group T1) received the basic diet. The findings revealed that supplementation with CSFBP-Fermented feed reduced ADFI and FCR and improved ADG in birds (P < 0.05). MDA levels in the serum of birds fed CSFBP-fermented feed were lower than in the control group (P < 0.05). The CAT activity in the serum of broilers increased after supplementation with 3% CSFBP-Fermented feed (P < 0.05). Supplementing broilers with CSFBP-fermented feed enhanced VH in the ileum, jejunum, and duodenum (P < 0.05). The addition of 3% CSFBP-Fermented feed decreased CD in the jejunum (P < 0.05). The addition of 3% and 5% CSFBP-Fermented feed increased the mRNA expression of ZO-1 and Occludin in the jejunum of broiler chickens and reduced the mRNA expression of IL-6 (P < 0.05). The addition of 3% CSFBP-Fermented feed increased the mRNA expression of Claudin in the jejunum of broiler chickens and reduced IL-1β mRNA expression (P < 0.05). Compared to the control group, all experimental groups exhibited decreased mRNA expression of TNF-α and INF-γ in the jejunal mucosa of the birds (P < 0.05). According to research using high-throughput sequencing of microorganisms' 16S rDNA, and an analysis of α-diversity found that supplementing broilers with 3% CSFBP-Fermented feed decreased the number of bacteria in their cecum (P < 0.05). Bacteroidota was higher in all groups after supplementation with CSFBP-Fermented feed. At the genus level, after addition with 3% CSFBP-Fermented feed, the abundance of Bacteroide and Prevotellaceae_Ga6A1_group were higher than the control group (33.36% vs 29.95%, 4.35% vs 2.94%). The abundance of Rikenellaceae_RC9_gut_group and Fusobacterium were lower than the control group (5.52% vs. 7.17%,0.38% vs. 1.33%). In summary, supplementing the diet with CSFBP-Fermented feed can promote the growth of performance by enhancing intestinal morphology, and barrier function, as well as modulating intestinal inflammatory factors and microbial composition in broilers.

Predicting foodborne pathogens and probiotics taxa within poultry-related microbiomes using a machine learning approach

BACKGROUND

Microbiomes that can serve as an indicator of gut, intestinal, and general health of humans and animals are largely influenced by food consumed and contaminant bioagents. Microbiome studies usually focus on estimating the alpha (within sample) and beta (similarity/dissimilarity among samples) diversities. This study took a combinatorial approach and applied machine learning to microbiome data to predict the presence of disease-causing pathogens and their association with known/potential probiotic taxa. Probiotics are beneficial living microorganisms capable of improving the host organism's digestive system, immune function and ultimately overall health. Here, 16 S rRNA gene high-throughput Illumina sequencing of temporal pre-harvest (feces, soil) samples of 42 pastured poultry flocks (poultry in this entire work solely refers to chickens) from southeastern U.S. farms was used to generate the relative abundance of operational taxonomic units (OTUs) as machine learning input. Unique genera from the OTUs were used as predictors of the prevalence of foodborne pathogens (Salmonella, Campylobacter and Listeria) at different stages of poultry growth (START (2-4 weeks old), MID (5-7 weeks old), END (8-11 weeks old)), association with farm management practices and physicochemical properties.

RESULT

While we did not see any significant associations between known probiotics and Salmonella or Listeria, we observed significant negative correlations between known probiotics (Bacillus and Clostridium) and Campylobacter at the mid-time point of sample collection. Our data indicates a negative correlation between potential probiotics and Campylobacter at both early and end-time points of sample collection. Furthermore, our model prediction shows that changes in farm operations such as how often the houses are moved on the pasture, age at which chickens are introduced to the pasture, diet composition and presence of other animals on the farm could favorably increase the abundance and activity of probiotics that could reduce Campylobacter prevalence.

CONCLUSION

Integration of microbiome data with farm management practices using machine learning provided insights on how to reduce Campylobacter prevalence and transmission along the farm-to-fork continuum. Altering management practices to support proliferation of beneficial probiotics to reduce pathogen prevalence identified here could constitute a complementary method to the existing but ineffective interventions such as vaccination and bacteriophage cocktails usage. Study findings also corroborate the presence of bacterial genera such as Caloramator, DA101, Parabacteroides and Faecalibacterium as potential probiotics.

A comprehensive longitudinal study of gut microbiota dynamic changes in laying hens at four growth stages prior to egg production

OBJECTIVE

The poultry industry is a primary source of animal protein worldwide. The gut microbiota of poultry birds, such as chickens and ducks, is critical in maintaining their health, growth, and productivity. This study aimed to identify longitudinal changes in the gut microbiota of laying hens from birth to the pre-laying stage.

METHODS

From a total of 80 Hy-Line Brown laying hens, birds were selected based on weight at equal intervals to collect feces (n = 20 per growth) and ileal contents (n = 10 per growth) for each growth stage (days 10, 21, 58, and 101). The V4 regions of the 16S rRNA gene were amplified after extracting DNA from feces and ileal contents. Amplicon sequencing was performed using Illumina, followed by analysis.

RESULTS

Microbial diversity increased with growth stages, regardless of sampling sites. Microbial community analysis indicated that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla in the feces and ileal. The abundance of Lactobacillus was highest on day 10, and that of Escherichia-shigella was higher on day 21 than those at the other stages at the genus level (for the feces and ileal contents; p<0.05). Furthermore, Turicibacter was the most abundant genus after changing feed (for the feces and ileal contents; p<0.05). The fecal Ruminococcus torques and ileal Lysinibacillus were negatively correlated with the body weights of chickens (p<0.05).

CONCLUSION

The gut microbiota of laying hens changes during the four growth stages, and interactions between microbiota and feed may be present. Our findings provide valuable data for understanding the gut microbiota of laying hens at various growth stages and future applied studies.

Dynamic distribution of gut microbiota in posthatching chicks and its relationship with average daily gain

The colonization and development of gut microbiota are essential for the health and growth of chicks after hatching. However, the colonization and prevalence of gut microbiota have not been well characterized, and knowledge of which microbes and their relationship with average daily gain in chicks is still limited. This study characterized the dynamic succession of microbiota in the intestinal tract of chicks and investigated its relationship with daily weight gain. A total of 121 fecal samples across 7 time points from d 0 to 10 posthatching were collected from 19 chicks randomly selected from 1,950 chicks. Using 16S rRNA gene sequencing examined microbial composition of fecal samples. The observed species index of alpha diversity increased with age, gradually achieving stability at 3 d of age. The microbiota of chicks after hatching was primarily Clostridium_sensu_stricto_1 (34.49%), and its relative abundance diminishes with age. In contrast, Lactobacillus had a low relative abundance in the first 2 d after hatching and gradually increased with age. Predicted functional capacities found that the microbiota of early-stage posthatching (d 0 and 1 after hatching) was involved in metabolism, including amino acid metabolism, metabolism of cofactors and vitamins, and nitrogen metabolism. However, at the later stage posthatching (from d 3-10 after hatching), the intestinal microbial function was involved in carbohydrate metabolism, amino acid metabolism, cell growth and death, and methane metabolism. It was identified that 47 operational taxonomic units were associated with average daily gain of chicks, 12 of which were annotated with Lactobacillus and significantly positive associated with average daily gain. In addition, Clostridium_sensu_stricto_1 was significantly negatively associated with average daily gain. Taken together, we characterized the dynamic successions of intestinal microbiota in hatching chicks. The intestinal microbiota of chicks has an impact on the host average daily gain. Our findings should be instrumental in improving local chick production.

Dietary supplementation of microalgae mitigates the negative effects of heat stress in broilers

Heat stress in poultry is a serious concern, affecting their health and productivity. To effectively address the issue of heat stress, it is essential to include antioxidant-rich compounds in the poultry diet to ensure the proper functioning of the redox system. Microalgae (Spirulina platensis) are rich in antioxidants and have several health benefits in humans and animals. However, its role in health and production and the underlying mechanism in heat-stressed broilers are poorly understood. This study aimed to determine the effect of microalgae supplementation on the health and production of heat-stressed broilers. Cobb500 day-old chicks (N = 144) were raised in litter floor pens (6 pens/treatment and 8 birds/pen). The treatment groups were: 1) no heat stress (NHS), 2) heat stress (HS), and 3) heat stress + 3% microalgae (HS+MAG). The broilers in the HS+MAG group were fed a diet supplemented with 3% microalgae, whereas NHS and HS groups were fed a standard broiler diet. Broilers in the NHS were raised under standard temperature (20°C-24°C), while HS and HS+MAG broilers were subjected to cyclic heat stress from d 22 to 35 (32°C-33°C for 8 h). Heat stress significantly decreased the final body weight, whereas the supplementation of microalgae increased the final body weight of broilers (P < 0.05). The expressions of ileal antioxidant (GPX3), immune-related (IL4), and tight-junction (CLDN2) genes were increased in microalgae-supplemented broilers compared to heat-stressed broilers (P < 0.05). The ileal villus height to crypt depth ratio was improved in microalgae-supplemented broilers (P < 0.05). In addition, microbial alpha, and beta diversities were higher in the HS+MAG group compared to the HS group (P < 0.05). There was an increase in volatile fatty acid-producing bacteria at the genus level, such as Ruminococcus, Ocillospira, Lactobacillus, Oscillobacter, Flavonifractor, and Colidextribacter in the group that received microalgae supplementation. In conclusion, dietary supplementation of microalgae improved the growth performances of heat-stressed broilers by improving their physiogenomics. Thus, the dietary inclusion of microalgae can potentially mitigate heat stress in broilers.

