Contact with adult hen affects development of caecal microbiota in newly hatched chicks

Multi-omics analyses reveal differences in intestinal flora composition and serum metabolites in Cherry Valley broiler ducks of different body weights

Fledgling broiler ducks vary in body weight and growth rate. The aim of this study was to investigate the relationship between serum metabolites and the intestinal microbiota in Cherry Valley broiler ducks with different finishing weights and to reveal differences in their metabolic regulation and microbial composition. Serum and cecum content samples were collected from Cherry Valley broiler ducks of different finishing weights. Metabolites were identified and compared using untargeted metabolomics, 16S rRNA gene sequencing, multivariate statistics and bioinformatics. Six key findings emerged. First, serum biochemical parameters showed that AST and ALT levels were significantly lower in the high weight group (Group H) than in the low weight group (Group L), and serum immunoglobulin IgG levels were significantly higher in group H. Second, the chorionic height to crypt depth ratio of the duodenum was significantly higher in group H than in group L. Third, the gut microbial community diversity or abundance was lower in broiler ducks in group L. Fourth, LEfSe analysis showed that the biomarker for group L was Streptococcus, whereas for group H it was Faecalibacterium. Fifth, a total of 127 differential metabolites were identified (49 up-regulated and 78 down-regulated). Finally, Spearman's correlation analysis showed that Spearman's correlation analyses showed that the Lipid-related serum metabolites were higher in low-body recombinant broiler ducks, mainly Lathosterol, Cholesterol, Cynaratriol and Leukotriene B4. In addition to lipid-associated serum metabolites in high-body recombination, The water-soluble vitamin-like metabolite Pantothenate and the antibiotic-like metabolite Tylosin were high. The cecum microbiota is strongly associated with metabolites, especially Faecalibacterium, unclassified Tannerellaceae, Subdoligranulum, Alistipes, and [Ruminococcus] torques_group, with which it exhibits strong Correlation. Broiler ducks with higher body weights have a better intestinal villous structure, enhanced digestion and absorption, higher levels of immunoglobulin secretion and superior growth performance. Broiler ducks with different body weights differed in plasma metabolites and cecum flora. Spearman's correlation analyses showed that the Correlation between differential metabolites and differential gut microbial genera.

Dietary polyunsaturated fatty acids effect on cecal microbiome profile of maturing broiler chicken

Diet has been reported to impact the diversity and function of gut microbiota. Our study investigated the effect of dietary fat types on cecal microbial composition and predicted function in broiler chickens at days 41 and 55 of age. Four dietary fat sources were evaluated and compared to a control dietary fat source of poultry fat. These were for two diets rich in omega-3 polyunsaturated fatty acids (PUFA) - fish oil and flaxseed oil, a diet rich in long-chain saturated fatty acid (SFA) - lard, and a diet rich in medium-chain saturated fatty acid - coconut oil. At day 55, broiler chickens fed a PUFA-rich diet maintained cecal microbial diversity while broiler chickens fed a SFA-rich diet exhibited a significant reduction in diversity compared to the control diet-fed chickens. More specifically, PUFA intake was associated with elevated levels of microbial carbohydrate metabolizing capability, contributing to efficient energy utilization and enhanced short-chain fatty acid production capability. In contrast, SFA-rich diets lowered abundances for key microbial families like Lachnospiraceae and Bifidobacteriaceae hampering nutrient digestibility and pathogen resistance. The microbiomes for chickens fed lard and coconut oil diets showed a significant reduction in SCFA-producing microbial taxa abundance while the microbial functional profile indicated reduced carbohydrate metabolism. Our findings underscore the contrasting effects of SFA-rich fat and PUFA-rich fat on the cecal microbiota of broiler chickens. The results suggest that incorporating PUFA-rich dietary fats into broiler feed may offer potential benefits by modulating the cecal gut microbiota toward outcomes associated with elevated carbohydrate utilization without hampering nutrient digestibility and pathogen resistance.

Effect of inulin supplementation in maternal fecal microbiota transplantation on the early growth of chicks

BACKGROUND

Fecal microbial transplantation (FMT) is an important technology for treating diarrhea and enteritis. Additionally, FMT has been applied to improve productivity, alter abnormal behavior, relieve stress, and reduce burdens. However, some previous studies have reported that FMT may cause stress in acceptor animals. Inulin, a prebiotic, can promote growth, enhance immunity, and balance the gut microbiota. Currently, there are limited reports on the effects of combining FMT with inulin on early growth performance in chicks.

RESULTS

In this study, a total of 90 1-day-old chicks were randomly divided into the control group (CON), FMT group, and inulin group (INU). The CON group was fed a basic diet, whereas the FMT and INU groups received fecal microbiota transplantation and FMT with inulin treatment, respectively. Compared with the FMT and CON groups, the INU group presented significantly greater average daily gain (ADG) and average daily feed intake (ADFI) values (P < 0.05). However, the organ indices did not significantly change (P > 0.05). The ratio of the villi to crypts in the ileum significantly differed at 21 and 35 days (P < 0.05). In addition, the cecum concentrations of acetic acid and butyric acid significantly increased in the INU group (P < 0.05). In addition, gut inflammation and serum inflammation decreased in the INU group, and immune factors increased after inulin supplementation. (P < 0.05). Firmicutes and Bacteroidetes were the dominant phyla, with more than 90% of all sequences being identified as originating from these two phyla. Inulin supplementation during mother-sourced microbial transplantation significantly increased the abundance of Rikenella, Butyricicoccus, and [Ruminococcus], which contributed positively to the promotion of early intestinal health and facilitated the early growth of chicks.

CONCLUSION

The results of this study suggest that inulin supplementation in maternal fecal microbiota transplantation can effectively promote early growth and probiotic colonization, which favors the health of chicks. Video Abstract.

Effects of early access to feed and water in hatchers on growth performance in broiler chickens

Conventional hatchers do not provide feed or water to chicks during hatch, which may negatively affect chick development, especially in early hatchlings subjected to prolonged feed deprivation due to biological variation in hatch time. This study aimed to evaluate the effects of early access to feed, water and a synbiotic product on performance, caecal microbiota development, organ development, intestinal morphology, total serum immunoglobulin (Ig) Y and antibody response to vaccination in Ross-308 chickens. A total of 330 chicks hatched in a specialised hatcher were divided into three hatch treatment groups: access to feed, water and synbiotic additive (PS); access to feed and water (PosC); no access to feed and water (NegC). Ten birds per hatch treatment were euthanised for organ sampling at placement, and the remaining 300 chicks were randomly allocated to 30 pens. All chicks received feed and water, and half the chicks in each treatment group received the synbiotic additive for 3 consecutive days (giving three hatching treatments and two postplacement treatments). All chicks were vaccinated against avian pneumovirus (APV) at 10 days of age. Blood sampling was performed weekly on three focal birds per pen for analysis of total serum IgY and antibodies to APV. Organ sampling was performed on days 11 and 32. Feed intake (FI) and BW were recorded weekly. The NegC group exhibited reduced early growth and lower FI throughout the study. At 25 days, they also demonstrated an inferior feed conversion ratio (FCR) compared with the other groups. At 4 and 25 days chickens that did not receive any postplacement treatment, None had superior FCR compared to those receiving PS also postplacement. There was also an effect of postplacement treatment where the None group weighed more compared to the PS group on almost all occasions. The NegC group had higher concentrations of IgY in serum compared to the PosC group at 3 days of age, an effect that remained a tendency until 25 days of age. No differences between treatments were found for antibody responses to APV vaccination. Some differences in relative weights of digestive organs between hatching groups were detected at the end of study, while no persistent effects on caecal microbiota composition were observed. In conclusion, delayed access to feed and water had adverse effects on productivity traits, lasting throughout the study. These findings warrant further validation in a practical context with higher stocking densities and pathogen loads.

