Raw data for Study 1 and 2 and metadata

Due to the evolution of welfare laws and the search for novel methods to study pig microbiota, the development of precise and non-invasive sampling methods is key to studying the microbial communities that inhabit the gut of the pigs. Administering swallowable devices to pigs is always a challenge due to factors like anatomy,specific materials required, and the need to restrain the animals. In this study, we describe a step-by-step protocol on how to administrate a Capsule for Sampling (CapSa), a biocompatible non-invasive device to study pig’s microbiota without harming the animals. The validation of the administering protocol was done through two different studies. In study 1, a total of 92 Swiss Large White pigs (from 6.45 to 71.3 kg BW) were administrated two capsules each and monitored for the following three days for capsule retrieval. On day 3, all pigs were euthanised to locate the missing capsules directly from the gastrointestinal tract of the pig. In study 2, 16 Swiss Large White pigs were selected at weaning and administered CapSas at five different timepoints (T1: 52 ± 3; T2: 70 ± 3; T3: 83 ± 3; T4: 110 ± 3; T5: 126 ± 3 days of age). To retrieve the capsules in the feces, pigs were monitored during three days post-administration. At T5, pigs were slaughtered and missing capsules were searched in the gastrointestinal tract. The protocol entails acclimation of the animals, housing modifications, administration of a prokinetic agent (prucalopride) to facilitate gastric emptying and oesophageal intubations to overcome challenges related to administration, gastric blockage and retrieval of the capsules.The present study describes a valid procedure to administer CapSa or any other swallowable devices in pigs. Moreover, this procedure is applicable for singular as well as repetitive administrations over the lifespan of the pigs.