Composition and Function of Chicken Gut Microbiota

Investigation into the supplementation of a ferric sillen core-linked polymer on the health and physiological performance of broiler chickens

Poultry is a ubiquitous and highly sought-after protein source valued for its accessibility, notable protein content, and lack of religious constraints. However, the demand for poultry has resulted in a surge in intensive production practices. The transition from subsistence agricultural practices to intensive food production resulted in the widespread adoption of antibiotics for both therapeutic and economic purposes. These interventions were intended to enhance meat yield, promote bird health, and enhance cost-effectiveness of production. However, this inadvertently contributed to the rise of antimicrobial resistance (AMR). Therefore, the need to explore alternative approaches to mitigate the problems associated with AMR has become increasingly pressing. In response, metal-based compounds have emerged as a promising substitute to conventional antibiotics. In this study, the effects of a water soluble metallo-antimicrobial supplement, ferric sillen core-linked polymer (FSCLP), on body weight gain, feed conversion, water intake, volatile fatty acid (VFA) production, cecal microbiome and intestinal morphology in broilers was examined. The findings of this study suggested that the addition of the FSCLP resulted in better bird performance, even during a period of heat stress. Volatile fatty acids analysis of cecal contents indicated that there were significantly higher levels (p < 0.05) of butyric and valeric acids. Cecal microbiome analysis confirmed significantly lower abundance (p < 0.05) of Proteobacteria (e.g., E. coli) and a significantly greater abundance of VFA-producing bacteria such as Intestinimonas butyriciproducens, Blautia and Lachnospiraceae. The intestinal morphology data showed supplementation with the FSCLP at 80 ppm resulted in a significantly higher (p < 0.05) villus height of the jejunum. This study emphasises the potential of FSCLP as a feasible solution to the issues faced by AMR in chicken production, providing insights into its beneficial impacts on performance, microbial composition, and intestinal health.

Microbial-transcriptome integrative analysis of heat stress effects on amino acid metabolism and lipid peroxidation in poultry jejunum

Despite the significant threat of heat stress to livestock animals, only a few studies have considered the potential relationship between broiler chickens and their microbiota. Therefore, this study examined microbial modifications, transcriptional changes and host-microbiome interactions using a predicted metabolome data-based approach to understand the impact of heat stress on poultry. After the analysis, the host functional enrichment analysis revealed that pathways related to lipid and protein metabolism were elevated under heat stress conditions. In contrast, pathways related to the cell cycle were suppressed under normal environmental temperatures. In line with the transcriptome analysis, the microbial analysis results indicate that taxonomic changes affect lipid degradation. Heat stress engendered statistically significant difference in the abundance of 11 microorganisms, including Bacteroides and Peptostreptococcacea. Together, integrative approach analysis suggests that microbiota-induced metabolites affect host fatty acid peroxidation metabolism, which is correlated with the gene families of Acyl-CoA dehydrogenase long chain (ACADL), Acyl-CoA Oxidase (ACOX) and Acetyl-CoA Acyltransferase (ACAA). This integrated approach provides novel insights into heat stress problems and identifies potential biomarkers associated with heat stress.

Zearalenone-induced hepatointestinal toxicity in laying hens: unveiling the role of gut microbiota and fecal metabolites

Zearalenone (ZEN), a mycotoxin produced by Fusarium species, is known for its reproductive toxicity as an estrogen analogue. However, there are limited knowledge about its hepatointestinal toxicity, as well as the role that gut microbiota and metabolites play in this process. In this study, a total of 24 thirty-week-old hens were fed to investigate the hepatointestinal toxicity subjected to long-term ZEN consumption at 2.0 mg/kg for 90 d. And we employed uncultured 16S rRNA sequencing for gut microbiota and untargeted metabolomics for fecal metabolites assessment. Notably, ZEN induced significant hepatic damage, as evidenced by hepatocyte necrosis, inflammatory cell infiltrate, increased liver lipopolysaccharide (LPS) and blood aspartate aminotransferase (AST) levels (P < 0.05). The decreased villus height, disruption of simple columnar epithelial cells, and exposure of the mucosal intrinsic layer were observed in the intestine. The gut microbial community composition and metabolites differed between ZEN group and control group. ZEN group exhibited higher gut microbial diversity (P < 0.05), lower Firmicutes/Bacteroidetes ratio and Lactobacillus abundance, and higher abundance in the genus such as Bacteroidetes, Parabacteroidetes and Desulfovibrio. Metabolomic analysis showed that ZEN treatment altered biosynthesis of siderophore group nonribosomal peptides and phenylpropanoids, metabolism of amino acid, digestion and absorption of vitamin and ABC transporters. Differential metabolites suggested that ZEN increase the risk of estrogen disorder, nucleic acid degradation, intestinal oxidative stress and inflammation. Neural network analysis showed that Ruminococcus was positively correlated with glyceric acid, and Prevotella was positively correlated with phenylacetylglycine. Both metabolites were positively correlated with blood AST level (P < 0.05), suggesting that intestinal microbe Ruminococcus and Prevotella might exacerbate liver damage by producing these harmful metabolites. Overall, we conclude that ZEN has damaged hepatointestinal system and the altered gut microbiota with resultant metabolite changes contribute to the adverse hepatointestinal effects of ZEN on laying hens. This study underscores the need for monitoring and mitigating ZEN exposure in poultry diets, highlighting its broader implications for animal health and food safety.

Longitudinal survey of total airborne bacterial and archaeal concentrations and bacterial diversity in enriched colony housing and aviaries for laying hens

Conventional cages for laying hens will be banned in Canada as of 2036, and the egg industry is transitioning toward enriched colony housing and aviaries. While higher concentrations of particulate matter have been previously reported in aviaries and other cage-free housing systems, concentrations of total bacteria and archaea suspended in the air are still uncharacterized in Canadian enriched colonies and aviaries. The aim of the present study was to conduct a longitudinal survey of airborne total bacteria and of airborne total archaea in twelve enriched colonies and twelve aviaries in Eastern Canada during a whole laying period. High-throughput sequencing of 16S rRNA gene amplicons was used to reveal and compare bacterial diversity at the start and the end of the production cycle, and during the cold and the warm seasons. Total bacterial and archaeal concentrations were significantly higher in aviaries (p < 0.05) versus enriched colonies, and in the cold season for both housing types (p < 0.05). While flock age did not have a significant effect on total bacterial and archaeal concentrations, it did on bacterial diversity in both enriched colony houses and aviaries (p < 0.05). The 2 housing systems were significantly different in their diversity of bacteria.

Selection for amoxicillin-, doxycycline-, and enrofloxacin-resistant Escherichia coli at concentrations lower than the ECOFF in broiler-derived cecal fermentations

Antimicrobial resistance (AMR) is an emerging worldwide problem and a health threat for humans and animals. Antimicrobial usage in human and animal medicine or in agriculture results in selection for AMR. The selective concentration of antimicrobial compounds can be lower than the minimum inhibitory concentration and differs between environments, which can be a reason for bacterial resistance. Therefore, knowledge of the minimal selective concentration (MSC), under natural conditions, is essential to understand the selective window of bacteria when exposed to residual antimicrobials. In this study, we estimated the MSCs of three antimicrobials, amoxicillin, doxycycline, and enrofloxacin in a complex microbial community by conducting fermentation assays with cecal material derived from broilers. We examined the phenotypic resistance of Escherichia coli, resistome, and microbiome after 6 and 30 hours of fermenting in the presence of the antimicrobials of interest. The concentrations were estimated to be 10-100 times lower than the epidemiological cut-off values in E. coli for the respective antimicrobials as determined by EUCAST, resulting in an MSC between 0.08 and 0.8 mg/L for amoxicillin, 0.4 and 4 mg/L for doxycycline, and 0.0125 and 0.125 mg/L for enrofloxacin. Additionally, resistome analysis provided an MSC for doxycycline between 0.4 and 4 mg/L, but amoxicillin and enrofloxacin exposure did not induce a significant difference. Our findings indicate at which concentrations there is still selection for antimicrobial-resistant bacteria. This knowledge can be used to manage the risk of the emergence of antimicrobial-resistant bacteria.IMPORTANCEAntimicrobial resistance possibly affects human and animal health, as well as economic prosperity in the future. The rise of antimicrobial-resistant bacteria is a consequence of using antimicrobial compounds in humans and animals selecting for antimicrobial-resistant bacteria. Concentrations reached during treatment are known to be selective for resistant bacteria. However, at which concentrations residues are still selective is important, especially for antimicrobial compounds that remain in the environment at low concentrations. The data in this paper might inform decisions regarding guidelines and regulations for the use of specific antimicrobials. In this study, we are providing these minimal selective concentrations for amoxicillin, doxycycline, and enrofloxacin in complex environments.

Chronological dynamics of the gut microbiome in response to the pasture grazing system in geese

It is commonly accepted that dietary fibers are good for gut health. The effect of fibers on the diversity and metabolic activities of the cecal microflora, however, differ with the passage of time. Therefore, we investigated the time-series impacts of the pasture grazing system (a high dietary fiber source) on the cecal microbiome and short-chain fatty acids in Wanpu geese, comparing it to commercial feeding (a low dietary fiber source). The cecal microbiota composition and SCFA concentrations were evaluated by 16S rRNA gene sequencing and gas chromatography, respectively. We found that pasture produced a generally quick positive response to Bacteroidales, Lactobacillales, Gastranaerophilales (at 45 days), Lachnospirales, and Oscillospirales (at 60 days and 90 days) irrespective of Erysipelotrichales (at 45 days), Clostridia_UCG-014, RF39 (at 60 days), Christensenellales, and Peptostreptococcales-Tissierellales (at 90 days) in geese. Meanwhile, we found that Lactobacillales, Gastranaerophilales, Lachnospirales, and Oscillospirales were significantly correlated with short-chain fatty acids in pasture grazing geese. Indeed, the correlation of cecal microbiota with SCFAs led to altered microbial functions evinced by COG; KEGG pathway levels 1, 2, and 3; BugBase; and FAPROTAX databases. This study emphasizes the importance of dietary fiber sources in influencing beneficial impacts in regulating geese microbiota homeostasis and metabolic functions such as energy and lipid metabolism.IMPORTANCELow dietary fiber diet sources cause gut microbial and short-chain fatty acid alterations that lead to compromised animal health. The establishment of an artificial pasture grazing system at the expense of ryegrass is a good source of dietary fiber for geese. Our results described the importance of pasture in maintaining the gut microbiota, SCFAs, and potential microbial functions reported by COG; KEGG pathway levels 1, 2, and 3; BugBase; and FAPROTAX databases.