Species and functional composition of cecal microbiota and resistance gene diversity in different Yunnan native chicken breeds: A metagenomic analysis

The gut microbiota of chickens not only modulates host immune function and production performance through nutrient metabolism but also serves as a reservoir for antibiotic resistance genes (ARGs), whose accumulation exacerbates bacterial resistance. This study integrated 108 cecal microbiome samples from six Yunnan native chicken breeds under free-range and caged farming systems, constructing a comprehensive catalog comprising 12,715 microbial genomes. We systematically revealed the dual mechanisms by which the gut microbiota regulates host phenotypes and ARG dissemination. Metagenomic analysis demonstrated that Alistipes, Prevotella, and Spirochaeta synergistically regulate body weight and immune indices through metabolic networks, which are linked to the significant enrichment of carbohydrate-active enzymes. GH23 and GT2 presented the greatest abundance, highlighting their pivotal role in dietary fiber metabolism. A total of 1327 ARGs were identified, spanning seven resistance mechanisms dominated by antibiotic efflux and target alteration. Alistipes_sp._CAG:831 presented the highest ARG abundance and diversity, with ARG levels strongly correlated with host bacterial abundance. Metagenomic-phenotype association networks further revealed that environmental stress drives disparities in ARG enrichment by altering the microbial community structure. This study elucidates the gut microbiota-host interaction network in Yunnan native chickens and provides critical insights into ARG transmission dynamics, offering a theoretical foundation for antibiotic resistance risk assessment and sustainable poultry farming strategies.

Fecal microbiota transplantation combined with inulin promotes the development and function of early immune organs in chicks

Modern management of chicks hinders the vertical transmission of intestinal microbiota, which is closely related to immunity. Inulin is a substrate that can be utilized by the microbiota. This study aimed to determine whether fecal microbiota transplantation (FMT) combined with inulin played a "1 + 1 > 2" role in enhancing the development and function of immune organs. Chicks were treated with 1 % inulin and/or fecal microbiota suspension on days 1-6. The growth performance, immune organ development, and immune indicators were evaluated on days 7, 14, and 21. Results showed that the combination of FMT and inulin significantly increased the immune organ index on day 7 and promoted the morphological structure and the expression of proliferating cell nuclear antigen (PCNA) in immune organs on days 7, 14, and 21. Each treatment increased the gene expression of interferon-gamma (IFN-γ), interleukin-4 (IL-4), interleukin-2 (IL-2), B cell-activating factor receptor (BAFFR), B cell linker (BLNK), C-X-C Motif Chemokine Ligand 12 (CXCL12), C-X-C Motif Chemokine Receptor 4 (CXCR4), and Biotin (Bu-1) to varying degrees. FMT combined with inulin significantly increased the expression of IgA-positive cells on days 7 and 14. In conclusion, the synergistic effect of FMT and inulin had beneficial impacts on the development and function of immune organs.

Effect of gum Arabic as natural prebiotic on intestinal ecosystem of post-hatched broiler chicks

The purpose of the current study was to investigate the effects of gum Arabic supplementation on short-chain fatty acids, cecal microbiota, immune-related gene expression, and small intestinal morphology in post-hatched broiler chicks. On the day of hatching, four hundred thirty-two commercial male broiler chicks were randomly allocated into six treatments with twelve cages as replicates of six chicks each for 24 days. Dietary treatments (T1 to T6) were supplemented with 0.0, 0.12, 0.25, 0.50, 0.75, and 1.0% gum Arabic to the basal diet, respectively. Performance parameters, short-chain fatty acid concentration, quantification of microbiota and immune response gene expression (pre-inflammatory cytokines, mucin-2, and secretory immunoglobulin A), and histomorphometry of the small intestine were measured. According to our results, daily weight gains in T2 and the production efficiency index increased in T2 to T4, whereas daily feed intake decreased in T2, T3, T5, and T6, but feed conversion ratio improved. Concentration of lactate, acetate, butyrate, and total short-chain fatty acid increased in T2, T3, T5, and T6. Propionate ‎in T2 T3, T4, and T6 and format in T2, T5, and T6 also increased. Lactobacillus spp. quantitatively increased from T3 to T6, whereas Bacteroides spp. decreased in T3 and T5. Other microbiota quantitatively showed no effect of dietary supplements. IL-1β, TNF-α, and MUC-2 decreased in T2 to T6 and IL-12 in T3, whereas INF-Y increased in T4 to T6 and SIgA in T4. All histometeric parameters of the duodenum, jejunum, and ileum improved with dietary supplementation. We conclude that the administration of gum Arabic resulted in an improvement in overall performance, fermentation metabolites, and modification of microbiota and immune response with improved histomorphometry in the intestines of young chicks.

Biosensors for Monitoring, Detecting, and Tracking Dissemination of Poultry-Borne Bacterial Pathogens Along the Poultry Value Chain: A Review

The poultry industry plays a crucial role in global food production, with chickens being the most widely consumed as a rich protein source. However, infectious diseases pose significant threats to poultry health, underscoring the need for rapid and accurate detection to enable timely intervention. In recent years, biosensors have emerged as essential tools to facilitate routine surveillance on poultry farms and rapid screening at slaughterhouses. These devices provide producers and veterinarians with timely information, thereby promoting proactive disease management. Biosensors have been miniaturized, and portable platforms allow for on-site testing, thereby enhancing biosecurity measures and bolstering disease surveillance networks throughout the poultry supply chain. Consequently, biosensors represent a transformative advancement in poultry disease management, offering rapid and precise detection capabilities that are vital for safeguarding poultry health and ensuring sustainable production systems. This section offers an overview of biosensors and their applications in detecting poultry diseases, with a particular emphasis on enteric pathogens.

Probiotic Mixtures Consisting of Representatives of Bacteroidetes and Selenomonadales Increase Resistance of Newly Hatched Chicks to Salmonella Enteritidis Infection

There are extensive differences in the caecal microbiota of chicks from hatcheries and those inoculated with faecal material from adult hens. Besides differences in microbial composition, the latter chickens are highly resistant to Salmonella Enteritidis challenges, while the former are susceptible. In this study, we tested whether strains from genera Bacteroides, Megamonas, or Megasphaera can increase chicken resistance to Salmonella and Campylobacter jejuni when defined microbial mixtures consisting of these bacterial genera are administered. Mixtures consisting of different species and strains from the above-mentioned genera efficiently colonised the chicken caecum and increased chicken resistance to Salmonella by a factor of 50. The tested mixtures were even more effective in protecting chickens from Salmonella in a seeder model of infection (3-5 log reduction). The tested mixtures partially protected chickens from C. jejuni infection, though the effect was lower than that against Salmonella. The obtained data represent a first step for the development of a new type of probiotics for poultry.

Immunoglobulin secretion influences the composition of chicken caecal microbiota

The chicken caecum is colonised by hundreds of different bacterial species. Which of these are targeted by immunoglobulins and how immunoglobulin expression shapes chicken caecal microbiota has been addressed in this study. Using cell sorting followed by sequencing of V3/V4 variable region of 16S rRNA, bacterial species with increased or decreased immunoglobulin coating were determined. Next, we determined also caecal microbiota composition in immunoglobulin knockout chickens. We found that immunoglobulin coating was common and major taxa were coated with immunoglobulins. Similarly, more taxa required immunoglobulin production for caecum colonisation compared to those which became abundant in immunoglobulin-deficient chickens. Taxa with low immunoglobulin coating such as Lactobacillus, Blautia, [Eubacterium] hallii, Megamonas, Fusobacterium and Desulfovibrio all encode S-layer proteins which may reduce interactions with immunoglobulins. Although there were taxa which overgrew in Ig-deficient chickens (e.g. Akkermansia) indicating immunoglobulin production acted to exclude them from the chicken caecum, in most of the cases, immunoglobulin production more likely contributed to fixing the desired microbiota in the chicken caecum.

