Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks

The effect of peanut skins as a natural antimicrobial feed additive on ileal and cecal microbiota in broiler chickens inoculated with Salmonella enterica Enteritidis

The consumption of poultry products contaminated with Salmonella species is one of the most common causes of Salmonella infections. In vivo studies demonstrated the potential application of peanut skins (PS) as an antimicrobial poultry feed additive to help mitigate the proliferation of Salmonella in poultry environments. Tons of PS, a waste by-product of the peanut industry, are generated and disposed in U.S. landfills annually. Peanut skins and extracts have been shown to possess antimicrobial and antioxidant properties. Hence, we aimed to determine the effect of PS as a feed additive on the gut microbiota of broilers fed a control or PS supplemented (4% inclusion) diet and inoculated with or without Salmonella enterica Enteritidis (SE). At hatch 160 male broilers were randomly assigned to 4 treatments: 1) CON-control diet without SE, 2) PS-PS diet without SE, 3) CONSE-control diet with SE, 4) PSSE-PS diet with SE. On d 3, birds from CONSE and PSSE treatments were inoculated with 4.2 × 109 CFU/mL SE. At termination (4 wk), 10 birds/treatment were euthanized and ileal and cecal contents were collected for 16S rRNA analysis using standard methodologies. Sequencing data were analyzed using QIIME2. No effect of PS or SE was observed on ileal alpha and beta diversity, while evenness, richness, number of amplicon sequence variants (ASV) and Shannon, as well as beta diversity were significantly (P < 0.05) affected in ceca. Similarly, more differentially abundant taxa between treatment groups were identified in ceca than in ileum. However, more microbiota functional changes, based on the PICRUST2 prediction, were observed in ileum. Overall, relatively minor changes in microbiota were observed during SE infection and PS treatment, suggesting that PS addition may not attenuate the SE proliferation, as shown previously, through modulation of microbiota in gastrointestinal tract. However, while further studies are warranted, these results suggest that PS may potentially serve as a functional feed additive for poultry for improvement of animal health.

Breaking the Cycle: A Yeast Mannan-Rich Fraction Beneficially Modulates Egg Quality and the Antimicrobial Resistome Associated with Layer Hen Caecal Microbiomes under Commercial Conditions

Antibiotics and antibiotic growth promoters have been extensively employed in poultry farming to enhance growth performance, maintain bird health, improve nutrient uptake efficiency, and mitigate enteric diseases at both sub-therapeutic and therapeutic doses. However, the extensive use of antimicrobials in poultry farming has led to the emergence of antimicrobial resistance (AMR) in microbial reservoirs, representing a significant global public health concern. In response, non-antibiotic dietary interventions, such as yeast mannan-rich fraction (MRF), have emerged as a promising alternative to modulate the gut microbiota and combat the AMR crisis. This study investigated whether a yeast mannan-rich fraction containing feed supplement impacted the performance of laying hens, their microbiomes, and the associated carriage of antimicrobial resistance genes under commercial conditions. High-throughput DNA sequencing was utilised to profile the bacterial community and assess changes in the antibiotic resistance genomes detected in the metagenome, the "resistome", in response to MRF supplementation. It was found that supplementation favourably influenced laying hen performance and microbial composition. Notably, there was a compositional shift in the MRF supplemented group associated with a lower relative abundance of pathobionts, e.g., Escherichia, Brachyspira and Trueperella, and their AMR-encoded genes, relative to beneficial microbes. Overall, the findings further demonstrate the ability of prebiotics to improve laying hen performance through changes associated with their microbiome and resistome.

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.

A live attenuated Salmonella Typhimurium vaccine dose and diluent have minimal effects on the caecal microbiota of layer chickens

Among the Salmonella reduction strategies in poultry production, one option is to use a Salmonella vaccine. The aim of vaccinating layer flocks is to reduce the shedding of wild-type Salmonella in the poultry environment, thereby reducing the contamination of poultry products (eggs and meat). Nutritive diluent and a higher dose of vaccine may enhance its colonization potential in the gut of chickens. In this study, a commercially available live attenuated vaccine (Vaxsafe® ST) was reconstituted in different media and delivered orally to day-old chicks at three different doses (107, 108, and 109 CFU/chick). Gut colonization of the vaccine strain and the effects of vaccination on gut microbiota were assessed in commercial-layer chickens. The vaccine diluent and dosage minimally affected microbiota alpha diversity. Microbiota beta diversity was significantly different (P < 0.05) based on the vaccine diluent and dose, which indicated that the vaccinated and unvaccinated chickens had different gut microbial communities. Differences were noted in the abundance of several genera, including Blautia, Colidextribacter, Dickeya, Enterococcus, Lactobacillus, Pediococcus, and Sellimonas. The abundance of Colidextribacter was significantly lower in chickens that received vaccine reconstituted in Marek's and water diluents, while Lactobacillus abundance was significantly lower in the water group. The highest vaccine dose (109 CFU/chick) did not significantly alter (P > 0.05) the abundance of microbial genera. Chicken age affected the microbiota composition more significantly than the vaccine dose and diluent. The abundance of Lactobacillus, Blautia, Caproiciproducens, Pediococcus, and Colidextribacter was significantly higher on day 14 compared with day 7 post-vaccination. The Salmonella Typhimurium vaccine load in the caeca was not significantly affected by diluent and vaccine dose; however, it was significantly lower (P < 0.0001) on day 14 compared with day 7 post-vaccination. Overall, the S. Typhimurium vaccine minimally affected the gut microbiota structure of layer chicks, whereas changes in microbiota were more significant with chicken age.

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

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

Comparing microbiotas of foals and their mares' milk in the first two weeks after birth

BACKGROUND

The mare-foal relationship is essential for the well-being and growth of a foal. Mare's milk provides a foal with nutrients, protective immunity, and microbes. Within the first two weeks of life, there is a risk for a foal to suffer from diarrhea, particularly "foal heat diarrhea" which happens at about the time of a mare's estrus cycle but is more likely due to transitions in the microbiota in the foal's gastrointestinal (GI) tract. We hypothesized that this GI microbiota transition could be caused by changes in lysozyme and microbial populations in the mare's milk. To test this hypothesis, fifteen mare-foal pairs were followed in the first 15 days post-foaling. Every other day milk was collected from mares and rectal swabs were collected from foals. Lysozyme activity in the mare's milk was measured using a fluorescence assay. Microbial DNA was isolated from the milk and swabs and the V4 domain of 16 S rRNA genes were PCR amplified and sequenced using Illumina MiSeq technology. Microbial populations were analyzed using DADA2 and phyloseq within R.

RESULTS

Mare's milk lysozyme activity peaked for samples at Day 1 and levels dropped to 72.5% of Day 1 activity by Day 15; however, microbial populations in the mare's milk did not vary significantly over the two weeks. Furthermore, levels of microbial diversity found in foal rectal swabs were initially similar to microbial diversity seen in mare's milk; however, over the first fifteen days, diversity increased for the foal rectal swab microbiota and swab microbial populations differed from milk microbes. A transition occurred shifting from microbes from the phylum Proteobacteria early in rectal swabs to those primarily from the phyla Firmicutes and Bacteroidota after the first few days post-foaling. These phyla contained several families and genera of microbes that promote utilization of milk components in healthy gut transition. Microbial abundance levels correlated more with days post-parturition than with lysozyme activity and mare's milk microbial populations.

CONCLUSIONS

The findings suggest that much of the microbial populations responsible for the transition of the foal's gut comes from sources outside of mare's milk species and levels of lysozyme activity.

Animal and In Vitro Models as Powerful Tools to Decipher the Effects of Enteric Pathogens on the Human Gut Microbiota

Examining the interplay between intestinal pathogens and the gut microbiota is crucial to fully comprehend the pathogenic role of enteropathogens and their broader impact on human health. Valid alternatives to human studies have been introduced in laboratory practice to evaluate the effects of infectious agents on the gut microbiota, thereby exploring their translational implications in intestinal functionality and overall health. Different animal species are currently used as valuable models for intestinal infections. In addition, considering the recent advances in bioengineering, futuristic in vitro models resembling the intestinal environment are also available for this purpose. In this review, the impact of the main human enteropathogens (i.e., Clostridioides difficile, Campylobacter jejuni, diarrheagenic Escherichia coli, non-typhoidal Salmonella enterica, Shigella flexneri and Shigella sonnei, Vibrio cholerae, and Bacillus cereus) on intestinal microbial communities is summarized, with specific emphasis on results derived from investigations employing animal and in vitro models.

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.

Modulation of Caecal Microbiota and Metabolome Profile in Salmonella-Infected Broilers by Phage Therapy

Bacteriophage therapy is considered one of the most promising tools to control zoonotic bacteria, such as Salmonella, in broiler production. Phages exhibit high specificity for their targeted bacterial hosts, causing minimal disruption to the niche microbiota. However, data on the gut environment's response to phage therapy in poultry are limited. This study investigated the influence of Salmonella phage on host physiology through caecal microbiota and metabolome modulation using high-throughput 16S rRNA gene sequencing and an untargeted metabolomics approach. We employed 24 caecum content samples and 24 blood serum samples from 4-, 5- and 6-week-old broilers from a previous study where Salmonella phages were administered via feed in Salmonella-infected broilers, which were individually weighed weekly. Phage therapy did not affect the alpha or beta diversity of the microbiota. Specifically, we observed changes in the relative abundance of 14 out of the 110 genera using the PLS-DA and Bayes approaches. On the other hand, we noted changes in the caecal metabolites (63 up-accumulated and 37 down-accumulated out of the 1113 caecal metabolites). Nevertheless, the minimal changes in blood serum suggest a non-significant physiological response. The application of Salmonella phages under production conditions modulates the caecal microbiome and metabolome profiles in broilers without impacting the host physiology in terms of growth performance.