Yacon (Smallanthus sonchifolius) root extracts affect laying performance, egg quality, serum biochemical parameters and intestinal microbiota in hens

OBJECTIVE

The objective of this study was to investigate the influence of yacon root extracts (YREs) on productive performance and health of laying hens.

METHODS

Six hundred 30-week-old Xiaoshan Chicken layers were divided into 5 groups, control group, antibiotic positive control group, and 3 YREs treatment groups. In a 9-wk feeding experiment, at the end of wk 3, 6, and 9, twenty eggs were collected from each replicate to measure egg qualities. At the end of wk 9, three hen serum samples, and 5 hen cecal content samples were collected from each replicate.

RESULTS

Compared to the control group, 0.8%, 1.6%, and 2.4% YREs treatments could increase hens' daily feed intake, and YREs supplementation affected daily feed intake in linear manner. YREs did not change egg size, but 0.8% and 2.4% YREs changed egg shape by decreasing the egg shape index and sphericity, and 0.8% YREs tended to improve the eggshell breaking strength. Diet supplemented with 1.6% YREs might decrease yolk color grade but optimize the pH of thick egg white in fresh egg; moreover, 1.6% and 2.4% YREs might be helpful for eggs to inhibit water loss during storage, and YREs supplementation affected water loss rate in linear manner. 2.4% YREs could decrease the serum lactate dehydrogenases (LDH) level, and YREs supplemental levels linearly affected serum LDH content. Finally, YREs could enrich the diversity of intestinal microbiota of hens fed with 0.8% and be beneficial for the relative abundance of phylum Bacteroidota and Halobacterota; 2.4% YREs might increase the abundance of phylum Actinobacteriota and genus Bifidobacterium, while decrease genus Bacteroides; YREs supplemental levels affected the abundance of phylum Actinobacteriota, and genera Bifidobacterium and Bacteroides in linear manner.

CONCLUSION

Dietary supplementation with YREs could affect egg quality, protect the health of organs and exhibit prebiotic activity.

Intestinal microbiota diversity from broilers with runting and stunting syndrome performed by metagenomics

Runting and stunting syndrome (RSS) is an enteric viral disease in commercial poultry that directly affects gut health; however, its influence on gut microbiota remains unknown. This study aimed to investigate the compositional changes in the bacterial community of the ileum of 7-day-old broiler chicks naturally affected or not affected by RSS, using next-generation sequencing (NGS) technology. Twenty-one samples were obtained from the ileal contents and mucosa of 11 chicks with RSS and 10 healthy chicks, raised in a dark house system located on a farm in the state of Minas Gerais, Brazil. The results revealed overall changes in the gut microbiota of the chicks with RSS, including a decrease in microbial richness and diversity. In particular, there was a decrease in Lactobacillus and an increase in Candidatus Arthromitus and Clostridium sensu stricto 1. These results indicate a relationship between viral infection and the gut microbial composition, which can cause gut dysbiosis and may influence inflammation in this organ.RESEARCH HIGHLIGHTS RSS causes dysbiosis of the gut microbiota of the ilea of chicks.A difference was found in gut microbiota between chicks with or without RSS.Candidatus Arthromitus was predominant in chicks with RSS.Clostridium sensu stricto 1 was strictly associated with chicks with RSS.

The Influence of Dietary Supplementation with Dried Olive Pulp on Gut Microbiota, Production Performance, Egg Quality Traits, and Health of Laying Hens

This study examines the dietary effect of dried olive pulp (OP) on the overall performance, egg quality, health, and gut microbiota of laying hens during a 36-week trial. A total of 180 Isa Brown layers, aged 23 weeks, were assigned to 15-floor pens and divided into three feeding groups (CON, OP4, and OP6) based on the dietary level of OP. Egg quality and biochemical parameters were assessed in 39- and 59-week-old hens. Fecal samples were collected for microbiota analysis. Data were analyzed with an Analysis of Variance. The percentage of broken eggshells was found to be 15-34% lower in the OP groups compared to the CON groups. At 59 weeks of age, a significant reduction in shell thickness was observed in the CON eggs compared to the OP eggs (p < 0.05). At 39 weeks of age, OP6 eggs had the darkest yolk color of all groups (p < 0.05). Fecal microbial diversity was affected only by hens' age. However, an enrichment in bacterial species belonging to the genera Megasphaera and Megamonas was found in the OP groups at 59 weeks of age. Our results demonstrate that OP feeding beneficially affects egg quality and promotes the proliferation of bacteria involved in the degradation of complex plant compounds, potentially contributing to the overall health of the gut microbiota.

Dietary Kluyveromyces marxianus hydrolysate alters humoral immunity, jejunal morphology, cecal microbiota and metabolic pathways in broiler chickens raised under a high stocking density

This study investigated the impact of dietary supplementation with hydrolyzed yeast (Kluyveromyces marxianus) on growth performance, humoral immunity, jejunal morphology, cecal microbiota and metabolic pathways in broilers raised at 45 kg/m2. A total of 1,176 mixed sex 1-day-old Ross 308 broilers were distributed into 42 pens and randomly assigned to either the control group, the control + 250 g hydrolyzed yeast (HY)/ton, 250HY group, or the control + 500 g HY/ton, 500HY group for 42 d. HY did not affect growth performance. However, HY reduced (P < 0.05) mortality at 25 to 35 d. Dietary HY lowered the heterophil/lymphocyte ratio and enhanced the villus height/crypt depth ratio and Newcastle disease titer (P < 0.05). Compared with HY250 and the control, HY500 upregulated (P < 0.05) IL-10. HY enhanced the α diversity, inferring the richness and evenness of the ceca microbiota. HY500 had greater β diversity than the control (P < 0.05). Six bacterial phyla, namely, Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Verrucomicrobia, and Cyanobacteria, were found. The relative abundance of Firmicutes was greater in the HY500 treatment group than in the HY250 and control groups. HY decreased the abundance of Actinobacteria. HY supplementation altered (P < 0.05) the abundance of 8 higher-level taxa consisting of 2 classes (Bacilli and Clostridia), 1 order (Lactobacillales), 1 family (Streptococcaceae), and five genera (Streptococcus, Lachnospiraceae_uc, Akkermansiaceae, PACO01270_g, and LLKB_g). HY500 improved (P < 0.05) the abundance of Bacilli, Clostridia, Lactobacillales, Streptococcaceae, Streptococcus, PACO01270_g, and Lachnospiraceae_uc, while HY250 enhanced (P < 0.05) the abundance of Akkermansiaceae and LLKB_g. HY improved the abundance of Lactobacillus and Akkermansia spp. Minimal set of pathway analyses revealed that compared with the control, both HY250 and HY500 regulated 20 metabolic pathways. These findings suggest that dietary K. marxianus hydrolysate, especially HY500, improved humoral immunity and jejunal morphology and beneficially altered the composition and metabolic pathways of the cecal microbiota in broilers raised at 45 kg/m2.

Effects of chlorogenic acid on productive and reproductive performances, egg quality, antioxidant functions, and intestinal microenvironment in aged breeder laying hens

This study investigated the effects of dietary chlorogenic acid (CGA) on the productive and reproductive performance, egg quality, antioxidant function, and intestinal microenvironment of laying hens. Thus, 162 healthy Hy-Line Brown breeding hens (63 weeks old) were randomly allocated to 3 groups, each receiving a basal diet plus supplementation: 0, 250, and 500 mg/kg CGA, respectively. Per the in vitro test, CGA had obvious inhibitory effects on Salmonella enteritis and avian pathogenic Escherichia coli and strong free radical scavenging ability. Per the breeder laying hen experiment, the CGA diets had no significant influence on egg production or reproductive performance (P < 0.05). Nevertheless, compared with the control diet, 250 mg/kg CGA significantly increased eggshell thickness, egg weight, yolk color, and Haugh unit (P < 0.05). Compared with the control diet and 500 mg/kg CGA, 250 mg/kg CGA significantly (P < 0.05) elevated antioxidant capacity by reducing serum malondialdehyde content, upregulating heme oxygenase-1, and downregulating heat shock proteins mRNA levels in the ileum. Compared with the control diet and 500 mg/kg CGA, 250 mg/kg CGA (P < 0.05) enhanced intestinal barrier function, shown by the upregulation of ileal Occludin and Mucin-2 mRNA levels; furthermore, 250 mg/kg CGA (P < 0.05) increased anti-apoptotic capacity by increasing B-cell leukemia/lymphoma 2 gene expression and downregulated Bcl2 Associated X mRNA levels in the liver and ileum of late breeder laying hens (P < 0.05). Lastly, 250 mg/kg CGA (P < 0.05) increased cecal g_CHKCI001 and short-chain fatty acid-producing bacteria g_Prevotellaceae UCG-001, positively related to gut health, and in the cecum, 500 mg/kg CGA significantly (P < 0.05) increased g_Shuttleworthia abundance, negatively related to gut health. Our findings suggest that dietary inclusion of 250 mg/kg CGA promotes egg quality, intestinal microbial composition, gut barrier integrity, and the antioxidant capacity of aged breeder laying hens.

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.

Drinking Water and Biofilm as Sources of Antimicrobial Resistance in Free-Range Organic Broiler Farms

Drinking water distribution systems (DWDSs) represent an ideal environment for biofilm formation, which can harbor pathogenic and antimicrobial-resistant bacteria. This study aimed to assess longitudinally the microbial community composition and antimicrobial resistance (AMR), as determined by 16S rRNA NGS and qPCR, respectively, in drinking water (DW) and biofilm from DWDSs, as well as faeces, of free-range organic broiler farms. The role of DWDSs in AMR gene (ARG) dissemination within the farm environment and transmission to animals, was also assessed. DW and biofilm microbial communities differed from those of faecal samples. Moreover, potentially pathogenic and opportunistic bacteria (e.g., Staphylococcaceae) were identified in water and biofilms. High prevalence and abundance of ARGs conferring resistance to carbapenems (i.e., blaNDM), 3rd and 4th generation cephalosporins (i.e., blaCMY-2), (fluoro)quinolones (i.e., qnrS), and polymyxins (i.e., mcr-3 and mcr-5) were detected in DW, biofilm, and faecal samples, which is of concern for both animal and human health. Although other factors (e.g., feed, pests, and wildlife) may contribute to the dissemination of AMR in free-range organic poultry farms, this study indicates that DWDSs can also play a role.