Insights into the intestinal microbiota of Exopalaemon annandalei and Exopalaemon carinicauda in the Yangtze River estuary

The gut microbiota plays a crucial role in food webs, carbon cycling, and related elements. Exopalaemon annandalei and Exopalaemon carinicauda are two important forage species in the Yangtze River estuary with extremely similar living habits and morphological characteristics. Exploring the microorganisms in the guts of these two shrimp species can help us understand the survival status of forage species and gut microbiota in the Yangtze River estuary. Therefore, this study analyzed the similarities and differences in the intestinal flora of E. annandalei and E. carinicauda through high-throughput sequencing of 16S rRNA gene amplicons. The results showed that the dominant bacteria in the intestinal flora of E. annandalei and E. carinicauda at the phylum level were Proteobacteria and Firmicutes, respectively. At the genus level, the intestinal flora had higher concentrations of Psychrobacter, Bacillus, Pseudomonas, Acinetobacter, and Macrococcus. In both shrimp species, the contents of Acinetobacter and Macrococcus were higher in spring than in winter. The most important potential functions of the intestinal microbiota were amino acid metabolism and purine metabolism. Additionally, the functions of metabolism and diseases in the intestinal microbiota of E. annandalei were greatly influenced by the season. Furthermore, the experimental results indicated that a lower ratio of Firmicutes to Bacteroidetes was associated with a larger body weight in shrimp. Overall, this study provides a theoretical reference for understanding the intestinal bacterial community of shrimp in estuaries and the healthy cultivation of E. annandalei and E. carinicauda.

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.

The gut microbiota and its metabolite butyrate shape metabolism and antiviral immunity along the gut-lung axis in the chicken

The gut microbiota exerts profound influence on poultry immunity and metabolism through mechanisms that yet need to be elucidated. Here we used conventional and germ-free chickens to explore the influence of the gut microbiota on transcriptomic and metabolic signatures along the gut-lung axis in poultry. Our results demonstrated a differential regulation of certain metabolites and genes associated with innate immunity and metabolism in peripheral tissues of germ-free birds. Furthermore, we evidenced the gut microbiota's capacity to regulate mucosal immunity in the chicken lung during avian influenza virus infection. Finally, by fine-analysing the antiviral pathways triggered by the short-chain fatty acid (SCFA) butyrate in chicken respiratory epithelial cells, we found that it regulates interferon-stimulated genes (ISGs), notably OASL, via the transcription factor Sp1. These findings emphasize the pivotal role of the gut microbiota and its metabolites in shaping homeostasis and immunity in poultry, offering crucial insights into the mechanisms governing the communication between the gut and lungs in birds.

Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota

The chicken immune system and microbiota play vital roles in maintaining gut homeostasis and protecting against pathogens. In mammals, XCR1+ conventional dendritic cells (cDCs) are located in the gut-draining lymph nodes and play a major role in gut homeostasis. These cDCs sample antigens in the gut luminal contents and limit the inflammatory response to gut commensal microbes by generating appropriate regulatory and effector T-cell responses. We hypothesized that these cells play similar roles in sustaining gut homeostasis in chickens, and that chickens lacking XCR1 were likely to contain a dysbiotic caecal microbiota. Here we compare the caecal microbiota of chickens that were either heterozygous or homozygous XCR1 knockouts, that had or had not been vaccinated for infectious bronchitis virus (IBV). We used short-read (Illumina) and long-read (PacBio HiFi) metagenomic sequencing to reconstruct 670 high-quality, strain-level metagenome assembled genomes. We found no significant differences between alpha diversity or the abundance of specific microbial taxa between genotypes. However, IBV vaccination was found to correlate with significant differences in the richness and beta diversity of the microbiota, and to the abundance of 40 bacterial genera. In conclusion, we found that a lack of XCR1 was not correlated with significant changes in the chicken microbiota, but IBV vaccination was.

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia

BACKGROUND

Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies.

RESULTS

Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database.

CONCLUSIONS

The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. Video Abstract.

In Vivo Expression of Chicken Gut Anaerobes Identifies Carbohydrate- or Amino Acid-Utilising, Motile or Type VI Secretion System-Expressing Bacteria

Complex gut microbiota increases chickens' resistance to enteric pathogens. However, the principles of this phenomenon are not understood in detail. One of the possibilities for how to decipher the role of gut microbiota in chickens' resistance to enteric pathogens is to systematically characterise the gene expression of individual gut microbiota members colonising the chicken caecum. To reach this aim, newly hatched chicks were inoculated with bacterial species whose whole genomic sequence was known. Total protein purified from the chicken caecum was analysed by mass spectrometry, and the obtained spectra were searched against strain-specific protein databases generated from known genomic sequences. Campylobacter jejuni, Phascolarctobacterium sp. and Sutterella massiliensis did not utilise carbohydrates when colonising the chicken caecum. On the other hand, Bacteroides, Mediterranea, Marseilla, Megamonas, Megasphaera, Bifidobacterium, Blautia, Escherichia coli and Succinatimonas fermented carbohydrates. C. jejuni was the only motile bacterium, and Bacteroides mediterraneensis expressed the type VI secretion system. Classification of in vivo expression is key for understanding the role of individual species in complex microbial populations colonising the intestinal tract. Knowledge of the expression of motility, the type VI secretion system, and preference for carbohydrate or amino acid fermentation is important for the selection of bacteria for defined competitive exclusion products.

Fecal Microbial Communities of Nellore and Crossbred Beef Calves Raised at Pasture

This study aimed to investigate the effect of age and genetics on the fecal microbiota of beef calves. Ten purebred Nellore (Bos taurus indicus) and ten crossbreed 50% Nellore-50% European breed (Bos taurus taurus) calves co-habiting on the same pasture paddock had fecal samples collected on days five (5 d), 14 d, 28 d, 60 d, 90 d, 180 d, 245 d (weaning) and 260 d after birth. All calves were kept with their mothers, and six Nellore dams were also sampled at weaning. Microbiota analysis was carried out by amplification of the V4 region of the 16S rRNA gene following high-throughput sequencing with a MiSeq Illumina platform. Results revealed that bacterial richness increased with age and became more similar to adults near weaning. Differences in microbiota membership between breeds were found at 60 d and 90 d and for structure at 60 d, 90 d, 245 d, and 260 d (p < 0.05). In addition, crossbreed calves presented less variability in their microbiota. In conclusion, the genetic composition significantly impacted the distal gut microbiota of calves co-habiting in the same environment, and further studies investigating food intake can reveal possible associations between microbiota composition and performance.

Combined analysis of the microbiome, metabolome and transcriptome of silkie chickens in response to avian pathogenic E. coli (APEC)

Avian colibacillosis is a bacterial disease caused by avian pathogenic Escherichia coli (APEC) that results in great losses in the poultry industry every year. Individual Silkie chickens of the same breed that are given the same feed in the same feeding conditions have different levels of resistance or susceptibility to APEC. Differences in gut microbes, gut metabolites, and gene expression in the spleen of APEC-resistant and APEC-susceptible chickens were compared, and multiple omics associations were analyzed to explore the mechanism of resistance to APEC in Silkie chickens. Compared with those in the APEC-susceptible group, the APEC-resistant group showed significantly increased abundances of many gut microorganisms, including Bacillus, Thermoactinomyces, Arthrobacter, and Ureibacillus, which were positively correlated with norvaline, l-arginine, and valyl-glycine levels. Intestinal tryptophan, indole, and indole derivative-related differentially abundant metabolites played an active role in combatting APEC infection. In the spleen, "response to stimulus" was the most significantly enriched GO term, and "cytokine‒cytokine receptor interaction" was the most significantly enriched KEGG pathway. The arginine biosynthesis and PPAR signaling pathways were the KEGG pathways that were significantly enriched with differentially abundant metabolites and differentially expressed genes. This study provides new insight into the prevention and treatment of APEC infection in Silkie chickens and lays a foundation to study the mechanism of APEC infection in poultry.

Contact with adult hens affects the composition of skin and respiratory tract microbiota in newly hatched chicks

Chickens in commercial production are hatched in hatcheries without any contact with their parents and colonization of their skin and respiratory tract is therefore dependent on environmental sources only. However, since chickens evolved to be hatched in nests, in this study we evaluated the importance of contact between hens and chicks for the development of chicken skin and tracheal microbiota. Sequencing of PCR amplified V3/V4 variable regions of the 16S rRNA gene showed that contact with adult hens decreased the abundance of E. coli, Proteus mirabilis and Clostridium perfringens both in skin and the trachea, and Acinetobacter johnsonii and Cutibacterium acnes in skin microbiota only. These species were replaced by Lactobacillus gallinarum, Lactobacillus aviarius, Limosilactobacillus reuteri, and Streptococcus pasterianus in the skin and tracheal microbiota of contact chicks. Lactobacilli can be therefore investigated for their probiotic effect in respiratory tract in the future. Skin and respiratory microbiota of contact chickens was also enriched for Phascolarctobacterium, Succinatimonas, Flavonifractor, Blautia, and [Ruminococcus] torque though, since these are strict anaerobes from the intestinal tract, it is likely that only DNA from nonviable cells was detected for these taxa.