Honeybee as a food nutrition analysis model of neural development and gut microbiota

Research on the relationships between the gut microbiota and the neurophysiology and behavior of animals has grown exponentially in just a few years. Insect behavior may be controlled by molecular mechanisms that are partially homologous to those in mammals, and swarming insects may be suitable as experiment models in these types of investigations. All core gut bacteria in honeybees can be cultivated in vitro. Certain gut microflora of bees can be genetically engineered or sterilized and colonized. The bee gut bacteria model is established more rapidly and has a higher flux than other sterile animal models. It may help elucidate the pathogenesis of intestinal diseases and identify effective molecular therapeutic targets against them. In the present review, we focused on the contributions of the honeybee model in learning cognition and microbiome research. We explored the relationship between honeybee behavior and neurodevelopment and the factors determining the mechanisms by which the gut microbiota affects the host. In particular, we concentrated on the correlation between gut microbiota and brain development. Finally, we examined strategies for the effective use of simple animal models in animal cognition and microbiome research.

Heat stress exposure cause alterations in intestinal microbiota, transcriptome, and metabolome of broilers

Introduction

Heat stress can affect the production of poultry through complex interactions between genes, metabolites and microorganisms. At present, it is unclear how heat stress affects genetic, metabolic and microbial changes in poultry, as well as the complex interactions between them.

Methods

Thus, at 28  days of age a total of 200 Arbor Acres broilers with similar body weights were randomly divided into the control (CON) and heat stress treatment (HS). There were 5 replicates in CON and HS, respectively, 20 per replication. From the 28-42  days, the HS was kept at 31 ± 1°C (9:00-17:00, 8 h) and other time was maintained at 21 ± 1°C as in the CON. At the 42nd day experiment, we calculated the growth performance (n = 8) of broilers and collected 3 and 6 cecal tissues for transcriptomic and metabolomic investigation and 4 cecal contents for metagenomic investigation of each treatment.

Results and discussion

The results indicate that heat stress significantly reduced the average daily gain and body weight of broilers (value of p < 0.05). Transcriptome KEGG enrichment showed that the differential genes were mainly enriched in the NF-kB signaling pathway. Metabolomics results showed that KEGG enrichment showed that the differential metabolites were mainly enriched in the mTOR signaling pathway. 16S rDNA amplicon sequencing results indicated that heat stress increased the relative abundance of Proteobacteria decreased the relative abundance of Firmicutes. Multi-omics analysis showed that the co-participating pathway of differential genes, metabolites and microorganisms KEGG enrichment was purine metabolism. Pearson correlation analysis found that ornithine was positively correlated with SULT1C3, GSTT1L and g_Lactobacillus, and negatively correlated with CALB1. PE was negatively correlated with CALB1 and CHAC1, and positively with g_Alistipes. In conclusion, heat stress can generate large amounts of reactive oxygen and increase the types of harmful bacteria, reduce intestinal nutrient absorption and antioxidant capacity, and thereby damage intestinal health and immune function, and reduce growth performance indicators. This biological process is manifested in the complex regulation, providing a foundational theoretical basis for solving the problem of heat stress.

The Functional Roles of Methionine and Arginine in Intestinal and Bone Health of Poultry: Review

This review explores the roles of methionine and arginine in promoting the well-being of poultry, with a specific focus on their impacts on intestinal and bone health. The metabolic pathways of methionine and arginine are elucidated, highlighting their distinct routes within the avian system. Beyond their fundamental importance in protein synthesis, methionine and arginine also exert their functional roles through their antioxidant capacities, immunomodulating effects, and involvement in the synthesis of metabolically important molecules such as S-adenosylmethionine, nitric oxide, and polyamines. These multifaceted actions enable methionine and arginine to influence various aspects of intestinal health such as maintaining the integrity of the intestinal barrier, regulating immune responses, and even influencing the composition of the gut microbiota. Additionally, they could play a pivotal role in promoting bone development and regulating bone remodeling, ultimately fostering optimal bone health. In conclusion, this review provides a comprehensive understanding of the potential roles of methionine and arginine in intestinal and bone health in poultry, thereby contributing to advancing the nutrition, overall health, and productivity of poultry in a sustainable manner.

Recent Review on the Extraction and Qualitative Assay of Cysteine and Other Amino Acids from Vellore Feather Waste and Molecular Docking Studies of Cysteine for Pharmacological Applications

Products produced from waste are a relatively recent innovation. Feather substrates are abundant in keratin content and improper disposal can cause ecosystem contamination. However, these pollutants can be transformed into value-added products for industrial application. Physical, chemical and cutting-edge microbiological methods were utilized for decomposing keratin and aid in the identification and estimation of amino acids from poultry feather wastes. These beneficial approaches are receiving more attention due to their retrieval of harmless and value added byproducts. These keratin-based compounds are used widely in pharmaceutical, livestock feed, fertilizer, and a variety of other industrial sectors. Since keratin is primarily consisting of amino acids, it can be utilized to affirm and estimate the amino acids in these feather substrates. This study primarily highlights the various methodologies employed for the qualitative estimation of amino acids in feather waste samples and the inhibitory activity of keratinase enzyme by EDTA and pepstatin in order to accumulate amino acids for drug delivery purpose and their importance in various pharmaceutical industries. In addition to that, molecular docking studies of cysteine with many standard pharmaceutical drugs like acetaminophen, pethidine, methylphenidate, carbamazepine, cillin and amlodipine were performed using autodock to demonstrate how cysteine greatly reduces conventional drug toxicity and its side effects.

Phenotype Alterations in the Cecal Ecosystem Involved in the Asymptomatic Intestinal Persistence of Paratyphoid Salmonella in Chickens

The gastrointestinal ecosystem involves interactions between the host, gut microbiota, and external environment. To colonize the gut of poultry, Salmonella must surmount barriers levied by the intestine including mucosal innate immune responses and microbiota-mediated niche restrictions. Accordingly, comprehending Salmonella intestinal colonization in poultry requires an understanding of how the pathogen interacts with the intestinal ecosystem. In chickens, the paratyphoid Salmonella have evolved the capacity to survive the initial immune response and persist in the avian ceca for months without triggering clinical signs. The persistence of a Salmonella infection in the avian host involves both host defenses and tolerogenic defense strategies. The initial phase of the Salmonella-gut ecosystem interaction is characteristically an innate pro-inflammatory response that controls bacterial invasion. The second phase is initiated by an expansion of the T regulatory cell population in the cecum of Salmonella-infected chickens accompanied by well-defined shifts in the enteric neuro-immunometabolic pathways that changes the local phenotype from pro-inflammatory to an anti-inflammatory environment. Thus, paratyphoid Salmonella in chickens have evolved a unique survival strategy that minimizes the inflammatory response (disease resistance) during the initial infection and then induces an immunometabolic reprogramming in the cecum that alters the host defense to disease tolerance that provides an environment conducive to drive asymptomatic carriage of the bacterial pathogen.

Dietary supplementation of solubles from shredded, steam-exploded pine particles modulates cecal microbiome composition in broiler chickens

This study evaluated the effects of supplementing solubles from shredded, steam-exploded pine particles (SSPP) on growth performances, plasma biochemicals, and microbial composition in broilers. The birds were reared for 28 days and fed basal diets with or without the inclusion of SSPP from 8 days old. There were a total of three dietary treatments supplemented with 0% (0% SSPP), 0.1% (0.1% SSPP) and 0.4% (0.4% SSPP) SSPP in basal diets. Supplementation of SSPP did not significantly affect growth or plasma biochemicals, but there was a clear indication of diet-induced microbial shifts. Beta-diversity analysis revealed SSPP supplementation-related clustering (ANOSIM: r = 0.31, p < 0.01), with an overall lower (PERMDISP: p < 0.05) individual dispersion in comparison to the control group. In addition, the proportions of the Bacteroides were increased, and the relative abundances of the families Vallitaleaceae, Defluviitaleaceae, Clostridiaceae, and the genera Butyricicoccus and Anaerofilum (p < 0.05) were significantly higher in the 0.4% SSPP group than in the control group. Furthermore, the linear discriminant analysis effect size (LEfSe) also showed that beneficial bacteria such as Ruminococcus albus and Butyricicoccus pullicaecorum were identified as microbial biomarkers of dietary SSPP inclusion (p < 0.05; | LDA effect size | > 2.0). Finally, network analysis showed that strong positive correlations were established among microbial species belonging to the class Clostridia, whereas Erysipelotrichia and Bacteroidia were mostly negatively correlated with Clostridia. Taken together, the results suggested that SSPP supplementation modulates the cecal microbial composition of broilers toward a "healthier" profile.

Brief exposure to captivity in a songbird is associated with reduced diversity and altered composition of the gut microbiome

The gut microbiome is important for host fitness and is influenced by many factors including the host's environment. Captive environments could potentially influence the richness and composition of the microbiome and understanding these effects could be useful information for the care and study of millions of animals in captivity. While previous studies have found that the microbiome often changes due to captivity, they have not examined how quickly these changes can occur. We predicted that the richness of the gut microbiome of wild-caught birds would decrease with brief exposure to captivity and that their microbiome communities would become more homogeneous. To test these predictions, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure their gut microbiomes immediately after capture ("wild sample") and again 5-10 days after capture ("captive sample"). There were significant differences in beta diversity between the wild and captive samples, and captive microbiome communities were more homogenous but only when using nonphylogenetic measures. Alpha diversity of the birds' microbiomes also decreased in captivity. The functional profiles of the microbiome changed, possibly reflecting differences in stress or the birds' diets before and during captivity. Overall, we found significant changes in the richness and composition of the microbiome after only a short exposure to captivity. These findings highlight the necessity of considering microbiome changes in captive animals for research and conservation purposes.