Prebiotic galactooligosaccharide feed modifies the chicken gut microbiota to efficiently clear Salmonella

Chicken meat is contaminated with Salmonella from the gut of infected chickens during slaughter. Eradication of Salmonella from broiler chickens through hygiene measures and/or vaccination is not cost-effective; complementary approaches are required. A mature gut microbiota obstructs Salmonella infection in chickens, and deliberate fortification of colonization resistance through prebiotic feed formulations would benefit public health and poultry production. Prebiotic galactooligosaccharides hastens Salmonella clearance from the gut of infected chickens. To better understand the role of galactooligosaccharides in colonization resistance, broiler chickens were raised on a wheat-soybean meal-based feed, with or without galactooligosaccharides for the first 24 days of life. Chickens were orally challenged with Salmonella enterica serovar Enteritidis at 20 days and the effect of supplementary galactooligosaccharides characterized by profiling Salmonella colonization, gut microbiota, innate immune response, and cecal short-chain fatty acid concentrations. Exposure to dietary galactooligosaccharides shortened the time to clear S. Enteritidis from the ceca. Differential abundance analysis of the cecal microbiota associated Salmonella challenge with a bacterial taxon belonging to the Acidaminococcaceae family (P < 0.005). Increased cecal concentrations of the short-chain fatty acids propionate and valerate were measured in Salmonella-challenged chickens sustained on either control or galactooligosaccharide-supplemented feed relative to mock-challenged controls; but far greater concentrations were detected in chickens fed a galactooligosaccharide-supplemented diet in early life. The abundance of the Acidaminococcaceae taxon exhibited a positive correlation with the cecal concentrations of propionate (ρ = 0.724, P = 0.008) and valerate (ρ = 0.71, P = 0.013). The absence of cecal pro-inflammatory transcriptional responses suggest that the rapid Salmonella clearance observed for the galactooligosaccharide-supplemented diet was not linked to innate immune function.

IMPORTANCE

Work presented here identifies bacterial taxa responsible for colonization resistance to Salmonella in broiler chickens. Deliberate cultivation of these taxa with prebiotic galactooligosaccharide has potential as a straight-forward, safe, and cost-effective intervention against Salmonella. We hypothesize that catabolism of galactooligosaccharide and its breakdown products by indigenous microorganisms colonizing the chicken gut produce excess levels of propionate. In the absence of gross inflammation, propionate is inimical to Salmonella and hastens intestinal clearance.

Modulation of Poultry Cecal Microbiota by a Phytogenic Blend and High Concentrations of Casein in a Validated In Vitro Cecal Chicken Alimentary Tract Model

Phytogenic blends (PBs) consist of various bioactive plant-derived compounds that are used as growth promoters for farm animals. Feed additives based on PBs have beneficial effects on farm animals' production performance, health, and overall well-being, as well as positive modulating effects on gut microbiota. In this study, we used a validated in vitro cecal chicken alimentary tract model (CALIMERO-2) to evaluate the effects of a PB (a mix of components found in rosemary, cinnamon, curcuma, oregano oil, and red pepper), alone or in combination with casein (control), on poultry cecal microbiota. Supplementation with the PB significantly increased the abundance of bacteria associated with energy metabolism (Monoglobus) and growth performance in poultry (Lachnospiraceae UCG-010). The PB also decreased the abundance of opportunistic pathogens (Escherichia-Shigella) and, most importantly, did not promote other opportunistic pathogens, which indicates the safety of this blend for poultry. In conclusion, the results of this study show promising perspectives on using PBs as feed additives for poultry, although further in vivo studies need to prove these data.

The Influence of Cecal Microbiota Transplantation on Chicken Injurious Behavior: Perspective in Human Neuropsychiatric Research

Numerous studies have evidenced that neuropsychiatric disorders (mental illness and emotional disturbances) with aggression (or violence) pose a significant challenge to public health and contribute to a substantial economic burden worldwide. Especially, social disorganization (or social inequality) associated with childhood adversity has long-lasting effects on mental health, increasing the risk of developing neuropsychiatric disorders. Intestinal bacteria, functionally as an endocrine organ and a second brain, release various immunomodulators and bioactive compounds directly or indirectly regulating a host's physiological and behavioral homeostasis. Under various social challenges, stress-induced dysbiosis increases gut permeability causes serial reactions: releasing neurotoxic compounds, leading to neuroinflammation and neuronal injury, and eventually neuropsychiatric disorders associated with aggressive, violent, or impulsive behavior in humans and various animals via a complex bidirectional communication of the microbiota-gut-brain (MGB) axis. The dysregulation of the MGB axis has also been recognized as one of the reasons for the prevalence of social stress-induced injurious behaviors (feather pecking, aggression, and cannibalistic pecking) in chickens. However, existing knowledge of preventing and treating these disorders in both humans and chickens is not well understood. In previous studies, we developed a non-mammal model in an abnormal behavioral investigation by rationalizing the effects of gut microbiota on injurious behaviors in chickens. Based on our earlier success, the perspective article outlines the possibility of reducing stress-induced injurious behaviors in chickens through modifying gut microbiota via cecal microbiota transplantation, with the potential for providing a biotherapeutic rationale for preventing injurious behaviors among individuals with mental disorders via restoring gut microbiota diversity and function.

Intestinal Microbiome Profiles in Broiler Chickens Raised with Different Probiotic Strains

The composition of the intestinal microbiota can influence the metabolism and overall functioning of avian organisms. Therefore, the objective of this study was to evaluate the effect of three different probiotics and an antibiotic on the microbiomes of 1.400 male Cobb® broiler raised for 42 days. The experiment was conducted with the following treatments: positive control diet (basal diet + antibiotic); negative control diet (basal diet without antibiotic and without probiotic); basal diet + Normal Avian Gut Flora (NAGF); basal diet + multiple colonizing strain probiotics (MCSPs); and basal diet + non-colonizing single strain probiotics (NCSSPs). The antibiotic (enramycin-antibiotic growth promoter) and probiotics were administered orally during all experiment (1 to 42 days), mixed with broiler feed. To determine the composition of the microbiota, five samples of ileal digesta were collected from 42-day-old chickens of each experimental group. The alpha and beta diversity of the ileal microbiota showed differences between the groups. MCSPs presented greater richness and uniformity compared to the positive control, negative control, and NCSSPs treatments, while the negative control exhibited greater homogeneity among samples than NCSSPs. MCSPs also showed a higher abundance of the genus Enterococcus. There were differences between the groups for low-abundance taxa (<0.5%), with NAGF showing higher levels of Delftia, Brevibacterium, and Bulleidia. In contrast, NCSSPs had a higher abundance of Ochrobactrum, Rhodoplanes, and Nitrospira. It was concluded that the treatments analyzed in this study induced modulations in the ileal microbiota of the chickens examined.

Impacts of access to legume- or grass-based pasture on behaviour, physiological responses and bacterial load of laying hens

Despite the plethora of studies on the impacts of access to runs on chickens, there is a paucity of information on the welfare and behavioural repertoire of hens raised in the deep litter houses with or without access to legume- or grass-based pasture. Therefore, this study aimed to evaluate the impact of access to grass or legume pastures by laying hens on behaviour, physiological responses and bacterial load. The study was conducted to evaluate the influence of exposure of egg-type chickens to runs on grass or legume pastures on their welfare and behaviours. The study involved the use of 240 ISA brown pullets from 12 weeks of age and and lasted for 48 weeks. The treatments were deep litter housing with grass-based pasture run (PG), deep litter housing with legume-based pasture run (PL) and deep litter housing without runs (LD) having 80 pullets with four replicates of twenty birds each. Behavioural observations of the hens in each pen were made at 52 weeks of age and tonic immobility was assessed by making the birds lie on their back with their head resting in a U-shaped wooden cradle. The measurements of the respiratory rate and rectal temperature of the hens were assessed at 1:00 p.m. at different laying phases. The gastrointestinal and egg bacterial counts were conducted at 60 weeks of age. Results revealed that the proportion of time spent eating was highest (p < 0.05) in the deep litter housing system, while the legume and grass pasture were similar. The hens spent most of their time standing and eating in the three treatments. However, the time spent standing in PL and PG was similar but significantly higher (p < 0.05) than in LD. Results on tonic immobility duration showed that the time spent by the hens in LD during the reaction was significantly longer than those of the PL and PG in the first, second and third phases of the experiments. However, the time spent by the hens in PL and PG was similar. The rectal temperatures of PL and PG birds were comparable and higher than those of LD during the second phase. On the other hand, there was no difference in the respiratory rate. Plasma triiodothyronine (T3) of the hens did not follow a consistent pattern. The bacterial count in the large intestine in LD and PL was similar but significantly (P < 0.05) higher than that of the PG. It was concluded that access to pasture influenced the behaviours of hens and that tonic immobility duration was shorter in the hens on the pasture, suggesting that access to pasture favoured hens' welfare.

Assessing the impact of hatching system and body weight on the growth performance, caecal short-chain fatty acids, and microbiota composition and functionality in broilers

BACKGROUND

Variations in body weight (BW) remain a significant challenge within broiler flocks, despite uniform management practices. Chicken growth traits are influenced by gut microbiota, which are in turn shaped by early-life events like different hatching environments and timing of first feeding. Chicks hatched in hatcheries (HH) experience prolonged feed deprivation, which could adversely impact early microbiota colonization. Conversely, hatching on-farm (HOF) allows early feeding, potentially fostering a more favorable gut environment for beneficial microbial establishment. This study investigates whether BW differences among broilers are linked to the disparities in gut microbiota characteristics and whether hatching systems (HS) impact the initial microbial colonization of broilers differing in BW, which in turn affects their growth patterns. Male Ross-308 chicks, either hatched in a hatchery or on-farm, were categorized into low (LBW) and high (HBW) BW groups on day 7, making a two-factorial design (HS × BW). Production parameters were recorded periodically. On days 7, 14, and 38, cecal volatile fatty acid (VFA) and microbiota composition and function (using 16 S rRNA gene sequencing and PICRUSt2) were examined.

