Microbial compositional changes in broiler chicken cecal contents from birds challenged with different Salmonella vaccine candidate strains

Vaccine protection of broilers against various doses of wild-type Salmonella Typhimurium and changes in gut microbiota

This study evaluated the impact of vaccine diluents (peptone or water) on the protective effects of Salmonella Typhimurium (S. Typhimurium) vaccine. Vaccinated broilers were challenged with different doses of wild-type S. Typhimurium through dust. At the time of cull, vaccine load was highest in caeca and lowest in spleen. Wild-type S. Typhimurium was detectable after 24 hrs only in the vaccinated birds challenged with 108 CFU and positive control. S. Typhimurium load was lower in the organs of the groups challenged with 104 and 106 compared to the 108 CFU group. The caecal microbiota alpha diversity of the vaccinated or vaccinated and challenged chickens differed from the positive and negative control groups. Beta diversity of the positive control clustered separately from all other treatment groups, showing that vaccine caused minimal changes in gut microbiota structure. The vaccinated and/or wild-type challenged chickens showed significantly higher abundance of Anaerostignum, Lachnoclostridium, Intestinimonas, Colidextribacter, Monoglobus, Acetanaerobacterium and Subdoligranulum. Outcomes from this study demonstrate that the vaccine effectively protected broiler chickens from S. Typhimurium infection and helped maintain a more stable gut microbiota structure, reducing the impact of S. Typhimurium on gut health. Vaccine diluent did not affect gut microbiota composition.

Deaminase inhibitor and casein hydrolysates drive microbial shifts favoring Campylobacter jejuni in an in vitro poultry cecal model

AIM

The dietary proteins in poultry feeds, including the polypeptide chain size, influence gut microbial composition and function. This study assessed the microbial preference for peptide size using the same protein source in three polypeptide forms.

METHODS AND RESULTS

We investigated the effects of diphenyliodonium chloride (DIC) on poultry cecal microbiota inoculated with Campylobacter jejuni and supplemented with various casein hydrolysates (intact casein, enzyme hydrolysate, acid hydrolysate, and a mix of all three) using an in vitro cecal model. The incubation occurred over 18 h at 42°C under microaerophilic conditions. We hypothesized a decrease in C. jejuni abundance by limiting nitrogenous metabolites while promoting the growth of protein fermentative bacteria. Additionally, we speculated that the response to DIC would vary with different polypeptides. Genomic DNA was extracted, amplified, and sequenced on an Illumina MiSeq platform. Analysis within QIIME2-2021.11 showed that DIC treatments did not significantly affect C. jejuni abundance but drastically decreased Enterobacteriaceae abundance (ANCOM, P < 0.05). DIC-treated groups exhibited a more stable community structure, especially in the peptide-amended group. Microbial interactions likely aided C. jejuni survival in DIC groups with casein hydrolysates. Methanocorpusculum, Phascolarctobacterium, and Campylobacter formed a core microbial community in both DIC-treated and non-treated groups. DIC altered co-occurrence patterns among core members and differentiated taxa in abundance in acid and peptide-DIC treated groups, changing negative relationships to positive ones (Spearman's Correlation, P < 0.05). Variations in polypeptide composition affected metabolite abundance, notably impacting the urea cycle in Campylobacter and Clostridiaceae. DIC shifted communal energy metabolism in microbiota on casein sources.

CONCLUSION

Campylobacter's adaptability to the deaminase inhibitor indicates reliance on the microbial community and their metabolic products, showcasing its metabolic versatility.

Co-exposure to polyethylene fiber and Salmonella enterica serovar Typhimurium alters microbiome and metabolome of in vitro chicken cecal mesocosms

Humans and animals encounter a summation of exposures during their lifetime (the exposome). In recent years, the scope of the exposome has begun to include microplastics. Microplastics (MPs) have increasingly been found in locations, including in animal gastrointestinal tracts, where there could be an interaction with Salmonella enterica serovar Typhimurium, one of the commonly isolated serovars from processed chicken. However, there is limited knowledge on how gut microbiomes are affected by microplastics and if an effect would be exacerbated by the presence of a pathogen. In this study, we aimed to determine if acute exposure to microplastics in vitro altered the gut microbiome membership and activity. The microbiota response to a 24 h co-exposure to Salmonella enterica serovar Typhimurium and/or low-density polyethylene (PE) microplastics in an in vitro broiler cecal model was determined using 16S rRNA amplicon sequencing (Illumina) and untargeted metabolomics. Community sequencing results indicated that PE fiber with and without S. Typhimurium yielded a lower Firmicutes/Bacteroides ratio compared with other treatment groups, which is associated with poor gut health, and overall had greater changes to the cecal microbial community composition. However, changes in the total metabolome were primarily driven by the presence of S. Typhimurium. Additionally, the co-exposure to PE fiber and S. Typhimurium caused greater cecal microbial community and metabolome changes than either exposure alone. Our results indicate that polymer shape is an important factor in effects resulting from exposure. It also demonstrates that microplastic-pathogen interactions cause metabolic alterations to the chicken cecal microbiome in an in vitro chicken cecal mesocosm.