Mechanisms underlying the Effects of Heat Stress on Intestinal Integrity, Inflammation, and Microbiota in Chickens

Poultry meat and egg production benefits from a smaller carbon footprint, as well as feed and water consumption, per unit of product, than other protein sources. Therefore, maintaining a sustainable production of poultry meat is important to meet the increasing global demand for this staple. Heat stress experienced during the summer season or in tropical/subtropical areas negatively affects the productivity and health of chickens. Crucially, its impact is predicted to grow with the acceleration of global warming. Heat stress affects the physiology, metabolism, and immune response of chickens, causing electrolyte imbalance, oxidative stress, endocrine disorders, inflammation, and immunosuppression. These changes do not occur independently, pointing to a systemic mechanism. Recently, intestinal homeostasis has been identified as an important contributor to nutrient absorption and the progression of systemic inflammation. Its mechanism of action is thought to involve neuroendocrine signaling, antioxidant response, the presence of oxidants in the diet, and microbiota composition. The present review focuses on the effect of heat stress on intestinal dysfunction in chickens and the underlying causative factors. Understanding these mechanisms will direct the design of strategies to mitigate the negative effect of heat stress, while benefiting both animal health and sustainable poultry production.

Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China

China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the surveillance of ten large-scale chicken farms and four connected abattoirs in three Chinese provinces over 2.5 years. Using a data mining approach based on machine learning, we analysed 461 microbiomes from birds, carcasses and environments, identifying 145 potentially mobile antibiotic resistance genes (ARGs) shared between chickens and environments across all farms. A core set of 233 ARGs and 186 microbial species extracted from the chicken gut microbiome correlated with the AMR profiles of Escherichia coli colonizing the same gut, including Arcobacter, Acinetobacter and Sphingobacterium, clinically relevant for humans, and 38 clinically relevant ARGs. Temperature and humidity in the barns were also correlated with ARG presence. We reveal an intricate network of correlations between environments, microbial communities and AMR, suggesting multiple routes to improving AMR surveillance in livestock production.

Characterizing the gut microbiome of broilers raised under conventional and no antibiotics ever practices

Meat from broilers raised without the use of antibiotics is becoming increasingly popular among consumers. Consequently, interest in the microbial profiling of chickens produced under nonconventional practices is growing, however, research on this topic is lacking. The current study was designed to characterize the dynamics of gut microbial populations of broilers raised under conventional and no antibiotics ever (NAE) practices. Four commercial farms (2 conventional and 2 NAE) were included in this study. On each farm, cecal (n = 224) and ileal (n = 224) contents were collected from birds at different stages during the grow out of a single flock and following transportation to the processing facility. Cecal microbiota was dominated by the genera Escherichia and Enterococcus upon hatching in both conventional and NAE flocks, shifting with time toward predominantly Faecalibacterium and Bacteroides. The composition of cecal microbial communities of NAE broilers was different than that of conventional chickens (P ≤ 0.05). Conventional broilers harbored a rich, but less diverse cecal microbiota than NAE, while the ileal microbiota was primarily populated with genera previously named Lactobacillus, which exhibited a higher abundance in NAE broilers (P ≤ 0.05). In both production systems, the microbiota followed a similar temporal succession that was more evident in the ceca. Transportation to the processing plant impacted the microbial composition of the ileum (P ≤ 0.05), characterized by an increase in the relative abundance of Psychrobacter. Finally, differential abundance analysis showed a positive correlation between Campylobacter and Enorma within the cecum microbiota, and a negative correlation with Salmonella.

An Overview of the Use and Applications of Limosilactobacillus fermentum in Broiler Chickens

The implementation of government regulations on antibiotic use, along with the public's concern for drug resistance, has strengthened interest in developing alternatives not only aimed at preserving animal production but also at reducing the effects of pathogenic infections. Probiotics, in particular, are considered microorganisms that induce health benefits in the host after consumption of adequate amounts; they have been established as a potential strategy for improving growth, especially by stimulating intestinal homeostasis. Probiotics are commonly associated with lactic acid bacteria, and Limosilactobacillus fermentum is a well-studied species recognized for its favorable characteristics, including adhesion to epithelial cells, production of antimicrobial compounds, and activation of receptors that prompt the transcription of immune-associated genes. Recently, this species has been used in animal production. Different studies have shown that the application of L. fermentum strains not only improves the intestinal ecosystem but also reduces the effects caused by potentially pathogenic microorganisms. These studies have also revealed key insights into the mechanisms behind the actions exerted by this probiotic. In this manuscript, we aim to provide a concise overview of the effects of L. fermentum administration on broiler chicken health and performance.

Effects of bacteriophage on Salmonella Enteritidis infection in broilers

Bacteriophages (BP) are viruses that can infect bacteria. The present study evaluated the effect of BP on Salmonella infected broilers. A number of 150 day-old broilers were used in a completely randomized design with five treatments that included: (1) basal diet from day 0 to 28; (2) basal diet + 0.3 g/kg of colistin from day 0 to 28; (3) basal diet from day 1 to 13, and basal diet + 0.4 g/kg of colistin from day 14 to 28; (4) basal diet + 1 g/kg of BP from day 0 to 28; (5) basal diet + 1.5 g/kg of BP from day 0 to 28. On day 13, 15 chickens from each treatment were challenged by Salmonella Enteritidis (SE), while fifteen from each treatment were not; instead, they were kept in the same cage with the challenged chickens (exposed chickens). At 7 and 14 days post-challenge, the number of SE and coliform bacteria in the cecum and liver of colistin and BP-fed birds was lower than the control treatment. In exposed and challenged chickens, the height and surface area of villus were greater in the BP and colistin-supplemented groups. Serum concentrations of aspartate aminotransferase and alanine transaminase were greater, while serum albumin and triglycerides concentrations were lower in the control treatment. The liver of the challenged chickens had more pathological lesions than exposed birds. BP significantly decreased PPARγ gene expression in exposed chickens. In the challenged and exposed chickens, TLR4 gene expression was lower in BP and colistin-treated birds as compared to the control. In conclusion, adding BP to the diet from the day of age prevents the spread of Salmonella.

Carvacrol attenuated lipopolysaccharide-induced intestinal injury by down-regulating TLRs gene expression and regulating the gut microbiota in rabbit

Carvacrol (CAR) is a plant extract that has been reported to enhance antioxidant activity in animals. However, the effect of CAR on the intestinal health of rabbits is poorly understood. Here, we investigated whether CAR exerts protective effects on the intestinal health of rabbits following lipopolysaccharide (LPS) challenge and whether these effects were mediated via the reduction of intestinal inflammation and the regulation of the intestinal flora. Intestinal damage was assessed in LPS-challenged rabbits treated or not with CAR. The serum levels of inflammatory factors were assessed by enzyme-linked immunosorbent assay. Histopathological changes in the ileum and cecum were examined using hematoxylin and eosin staining. The relative gene expression levels of inflammatory factors and tight junction proteins in the rabbit cecum were determined by qRT-PCR. High-throughput sequencing analysis of the microbial 16S rRNA gene was performed using the Illumina NovaSeq Platform. The results showed that CAR can prevent intestinal inflammation and damage as well as mitigate gut dysbiosis in rabbits following LPS challenge. Our study provides a theoretical reference for the application of dietary CAR in rabbit production.

Comparative analysis of clinical breakpoints, normalized resistance interpretation and epidemiological cut-offs in interpreting antimicrobial resistance of Escherichia coli isolates originating from poultry in different farm types in Tanzania

Introduction

Existing breakpoint guidelines are not optimal for interpreting antimicrobial resistance (AMR) data from animal studies and low-income countries, and therefore their utility for analysing such data is limited. There is a need to integrate diverse data sets, such as those from low-income populations and animals, to improve data interpretation.

Gap statement

There is very limited research on the relative merits of clinical breakpoints, epidemiological cut-offs (ECOFFs) and normalized resistance interpretation (NRI) breakpoints in interpreting microbiological data, particularly in animal studies and studies from low-income countries.

Aim

The aim of this study was to compare antimicrobial resistance in Escherichia coli isolates using ECOFFs, CLSI and NRI breakpoints.

Methodology

A total of 59 non-repetitive poultry isolates were selected for investigation based on lactose fermentation on MacConkey agar and subsequent identification and confirmation as E. coli using chromogenic agar and uidA PCR. Kirby Bauer disc diffusion was used for susceptibility testing. For each antimicrobial agent, inhibition zone diameters were measured, and ECOFFs, CLSI and NRI bespoke breakpoints were used for resistance interpretation.

Results

According to the interpretation of all breakpoints except ECOFFs, tetracycline resistance was significantly higher (TET) (67.8 -69.5 %), than those for ciprofloxacin (CIPRO) (18.6 -32.2 %), imipenem (IMI) (3.4 -35 %) and ceftazidime (CEF) (1.7 -45.8 %). Prevalence estimates of AMR using CLSI and NRI bespoke breakpoints did not differ for CEF (1.7 % CB and 1.7 % COWT), IMI (3.4 % CB and 4.0 % COWT) and TET (67.8 % CB and 69.5 % COWT). However, with ECOFFs, AMR estimates for CEF, IMI and CIP were significantly higher (45.8, 35.6 and 64.4 %, respectively; P<0.05). Across all the three breakpoints, resistance to ciprofloxacin varied significantly (32.2 % CB, 64.4 % ECOFFs and 18.6 % COWT, P<0.05).

Conclusion

AMR interpretation is influenced by the breakpoint used, necessitating further standardization, especially for microbiological breakpoints, in order to harmonize outputs. The AMR ECOFF estimates in the present study were significantly higher compared to CLSI and NRI.

