Fig. 1

Sampling scheme of the study. From a cohort of 513 pigs, 103 initial RWA pigs were followed in detail along with 99 progressively enrolled pigs from an initial pool of 410 untreated buffer pigs. One hundred and three pigs were initially followed regardless of treatment (study pigs). For example, in week 2, 84 animals remained RWA, while 14 animals had received antibiotic treatment. In the buffer group, 42 animals had received antibiotic treatment by week 2 and where hence enrolled for sampling downstream, resulting in 140 total pigs registered in that week. Of these 140 pigs, 93 were successfully used for analyses, i.e. had full metadata and complete 16S and qPCR data. Due to logistics and internal movement of the pigs between farm units, some sampling weeks where either under-sampled (week 3) or disturbed by ongoing transfer of pigs between units (weeks 12, 24 and 26) and were hence excluded from statistical testing