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J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Campylobacter jejuni is a leading foodborne pathogen that commonly colonizes the intestinal tract of broiler chickens and represents a significant food safety concern. Dietary intervention may provide a practical approach to modulate the gut microbiota and reduce pathogen colonization. This study investigated the effects of oat supplementation on C. jejuni colonization and dissemination, cecal microbiota and predicted functions, and cecal short-chain fatty acids (SCFAs) and ileal amino acid profiles during early-life infection in broiler chickens. One-day-old Ross 308 broiler chickens were fed a basal diet or diets containing 10% oat (MDF) or 20% oat (HDF) and orally infected with C. jejuni at 2 days of age. C. jejuni loads in the cecum, jejunum, liver, and spleen were quantified by culture. Cecal microbiota composition and predicted functional profiles were characterized by shotgun metagenomic sequencing, while cecal SCFAs and ileal amino acids were quantified at 21 and 35 dpi using gas chromatography and an automatic amino acid analyzer, respectively. Oat supplementation reduced intestinal C. jejuni loads and limited dissemination to the liver and spleen, with the MDF diet reducing cecal loads by up to 3.3 log10 CFU\/g at 35 dpi (p &lt; 0.05). Infection altered cecal microbial diversity and community structure, while oat supplementation modified these infection-associated microbial patterns, with MDF showing the most consistent effects. Differential abundance analysis identified changes in taxa, including Bacteroides, Parabacteroides, and Phocaeicola, together with changes in predicted functions related to motility and chemotaxis, iron acquisition, and dormancy\/sporulation. These microbial changes coincided with alterations in cecal isobutyrate and ileal amino acids, particularly glutamate, serine, proline, and aspartate, in MDF-fed infected chickens. Overall, MDF supplementation was most consistently associated with reduced C. jejuni colonization and dissemination and concurrent changes in the developing cecal microbial and metabolic profiles.<\/jats:p>","DOI":"10.3390\/ijms27198607","type":"journal-article","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T16:50:54Z","timestamp":1790614254000},"page":"8607","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Early-Life Oat Supplementation Is Associated with Altered Cecal Microbiota and Microbial Metabolic Profiles and Reduced Campylobacter jejuni Colonization in Broiler Chickens"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1030-7324","authenticated-orcid":false,"given":"Bereket","family":"Dessalegn","sequence":"first","affiliation":[{"name":"Clinical Unit for Poultry Medicine, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine, 1210 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3182-9810","authenticated-orcid":false,"given":"Motuma","family":"Debelo","sequence":"additional","affiliation":[{"name":"Clinical Unit for Poultry Medicine, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine, 1210 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Nicola","family":"Palmieri","sequence":"additional","affiliation":[{"name":"Clinical Unit for Poultry Medicine, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine, 1210 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6913-219X","authenticated-orcid":false,"given":"K\u00e1roly","family":"Dublecz","sequence":"additional","affiliation":[{"name":"Institute of Physiology and Nutrition, Georgikon Campus, Hungarian University of Agriculture and Life Science, 8360 Keszthely, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6991-0120","authenticated-orcid":false,"given":"Michael","family":"Hess","sequence":"additional","affiliation":[{"name":"Clinical Unit for Poultry Medicine, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine, 1210 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0843-2089","authenticated-orcid":false,"given":"Wageha A.","family":"Awad","sequence":"additional","affiliation":[{"name":"Clinical Unit for Poultry Medicine, Clinical Department for Farm Animals and Food System Transformation, University of Veterinary Medicine, 1210 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Al Hakeem, W.G., Fathima, S., Shanmugasundaram, R., and Selvaraj, R.K. (2022). Campylobacter jejuni in Poultry: Pathogenesis and Control Strategies. Microorganisms, 10.","DOI":"10.3390\/microorganisms10112134"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Veronese, P., and Dodi, I. (2024). Campylobacter jejuni\/coli Infection: Is It Still a Concern?. Microorganisms, 12.","DOI":"10.3390\/microorganisms12122669"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"European Food Safety Authority (EFSA), and European Centre for Disease Prevention and Control (ECDC) (2025). The European Union One Health 2024 Zoonoses Report. EFSA J., 23, e9759.","DOI":"10.2903\/j.efsa.2025.9759"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"584","DOI":"10.15585\/mmwr.mm7326a1","article-title":"Reported Incidence of Infections Caused by Pathogens Transmitted Commonly Through Food: Impact of Increased Use of Culture-Independent Diagnostic Tests-Foodborne Diseases Active Surveillance Network, 1996\u20132023","volume":"73","author":"Shah","year":"2024","journal-title":"MMWR. Morb. Mortal. Wkly. Rep."