Colonization of chickens with competitive exclusion products results in extensive differences in metabolite composition in cecal digesta

The concept of competitive exclusion is well established in poultry and different products are used to suppress the multiplication of enteric pathogens in the chicken intestinal tract. While the effect has been repeatedly confirmed, the specific principles of competitive exclusion are less clear. The aim of the study was to compare metabolites in the cecal digesta of differently colonized chickens. Metabolites in the cecal contents of chickens treated with a commercial competitive exclusion product or with an experimental product consisting of 23 gut anaerobes or in control untreated chickens were determined by mass spectrometry. Extensive differences in metabolite composition among the digesta of all 3 groups of chickens were recorded. Out of 1,706 detected compounds, 495 and 279 were differently abundant in the chicks treated with a commercial or experimental competitive exclusion product in comparison to the control group, respectively. Soyasaponins, betaine, carnitine, glutamate, tyramine, phenylacetaldehyde, or 3-methyladenine were more abundant in the digesta of control chicks while 4-oxododecanedioic acid, nucleotides, dipeptides, amino acids (except for glutamate), and vitamins were enriched in the digesta of chickens colonized by competitive exclusion products. Metabolites enriched in the digesta of control chicks can be classified as of plant feed origin released in the digesta by degradative activities of the chicken. Some of these molecules disappeared from the digesta of chicks colonized by complex microbiota due to them being metabolized. Instead, nucleotides, amino acids, and vitamins increased in the digesta of colonized chicks as a consequence of the additional digestive potential brought to the cecum by microbiota from competitive exclusion products. It is therefore possible to affect metabolite profiles in the chicken cecum by its colonization with selected bacterial species.

Vertical transmission of gut bacteria in commercial chickens is limited

The existence of vertical transmission in chickens under commercial settings, where chicks are raised separately from adults, is unclear. To answer this question, the fecal microbiota of chicks hatched and grown separately was compared with their mothers' microbiota. Most amplicon sequence variants (ASVs) identified in hens were not detected at all in chicks up to two weeks of age by 16S rDNA sequencing, and those that were detected had a low incidence among the chicks. Nevertheless, a few ASVs that were common with the hens were highly prevalent among the chicks, implying that they were efficiently transmitted to chicks. These ASVs were culturable from the reproductive tract of hens and eggshells. Furthermore, interventions attempting to disrupt transmission resulted in a reduction in the prevalence of specific phylogenetic groups in chicks. To conclude, vertical transmission in commercial poultry grown separately from adults likely exists but is not efficient, possibly resulting in impairment of microbiota function. This implies that artificial exposure to adult bacterial strains might improve microbiota functioning.

Investigating the cecal microbiota of broilers raised in extensive and intensive production systems

Intensive broiler production practices are structured to prevent the introduction and spread of pathogens; however, they can potentially minimize the exposure of broilers to beneficial commensal bacteria. In this study, we used 16S rRNA amplicon sequencing to characterize the cecal microbiota of 35-day-old broilers from 22 independent commercial farms rearing broilers under intensive (IPS) or extensive production systems (EPS). We aimed to determine which bacteria are normal inhabitants of the broiler ceca and which bacteria might be missing from broilers in IPS. In addition, we generated a collection of 410 bacterial isolates, including 87 different species, to be used as a resource to further explore the effects of selected isolates on bird physiology and to elucidate the role of individual species within the cecal microbial community. Our results indicated significant differences in the microbiota of broilers between systems: the microbiota of broilers from EPS was dominated by Bacteroidetes {55.2% ± 8.9 [mean ± standard deviation (SD)]}, whereas Firmicutes dominated the microbiota of broilers from IPS (61.7% ± 14.4, mean ± SD). Bacterial taxa found to be core in the EPS microbiota, including Olsenella, Alistipes, Bacteroides, Barnesiella, Parabacteroides, Megamonas, and Parasutterella, were shown to be infrequent or absent from the IPS microbiota, and the EPS microbiota presented higher phylogenetic diversity and greater predicted functional potential than that of broilers in IPS. The bacteria shown to be depleted in broilers from IPS should be further investigated for their effects on bird physiology and potential application as next-generation probiotics. IMPORTANCE Production practices in intensive farming systems significantly reduce the introduction and spread of pathogens; however, they may potentially minimize the exposure of animals to beneficial commensal microorganisms. In this study, we identified core bacteria from the cecal microbiota of broilers raised in extensive production systems that are missing or reduced in birds from intensive systems, including Olsenella, Alistipes, Bacteroides, Barnesiella, Parabacteroides, Megamonas, and Parasutterella. Furthermore, the cecal microbiota of broilers from extensive systems showed higher diversity and greater functional potential than that of broilers from intensive systems. In addition, a collection of bacterial isolates containing 87 different species was generated from the current study, and this important resource can be used to further explore the role of selected commensal bacteria on the microbial community and bird physiology.

Colonization of the Gastrointestinal Tract of Chicks with Different Bacterial Microbiota Profiles

This study aimed to investigate the consequences of early-life microbiota transplantation using different caecal content sources in broiler chicks. We hypothesized that chicks receiving at-hatch microbiota from organic hens would harbour a distinct microbiota from chicks receiving industry-raised broiler microbiota after six weeks of age. Three hundred Cobb broilers eggs were randomly assigned to one of four groups according to the caecal content received: organic laying hens (Organic); autoclaved caecal content of organic laying hens (Autoclaved); conventionally grown broilers (Conventional); and sterile saline (Control). caecal microbiota transplantation was given by gavage on day 1. Ten birds/group were euthanized on days 2, 7, 14, 28, and 42. The caecal tonsils and contents were collected for cytokines and microbiota analyses. The microbiota from chicks receiving live inocula resembled the donors' microbiota from day seven until day 42. The microbiota composition from the chickens who received the Organic inoculum remained markedly different. Starting on day 7, the Organic group had higher richness. Simpson and Shannon's indices were higher in the Conventional group on days 2 and 7. Chickens in the Conventional group presented higher production of IL-1β and IL-6 in plasma on days 2 and 28, increased IL-6 expression in the caecal tonsils at days 7 and 42, and increased IL-12 expression on day 7. However, the Conventional group was infected with Eimeria spp., which likely caused inflammation. In conclusion, microbiota transplantation using different microbiota profiles persistently colonized newly hatched broiler chicks. Future studies evaluating the importance of microbiota composition during infections with common enteropathogens are necessary. This study also highlights the need for a strict screening protocol for pathogens in the donors' intestinal content.

The abundance and diversity of antibiotic resistance genes in layer chicken ceca is associated with farm enviroment

Industrialized layer chicken feedlots harbor complex environmental microbial communities that affect the enrichment and exchange of gut bacteria and antibiotic resistance genes (ARGs). However, the contribution of different environmental sources to the gut ARGs of layer chickens is not clear. Here, layer chicken gut and environmental samples (air, water, feed, cage, feather, maternal hen feces, uropygial glands) were collected during the early 3 month period before the laying of eggs, and the source and characteristics of the gut microorganisms and ARGs were analyzed by performing 16S rRNA and metagenomic sequencing. The results showed that the abundances of Bacteroidetes and Actinobacteria in cecum of layer chickens gradually increased, while that of Proteobacteria decreased with age, and the number and relative abundance of ARGs decreased significantly with age. On day 5, 57% of the layer chicken cecal ARGs were from feather samples, and 30% were from cage samples. Subsequently, the contribution of cage ARGs became progressively more prominent over time. At days 30 and 57, the contribution of cage ARGs to the chick cecal ARGs reached 63.3 and 69.5%, respectively. The bacterial community composition (especially the abundances of Klebsiella pneumoniae and Escherichia coli) was the major factor impacting the ARG profile. K. pneumoniae and E. coli were mainly transmitted from feathers to the layer chicken cecum, and the contribution rates were 32 and 3.4%, respectively. In addition, we observed the transmission of ARG-carrying bacteria (Bacteroides fragilis) from the cage to the gut, with a contribution rate of 11.5%. It is noteworthy that B. fragilis is an opportunistic pathogen that may cause diarrhea in laying hens. These results can provide reference data for the healthy breeding of layer chickens and the prevention and control of ARG pollution.