RESULTS

HOF chicks had higher day 1 BW, but HH chicks caught up within first week, with no further HS-related performance differences. The HBW chicks remained heavier attributed to higher feed intake rather than improved feed efficiency. HBW group had higher acetate concentration on day 14, while LBW group exhibited higher isocaproate on day 7 and isobutyrate on days 14 and 38. Microbiota analyses revealed diversity and composition were primarily influenced by BW than by HS, with HS having minimal impact on BW-related microbiota. The HBW group on various growth stages was enriched in VFA-producing bacteria like unclassified Lachnospiraceae, Alistipes and Faecalibacterium, while the LBW group had higher abundances of Lactobacillus, Akkermansia and Escherichia-Shigella. HBW microbiota presented higher predicted functional potential compared to the LBW group, with early colonizers exhibiting greater metabolic activity than late colonizers.

CONCLUSIONS

Despite differences in hatching conditions, the effects of HS on broiler performance were transient, and barely impacting BW-related microbiota. BW variations among broilers are likely linked to differences in feed intake, VFA profiles, and distinct microbiota compositions and functions.

Persistence of commensal multidrug-resistant Escherichia coli in the broiler production pyramid is best explained by strain recirculation from the rearing environment

Despite the success of mitigation policies in several countries to reduce the use of antibiotics in veterinary medicine, pathogenic and commensal bacteria resistant to antibiotics are still circulating in livestock animals. However, factors contributing the most to antimicrobial resistance (AMR) persistence in these settings are yet not clearly identified. The broiler production, with its highly segmented, pyramidal structure offers an ideal context to understand and control the spread of resistant bacteria. By taking advantage of an experimental facility reproducing the whole broiler production pyramid, we demonstrate that resistant E. coli persist in our system primarily though recirculation of a few commensal clones surviving in the rearing environment. No vertical transmission from hens to offspring nor strain acquisition at the hatchery were detected, while import of new strains from outside the facility seems limited. Moreover, each clone carries its own resistance-conferring plasmid(s), and a single putative plasmid horizontal transfer could have been inferred. These results, observed for now in a small experimental facility with high level of biosecurity, must be confirmed in a commercial farm context but still provide invaluable information for future mitigation policies.

The Association between Broiler Litter Microbiota and the Supplementation of Bacillus Probiotics in a Leaky Gut Model

Probiotics provided from hatch have a major influence on microbiota development, and together with environmental and bedding microbiota, shape the microbial community of the litter. We investigated the influence of probiotic supplementation and a leaky gut challenge induced using dexamethasone (DEX) on the litter microbial community and litter parameters. The probiotic product was a mix of three Bacillus amyloliquefaciens strains. The litter microbiota were compared to the microbial communities from other gut sections. The litter samples had higher microbial diversity compared to the caecum, gizzard, jejunum, and jejunal mucosa. The high similarity between the litter phylum-level microbiota and gizzard microbiota detected in our study could be a consequence of ingested feed and litter passing through the gizzard. Moreover, the litter microbial community is fundamentally distinct from the intestinal microbiota, as evidenced by the number of genera present in the litter but absent from all the intestinal sections and vice versa. Furthermore, LEfSe analysis identified distinct microbial taxa across different groups, with specific genera associated with different treatments. In terms of litter quality, the birds in the DEX groups had a significantly higher moisture content, indicating successful leaky gut challenge, while probiotic supplementation did not significantly affect the moisture levels. These findings provide comprehensive insights into the distinct microbiota characteristics of litter.

Microbiome analyses of poultry feeds: Part II. Comparison of different poultry feeds

Within the realm of poultry feed mill operations, the persistent concern over microbial feed quality necessitates the establishment of a robust baseline for enhancing and sustaining the standards of commercial feeds. This dual-phase investigation, comprising Parts I, was previously published, and the current study presented here as Part II aimed to illuminate this baseline using 16S rRNA gene sequencing. In Part II, nine distinct commercial poultry feeds formulated as starters, growers, starter/growers, or supplements, the selected feeds underwent genomic DNA extraction, amplification with custom dual-indexed primers, and subsequent Illumina MiSeq sequencing. Through data analysis in QIIME2-2021.4 and R Studio, the study unveils alpha (Kruskal-Wallis) and beta (ANOSIM) diversity, taxonomic differences (ANCOM), and core microbiomes (core_members), deeming main and pairwise effects statistically significant at p < 0.05 and Q < 0.05. Notably, the investigation identified 30% common core microbial members across the nine feed types, shedding light on potential foodborne poultry pathogens such as Helicobacter and Campylobacter. Probiotic-associated feeds exhibited distinct microbial communities, emphasizing the need to explore their impact on the early poultry gastrointestinal tract (GIT) further.

Comparison of gut microbiota immunity and pathology in specific-pathogen-free chickens with glandular and muscular gastritis using different methods

The objective of this study is to review different methods to screen for the optimal model for preventing and treating chicken glandular and muscular gastritis syndrome. Twenty-four 40-day-old specific pathogen-free (SPF) chickens were randomly allocated into four groups (N = 6): polyethylene glycol + ammonium chloride group (M1 group), acetic acid + rhubarb group (M2 group), polyethylene glycol + rhubarb group (M3 group), and control group. The control group had free access to water, while the remaining groups received different doses of molding reagents added to their drinking water. The animal models were assessed based on clinical manifestations, histopathology findings, serological analysis, and composition of intestinal microbiota to establish an optimal approach for constructing an avian model of glandular and muscular gastritis. The SPF chickens in each model group exhibited typical symptoms of glandular and muscular gastritis, poor spirit, yellow loose stools with undigested feed, and enlargement and ulceration of the glandular and muscular stomach. Among these groups, the M3 group had the highest incidence rate of 100%. Compared to the control group, the body weight and body temperature of the chicken in the three model groups were reduced, and the glandular and muscular stomachs and duodenum showed different degrees of bleeding, mucosal abscission, and other pathological injuries. Additionally, the levels of serum IL-2 and α-amylase activity decreased while the content of IL-4 increased. After conducting 16s rDNA sequencing, it was observed that the abundance of Bacteroides, Faecalibacterium, and Ruminococcaceae UCG-014 was significantly increased in the model group compared to the control group. Conversely, there was a notable decrease in the levels of Megamonas and Lactobacillus, which are speculated to be associated with arachidonic acid metabolism, the NF-κB signaling pathway, and TNF signaling pathways. The combination of polyethylene glycol and rhubarb emerged as the most effective method for establishing the glandular and muscular gastritis model in SPF chickens. This constructed chicken model displayed distinct signs of damage to the glandular and muscular stomach, inflammatory response, and disturbance in the intestinal flora, thereby providing a foundation for future research on the prevention and treatment of this syndrome.

Dust sprinkling as an effective method for infecting layer chickens with wild-type Salmonella Typhimurium and changes in host gut microbiota

Role of dust in Salmonella transmission on chicken farms is not well characterised. Salmonella Typhimurium (ST) infection of commercial layer chickens was investigated using a novel sprinkling method of chicken dust spiked with ST and the uptake compared to a conventional oral infection. While both inoculation methods resulted in colonisation of the intestines, the Salmonella load in liver samples was significantly higher at 7 dpi after exposing chicks to sprinkled dust compared to the oral infection group. Infection of chickens using the sprinkling method at a range of doses showed a threshold for colonisation of the gut and organs as low as 1000 CFU/g of dust. Caecal content microbiota analysis post-challenge showed that the profiles of chickens infected by the sprinkling and oral routes were not significantly different; however, both challenges induced differences when compared to the uninfected negative controls. Overall, the study showed that dust sprinkling was an effective way to experimentally colonise chickens with Salmonella and alter the gut microbiota than oral gavage at levels as low as 1000 CFU/g dust. This infection model mimics the field scenario of Salmonella infection in poultry sheds. The model can be used for future challenge studies for effective Salmonella control.

Insect live larvae as a new nutritional model in duck: effects on gut health

BACKGROUND

This study aimed to evaluate the effects of Hermetia illucens (Black soldier fly-BSF) and Tenebrio molitor (Yellow mealworm-YMW) live larvae as a new nutritional model on duck's gut health, considering gut histomorphometry, mucin composition, cytokines transcription levels, and microbiota. A total of 126, 3-days-old, females Muscovy ducks were randomly allotted to three dietary treatments (6 replicates/treatment, 7 birds/pen): (i) C: basal diet; (ii) BSF: C + BSF live larvae; (iii) YMW: C + YMW live larvae. BSF and YMW live larvae were administered on top of the basal diet, based on the 5% of the expected daily feed intake. The live weight, average daily gain, average daily feed intake and feed conversion ratio were evaluated for the whole experimental period. On day 52, 12 ducks/treatment (2 birds/replicate) were slaughtered and samples of duodenum, jejunum, ileum, spleen, liver, thymus and bursa of Fabricius were collected for histomorphometry. Mucin composition was evaluated in the small intestine through histochemical staining while jejunal MUC-2 and cytokines transcription levels were evaluated by rt-qPCR. Cecal microbiota was also analyzed by means of 16 S rRNA gene sequencing.

RESULTS

Birds' growth performance and histomorphometry were not influenced by diet, with a proximo-distal decreasing gradient from duodenum to ileum (p < 0.001), respecting the physiological gut development. Mucin staining intensity and MUC-2 gene expression did not vary among dietary treatments, even though mucin intensity increased from duodenum to ileum, according to normal gut mucus physiology (p < 0.001). Regarding local immune response, IL-6 was higher in YMW group when compared to the other groups (p = 0.009). Insect live larvae did not affect cecal microbiota diversity, but BSF and YMW groups showed a higher presence of Helicobacter, Elusimicrobium, and Succinatimonas and a lower abundance of Coriobacteriaceae and Phascolarctobacterium compared to C birds (p < 0.05).