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.cmi.2015.11.019","article-title":"Campylobacteriosis: The Role of Poultry Meat","volume":"22","author":"Skarp","year":"2016","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"105368","DOI":"10.1016\/j.psj.2025.105368","article-title":"In-Ovo Stimulation Trains Innate Immunity to Mitigate Campylobacter jejuni in Broiler Chickens","volume":"104","author":"Hickey","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1186\/s13099-025-00760-x","article-title":"Effects of Exogenous Protease Supplementation of Diets Containing Animal Proteins or Not on Campylobacter jejuni Colonization and on the Intestinal Microbiota of Broiler Chickens","volume":"17","author":"Chagneau","year":"2025","journal-title":"Gut Pathog."},{"key":"ref_8","first-page":"100197","article-title":"An Updated Assessment of the Effect of Control Options to Reduce Campylobacter Concentrations in Broiler Caeca on Human Health Risk in the European Union","volume":"21","author":"Nauta","year":"2022","journal-title":"Microb. Risk Anal."},{"key":"ref_9","first-page":"4989","article-title":"Approaches to Prevent and Control Campylobacter spp. Colonization in Broiler Chickens: A Review","volume":"28","author":"Shehata","year":"2020","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Al Hakeem, W.G., Acevedo Villanueva, K.Y., and Selvaraj, R.K. (2023). The Development of Gut Microbiota and Its Changes Following C. jejuni Infection in Broilers. Vaccines, 11.","DOI":"10.3390\/vaccines11030595"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Patuzzi, I., Orsini, M., Cibin, V., Petrin, S., Mastrorilli, E., Tiengo, A., Gobbo, F., Catania, S., Barco, L., and Ricci, A. (2021). The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time. Microorganisms, 9.","DOI":"10.3390\/microorganisms9020221"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Awad, W.A., Mann, E., Dzieciol, M., Hess, C., Schmitz-Esser, S., Wagner, M., and Hess, M. (2016). Age-Related Differences in the Luminal and Mucosa-Associated Gut Microbiome of Broiler Chickens and Shifts Associated with Campylobacter jejuni Infection. Front. Cell. Infect. Microbiol., 6.","DOI":"10.3389\/fcimb.2016.00154"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"5372","DOI":"10.1128\/AEM.69.9.5372-5379.2003","article-title":"Effect of Campylobacter-Specific Maternal Antibodies on Campylobacter jejuni Colonization in Young Chickens","volume":"69","author":"Sahin","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1186\/s40168-018-0477-5","article-title":"The Effect of the Timing of Exposure to Campylobacter jejuni on the Gut Microbiome and Inflammatory Responses of Broiler Chickens","volume":"6","author":"Connerton","year":"2018","journal-title":"Microbiome"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"8605","DOI":"10.1128\/AEM.01090-10","article-title":"Biosecurity-Based Interventions and Strategies to Reduce Campylobacter spp. on Poultry Farms","volume":"77","author":"Newell","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e30","DOI":"10.1637\/9248.1","article-title":"Investigation of the Presence and Protective Effects of Maternal Antibodies Against Campylobacter jejuni in Chickens","volume":"5","author":"Cawthraw","year":"2010","journal-title":"Avian Dis. Dig."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Szott, V., Reichelt, B., Friese, A., and Roesler, U. (2022). A Complex Competitive Exclusion Culture Reduces Campylobacter jejuni Colonization in Broiler Chickens at Slaughter Age In Vivo. Vet. Sci., 9.","DOI":"10.3390\/vetsci9040181"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/s41579-022-00833-7","article-title":"Microbiota-Mediated Colonization Resistance: Mechanisms and Regulation","volume":"21","author":"Pickard","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Haems, K., Strubbe, D., Van Rysselberghe, N., Rasschaert, G., Martel, A., Pasmans, F., and Garmyn, A. (2024). Role of Maternal Antibodies in the Protection of Broiler Chicks against Campylobacter Colonization in the First Weeks of Life. Animals, 14.","DOI":"10.3390\/ani14091291"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1080\/1828051X.2024.2310588","article-title":"The Effect of Campylobacter jejuni Challenge on the Ileal Microbiota and Short-Chain Fatty Acids at 28 and 35 Days of Age","volume":"23","author":"Cason","year":"2024","journal-title":"Ital. J. Anim. Sci."