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.

Poultry gut health and beyond

Intestinal health is critically important for the digestion and absorption of nutrients and thus is a key factor in determining performance. Intestinal health issues are very common in high performing poultry lines due to the high feed intake, which puts pressure on the physiology of the digestive system. Excess nutrients which are not digested and absorbed in the small intestine may trigger dysbiosis, i.e. a shift in the microbiota composition in the intestinal tract. Dysbiosis as well as other stressors elicit an inflammatory response and loss of integrity of the tight junctions between the epithelial cells, leading to gut leakage. In this paper, key factors determining intestinal health and the most important nutritional tools which are available to support intestinal health are reviewed.

Pioneer colonizers: Bacteria that alter the chicken intestinal morphology and development of the microbiota

Microbes commonly administered to chickens facilitate development of a beneficial microbiome that improves gut function, feed conversion and reduces pathogen colonization. Competitive exclusion products, derived from the cecal contents of hens and shown to reduce Salmonella colonization in chicks, possess important pioneer-colonizing bacteria needed for proper intestinal development and animal growth. We hypothesized that inoculation of these pioneer-colonizing bacteria to day of hatch chicks would enhance the development of their intestinal anatomy and microbiome. A competitive exclusion product was administered to broiler chickens, in their drinking water, at day of hatch, and its impact on intestinal morphometrics, intestinal microbiome, and production parameters, was assessed relative to a control, no treatment group. 16S rRNA gene, terminal restriction fragment length polymorphism (T-RFLP) was used to assess ileal community composition. The competitive exclusion product, administered on day of hatch, increased villus height, villus height/width ratio and goblet cell production ∼1.25-fold and expression of enterocyte sugar transporters 1.25 to 1.5-fold in chickens at 3 days of age, compared to the control group. As a next step, chicks were inoculated with a defined formulation, containing Bacteroidia and Clostridia representing pioneer-colonizing bacteria of the two major bacterial phyla present in the competitive exclusion product. The defined formulation, containing both groups of bacteria, were shown, dependent on age, to improve villus height (jejunum: 1.14 to 1.46-fold; ileum: 1.17-fold), goblet cell numbers (ileum 1.32 to 2.51-fold), and feed efficiency (1.18-fold, day 1) while decreasing Lactobacillus ileal abundance by one-third to half in birds at 16 and 42 days of age, respectively; compared to the phosphate buffered saline treatment group. Therefore, specific probiotic formulations containing pioneer colonizing species can provide benefits in intestinal development, feed efficiency and body weight gain.

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.

Week-Old Chicks with High Bacteroides Abundance Have Increased Short-Chain Fatty Acids and Reduced Markers of Gut Inflammation

As important commensals in the chicken intestine, Bacteroides are essential complex carbohydrate degraders, and short-chain fatty acid (SCFA) producers that are highly adapted to the distal gut. Previous studies have shown large variation in Bacteroides abundance in young chickens. However, limited information is available regarding how this variation affects the gut microbiome and host immunity. To investigate how elevated or depleted Bacteroides levels affect gut microbial functional capacity and impact host response, we sampled 7-day-old broiler chickens from 14 commercial production flocks. Week-old broiler chickens were screened and birds with low Bacteroides (LB) and high Bacteroides (HB) abundance were identified via 16S rRNA gene amplicon sequencing and quantitative PCR (qPCR) assays. Cecal microbial functionality and SCFA concentration of chickens with distinct cecal Bacteroides abundance were profiled by shotgun metagenomic sequencing and gas chromatography, respectively. The intestinal immune responses of LB and HB chickens were assessed via reverse transcription qPCR. Results showed that the gut microbiota of the LB group had increased abundance of lactic acid bacteria pyruvate fermentation pathway, whereas complex polysaccharide degradation and SCFA production pathways were enriched in the HB group (P < 0.05), which was supported by increased SCFA concentrations in the ceca of HB chickens (P < 0.05). HB chickens also showed decreased expression of interleukin-1β and increased expression of interleukin-10 and tight-junction protein claudin-1 (P < 0.05). Overall, the results indicated that elevated Bacteroides may benefit the 7-day broiler gut and that further work should be done to confirm the causal role of Bacteroides in the observed positive outcomes. IMPORTANCE To date, limited information is available comparing distinct Bacteroides compositions in the chicken gut microbial communities, particularly in the context of microbial functional capacities and host responses. This study showed that possessing a microbiome with elevated Bacteroides in early life may confer beneficial effects to the chicken host, particularly in improving SCFA production and gut health. This study is among the first metagenomic studies focusing on the early life chicken gut microbiota structure, microbial functionality, and host immune responses. We believe that it will offer insights to future studies on broiler gut microbial population and their effects on host health.

Research Note: A mixture of Bacteroides spp. and other probiotic intestinal anaerobes reduces colonization by pathogenic E. coli strain O78:H4-ST117 in newly hatched chickens

An experimental group of one-day-old chicken from a commercial hatchery was given a defined mixture of 7 gut anaerobes. The next day the chicks were inoculated by an APEC strain O78:H4-ST117 resistant to ciprofloxacin, alongside with the control group and monitored for 4 wk after the inoculation for the presence of the colonizing strains and ciprofloxacin-resistant E. coli. Significant reduction of colonization rates in the first 2 wk was recorded in the experimental group for the numbers of ciprofloxacin-resistant E. coli. The results show that colonization of chicken by defined anaerobic mixtures may provide a decisive protection during the critical period of the chicken intestinal microflora development.

Microbiota of Chickens and Their Environment in Commercial Production

Chickens in commercial production are subjected to constant interaction with their environment, including the exchange of microbiota. In this review, we therefore focused on microbiota composition in different niches along the whole line of chicken production. We included a comparison of microbiota of intact eggshells, eggshell waste from hatcheries, bedding, drinking water, feed, litter, poultry house air and chicken skin, trachea, crop, small intestine, and cecum. Such a comparison showed the most frequent interactions and allowed for the identification of microbiota members that are the most characteristic for each type of sample as well as those that are the most widespread in chicken production. Not surprisingly, Escherichia coli was the most widely distributed species in chicken production, although its dominance was in the external aerobic environment and not in the intestinal tract. Other broadly distributed species included Ruminococcus torque, Clostridium disporicum, and different Lactobacillus species. The consequence and meaning of these and other observations are evaluated and discussed.

Effects of access to feed, water, and a competitive exclusion product in the hatcher on some immune traits and gut development in broiler chickens

This study evaluated the effect of access to feed, water, and the competitive exclusion (CE) product Broilact®, administered in the hatcher, on broiler performance, caecal microbiota development, organ development, intestinal morphology, serum levels of IgY and vaccine-induced antibody responses.In total, 250 chicks were hatched in a HatchCare^TM hatcher and divided into four groups, given access to feed, water and the CE product sprayed on the chicks (CEs); access to feed, water, and the CE product in water (CEw); access to feed and water (Cpos); or no access to feed and water (Cneg) in the hatcher. At the research facility, 10 chicks per hatching treatment were euthanized for organ measurements. The remaining 200 chicks were randomly distributed to 20 pens. On d 11, all birds were vaccinated against avian pneumovirus (APV). Three focal birds per pen were blood-sampled weekly for quantification of IgY and serum antibodies to APV. On d 11 and 32, two birds per replicate pen were euthanised for organ measurements and sample collection. Feed intake and body weight were recorded weekly.Delayed access to feed and water reduced weight gain and feed intake early in life. At the end of the study, no differences in body weight remained.There were some early effects on organs, with depressed intestinal development and higher relative gizzard weight for the Cneg group at placement. No treatment effects on the immune traits measured were detected. The relative abundance of seven bacterial genera differed between treatment groups at d 11 of age. The results suggested that chickens are capable of compensating for 40 h feed and water deprival post-hatch. Provision of Broilact® did not have any persistent performance-enhancing properties, although different outcomes under rearing conditions closer to commercial production cannot be ruled out.