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

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

A Two Bacteriocinogenic Ligilactobacillus Strain Association Inhibits Growth, Adhesion, and Invasion of Salmonella in a Simulated Chicken Gut Environment

In this study, we aimed to develop a protective probiotic coculture to inhibit the growth of Salmonella enterica serovar Typhimurium in the simulated chicken gut environment. Bacterial strains were isolated from the digestive mucosa of broilers and screened in vitro against Salmonella Typhimurium ATCC 14028. A biocompatibility coculture test was performed, which identified two biocompatible strains, Ligilactobacillus salivarius UO.C109 and Ligilactobacillus saerimneri UO.C121 with high inhibitory activity against Salmonella. The cell-free supernatant (CFS) of the selected isolates exhibited dose-dependent effects, and the inhibitory agents were confirmed to be proteinaceous by enzymatic and thermal treatments. Proteome and genome analyses revealed the presence of known bacteriocins in the CFS of L. salivarius UO.C109, but unknown for L. saerimneri UO.C121. The addition of these selected probiotic candidates altered the bacterial community structure, increased the diversity of the chicken gut microbiota challenged with Salmonella, and significantly reduced the abundances of Enterobacteriaceae, Parasutterlla, Phascolarctobacterium, Enterococcus, and Megamonas. It also modulated microbiome production of short-chain fatty acids (SCFAs) with increased levels of acetic and propionic acids after 12 and 24 h of incubation compared to the microbiome challenged with S. Typhimurium. Furthermore, the selected probiotic candidates reduced the adhesion and invasion of Salmonella to Caco-2 cells by 37-39% and 51%, respectively, after 3 h of incubation, compared to the control. These results suggest that the developed coculture probiotic strains has protective activity and could be an effective strategy to control Salmonella infections in poultry.

Dietary supplemental coated essential oils and organic acids mixture improves growth performance and gut health along with reduces Salmonella load of broiler chickens infected with Salmonella Enteritidis

BACKGROUND

Reducing Salmonella infection in broiler chickens by using effective and safe alternatives to antibiotics is vital to provide safer poultry meat and minimize the emergence of drug-resistant Salmonella and the spread of salmonellosis to humans. This study was to first evaluate the protective efficacy of feeding coated essential oils and organic acids mixture (EOA) on broiler chickens infected with Salmonella Enteritidis (S. Enteritidis, SE), and then its action mechanism was further explored.

METHODS

A total of 480 1-day-old Arbor Acres male chickens were randomly assigned into five treatments with six replicates, including non-challenged control fed with basal diet (A), SE-challenged control (B), and SE-infected birds fed a basal diet with 300 mg/kg of EOA (BL), 500 mg/kg of EOA (BM) and 800 mg/kg of EOA (BH), respectively. All birds on challenged groups were infected with Salmonella Enteritidis on d 13.  RESULTS: Feeding EOA showed a reversed ability on negative effects caused by SE infection, as evidenced by decreasing the feed conversion rate (FCR) and the ratio of villus height to crypt depth (VH/CD) (P < 0.05), obviously decreasing intestinal and internal organs Salmonella load along with increasing cecal butyric acid-producing bacteria abundance (P < 0.05). Moreover, supplemental different levels of EOA notably up-regulated claudin-1 (CLDN-1), occludin (OCLN), zonula occludens-1 (ZO-1), mucin-2 (MUC-2), fatty acid binding protein-2 (FABP-2), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), myeloid differential protein-88 (MyD88) and interleukin-6 (IL-6) mRNA levels in the ileum of the infected chickens after challenge, whereas down-regulated toll-like receptor-4 (TLR-4) mRNA levels (P < 0.05). Linear discriminant analysis combined effect size measurements analysis (LEfSe) showed that the relative abundance of g_Butyricicoccus, g_Anaerotruncus and g_unclassified_f_Bacillaceae significantly was enriched in infected birds given EOA. Also, phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis showed that alpha-linolenic acid metabolism, fatty acid metabolism and biosynthesis of unsaturated fatty acids were significantly enriched in the EOA group.

CONCLUSION

Our data suggest that the essential oils and organic acids mixture can be used as an effective strategy to ameliorate and alleviate Salmonella Enteritidis infection in broilers.

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.

Timing and delivery route effects of cecal microbiome transplants on Salmonella Typhimurium infections in chickens: potential for in-hatchery delivery of microbial interventions

BACKGROUND

Exposure to microbes early in life has long-lasting effects on microbial community structure and function of the microbiome. However, in commercial poultry settings chicks are reared as a single-age cohort with no exposure to adult birds which can have profound effects on microbiota development and subsequent pathogen challenge. Microbiota manipulation is a proven and promising strategy to help reduce pathogen load and transmission within broiler flocks. However, administration of microbiota transplant products in a hatchery setting may prove challenging. Effective administration strategies are dependent on key factors, such as; the age of chicks receiving interventions and mode of delivery. This study aimed to assess these two aspects to provide supporting evidence towards microbiome manipulation strategies for use in commercial hatcheries.

RESULTS

Manipulation of the microbiota between 4 and 72 h of hatch markedly reduced faecal shedding and colonisation with the foodborne pathogen Salmonella enterica serovar Typhimurium (ST4/74). Administration of transplant material via spray or gel drop delivery systems had minimal effect on the protection conferred with fewer birds in transplant groups shown to shed ST4/74 in the faeces compared to PBS-gavaged control birds. Analysis of the microbiome following transplantation demonstrated that all transplant groups had higher diversity and species richness than non-transplant groups during the first week of life and the early stages of infection with ST47/4.The relative abundance of the bacterium Faecalibacterium prausnitzii was significantly higher in CMT groups compared to PBS controls. The presence of F. prausnitzii was also shown to increase in PBS-challenged birds compared to unchallenged birds potentially indicating a role of this bacterium in limiting Salmonella infections.

CONCLUSIONS

This study demonstrated that administration of microbiome transplants, using methods that would align with hatchery practices, effectively reduced colonisation and shedding of Salmonella in chickens. Age of chicks at microbiome administration had limited effect on the diversity and composition of the microbiome and conferred protection against Salmonella infections. Traditional hatchery delivery systems, such as spray or gel-drop, are sufficient to transfer donor material, alter the microbiome and confer protection against Salmonella. This study helps highlight the opportunity for use of microbiome modification methods within the hatchery.

Dietary Supplementation with Botanical Blends Modified Intestinal Microbiota and Metabolomics of Weaned Pigs Experimentally Infected with Enterotoxigenic Escherichia coli

The objective of this study was to investigate supplementation of botanical blends (BB) comprised of 0.3% capsicum oleoresin and 12% garlic oil on gut microbiota and metabolomic profiles in serum and ileal mucosa of Escherichia coli infected pigs. Sixty weaned pigs were assigned to one of five treatments: negative control (CON-), positive control (CON+), dietary supplementation of 100 ppm BB1, 50 or 100 ppm BB2. All pigs, except CON-, were orally inoculated with 10¹⁰ CFU F18 ETEC/3-mL dose for 3 consecutive days after 7 d adaption. Feces, ileal digesta and cecal content were collected for 16S rRNA amplicon sequencing. Serum and ileal mucosa underwent primary metabolomics analysis. Supplementing 100 ppm BB1 increased (p < 0.05) relative abundances of Enterobacteriaceae and Escherichia-Shigella in ileum, and the relative abundances of Bacteroidota and Prevotellaceae in cecum than CON+ on d 5 post-inoculation (PI). Supplementing 100 ppm BB2 upregulated serum pinitol on d 4 PI and serum cholesterol and aminomalonic acids on d 21 PI, while supplementing 50 ppm BB2 reduced asparagine in ileal mucosa on d 5 PI than CON+. Supplementation with botanical blends modulated ileal and cecal microbiota and serum metabolomics profiles in weaned pigs under Escherichia coli challenge.

Weaning diet supplemented with health-promoting feed additives influences microbiota and immune response in piglets challenged with Salmonella

The aim of this study was to evaluate the potential of micronutrients and feed additives to modulate intestinal microbiota and systemic and mucosal immune responses in weaned pigs infected with Salmonella. At weaning, 32 litters of 12 piglets each were allocated to four dietary treatments: 1) control diet (CTRL), 2) CTRL supplemented with chlortetracycline (ATB), 3) CTRL supplemented with a cocktail of feed additives (CKTL); and 4) CKTL diet containing bovine colostrum in replacement of spray-dry animal plasma (CKTL+COL). The CKTL supplement included cranberry extract, encapsulated carvacrol and yeast-derived products and an enriched selenium and vitamin premix. Three weeks after weaning, four pigs per litter were orally inoculated with Salmonella Typhimurium DT104. Half of them were euthanized 3 days post-infection (dpi) and the other half, 7 dpi. The expression of IL6, TNF, IL8, monocyte chemoattractant protein 1 (MCP1), IFNG, cyclooxygenase 2 (COX2), glutathione peroxidase 2 (GPX2) and β-defensin 2 (DEFB2) showed a peaked response at 3 dpi (P < 0.05). Results also revealed that DEFB2 expression was higher at 3 dpi in CTRL and CKTL groups than in ATB (P = 0.01 and 0.06, respectively) while GPX2 gene was markedly increased at 3 and 7 dpi in pigs fed CKTL or CKTL+COL diet compared to CTRL pigs (P < 0.05). In piglets fed CKTL or CKTL+COL diet, intestinal changes in microbial communities were less pronounced after exposure to Salmonella compared to CTRL and progressed faster toward the status before Salmonella challenge (AMOVA P < 0.01). Furthermore, the relative abundance of several families was either up- or down-regulated in pigs fed CKTL or CKTL+COL diet after Salmonella challenge. In conclusion, weaning diet enriched with bovine colostrum, vitamins and mixture of feed additives mitigated the influence of Salmonella infection on intestinal microbial populations and modulate systemic and intestinal immune defences.