CONCLUSIONS

The use of BSF and YMW live larvae as new nutritional model did not impair gut development and mucin composition of Muscovy ducks, but slightly improved the intestinal immune status and the microbiota composition by enhancing regulatory cytokine IL-6 and by increasing minor Operational Taxonomic Units (OTUs) involved in short-chain fatty acids production.

Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the cecum and ileum in broiler chickens

Coccidiosis, an intestinal disease caused by Eimeria parasites, is responsible for major losses in the poultry industry by impacting chicken health. The gut microbiota is associated with health factors, such as nutrient exchange and immune system modulation, requiring understanding on the effects of Eimeria infection on the gut microbiota. This study aimed to determine the effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the cecum (CeL and CeM) and ileum (IlL and IlM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. E. acervulina infection decreased evenness in CeL microbiota at day 10, increased richness in CeM microbiota at day 3 before decreasing richness at day 14, and decreased richness in IlL microbiota from day 3 to 10. CeL, CeM, and IlL microbiota differed between infected and control birds based on beta diversity at varying time points. Infection reduced relative abundance of bacterial taxa and some predicted metabolic pathways known for short-chain fatty acid production in CeL, CeM, and IlL microbiota, but further understanding of metabolic function is required. Despite E. acervulina primarily targeting the duodenum, our findings demonstrate the infection can impact bacterial diversity and abundance in the cecal and ileal microbiota.

Host genetics drives differences in cecal microbiota composition and immune traits of laying hens raised in the same environment

Vaccination is one of the most effective strategies for preventing infectious diseases but individual vaccine responses are highly heterogeneous. Host genetics and gut microbiota composition are 2 likely drivers of this heterogeneity. We studied 94 animals belonging to 4 lines of laying hens: a White Leghorn experimental line genetically selected for a high antibody response against the Newcastle Disease Virus (NDV) vaccine (ND3) and its unselected control line (CTR), and 2 commercial lines (White Leghorn [LEG] and Rhode Island Red [RIR]). Animals were reared in the same conditions from hatching to 42 d of age, and animals from different genetic lines were mixed. Animals were vaccinated at 22 d of age and their humoral vaccine response against NDV was assessed by hemagglutination inhibition assay and ELISA from blood samples collected at 15, 19, and 21 d after vaccination. The immune parameters studied were the 3 immunoglobulins subtypes A, M, and Y and the blood cell composition was assessed by flow cytometry. The composition of the cecal microbiota was assessed at the end of the experiment by analyzing amplified 16S rRNA gene sequences to obtain amplicon sequence variants (ASV). The 4 lines showed significantly different levels of NDV vaccine response at the 3 measured points, with, logically, a higher response of the genetically selected ND3 line, and intermediate and low responses for the unselected CTR control line and for the 2 commercial lines, respectively. The ND3 line displayed also a higher proportion of immunoglobulins (IgA, IgM, and IgY). The RIR line showed the most different blood cell composition. The 4 lines showed significantly different microbiota characteristics: composition, abundances at all taxonomic levels, and correlations between genera and vaccine response. The tested genetic lines differ for immune parameters and gut microbiota composition and functions. These phenotypic differences can be attributed to genetic differences between lines. Causal relationships between both types of parameters are discussed and will be investigated in further studies.

Investigating antibiotic free feed additives for growth promotion in poultry: effects on performance and microbiota

The poultry industry is evolving towards antibiotic-free production to meet market demands and decelerate the increasing spread of the antimicrobial resistance. The growing need for antibiotic free products has challenged producers to decrease or completely stop using antimicrobials as feed supplements in broiler diet to improve feed efficiency, growth rate, and intestinal health. Natural feed additives (e.g., probiotics and phytobiotics) are promising alternatives to substitute antimicrobial growth promoters. The goal of our study was to characterize the effects of a Probiotic and an Essential Oils blend on broilers' performance and perform a time-series analysis to describe their excreta microbiome. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 d in 32 randomly allocated cages. Treatments consisted of 4 experimental diets: a basal diet, and a basal diet mixed with an Antibiotic (bacitracin methylene disalicylate), an essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Body weight (on 1, 10, and 21d), and feed intake (10d and 21d) were recorded and feed conversion ratio was calculated. Droppings were collected daily (1-21d) to characterize broilers' excreta microbiota by targeted sequencing of the bacterial 16S rRNA gene. The Probiotic significantly improved feed conversion ratio for starter phase 1 to 10d (P = 0.03), grower phase 10 to 21d (P = 0.05), and total period 1 to 21d (P = 0.01) compared to the Antibiotic. Feed supplements did not affect alpha diversity but did impact microbial beta diversity (P < 0.01). Age also impacted microbiome turnover as differences in alpha and beta diversity were detected. Furthermore, when compared to the basal diet, the probiotic and antibiotic significantly impacted relative abundance of Bifidobacterium (log2 fold change -1.44, P = 0.03), Intestinimonas (log2 fold change 0.560, P < 0.01) and Ligilactobacillus (log2 fold change -1.600, P < 0.01). Overall, Probiotic supplementation but not essential oils supplementation positively impacted broilers' growth performance by directly causing directional shifts in broilers' excreta microbiota structure.

Beyond probiotics, uses of their next-generation for poultry and humans: A review

The production of healthy food is one of the basic requirements and challenges. Research efforts have been introduced in the human's food industry to reduce the microbial resistance and use safe and healthy alternatives with a high durability. However, the conducted work about these issues in the field of livestock animal production have been started since 2015. Inappropriate and extensive use of antibiotics has resulted in the increase of antimicrobial resistance, presence of drug residues in tissues, and destruction of the gut microbiome. Therefore, discovering and developing antibiotic substitutes were urgent demands. Probiotic compounds containing living micro-organisms are important antibiotic alternative that have been beneficially and extensively used in humans, animals, and poultry. However, some probiotics show some obstacles during production and applications. Accordingly, this review article proposes a comprehensive description of the next-generation of probiotics including postbiotics, proteobiotics, psychobiotics, immunobiotics and paraprobiotics and their effects on poultry production and human's therapy. These compounds proved great efficiency in terms of restoring gut health, improving performance and general health conditions, modulating the immune response and reducing the pathogenic micro-organisms. However, more future research work should be carried out regarding this issue.

Isolation and Identification of Chicken-Derived Lactic Acid Bacteria: In Vitro Probiotic Properties and Antagonistic Effects against Salmonella pullorum, Staphylococcus aureus, and Escherichia coli

The development of probiotics capable of quickly colonizing the intestines of animals is important in promoting the healthy growth of livestock. The aim of this study was to screen lactic acid bacteria (LAB) from the intestinal microbiota of chickens with potential applications, and to evaluate their probiotic properties and antagonistic abilities against Salmonella pullorum, Staphylococcus aureus, and Escherichia coli. The results showed that a total of 79 strains with the characteristics of LAB were isolated from the chicken cecum microbiota, of which 7 strains exhibited strong inhibitory activity against S. pullorum, S. aureus, and E. coli. Performing 16s rDNA sequencing revealed that these seven strains were Lactiplantibacillus pentosus (n = 1), Lactiplantibacillus plantarum (n = 3), Lactiplantibacillus paraplantarum (n = 1), Lactiplantibacillus argentoratensis (n = 1), and Lactiplantibacillus fabifermentans (n = 1). Among them, L. pentosus R26 and L. plantarum R32 exhibited superior antibacterial activity. These two strains demonstrated high lactic acid production ability, with survival rates of 86.29% and 87.99% after 3 h of treatment at pH 1.5, 86.66% and 85.52% after 3 h of treatment with 0.5% bile salts, 90.03% and 88.16% after 2 h of treatment with simulated gastric fluid, and 98.92% and 98.22% after 2 h of treatment with simulated intestinal fluid, respectively. Co-cultivation with L. pentosus R26 for 24 h resulted in 50% of the pathogens being antagonized, while almost complete inhibition was observed following 72 h of co-cultivation. In conclusion, L. pentosus R26 and L. plantarum R32 exhibited high antibacterial activity and acid production capability, while also demonstrating satisfactory tolerance to low pH values and high concentrations of bile salts and digestive fluid. The probiotic characteristics and stress resistance of L. pentosus R26 were slightly superior to those of L. plantarum R32, indicating its potential for development as a probiotic.

Diet replacement with whole insect larvae affects intestinal morphology and microbiota of broiler chickens

Insect-based diets are gaining interest as potential ingredients in improving poultry gut health. This study assessed the dietary treatment with whole dried Tenebrio molitor larvae (TM) on broiler chickens' gut microbiota and morphology. 120 Ross-308 broilers received treated diets with 5% (TM5) and 10% (TM10) replacement ratio in a 35-day trial. Intestinal histomorphometry was assessed, as well as claudin-3 expression pattern and ileal and caecal digesta for microbial community diversity. Null hypothesis was tested with two-way ANOVA considering the intestinal segment and diet as main factors. The TM5 group presented higher villi in the duodenum and ileum compared to the other two (P < 0.001), while treated groups showed shallower crypts in the duodenum (P < 0.001) and deeper in the jejunum and ileum than the control (P < 0.001). Treatments increased the caecal Firmicutes/Bacteroidetes ratio and led to significant changes at the genus level. While Lactobacilli survived in the caecum, a significant reduction was evident in the ileum of both groups, mainly owed to L. aviarius. Staphylococci and Methanobrevibacter significantly increased in the ileum of the TM5 group. Results suggest that dietary supplementation with whole dried TM larvae has no adverse effect on the intestinal epithelium formation and positively affects bacterial population richness and diversity.

Yeast mannan rich fraction positively influences microbiome uniformity, productivity associated taxa, and lay performance

BACKGROUND

Alternatives to antibiotic as growth promoters in agriculture, such as supplemental prebiotics, are required to maintain healthy and high performing animals without directly contributing to antimicrobial resistance bioburden. While the gut microbiota of broiler hens has been well established and successfully correlated to performance, to our knowledge, a study has yet to be completed on the effect of prebiotic supplementation on correlating the mature laying hen productivity and microbiota. This study focused on establishing the impact of a yeast derived prebiotic, mannan rich fraction (MRF), on the cecal microbiota of late laying hens. This study benefitted from large sample sizes so intra- and intergroup variation effects could be statistically accounted for.