IMPORTANCE

Researching the exposome, a summation of exposure to one's lifespan, will aid in determining the environmental factors that contribute to disease states. There is an emerging concern that microplastic-pathogen interactions in the gastrointestinal tract of broiler chickens may lead to an increase in Salmonella infection across flocks and eventually increased incidence of human salmonellosis cases. In this research article, we elucidated the effects of acute co-exposure to polyethylene microplastics and Salmonella enterica serovar Typhimurium on the ceca microbial community in vitro. Salmonella presence caused strong shifts in the cecal metabolome but not the microbiome. The inverse was true for polyethylene fiber. Polyethylene powder had almost no effect. The co-exposure had worse effects than either alone. This demonstrates that exposure effects to the gut microbial community are contaminant-specific. When combined, the interactions between exposures exacerbate changes to the gut environment, necessitating future experiments studying low-dose chronic exposure effects with in vivo model systems.

Salmonella in eggs and egg-laying chickens: pathways to effective control

Eggs contaminated with Salmonella have been internationally significant sources of human illness for several decades. Most egg-associated illness has been attributed to Salmonella serovar Enteritidis, but a few other serovars (notably S. Heidelberg and S. Typhimurium) are also sometimes implicated. The edible interior contents of eggs typically become contaminated with S. Enteritidis because the pathogen's unique virulence attributes enable it to colonize reproductive tissues in systemically infected laying hens. Other serovars are more commonly associated with surface contamination of eggshells. Both research and field experience have demonstrated that the most effective overall Salmonella control strategy in commercial laying flocks is the application of multiple interventions throughout the egg production cycle. At the preharvest (egg production) level, intervention options of demonstrated efficacy include vaccination and gastrointestinal colonization control via treatments such as prebiotics, probiotics, and bacteriophages, Effective environmental management of housing systems used for commercial laying flocks is also essential for minimizing opportunities for the introduction, transmission, and persistence of Salmonella in laying flocks. At the postharvest (egg processing and handling) level, careful regulation of egg storage temperatures is critical for limiting Salmonella multiplication inside the interior contents.

Co-exposure to Polyethylene Fiber and Salmonella enterica Typhimurium Alters Microbiome and Metabolome of in vitro Chicken Cecal Mesocosms

Humans and animals encounter a summation of exposures during their lifetime (the exposome). In recent years, the scope of the exposome has begun to include microplastics. Microplastics (MPs) have increasingly been found in locations where there could be an interaction with Salmonella enterica Typhimurium, one of the commonly isolated serovars from processed chicken. In this study, the microbiota response to a 24-hour co-exposure to Salmonella enterica Typhimurium and/or low-density polyethylene (PE) microplastics in an in vitro broiler cecal model was determined using 16S rRNA amplicon sequencing (Illumina) and untargeted metabolomics. Community sequencing results indicated that PE fiber with and without S. Typhimurium yielded a lower Firmicutes/Bacteroides ratio compared to other treatment groups, which is associated with poor gut health, and overall had greater changes to the cecal microbial community composition. However, changes in the total metabolome were primarily driven by the presence of S. Typhimurium. Additionally, the co-exposure to PE Fiber and S. Typhimurium caused greater cecal microbial community and metabolome changes than either exposure alone. Our results indicate that polymer shape is an important factor in effects resulting from exposure. It also demonstrates that microplastic-pathogen interactions cause metabolic alterations to the chicken cecal microbiome in an in vitro chicken cecal model.

