New strategies to reduce diseases on organic broiler farms with special consideration of the gut microbiome ("ProBioHuhn")

Animal welfare, the gut microbiome and the prevalence of antibiotic resistance were studied longitudinally across four fattening cycles on 14 organic broiler farms, involving three fattening types (slower growing broilers, dual-purpose cockerels and male layer hybrids), and strategies to reduce disease were worked on with livestock farmers and advisory services. 

All fattening types exhibited a gut microbiome dominated by lactic acid bacteria. With increasing age, the composition and functional gene profile of the microbiome became more differentiated, with a clear transition after access to the free-range. 

Low resistance rates among commensal E. coli were associated with occasional on-farm use of antibiotics and the hatchery as a potential source of introduction. Thermotolerant Campylobacter spp. were found often at the end of the fattening period. They exhibited high resistance rates, which were, however, not associated with on-farm antibiotic use. 

For many animal welfare indicators, low average prevalences of severe impairments were observed. However, keel bone damage and comb injuries were more frequent in dual-purpose cockerels, while skin lesions on the trunk and footpad dermatitis were more common in broilers; the latter being also partly problematic in the other fattening types. No differences regarding endoparasite infection and fear behaviour was apparent. The extent of health impairments increased along the fattening period, but earlier critical time points were also observed, depending on the farm and the specific indicator. 

The heterogeneous feeding practices were frequently associated with deviations from recommended values, particularly regarding essential amino acids, minerals and feed structure. The crude fibre content influenced the gut microbiome in a fattening-type-specific manner, but to limited extent. 

Information and communication gaps regarding animal welfare issues were identified, and recommendations for action were developed; the implementation of the latter often led to improving animal welfare levels over the course of the project. Participatory advisory and exchange formats, which facilitate continuous collaboration and the joint development of solutions, were assessed as particularly conducive to improving animal welfare.

The final project report can be found here.

Dr. Margret Krieger

margret.krieger[at]uni-kassel[dot]de

Cheng YC, Camarinha-Silva A (2026). ProBioHuhn: Dynamic changes in the organic chicken gut microbiome driven by genetic and environmental variation. Annual Conference of the Association for General and Applied Microbiology, March 22–25, 2026, Berlin, Germany.

Cheng YC, Camarinha-Silva A (2026). ProBioHuhn: Temporal variation in the organic chicken gut microbiota and influencing factors. Annual Meeting of the Society for Nutritional Physiology. March 3–5, 2026, Göttingen, Germany

Korves AM, Grobbel M, Tenhagen BA (2026). Antimicrobial resistance of commensal and extended-spectrum β-lactamase/AmpC-producing Escherichia coli in organic meat chicken farms. Poultry Science, 105 (4), 106559. doi.org/10.1016/j.psj.2026.106559

Korves-Wilm AM, Stingl K, Krieger M, Grobbel M, Tenhagen B (2026). Longitudinal study of the prevalence and antimicrobial resistance of thermotolerant Campylobacter spp. in German organic broiler farms. Microbiol Spectr 14:e01012-26. doi.org/10.1128/spectrum.01012-26

Krieger M, Horbach S, Ebinghaus A, Knierim U (2026). Feeding management of different types of organic broiler chickens. IFOAM Animal Husbandry Alliance Conference 2026. Animal - Science Proceedings 17, 1–152. doi: 10.1016/j.anscip.2026.03.099

Krieger M, Horbach S, Ebinghaus A, Knierim U (2026). Changes in the footpads of organic broiler farms with different fattening systems over the course of fattening. 18th Scientific Conference on Organic Agriculture, March 3–6, 2026, Bonn. doi.org/10.48565/qysm-nt77

Krieger M, Horbach S, Ahlers C, Ebinghaus A, Knierim U (2026). Animal Welfare in Organically Raised Broiler Chickens—Results from the ProBioHuhn Project. Leipziger Blaue Hefte, Proceedings of the Leipzig Veterinary Congress, January 15–17, 2026, Volume 3, 329–332.

Cheng YC, Krieger M, Korves AM, Camarinha-Silva A (2025). The chicken gut microbiome in conventional and alternative production systems. Journal of Animal Science and Biotechnology, 16, 153. doi.org/10.1186/s40104-025-01293-8

Cheng YC, Camarinha-Silva A (2025). ProBioHuhn: Temporal and Spatial Variation of Gut Microbiota in Organic Chicken Farms in Germany. Annual Meeting of the Society for Nutritional Physiology. March 4–6, 2025, Göttingen.

Horbach S, Krieger M, Ebinghaus A, Knierim U (2025). Do slow-growing broiler hybrids, male layer hybrids, and dual-purpose roosters differ in their reactions to humans and unfamiliar objects? In: Current Research on Species-Appropriate Animal Husbandry 2025, Darmstadt, Board of Trustees for Technology and Construction in Agriculture, 189–199.

Korves AM, Sardogan B, Oelgeschläger K, Skladnikiewicz-Ziemer T, Umbach F, Krieger M, Flor M, Grobbel M, Käsbohrer A, Tenhagen BA, Binsker U (2025). Importance of chick origin in introducing multidrug-resistant and extended-spectrum beta-lactamase-producing Enterobacteriaceae into an organic broiler farm. Microbiol Res. Dec. 2025;301:128291. doi: 10.1016/j.micres.2025.128291

Bolten A, Krieger M, Knierim U (2024). Attitudes and Motivation Regarding Animal Welfare on Organic Broiler Farms. 34th Annual Conference of the Austrian Society for Agricultural Economics, September 19–20, 2024, University of Natural Resources and Life Sciences, Vienna.

Bolten A, Krieger M, Knierim U (2024). Attitudes and Motivation Regarding Animal Welfare on Organic Broiler Farms. 17th Scientific Conference on Organic Agriculture, March 5–8, 2024, Giessen. orgprints.org/id/eprint/53808/

Cheng YC, Camarinha-Silva A (2024). ProBioHuhn: Variations in the gut microbiome of three organic chicken types across different fattening periods and environments. The 75th EAAP Annual Meeting. September 1–5, 2024, Florence, Italy, p. 932

Gieseke D, Knierim U, Krieger M, Tiemann I, Hörning B (2024) Rearing young roosters in organic farming—which production system is best suited for the farm? 17th Scientific Conference on Organic Farming, March 5–8, 2024, Giessen. orgprints.org/id/eprint/53922/

Matoni L, Krieger M, Umbach F, Jung L, Ahlers C, Bolten A, Knierim U (2024). Preliminary results from the ProBioHuhn project on animal welfare in broiler hybrids, dual-purpose roosters, and laying hybrid roosters on organic broiler farms. 17th Scientific Conference on Organic Farming, March 5–8, 2024, Giessen. orgprints.org/id/eprint/53817/