RESULTS

Taxonomic richness was significantly greater at all taxonomic ranks and taxonomic evenness was significantly lower for all taxonomic ranks in MRF-supplemented birds (P < 0.005). Use of principal coordinate analyses and principal component analyses found significant variation between treatment groups. When assessed for compositional uniformity (an indicator of flock health), microbiota in MRF-supplemented birds was more uniform than control birds at the species level. From a food safety and animal welfare perspective, Campylobacter jejuni was significantly lower in abundance in MRF-supplemented birds. In this study, species associated with high weight gain (an anticorrelator of performance in laying hens) were significantly lower in abundance in laying hens while health-correlated butyrate and propionate producing species were significantly greater in abundance in MRF-supplemented birds.

CONCLUSIONS

The use of prebiotics may be a key factor in controlling the microbiota balance limiting agri-food chain pathogen persistence and in promoting uniformity. In previous studies, increased α- and β-diversity indices were determinants of pathogen mitigation and performance. MRF-supplemented birds in this study established greater α- and β-diversity indices in post-peak laying hens, greater compositional uniformity across samples, a lower pathogenic bioburden and a greater abundance of correlators of performance.

Live black soldier fly (Hermetia illucens) larvae in feed for laying hens: effects on hen gut microbiota and behavior

This study examined the effects of including live black soldier fly (BSF, Hermetia illucens) larvae in the diet of laying hens on gut microbiota, and the association between microbiota and fearfulness. A total of 40 Bovans White laying hens were individually housed and fed 1 of 4 dietary treatments that provided 0, 10, 20%, or ad libitum daily dietary portions of live BSF larvae for 12 wk. Cecum microbiota was collected at the end of the experiment and sequenced. Behavioral fear responses to novel objects and open field tests on the same hens were compared against results from gut microbiota analyses. The results showed that the bacteria genera Enterococcus, Parabacteroides, and Ruminococcus torques group were positively associated with increased dietary portion of live larvae, while Lactobacillus, Faecalibacterium, Bifidobacterium, Subdoligranulum, and Butyricicoccus were negatively associated with larvae in the diet. Inclusion of larvae did not affect fear behavior, but the relative abundance of Lachnospiraceae CHKCI001 and Erysipelatoclostridium was associated with fear-related behaviors. Further studies are needed to determine whether the change in gut microbiota affects fearfulness in the long-term.

Enhancing Weaned Piglet Health and Performance: The Role of Autolyzed Yeast (Saccharomyces cerevisiae) and β-Glucans as a Blood Plasma Alternative in Diets

The objective of this study was to evaluate the inclusion of the autolyzed yeast (AY) Saccharomyces cerevisiae with or without an immunomodulator (1,3/1,6 β-glucans) as a total/partial substitute for blood plasma (BP) in the diet of post-weaning piglets; zootechnical performance, intestinal health and microbiota, immune responses and energy metabolism were assessed. A total of 240 castrated male and female piglets, with a mean age of 22 days and mean initial weight of 5.24 ± 0.82 kg, were randomly divided into blocks of four treatments with 12 replicates. The dietary inclusions were blood plasma (BP), autolyzed yeast (AY), autolyzed yeast + immunomodulator (AYI) and 50% BP and 50% AY (BPAY). In pre-initial phase II (29-35 days), piglets fed AY showed better feed conversion (FCR = 1.358) than the piglets in the BP (1.484), AYI (1.379) and BPAY (1.442) groups, i.e., 8.49% (0.126), 1.52% (0.021) and 4.50% (0.084), respectively (p = 0.0293). In the total period (21-42 days), better FCR was observed in the AYI (1.458) group, i.e., 4.64% (0.071), 1.15% (0.017) and 4.58% (0.070), than in the BP (1.529), AY (1.475) and BPAY (1.528) groups, respectively (p = 0.0150). In piglets fed AY (n = 3) and BPAY (n = 2), there was a reduction in the number of medications, i.e., 82.35% (-14n) and 88.23% (-15n), respectively (p = 0.0001), compared with that in the BP group (n = 17). In the AY group (73.83 mg/dL), AYI group (69.92 mg/dL), and BPAY group (69.58 mg/dL), piglets exhibited increases in triglyceride levels of 79.32%, 69.83%, and 69.00%, respectively, in comparison to those in the BP group, which had triglyceride levels of 41.17 mg/dL (p = 0.0400). The beta-hydroxybutyrate concentration in the AY group (79.96 ng/μL) was lower by 31.95%, 22.64%, and 5.89% compared to the BP group (117.50 ng/μL), AYI group (103.36 ng/μL), and BPAY group (84.67 ng/μL), respectively (p = 0.0072). In the AYI group, there was modulation of the microbiota, with an increase in the relative abundance of bacteria of the genera Lactobacillus, Collinsella and Bulleidia. AY, associated or not associated with an immunomodulator, is a potential substitute for BP in diets for piglets in the nursery phase, with positive effects on immune, metabolic, and intestinal microbial performance.

Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties

BACKGROUND

Chickens are one of the most widely farmed animals worldwide and play a crucial role in meat and egg production. Gut microbiota is essential for chickens' health, disease, growth, and egg production. However, native chickens such as Jianghan chickens have better meat and egg production quality than centralized chickens, their intestinal microbial diversity is richer, and the potential gut microbial resources may bring health benefits to the host.

RESULTS

The bacterial species composition in the gut microbiota of Jianghan chickens is similar to that of other chicken breeds, with Phocaeicola and Bacteroides being the most abundant bacterial genera. The LEfSe analysis revealed significant differences in species composition and functional profiles between samples from Jingzhou and the other three groups. Functional annotation indicated that the gut microbiota of Jianghan chickens were dominated by metabolic genes, with the highest number of genes related to carbohydrate metabolism. Several antibiotic resistance genes (ARGs) were found, and the composition of ARGs was similar to that of factory-farmed chickens, suggesting that antibiotics were widely present in the gut microbiota of Jianghan chickens. The resistance genes of Jianghan chickens are mainly carried by microorganisms of the Bacteroidota and Bacillota phylum. In addition, more than 829 isolates were selected from the microbiota of Jianghan chickens. Following three rounds of acid and bile tolerance experiments performed on all the isolated strains, it was determined that six strains of Pediococcus acidilactici exhibited consistent tolerance. Further experiments confirmed that three of these strains (A4, B9, and C2) held substantial probiotic potential, with P. acidilactici B9 displaying the highest probiotic potential.

CONCLUSIONS

This study elucidates the composition of the intestinal microbiota and functional gene repertoire in Jianghan chickens. Despite the absence of antibiotic supplementation, the intestinal microbial community of Jianghan chickens still demonstrates a profile of antibiotic resistance genes similar to that of intensively reared chickens, suggesting resistance genes are prevalent in free-ranging poultry. Moreover, Jianghan and intensively reared chickens host major resistance genes differently, an aspect seldom explored between free-range and pastured chickens. Furthermore, among the 829 isolates, three strains of P. acidilatici exhibited strong probiotic potential. These findings provide insights into the unique gut microbiota of Jianghan chickens and highlight potential probiotic strains offering benefits to the host. Video Abstract.

The effect of sex and dietary crude protein level on nutrient transporter gene expression and cecal microbiota populations in broiler chickens

It is well known that male and female broilers differ in their growth performance and that many physiological factors contribute to this difference. The aim of this experiment is to investigate if there are differences between male and female broilers in cecal microbiota and nutrient transporter gene expression and if these differences play a role in the growth performance of broilers. The possible effect of protein level and its interaction with sex on microbiota and expression of the nutrient transporters were also investigated. Samples were collected from male and female birds fed either standard crude protein (SCP) or reduced crude protein diets (RCP) at the age of d 35. The experiment was designed as a 2 × 2 factorial arrangement of treatments consisting of 448 Cobb 500 broilers assigned to 32-floor pens with 4 treatments, 8 replicates, and 14 birds per pen for performance measurements. The factors were sex (male or female) and dietary crude protein (CP) level (standard or reduced). Body weight gain (BWG), feed intake and feed conversion ratio were recorded for each pen. Sex had a significant effect on BWG and FCR (P < 0.001) where males had a significantly higher BWG and better FCR compared to females. There was a significant interaction between sex and protein level on feed intake (FI) (P < 0.05), where male birds had a higher FI compared to female birds only when the birds were fed SCP but not RCP diets. There was a significant interaction between CP level and sex on the expression of CAT2 (P = 0.02) and PEPT2 (P = 0.026) where the genes were significantly upregulated in females but only when the RCP diet was fed. The RCP diet upregulated the expression of BoAT (P = 0.03) as a main effect. Female birds had significantly higher expression of the PepT-2 gene compared to the males. The alpha diversity of the cecal microbiota showed differences among the treatments. The Shannon diversity index was statistically higher (P = 0.036) for males fed the SCP diet and the Chao1 index for evenness was statistically higher (P = 0.027) in females fed the SCP diet. There was also a difference in the relative abundance of the 15 most common genera found in the cecal content of the broilers in this experiment and lastly, the differential composition of microbiota between the different treatments was also significantly different. This study suggests that chickens are able to compensate for a reduction in AA substrates when fed a low CP diet through the upregulation of certain AA transporters, females may adapt to low CP diets better by such upregulation compared to males, and lastly, sex has an effect on the cecal microbial population and these differences contribute towards the performance differences between male and female broilers.

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.

Genomic characterization of Pseudomonas spp. on food: implications for spoilage, antimicrobial resistance and human infection

BACKGROUND

Pseudomonas species are common on food, but their contribution to the antimicrobial resistance gene (ARG) burden within food or as a source of clinical infection is unknown. Pseudomonas aeruginosa is an opportunistic pathogen responsible for a wide range of infections and is often hard to treat due to intrinsic and acquired ARGs commonly carried by this species. This study aimed to understand the potential role of Pseudomonas on food as a reservoir of ARGs and to assess the presence of potentially clinically significant Pseudomonas aeruginosa strains on food. To achieve this, we assessed the genetic relatedness (using whole genome sequencing) and virulence of food-derived isolates to those collected from humans.