Effects of organic zinc on production performance, meat quality, apparent nutrient digestibility and gut microbiota of broilers fed low-protein diets

The high cost of feed and nitrogen pollution caused by high-protein diets have become major challenges restricting sustainable development in China's animal husbandry sector. Properly reducing protein levels and improving protein utilization in feed are effective approaches to solving this problem. To determine the optimal dose of methionine hydroxyl analogue chelated zinc (MHA-Zn) in broiler diets with a 1.5% reduction in crude protein (CP), a total of 216 1-day-old broilers were randomly assigned into 4 groups (each group consisted of 3 replications with 18 broilers per replicate), and growth and development indexes were assessed after 42 days. The broilers in control group were fed a basic diet, whereas those in the three test groups were fed diets with a 1.5% reduction in CP. The results showed no significant difference in the edible parts of broilers between low-protein (LP) diet group (90 mg/kg MHA-Zn) and normal diet group (p > 0.05), and adding 90 mg/kg MHA-Zn to LP diet significantly improved ileum morphology and apparent total tract digestibility (ATTD) of nutrient (p < 0.01; p < 0.05). A 16S rRNA sequencing analysis indicated that supplementing the LP diet with 90 mg/kg MHA-Zn was adequate for production performance of broilers and promoted beneficial bacteria in the cecum (Lactobacillus, Butyricoccus, Oscillospira, etc.) (p < 0.01). In summary, adding an optimal dose of organic zinc (90 mg/kg MHA-Zn) in low protein diets led to enhanced production performance of broilers and optimized cecum microbiota. Additionally, the reduction of crude protein consumption in broiler production proved to be a cost-effective measure, while also mitigated nitrogen pollutant emissions in the environment.

Characterization of potential probiotics Lactobacillus species isolated from the gastrointestinal tract of Rhode Island Red (RIR) chicken in Ethiopia

Background and aims

Nowadays, probiotic microorganisms are given high attention due to their potential for the improvement of animal production and productivity. The natural gut microflora of poultry can serve as an excellent source of optimum probiotic strains. Therefore, this study isolated, identified and characterized potential probiotic Lactobacillus strains from the digestive tract content of RIR chicken in Ethiopia.

Methods

A total of five RIR chickens were randomly taken and a sample was taken from each gastrointestinal content for further analysis. For further characterization, among 190 isolates only 10 representative isolates were randomly taken for further in vitro probiotic potential characterization. The selected isolates were screened and identified based on the biochemical, morphological, and 16S rRNA gene sequences.

Results

Survival isolates of IS3, IS4, IS6, and IS7 were significantly different (P < 0.05) at pH 2. IS3, IS4, IS6, and IS7 showed tolerance for 0.3% bile salt. Isolates of IS1, IS2, IS5, IS7, and IS8 were ampicillin-resistant, and chloramphenicol, ciprofloxacin, and erythromycin were used as antibiotics. All ten isolates showed antagonistic activity against Escherichia coli, Staphylococcus aureus, Salmonella typhimurium, Staphylococcus intermedius, and Salmonella enteritidis. The optimum temperature for all isolates was 45 °C, and all the isolates could grow at 0.69 mol/L of NaCl. Using phylogenetic analysis of the 16SrRNA gene sequence; IS3 was identified as Lactobacillus salivarius, while IS4, IS6, and IS7 were identified as Lactobacillus reuteri.

Conclusions

The results indicated that the selected Lactobacillus isolates can survive the stress conditions of the gastrointestinal tract and can thus be considered potential probiotic candidates for chickens.

Deciphering the Association between Campylobacter Colonization and Microbiota Composition in the Intestine of Commercial Broilers

Campylobacter is a major food safety concern and is transmitted mainly via poultry meat. We previously found that some commercial broiler farms consistently produced Campylobacter-negative flocks while others were consistently Campylobacter-positive for consecutive production cycles although the farms operated under similar management practices. We hypothesized that this difference in Campylobacter colonization might be associated with the gut microbiota composition. To address this, six commercial broiler farms were selected based on their Campylobacter status (three negative and three positive) to evaluate the microbiota differences between each farm category. For each farm on each production cycle (2-3 cycles), 40 ceca collected from five-week-old broilers were processed for microbiota analysis via 16S rRNA gene sequencing. Cecal microbiota species richness, phylogenetic diversity, community structure, and composition of Campylobacter-positive farms were noticeably different from those of Campylobacter-negative farms. Rikenella, Methanocorpusculum, Barnesiella, Parasutterella, and Helicobacter were significantly more abundant among Campylobacter-positive farms. In contrast, Ruminococcaceae, Streptococcus, Escherichia, Eggerthellaceae, Lactobacillus, Monoglobus, and Blausia were more abundant in Campylobacter-negative farms. Eggerthellaceae, Clostridia, Lachnospiraceae, Lactobacillus, Monoglobus, and Parabacteroides were significantly negatively correlated with Campylobacter abundance. These findings suggest that specific members of cecal microbiota may influence Campylobacter colonization in commercial broilers and may be further explored to control Campylobacter in poultry.

Effects of tea residues-fermented feed on production performance, egg quality, antioxidant capacity, caecal microbiota, and ammonia emissions of laying hens

This study was to assess the effects of tea residues-fermented feed (TR-fermented feed) on production performance, egg quality, serum antioxidant capacity, caecal microbiota, and ammonia emissions of laying hens. A total of 1,296 Lohmann laying hens have randomly distributed four groups with six parallels and fed with diets TR-fermented feed at the rates of 0 (control), 1, 3, and 5%. The inclusion of 1% (TR)-fermented feed resulted in a significant increase in egg-laying rate and average egg weight of birds, and a reduction in the feed-to-egg ratio when compared to the control group (p < 0.05). The addition of 1 and 3% of (TR)-fermented feed significantly improved the Haugh unit of eggs (p < 0.05). The eggshell thickness was observed to increase by almost one-fold upon the inclusion of 3 and 5% (TR)-fermented feed in the basal diet (p < 0.05). The supplementation of 3% (TR)-fermented feed significantly increased the content of methionine, tyrosine, proline, essential amino acids (EAA), alpha linoleic acid (C18:3n6), docosanoic acid (C22:0), docosahexaenoic acid (C22:6n3), twenty-three carbonic acids (C23:0), ditetradecenoic acid (C24:1) and total omega-3 polyunsaturated fatty acids (∑ω-3 PUFA) in the eggs (p < 0.05). The addition of a certain amount of (TR)-fermented feed can enhance the activity of glutathione peroxidase (GSH-PX) and superoxide dismutase (SOD) in chicken serum, and reduce the level of malondialdehyde (MDA) (p < 0.05). The ammonia concentration in the hen house of laying hens in the treatment groups decreased significantly (p < 0.05). Bacteroidetes and Firmicutes, the main phyla in the cecal bacterial community, were differentially abundant in each group, comprising greater than 55 and 33%, respectively. Collectively, this research indicates that (TR)-fermented feed supplementation improves the performance of laying hens and reduces ammonia emissions and can be used in industry-scale layer production.

Influence of Live Attenuated Salmonella Vaccines on Cecal Microbiome Composition and Microbiota Abundances in Young Broiler Chickens

Salmonellosis is a global food safety challenge caused by Salmonella, a gram-negative bacterium of zoonotic importance. Poultry is considered a major reservoir for the pathogen, and humans are exposed through consumption of raw or undercooked products derived from them. Prophylaxis of Salmonella in poultry farms generally mainly involves biosecurity measures, flock testing and culling, use of antibiotics, and vaccination programs. For decades, the use of antibiotics has been a common practice to limit poultry contamination with important pathogenic bacteria such as Salmonella at the farm level. However, due to an increasing prevalence of resistance, non-therapeutic use of antibiotics in animal production has been banned in many parts of the world. This has prompted the search for non-antimicrobial alternatives. Live vaccines are among the developed and currently used methods for Salmonella control. However, their mechanism of action, particularly the effect they might have on commensal gut microbiota, is not well understood. In this study, three different commercial live attenuated Salmonella vaccines (AviPro^® Salmonella Vac T, AviPro^® Salmonella DUO, and AviPro^® Salmonella Vac E) were used to orally vaccinate broiler chickens, and cecal contents were collected for microbiomes analysis by 16S rRNA next generation sequencing. Quantitative real-time PCR (qPCR) was used to study the cecal immune-related genes expression in the treatment groups, while Salmonella-specific antibodies were analyzed from sera and cecal extracts by enzyme-linked immunosorbent assay (ELISA). We show that vaccination with live attenuated Salmonella vaccines had a significant influence on the variability of the broiler cecal microbiota (p = 0.016). Furthermore, the vaccines AviPro^® Salmonella Vac T and AviPro^® Salmonella DUO, but not AviPro^® Salmonella Vac E, had a significant effect (p = 0.024) on microbiota composition. This suggests that the live vaccine type used can differently alter the microbiota profiles, driving the gut colonization resistance and immune responses to pathogenic bacteria, and might impact the overall chicken health and productivity. Further investigation is, however, required to confirm this.

Cecal Microbiota Development and Physiological Responses of Broilers Following Early Life Microbial Inoculation Using Different Delivery Methods and Microbial Sources

Broilers in intensive systems may lack commensal microbes that have coevolved with chickens in nature. This study evaluated the effects of microbial inocula and delivery methods applied to day-old chicks on the development of the cecal microbiota. Specifically, chicks were inoculated with cecal contents or microbial cultures, and the efficacies of three delivery methods (oral gavage, spraying inoculum into the bedding, and cohousing) were evaluated. Also, a competitive study evaluated the colonization ability of bacteria sourced from extensive or intensive poultry production systems. The microbiota of inoculated birds presented higher phylogenetic diversity values (PD) and higher relative abundance values of Bacteroidetes, compared with a control. Additionally, a reduction in the ileal villus height/crypt depth ratio and increased cecal IL-6, IL-10, propionate, and valerate concentrations were observed in birds that were inoculated with cecal contents. Across the experiments, the chicks in the control groups presented higher relative abundance values of Escherichia/Shigella than did the inoculated birds. Specific microbes from intensively or extensively raised chickens were able to colonize the ceca, and inocula from intensive production systems promoted higher relative abundance values of Escherichia/Shigella. We concluded that Alistipes, Bacteroides, Barnesiella, Mediterranea, Parabacteroides, Megamonas, and Phascolarctobacterium are effective colonizers of the broiler ceca. In addition, oral gavage, spray, and cohousing can be used as delivery methods for microbial transplantation, as indicated by their effects on the cecal microbiota, intestinal morphology, short-chain fatty acids concentration, and cytokine/chemokine levels. These findings will guide future research on the development of next-generation probiotics that are able to colonize and persist in the chicken intestinal tract after a single exposure. IMPORTANCE The strict biosecurity procedures employed in the poultry industry may inadvertently hinder the transmission of beneficial commensal bacteria that chickens would encounter in natural environments. This research aims at identifying bacteria that can colonize and persist in the chicken gut after a single exposure. We evaluated different microbial inocula that were obtained from healthy adult chicken donors as well as three delivery methods for their effects on microbiota composition and bird physiology. In addition, we conducted a competitive assay to test the colonization abilities of bacteria sourced from intensively versus extensively raised chickens. Our results indicated that some bacteria are consistently increased in birds that are exposed to microbial inoculations. These bacteria can be isolated and employed in future research on the development of next-generation probiotics that contain species that are highly adapted to the chicken gut.