Cytokines and cecal microbiome modulations conferred by a dual vaccine in Salmonella-infected layers

Zoonotic Salmonella infection is a critical and challenging issue for public health. Since human infections are mainly associated with consuming contaminated chicken products, strategies to reduce Salmonella carriage and shedding are essential. Here we investigate the mechanisms of the live attenuated Salmonella vaccine (AviPro Salmonella Duo) against Salmonella Enteritidis (SE) infection. We focused on inflammatory-related cytokine expressions and cecal microbiota modulations in specific-pathogen-free (SPF) and field layers. Forty-eight 2-day-old SPF layers were randomly allotted into S.SEvc, S.SEc, S.Vc, and S.Ct groups in trial 1. The equal number of filed layers at 25 wk were allocated into SEvc, SEc, Vc, and Ct groups in trial 2. Each group contained 12 layers. Groups were further assigned for vaccination (S.Vc and Vc groups), SE challenge (S.SEc and SEc groups), vaccination and the following SE challenge (S.SEvc and SEvc groups), or the placebo treatment (S.Ct and Ct groups). Cecal tissues and contents of layers on day 14 post-SE-challenges were collected for cytokine mRNA expression and 16S rRNA metagenomic analyses. We found that SE challenges significantly upregulated expressions of IFNγ, IL-1β, IL-12β, and NFκB1A in SPF layers. The vaccine notably counteracted the levels of IFNα, IFNγ, and NFκB1A activated by SE attacks. The vaccination, SE challenge, and their combination did not significantly affect alpha diversities but promoted dissimilarities in microbial communities between groups. Eubacterium_coprostanoligenes and Faecalibacterium_prausnitzii were identified as contributory taxa in the cecal microbiota of SE-challenged and vaccinated SPF layers. A significantly higher abundance of Faecalibacterium_prausnitzii in the ceca further correlated with the vaccination conferred protection against SE infection. In contrast, Oscillibacter_valericigenes and Mediterraneibacter_glycyrrhizinilyticus were featured taxa in Salmonella-infected field layers. Megamonas_hypermegale and Megamonas_rupellensis were identified as featured taxa in vaccinated field layers compared to SE-infected layers. To conclude, applying a dual Salmonella vaccine in this study modulated expressions of inflammatory-related cytokines and the cecal microbiome in layers, contributing to protection against SE infection. The feature microbes are promising for developing predictive indices and as antibiotic alternatives added to feed to reduce the risk of Salmonella shedding and contamination.

Symbiotic bacteria stabilize the intestinal environment by producing phenylpropanoids

Salmonella enterica serovar Enteritidis (S. Enteritidis) can colonize in the intestinal tract of chickens and transmit to humans. In order to decrypt the mechanism of avian resistance to S. Enteritidis, we utilized two China local chicken breeds to generate the reciprocal crosses (the Cross and the Reverse-cross). The two lines of hybrids were orally inoculated with S. Enteritidis at 2-day old and sampled at 3 days post-inoculation. Along the analysis direction of multi-omics, differential metabolites, functional pathways and correlated microbes, we found that 12 species of microbes thrived upon S. Enteritidis challenge and probably contributed to the intestinal stability in the Cross by enhancing the production of phenylpropanoids. Our findings can help to understand the symbiotic and resistant mechanisms derived from the intestinal microbiota.

Effect of Lactobacillus reuteri S5 Intervention on Intestinal Microbiota Composition of Chickens Challenged with Salmonella enteritidis

To understand the mechanism of lactic acid bacteria against Salmonella enteritidis infection; we examined how lactic acid bacteria regulated the intestinal microbiota to resist infection by pathogenic bacteria. The probiotic strain Lactobacillus reuteri S5 was used to construct an animal model of S. enteritidis infected broilers. A high-throughput sequencing technology was used to analyze the regulatory effects of L. reuteri S5 on the structure of the intestinal microbiota of broilers infected with S. enteritidis; and to examine the possible defense mechanism they used. Our results showed that the administration of L. reuteri S5 reduced colonization of S. enteritidis (p < 0.05), decreased intestinal permeability (p < 0.05), and reduced the bacterial displacement likely due by S. enteritidis colonization (p < 0.05), suggesting some enhancement of the intestinal barrier function. Furthermore, L. reuteri S5 increased the number of operational taxonomic units (OTUs) in the chicken cecal microflora and the relative abundance of Lactobacillaceae and decreased the relative abundance of Enterobacteriaceae. These results suggest that the lactic acid bacterium L. reuteri S5 protected the intestinal microbiota of chickens against S. enteritidis infection.

The response of cecal microbiota to inflammatory state induced by Salmonella enterica serovar Enteritidis

By combining the experiments of reciprocal crosses of chicken infected with Salmonella enterica serovar Enteritidis (S. Enteritidis), we focused on the common response of cecal microbiota to an inflammatory state in respect of transcriptome and microbiome. The inoculation of S. Enteritidis improved the microbial diversity and promoted the microbiota evolution in our infection model. Correlation analysis between bacteria and inflammation-related genes showed that some intestinal microorganisms were “inflammophile” and thrived in an inflamed environment. The global function of cecal microbiome was to maintain the homeostasis likely by the up-regulation of microbial metabolism pathway in bacitracin, putrescine, and flavonoids production, although the bacitracin may affect the symbiotic bacteria Enterococcus. The action of S. Enteritidis had close relationships with multiple inflammation-related genes, including the genes PTAFR, LY96, and ACOD1 which proteins are related to the binding and tolerance of LPS, and the genes IL-18, IL-18R1 and IL-18RAP which products can form a functional complex and transmit IL-18 pro-inflammatory signal. Additionally, the infection of S. Enteritidis aroused the transcription of EXFABP, which protein has a potential to sequestrate the siderophore and might cause the decline of Escherichia-Shigella and Enterococcus. S. Enteritidis can escape from the sequestrating through the salmochelin, another kind of siderophore which cannot be recognized by EXFABP. Probably by this way, S. Enteritidis competed with the symbiotic bacteria and edged out the niches. Our research can help to understand the interplay between host, pathogen, and symbiotic bacteria.

Dietary selenium sources alleviate immune challenge induced by Salmonella Enteritidis potentially through improving the host immune response and gut microbiota in laying hens

The aim of this study was to evaluate the effects of different selenium (Se) sources on the immune responses and gut microbiota of laying hens challenged with Salmonella enteritidis (S. Enteritidis). A total of 240 45-week-old layers were randomly divided into eight groups with six replicates per group according to a 4 × 2 factorial design, including a blank diet without Se supplementation (CON group) and three diets with 0.3 mg/kg Se supplementation from sodium selenite (IS group), yeast Se (YS group), and selenium-enriched yeast culture (SYC group), respectively. After 8 weeks of feeding, half of them were orally challenged with 1.0 ml suspension of 109 colony-forming units per milliliter of S. Enteritidis daily for 3 days. The serum was collected on days 3, 7, and 14, and the cecum content was collected on day 14 after challenge. There was no significant difference in laying performance among the eight groups before challenge. The S. Enteritidis challenge significantly decreased the laying performance, egg quality, GSH-Px, IgG, and IgM and increased the ratio of feed and egg, malondialdehyde (MDA), Salmonella-specific antibody (SA) titers, IL-6, IL-2, IL-1β, and INF-γ. However, SYC increased the level of GSH-Px and IgG and decreased IL-6, while YS decreased the level of IL-2 and IL-1β. What is more, Se supplementation decreased the SA titers to varying degrees and reduced the inflammatory cell infiltration in the lamina propria caused by S. Enteritidis infection. In addition, the S. Enteritidis challenge disrupted the intestinal flora balance by reducing the abundance of the genera Clostridium innocuum, Lachnospiraceae, and Bifidobacterium and increasing the genera Butyricimonas and Brachyspira, while Se supplementation increased the gut microbial alpha diversity whether challenged or not. Under the S. Enteritidis challenge condition, the alteration of microbial composition by the administration of different Se sources mainly manifested as IS increased the relative abundance of the genera Lachnospiraceae and Christensenellaceae, YS increased the relative abundance of the genera Megamonas and Sphingomonas, and SYC increased the genera Fusobacterium and Lactococcus. The alteration of gut microbial composition had a close relationship with antioxidant or immune response. To summarize, different Se sources can improve the egg quality of layers challenged by S. Enteritidis that involves elevating the immunity level and regulating the intestinal microbiota.