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

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

Attenuated Streptococcus agalactiae WC1535 ∆Sia perturbs the gut microbiota of Oreochromis niloticus, massively colonizes the intestine, and induces intestinal mucosal immunity after intraperitoneal inoculation

We previously developed and assessed the effectiveness of the attenuated Streptococcus agalactiae (Group B Streptococcus, GBS) strain WC1535 ∆Sia (with neuA-D gene cluster deletion) vaccine in tilapia (Oreochromis niloticus). In this study, we characterized the bacterial communities of the tilapia intestines by 16S rRNA high-throughput sequencing and assessed the serum antibody response, expression of immune-related genes, and histological changes following formalin-killed GBS vaccine (FKV) and the live attenuated vaccine ∆Sia (LAV). Results showed that FKV and LAV induced robust systemic and intestinal mucosal immune responses in tilapia without causing obvious pathological changes in the hindgut, spleen, and head kidney but exerted different effects on intestinal bacterial communities. The richness or diversity of the intestinal bacterial community of FKV tilapia showed no significant changes compared with that of the control fish (p &gt; 0.05) at either day 21 post-initial vaccination (21 dpiv) or day 35 (day 14 after the second immunization) (35 dpiv). The community composition of FKV tilapia and controls was significantly similar, although the relative abundance of some genera was significantly altered. Relative to control fish, the gut ecosystem of LAV tilapia was significantly disturbed with a substantial increase in community diversity at 21 dpiv (p &lt; 0.05) and a significant decrease at 35 dpiv in fish with high serum antibody response (ΔSia35H) (p &lt; 0.05). However, there was no significant difference between ΔSia35H and ΔSia35L (low serum antibody response) fish (p &gt; 0.05). Moreover, the community composition of LAV tilapia at 21 dpiv or 35 dpiv was considerably different from that of the controls. Particularly, GBS ∆Sia was found to be abundant in the intestine at 21 and 35 dpiv. This result suggested that the parenteral administration of the LAV (∆Sia) may also have the effect of oral vaccination in addition to the immune effect of injection vaccination. In addition, a significant correlation was found between the expression of immune-related genes and certain bacterial species in the intestinal mucosal flora. Our findings will contribute to a better understanding of the effects of inactivated and attenuated vaccines on gut microbiota and their relationship with the immune response.

Ileal and cecal microbiota response to Salmonella Typhimurium challenge in conventional and slow-growing broilers

Despite the negative impacts of Salmonella intestinal colonization on human health, Salmonella is a natural colonizer of the gastrointestinal tract and is not overtly pathogenic to the avian host. It is of interest to understand the impacts and colonization rates of Salmonella across selected genetic lines such as slow-growing (SG) and conventional (CONV) broilers. The objective of this study was to characterize the relationship between Salmonella enterica serovar Typhimurium challenge and selected broiler genetic lines on the ileal and cecal microbiome. Male chicks of two broiler breeds (n = 156/breed) were cohoused in an open floor pen until day 7. On day 13, the chicks were then separated into 12 isolators per breed (4 rooms, 6 isolators/room, 11 chicks/isolator). On day 14, chicks in the 12 treatment isolators (6 isolators/breed, 108 total) were challenged with Salmonella Typhimurium (ST) (1 × 108 CFU/ml) via oral gavage while the remaining chicks (n = 108) were given an oral gavage of sterile tryptic soy broth control (C). Ileal and cecal contents were collected on day 7 from 24 chicks of each breed, and on days 13, 17, 21, and 24 from two chicks per isolator. Samples underwent DNA extraction and PCR amplification to obtain 16S rRNA amplicons that were sequenced with Illumina MiSeq. Salmonella Typhimurium colonization in the cecum was not different in the two broiler breeds. The main effect of breed had the greatest impact on the ileum microbiota of broilers 7 days of age where SG broilers had significantly lower diversity and richness compared to CONV broilers (p < 0.05). Salmonella Typhimurium challenge consistently caused a change in beta diversity. Regardless of day or intestinal location, challenged broilers had many amplicon sequence variants (ASVs) with decreased abundance of likely beneficial bacteria such as Mollicutes RF39, Shuttleworthia, Flavonifractor, and Oscillibacter compared to broilers that were unchallenged with Salmonella Typhimurium (p < 0.05). Additionally, there was a difference in the timing of when the microbiota alpha and beta diversity of each breed responded to Salmonella Typhimurium challenge. Thus, both broiler breed and Salmonella Typhimurium can impact the intestinal microbiota.