An Edible Biopolymeric Microcapsular Wrapping Integrating Lytic Bacteriophage Particles for Salmonella enterica: Potential for Integration into Poultry Feed

This research work aimed at developing an edible biopolymeric microcapsular wrapping (EBMW) integrating lytic bacteriophage particles for Salmonella enterica, with potential application in poultry feed for biocontrol of that pathogen. This pathogen is known as one of the main microorganisms responsible for contamination in the food industry and in foodstuff. The current techniques for decontamination and pathogen control in the food industry can be very expensive, not very selective, and even outdated, such as the use of broad-spectrum antibiotics that end up selecting resistant bacteria. Hence, there is a need for new technologies for pathogen biocontrol. In this context, bacteriophage-based biocontrol appears as a potential alternative. As a cocktail, both phages were able to significantly reduce the bacterial load after 12 h of treatment, at either multiplicity of infection (MOI) 1 and 10, by 84.3% and 87.6%, respectively. Entrapment of the phage virions within the EBMW matrix did not exert any deleterious effect upon their lytic activity. The results obtained showed high promise for integration in poultry feed aiming at controlling Salmonella enterica, since the edible biopolymeric microcapsular wrapping integrating lytic bacteriophage particles developed was successful in maintaining lytic phage viability while fully stabilizing the phage particles.

Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces

American cranberry (Vaccinium macrocarpon) and lowbush/wild blueberry (V. angustifolium) pomace are polyphenol-rich products having potentially beneficial effects in broiler chickens. This study investigated the cecal microbiome of broiler-vaccinated or non-vaccinated birds against coccidiosis. Birds in each of the two groups (vaccinated or non-vaccinated) were fed a basal non-supplemented diet (NC), a basal diet supplemented with bacitracin (BAC), American cranberry (CP), and lowbush blueberry (BP) pomace alone or in combination (CP + BP). At 21 days of age, cecal DNA samples were extracted and analyzed using both whole-metagenome shotgun sequencing and targeted-resistome sequencing approaches. Ceca from vaccinated birds showed a lower abundance of Lactobacillus and a higher abundance of Escherichia coli than non-vaccinated birds (p < 0.05). The highest and lowest abundance of L. crispatus and E. coli, respectively, were observed in birds fed CP, BP, and CP + BP compared to those from NC or BAC treatments (p < 0.05). Coccidiosis vaccination affected the abundance of virulence genes (VGs) related to adherence, flagella, iron utilization, and secretion system. Toxin-related genes were observed in vaccinated birds (p < 0.05) in general, with less prevalence in birds fed CP, BP, and CP + BP than NC and BAC (p < 0.05). More than 75 antimicrobial resistance genes (ARGs) detected by the shotgun metagenomics sequencing were impacted by vaccination. Ceca from birds fed CP, BP, and CP + BP showed the lowest (p < 0.05) abundances of ARGs related to multi-drug efflux pumps, modifying/hydrolyzing enzyme and target-mediated mutation, when compared to ceca from birds fed BAC. Targeted metagenomics showed that resistome from BP treatment was distant to other groups for antimicrobials, such as aminoglycosides (p < 0.05). Significant differences in the richness were observed between the vaccinated and non-vaccinated groups for aminoglycosides, β-lactams, lincosamides, and trimethoprim resistance genes (p < 0.05). Overall, this study demonstrated that dietary berry pomaces and coccidiosis vaccination significantly impacted cecal microbiota, virulome, resistome, and metabolic pathways in broiler chickens.

Supplemental enzymes and probiotics on the gut health of broilers fed with a newly harvested corn diet

Gut health is important for digestion and absorption of nutrient for animals. The purpose of this study was to investigate the therapeutic effect of enzymes and probiotics alone or in combination on the gut health of broilers fed with newly harvested corn diets. A total of 624 Arbor Acres Plus male broiler chickens were randomly divided into 8 treatment groups (PC: normal corn diet, NC: newly harvested corn diet, DE: NC + glucoamylase, PT: NC + protease, XL: NC + xylanase, BCC: NC + Pediococcus acidilactici BCC-1, DE + PT: NC + glucoamylase + protease, XL+BCC: NC + xylanase + Pediococcus acidilactici BCC-1). Each group was divided into 6 replicates, with 13 birds each. On d 21, intestinal morphological, intestinal tight junction and aquaporins gene expression, cecal short-chain fatty acid concentrations, and microflora were measured. Compared with the newly harvested corn diets (NC), supplemental glucoamylase (DE) significantly increased the relative abundance of Lachnospiraceae (P < 0.05) and decreased the relative abundance of Moraxellaceae (P < 0.05). Supplemental protease (PT) significantly increased the relative abundance of Barnesiella (P < 0.05), but the relative abundance of Campylobacter decreased by 44.4%. Supplemental xylanase (XL) significantly increased the jejunal mRNA expressions of MUC2, Claudin-1, and Occludin (P < 0.01), as well as the cecal digesta contents of acetic acid, butyric acid, and valeric acid (P < 0.01). Supplemental DE combined with PT increased the ileal mRNA expressions of aquaporins (AQP) 2, AQP5, and AQP7 (P < 0.01). Supplemental BCC significantly increased the jejunal villus height and crypt depth (P < 0.01), the jejunal mRNA expressions of MUC2, Claudin-1 and Occludin (P < 0.01), and the relative abundance of Bacteroides (P < 0.05). Supplemental xylanase in combination with BCC significantly increased jejunal villus height and crypt depth (P < 0.01), the ileal mRNA expressions of AQP2, AQP5 and AQP7 (P < 0.01), and the cecal digesta contents of acetic acid, butyric acid, and valeric acid (P < 0.01). This suggests that inclusions of supplemental protease (12,000 U/kg), glucoamylase (60,000 U/kg), or Pediococcus acidilactici BCC-1 (10⁹ cfu/kg) individually or in combination with xylanase (4,800 U/kg) in the newly harvested corn diets can alleviate diarrhea in broilers, and be beneficial for the gut health.

Effects of indoor and outdoor rearing system on geese biochemical parameters and cecal microbial composition

The present study aimed to investigate the impact of indoor and outdoor rearing systems on the biochemistry and microbial composition of White Roman geese, with a particular focus on the gut microbiome. Our results showed that geese reared in an outdoor system had significantly lower serum aspartate aminotransferase (AST) compared to those reared indoors, but lower levels of high-density lipoprotein (HDL) and higher levels of low-density lipoprotein (LDL). Moreover, the cecal microbiota of geese reared outdoors exhibited higher species evenness and increased alpha diversity, with a significant alteration in the F/B ratios. The bacterial taxonomy composition also differed between the 2 rearing systems, with higher relative abundances of the Firmicutes and Actinobacteria and lower relative abundances of the Bacteroidetes and Proteobacteria in the outdoor system. These findings suggest that rearing systems may play a critical role in shaping the gut microbiome and overall health of geese. Notably, our data demonstrated that indoor rearing was associated with a higher abundance of pathogenic genera and a lower abundance of commensal genera compared to outdoor rearing. Our study supports the hypothesis that rearing systems may alter the physiological functions and microbial composition of geese, and highlights the need for further research to confirm and expand upon these findings. In summary, our study underscores the importance of considering the impact of rearing systems on the gut microbiome and health of geese.

Dietary muramidase improved growth performance, feed efficiency, breast meat yield, and welfare of turkeys from hatch to market

Muramidase is an enzyme that hydrolyzes peptidoglycans of bacterial cell walls and improves performance of broilers in a dose-dependent manner. An experiment was conducted to evaluate muramidase supplementation, at a high or step-down dose, in turkeys from hatch to market. Male, B.U.T. 6 turkey poults were placed in 24 floor pens at 32 birds per pen. Poults were fed 1 of 3 diets from d 1 to 126 of age. There were 8 replicate pens per treatment. The treatments were a control (CTL) diet, the CTL plus muramidase at 45,000 LSU(F)/kg from phase 1 to 6 (BAL45), and the CTL plus muramidase at 45,000 LSU(F)/kg from phase 1 to 3 and decreased to 25,000 LSU(F)/kg from phase 4 to 6 (BAL45-25). Data were analyzed using SAS. The model included treatment and block and means were separated by Fisher LSD test. Birds fed BAL45 were heavier (P < 0.05) and had a greater (P < 0.05) average daily gain compared with birds fed the CTL from hatch to d 126 of age. Birds fed BAL45-25 had a final BW and average daily gain intermediate to or equivalent to birds fed BAL45 at the same phases. Feed conversion ratio was improved (P < 0.05) in birds fed BAL45 compared with birds fed the CTL and intermediate in birds fed BAL45-25. Breast meat yield was greater (P < 0.05) in turkeys fed muramidase, regardless of dose, compared with birds fed the CTL. There was no effect of treatment on muramic acid content in the jejunum digesta or litter scores. The frequency of pododermatitis score 1 was greater (P < 0.05) and score 2 was lower (P < 0.05) in birds fed muramidase, regardless of dose, compared with birds fed the CTL diet. In conclusion, muramidase supplementation improved performance, breast meat yield, feed efficiency and some markers of welfare, proportional to the dose in the diets.