Caecal microbiota composition of experimental inbred MHC-B lines infected with IBV differs according to genetics and vaccination

Interactions between the gut microbiota and the immune system may be involved in vaccine and infection responses. In the present study, we studied the interactions between caecal microbiota composition and parameters describing the immune response in six experimental inbred chicken lines harboring different MHC haplotypes. Animals were challenge-infected with the infectious bronchitis virus (IBV), and half of them were previously vaccinated against this pathogen. We explored to what extent the gut microbiota composition and the genetic line could be related to the immune response, evaluated through flow cytometry. To do so, we characterized the caecal bacterial communities with a 16S rRNA gene amplicon sequencing approach performed one week after the IBV infectious challenge. We observed significant effects of both the vaccination and the genetic line on the microbiota after the challenge infection with IBV, with a lower bacterial richness in vaccinated chickens. We also observed dissimilar caecal community profiles among the different lines, and between the vaccinated and non-vaccinated animals. The effect of vaccination was similar in all the lines, with a reduced abundance of OTU from the Ruminococcacea UCG-014 and Faecalibacterium genera, and an increased abundance of OTU from the Eisenbergiella genus. The main association between the caecal microbiota and the immune phenotypes involved TCR_ϒδ expression on TCR_ϒδ⁺ T cells. This phenotype was negatively associated with OTU from the Escherichia-Shigella genus that were also less abundant in the lines with the highest responses to the vaccine. We proved that the caecal microbiota composition is associated with the IBV vaccine response level in inbred chicken lines, and that the TCR_ϒδ⁺ T cells (judged by TCR_ϒδ expression) may be an important component involved in this interaction, especially with bacteria from the Escherichia-Shigella genus. We hypothesized that bacteria from the Escherichia-Shigella genus increased the systemic level of bacterial lipid antigens, which subsequently mitigated poultry γδ T cells.

The Game for Three: Salmonella–Host–Microbiota Interaction Models

Colonization of the gastrointestinal (GI) tract by enteric pathogens occurs in a context strongly determined by host-specific gut microbiota, which can significantly affect the outcome of infection. The complex gameplay between the trillions of microbes that inhabit the GI tract, the host, and the infecting pathogen defines a specific triangle of interaction; therefore, a complete model of infection should consider all of these elements. Many different infection models have been developed to explain the complexity of these interactions. This review sheds light on current knowledge, along with the strengths and limitations of in vitro and in vivo models utilized in the study of Salmonella–host–microbiome interactions. These models range from the simplest experiment simulating environmental conditions using dedicated growth media through in vitro interaction with cell lines and 3-D organoid structure, and sophisticated “gut on a chip” systems, ending in various animal models. Finally, the challenges facing this field of research and the important future directions are outlined.

Intestinal Mucosal Immunity-Mediated Modulation of the Gut Microbiome by Oral Delivery of Enterococcus faecium Against Salmonella Enteritidis Pathogenesis in a Laying Hen Model

Enterococcus faecium (E. faecium) is a protective role that has crucial beneficial functions on intestinal homeostasis. This study aimed to investigate the effects of E. faecium on the laying performance, egg quality, host metabolism, intestinal mucosal immunity, and gut microbiota of laying hens under the Salmonella Enteritidis (S. Enteritidis) challenge. A total of 400 45-week-old laying hens were randomly divided into four treatments (CON, EF, SCON, and SEF groups) with five replicates for each group and 20 hens per replicate and fed with a basal diet or a basal diet supplemented with E. faecium (2.5 × 10⁸ cfu/g feed). The experiment comprised two phases, consisting of the pre-salmonella challenged phase (from day 14 to day 21) and the post-salmonella challenged phase (from day 21 to day 42). At day 21 and day 22, the hens in SCON and SEF groups were orally challenged with 1.0 ml suspension of 10⁹ cfu/ml S. Enteritidis (CVCC3377) daily, whereas the hens in CON and EF groups received the same volume of sterile PBS. Herein, our results showed that E. faecium administration significantly improved egg production and shell thickness during salmonella infection. Also, E. faecium affected host lipid metabolism parameters via downregulating the concentration of serum triglycerides, inhibited oxidative stress, and enhanced immune functions by downregulating the level of serum malondialdehyde and upregulating the level of serum immunoglobulin G. Of note, E. faecium supplementation dramatically alleviated intestinal villi structure injury and crypt atrophy, and improved intestinal mucosal barrier injuries caused by S. Enteritidis challenge. Moreover, our data revealed that E. faecium supplementation ameliorated S. Enteritidis infection-induced gut microbial dysbiosis by altering the gut microbial composition (reducing Bacteroides, Desulfovibrio, Synergistes, and Sutterella, and increasing Barnesiella, Butyricimonas, Bilophila, and Candidatus_Soleaferrea), and modulating the gut microbial function, such as cysteine and methionine metabolism, pyruvate metabolism, fatty acid metabolism, tryptophan metabolism, salmonella infection, and the PI3K-Akt signaling pathway. Taken together, E. faecium has a strong capacity to inhibit the S. Enteritidis colonization of hens. The results highlight the potential of E. faecium supplementation as a dietary supplement to combat S. Enteritidis infection in animal production and to promote food safety.

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.

Differences in caecal microbiota composition and Salmonella carriage between experimentally infected inbred lines of chickens

BACKGROUND

Salmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication resulting from consumption of contaminated poultry products. Genetic selection of animals that are more resistant to Salmonella carriage and modulation of the gut microbiota are two promising ways to decrease individual Salmonella carriage. The aims of this study were to identify the main genetic and microbial factors that control the level of Salmonella carriage in chickens (Gallus gallus) under controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines N and 61 were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce recontamination of birds by Salmonella. Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition, using a 16S rRNA gene high-throughput sequencing approach.

RESULTS

Our results confirmed that the N line is more resistant to Salmonella carriage than the 61 line, and that intra-line variability is higher for the 61 line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Among the 617 operational taxonomic units (OTU) observed, more than 390 were differentially abundant between the two lines. Furthermore, within the 61 line, we found a difference in the microbiota taxonomic composition between the high and low Salmonella carriers, with 39 differentially abundant OTU. Using metagenome functional prediction based on 16S data, several metabolic pathways that are potentially associated to microbiota taxonomic differences (e.g. short chain fatty acids pathways) were identified between high and low carriers.

CONCLUSIONS

Overall, our findings demonstrate that the caecal microbiota composition differs between genetic lines of chickens. This could be one of the reasons why the investigated lines differed in Salmonella carriage levels under experimental infection conditions.

The Interplay between Salmonella and Intestinal Innate Immune Cells in Chickens

Salmonellosis is a common infection in poultry, which results in huge economic losses in the poultry industry. At the same time, Salmonella infections are a threat to public health, since contaminated poultry products can lead to zoonotic infections. Antibiotics as feed additives have proven to be an effective prophylactic option to control Salmonella infections, but due to resistance issues in humans and animals, the use of antimicrobials in food animals has been banned in Europe. Hence, there is an urgent need to look for alternative strategies that can protect poultry against Salmonella infections. One such alternative could be to strengthen the innate immune system in young chickens in order to prevent early life infections. This can be achieved by administration of immune modulating molecules that target innate immune cells, for example via feed, or by in-ovo applications. We aimed to review the innate immune system in the chicken intestine; the main site of Salmonella entrance, and its responsiveness to Salmonella infection. Identifying the most important players in the innate immune response in the intestine is a first step in designing targeted approaches for immune modulation.

Microbiota from Specific Pathogen-Free Mice Reduces Campylobacter jejuni Chicken Colonization

Campylobacter jejuni, a prevalent foodborne bacterial pathogen, is mainly transmitted from poultry with few effective prevention approaches. In this study, we aimed to investigate the role of microbiota on C. jejuni chicken colonization. Microbiota from specific pathogen-free (SPF) mouse stools were collected as SPF-Aerobe and SPF-Anaerobe. Birds were colonized with SPF-Aerobe or SPF-Anaerobe at day 0 and infected with C. jejuni AR101 at day 12. Notably, C. jejuni AR101 colonized at 5.3 and 5.6 log₁₀ C. jejuni CFU/g chicken cecal digesta at days 21 and 28, respectively, while both SPF-Aerobe and SPF-Anaerobe microbiota reduced pathogen colonization. Notably, SPF-Aerobe and SPF-Anaerobe increased cecal phylum Bacteroidetes and reduced phylum Firmicutes compared to those in the nontransplanted birds. Interestingly, microbiota from noninfected chickens, SPF-Aerobe, or SPF-Anaerobe inhibited AR101 in vitro growth, whereas microbiota from infected birds alone failed to reduce pathogen growth. The bacterium Enterobacter102 isolated from infected birds transplanted with SPF-Aerobe inhibited AR101 in vitro growth and reduced pathogen gut colonization in chickens. Together, SPF mouse microbiota was able to colonize chicken gut and reduce C. jejuni chicken colonization. The findings may help the development of effective strategies to reduce C. jejuni chicken contamination and campylobacteriosis.

Association of quorum sensing and biofilm formation with Salmonella virulence: story beyond gathering and cross-talk

Enteric fever (typhoid and paratyphoid fever) is a public health concern which contributes to mortality and morbidity all around the globe. It is caused mainly due to ingestion of contaminated food and water with a gram negative, rod-shaped, flagellated bacterium known as Salmonella enterica serotype typhi (typhoid fever) or paratyphi (paratyphoid fever). Clinical problems associated with Salmonellosis are mainly bacteraemia, gastroenteritis and enteric fever. The bacteria undergo various mechanisms to escape itself from immune reaction of the host, modulating immune response at the site of infection leading to virulence factor production and anti-microbial resistance. Biofilm is one of the adaptation mechanisms through which Salmonella survives in unfavourable conditions and thus is considered as a major threat to public health. Another property of the bacteria is "Quorum Sensing", which is a cell-cell communication and most of the pathogenic bacteria use it to coordinate the production of several virulence factors and other behaviours such as swarming and biofilm formation. Earlier, quorum sensing was believed to be just a medium for communication but, later on, its role in virulence has been studied. However, there are negligible information relating to interaction between quorum sensing and biofilm formation and how these events play crucial role in Salmonella pathogenesis. The review is a summary of updated information regarding how Salmonella uses these properties to spread more and survive better, making a challenge for clinicians and public health experts. Therefore, this review would help bring an insight regarding how biofilm formation and quorum sensing are inter-related and their role in pathogenesis and virulence of Salmonella.