Microbiome Applications for Laying Hen Performance and Egg Production

Management of laying hens has undergone considerable changes in the commercial egg industry. Shifting commercial production from cage-based systems to cage-free has impacted the housing environment and created issues not previously encountered. Sources of microorganisms that become established in the early stages of layer chick development may originate from the hen and depend on the microbial ecology of the reproductive tract. Development of the layer hen GIT microbiota appears to occur in stages as the bird matures. Several factors can impact the development of the layer hen GIT, including pathogens, environment, and feed additives such as antibiotics. In this review, the current status of the laying hen GIT microbial consortia and factors that impact the development and function of these respective microbial populations will be discussed, as well as future research directions.

Role of the gut microbiota in airway immunity and host defense against respiratory infections

Colonization of the intestine with commensal bacteria is known to play a major role in the maintenance of human health. An altered gut microbiome is associated with various ensuing diseases including respiratory diseases. Here, we summarize current knowledge on the impact of the gut microbiota on airway immunity with a focus on consequences for the host defense against respiratory infections. Specific gut commensal microbiota compositions and functions are depicted that mediate protection against respiratory infections with bacterial and viral pathogens. Lastly, we highlight factors that have imprinting effects on the establishment of the gut microbiota early in life and are potentially relevant in the context of respiratory infections. Deepening our understanding of these relationships will allow to exploit the knowledge on how gut microbiome maturation needs to be modulated to ensure lifelong enhanced resistance towards respiratory infections.

Buffered formic acid and a monoglyceride blend coordinately alleviate subclinical necrotic enteritis impact in broiler chickens

The objective of this study was to evaluate the effect of 2 different doses of a partially buffered formic acid product (Amasil NA; 61% formic acid, 20.5% sodium formate), and a monoglyceride blend of short- and medium-chain fatty acids (BalanGut LS P) on necrotic enteritis (NE) infected broilers in terms of performance, intestinal microbial population and short-chain fatty acids concentrations in the gastrointestinal tract. A total of 528-day-old as hatched Ross 308 broilers were allocated to 48 pens with 11 birds in each pen. Six dietary treatments applied in the study were: T1) nonsupplemented diet (Control); T2) antibiotic supplemented diets; T3) and T4) high (Starter: 0.5%; Grower and Finisher: 0.5%) and low (Starter: 0.3%; Grower and Finisher: 0.2%) dose of Amasil NA; and groups T5) and T6) high (Starter: 0.3%; Grower and Finisher: 0.2%) and low dose (Starter: 0.3%; Grower: 0.15%; Finisher: 0.075%) of (BalanGut LS P). All birds in this study were fed starter (d 0-10), grower (d 11-24) and finisher (d 25-35) diets and challenged with NE. To induce subclinical NE, oral administrations of Eimeria oocysts (d 9) followed by inoculation of Clostridium perfringens strains (d 14 and 15) were applied. Results showed that birds fed the high dose of Amasil NA, had a higher feed conversion ratio (FCR,P < 0.05) compared to the nonsupplemented group during the starter period. Antibiotic supplementation reduced FCR during the grower (P < 0.001), finisher (P < 0.05) and overall (P < 0.001) periods of the experiment. Both levels of BalanGut LS P and low levels of Amasil NA enhanced overall FCR (P < 0.05) compared to the birds in the nonsupplemented group. Compared to the nonsupplemented group, high levels of Amasil NA and low levels of BalanGut LS P improved FCR in the finisher stage (P < 0.05). On d 16, cecum digesta of birds fed with antibiotic supplemented diets showed a significantly lower number of C. perfringens (P < 0.001) compared to the nonsupplemented and high level of BalanGut LS P group. Bacillus (P < 0.01) and Ruminococcus numbers were significantly lower in the birds fed with high level of Amasil NA (P < 0.05) compared to the antibiotic supplemented diets. High doses of Amasil NA, showed the highest propionate concentration in the cecum (P < 0.001). The study suggests that supplementation of BalanGut LS P and Amasil NA at different feeding phases may achieve optimal performance improvement in broilers under NE challenge.

Challenges in Vaccinating Layer Hens against Salmonella Typhimurium

Salmonella Typhimurium is among the most common causes of bacterial foodborne gastrointestinal disease in humans. Food items containing raw or undercooked eggs are frequently identified during traceback investigation as the source of the bacteria. Layer hens can become persistently infected with Salmonella Typhimurium and intermittently shed the bacteria over the course of their productive lifetime. Eggs laid in a contaminated environment are at risk of potential exposure to bacteria. Thus, mitigating the bacterial load on farms aids in the protection of the food supply chain. Layer hen producers use a multifaceted approach for reducing Salmonella on farms, including the all-in-all-out management strategy, strict biosecurity, sanitization, and vaccination. The use of live attenuated Salmonella vaccines is favored because they elicit a broader host immune response than killed or inactivated vaccines that have been demonstrated to provide cross-protection against multiple serovars. Depending on the vaccine, two to three doses of Salmonella Typhimurium vaccines are generally administered to layer hens within the first few weeks. The productive life of a layer hen, however, can exceed 70 weeks and it is unclear whether current vaccination regimens are effective for that extended period. The objective of this review is to highlight layer hen specific challenges that may affect vaccine efficacy.