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"102265","DOI":"10.1016\/j.psj.2022.102265","article-title":"Modified Dietary Fiber from Cassava Pulp Affects the Cecal Microbial Population, Short-Chain Fatty Acid, and Ammonia Production in Broiler Chickens","volume":"102","author":"Okrathok","year":"2023","journal-title":"Poult. Sci."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e0206523","DOI":"10.1128\/spectrum.02065-23","article-title":"Microbiota-Accessible Fiber Activates Short-Chain Fatty Acid and Bile Acid Metabolism to Improve Intestinal Mucus Barrier in Broiler Chickens","volume":"12","author":"Yang","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1038\/nrmicro1817","article-title":"Polysaccharide Utilization by Gut Bacteria: Potential for New Insights from Genomic Analysis","volume":"6","author":"Flint","year":"2008","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2583","DOI":"10.1111\/1750-3841.16580","article-title":"Combined Effect of Metabolites Produced by a Modified Lactobacillus casei and Berry Phenolic Extract on Campylobacter and Microbiome in Chicken Cecum Contents","volume":"88","author":"Tabashsum","year":"2023","journal-title":"J. Food Sci."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Wu, G., Tang, X., Fan, C., Wang, L., Shen, W., Ren, S., Zhang, L., and Zhang, Y. (2022). Gastrointestinal Tract and Dietary Fiber Driven Alterations of Gut Microbiota and Metabolites in Durco \u00d7 Bamei Crossbred Pigs. Front. Nutr., 8.","DOI":"10.3389\/fnut.2021.806646"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"5474","DOI":"10.1002\/jsfa.13378","article-title":"Supplementation of Lactobacillus-Fermented Rapeseed Meal in Broiler Diet Reduces Campylobacter jejuni Cecal Colonization and Limits the l-Tryptophan and l-Histidine Biosynthesis Pathways","volume":"104","author":"Khattak","year":"2024","journal-title":"J. Sci. Food Agric."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1637\/aviandiseases-D-23-00003","article-title":"The Role of Dietary Supplementation of Yeast Cell Walls in Response to a Campylobacter jejuni Inoculation in Broiler Chickens","volume":"67","author":"Munoz","year":"2023","journal-title":"Avian Dis."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Olson, E.G., Dittoe, D.K., Chatman, C.C., Majumder, E.L.W., and Ricke, S.C. (2024). Campylobacter jejuni and Casein Hydrolysate Addition: Impact on Poultry in Vitro Cecal Microbiota and Metabolome. PLoS ONE, 19.","DOI":"10.1371\/journal.pone.0303856"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"115217","DOI":"10.1016\/j.anifeedsci.2022.115217","article-title":"Efficacy of Scrophularia Striata Hydroalcoholic Extract and Mannan-Oligosaccharide on Productive Performance, Intestinal Bacterial Community, and Immunity in Broiler Chickens after Infection with Campylobacter jejuni","volume":"285","author":"Rostami","year":"2022","journal-title":"Anim. Feed Sci. Technol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Singh, A.K., and Kim, W.K. (2021). Effects of Dietary Fiber on Nutrients Utilization and Gut Health of Poultry: A Review of Challenges and Opportunities. Animals, 11.","DOI":"10.3390\/ani11010181"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"4776","DOI":"10.1016\/j.psj.2020.06.061","article-title":"In Ovo Supplementation of Chitooligosaccharide and Chlorella Polysaccharide Affects Cecal Microbial Community, Metabolic Pathways, and Fermentation Metabolites in Broiler Chickens","volume":"99","author":"Zhang","year":"2020","journal-title":"Poult. Sci."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"105207","DOI":"10.1016\/j.psj.2025.105207","article-title":"Research Note: Complex Evaluation of Whole Oats and Dehulled Oats as Feedstuffs for Broiler Chickens","volume":"104","author":"Such","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Fabiano, G.A., Shinn, L.M., and Antunes, A.E.C. (2023). Relationship between Oat Consumption, Gut Microbiota Modulation, and Short-Chain Fatty Acid Synthesis: An Integrative Review. Nutrients, 15.","DOI":"10.3390\/nu15163534"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Joyce, S.A., Kamil, A., Fleige, L., and Gahan, C.G.M. (2019). The Cholesterol-Lowering Effect of Oats and Oat Beta Glucan: Modes of Action and Potential Role of Bile Acids and the Microbiome. Front. Nutr., 