Utilizing the Microbiota and Machine Learning Algorithms To Assess Risk of Salmonella Contamination in Poultry Rinsate

ABSTRACT

Traditional microbiological testing methods are slow, and many molecular-based techniques rely on culture-based enrichment to overcome low limits of detection. Recent advancements in sequencing technologies may make it possible to utilize machine learning to identify patterns in microbiome data to potentially predict the presence or absence of pathogens. In this study, 299 poultry rinsate samples from various points in the processing chain were analyzed to determine if microbiota could inform about a sample's risk for containing Salmonella. Samples were culture confirmed as Salmonella positive or negative following modified U.S. Department of Agriculture Microbiological Laboratory Guidebook protocols. The culture confirmation result was used as a reference to compare with 16S sequencing data. Prechill samples tested positive (71 of 82) at a higher frequency than postchill samples (30 of 217) and contained greater microbial diversity. Due to the larger sample size, postchill samples were analyzed more thoroughly. Analysis of variance identified a significant effect of chilling on the number of genera (P < 0.001), but analysis of similarities failed to provide evidence for microbial dissimilarity between pre- and postchill samples (P = 0.001, R = 0.443). Various machine learning models were trained by using postchill samples to predict if a sample contained Salmonella on the basis of the samples' microbiota preenrichment. The optimal model was a random forest-based model with a performance as follows: accuracy (88%), sensitivity (85%), and specificity (90%). Although the algorithms described in this article are prototypes, these risk-based algorithms demonstrate the potential and need for further studies to provide insight alongside diagnostic tests. Combining risk-based information with diagnostic tools can help poultry processors make informed decisions to help identify and prevent the spread of Salmonella. These data add to the growing body of literature exploring novel ways to utilize microbiome data for predictive food safety.

HIGHLIGHTS

Understanding the effects of intramuscular injection and feed withdrawal on Salmonella Typhimurium shedding and gut microbiota in pullets

Background

Gut microbiota plays a key role in health, immunity, digestion, and production in layers. Factors such as environment, diet, diseases, stress, and flock management significantly affect gut microbiota; however, it is not known how potential stressors such as intramuscular injections or feed withdrawal alter the composition of gut microbiota that result in increased the shedding level of foodborne pathogens. In the current study, the effects of intramuscular corticosterone injection and feed withdrawal were evaluated to understand their role in Salmonella Typhimurium shedding and changes in the composition of gut microbiota in layers.

Results

Salmonella shedding was observed for 8 weeks post-infection. There was a significant increase in Salmonella Typhimurium count after intramuscular injection and feed withdrawal. The Salmonella infected and the negative control groups showed significant differences in the abundance of different genera in gut microbiota at week 1 and up to week 7 post infection. The infected group showed a significant reduction in alpha diversity of gut microbiota. Firmicutes reduced significantly (P < 0.05) after intramuscular injection, while the feed withdrawal groups did not cause any significant changes in Proteobacteria-Firmicutes ratio. Furthermore, intramuscular injection resulted in a significant change in alpha diversity of gut microbiota.

Conclusions

Exposure of chicks to relatively low dose of Salmonella Typhimurium can lead to persistent shedding in pullets. The Salmonella Typhimurium infection disrupted the gut microbiota composition immediately after infection. The potential stress of intramuscular injection and feed withdrawal significantly increased the Salmonella Typhimurium count in faeces. The intramuscular injection also resulted in a significant alteration of the Proteobacteria-Firmicutes ratio, which could increase the risk of dysbiosis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-021-00597-9.

Effect of inclusion of micronized camelina, sunflower, and flax seeds in the broiler chicken diet on performance productivity, nutrient utilization, and intestinal microbial populations

The aim of the study was to evaluate the effect of inclusion of micronized full-fat camelina, flax, or sunflower seeds in the diet for broiler chickens on the performance productivity, nutrient utilization, and composition of intestinal microbial populations and to assess the possibility of modification of the resistance of isolated bacteria to chemotherapeutic agents with different mechanisms of action. The use of micronized oilseeds improved the broiler chicken body weight (P = 0.035) and the FCR value (P = 0.045) in the final rearing stage by enhancement of the utilization of total protein and organic matter. Lactobacillus-Enterococcus spp., Bifidobacterium spp., Escherichia coli, and Salmonella spp. were isolated from small intestinal contents, and Enterobacteriaceae taxa were detected in the cecum and cloaca of the broiler chickens. The addition of micronized camelina seeds (CAM.IR) contributed to an increase in the Bifidobacterium counts in the small intestine, compared with the control treatment (P < 0.050). Escherichia coli bacteria were not isolated only in the CAM.IR treatment. Nitrofurantoin and chloramphenicol were the most effective agents against the isolates from the cecum and cloaca in all oilseed treatments, whereas streptomycin exhibited the lowest efficacy. In the CAM.IR and micronized sunflower seed (SUN.IR) treatments, there were higher counts of trimethoprim/sulfamethoxazole-resistant Enterobacteriaceae strains than in the control and micronized flax seed (FLA.IR) treatments (P < 0.05). There was a difference between strains isolated from the cecum and cloaca only in the FLA.IR treatment, i.e., increased tetracycline sensitivity was exhibited by strains isolated from the cloaca (13% vs. 50%), also in comparison with the control treatments (P = 0.054). In comparison with the CAM.IR and control treatments, reduced numbers of multi-resistant strains were found in the cloaca isolates from the for FLA.IR and SUN.IR variants. Micronized camelina, flax, and sunflower seeds can be used as part of an effective nutritional strategy focused on optimization of the efficiency of rearing broiler chickens, as they positively modify intestinal microbial populations and increase bacterial sensitivity to the analyzed chemotherapeutic agents.

Temporal dynamics of gut microbiota in caged laying hens: a field observation from hatching to end of lay

Gut health has major implications for the general health of food-producing animals such as the layer birds used in the egg industry. In order to modulate gut microbiota for the benefit of gut health, an understanding of the dynamics and details of the development of gut microbiota is critical. The present study investigated the phylogenetic composition of the gut microbiota of a commercial layer flock raised in cages from hatch to the end of the production cycle. This study also aimed to understand the establishment and development of gut microbiota in layer chickens. Results showed that the faecal microbiota was dominated by phyla Firmicutes and Proteobacteria in the rearing phase, but Bacteroidetes in mid lay and late lay phase. The gut microbiota composition changed significantly during the transfer of the flock from the rearing to the production shed. The richness and diversity of gut microbiota increased after week 6 of the flocks age and stabilized in the mid and late lay phase. The overall dynamics of gut microbiota development was similar to that reported in earlier studies, but the phylogenetic composition at the phylum and family level was different. The production stage of the birds is one of the important factors in the development of gut microbiota. This study has contributed to a better understanding of baseline gut microbiota development over the complete life cycles in layer chickens and will help to develop strategies to improve the gut health. KEY POINTS: • Faecal microbiota of caged hens was dominated by phyla Firmicutes and Proteobacteria in the rearing phase. • The gut microbiota composition changed significantly during the transfer of the flock from the rearing to the production shed. • The richness and diversity of gut microbiota increased after week 6 of the flocks age and stabilized in the mid and late lay phase.

Apple Pomace and Performance, Intestinal Morphology and Microbiota of Weaned Piglets-A Weaning Strategy for Gut Health?

Apple pomace (AP) is known to be rich in biomolecules beneficial for health and it may advantageously be used to overcome the critical step of piglets’ weaning. The study aimed to determine the effect of two levels of incorporation of AP on the performance, intestinal morphology, and microbiota of weaned piglets and investigate this feed ingredient as a weaning strategy. An experiment was performed with 42 piglets from weaning (28 days old) over a five-week period, including three iso-energetic and iso-nitrogenous diets (0%, 2%, and 4% dried AP diets) with seven pen-repetitions per diet (two pigs per pen). AP diets were beneficial for the average daily gain calculated on week 3 (p = 0.038) and some parameters of the intestinal architecture on the 35 post-weaning day. The 4% AP diet was beneficial for the feed conversion ratio (p = 0.002) and the energetic feed efficiency (p = 0.004) on the 35 post-weaning day. AP tended to influence the consistency of feces (softer to liquid, p = 0.096) and increased the counts of excreted pathogens (p = 0.072). Four percent AP influenced the richness of the microbiota and the bacteria profile as observed for the phylum Bacteroidetes or the class Clostridia. The 4% AP diet appeared as an interesting weaning strategy that should be evaluated in a large cohort.

Evaluation of curcumin and copper acetate against Salmonella Typhimurium infection, intestinal permeability, and cecal microbiota composition in broiler chickens

BACKGROUND

Interest in the use of natural feed additives as an alternative to antimicrobials in the poultry industry has increased in recent years because of the risk of bacterial resistance. One of the most studied groups are polyphenolic compounds, given their advantages over other types of additives and their easy potentiation of effects when complexes are formed with metal ions. Therefore, the objective of the present study was to evaluate the impact of dietary supplementation of copper acetate (CA), curcumin (CR), and their combination (CA-CR) against Salmonella Typhimurium colonization, intestinal permeability, and cecal microbiota composition in broiler chickens through a laboratory Salmonella infection model. S. Typhimurium recovery was determined on day 10 post-challenge by isolating Salmonella in homogenates of the right cecal tonsil (12 chickens per group) on Xylose Lysine Tergitol-4 (XLT-4) with novobiocin and nalidixic acid. Intestinal integrity was indirectly determined by the fluorometric measurement of fluorescein isothiocyanate dextran (FITC-d) in serum samples from blood obtained on d 10 post-S. Typhimurium challenge. Finally, microbiota analysis was performed using the content of the left caecal tonsil of 5 chickens per group by sequencing V4 region of 16S rRNA gene.