Respiratory and Gut Microbiota in Commercial Turkey Flocks with Disparate Weight Gain Trajectories Display Differential Compositional Dynamics

Communities of gut bacteria (microbiota) are known to play roles in resistance to pathogen infection and optimal weight gain in turkey flocks. However, knowledge of turkey respiratory microbiota and its link to gut microbiota is lacking. This study presents a 16S rRNA gene-based census of the turkey respiratory microbiota (nasal cavity and trachea) alongside gut microbiota (cecum and ileum) in two identical commercial Hybrid Converter turkey flocks raised in parallel under typical field commercial conditions. The flocks were housed in adjacent barns during the brood stage and in geographically separated farms during the grow-out stage. Several bacterial taxa, primarily Staphylococcus, that were acquired in the respiratory tract at the beginning of the brood stage persisted throughout the flock cycle. Late-emerging predominant taxa in the respiratory tract included Deinococcus and Corynebacterium Tracheal and nasal microbiota of turkeys were identifiably distinct from one another and from gut microbiota. Nevertheless, gut and respiratory microbiota changed in parallel over time and appeared to share many taxa. During the brood stage, the two flocks generally acquired similar gut and respiratory microbiota, and their average body weights were comparable. However, there were qualitative and quantitative differences in microbial profiles and body weight gain trajectories after the flocks were transferred to geographically separated grow-out farms. Lower weight gain corresponded to the emergence of Deinococcus and Ornithobacterium in the respiratory tract and Fusobacterium and Parasutterella in gut. This study provides an overview of turkey microbiota under field conditions and suggests several hypotheses concerning the respiratory microbiome.IMPORTANCE Turkey meat is an important source of animal protein, and the industry around its production contributes significantly to the agricultural economy. The microorganisms present in the gut of turkeys are known to impact bird health and flock performance. However, the respiratory microbiota in turkeys is entirely unexplored. This study has elucidated the microbiota of respiratory tracts of turkeys from two commercial flocks raised in parallel throughout a normal flock cycle. Further, the study suggests that bacteria originating in the gut or in poultry house environments influence respiratory communities; consequently, they induce poor performance, either directly or indirectly. Future attempts to develop microbiome-based interventions for turkey health should delimit the contributions of respiratory microbiota and aim to limit disturbances to those communities.

Two different Clostridium perfringens strains produce different levels of necrotic enteritis in broiler chickens

Subclinical necrotic enteritis (NE) is primarily caused by the gram-positive bacterium, Clostridium perfringens (Cp). The trend towards removal of in-feed antimicrobials and subsequent increased emergence of infection in poultry has resulted in a wide interest in better understanding of the mechanism behind this disease. The virulence of NE, to a large extent, depends on the virulence of Cp strains. Thus, this study was to assess how 2 different strains of Cp affect performance and gut characteristics of broiler chickens. Ross 308 male broilers (n = 468) were assigned to a 2 × 3 factorial arrangement of treatments with antibiotics (Salinomycin at 72 ppm and zinc bacitracin at 50 ppm -, or +) and challenge (non-challenge, Cp EHE-NE18, or Cp WER-NE36). Oral administration of Eimeria oocysts (day 9) followed by inoculation with 1 mL 108 CFU Cp strains (day 14 and 15) were used to induce NE. Broiler performance was analyzed at day 10, 24, and 35. On day 16, intestinal lesion score and intestinal pH were evaluated and samples of cecal content were analyzed for bacterial counts and short-chain fatty acid concentrations (SCFA). Birds in both challenged groups showed higher feed conversion ratio (FCR), lower weight gain (P < 0.001), increased lesion scores in the jejunum (P < 0.01), and reduced pH in the ileum and cecum (P < 0.01), compared to the non-challenged birds. They also showed decreased numbers of Bacillus spp. (P < 0.001), and Ruminococcus spp. (P < 0.01) in the cecal content. On day 35, the NE36 challenged birds had a lower weight gain (P < 0.001) and higher FCR (P < 0.001) compared to the NE18 challenged birds. Interestingly, cecal Lactobacillus and lactate were increased by the NE challenge (P < 0.001), and to a greater extent in birds challenged with NE36 compared to the NE18 strain (P < 0.001). This study suggests that Cp strains varying in virulence produce different levels of disease in broiler chickens through modulating the gut environment, intestinal microbiota, and SCFA profile to different extents.

