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ARS Home Plains Area College Station, Texas Southern Plains Agricultural Research Center Food and Feed Safety Research Research





- Kogut, Michael - Mike
- Byrd Ii, James - Allen
- Genovese, Kenneth - Ken
- Poole, Toni
- Swaggerty, Christina - Christi
- 2023
- 2022
- 2021
- Publications
- Food Safety, (Animal and Plant Products) (108)

Research Project: Immunological and Practical Approaches to Manipulate the Ecological Niches and Reduce Foodborne Pathogens in Poultry **Location:
                            Food and Feed Safety Research** 2022 Annual Report **Objectives**
                                

Objective 1:  Characterize the immune-metabolic signatures of the host:pathogen interactome following Salmonella and Campylobacter infection in the cecum that transforms host defenses from 'disease resistance' to 'disease tolerance' and mitigates long-term persistent intestinal infection in broilers chickens.
Objective 2:  Determine the intestinal kinome profile and antimicrobial resistance patterns associated with Salmonella and Campylobacter colonization in broiler chickens with high or low concentrations of these foodborne pathogens.
Objective 3:  Develop new strategies (including immunologic training) to reduce foodborne pathogens by targeting neonatal poultry gut health via stimulating the development and maturation of the intestinal immune system.
Sub-objective 3.A: Deliver non-nutritional dietary feed additives to breeder chickens (hens and roosters) to induce /enhance trans-generational trained innate immunity as both a prophylactic and as a therapeutic agent in neonatal chickens against foodborne pathogens.
Sub-objective 3.B: Evaluate a novel innate immune therapeutic as an alternative to antibiotics that targets innate immunity based on the ability of the immune system to detect bacterial viability through the recognition of viability-associated microbial associated molecular patterns (vita-MAMPs).
Sub-objective 3.C: Develop a novel immunogenic probiotic to improve neonatal poultry gut health and stimulate the development and maturation of the intestinal immune system.
Objective 4:  Develop intervention strategies and alternatives to antibiotics to reduce the bacterial load of foodborne pathogens during pre-harvest poultry production.
Objective 5:  Investigate the interaction between yeast and fungi and foodborne bacteria to determine their role as commensals, inhibitors, or their use as alternatives to antibiotics as pre-and probiotics. **Approach**
                                

Despite control efforts, foodborne illnesses due to Salmonella continues to impact the consumer.  Poultry are commonly identified as a major source of Salmonella.  We will take a multi-faceted approach to develop urgently needed new control strategies against Salmonella, and our integrated approaches will identify and evaluate applied and basic pre-harvest approaches to reduce Salmonella in poultry.  Based on previous research and collaborations with industry, we will identify and/or modify management practices to reduce foodborne pathogen load and will address environmental conditions associated with higher risks that enable pathogen survival and growth.  Direct and indirect modulation of gut microbiome-innate immune interactome will be evaluated to determine which natural host mechanisms can be exploited to strengthen therapeutic benefit.  Modulating the innate immune response has considerable potential to induce a profound and rapid cross-protection against multiple serovars of foodborne pathogens.  Salmonella have evolved a unique survival strategy in poultry that minimizes host defenses during the initial infection and then exploits and/or induces a dramatic immunometabolic reprogramming in the cecum that alters the host defense to induce a disease tolerance.  Therefore, a component of the research will concentrate on modulatory mechanisms (vaccination, pro- and postbiotic) to counter these reprogramming mechanisms and lead to the development of novel immunometabolic therapeutic strategies.  This research will enhance the microbiological safety of poultry and reduce potential antimicrobial resistance in animal agriculture and public health. **Progress Report**
                                

Work under Objective 3 in fiscal year (FY) 2022 provided evidence that segmented filamentous bacteria (SFB) may be a useful probiotic to improve chicken health in early life. SFB are a keystone taxon that intimately binds to the intestine of the chicken. Project work evaluated the probiotic potential of SFB and found that it significantly reduced Salmonella load in chickens in a T helper 17-mediated manner. T helper 17 cells are predominantly in the intestine and their function is an important part of the poultry immune system. Work under Objectives 1 and 2 identified crucial elements of the intestinal mucosal immune system that enhance the ability of birds to fight off pathogenic microbes while maintaining a state of tolerance to the diverse and beneficial intestinal microbes. Under Objective 4, routes by which Salmonella infects turkeys and potentially contaminates ground turkey were identified; the findings have significant food safety implications in commercial turkey production because the data suggest that Salmonella can cause infection in turkeys via routes other than fecal-oral. This research is of high interest to the poultry industry given its promise of developing pre-harvest intervention strategies that can be incorporated into commercial turkey production practices to enhance microbial food safety. Under Objective 5, by using a novel tag bacterial diversity amplification method to determine the diversity within the intestinal microbiota of poultry under commercial conditions, we found slight differences in the bacterial profile in the ceca and dramatic differences in the fungal profiles within the ceca of 30 to 40-day-old broilers. **Accomplishments**
                                