RESULTS

The results showed that in two independent studies, all experimental treatments were able to significantly reduce the S. Typhimurium colonization in cecal tonsils (CT, P < 0.0001) compared to the positive control (PC) group. However, only CA-CR was the most effective treatment in reducing S. Typhimurium counts in both independent studies. Furthermore, the serum fluorescein isothiocyanate dextran (FITC-d) concentration in chickens treated with CR was significantly lower when compared to PC (P = 0.0084), which is related to a decrease in intestinal permeability and therefore intestinal integrity. The effect of dietary treatments in reducing Salmonella was further supported by the analysis of 16S rRNA gene sequences using Linear discriminant analysis effect size (LEfSe) since Salmonella was significantly enriched in PC group (LDA score > 2.0 and P < 0.05) compared to other groups. In addition, Coprobacillus, Eubacterium, and Clostridium were significantly higher in the PC group compared to other treatment groups. On the contrary, Fecalibacterium and Enterococcus in CR, unknown genus of Erysipelotrichaceae at CA-CR, and unknown genus of Lachnospiraceae at CA were significantly more abundant respectively.

CONCLUSIONS

CR treatment was the most effective treatment to reduce S. Typhimurium intestinal colonization and maintain better intestinal homeostasis which might be achieved through modulation of cecal microbiota.

Bacterial meta-analysis of chicken cecal microbiota

Poultry production is an industry that generates 90,000 metric tons of chicken meat worldwide. Thus, optimizing chicken growth and sustainable production is of great importance. A central factor determining not only production parameters, but also stability of the immune system and chicken health, is the diversity and variability of the microbiota present throughout the gastrointestinal tract. To date, several studies have investigated the relationship between bacterial communities and the gut microbiome, with limited data to compare. This study aims to create a bacterial meta-analysis based on studies using amplicon sequencing with Illumina sequencing technologies in order to build a baseline for comparison in future analyses of the cecal bacterial composition in chicken. A systematic literature review was performed (SYRF ID: e84f0468-e418-4eec-9da4-b517f1b4809d. Full project URL: https://app.syrf.org.uk/projects/e84f0468-e418-4eec-9da4-b517f1b4809d/detail). From all the available and analyzed manuscripts only nine contained full raw-sequence data available and the corresponding metadata. A total of 324 samples, comprising three different regions within the 16S rRNA gene, were analyzed. Due to the heterogeneity of the data, each region was analyzed independently and an effort for a joint analysis was performed as well. Taxonomic profiling revealed 11 phyla, with Firmicutes as the most prevalent phylum, followed by Bacteroidetes and Proteobacteria. At genus level, 109 genera were found. Shannon metric for alpha diversity showed that factors like type of chickens (Commercial or experimental) and 16S rRNA gene subregion have negligible effect on diversity. Despite the large number of parameters that were taken into account, the identification of common bacteria showed five genera to be common for all sets in at least 50% of the samples. These genera are highly associated to cellulose degradation and short chain fatty acids synthesis. In general, it was possible to identify some commonalities in the bacterial cecal microbial community despite the extensive variability and factors differing from one study to another.

A Role for the Microbiota in the Immune Phenotype Alteration Associated with the Induction of Disease Tolerance and Persistent Asymptomatic Infection of Salmonella in the Chicken

Previous studies have shown a tissue immune phenotype-altering event occurring on days 2 and 4 in the ceca post-Salmonella challenge. To evaluate the involvement of the cecal microbiota in the phenotype reprogramming, we hypothesized that the addition of subtherapeutic bacitracin (BMD) will affect the cecal microbiota. Therefore, the objective of this study was to determine if the antibiotic-mediated changes in the microbiota composition influenced the immune phenotype induced by Salmonella enteritidis infection of the chicken cecum. A total of 112 fertile eggs were obtained for each experiment, repeated for a total of three separate times. The ceca and cecal contents were collected on days 2 and 4 post-infection for mRNA expression TaqMan assay and 16S rRNA gene microbiota sequencing. The results demonstrate the effects of bacitracin on cecal composition and its interaction with Salmonella enteritidis in young chicks. There is a preliminary indication of phenotype change in the Salmonella-challenged group provided subtherapeutic BMD due to the shifting cecal microbiota and cecal immune response, indicating the addition of bacitracin during infection altered the cecal phenotype. These data demonstrate the potential involvement of the microbiota in reprogramming immune phenotype (disease resistance to disease tolerance) induced by Salmonella in the chicken cecum.

Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota

In the past decade, the initial studies of the gut microbiota started focusing on the correlation of the composition of the gut microbiota and the health or diseases of the host, and there are extensive literature reviews pertaining to this theme. However, little is known about the association between the microbiota, the host, and pathogenic bacteria, such as Salmonella enterica, which is among the most important foodborne pathogens and identified as the source of multiple outbreaks linked to contaminated foods causing salmonellosis. Secretion systems, flagella, fimbriae, endotoxins, and exotoxins are factors that play the most important roles in the successful infection of the host cell by Salmonella. Infections with S. enterica, which is a threat to human health, can alter the genomic, taxonomic, and functional traits of the gut microbiota. The purpose of this review is to outline the state of knowledge on the impacts of S. enterica on the intestinal microbiota and highlight the need to identify the gut bacteria that could contribute to salmonellosis.

Associations between phenotypic characteristics and clinical parameters of broilers and intestinal microbial development throughout a production cycle: A field study

Disturbances in intestinal health are a common problem affecting commercial broiler chickens worldwide. Several studies have revealed associations between health, production performance, and intestinal microbiota. This study aimed to describe the development of the intestinal microbiota of broilers within a production cycle to evaluate to what extent clinical parameters and phenotypic characteristics can explain the intestinal microbiota variation. Of four well-performing flocks within two farms, the cecal content was collected of nine broilers at 0, 2, 4, or 5, 7, 11, or 12, 14, 21, 28, 35, and 40 days of the production cycle. In total, 342 samples were analyzed using 16S ribosomal RNA gene amplicon sequencing. Variables as macroscopic gut abnormalities, gut lesions, age, individual body weight, sex, footpad integrity, the color of ceca, and foam in cecal content were determined. Ileum tissue was collected for histological quantification of villus length and crypt depth. Flock infection levels of the intestinal disease coccidiosis were measured in pooled feces from the poultry house. Increases in phylogenetic diversity were observed from hatch until day 21 of age. Constrained multivariate analysis indicated that age, farm, body weight, ileum crypt depth, cecal color, and the coccidiosis lesion score were important variables to describe the variation in cecal microbiota. These results contribute to determining relevant variables in flocks that may be indicative of the intestinal microbiota composition. Moreover, this knowledge increases the awareness of interactions between the intestinal microbiota and broiler health as well as their relative importance.

Salmonella enterica Serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses To Overcome Colonization Resistance in Swine

Salmonella enterica serovar Typhimurium is a prevalent incitant of enteritis in human beings and nonhuman animals. It has been proposed that host defense responses incited by Salmonella allow the bacterium to overcome colonization resistance. Piglets (n = 24) were orally inoculated with S. enterica serovar Typhimurium DT104 or buffer alone, and the host and microbial responses were temporally examined at the acute (2 days postinoculation [dpi]), subacute (6 dpi), and recovery (10 dpi) stages of salmonellosis. At the acute stage of disease, body temperatures were elevated, and feed consumption and weight gain were reduced. The densities of Salmonella associated with the gut mucosa decreased over time, with higher densities of the bacterium in the ileum and the large intestine. Moreover, substantive histopathological changes were observed as a function of time, with prominent epithelial injury and neutrophil infiltration observed at 2 dpi. Correspondingly, a variety of host metrics were temporally affected in piglets with salmonellosis (e.g., TNFα, IFNγ, PR39, βD2, iNOS, IL8, REGIIIγ). The enteric microbiota was characterized using culture-independent and -dependent methods in concert, and taxon- and location-specific changes to the microbiota were observed in infected piglets. Bacteroides spp. (e.g., Bacteroides uniformis, Bacteroides fragilis), Streptococcus spp. (e.g., Streptococcus gallolyticus), and various Gammaproteobacteria were highly associated with inflamed tissues, while bacteria within the Ruminococcaceae and Veillonellaceae families were mainly associated with healthy mucosae. In conclusion, the study findings showed that S Typhimurium incited temporal and spatial modifications to the swine autochthonous microbiota, and to host defense responses, that were consistent with overcoming colonization resistance to incite salmonellosis in swine.IMPORTANCE Limited information is available on host and enteric microbiota responses incited by Salmonella enterica serovar Typhimurium in swine and on possible mechanisms by which the bacterium overcomes colonization resistance to incite salmonellosis. Temporal characterization of a variety of host metrics in piglets (e.g., physiological, histopathological, and immunological) showed the importance of studying the progression of salmonellosis. A number of host responses integrally associated with disease development were identified. Utilization of next-generation sequence analysis to characterize the enteric microbiota was found to lack sufficient resolution; however, culture-dependent and -independent methods in combination identified taxon- and location-specific changes to bacterial communities in infected piglets. The study identified bacterial and host responses associated with salmonellosis, which will be beneficial in understanding colonization resistance and in the development of effective alternatives to antibiotics to mitigate salmonellosis.