Subclinical doses of dietary fumonisins and deoxynivalenol cause cecal microbiota dysbiosis in broiler chickens challenged with Clostridium perfringens

Fusarium toxins are one of the most common contaminants in poultry diets. The co-occurrence of fumonisins (FUM) and deoxynivalenol (DON), even at a subclinical dose, negatively affects the growth performance, intestinal integrity and induce subclinical necrotic enteritis in broiler chickens. Loss of gut integrity can be expected to alter the intestinal microbiota’s composition. The objective of this study was to identify the effects of combined FUM and DON on the cecal microbiome profile and predicted metabolic functions and a short chain fatty acid profile in broilers challenged with Clostridium perfringens. A total of 240 1 day-old chicks were randomly assigned to two treatments: a control diet and the control diet with 3 mg/kg FUM + 4 mg/kg DON each with eight replications. All the birds were received cocci vaccine at d0. All birds in both treatment groups were challenged with C. perfringens 1 × 108 CFU via feed on d 19 and 20 to achieve 5% mortality. On d 35, the FUM and DON contaminated diet numerically (P = 0.06) decreased the body weight gain (BWG) by 84 g compared to the control group. The bacterial compositions of the cecal contents were analyzed by sequencing the V3–V4 region of the 16S rRNA gene. Overall, microbial richness and diversity increased (P &lt; 0.02) during the studied period (d 21–35). Cecal contents of birds in the FUM + DON group had greater (P &lt; 0.05) microbial evenness and diversity (Shannon index) compared to the control group. FUM + DON exposure decreased (P = 0.001) the relative abundance of Proteobacteria in the cecal content, compared to the control group. The combined FUM + DON significantly increased the relative abundance of the Defluviitaleaceae and Lachnospiraceae families (P &lt; 0.05) but decreased the abundances of the Moraxellaceae and Streptococcaceae (P &lt; 0.05) compared to the control group birds. At the genus level, FUM + DON exposure decreased (P &lt; 0.05) Acinetobacter and Pseudomonas abundance and had a tendency (P = 0.08) to decrease Thermincola abundance compared to the control group. In the ileum, no NE-specific microscopic abnormalities were found; however, the tip of the ileal villi were compromised. The present findings showed that dietary FUM and DON contamination, even at subclinical levels, altered cecal microbial composition, dysregulated intestinal functions, and impaired the gut immune response, potentially predisposing the birds to necrotic enteritis.

Amorphous solid dispersion preparation via co-precipitation improves the dissolution, oral bioavailability and intestinal health enhancement properties of magnolol

Magnolol (MAG) is a multifunctional plant polyphenol with anti-inflammatory, antibacterial, antioxidant and antitumor properties. In poultry, it has been shown to improve growth performance, antioxidant, immune functions and intestinal health. However, its applications are limited by poor solubility and low oral bioavailability. This study aimed at improving the water solubility of MAG through solid dispersion and investigating its effects in Arbor Acre (AA) broilers. Hydroxypropyl methylcellulose succinic acid (HPMCAS) was used as a carrier to prepare magnolol solid dispersions (MAG-HPMCAS SD) via antisolvent coprecipitation, which were characterized thereafter. Optimal formulation proportions for SD were screened by in vitro dissolution assays, while its effects on improving absorption were investigated via in vivo pharmacokinetic assays. In addition, we evaluated the effects of MAG-HPMCAS SD on growth performance, antioxidant status, and gut microbiota in AA broilers. The powder samples prepared via antisolvent coprecipitation did not exhibit a crystal diffraction peak of MAG in powder X-ray diffractions or melting point peak in differential scanning calorimetry, proving the successful preparation of an amorphous solid dispersion system. The in vitro dissolution assay showed that the cumulative dissolution rate of MAG-HPMCAS(LF) SD (2:8, w/w) was 100%. Pharmacokinetic analyses revealed that the peak concentration (C_max) of MAG-HPMCAS SD was 5.07 ± 0.73 μg/mL, which was 1.76 times greater than that of MAG. In addition, AUC_0-48 and t_1/2 of MAG-HPMCAS SD were 40.49 ± 6.29 g·h/mL and 9.15 ± 3.23 h, respectively, which were 2.17 and 2.56 times higher than those of MAG. Supplementation of MAG-HPMCAS SD in AA broilers significantly increased ADG (7-14 d and 15-21 d) and reduced feed conversion ratio (15-21 d) (P < 0.05). Bacterial diversity in the MAG-HPMCAS SD-supplemented group was greater than in the Control and MAG-supplemented group. Supplementation of MAG-HPMCAS SD stimulated the proliferation of beneficial bacteria, such as Lactobacillaceae and Bifidobacteriaceae. In conclusion, the MAG-HPMCAS SD prepared by coprecipitation improved the dissolution rate, the bioavailability of MAG, growth promotion, antioxidant effects and gut health in broilers.

Microbial diversity and community composition of fecal microbiota in dual-purpose and egg type ducks

Introduction

Ducks are important agricultural animals, which can be divided into egg and dual-purpose type ducks according to economic use. The gut microbiota of ducks plays an important role in their metabolism, immune regulation, and health maintenance.

Methods

Here, we use 16S rDNA V4 hypervariable amplicon sequencing to investigate the compositions and community structures of fecal microbiota between egg (five breeds, 96 individuals) and dual-purpose type ducks (four breeds, 73 individuals) that were reared under the same conditions.

Results

The alpha diversity of fecal microflora in egg type ducks was significantly higher than that in dual-type ducks. In contrast, there is no significant difference in the fecal microbial community richness between the two groups. MetaStat analysis showed that the abundance of Peptostreptococcaceae, Streptococcaceae, Lactobacillus, Romboutsia, and Campylobacter were significantly different between the two groups. The biomarkers associated with the egg and dual-purpose type ducks were identified using LEfSe analysis and IndVal index. Function prediction of the gut microbiota indicated significant differences between the two groups. The functions of environmental information processing, carbohydrate metabolism, lipid metabolism, xenobiotic biodegradation and metabolism, and metabolism of terpenoids and polyketides were more abundant in egg type ducks. Conversely, the genetic information processing, nucleotide metabolism, biosynthesis of amino acids and secondary metabolites, glycan biosynthesis and metabolism, fatty acid elongation, and insulin resistance were significantly enriched in dual-purpose type ducks.

Discussion

This study explored the structure and diversity of the gut microbiota of ducks from different economic-use groups, and provides a reference for improving duck performance by using related probiotics in production.

The Gut Microbiota of Broilers Reared with and without Antibiotic Treatment

The aim of this study was to examine the microbiota in broilers reared with and without antibiotics and to investigate differences between the upper, middle and lower sections of the gastrointestinal tract (GIT). One of two commercial flocks was treated with an antibiotic (T) (20 mg trimethoprim and 100 mg sulfamethoxazole per ml in the drinking water for 3 days) and the other was left untreated (UT). The GIT contents of 51 treated and untreated birds were aseptically removed from the upper (U), middle (M) and lower (L) sections. These were pooled in triplicate (n = 17 per section per flock), the DNA extracted and purified, 16S amplicon metagenomic sequencing performed and the resultant data analysed using a range of bioinformatics software. There were significant differences in the microbiota of the upper, middle and lower GIT, and treatment with the antibiotic significantly affected the microbiota in each of these sections. This study provides new data on broiler GIT microbiota and suggests that GIT location is a more important determinant of the constituent bacterial flora rather than the use or otherwise of antimicrobial treatments, at least when applied early in the production cycle.

No evidence for associations between brood size, gut microbiome diversity and survival in great tit (Parus major) nestlings

BACKGROUND

The gut microbiome forms at an early stage, yet data on the environmental factors influencing the development of wild avian microbiomes is limited. As the gut microbiome is a vital part of organismal health, it is important to understand how it may connect to host performance. The early studies with wild gut microbiome have shown that the rearing environment may be of importance in gut microbiome formation, yet the results vary across taxa, and the effects of specific environmental factors have not been characterized. Here, wild great tit (Parus major) broods were manipulated to either reduce or enlarge the original brood soon after hatching. We investigated if brood size was associated with nestling bacterial gut microbiome, and whether gut microbiome diversity predicted survival. Fecal samples were collected at mid-nestling stage and sequenced with the 16S rRNA gene amplicon sequencing, and nestling growth and survival were measured.

RESULTS

Gut microbiome diversity showed high variation between individuals, but this variation was not significantly explained by brood size or body mass. Additionally, we did not find a significant effect of brood size on body mass or gut microbiome composition. We also demonstrated that early handling had no impact on nestling performance or gut microbiome. Furthermore, we found no significant association between gut microbiome diversity and short-term (survival to fledging) or mid-term (apparent juvenile) survival.

CONCLUSIONS

We found no clear association between early-life environment, offspring condition and gut microbiome. This suggests that brood size is not a significantly contributing factor to great tit nestling condition, and that other environmental and genetic factors may be more strongly linked to offspring condition and gut microbiome. Future studies should expand into other early-life environmental factors e.g., diet composition and quality, and parental influences.

Growth performance, caecal microbiome profile, short-chain fatty acids, and litter characteristics in response to placement on reused litter and combined threonine, arginine and glutamine supplementation to juvenile male broiler chickens

BACKGROUND

Exposure of broilers to litter microbiome may increase specific amino acid (AA) requirements towards activated immune responses. This may challenge the generality of the ideal protein (IP) concept, in which dietary essential AA to lysine ratios aimed to mimic presumably constant AA to lysine ratios in whole bird requirements. Therefore, we tested the effect of threonine, arginine and glutamine (TAG) supplementation to IP-based control diets (C) on performance, caecal microbiome composition, short-chain fatty acids and litter characteristics of broiler chickens placed on reused litter.