1. Nutritional mediated induction of immunity in breeder hens increases immune protection in chicks. Young chicks are susceptible to many different pathogens, including Salmonella, during the first week after hatch. Salmonella colonizes the intestinal tract of young poultry and is one of the leading causes of human foodborne illness. As poultry producers move away from the routine use of antibiotics, there is a growing need to identify alternative approaches to protect and boost the natural immune responsiveness of newly hatched chicks. ARS researchers at College Station, Texas, working closely with industry and academic partners, showed it was possible to confer transgenerational protection against Salmonella colonization in young chicks by feeding the parent hens a diet supplemented with a blend of natural botanicals. This accomplishment demonstrated that by feeding hens a natural antibiotic alternative, the hens produce chicks having a more robust immune response and that are more resistant to colonization by Salmonella. The work represents a significant contribution to the goal of producing poultry products for the U.S. consumer that are microbiologically safe. 2. Non-fecal-oral routes of Salmonella infection in turkeys. As with other poultry species reared commercially for food production, young turkeys are susceptible to colonization by a number of bacterial species that can cause food poisoning in humans if the meat products are contaminated during processing. The turkey industry is in critical need of effective strategies to assure that turkey food products reaching the consumer are microbiologically safe. ARS researchers at College Station, Texas, working closely with key turkey industry scientists and managers, established the various routes by which the growing birds can be infected by Salmonella, one of the more important problematic bacteria. This accomplishment is important because understanding how growing turkeys can be infected by dangerous microorganisms is critical to development of new technology and/or management strategies that will assure microbiological safety of turkey food products. The industry and relevant U.S. regulatory agencies are aware of and highly supportive of this work. 3. Anti-inflammatory mechanism of feeding sub-therapeutic bacitracin to broiler chickens. For decades, poultry farmers fed low levels of antibiotic growth promoters (AGPs) to chickens because the antibiotics seemed to cause increased growth in a shorter amount of time. Although no one understood exactly why antibiotics provided this effect, it was not because the antibiotics killed germs; the doses given to the chicks were much less than the amount needed to kill pathogenic microorganisms. Because consumers have demanded the removal of antibiotics from animal feed to prevent antibiotic resistance in germs that infect humans, there is need for development of alternatives to antibiotics that provide the growth promoting aspects without drug resistance. One of the great stumbling blocks in identifying new alternatives to antibiotics has been the lack of knowledge of how they increased growth of the chicks. ARS researchers at College Station, Texas, identified a potential mechanism of the growth promoting abilities of AGPs: suppressing immune function in the gut. Now that we potentially understand how AGPs work, new alternatives can hopefully be developed that will use these same mechanisms without harming the ability of the chicks to fight infections. These results are important to the poultry industry and to U.S. consumers in providing a new approach to managing harmful bacteria in meat products. 4. Development of a diet-induced low grade chronic inflammatory model in boiler chickens. Until recently, poultry producers have relied on antibiotics to compensate for potential poor husbandry and management issues. However, with the removal of growth-promoting antimicrobials in poultry feed, intestinal inflammation has become more of an issue worldwide. For the poultry producer, chronic low-grade intestinal inflammation has a negative impact on the productivity of the poultry operation by impairing the birds' ability to absorb nutrients and reach 100% of their growth and genetic potential. Although chronic intestinal inflammation can be induced by a number of environmental factors, diet is the main cause given some feed ingredients, such as soybean meal, are potent stimulators of the