Psyllium supplementation is associated with changes in the fecal microbiota of horses

OBJECTIVE

Prophylactic supplementation of psyllium husk is recommended to enhance passage of ingested sand from the gastrointestinal tracts of horses. We hypothesized that psyllium supplementation would increase fecal sand passage and favorably alter bacterial populations in the hindgut. Six yearlings and six mature mares were fed a psyllium supplement in the diet daily for seven days. Voluntarily-voided feces were collected over the course of 29 days, prior, during, and after treatment. Feces were analyzed for acid detergent fiber (ADF) and acid detergent insoluble ash analyses. Microbial DNA was also isolated, and the V4 region of the 16S ribosomal RNA gene was PCR-amplified and sequenced using MiSeq technology.

RESULTS

Fecal ADF concentration was greater in adults while silica concentration was greater in yearlings. Mature mare fecal ADF decreased during and just after supplementation but thereafter increased. No changes in silica levels were noted in either group over time. Fecal microbial population phylogenetic diversity was greatest mid-supplementation and lowest at 11 days post-supplementation. Functional profiles of the microbial communities presented some benefits for psyllium supplementation. These findings provide compelling evidence for further detailed studies of prophylactic psyllium supplementation.

Synergistic effects of the early administration of Lactobacillus kefiranofaciens DN1 and Kluyveromyces marxianus KU140723-05 on the inhibition of Salmonella Enteritidis colonization in young chickens

In this study, we aimed to assess the feasibility of the lactic acid bacterium Lactobacillus kefiranofaciens DN1 (LKF_DN1) and the yeast Kluyveromyces marxianus KU140723-05 (KMA5), recently isolated from kefir, as probiotics. Specifically, we evaluated the effect of early administration of these 2 microbes on the inhibition of Salmonella Enteritidis (SE) colonization in neonatal chicks. We also examined the effects of exposure of chicks to probiotics before SE exposure on the reduction in the number of gut SE. A total of 108 1-day-old specific-pathogen-free male layer chicks were used for 3 independent experiments. The experimental chicks were randomly divided into 6 groups (negative control: basal diet [BD] without probiotics and SE; positive control: BD; probiotic group [PG] 1: BD + LKF_DN1; PG2: BD + KMA5; PG3: BD + LKF_DN1 + KMA5; and PG4: BD+ a commercial product IDF-7), all of which, except negative control, were coadministered with SE strain resistant to rifampicin (SERR). We found that the administration of LKF_DN1 and/or KMA5 reduced the number of viable cells of the SERR strain in chicks by up to 1.90 log₁₀, relative to positive control chicks. Compared with late administration (day [D] 10 and D11), early administration (D1 and D2) of the probiotics was more effective in reducing SERR cell numbers in the gut. Furthermore, we detected no significant difference in the reduction of gut SERR cell numbers in chicks from the same groups exposed to the probiotics at D10 and D11 before and after administration with SERR. Collectively, our findings indicate that, as dietary additives, LKF_DN1 and KMA5 showed potential probiotic activity in chicks. Moreover, the combination of the lactic acid bacteria and/or yeast strain was found to rapidly reduce SE numbers in the chick gut and showed a prolonged inhibitory effect against SE colonization. We, thus, propose that the administration of these 2 probiotics, as early as possible after hatching, would be considerably effective in controlling SE colonization in the guts of chicks.

Dietary supplementation with vitamin C ameliorates the adverse effects of Salmonella Enteritidis-challenge in broilers by shaping intestinal microbiota

Salmonella Enteritidis (SE) infection is not only a leading cause of poor production performance and compromised animal welfare in broilers but also a potential threat to public health. Two experiments were conducted to evaluate the effects of dietary supplemental vitamin C (VC) on SE challenged-broilers. In experiment 1, one hundred eighty 1-day-old Arbor Acre broilers were randomly allocated into 3 treatments, with 0, 500, or 1,000 mg/kg VC included in the diet. In experiment 2, dietary VC at 0 or 500 mg/kg, with or without SE challenge was applied in a 2 × 2 factorial arrangement in 6 randomized complete blocks. In experiment 1, addition with 500 mg/kg VC increased BW and infectious bursal disease (IBD) titer of broilers on 35 D (P < 0.05), whereas 1,000 mg/kg VC had no effects on the IBD titer (P > 0.05) compared with the control group. In experiment 2, SE challenge depressed BW on 11 and 21 D (P < 0.05 and P = 0.088, respectively), whereas increased mortality and hepatic bacterial translocation (P < 0.05) on 21 D. Further, SE challenge resulted in lower villus height in jejunum, lower microbial richness, and diversity, whereas higher abundance of Enterobacteriaceae in cecum (P < 0.05). Importantly, supplementation with VC increased BW on both 21 and 35 D (P < 0.05 and P = 0.088, respectively) and enhanced the intestinal health by improving villus morphology and microbial structure as indicated by higher cecal microbial richness and Firmicutes to Bacteroidetes ratio, while lower abundance of Enterobacteriaceae (P < 0.05). In addition, birds fed with 500 mg/kg VC in the diet had significantly increased jejunal secretory immunoglobulin A levels, T lymphocytes stimulation index, and serum total antioxidant capability compared with groups without VC (P < 0.05). In conclusion, SE challenge induced lower production performance and higher mortality in broilers. However, dietary supplementation with VC ameliorated SE-caused damage in broilers by improving the intestinal health, partly mediated by shaping the structure of cecal microbiota.

Microbiome and pathogen interaction with the immune system

The intestinal tract harbors a diverse community of microbes that have co-evolved with the host immune system. Although many of these microbes execute functions that are critical for host physiology, the host immune system must control the microbial community so that the dynamics of this interdependent relationship is maintained. To facilitate host homeostasis, the immune system ensures that the microbial load is tolerated, but anatomically contained, while remaining reactive to microbial invasion. Although the microbiota is required for intestinal immune development, immune responses regulate the structure and composition of the intestinal microbiota by evolving unique immune adaptations that manage this high-bacterial load. The immune mechanisms work together to ensure that commensal bacteria rarely breach the intestinal barrier and that any that do invade should be killed rapidly to prevent penetration to systemic sites. The communication between microbiota and the immune system is mediated by the interaction of bacterial components with pattern recognition receptors expressed by intestinal epithelium and various antigen-presenting cells resulting in activation of both innate and adaptive immune responses. Interaction between the microbial community and host plays a crucial role in the mucosal homeostasis and health status of the host. In addition to providing a home to numerous microbial inhabitants, the intestinal tract is an active immunological organ, with more resident immune cells than anywhere else in the body, organized in lymphoid structures called Peyer's patches and isolated lymphoid follicles such as the cecal tonsils. Macrophages, dendritic cells, various subsets of T cells, B cells and the secretory immunoglobulin A (IgA) they produce, all contribute to the generation of a proper immune response to invading pathogens while keeping the resident microbial community in check without generating an overt inflammatory response to it. IgA-producing plasma cells, intraepithelial lymphocytes, and γδT cell receptor-expressing T cells are lymphocytes that are uniquely present in the mucosa. In addition, of the γδT cells in the intestinal lamina propria, there are significant numbers of IL-17-producing T cells and regulatory T cells. The accumulation and function of these mucosal leukocytes are regulated by the presence of intestinal microbiota, which regulate these immune cells and enhance the mucosal barrier function allowing the host to mount robust immune responses against invading pathogens, and simultaneously maintains immune homeostasis.

Salmonella Typhimurium infection disrupts but continuous feeding of Bacillus based probiotic restores gut microbiota in infected hens

Background

The gut microbiota plays an important role in the colonisation resistance and invasion of pathogens. Salmonella Typhimurium has the potential to establish a niche by displacing the microbiota in the chicken gut causing continuous faecal shedding that can result in contaminated eggs or egg products. In the current study, we investigated the dynamics of gut microbiota in laying chickens during Salmonella Typhimurium infection. The optimisation of the use of an infeed probiotic supplement for restoration of gut microbial balance and reduction of Salmonella Typhimurium load was also investigated.

Results

Salmonella infection caused dysbiosis by decreasing (FDR < 0.05) the abundance of microbial genera, such as Blautia, Enorma, Faecalibacterium, Shuttleworthia, Sellimonas, Intestinimonas and Subdoligranulum and increasing the abundance of genera such as Butyricicoccus, Erysipelatoclostridium, Oscillibacter and Flavonifractor. The higher Salmonella Typhimurium load resulted in lower (P < 0.05) abundance of genera such as Lactobacillus, Alistipes, Bifidobacterium, Butyricimonas, Faecalibacterium and Romboutsia suggesting Salmonella driven gut microbiota dysbiosis. Higher Salmonella load led to increased abundance of genera such as Caproiciproducens, Acetanaerobacterium, Akkermansia, Erysipelatoclostridium, Eisenbergiella, EscherichiaShigella and Flavonifractor suggesting a positive interaction of these genera with Salmonella in the displaced gut microbiota. Probiotic supplementation improved the gut microbiota by balancing the abundance of most of the genera displaced by the Salmonella challenge with clearer effects observed with continuous supplementation of the probiotic. The levels of acetate and butyrate in the faeces were not affected (P > 0.05) by Salmonella challenge and the butyrate level was increased by the continuous feeding of the probiotic. Probiotic supplementation in Salmonella challenged chickens resulted in higher level of propionate. Continuous probiotic supplementation decreased (P < 0.05) the overall mean load of Salmonella in faeces and had a significant effect on Salmonella load reduction in internal organs.

