Role of diet-microbiota interactions in precision nutrition of the chicken: facts, gaps, and new concepts

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

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

Cell-Free Culture Supernatant of Lactobacillus acidophilus AG01 and Bifidobacterium animalis subsp. lactis AG02 Reduces the Pathogenicity of NetB-Positive Clostridium perfringens in a Chicken Intestinal Epithelial Cell Line

The worldwide reduction in the use of antibiotics in animal feed is fueling the need for alternatives for the prevention and control of poultry intestinal diseases such as necrotic enteritis (NE), which is caused by Clostridium perfringens. This is the first report on the use of an intestinal epithelial chicken cell line (CHIC-8E11) to study the pathogenic traits of C. perfringens and to investigate the mode of action of cell-free supernatants (CFS) from probiotic Lactobacillus acidophilus AG01 and Bifidobacterium animalis subsp. lactis AG02 in reducing the pathogenicity of C. perfringens. The cell adhesion, permeability and cytotoxicity were assessed under challenge with four C. perfringens strains isolated from broiler NE episodes of differing geographical origin (CP1-UK; CP10-Sweden; 25037-CP01 and CP22-USA). All the C. perfringens strains could adhere to the CHIC-8E11 cells, with varying affinity (0.05-0.48% adhesion across the strains). The CFS from one out of two strains (CP22) increased the cell permeability (+4.5-fold vs. the control, p < 0.01), as measured by the fluorescein isothiocyanate-dextran (FD4) content, with NetB toxin implicated in this effect. The CFS from all the strains was cytotoxic against the CHIC-8E11 cells in a dose- and strain-dependent manner (cytotoxicity 23-62% across the strains when dosed at 50 µL/mL, as assessed by the MTT cell viability assay). Pre-treatment of the cells with CFS from B. animalis subsp. lactis AG02 but not L. acidophilus AG01 reduced the cell adhesion of three out of four C. perfringens strains (by 77-85% vs. the control, p < 0.001) and reduced the negative effect of two NetB-positive strains on the cell permeability. The CFS of both probiotics alleviated the cytotoxicity of all the C. perfringens strains, which was dependent on the dose. The results confirm the suitability of the CHIC-8E11 cell line for the study of host-pathogen cell interactions in the context of NE caused by C. perfringens and reveal a beneficial mode of action of B. animalis subsp. lactis AG02 in reducing C. perfringens cell adhesion and, together with L. acidophilus AG01, in reducing C. perfringens cytotoxicity.

Impact of housing system on intestinal microbiota of laying hens - A systematic review

Studies on the housing system's impact on laying hens' intestinal microbiota were retrieved from the Web of Science, PubMed, and Scopus (between 2017 and 2022). Inclusion criteria were studies that discussed measurable effects related to the topic written in English, Portuguese, and Spanish. Of 3281 articles in the identification stage, 12 studies were used in the systematic review. Asia developed most research relating to the subject. Most studies compared the intestinal microbiota of laying hens from conventional cages versus Cage-Free or Free-Range. However, no study has evaluated the intestinal microbiota of laying hens maintained in an organic system. Greengene and Silva were the most used reference in the studies. According to the results observed in the studies included in the systematic review, there is greater alpha diversity in the alternative system and a high dissimilarity between the conventional and alternative systems. Exposure to environmental factors such as soil, vegetation, natural lighting, access to pastures, and ingesting fibrous foods can lead to changes in the intestinal microbiota. A brief outline of published scientific evidence demonstrates that the housing system can change the gut microbiome of hens. This study summarises the relationship between the housing system and the intestinal microbiome of laying hens and provides a roadmap for future research regarding the gut microbiome of hens.

Necrotic enteritis and antibiotic-free production of broiler chickens: Challenges in testing and using alternative products

The global trend towards raising broiler chickens without the use of in-feed antibiotics (IFAs) means that there is an ongoing need to develop alternative treatments capable of delivering the benefits that IFAs previously provided. IFAs supported the productivity performance of chickens and played a key role in maintaining their health. Necrotic enteritis (NE) is an important disease of broilers that affects health, productivity, and welfare, and was previously well controlled by IFAs. However, with the reduction in IFA use, NE is resurgent in some countries. Vaccines and various feed additives, including pre-, pro-, and postbiotics, phytobiotics, fatty acids, and phage therapies have been introduced as alternative methods of NE control. While some of these feed additives have specific activity against the NE pathogen, Clostridium perfringens, most have the more general goal of reinforcing gut health. Extensive reviews of the effects of many of these feed additives on gut health have been published recently. Hence, rather than cover previously well reviewed areas of research this review focuses on the challenges and pitfalls in undertaking experimental assessment of alternative NE treatments and translating laboratory research to real world commercial production settings. The review is based on the author's particular experience, reading, thoughts, and analysis of the available information and inevitably presents a particular understanding that is likely to be at odds with others thinking on these issues. It is put forward to stimulate thinking and discussion on the issues covered.