Bacterial composition of a competitive exclusion product and its correlation with product efficacy at reducing Salmonella in poultry

The mature intestinal microbiome is a formidable barrier to pathogen colonization. Day-old chicks seeded with cecal contents of adult hens are resistant to colonization with Salmonella, the basis of competitive exclusion. Competitive exclusion products can include individual microbes but are commonly undefined intestinal communities taken from adult animals and in commercial production is amplified in fermentator and sold commercially in freeze dried lots. While superior to single and multiple species probiotics, reducing Salmonella colonization by multiple logs, undefined products have limited acceptance because of their uncharacterized status. In this study, the bacterial composition of the master stock, preproduction seed stocks and commercial lots of a poultry competitive exclusion product, was defined by 16S rRNA sequence analysis, targeting the 16S rRNA variable region (V1-V3). The samples contained a diversity of genera (22-52 distinct genera) however, the commercial lots displayed less diversity compared to the seeds and the master stock. Community composition varied between seeds and the master stock and was not a good predictor of potency, in terms of log₁₀ reduction in Salmonella abundance. While there was significant correlation in composition between seeds and their commercial lots, this too was a not a good predictor of potency. There was linear correlation between unclassified Actinobacteria, Peptococcus, and unclassified Erysipelotrichaceae, and Salmonella abundance (r ² > .75) for commercial seeds. However, upon review of the literature, these three genera were not consistently observed across studies or between trials that examined the correlation between intestinal community composition and Salmonella prevalence or abundance.

Uncovering the core principles of the gut-lung axis to enhance innate immunity in the chicken

Research in mammals has evidenced that proper colonization of the gut by a complex commensal microbial community, the gut microbiota (GM), is critical for animal health and wellbeing. It greatly contributes to the control of infectious processes through competition in the microbial environment while supporting proper immune system development and modulating defence mechanisms at distant organ sites such as the lung: a concept named ‘gut-lung axis’. While recent studies point to a role of the GM in boosting immunity and pathogen resilience also in poultry, the mechanisms underlying this role are largely unknown. In spite of this knowledge gap, GM modulation approaches are today considered as one of the most promising strategies to improve animal health and welfare in commercial poultry production, while coping with the societal demand for responsible, sustainable and profitable farming systems. The majority of pathogens causing economically important infectious diseases in poultry are targeting the respiratory and/or gastrointestinal tract. Therefore, a better understanding of the role of the GM in the development and function of the mucosal immune system is crucial for implementing measures to promote animal robustness in commercial poultry production. The importance of early gut colonization in the chicken has been overlooked or neglected in industrial poultry production systems, where chicks are hampered from acquiring a complex GM from the hen. Here we discuss the concept of strengthening mucosal immunity in the chicken through GM modulation approaches favouring immune system development and functioning along the gut-lung axis, which could be put into practice through improved farming systems, early-life GM transfer, feeding strategies and pre-/probiotics. We also provide original data from experiments with germ-free and conventional chickens demonstrating that the gut-lung axis appears to be functional in chickens. These key principles of mucosal immunity are likely to be relevant for a variety of avian diseases and are thus of far-reaching importance for the poultry sector worldwide.

Poor body condition is associated with lower hippocampal plasticity and higher gut methanogen abundance in adult laying hens from two housing systems

It is still unclear which commercial housing system provides the best quality of life for laying hens. In addition, there are large individual differences in stress levels within a system. Hippocampal neurogenesis or plasticity may provide an integrated biomarker of the stressors experienced by an individual. We selected 12 adult hens each with good and poor body condition (based on body size, degree of feather cover and redness of the comb) from a multi-tier free range system containing H&N strain hens, and from an enriched cage system containing Hy-Line hens (n = 48 total). Immature neurons expressing doublecortin (DCX) were quantified in the hippocampus, contents of the caecal microbiome were sequenced, and expression of inflammatory cytokines was measured in the spleen. DCX⁺ cell densities did not differ between the housing systems. In both systems, poor condition hens had lower DCX⁺ cell densities, exhibited elevated splenic expression of interleukin-6 (IL6) mRNA, and had a higher relative caecal abundance of methanogenic archea Methanomethylophilaceae. The findings suggest poor body condition is an indicator that individual hens have experienced a comparatively greater degree of cumulative chronic stress, and that a survey of the proportion of hens with poor body conditions might be one way to evaluate the impact of housing systems on hen welfare.

Insight into dominant intestinal microbiota and the fatty acids profile of turkeys following the administration of synbiotic preparations

BACKGROUND

Probiotics and prebiotics are widely used as natural feed additives in the nutrition of farm animals, including poultry. The using of this type of preparation has a positive effect on animal welfare, human health and the environment. High potential is attributed to preparations combining probiotics and prebiotics, called synbiotics. The aim of the research was to confirm the beneficial effects of synbiotics on the performance of turkeys and the number of dominant intestinal microbiota. In addition, we also investigated the concentration of organic acids (lactic acid, short-chain and branched-chain fatty acids) in the excreta of turkeys.

RESULTS

The synbiotic supplementation of turkeys caused statistically significant (P < 0.05) differences in body weight of animals and European production efficiency factor (EPEF) compared to control group after 15 weeks of rearing. Administration of the synbiotics resulted in a significant (P < 0.05) reduction in the count of potential pathogens (Clostridium spp., Clostridium coccoides and Escherichia coli) but a significant (P < 0.05) increase in the count of beneficial microorganisms (lactobacilli and Bifidobacterium spp.) in the excreta of turkeys. Results of synbiotic supplementation showed that the short-chain fatty acids and lactic acid concentration were significantly (P < 0.05) increased, while the concentration of branched-chain fatty acids was decreased.

CONCLUSION

The results showed a beneficial influence of the synbiotics on the animals' performance, dominant intestinal microbiota and fatty acid profile in the excreta of turkeys. The developed synbiotics can be effectively used in nutrition of turkeys. © 2022 Society of Chemical Industry.

Microbiota Transplantation in Day-Old Broiler Chickens Ameliorates Necrotic Enteritis via Modulation of the Intestinal Microbiota and Host Immune Responses

A microbiota transplant (MT) originating from mature adult chicken ceca and propagated in bioreactors was administered to day-old broiler chicks to ascertain the degree to which, and how, the MT affects Clostridium perfringens (Cp)-incited necrotic enteritis (NE). Using a stress predisposition model of NE, birds administered the MT and challenged with Cp showed fewer necrotic lesions, and exhibited a substantially higher α- and β-diversity of bacteria in their jejunum and ceca. Birds challenged with Cp and not administered the MT showed decreased Lactobacillus and increased Clostridium sensu strico 1 in the jejunum. In ceca, Megamonas, a genus containing butyrate-producing bacteria, was only present in birds administered the MT, and densities of this genus were increased in birds challenged with Cp. Metabolite profiles in cecal digesta were altered in birds administered the MT and challenged with the pathogen; 59 metabolites were differentially abundant following MT treatment, and the relative levels of short chain fatty acids, butyrate, valerate, and propionate, were decreased in birds with NE. Birds administered the MT and challenged with Cp showed evidence of enhanced restoration of intestinal barrier functions, including elevated mRNA of MUC2B, MUC13, and TJP1. Likewise, birds administered the MT exhibited higher mRNA of IL2, IL17A, and IL22 at 2-days post-inoculation with Cp, indicating that these birds were better immunologically equipped to respond to pathogen challenge. Collectively, study findings demonstrated that administering a MT containing a diverse mixture of microorganisms to day-old birds ameliorated NE in broilers by increasing bacterial diversity and promoting positive immune responses.

Delayed access to feed early post-hatch affects the development and maturation of gastrointestinal tract microbiota in broiler chickens

Background

The first two weeks of post-hatch (PH) growth in broilers (meat-type birds) are critical for gut development and microbiota colonization. In the current broiler production system, chicks may not receive feed and water for 24 to 72 h due to variations in hatching time and hatchery management. Post-hatch feed delay affects body weight, feed efficiency, mortality, and gut development. The goal of this study was to investigate changes in the microbiome in broiler chickens early PH and the effect of delayed access to feed on the microbiota.