Conclusions

Salmonella challenge negatively impacts the diversity and abundance of many gut microbial genera involved in important functions such as organic acid and vitamin production. Strategic feeding of a Bacillus based probiotic helps in restoring many of the microbial genera displaced by Salmonella Typhimurium challenge.

Integrative analysis of gut microbiome and metabolites revealed novel mechanisms of intestinal Salmonella carriage in chicken

Intestinal carriage of Salmonella Enteritidis (SE) in the chicken host serves as a reservoir for transmission of Salmonella to humans through the consumption of poultry products. The aim of the current study was to examine the three-way interaction that occurred between host metabolites, resident gut microbiota and Salmonella following inoculation of SE in two-week-old layer chicks. Our results revealed an overall alteration in gut microbiome and metabolites in association with SE infection. Enriched colonization by different microbial members throughout the course of experimental infection highlighted significant fluctuation in the intestinal microbial community in response to Salmonella infection. As changes in community membership occurred, there was also subsequent impact on differential regulation of interlinked predicted functional activities within the intestinal environment dictated by Salmonella-commensal interaction. Alteration in the overall microbial community following infection also has a ripple effect on the host regulation of cecum-associated metabolic networks. The findings showed that there was differential regulation in many of the metabolites in association with SE colonization in chickens. Perturbation in metabolic pathways related to arginine and proline metabolism as well as TCA cycle was most prominently detected. Taken together, the present findings provided a starting point in understanding the effect of intestinal Salmonella carriage on the microbiome and metabolome of developing young layer chicks.

Effects of Bacillus subtilis and coccidial vaccination on cecal microbial diversity and composition of Eimeria-challenged male broilers

In a companion study, the effects of dietary antibiotic alternative and coccidial vaccination on the growth performance of male broilers have been reported. In this paper, the effects of dietary probiotics and coccidial vaccination on diversity and composition of cecal microbiota were investigated using a 3 (diets) × 2 (vaccinated or non-vaccinated) factorial setting of treatments. Three diets, including a corn and soybean-meal control diet, an antibiotic diet (a control diet supplemented with bacitracin and salinomycin), and a probiotic diet (a control diet supplemented with Bacillus subtilis) were provided to broiler chicken from day 0 to 42. To simulate an Eimeria challenge in the field, all chicks were gavaged with a 20× dose of commercial coccidial vaccine containing live Eimeria oocysts on day 14. Cecal contents were collected on day 42. High-throughput sequencing of the 16S rRNA gene was used to determine microbial diversity and composition. Coccidial vaccination to broilers reduced bacterial diversity (Shannon index) of the cecal microbiota. There was a significant interaction between the dietary additive and coccidial vaccination on the observed bacterial species number. Diets supplemented with B. subtilis increased bacterial species of non-vaccinated broilers but decreased bacterial species of vaccinated broilers. In contrast, diets supplemented with antibiotics reduced bacterial species of broilers from both groups. Interactions between dietary additive and coccidial vaccination were also observed on microbial composition. Vaccinated broilers fed the B. subtilis diet exhibited the lowest Firmicutes percentage and highest Bacteroidetes percentage within the microbial community. In addition, vaccinated broilers fed the B. subtilis diet exhibited the highest Rikenella microfusus percentage. From this study, the coccidial vaccination on the day of hatch reduced the microbial diversity of broilers at a later age. The inclusion of B. subtilis-probiotics in the feed of vaccinated broilers may reduce microbial diversity in cecal content by increasing the proportion of a predominant bacterial species, R. microfusus, in the microbial community.

Organic Acids Modulate Systemic Metabolic Perturbation Caused by Salmonella Pullorum Challenge in Early-Stage Broilers

The objectives of this study were to determine the protective effects of organic acids (OA) in broilers exposed to Salmonella Pullorum challenge at early stage and to explore the potential benefits of OA by metabolomics analysis. The treatment groups included non-challenged, S. Pullorum-challenged, challenged group supplemented with virginiamycin, challenged group supplemented with OA in drinking water, challenged group supplemented with OA in feed, and challenged group supplemented with OA in combination in drinking water and feed. Results showed that early Salmonella challenge induced an acute systemic infection of broilers in the starter phase, followed by the grower phase without triggering clinical signs. OA supplementation promoted growth during the grower phase, and while OA in water contributed more, the positive effects of OA in combination were comparable to those of virginiamycin supplementation in challenged birds. Furthermore, OA could modulate the systemic metabolic perturbation caused by challenge as it alleviated stress responses mediated by steroid hormone, potentially attenuated antioxidant or immune defense, and modified intestinal microbiota metabolism. These results show a metabolic mechanism that may partly explain the potential benefits of OA in Salmonella challenged birds, and may contribute to the use of OA to control or reduce S. Pullorum infection in farm animals.

Effects of multi-strain probiotic supplementation on intestinal microbiota, tight junctions, and inflammation in young broiler chickens challenged with Salmonella enterica subsp. enterica

Objective

This study assessed the effects of probiotics on cecal microbiota, gene expression of intestinal tight junction proteins, and immune response in the cecal tonsil of broiler chickens challenged with Salmonella enterica subsp. enterica.

Methods

One-day-old broiler chickens (n = 240) were randomly allocated to four treatments: negative control (Cont), multi-strain probiotic-treated group (Pro), Salmonella-infected group (Sal), and multi-strain probiotic-treated and Salmonella-infected group (ProSal). All chickens except those in the Cont and Pro groups were gavaged with 1×10⁸ cfu/mL of S. enterica subsp. enterica 4 days after hatching.

Results

Our results indicated that body weight, weight gain, and feed conversion ratio of birds were significantly reduced (p<0.05) by Salmonella challenge. Chickens challenged with Salmonella decreased cecal microbial diversity. Chickens in the Sal group exhibited abundant Proteobacteria than those in the Cont, Pro, and ProSal groups. Salmonella infection downregulated gene expression of Occludin, zonula occludens-1 (ZO1), and Mucin 2 in the jejunum and Occludin and Claudin in the ileum. Moreover, the Sal group increased gene expression of interferon-γ (IFN-γ), interleukin-6 (IL-6), IL-1β, and lipopolysaccharide-induced tumor necrosis factor-alpha factor (LITAF) and reduced levels of transforming growth factor-β4 and IL-10 compared with the other groups (p<0.05). However, chickens receiving probiotic diets increased Lactobacillaceae abundance and reduced Enterobacteriaceae abundance in the ceca. Moreover, supplementation with probiotics increased the mRNA expression of Occludin, ZO1, and Mucin 2 in the ileum (p<0.05). In addition, probiotic supplementation downregulated the mRNA levels of IFN-γ (p<0.05) and LITAF (p = 0.075) and upregulated IL-10 (p = 0.084) expression in the cecal tonsil.

Conclusion

The administration of multi-strain probiotics modulated intestinal microbiota, gene expression of tight junction proteins, and immunomodulatory activity in broiler chickens.

Evaluation of the Antimicrobial and Anti-inflammatory Properties of Bacillus-DFM (Norum™) in Broiler Chickens Infected With Salmonella Enteritidis

Restrictions of in-feed antibiotics use in poultry has pushed research toward finding appropriate alternatives such as Direct-Fed Microbials (DFM). In this study, previously tested Bacillus isolates (B. subtilis and B. amyloliquefaciens) were used to evaluate their therapeutic and prophylactic effects against Salmonella enterica serovar Enteritidis (S. Enteritidis) in broiler chickens. For this purpose, initial antibacterial activity of Bacillus-DFM (10⁴ spores/g or 10⁶ spores/g) against S. Enteritidis colonization in crop, proventriculus and intestine was investigated using an in vitro digestive model. Furthermore, to evaluate therapeutic and prophylactic effects of Bacillus-DFM (10⁴ spores/g) against S. Enteritidis colonization, altogether 60 (n = 30/group) and 30 (n = 15/group) 1-day-old broiler chickens were randomly allocated to either DFM or control group (without Bacillus-DFM), respectively. Chickens were orally gavaged with 10⁴ cfu of S. Enteritidis per chicken at 1-day old, and cecal tonsils (CT) and crop were collected 3 and 10 days later during the therapeutic study, whereas they were orally gavaged with 10⁷ cfu of S. Enteritidis per chicken at 6-day-old, and CT and crop were collected 24 h later from two independent trials during the prophylactic study. Serum superoxide dismutase (SOD), FITC-d and intestinal IgA levels were reported for both chicken studies, in addition cecal microbiota analysis was performed during the therapeutic study. DFM significantly reduced S. Enteritidis concentration in the intestine compartment, and in both proventriculus and intestine compartments as compared to the control when used at 10⁴ spores/g and 10⁶ spores/g, respectively (p < 0.05). DFM significantly reduced FITC-d and IgA as well as SOD and IgA levels (p < 0.05) compared to the control in therapeutic and prophylactic studies, respectively. Interestingly, in the therapeutic study, there were significant differences in bacterial community structure and predicted metabolic pathways between DFM and control. Likewise, phylum Actinobacteria and the genera Bifidobacterium, Roseburia, Proteus, and cc_115 were decreased, while the genus Streptococcus was enriched significantly in the DFM group as compared to the control (MetagenomeSeq, p < 0.05). Thus, the overall results suggest that the Bacillus-DFM can reduce S. Enteritidis colonization and improve the intestinal health in chickens through mechanism(s) that might involve the modulation of gut microbiota and their metabolic pathways.