Translating 'big data': better understanding of host-pathogen interactions to control bacterial foodborne pathogens in poultry

Recent technological advances has led to the generation, storage, and sharing of colossal sets of information ('big data'), and the expansion of 'omics' in science. To date, genomics/metagenomics, transcriptomics, proteomics, and metabolomics are arguably the most ground breaking approaches in food and public safety. Here we review some of the recent studies of foodborne pathogens (Campylobacter spp., Salmonella spp., and Escherichia coli) in poultry using big data. Genomic/metagenomic approaches have reveal the importance of the gut microbiota in health and disease. They have also been used to identify, monitor, and understand the epidemiology of antibiotic-resistance mechanisms and provide concrete evidence about the role of poultry in human infections. Transcriptomics studies have increased our understanding of the pathophysiology and immunopathology of foodborne pathogens in poultry and have led to the identification of host-resistance mechanisms. Proteomic/metabolomic approaches have aided in identifying biomarkers and the rapid detection of low levels of foodborne pathogens. Overall, 'omics' approaches complement each other and may provide, at least in part, a solution to our current food-safety issues by facilitating the development of new rapid diagnostics, therapeutic drugs, and vaccines to control foodborne pathogens in poultry. However, at this time most 'omics' approaches still remain underutilized due to their high cost and the high level of technical skills required.

Farm Stage, Bird Age, and Body Site Dominantly Affect the Quantity, Taxonomic Composition, and Dynamics of Respiratory and Gut Microbiota of Commercial Layer Chickens

The digestive and respiratory tracts of chickens are colonized by bacteria that are believed to play important roles in the overall health and performance of the birds. Most of the current research on the commensal bacteria (microbiota) of chickens has focused on broilers and gut microbiota, and less attention has been given to layers and respiratory microbiota. This research bias has left significant gaps in our knowledge of the layer microbiome. This study was conducted to define the core microbiota colonizing the upper respiratory tract (URT) and lower intestinal tract (LIT) in commercial layers under field conditions. One hundred eighty-one chickens were sampled from a flock of >80,000 birds at nine times to collect samples for 16S rRNA gene-based bacterial metabarcoding. Generally, the body site and age/farm stage had very dominant effects on the quantity, taxonomic composition, and dynamics of core bacteria. Remarkably, ileal and URT microbiota were compositionally more related to each other than to that from the cecum. Unique taxa dominated in each body site yet some taxa overlapped between URT and LIT sites, demonstrating a common core. The overlapping bacteria also contained various levels of several genera with well-recognized avian pathogens. Our findings suggest that significant interaction exists between gut and respiratory microbiota, including potential pathogens, in all stages of the farm sequence. The baseline data generated in this study can be useful for the development of effective microbiome-based interventions to enhance production performance and to prevent and control disease in commercial chicken layers.IMPORTANCE The poultry industry is faced with numerous challenges associated with infectious diseases and suboptimal performance of flocks. As microbiome research continues to grow, it is becoming clear that poultry health and production performance are partly influenced by nonpathogenic symbionts that occupy different habitats within the bird. This study has defined the baseline composition and overlaps between respiratory and gut bacteria in healthy, optimally performing chicken layers across all stages of the commercial farm sequence. Consequently, the study has set the groundwork for the development of interventions that seek to enhance production performance and to prevent and control infectious diseases through the modulation of gut and respiratory bacteria.

In-feed resin acids reduce matrix metalloproteinase activity in the ileal mucosa of healthy broilers without inducing major effects on the gut microbiota