Results

Chicks either received feed and water immediately after hatch or access to feed was delayed for 48 h to mimic commercial hatchery settings (treatment, TRT). Both groups were sampled (n = 6) at -48, 0, 4 h, and 1 (24 h), 2 (48 h), 3 (72 h), 4 (96 h), 6 (144 h), 8 (192 h), 10 (240 h), 12 (288 h) and 14 (336 h) days PH. Ileal (IL) and cecal (CE) epithelial scrapings (mucosal bacteria, M) and digesta (luminal bacteria, L) were collected for microbiota analysis. Microbiota was determined by sequencing the V3-V4 region of bacterial 16S rRNA and analyzed using QIIME2. The microbiota of early ileal and cecal samples were characterized by high abundance of unclassified bacteria. Among four bacterial populations (IL-L, IL-M, CE-L, CE-M), IL-M was the least affected by delayed access to feed early PH. Both alpha and beta diversities were affected by delayed access to feed PH in IL-L, CE-M and CE-L. However, the development effect was more pronounced. In all four bacterial populations, significant changes due to developmental effect (time relative to hatch) was observed in taxonomic composition, with transient changes of bacterial taxa during the first two weeks PH. Delayed access to feed has limited influence on bacterial composition with only a few genera and species affected in all four bacterial populations. Predicted function based on 16S rRNA was also affected by delayed access to feed PH with most changes in metabolic pathway richness observed in IL-L, CE-L and CE-M.

Conclusions

These results show transient changes in chicken microbiota biodiversity during the first two weeks PH and indicate that delayed access to feed affects microbiota development. Proper microbiota development could be an important factor in disease prevention and antibiotic use in broiler chickens. Moreover, significant differences in response to delayed access to feed PH between luminal and mucosal bacterial populations strongly suggests the need for separate analysis of these two populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02619-6.

The effect of Campylobacter jejuni and Campylobacter coli colonization on the gut morphology, functional integrity, and microbiota composition of female turkeys

BACKGROUND

Campylobacter (C.) species are the most common bacterial cause of foodborne diarrhea in humans. Despite colonization, most animals do not show clinical signs, making recognition of affected flocks and disruption of the infection chain before slaughter challenging. Turkeys are often cocolonized with C. jejuni and C. coli. To understand the pathogen-host-interaction in the context of two different Campylobacter species, we compared the colonization patterns and quantities in mono- and co-colonized female commercial turkeys. In three repeated experiments we investigated the impact on gut morphology, functional integrity, and microbiota composition as parameters of gut health at seven, 14, and 28 days post-inoculation.

RESULTS

Despite successful Campylobacter colonization, clinical signs or pathological lesions were not observed. C. coli persistently colonized the distal intestinal tract and at a higher load compared to C. jejuni. Both strains were isolated from livers and spleens, occurring more frequently in C. jejuni- and co-inoculated turkeys. Especially in C. jejuni-positive animals, translocation was accompanied by local heterophil infiltration, villus blunting, and shallower crypts. Increased permeability and lower electrogenic ion transport of the cecal mucosa were also observed. A lower relative abundance of Clostridia UCG-014, Lachnospiraceae, and Lactobacillaceae was noted in all inoculated groups compared to controls.

CONCLUSIONS

In sum, C. jejuni affects gut health and may interfere with productivity in turkeys. Despite a higher cecal load, the impact of C. coli on investigated parameters was less pronounced. Interestingly, gut morphology and functional integrity were also less affected in co-inoculated animals while the C. jejuni load decreased over time, suggesting C. coli may outcompete C. jejuni. Since a microbiota shift was observed in all inoculated groups, future Campylobacter intervention strategies may involve stabilization of the gut microbiota, making it more resilient to Campylobacter colonization in the first place.

High resolution parallel sequencing reveals multi-strain Campylobacter in broiler chicken flocks testing ‘negative’ by conventional culture methods: implications for control of Campylobacter infection

Contaminated chicken meat is a major source of human Campylobacteriosis and rates of infection remain high, despite efforts to limit the colonisation of broiler (meat) chicken flocks on farms. Using conventional testing methods of culture or qPCR, Campylobacter is typically detected amongst broiler flocks from 3 wk of age, leading to the assumption that infection is introduced horizontally into chicken rearing houses at this time. In this study, we use parallel sequencing of a fragment of the Campylobacter outer membrane protein, encoded by the porA gene, to test for presence of Campylobacter DNA amongst fresh fecal samples collected from broiler flocks aged 23 to 28 d. Campylobacter DNA was detected in all of the 290 samples tested using the porA target, and in 48% of samples using 16S bacterial profiling, irrespective of whether or not Campylobacter could be detected using conventional qPCR thresholds. A single porAf2 variant was predominant among flocks that would be determined to be Campylobacter ‘positive’ by conventional means, but a diverse pattern was seen among flocks that were Campylobacter ‘negative’. The ability to routinely detect low levels of Campylobacter amongst broiler flocks at a much earlier age than would conventionally be identified requires a re-examination of how and when biosecurity measures are best applied for live birds. In addition, it may be useful to investigate why single Campylobacter variants proliferate in some broiler flocks and not others.

Influence of the Gut Microbiome on Feed Intake of Farm Animals

With the advancement of microbiome research, the requirement to consider the intestinal microbiome as the “last organ” of an animal emerged. Through the production of metabolites and/or the stimulation of the host’s hormone and neurotransmitter synthesis, the gut microbiota can potentially affect the host’s eating behavior both long and short-term. Based on current evidence, the major mediators appear to be short-chain fatty acids (SCFA), peptide hormones such as peptide YY (PYY) and glucagon-like peptide-1 (GLP-1), as well as the amino acid tryptophan with the associated neurotransmitter serotonin, dopamine and γ-Aminobutyrate (GABA). The influence appears to extend into central neuronal networks and the expression of taste receptors. An interconnection of metabolic processes with mechanisms of taste sensation suggests that the gut microbiota may even influence the sensations of their host. This review provides a summary of the current status of microbiome research in farm animals with respect to general appetite regulation and microbiota-related observations made on the influence on feed intake. This is briefly contrasted with the existing findings from research with rodent models in order to identify future research needs. Increasing our understanding of appetite regulation could improve the management of feed intake, feed frustration and anorexia related to unhealthy conditions in farm animals.

Omics technologies in poultry health and productivity - part 1: current use in poultry research

In biology, molecular terms with the suffix "-omics" refer to disciplines aiming at the collective characterization of pools of molecules derived from different layers (DNA, RNA, proteins, metabolites) of living organisms using high-throughput technologies. Such omics analyses have been widely implemented in poultry research in recent years. This first part of a bipartite review on omics technologies in poultry health and productivity examines the use of multiple omics and multi-omics techniques in poultry research. More specific present and future applications of omics technologies, not only for the identification of specific diagnostic biomarkers, but also for potential future integration in the daily monitoring of poultry production, are discussed in part 2. Approaches based on omics technologies are particularly used in poultry research in the hunt for genetic markers of economically important phenotypical traits in the host, and in the identification of key bacterial species or functions in the intestinal microbiome. Integrative multi-omics analyses, however, are still scarce. Host physiology is investigated via genomics together with transcriptomics, proteomics and metabolomics techniques, to understand more accurately complex production traits such as disease resistance and fertility. The gut microbiota, as a key player in chicken productivity and health, is also a main subject of such studies, investigating the association between its composition (16S rRNA gene sequencing) or function (metagenomics, metatranscriptomics, metaproteomics, metabolomics) and host phenotypes. Applications of these technologies in the study of other host-associated microbiota and other host characteristics are still in their infancy.

Omics technologies in poultry health and productivity - part 2: future applications in the poultry industry

The increasing global demand for poultry products, together with the growing consumer concerns related to bird health and welfare, pose a significant challenge to the poultry industry. Therefore, the poultry industry is increasingly implementing novel technologies to optimize and enhance bird welfare and productivity. This second part of a bipartite review on omics technologies in poultry health and productivity highlights the implementation of specific diagnostic biomarkers based on omics-research in the poultry industry, as well as the potential integration of multi-omics in future poultry production. A general discussion of the use of multiple omics technologies in poultry research is provided in part 1. To date, approaches focusing on one or more omics type are widely used in poultry research, but the implementation of these omics techniques in poultry production is not expected in the near future. However, great potential lays in the development of diagnostic tests based on disease- or gut health-specific biomarkers, which are identified through omics research. As the cost of omics technologies is rapidly decreasing, implementation of multi-omics measurements in routine poultry monitoring systems might be feasible in the more distant future. Therefore, the opportunities, challenges and requirements to enable the integration of multi-omics-based monitoring of bird health and productivity in future poultry production are discussed.