6.","DOI":"10.3389\/fnut.2019.00171"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Li, X., Wu, Y., Duan, R., Yu, H., Liu, S., and Bao, Y. (2024). Research Progress in the Extraction, Structural Characteristics, Bioactivity, and Commercial Applications of Oat \u03b2-Glucan: A Review. Foods, 13.","DOI":"10.3390\/foods13244160"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"103607","DOI":"10.1016\/j.psj.2024.103607","article-title":"Systematic Review on Microbiome-Related Nutritional Interventions Interfering with the Colonization of Foodborne Pathogens in Broiler Gut to Prevent Contamination of Poultry Meat","volume":"103","author":"Mekonnen","year":"2024","journal-title":"Poult. Sci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"101922","DOI":"10.1016\/j.psj.2022.101922","article-title":"Research Note: The Gut Microbiota Varies with Dietary Fiber Levels in Broilers","volume":"101","author":"Qiu","year":"2022","journal-title":"Poult. Sci."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Zhang, C., Hao, E., Chen, X., Huang, C., Liu, G., Chen, H., Wang, D., Shi, L., Xuan, F., and Chang, D. (2023). Dietary Fiber Level Improve Growth Performance, Nutrient Digestibility, Immune and Intestinal Morphology of Broilers from Day 22 to 42. Animals, 13.","DOI":"10.3390\/ani13071227"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2259","DOI":"10.3382\/ps\/pew151","article-title":"Campylobacter jejuni Colonization Promotes the Translocation of Escherichia coli to Extra-Intestinal Organs and Disturbs the Short-Chain Fatty Acids Profiles in the Chicken Gut","volume":"95","author":"Awad","year":"2016","journal-title":"Poult. Sci."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"65","DOI":"10.3920\/JAAN2021.0003","article-title":"A Probiotic and Mixed-Enzymes Combination Reduces the Inflammatory Response, Faecal Shedding and Systemic Spread of Campylobacter jejuni in Broilers","volume":"9","author":"Gibbs","year":"2021","journal-title":"J. Appl. Anim. Nutr."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Thibodeau, A., Fravalo, P., Yergeau, E., Arsenault, J., Lahaye, L., and Letellier, A. (2015). Chicken Caecal Microbiome Modifications Induced by Campylobacter jejuni Colonization and by a Non-Antibiotic Feed Additive. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0131978"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"wrae133","DOI":"10.1093\/ismejo\/wrae133","article-title":"Diversity Alone Does Not Reliably Indicate the Healthiness of an Animal Microbiome","volume":"18","author":"Williams","year":"2024","journal-title":"ISME J."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Hou, L., Sun, B., and Yang, Y. (2020). Effects of Added Dietary Fiber and Rearing System on the Gut Microbial Diversity and Gut Health of Chickens. Animals, 10.","DOI":"10.3390\/ani10010107"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Al Hakeem, W.G., Cason, E.E., Adams, D., Fathima, S., Shanmugasundaram, R., Lourenco, J., and Selvaraj, R.K. (2024). Characterizing the Effect of Campylobacter jejuni Challenge on Growth Performance, Cecal Microbiota, and Cecal Short-Chain Fatty Acid Concentrations in Broilers. Animals, 14.","DOI":"10.3390\/ani14030473"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Pang, J., Beyi, A.F., Looft, T., Zhang, Q., and Sahin, O. (2023). Fecal Microbiota Transplantation Reduces Campylobacter jejuni Colonization in Young Broiler Chickens Challenged by Oral Gavage but Not by Seeder Birds. Antibiotics, 12.","DOI":"10.3390\/antibiotics12101503"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s42523-023-00287-z","article-title":"Dietary Novel Alkaline Protease from Bacillus licheniformis Improves Broiler Meat Nutritional Value and Modulates Intestinal Microbiota and Metabolites","volume":"6","author":"Yi","year":"2024","journal-title":"Anim. Microbiome"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Wassie, T., Cheng, B., Zhou, T., Gao, L., Lu, Z., Xie, C., and Wu, X. (2022). Microbiome-Metabolome Analysis Reveals Alterations in the Composition and Metabolism of Caecal Microbiota and Metabolites with Dietary Enteromorpha Polysaccharide and Yeast Glycoprotein in Chickens. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.996897"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"103897","DOI":"10.1016\/j.psj.2024.103897","article-title":"Assessment of Probiotic Bacillus velezensis Supplementation to Reduce Campylobacter jejuni Colonization in Chickens","volume":"103","author":"Cui","year":"2024","journal-title":"Poult. Sci."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"e00380-17","DOI":"10.1128\/IAI.00380-17","article-title":"Influence of the Gut Microbiota Composition on Campylobacter jejuni Colonization in Chickens","volume":"85","author":"Han","year":"2017","journal-title":"Infect. Immun."