RESULTS

A non-specific culturing approach for Pseudomonas recovered the bacterial genus from 28 of 32 (87.5%) retail food samples, although no P. aeruginosa was identified. The Pseudomonas species recovered were not clinically relevant, contained no ARGs and are likely associated with food spoilage. A specific culture method for P. aeruginosa resulted in the recovery of P. aeruginosa from 14 of 128 (11%) retail food samples; isolates contained between four and seven ARGs each and belonged to 16 sequence types (STs), four of which have been isolated from human infections. Food P. aeruginosa isolates from these STs demonstrated high similarity to human-derived isolates, differing by 41-312 single nucleotide polymorphisms (SNPs). There were diverse P. aeruginosa collected from the same food sample with distinct STs present on some samples and isolates belonging to the same ST differing by 19-67 SNPs. The Galleria mellonella infection model showed that 15 of 16 STs isolated from food displayed virulence between a low-virulence (PAO1) and a high virulence (PA14) control.

CONCLUSION

The most frequent Pseudomonas recovered from food examined in this study carried no ARGs and are more likely to play a role in food spoilage rather than infection. P. aeruginosa isolates likely to be able to cause human infections and with multidrug resistant genotypes are present on a relatively small but still substantial proportions of retail foods examined. Given the frequency of exposure, the potential contribution of food to the burden of P. aeruginosa infections in humans should be evaluated more closely.

General media over enrichment media supports growth of Campylobacter jejuni and maintains poultry cecal microbiota enabling translatable in vitro microbial interaction experiments

AIM

This study aimed to assess the suitability of two media types, Bolton enrichment broth (BEB) and anaerobic dilution solution (ADS), in replicating the poultry cecal environment to investigate metabolic interactions and Campylobacter presence within poultry ceca.

METHODS

Using an anaerobic in vitro poultry cecal model, cecal contents (free of culturable Campylobacter) were diluted in BEB and ADS, inoculated with 105 CFU of Campylobacter jejuni, and incubated for 48 h at 42°C under microaerophilic conditions. Samples were collected at 0, 24, and 48 h. Genomic DNA was extracted, amplified, and sequenced on Illumina MiSeq platform. Data underwent analysis within QIIME2-2021.11, including alpha and beta diversity assessments, ANOVA, ADONIS, ANCOM, and Bradford assay for protein concentration.

RESULTS

ADS supported a more diverse microbial population than BEB, influencing C. jejuni presence. ANCOM highlighted dominant genera in BEB (Lactobacillus and Campylobacter) and affirmed C. jejuni growth in ADS. Core microbiota analysis revealed unique associations with each media type, while the Bradford assay indicated ADS consistently yielded more uniform microbial growth.

CONCLUSIONS

ADS was identified as a preferred diluent for faithfully replicating cecal microbial changes in the presence of Campylobacter.

Association Between Escherichia coli Load in the Gut and Body Weight Gain in Broiler Chickens: A Systematic Review and Meta-Analysis

Escherichia coli is one of the first commensal bacteria to colonize the chicken gut, where it predominates at an early stage of broiler chick life. Escherichia coli can potentially cause colibacillosis in chickens, spreading to extraintestinal systemic organs, which results in high economic losses in poultry industry, as well as a potential risk to public health. Many studies conducted to investigate the effectiveness of natural products as alternatives to antibiotics and to enhance the production performance in broiler chickens have assessed E. coli load in the chicken gut, but it is still unknown how the E. coli count is linked to broiler growth performance. A systematic search of published research articles, including key terms of interest such as broiler chickens, growth performance, and E. coli count, was conducted using two main databases (PubMed and the Web of Science). A random effects metaregression model was built to evaluate the association between E. coli count and weight gain in untreated groups of broilers (negative controls) from eligible studies. Of 2108 articles in the initial screening, 60 were included in the final meta-analysis. After data extraction, records from the ileum and cecum at 21, 35, and 42 days of age were considered for the meta-analysis. The meta-analysis showed that the average E. coli count in both the ileum and cecum at 21 days of age was positively associated with the average weight gain in the studied broiler chickens, while no statistically significant associations were found at 35 and 42 days of age. In conclusion, the positive association between E. coli load and body weight gain in young broiler chickens may be attributed to the relative dominance of E. coli in the gut of this age group when the microbial population is less diverse. The dynamic association between the production performance and the load of E. coli that has dubious pathogenic potential suggests the importance of careful assessment of commensal E. coli to develop strategies to enhance production, particularly in young broiler chickens.

Effects of dietary Chinese herbal mixtures on productive performance, egg quality, immune status, caecal and offspring meconial microbiota of Wenchang breeder hens

This study aimed to evaluate the effects of Chinese herbal mixtures (CHMs) on productive performance, egg quality, immune status, anti-apoptosis ability, caecal microbiota, and offspring meconial microbiota in hens. A total of 168 thirty-week-old Wenchang breeder hens were randomly divided into two groups, with each group comprising six replicate pens of fourteen hens. The groups were fed a basal diet (CON group) and a basal diet with 1,000 mg/kg CHMs (CHMs group) for 10 weeks. Our results showed that dietary supplementation with CHMs increased the laying rate, average egg weight, hatch of fertile, and offspring chicks' weight while concurrently reducing the feed conversion ratio (FCR) and embryo mortality (p < 0.05). The addition of CHMs resulted in significant improvements in various egg quality parameters, including eggshell strength, albumen height, haugh unit, and the content of docosatetraenoic acid (C20:4n-6) in egg yolk (p < 0.05). The supplementation of CHMs had a greater concentration of IgA and IgG while decreasing the content of IL-6 in serum compared with the CON group (p < 0.05). Addition of CHMs to the diet increased the expression of Bcl-2 and IL-4 in liver and ovary, decreased the expression of IL-1β, Bax, and Caspase-8 in jejunum and ovary, and decreased the expression of NF-κB in liver, jejunum, and ovary (p < 0.05). Moreover, dietary CHMs reduced the abundance of Desulfovibrio in caecal microbiota as well as decreased the abundance of Staphylococcaceae_Staphylococcus and Pseudomonadaceae_Pseudomonas in the offspring meconial microbiota (p < 0.05). In conclusion, the CHMs could improve productive parameters by enhancing immune status, anti-apoptosis capacity, and modulating the caecal microbiota of Wenchang breeder hens, as well as maintaining the intestinal health of the offspring chicks.

Glycerol and reuterin-producing Limosilactobacillus reuteri enhance butyrate production and inhibit Enterobacteriaceae in broiler chicken cecal microbiota PolyFermS model

BACKGROUND

Administering probiotic strains of Limosilactobacillus reuteri to poultry has been shown to improve poultry performance and health. Some strains of L. reuteri taxa can produce reuterin, a broad-spectrum antimicrobial compound from glycerol conversion, with high inhibitory activity against enterobacteria. However, little is known about the metabolism of glycerol in the complex chicken cecal microbiota nor the effect of glycerol, either alone or combined with L. reuteri on the microbiota. In this study, we investigated the effect of L. reuteri PTA5_F13, a high-reuterin-producing chicken strain and glycerol, alone or combined, on broiler chicken cecal microbiota composition and activity using the continuous PolyFermS model recently developed to mimic chicken cecal fermentation.

METHODS

Three independent PolyFermS chicken cecal microbiota models were inoculated with immobilized cecal microbiota from different animals and operated continuously. The effects of two additional levels of glycerol (50 and 100 mM) with or without daily supplementation of chicken-derived L. reuteri PTA5_F13 (107 CFU/mL final concentration) were tested in parallel second-stage reactors continuously inoculated with the same microbiota. We analyzed the complex chicken gut microbiota structure and dynamics upon treatment using 16S rRNA metabarcoding and qPCR. Microbiota metabolites, short-chain and branched-chain fatty acids, and glycerol and reuterin products were analyzed by HPLC in effluent samples from stabilized reactors.

RESULTS

Supplementation with 100 mM glycerol alone and combined with L. reuteri PTA5_F13 resulted in a reproducible increase in butyrate production in the three modelled microbiota (increases of 18 to 25%). Glycerol alone resulted also in a reduction of Enterobacteriaceae in two of the three microbiota, but no effect was detected for L. reuteri alone. When both treatments were combined, all microbiota quantitatively inhibited Enterobacteriaceae, including in the last model that had very high initial concentrations of Enterobacteriaceae. Furthermore, a significant 1,3-PDO accumulation was measured in the effluent of the combined treatment, confirming the conversion of glycerol via the reuterin pathway. Glycerol supplementation, independent of L. reuteri addition, did not affect the microbial community diversity.

CONCLUSIONS

Glycerol induced a stable and reproducible butyrogenic activity for all tested microbiota and induced an inhibitory effect against Enterobacteriaceae that was strengthened when reuterin-producing L. reuteri was spiked daily. Our in vitro study suggests that co-application of L. reuteri PTA5_F13 and glycerol could be a useful approach to promote chicken gut health by enhancing metabolism and protection against Enterobacteriaceae.

Effects of dustbathing environment on gut microbiota and expression of intestinal barrier and immune-related genes of adult laying hens housed individually in modified traditional cage

Litters, the composition of sand and peat rich in microbiota, are essential to trigger the dustbathing behavior of chickens. To investigate the effects of a dustbathing environment (DE) on the intestinal health, gut microbiota, and immune responses of laying hens, a total of 72 healthy Hy-Line Brown laying hens at 69 wk of age (WOA) were housed individually in modified traditional cages and randomly divided into 2 groups: one group had free access to litters (CT), while the other one was restricted from litters (CC). The experiment lasted for 42 d. At the end of the experiment, the intestinal histomorphology and immune status of laying hens were determined, and the 16S rRNA sequencing method was used to assess the composition of the intestinal microbial community of birds. Intestinal histomorphology changed, including villus height and villus-to-crypt ratio significantly increased in the CT group (P < 0.01). DE reshaped the microbial community and increased the microbial richness with the higher indicators of Chao1 and observed species and the comparatively abundant beta diversity (P < 0.05). Ten genera, including Faecalibacterium and Coprococcus, declined in laying hens from the CT group (P < 0.05), while Alistipes increased in CT hens (P < 0.05) compared to those hens from the CC group. The expression levels of intestinal barrier-related genes of claudin-1, claudin-4, occludin, ZO-1, and ZO-2 and immune-related genes of IL-4, IL-6, IL-8, IFN-γ, IgA, TLR-2, and TLR-4 were significantly upregulated in the intestine of laying hens in CT group (P < 0.05). DE also increased the serum levels of IL-4, IL-6, IL-8, IFN-γ, and IgA (P < 0.01). The alteration of the gut microbiota by DE is closely related to host immune responses, including Lactobacillus positively correlated with IL-4 and IgA. Thus, a dustbathing environment can improve the welfare of laying hens by changing the intestinal histomorphology, immune response, and the gut microbial community.