Development of an environmental contamination model to simulate the microbial bloom that occurs in commercial hatch cabinets

Microbial blooms that emerge in commercial hatch cabinets consist of apathogenic and pathogenic microorganisms, including Escherichia coli, Enterococcus faecalis, and Aspergillus fumigatus. Objectives of the present study included the development of a multipathogen contamination model to mimic commercial conditions and optimization of sampling methods to quantify bacterial or fungal presence within the hatch cabinet. The pathogen challenge mix (PM) was recreated from select bacterial or fungal isolates recovered from an egg homogenate (EH) derived from the contents of infertile eggs and late embryonic mortalities. Isolates selected for PM included Enterococcus faecalis (∼10⁸ CFU/egg), Staphylococcus aureus (∼10⁷ CFU/egg), Staphylococcus chromogenes (∼10⁷ CFU/egg), Aspergillus fumigatus (∼10⁶ spores/egg), and 2 Escherichia coli (∼10⁸ CFU/egg) isolates. Challenge (100 μL of PM or EH) was administered using a sterile loop to a 28 mm area on the blunt end of the eggshell at day 19 of embryogenesis (DOE). In 3 experiments, microbiological data were collected from environmental hatcher samples (open-agar plate method), fluff samples, postmortem whole-body chick rinse samples, and gastrointestinal tract (GIT) samples to evaluate select bacteria and fungi circulating within the hatch cabinet and colonization of GIT. Cumulative bacterial and fungal recovery from the PM hatching environment from DOE20 to hatch was higher than the nonchallenged group (NC) and EH group at ∼860 and ∼1,730 CFU, respectively. Bacterial recovery from GIT, fluff, and chick rinse samples were similar for the PM and EH group in Exp. 1. However, Aspergillus fumigatus recovery from fluff and chick rinse samples for the PM group was significantly (P < 0.001) higher than the NC and EH group. In Exp. 2 and 3, PM challenge significantly (P < 0.05) increased Gram-negative bacterial recovery from the GIT, fluff and chick rinse samples compared to both the NC and EH group. These data suggest this innovative multispecies environmental contamination model using PM could be utilized to evaluate strategies to mitigate microbial contamination in commercial hatch cabinets in a laboratory setting.

Host Species Adaptation of Obligate Gut Anaerobes Is Dependent on Their Environmental Survival

The gut microbiota of warm-blooded vertebrates consists of bacterial species belonging to two main phyla; Firmicutes and Bacteroidetes. However, does it mean that the same bacterial species are found in humans and chickens? Here we show that the ability to survive in an aerobic environment is central for host species adaptation. Known bacterial species commonly found in humans, pigs, chickens and Antarctic gentoo penguins are those capable of extended survival under aerobic conditions, i.e., either spore-forming, aerotolerant or facultatively anaerobic bacteria. Such bacteria are ubiquitously distributed in the environment, which acts as the source of infection with similar probability in humans, pigs, chickens, penguins and likely any other warm-blooded omnivorous hosts. On the other hand, gut anaerobes with no specific adaptation for survival in an aerobic environment exhibit host adaptation. This is associated with their vertical transmission from mothers to offspring and long-term colonisation after administration of a single dose. This knowledge influences the design of next-generation probiotics. The origin of aerotolerant or spore-forming probiotic strains may not be that important. On the other hand, if Bacteroidetes and other host-adapted species are used as future probiotics, host preference should be considered.

Layers, broiler chickens and their F1 cross develop distinctly different caecal microbial communities when hatched and reared together

Aim

To compare the caecal microbiota of layer, broiler, and intermediate F1 layer × broiler cross birds with the hypothesis that significant differences in caecal microbial composition would persist between the three groups when host and environmental interactions were minimized.

Methods and Results

Caecal contents were characterized using 16S rRNA for males of broiler (n = 12), layer (n = 12) and F1 layer × broiler cross (n = 9) birds that were hatched and reared under the same conditions. The microbial community structure differed significantly between the three groups of birds at phylum, genus and OTU levels, with clear separation of the groups observed. Firmicutes was the phylum most represented across samples; however, the high abundance of Proteobacteria in the layer birds at d28 post‐hatch was unexpected, and driven by a higher abundance of E. coli.

Conclusions

The microbiota phylotype between broilers, layers and their F1 cross significantly differed in community structure, diversity and relative abundance in the absence of environmental confounding, which is generally difficult to avoid in microbial studies.

Significance and Impact of Study

The results provide a unique comparison and evidence that there is a strong genetic component driving microbial composition within poultry strains, despite the embryonic development occurring in ovo.

Effects of faecal microbiota transplantation on the growth performance, intestinal microbiota, jejunum morphology and immune function of laying-type chicks

Context Recent studies have indicated that the early stage of growth is a critical window for intestinal microbiota manipulation to optimise the immunity and body growth. Faecal microbiota transplantation (FMT) is often used to regulate intestinal microbiota colonisation. Aims The aim of this study was to explore the effect of FMT on the growth performance, intestinal microbiota, jejunum morphology and immune function of newly hatched laying-type chicks. Methods The chicks (Hy-line Brown) were randomly divided into the control group (CON) and FMT group (FMT), which were treated with sterile saline and faecal microbiota suspension of Hy-line Brown breeder hens on Days 1, 3 and 5 respectively. For each group, there were five replications of 12 birds each for 4 weeks. This study investigated the body weight, tibia length, intestinal microflora, jejunum morphology and immune indexes of the chicks. Key results The results showed that the body weight and tibia length of birds in the FMT group were significantly increased at 7, 14 and 21 days of age (P < 0.01). Furthermore, we found that FMT altered the intestinal microbiota community of the birds and improved the richness, evenness, diversity and stability of their intestinal microbiota (P < 0.05). The faecal microbiota of the donor hens and birds that received the transplantation were very similar. The villus height and the ratio of the villus to crypt of the birds in the FMT group were significantly (P < 0.0001) higher than those in the control group. In addition, Spearman’s correlation analysis showed that the villus height of the FMT group showed positive correlation with Bacteroides (P < 0.05), and the villus height and the ratio of the villus to crypt in the FMT group showed positive correlations with Megasphaera (P < 0.05). The birds in the FMT group had no significant difference in intestinal length, immune organ indexes, serum β-defensin and IgA concentrations. Conclusions In summary, FMT can promote the early growth performance and jejunum morphology of laying-type chicks and improve the intestinal microbiota. FMT has no significant effect on the immune function of chicks. Implications FMT may be a potential method to improve the health of chicks to enhance the poultry industry.

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

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

Effect of cecal microbiota transplantation between different broiler breeds on the chick flora in the first week of life

The cecal microbiota plays numerous roles in chicken health and nutrition. Where such microbiota differs between lines exhibiting distinct phenotypes, microbiota transplantation offers scope to dissect the role of gut microbial communities in those traits. However, the composition and stability of transplants over time is relatively ill-defined and varying levels of success have been reported. In this study, we transplanted cecal contents from adult Roslin broilers into chicks from a different broiler line. Within <12 h posthatch, Ross 308 chicks received an oral gavage of cecal contents (n = 26) or a PBS control (n = 24). Cecal contents samples were collected postmortem from birds on d 1, 2, 3, 4, and 7 posthatch. DNA was extracted from these samples and the transplant inoculum and the V4 region of the 16S rRNA gene was amplified and sequenced. The cecal microbiota of chickens receiving the microbiota transplant was significantly different in composition and significantly richer and more diverse, in comparison to control birds. At the final timepoint (d 7), of the 150 Operational Taxonomic Units (OTUs) that were >0.1% abundant (average) in the donor sample, 137 were detected in the treated group (75 were >0.1% abundant (average)) while only 88 were detected in the control group (29 were >0.1% abundant (average)). Our data therefore suggests that stable transplantation of the cecal microbiota between lines is achievable using the methods described in this paper.