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. colishort forEscherichia 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.