The chicken gut is constantly exposed to harmful molecules and microorganisms which endanger the integrity of the intestinal wall. Strengthening intestinal mucosal integrity is a key target for feed additives that aim to promote intestinal health in broilers. Recently, dietary inclusion of resin-based products has been shown to increase broiler performance. However, the mode of action is still largely unexplored. Coniferous resin acids are known for their anti-microbial, anti-inflammatory and wound-healing properties, all properties that might support broiler intestinal health. In the current study, the effect of pure resin acids on broiler intestinal health was explored. Ross 308 broilers were fed a diet supplemented with coniferous resin acids for 22 days, after which the effect on both the intestinal microbiota as well as on the intestinal tissue morphology and activity of host collagenases was assessed. Dietary inclusion of resin acids did not alter the morphology of the healthy intestine and only minor effects on the intestinal microbiota were observed. However, resin acids-supplementation reduced both duodenal inflammatory T cell infiltration and small intestinal matrix metalloproteinase (MMP) activity towards collagen type I and type IV. Reduced breakdown of collagen type I and IV might indicate a protective effect of resin acids on intestinal barrier integrity by preservation of the basal membrane and the extracellular matrix. Further studies are needed to explore the protective effects of resin acids on broiler intestinal health under sub-optimal conditions and to elaborate our knowledge on the mechanisms behind the observed effects.

Effects of Attenuated S. agalactiae Strain YM001 on Intestinal Microbiota of Tilapia Are Recoverable

Previously, we constructed and characterized the vaccine efficacy of attenuated S. agalactiae strain YM001 in tilapia. In this study, the potential impacts of YM001 on the tilapia intestinal microbiota were assessed by qPCR and 16S rRNA sequencing methods. The results showed that YM001 distributed unevenly in different parts of intestine, peaked in the intestine at 12 h after oral administration, and then declined gradually. YM001 caused 0% mortality of fish during the entire experimental period, while the referent strain HN016 caused 100% mortality at 3 d after oral administration. However, the intestinal microbiota could be changed by YM001, the diversity of intestinal microbiota decreased first and gradually recovered after oral administration. The diversity of intestinal microbiota of tilapia was negatively correlated with the content of HN016 in the intestinal tract. The oral YM001 mainly changed the abundance of Streptococcus, Cetobacterium, Akkermansia, Romboutsia, Bacteroides, Brevinema, Lachnospiraceae_NK4A136-group, coprothermobactter, presiomonas, and Roseburia in intestine. The present study indicate that oral administration of YM001 altered the diversity and composition of intestinal microbiota in tilapia, but these change were only temporary, non-lethal, and recoverable. The results provide a more comprehensive experimental basis for the safety of oral YM001 vaccines.

PLGA-encapsulated CpG ODN and Campylobacter jejuni lysate modulate cecal microbiota composition in broiler chickens experimentally challenged with C. jejuni

Campylobacter jejuni is a leading bacterial cause of human gastroenteritis. Reducing Campylobacter numbers in the intestinal tract of chickens will minimize transmission to humans, thereby reducing the incidence of infection. We have previously shown that oral pre-treatment of chickens with C. jejuni lysate and Poly D, L-lactide-co-glycolide polymer nanoparticles (PLGA NPs) containing CpG oligodeoxynucleotide (ODN) can reduce the number of C. jejuni in infected chickens. In the current study, the effects of these pre-treatments on the composition and functional diversity of the cecal microbiota, in chickens experimentally infected with C. jejuni, were investigated using next-generation sequencing. The taxonomic composition analysis revealed a reduction in cecal microbial diversity and considerable changes in the taxonomic profiles of the microbial communities of C. jejuni-challenged chickens. On the other hand, irrespective of the dose, the microbiota of PLGA-encapsulated CpG ODN- and C. jejuni lysate-treated chickens exhibited higher microbial diversity associated with high abundance of members of Firmicutes and Bacteroidetes and lower numbers of Campylobacter than untreated-chickens. These findings suggest that oral administration of encapsulated CpG ODN and C. jejuni lysate can reduce colonization by C. jejuni by enhancing the proliferation of specific microbial groups. The mechanisms that mediate these changes remain, however, to be elucidated.

A Consistent and Predictable Commercial Broiler Chicken Bacterial Microbiota in Antibiotic-Free Production Displays Strong Correlations with Performance