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Rawash, M.A., Farkas, V., Such, N., Mez\u0151laki, \u00c1., Menyh\u00e1rt, L., P\u00e1l, L., Csit\u00e1ri, G., and Dublecz, K. (2023). Effects of Barley- and Oat-Based Diets on Some Gut Parameters and Microbiota Composition of the Small Intestine and Ceca of Broiler Chicken. Agriculture, 13.","DOI":"10.3390\/agriculture13010169"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Thiam, M., Wang, Q., Barreto S\u00e1nchez, A.L., Zhang, J., Ding, J., Wang, H., Zhang, Q., Zhang, N., Wang, J., and Li, Q. (2022). Heterophil\/Lymphocyte Ratio Level Modulates Salmonella Resistance, Cecal Microbiota Composition and Functional Capacity in Infected Chicken. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.816689"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1152\/ajpgi.00319.2017","article-title":"Protein fermentation in the gut; implications for intestinal dysfunction in humans, pigs, and poultry","volume":"315","author":"Gilbert","year":"2018","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"lxad312","DOI":"10.1093\/jambio\/lxad312","article-title":"General Media over Enrichment Media Supports Growth of Campylobacter jejuni and Maintains Poultry Cecal Microbiota Enabling Translatable in Vitro Microbial Interaction Experiments","volume":"135","author":"Olson","year":"2024","journal-title":"J. Appl. Microbiol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Hankel, J., Jung, K., Kuder, H., Keller, B., Keller, C., Galvez, E., Strowig, T., and Visscher, C. (2019). Caecal Microbiota of Experimentally Campylobacter jejuni-Infected Chickens at Different Ages. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.02303"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s42003-022-03239-6","article-title":"Growth Promotion and Antibiotic Induced Metabolic Shifts in the Chicken Gut Microbiome","volume":"5","author":"Plata","year":"2022","journal-title":"Commun. Biol."},{"key":"ref_56","unstructured":"Aviagen (2019). Ross 308 Nutrition Specifications, Aviagen."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"13531","DOI":"10.1038\/s41598-025-97672-2","article-title":"Exposure of Broiler Chickens to Deoxynivalenol and Campylobacter jejuni Induces Substantial Changes in Intestinal Gene Expression","volume":"15","author":"Awad","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_58","unstructured":"Andrews, S. (2026, May 15). FastQC: A Quality Control Tool for High Throughput Sequence Data, Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"e107","DOI":"10.1002\/imt2.107","article-title":"Ultrafast One-Pass FASTQ Data Preprocessing, Quality Control, and Deduplication Using Fastp","volume":"2","author":"Chen","year":"2023","journal-title":"iMeta"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"btad728","DOI":"10.1093\/bioinformatics\/btad728","article-title":"Hostile: Accurate Decontamination of Microbial Host Sequences","volume":"39","author":"Constantinides","year":"2023","journal-title":"Bioinformatics"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved Metagenomic Analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Tewelde, K.G., Kiss, B., Csisz\u00e9r, T., P\u00e1l, L., Such, N., Bartos, \u00c1., and Dublecz, K. (2026). Feeding Low- and High-Fibre Sunflower Meal to Broiler Chickens\u2014Effects of Inclusion Rate and Age of Birds on the Production Traits, Carcass Composition, Nutrient Digestibility, Gut Viscosity, and Caecal Short-Chain Fatty Acid Content. Animals, 16.","DOI":"10.3390\/ani16020162"},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Such, N., Mez\u0151laki, \u00c1., Tewelde, K.G., P\u00e1l, L., Horv\u00e1th, B., Po\u00f3r, J., and Dublecz, K. (2024). Feeding Sunflower Meal with Pullets and Laying Hens Even at a 30% Inclusion Rate Does Not Impair the Ileal Digestibility of Most Amino Acids. Front. Vet. Sci., 11.","DOI":"10.3389\/fvets.2024.1347374"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1038\/s41592-025-02923-9","article-title":"MaAsLin 3: Refining and Extending Generalized Multivariable Linear Models for Meta-Omic Association Discovery","volume":"23","author":"Nickols","year":"2026","journal-title":"Nat. Methods"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/19\/8607\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T04:16:43Z","timestamp":1790655403000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/19\/8607"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,26]]},"references-count":64,"journal-issue":{"issue":"19","published-online":{"date-parts":[[2026,10]]}},"alternative-id":["ijms27198607"],"URL":"https:\/\/doi.org\/10.3390\/ijms27198607","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,26]]}}}