intestinal immune response. Research into understanding and regulating intestinal inflammation in poultry has been limited by two factors: development of a dependable in vivo model, and identification of non-invasive biomarkers. ARS researchers at College Station, Texas, characterized for the first time two in vivo models of chronic gut inflammation and identified novel inflammation-specific molecules present in the serum and feces that indicate an ongoing inflammatory response. The models will allow studies into methods of controlling inflammation, while the biomarkers will allow for in-the-field diagnosis of inflammation in intensive poultry farming; the work is a major contribution to poultry microbial food safety research. **Review Publications**
                            *Bortoluzzi, C., Lahaye, L., Oxford, J., Detzler, D., Eyng, C., Barbieri, N.L., Santin, E., Kogut, M.H. 2021. Protected organic acids and essential oils for broilers raised under field conditions: Intestinal health biomarkers and cecal microbiota. Frontiers in Physiology. 12. Article 722339. https://doi.org/10.3389/fphys.2021.722339.*
                                *Swaggerty, C.L., Bortoluzzi, C., Lee, A., Eyng, C., Dal Pont, G., Kogut, M.H. 2021. Potential replacements for antibiotic growth promoters in poultry: Interactions at the gut level and their impact on host immunity. Advances in Experimental Medicine and Biology. 1354:145-159. https://doi.org/10.1007/978-3-030-85686-1_8.*
                                *Kogut, M.H. 2021. Immunophysiology of the avian immune system. In: Scanes, C.G., Dridi, S., editors. Sturkie's Avian Physiology. 7th edition. Cambridge, MA: Academic Press. p. 591-609.*
                                *Emami, N., Greene, E., Kogut, M.H., Dridi, S. 2021. Heat stress and feed restriction distinctly affect performance, carcass and meat yield, intestinal integrity and inflammatory (chemo) cytokines in broiler chickens. Frontiers in Physiology. 12. Article 707757. https://doi.org/10.3389/fphys.2021.707757.*
                                *Redweik, G.A., Kogut, M.H., Arsenault, R.J., Lyte, M., Mellata, M. 2021. Reserpine improves Enterobacteriaceae resistance in chicken intestine via neuro-immunometabolic signaling and MEK1/2 activation. Communications Biology. 4. Article 1359. https://doi.org/10.1038/s42003-021-02888-3.*
                                *Shanmugasundaram, R., Acevedo-Villanueva, K., Akerele, G., Mortada, M., Selvaraj, R.K., Applegate, T.J., Kogut, M.H. 2021. Effects of Salmonella enterica ser. Enteritidis and Heidelberg on host CD4+CD25+ regulatory T cell suppressive immune responses in chickens. PLoS ONE. 16(11). Article e0260280. https://doi.org/10.1371/journal.pone.0260280.*
                                *Zhao, D., Farnell, M.B., Kogut, M.H., Genovese, K.J., Chapkin, R.S., Davidson, L.A., Berghman, L.R., Farnell, Y.Z. 2022. From crypts to enteroids: Establishment and characterization of avian intestinal organoids. Poultry Science. 101(3). Article 101642. https://doi.org/10.1016/j.psj.2021.101642.*
                                *Swaggerty, C.L., Byrd II, J.A., Arsenault, R.J., Perry, F., Johnson, C.N., Genovese, K.J., He, H., Kogut, M.H., Piva, A., Grilli, E. 2022. A blend of microencapsulated organic acids and botanicals reduces necrotic enteritis via specific signaling pathways in broilers. Poultry Science. 101(4). Article 101753. https://doi.org/10.1016/j.psj.2022.101753.*
                                *Kogut, M.H. 2022. Role of diet-microbiota interactions in precision nutrition of the chicken: facts, gaps, and new concepts. Poultry Science. 101(3). Article 101673. https://doi.org/10.1016/j.psj.2021.101673.*
                                *Kogut, M.H., Genovese, K.J., Byrd II, J.A., Swaggerty, C.L., He, L.H., Farnell, Y., Arsenault, R. 2022. Chicken-specific kinome analysis of early host immune signaling pathways in the cecum of newly hatched chicks infected with Salmonella enterica serovar Enteriditis. Frontiers in Cellular and Infection Microbiology. 12. Article 899395. https://doi.org/10.3389/fcimb.2022.899395.*
                                *Crippen, T.L., Singh, B., Anderson, R.C., Sheffield, C.L. 2022. Adult Alphitobius diaperinus microbial community during broiler production and in spent litter after stockpiling. Microorganisms. 10(1). Article 175. https://doi.org/10.3390/microorganisms10010175.*


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