Comparative profiling of gut microbiota and metabolome in diet-induced obese and insulin-resistant C57BL/6J mice

Diet-based models are commonly used to investigate obesity and related disorders. We conducted a comparative profiling of three obesogenic diets HFD, high fat diet; HFHF, high fat high fructose diet; and HFCD, high fat choline deficient diet to assess their impact on the gut microbiome and metabolome. After 20 weeks, we analyzed the gut microbiota and metabolomes of liver, plasma, cecal, and fecal samples. Fecal and plasma bile acids (BAs) and fecal short-chain fatty acids (SCFAs) were also examined. Significant changes were observed in fecal and cecal metabolites, with increased Firmicutes and decreased Bacteroidetes in the HFD, HFHF, and HFCD-fed mice compared to chow and LFD (low fat diet)-fed mice. Most BAs were reduced in plasma and fecal samples of obese groups, except taurocholic acid, which increased in HFCD mice's plasma. SCFAs like acetate and butyrate significantly decreased in obesogenic diet groups, while propionic acid specifically decreased in the HFCD group. Pathway analysis revealed significant alterations in amino acid, carbohydrate metabolism, and nucleic acid biosynthesis pathways in obese mice. Surprisingly, even LFD-fed mice showed distinct changes in microbiome and metabolite profiles compared to the chow group. This study provides insights into gut microbiome dysbiosis and metabolite alterations induced by obesogenic and LFD diets in various tissues. These findings aid in selecting suitable diet models to study the role of the gut microbiome and metabolites in obesity and associated disorders, with potential implications for understanding similar pathologies in humans.

Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples

Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.

Current State of Milk, Dairy Products, Meat and Meat Products, Eggs, Fish and Fishery Products Authentication and Chemometrics

Food fraud is a matter of major concern as many foods and beverages do not follow their labelling. Because of economic interests, as well as consumers' health protection, the related topics, food adulteration, counterfeiting, substitution and inaccurate labelling, have become top issues and priorities in food safety and quality. In addition, globalized and complex food supply chains have increased rapidly and contribute to a growing problem affecting local, regional and global food systems. Animal origin food products such as milk, dairy products, meat and meat products, eggs and fish and fishery products are included in the most commonly adulterated food items. In order to prevent unfair competition and protect the rights of consumers, it is vital to detect any kind of adulteration to them. Geographical origin, production methods and farming systems, species identification, processing treatments and the detection of adulterants are among the important authenticity problems for these foods. The existence of accurate and automated analytical techniques in combination with available chemometric tools provides reliable information about adulteration and fraud. Therefore, the purpose of this review is to present the advances made through recent studies in terms of the analytical techniques and chemometric approaches that have been developed to address the authenticity issues in animal origin food products.

Effect of microbial muramidase supplementation in diets formulated with different fiber profiles for broiler chickens raised under various coccidiosis management programs

The objective of the present study was to determine the effects of muramidase (MUR) supplemented to diets formulated with different fiber sources (inert or fermentable) on the growth performance and intestinal parameters of broiler chickens raised under different coccidiosis management programs. A total of 2,208 male Ross 308 broilers were housed in 96 floor pens and distributed into a 2 × 3 × 2 factorial arrangement in a completely randomized block design with 2 sources of fiber (inert or fermentable fiber), 3 coccidiosis management programs (none, vaccine, or Salinomycin), and with or without supplementation of MUR at 35,000 LSU(F)/kg of diet. Body weight gain (BWG), feed intake (FI), and feed conversion ratio (FCR) were calculated for each feeding phase (d 0-14, d 14-28, d 28-36) and from d 0 to 36. On d 17 and d 31, samples were taken to analyze several parameters. The experimental data were analyzed with 3-way ANOVA considering the main effect of fiber source, coccidiosis program, inclusion of MUR, and their interactions using JMP 16.2. 16S rDNA sequencing of the ileal and cecal content was carried out to analyze the diversity, composition, and predictive function of the microbiota. From d 0 to 36, BWG increased (P = 0.05) by 2.5% in birds supplemented with Salinomycin (P = 0.04), and by 2.2% with MUR supplementation (P = 0.02). Salinomycin and MUR improved FCR (P < 0.0001) when compared to nonsupplemented birds. The supplementation of MUR, regardless of the coccidiosis management program, reduced the intestinal viscosity (P = 0.03). On d 31, the highest blood concentration of carotenoids was observed in chickens fed diets supplemented with Salinomycin. MUR led to significant changes in the diversity, composition, and predictive function of the ileal microbiota, mainly on d 31. The results observed herein further explain the positive effects of MUR on the growth performance of broiler chickens.