Defining the baseline bacterial microbiome is critical to understanding its relationship with health and disease. In broiler chickens, the core microbiome and its possible relationships with health and disease have been difficult to define, due to high variability between birds and flocks. Presented here are data from a large, comprehensive microbiota-based study in commercial broilers. The primary goals of this study included understanding what constitutes the core bacterial microbiota in the broiler gastrointestinal, respiratory, and barn environments; how these core players change across age, geography, and time; and which bacterial taxa correlate with enhanced bird performance in antibiotic-free flocks. Using 2,309 samples from 37 different commercial flocks within a vertically integrated broiler system and metadata from these and an additional 512 flocks within that system, the baseline bacterial microbiota was defined using 16S rRNA gene sequencing. The effects of age, sample type, flock, and successive flock cycles were compared, and results indicate a consistent, predictable, age-dependent bacterial microbiota, irrespective of flock. The tracheal bacterial microbiota of broilers was comprehensively defined, and Lactobacillus was the dominant bacterial taxon in the trachea. Numerous bacterial taxa were identified, which were strongly correlated with broiler chicken performance across multiple tissues. While many positively correlated taxa were identified, negatively associated potential pathogens were also identified in the absence of clinical disease, indicating that subclinical dynamics occur that impact performance. Overall, this work provides necessary baseline data for the development of effective antibiotic alternatives, such as probiotics, for sustainable poultry production.IMPORTANCE Multidrug-resistant bacterial pathogens are perhaps the greatest medical challenge we will face in the 21st century and beyond. Antibiotics are necessary in animal production to treat disease. As such, animal production is a contributor to the problem of antibiotic resistance. Efforts are underway to reduce antibiotic use in animal production. However, we are also challenged to feed the world's increasing population, and sustainable meat production is paramount to providing a safe and quality protein source for human consumption. In the absence of antibiotics, alternative approaches are needed to maintain health and prevent disease, and probiotics have great promise as one such approach. This work paves the way for the development of alternative approaches to raising poultry by increasing our understandings of what defines the poultry microbiome and of how it can potentially be modulated to improve animal health and performance.

Salmonella Excludes Salmonella in Poultry: Confirming an Old Paradigm Using Conventional and Barcode-Tagging Approaches

Salmonella is one of the major foodborne bacterial pathogens, and the consumption of contaminated chicken meats isa primary route of Salmonella transmission into human food chains. However, the mechanism of Salmonella transmission within the chicken flock is not fully understood, including competition among Salmonella strains during chicken infection. The purpose of the present study was to evaluate the competitive exclusion (CE) between different or same Salmonella species consecutively challenged through the oral route. Two different approaches were used to evaluate the CE effect, including tracking Salmonella colonization by wild-type strains with difference in natural antibiotic resistance or DNA barcode-tagged isogenic strains. When day-of-hatch chicks were administered by wild-type S. Typhimurium (ST) on day 1, followed by infection on day 2 by S. Enteritidis (SE) or vice versa, most of the birds were colonized only by the first strains administered (82% by ST or 83% by SE). When similar experiments were performed using two different isogenic barcode-tagged SE strains, Illumina sequencing analysis of the barcode region showed that the first barcode-tagged strains administered were dominant strains, ranging from 92 to 99% of the Salmonella recovered from ceca. These results provide quantitative evidence supporting the CE theory that oral administration of Salmonella will produce predominant inhibition over the subsequent colonization of ceca by the following administration one day later by different or same Salmonella species. We also showed that the use of barcode-tagged isogenic strains in combination with deep profiling of barcodes by Illumina sequencing can serve as a quantitative method for studying complex dynamics of Salmonella infection, transmission and colonization in poultry.

Host and Environmental Factors Affecting the Intestinal Microbiota in Chickens

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

Impact of Dietary Galacto-Oligosaccharide (GOS) on Chicken's Gut Microbiota, Mucosal Gene Expression, and Salmonella Colonization

Preventing Salmonella colonization in young birds is key to reducing contamination of poultry products for human consumption (eggs and meat). While several Salmonella vaccines have been developed that are capable of yielding high systemic antibodies, it is not clear how effective these approaches are at controlling or preventing Salmonella colonization of the intestinal tract. Effective alternative control strategies are needed to help supplement the bird’s ability to prevent Salmonella colonization, specifically by making the cecum less hospitable to Salmonella. In this study, we investigated the effect of the prebiotic galacto-oligosaccharide (GOS) on the cecal microbiome and ultimately the carriage of Salmonella. Day-old pullet chicks were fed control diets or diets supplemented with GOS (1% w/w) and then challenged with a cocktail of Salmonella Typhimurium and Salmonella Enteritidis. Changes in cecal tonsil gene expression, cecal microbiome, and levels of cecal and extraintestinal Salmonella were assessed at 1, 4, 7, 12, and 27 days post infection. While the Salmonella counts were generally lower in the GOS-treated birds, the differences were not significantly different at the end of the experiment. However, these data demonstrated that treatment with the prebiotic GOS can modify both cecal tonsil gene expression and the cecal microbiome, suggesting that this type of treatment may be useful as a tool for altering the carriage of Salmonella in poultry.