Controlling Salmonella: strategies for feed, the farm, and the processing plant

Controlling Salmonella in poultry is an ongoing food safety measure and while significant progress has been made, there is a need to continue to evaluate different strategies that include understanding Salmonella-poultry interaction, Salmonella-microbiota interactions, Salmonella genetics and response to adverse conditions, and preharvest and postharvest parameters that enable persistence. The purpose of this symposium is to discuss different strategies to consider from feed milling to the farm to the processing environment. This Poultry Science Association symposium paper is divided into 5 different sections that covers 1) immunological aspects of Salmonella control, 2) application of Salmonella genetics for targeted control strategies in poultry production, 3) improving poultry feed hygienics: utilizing feed manufacture techniques and equipment to improve feed hygienics, 4) practical on farm interventions for controlling Salmonella-what works and what may not work, and 5) monitoring and mitigating Salmonella in poultry. These topics elucidate the critical need to establish control strategies that will improve poultry gut health and limit conditions that exposes Salmonella to stress causing alterations to virulence and pathogenicity both at preharvest and postharvest poultry production. This information is relevant to the poultry industry's continued efforts to ensure food safety poultry production.

Relationship of the Poultry Microbiome to Pathogen Colonization, Farm Management, Poultry Production, and Foodborne Illness Risk Assessment

Despite the continuous progress in food science and technology, the global burden of foodborne illnesses remains substantial, with pathogens in food causing millions of infections each year. Traditional microbiological culture methods are inadequate in detecting the full spectrum of these microorganisms, highlighting the need for more comprehensive detection strategies. This review paper aims to elucidate the relationship between foodborne pathogen colonization and the composition of the poultry microbiome, and how this knowledge can be used for improved food safety. Our review highlights that the relationship between pathogen colonization varies across different sections of the poultry microbiome. Further, our review suggests that the microbiome profile of poultry litter, farm soil, and farm dust may serve as potential indicators of the farm environment's food safety issues. We also agree that the microbiome of processed chicken samples may reveal potential pathogen contamination and food quality issues. In addition, utilizing predictive modeling techniques on the collected microbiome data, we suggest establishing correlations between particular taxonomic groups and the colonization of pathogens, thus providing insights into food safety, and offering a comprehensive overview of the microbial community. In conclusion, this review underscores the potential of microbiome analysis as a powerful tool in food safety, pathogen detection, and risk assessment.

Evaluation of the Immunoprotective Capacity of Five Vaccine Candidate Proteins against Avian Necrotic Enteritis and Impact on the Caecal Microbiota of Vaccinated Birds

Avian necrotic enteritis is an enteric disease of broiler chickens caused by certain pathogenic strains of Clostridium perfringens in combination with predisposing factors. A vaccine offering complete protection against the disease has not yet been commercialized. In a previous study, we produced five recombinant proteins predicted to be surface-exposed and unique to necrotic enteritis-causing C. perfringens and the immunogenicity of these potential vaccine candidates was assessed in broiler chickens. In the current work, the relative contribution of the antibodies raised by these putative antigens to protect broiler chickens was evaluated using an experimental necrotic enteritis induction model. Additionally, the link between the immune response elicited and the gut microbiota profiles in immunized birds subjected to infection with virulent C. perfringens was studied. The ELISA results showed that the IgY antibody titers in vaccinated birds on days 21 and 33 were significantly higher than those on days 7 and 14 and those in birds receiving the adjuvant alone, while the relative contribution of the specific immunity attributed to these antibodies could not be precisely determined using this experimental necrotic enteritis induction model. In addition, 16S rRNA gene amplicon sequencing showed that immunization of birds with recombinant proteins had a low impact on the chicken caecal microbiota.

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.

The Expression of Amino Acid and Fatty Acid Receptors Show an Age-Dependent Pattern Involving Oral Cavity, Jejunum and Lower Gut Sensing in Broiler Chickens

This work aimed to evaluate the gene expression of amino acids (AA) and fatty acids (FA) sensors in the gastrointestinal tract (GIT) of chickens at two different ages (7 and 26 days post-hatch). Sixteen broilers (Ross 308) were selected, and ten sections of the GIT, including upper (tongue base, upper palate, crop, proventriculus), middle (gizzard, duodenum, jejunum, ileum), and lower GIT section (cecum, colon) were collected for analysis. Relative gene expression of AA (T1R1, T1R3, mGluR1, mGluR4, CaSR, GPR139, GPRC6A, GPR92) and FA (FFAR2, FFAR3, FFAR4) sensors were assessed using qPCR. The statistical model included age, GIT section, and gene. In addition, the correlations between gene expressions were calculated. At day 7, a significantly (p = 0.004) higher expression of AA sensors in the oral cavity and FA sensors in the lower GIT section (i.e., cecum and colon) compared to the middle section was recorded. A higher expression of AA compared to FA sensors was detected at the upper GIT section in 7 (p < 0.001) and 26-day-old chickens (p = 0.026). Thus, at day 7, AA sensors were predominantly (p < 0.05) expressed in the upper GIT section (mainly oral cavity), while FA sensors were mainly expressed in the lower GIT section, at cecum (FFR2 and 4) or colon (FFAR3). These results may indicate that in early life, both ends of the GIT are fundamental for feed intake (oral cavity) and development of the microbiota (cecum and colon). In contrast, at 26 days of age, the results showed the emergence of both AA and FA sensors in the jejunum, presumably indicating the essential role of the jejunum in the digestion absorption of nutrients and the signaling to the brain (gut-brain axis) through the enteroendocrine system. Significant positive correlations were observed between T1R1 and T1R3 (r = 0.85, p < 0.001), CaSR and T1R1 (r = 0.78, p < 0.001), CaSR and T1R3 (r = 0.45, p < 0.050), and mGluR1 and FFAR3 (r = 0.46, p < 0.050). It is concluded that the gene expression is greater in the oral cavity for AA sensors and the lower gut for FA sensors. On day 26, the role of jejunum regarding nutrient sensing is highlighted.

Fecal Microbiota Transplantation Reduces Campylobacter jejuni Colonization in Young Broiler Chickens Challenged by Oral Gavage but Not by Seeder Birds

Campylobacter spp., particularly C. jejuni and C. coli, are major food safety concerns, transmitted to humans mainly via contaminated poultry meat. In a previous study, we found that some commercial broiler farms consistently produced Campylobacter-free flocks while others consistently reared Campylobacter-colonized flocks, and significant differences in the gut microbiota compositions between the two types of farm categories were revealed. Therefore, we hypothesized that gut microbiota influences Campylobacter colonization in poultry and that the microbiota from Campylobacter-free flocks may confer colonization resistance to Campylobacter in the chicken intestine. In this study, two fecal microbiota transplantation (FMT) trials were performed to test the hypothesis. Newly hatched chicks were given FMT via oral gavage of the cecal content of Campylobacter-free adult chickens (treatment groups) or PBS (control groups) before the feed consumption. Approximately two weeks after the FMT, the birds were challenged with C. jejuni either by oral gavage (trial 1) or by co-mingling with Campylobacter-colonized seeder birds (trial 2) to evaluate the potential protective effect of the FMT. Cecal contents were collected (3 times, 5 days apart) to determine the Campylobacter colonization levels via culture and microbiota compositions via 16S rRNA gene sequencing. FMT reduced cecal Campylobacter colonization significantly (log10 1.2-2.54 CFU/g) in trial 1 but not in trial 2, although FMT significantly impacted the diversity and compositions of the gut microbiota in both trials. Several genera, such as Butyricimonas, Parabacteroides, Parasutterella, Bilophila, Fournierella, Phascolarctobacterium, and Helicobacter, had increased abundance in the FMT-treated groups in both trials. Furthermore, Campylobacter abundance was found to be negatively correlated with the Escherichia and Ruminococcus_torques_group genera. These findings indicate that even though FMT with adult cecal microbiota can positively affect the subsequent development of the gut microbiota in young broilers, its inhibitory effect on Campylobacter colonization varies and appears to be influenced by the challenge models.

The digestive tract histology and geographical distribution of gastrointestinal microbiota in yellow-feather broilers

Exhaustive understanding of intestinal physiological characteristics is the critical precondition for the improvement of intestinal health and growth performance of yellow-feather broilers (YFB). As a vital part of gastrointestinal tract, the symbiotic, complex, and variable microbiota have a profound effect on the nutrition, immunity, health, and production of broilers. Hence, the development status of proventriculus, jejunum, and cecum, and spatial heterogeneity of bacterial community in crop, proventriculus, gizzard, jejunum, cecum, and rectum of adult YFB were detected in our study. The results revealed that proventriculus, jejunum, and cecum of broilers are well-developed based on morphological observation. The Chao and Shannon indexes in cecum and rectum are notably higher than other sections and their microbiota structure is also distinct from foregut. Firmicutes and Lactobacillus are the predominant phylum and genus in all gastrointestinal sections, respectively. As feature species of crop, Lactobacillus spp. mainly settle in foregut, whereas some Clostridia species (unclassified Lachnospiraceae, Faecalibacterium, Romboutsia and so on) are characteristic and more abundant in cecum and rectum. Interestingly, there are 2 Ruminococcus torques strains positively and negatively correlated with cecum development, respectively. In a whole, our findings reveal the specialized digestive physiology and regional distribution of intestinal microbiota in YFB, which provides a reference for the future study on the improvement of growth performance and intestinal development through microbiota manipulation in yellow-feather broilers.