Chicken adaptive response to nutrient density: immune function change revealed by transcriptomic analysis of spleen

Feed accounts for the largest portion (65-70%) of poultry production costs. The feed formulation is generally improved to efficiently meet the nutritional needs of chickens by reducing the proportion of crude protein (CP) and metabolizable energy (ME) levels in the diet. Although many studies have investigated the production performance during dietary restriction, there is a lack of research on the mechanisms by which immune cell function is altered. This study examined the effects of ME and CP restriction in the chicken diet on serum immunoglobulins and expression of immune function genes in spleen. Changes in serum immunoglobulins and immune-related gene expression were analyzed in 216 YS-909 broilers fed with 9 different dietary treatments, including experimental treatment diets containing low, standard, and high levels of ME or CP in the diet. At 42 days of age, serum immunoglobulins and expression of spleen immune genes in 6 female chickens selected randomly from each dietary treatment (3×3 factorial arrangement) group were measured by enzyme-linked immunosorbent assay (ELISA) and transcriptomic analysis using RNA sequencing, respectively. The results showed that the IgM level in the low ME group chickens was significantly (p < 0.05) lower than that in other groups. In addition, immune-related genes, such as MX1, USP18, TLR4, IFNG and IL18 were significantly upregulated when the dietary nutrient density was reduced, which may put the body in an inflammatory state. This study provided general information on the molecular mechanism of the spleen immune response to variable nutrient density.

Gut Microbiota Mediates Skin Ulceration Syndrome Outbreak by Readjusting Lipid Metabolism in Apostichopus japonicus

The intestinal tract is the most important location for symbiotes and pathogens, and the microbiota plays a crucial role in affecting the health of the gut and other host organs. Dysbacteriosis in the intestinal system has been proven to be significant in skin ulceration syndrome (SUS) in sea cucumbers. This study investigates whether the gut microbiota and lipid metabolites are relevant to the initiation and progression of SUS in a Vibrio-splendidus-infected sea cucumber model. The tight junction genes were downregulated and the inflammatory factor gene transcriptions were upregulated after V. splendidus infection in the intestinal tissue of the sea cucumber. V. splendidus infection modulated the gut microbiota by interacting with Psychromonas macrocephali, Propionigenium maris, Bacillus cereus, Lutibacter flavus, and Hoeflea halophila. Meanwhile, the metabolites of the long-chain fatty acids in the intestinal tissue, including triglycerides (TG), phosphatidylethanolamines (PE), and phosphatidylglycerols (PG), were altered after V. splendidus infection. V. splendidus engaged in positive interactions with PG and PE and negative interactions with specific TG. These results related to gut microbiota and metabolites can offer practical assistance in the identification of the inflammatory mechanisms related to SUS, and this study may serve as a reference for predicting the disease.

Recent developments in antimicrobial growth promoters in chicken health: Opportunities and challenges

With a continuously increasing human population is an increasing global demand for food. People in countries with a higher socioeconomic status tend to switch their preferences from grains to meat and high-value foods. Their preference for chicken as a source of protein has grown by 70% over the last three decades. Many studies have shown the role of feed in regulating the animal gut microbiome and its impact on host health. The microbiome absorbs nutrients, digests foods, induces a mucosal immune response, maintains homeostasis, and regulates bioactive metabolites. These metabolic activities are influenced by the microbiota and diet. An imbalance in microbiota affects host physiology and progressively causes disorders and diseases. With the use of antibiotics, a shift from dysbiosis with a higher density of pathogens to homeostasis can occur. However, the progressive use of higher doses of antibiotics proved harmful and resulted in the emergence of multidrug-resistant microbes. As a result, the use of antibiotics as feed additives has been banned. Researchers, regulatory authorities, and managers in the poultry industry have assessed the challenges associated with these restrictions. Research has sought to identify alternatives to antibiotic growth promoters for poultry that do not have any adverse effects. Modulating the host intestinal microbiome by regulating dietary factors is much easier than manipulating host genetics. Research efforts have led to the identification of feed additives, including bacteriocins, immunostimulants, organic acids, phytogenics, prebiotics, probiotics, phytoncides, and bacteriophages. In contrast to focusing on one or more of these alternative bioadditives, an improved feed conversion ratio with enhanced poultry products is possible by employing a combination of feed additives. This article may be helpful in future research towards developing a sustainable poultry industry through the use of the proposed alternatives.