RESULTS

Thirty-two pens with ten male broiler chickens each were used in a 2 × 2 factorial arrangement of two diet treatments (with or without TAG supplementation) and two litter treatments (placement on clean or reused litter) for 21 days (n = 8). Caecal contents were analysed for microbiome profile using percent guanine + cytosine (%G + C profile) method and short chain fatty acids. TAG-supplemented birds underperformed compared to C birds (P = 0.002), whereas birds placed on reused litter outperformed those on clean litter (P = 0.047). Diet, reused litter and their interaction impacted the %G + C profile at different ranges. Whilst TAG supplementation reduced bacterial abundance at %G + C 51-56 (P < 0.05), reused litter placement tended to reduce %G + C 23-31 and increase %G + C 56-59 (P < 0.10). However, TAG supplementation reduced bacterial abundance at %G + C 47-51 (P < 0.05) and increased caecal branched chain fatty acids on clean litter only (P = 0.025). Greater levels of propionic acid were observed for C birds placed on reused litter only (P = 0.008). Litter pH was greater for reused litter pens than clean litter pens at day 21 (P < 0.001). In addition, litter moisture content was less for TAG birds and reused litter pens compared to C birds (P = 0.041) and clean litter pens (P < 0.001), respectively.

CONCLUSIONS

These data support the view that irrespective of performance benefits arising from bird placement on reused litter, TAG supplementation to IP-formulated baseline rations impaired growth, supported by the lowered abundance of caecal bacteria known to dominate in well-performing birds and greater levels of caecal branched chain fatty acids.

Microbial diversity and metabolic function in duodenum, jejunum and ileum of emu (Dromaius novaehollandiae)

Emus (Dromaius novaehollandiae), a large flightless omnivorous ratite, are farmed for their fat and meat. Emu fat can be rendered into oil for therapeutic and cosmetic use. They are capable of gaining a significant portion of its daily energy requirement from the digestion of plant fibre. Despite of its large body size and low metabolic rate, emus have a relatively simple gastroinstetinal (GI) tract with a short mean digesta retention time. However, little is known about the GI microbial diversity of emus. The objective of this study was to characterize the intraluminal intestinal bacterial community in the different segments of small intestine (duodenum, jejunum, and ileum) using pyrotag sequencing and compare that with the ceca. Gut content samples were collected from each of four adult emus (2 males, 2 females; 5-6 years old) that were free ranged but supplemented with a barley-alfalfa-canola based diet. We amplified the V3-V5 region of 16S rRNA gene to identify the bacterial community using Roche 454 Junior system. After quality trimming, a total of 165,585 sequence reads were obtained from different segments of the small intestine (SI). A total of 701 operational taxonomic units (OTUs) were identified in the different segments of small intestine. Firmicutes (14-99%) and Proteobacteria (0.5-76%) were the most predominant bacterial phyla in the small intestine. Based on species richness estimation (Chao1 index), the average number of estimated OTUs in the small intestinal compartments were 148 in Duodenum, 167 in Jejunum, and 85 in Ileum, respectively. Low number of core OTUs identified in each compartment of small intestine across individual birds (Duodenum: 13 OTUs, Jejunum: 2 OTUs, Ileum: 14 OTUs) indicated unique bacterial community in each bird. Moreover, only 2 OTUs (Escherichia and Sinobacteraceae) were identified as core bacteria along the whole small intestine. PICRUSt analysis has indicated that the detoxification of plant material and environmental chemicals seem to be performed by SI microbiota, especially those in the jejunum. The emu cecal microbiome has more genes than SI segments involving in protective or immune response to enteric pathogens. Microbial digestion and fermentation is mostly in the jejunum and ceca. This is the first study to characterize the microbiota of different compartments of the emu intestines via gut samples and not fecal samples. Results from this study allow us to further investigate the influence of the seasonal and physiological changes of intestinal microbiota on the nutrition of emus and indirectly influence the fatty acid composition of emu fat.

Physiological effects of in ovo delivery of bioactive substances in broiler chickens

The poultry industry has improved genetics, nutrition, and management practices, resulting in fast-growing chickens; however, disturbances during embryonic development may affect the entire production cycle and cause irreversible losses to broiler chicken producers. The most crucial time in the chicks' development appears to be the perinatal period, which encompasses the last few days of pre-hatch and the first few days of post-hatch. During this critical period, intestinal development occurs rapidly, and the chicks undergo a metabolic and physiological shift from the utilization of egg nutrients to exogenous feed. However, the nutrient reserve of the egg yolk may not be enough to sustain the late stage of embryonic development and provide energy for the hatching process. In addition, modern hatchery practices cause a delay in access to feed immediately post-hatch, and this can potentially affect the intestinal microbiome, health, development, and growth of the chickens. Development of the in ovo technology allowing for the delivery of bioactive substances into chicken embryos during their development represents a way to accommodate the perinatal period, late embryo development, and post-hatch growth. Many bioactive substances have been delivered through the in ovo technology, including carbohydrates, amino acids, hormones, prebiotics, probiotics and synbiotics, antibodies, immunostimulants, minerals, and microorganisms with a variety of physiological effects. In this review, we focused on the physiological effects of the in ovo delivery of these substances, including their effects on embryo development, gastrointestinal tract function and health, nutrient digestion, immune system development and function, bone development, overall growth performance, muscle development and meat quality, gastrointestinal tract microbiota development, heat stress response, pathogens exclusion, and birds metabolism, as well as transcriptome and proteome. We believe that this method is widely underestimated and underused by the poultry industry.

A phytobiotic extract, in an aqueous or in a cyclodextrin encapsulated form, added in diet affects meat oxidation, cellular responses and intestinal morphometry and microbiota of broilers

The present trial examined the effects of diet supplementation with an extract including Greek oregano, garlic, rock samphire, and camelina, administered either in aqueous form or encapsulated in cyclodextrin, on broiler chickens. The duration of the trial was 35 days. Mixed broiler chicks (Ross-308, 120 individuals, 1 day old) were randomly allocated to one of three groups, each with four replicates. Control group A (CONTROL) was fed a basal diet consisting of maize and soybean. The diet of the AQORGCC and CDORGCC groups was further supplemented with aqueous and cyclodextrin-encapsulated herbal extracts, respectively. Levels of lipid and protein oxidation were determined in breast and thigh meat samples. Furthermore, to address cellular stress and signaling responses, the expression patterns of heat shock proteins (Hsp60, Hsp70, and Hsp90), mitogen-activated protein kinases (P38 and P44/42 MAPKs), and apoptotic-related proteins (Bcl-2/Bad ratio) were investigated in breast and thigh tissues using Western blot analysis. The intestinal morphometry of the duodenum, jejunum, and ileum was also assessed. To investigate ileal and cecal bacterial community diversity, 16S rRNA gene high-throughput amplicon sequencing on the V3–V4 hypervariable region was performed. The results showed that the herbal extract in cyclodextrin delayed meat lipid oxidation. According to the protein expression patterns, the formulated diets elicited tissue-specific cellular responses. Compared with the CONTROL group, dietary supplementation with the encapsulated form resulted in significant Hsp induction and MAPK activation, whereas, in the group whose diet was supplemented with the aqueous form, the expression of most of the examined proteins decreased or was maintained at a constant level. Villus height and lamina propria width were mostly affected by the aqueous herbal extract, whereas the number of goblet cells remained unchanged among the groups. Firmicutes, Proteobacteria, and Bacteroidota were the major phyla in mean relative abundance in all diets in both cecal and ileal samples. Alpha-diversity indices highlighted higher species richness and diversity in the cecum than in the ileum, as well as in chicks treated with the aqueous extract of the herbal mixture, but only in the cecum. Cecal beta-diversity differed between the cyclodextrin and the CONTROL groups, while ileal beta-diversity varied only between the aqueous-treated group and the CONTROL group. In conclusion, the dietary mixtures of herbal extracts (particularly those encapsulated in cyclodextrin) improved protein and lipid oxidation and increased the number of beneficial lactic acid-producing bacteria in the cecum, whereas the aqueous herbal extract mostly affected bacterial activity in the proximal part of the chicken intestine. Similarly, intestinal morphometry in the duodenum, jejunum, and ileum was mostly affected by the aqueous herbal extract, which seems to inhibit proteins associated with stress signaling in meat.

The Development of Gut Microbiota and Its Changes Following C. jejuni Infection in Broilers

The gut is home to more than millions of bacterial species. The gut bacteria coexist with the host in a symbiotic relationship that can influence the host's metabolism, nutrition, and physiology and even module various immune functions. The commensal gut microbiota plays a crucial role in shaping the immune response and provides a continuous stimulus to maintain an activated immune system. The recent advancements in high throughput omics technologies have improved our understanding of the role of commensal bacteria in developing the immune system in chickens. Chicken meat continues to be one of the most consumed sources of protein worldwide, with the demand expected to increase significantly by the year 2050. Yet, chickens are a significant reservoir for human foodborne pathogens such as Campylobacter jejuni. Understanding the interaction between the commensal bacteria and C. jejuni is essential in developing novel technologies to decrease C. jejuni load in broilers. This review aims to provide current knowledge of gut microbiota development and its interaction with the immune system in broilers. Additionally, the effect of C. jejuni infection on the gut microbiota is addressed.

Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses

In this study, we investigated the dynamics of the ceca and litter microbiome of chickens from post-hatch through pre-harvest. To achieve this, six hundred one-day old Cobb 500 broiler chicks were raised on floor pens for 49 days in two separate houses. We performed short-read and full-length sequencing of the bacterial 16S rRNA gene present in the meconium and in cecal and litter samples collected over the duration of the study. In addition, we determined the antimicrobial resistance (AMR) phenotype of Escherichia coli and Enterococcus spp. isolated from the meconium and the ceca of 49-day old chickens. We monitored the relative humidity, temperature, and ammonia in each house daily and the pH and moisture of litter samples weekly. The overall microbial community structure of the ceca and litter consistently changed throughout the course of the grow-out and correlated with some of the environmental parameters measured (p < 0.05). We found that the ceca and litter microbiome were similar in the two houses at the beginning of the experiment, but over time, the microbial community separated and differed between the houses. When we compared the environmental parameters in the two houses, we found no significant differences in the first half of the growth cycle (day 0-21), but morning temperature, morning humidity, and ammonia significantly differed (p < 0.05) between the two houses from day 22-49. Lastly, the prevalence of AMR in cecal E. coli isolates differed from meconium isolates (p < 0.001), while the AMR phenotype of cecal Enterococcus isolates differed between houses (p < 0.05).

Mapping chicken production and distribution networks in Vietnam: An analysis of socio-economic factors and their epidemiological significances

The growing chicken industry in Viet Nam has an increasingly important contribution to the country's food security, but its development requires careful planning to prevent disease risks. This study characterizes the chicken production and distribution networks in Vietnam and identifies potential factors that could promote disease emergence and transmission. Qualitative data were collected from interviews with 29 key informants from five stakeholder groups representing the main nodes from chicken production and distribution networks (PDN). Three main networks were identified based on production type: a colored broiler and spent hen network, a white (or exotic) broiler network, and an egg network. Colored chickens and spent hens are the most preferred commodity by vietnamese consumers and their PDN is composed of production units differing in their scale and management and with long distribution chains involving numerous small-scale independent stakeholders. Live bird markets plays a central role in this network, which is driven by consumers' preference for live chickens. The white chicken network presents an important duality, as it is composed of both a large number of independent household farms and traders operating independently with little chain coordination, and of large farms contracted by vertically-integrated companies. The egg PDN was the most organized network, being mostly controlled by large vertically-integrated companies. High level specialization and diversification of stakeholders is found in all three networks. Stakeholders' perceptions of the main factors promoting disease risk along the PDN were the low biosecurity in household farms and live bird markets, mobile traders, the informal slaughter of birds and the management of sick birds. Findings from this study can be used to plan future studies to support food system planners in the development of safer poultry production and distribution in Vietnam.

Dietary muramidase increases ileal amino acid digestibility of wheat and corn-based broiler diets without affecting endogenous amino acid losses

The objective of these studies was to evaluate the impact of dietary muramidase (MUR) on endogenous amino acids (AA) losses and digestibility of nutrients in wheat and corn-based broiler diets. In experiment 1, the effect of dietary MUR on the flow of endogenous AA (EAA) at the jejunum and terminal ileum of broilers were assessed using either the nitrogen (N) free diet method (NFD) or the highly digestible protein diet method (HDP; 100 g casein/kg diet). Sialic acid and muramic acid concentrations were measured in the jejunal content. In experiment 2, a 2x2x2 factorial arrangement of treatments with 2 base grains (wheat or corn), with low or high metabolizable energy (ME) levels, and without or with MUR supplementation was implemented. All diets contained phytase, xylanase, and cellulase. Apparent ileal digestibility (AID) of dry matter (DM), protein (CP), amino acids (AA), crude fat, and energy, as well as the apparent total tract metabolizability (ATTM) of DM, CP, and gross energy (GE) were determined. The standardized ileal digestibility (SID) of AA was obtained by correcting AID values for basal ileal EAA obtained from chicks fed with NFD or HDP in experiment 1, jejunal EAA flow of all AA was higher (P < 0.001) compared to the ileum, but this effect was method dependent. Jejunal, but not ileal, EAA flow measured with HDP was higher compared to NFD, as well as sialic acid (P < 0.001) and muramic acid (P < 0.004) concentrations. Muramidase inclusion had no effect on basal EAA flow, independently of the segment and the method used. In experiment 2, dietary MUR supplementation increased the AID of CP (P < 0.05), all AA, and tended (P = 0.07) to increase the AID of GE, independently of the cereal type used. However, ATTM of DM and GE, but not CP, increased with MUR inclusion compared with the control treatments, especially in wheat and low ME diets (P < 0.05). In conclusion, MUR supplementation improved AID of CP and AA without affecting EAA losses and increases energy utilization.

A meta-analysis of the effects of clay mineral supplementation on alkaline phosphatase, broiler health, and performance

The crucial constraint in the broiler production sector is feed efficiency; many feed additives have been widely employed to increase broiler growth. Nonetheless, some of these substances exacerbate health and animal-based food product safety concerns. This meta-analysis examines the effect of clay minerals on alkaline phosphatase (ALP), broiler health, and performance. Metadata was constructed from 369 data items that were harvested from 86 studies. The addition of clay minerals was set as a fixed effect and the difference between experiments was established as a random effect. The metadata were fitted using a linear mixed model. Due to the presence of clay minerals, growth performance as assessed by body weight (BW), average daily gain (ADG), and performance efficiency index (PEI) increased significantly (P < 0.01). In the total period, the increases of BW, ADG, and PEI were 4.12 g, 0.0714 g/d, and 0.648, respectively, per unit of clay minerals added. Clay minerals did not affect blood serum parameters (e.g., ALP and calcium). The IgA and IgM concentrations in the jejunum and ileum were significantly greater (P < 0.01) in the starter phase. Among clay minerals, broilers fed diets with aluminosilicate, halloysite, kaolin, and zeolite consistently exhibited higher (P < 0.05) BW, ADG, PEI, and lower feed conversion ratio (P < 0.05) in the finisher phase. Aluminosilicate was the only clay that increased (P < 0.05) secretory IgA concentration in both jejunum and ileum. In conclusion, clay minerals could be used as a growth promoter, especially during the finisher phase, without adversely affecting feed intake, liver function, and mineral metabolism in broiler chickens. Aluminosilicate was superior in improving the mucosal immunity status of broiler chickens.

An In Vitro Model of the Chicken Gastrointestinal Tract with Special Emphasis to the Cecal Microbiota

An in vitro model of the upper gastrointestinal tract as well as the chicken cecum was developed to have a predictive tool for estimating the production performance of animals by analyzing the feeding value of a certain diet. The upper gastrointestinal tract consists of a batch type model, whereas the cecal model is comprised of 4 semi-continuous connected vessels inoculated with cecal or fecal microbes. The upper gastrointestinal tract and cecal simulations were both run with a corn- and a wheat-based diet to simulate 2 typical feed types. Samples were collected after the 5-h cecal simulations and aliquots were frozen to assess inoculum stability. The microbiota was analyzed by 16S rRNA gene sequencing, whereas short chain fatty acids as microbial metabolites were analyzed by using gas chromatography. As expected, some significant differences in microbial abundance after simulation between the cecal and fecal slurry samples (P = 0.001) were detected, as well between the fresh and frozen status (P = 0.001), hence simulations inoculated with cecal and fresh samples being more diverse. For the measured metabolites, almost all of them increased (P < 0.05) significantly when comparing fresh and frozen inoculum. The present chicken intestinal in vitro model represents a rapid systematic screening system for studying dietary related microbial changes and reducing the need of animal sacrifice for experimentation.

How do living conditions affect the gut microbiota of endangered Père David's deer (Elaphurus davidianus)? Initial findings from the warm temperate zone

Reintroduction is an effective strategy in the conservation of endangered species under scientific monitoring. Intestinal flora plays an important role in the envir onmental adaptation of endangered Père David's deer (Elaphurus davidianus). In this study, 34 fecal samples from E. davidianus were collected from different habitats in Tianjin city of China to investigate differences in the intestinal flora under captive and semi-free-ranging conditions. Based on 16S rRNA high-throughput sequencing technology, a total of 23 phyla and 518 genera were obtained. Firmicutes was dominant in all individuals. At the genus level, UCG-005 (13.05%) and Rikenellaceae_RC9_gut_group (8.94%) were dominant in captive individuals, while Psychrobacillus (26.53%) and Pseudomonas (11.33%) were dominant in semi-free-ranging individuals. Alpha diversity results showed that the intestinal flora richness and diversity were significantly (P < 0.001) higher in captive individuals than in semi-free-ranging individuals. Beta diversity analysis also showed a significant difference (P = 0.001) between the two groups. In addition, some age- and sex-related genera such as Monoglobus were identified. In summary, the structure and diversity of intestinal flora showed significant habitat variation. This is the first time an analysis has been undertaken of the structural differences of the intestinal flora in Père David's deer, under different habitats in the warm temperate zone, providing a reference basis for the conservation of endangered species.

Current and future interventions for improving poultry health and poultry food safety and security: A comprehensive review

Poultry is thriving across the globe. Chicken meat is the most preferred poultry worldwide, and its popularity is increasing. However, poultry also threatens human hygiene, especially as a fomite of infectious diseases caused by the major foodborne pathogens (Campylobacter, Salmonella, and Listeria). Preventing pathogenic bacterial biofilm is crucial in the chicken industry due to increasing food safety hazards caused by recurring contamination and the rapid degradation of meat, as well as the increased resistance of bacteria to cleaning and disinfection procedures commonly used in chicken processing plants. To address this, various innovative and promising strategies to combat bacterial resistance and biofilm are emerging to improve food safety and quality and extend shelf-life. In particular, natural compounds are attractive because of their potential antimicrobial activities. Natural compounds can also boost the immune system and improve poultry health and performance. In addition to phytochemicals, bacteriophages, nanoparticles, coatings, enzymes, and probiotics represent unique and environmentally friendly strategies in the poultry processing industry to prevent foodborne pathogens from reaching the consumer. Lactoferrin, bacteriocin, antimicrobial peptides, cell-free supernatants, and biosurfactants are also of considerable interest for their prospective application as natural antimicrobials for improving the safety of raw poultry meat. This review aims to describe the feasibility of these proposed strategies and provide an overview of recent published evidences to control microorganisms in the poultry industry, considering the human health, food safety, and economic aspects of poultry production.