Chiara Vaggi (Centre for Animal Nutrition and Welfare, Clinical Department for Farm Animals and Food System Transformation, Departments, University of Veterinary Medicine Vienna) Chiara Vaggi Julia Vötterl (Centre for Veterinary Public Health and One Health, Clinical Department for Farm Animals and Food System Transformation, Departments, University of Veterinary Medicine Vienna) Julia Vötterl Frederike Lerch (Centre for Veterinary Public Health and One Health, Clinical Department for Farm Animals and Food System Transformation, Departments, University of Veterinary Medicine Vienna) Frederike Lerch Fitra Yosi (Centre for Veterinary Public Health and One Health, Clinical Department for Farm Animals and Food System Transformation, Departments, University of Veterinary Medicine Vienna) Fitra Yosi Simone Koger (Centre for Animal Nutrition and Welfare, Clinical Department for Farm Animals and Food System Transformation, Departments, University of Veterinary Medicine Vienna) Simone Koger Sara Ricci (Centre for Animal Nutrition and Welfare, Clinical Department for Farm Animals and Food System Transformation, Departments, University of Veterinary Medicine Vienna) Sara Ricci Doris Verhovsek (VetFarm, Central Special Facilities, University of Veterinary Medicine Vienna) Doris Verhovsek Barbara Metzler-Zebeli (Centre for Animal Nutrition and Welfare, Clinical Department for Farm Animals and Food System Transformation, Departments, University of Veterinary Medicine Vienna) Barbara Metzler-Zebeli Frontiers Media SA 2026 Fecal samples are widely used as a proxy for the large intestinal microbiota; however, phenotypic characteristics (e.g., color and consistency) may be associated with divergent microbial profiles, especially around weaning, when diet and physiological adaptation rapidly alter gut function. The relationship between fecal phenotype, sample type, and piglet gut microbiota under physiological conditions remains poorly understood. This study investigated the bacterial communities in different fecal phenotypes of piglets shortly before and immediately after weaning. The fecal consistency of 192 piglets across two replicate batches was scored daily from day of life (DoL) 28 to 36, and fecal or rectal swab samples were collected at DoL28 and DoL33. The samples were classified by type (feces/swab), color (brown/yellow), and consistency (balls/liquid). DNA was extracted for quantification of total bacterial gene copies and 16S rRNA gene sequencing, and microbial composition was analyzed using Quantitative Insights Into Microbial Ecology 2 (QIIME2), Statistical Analysis System (SAS), and R. Fecal consistency changed markedly over time, shifting from predominantly ball-shaped on DoL28-32 to softer feces thereafter (p < 0.001). Age strongly influenced microbiota structure, with marked increases in relative abundance of Prevotella and Alloprevotella from DoL28 to DoL33, whereas the abundance of Escherichia, Methanobrevibacter, and Fusobacterium declined. Microbial communities differed between sample types, with swabs potentially reflecting mucosa-associated taxa more closely than fecal samples. Shannon and Simpson indices indicated reduced diversity in yellow and liquid feces on DoL28 (p < 0.001). Swabs and yellow liquid feces on DoL28 showed higher relative abundances of Escherichia, Bacteroides, and Fusobacterium, whereas brown ball-shaped feces were enriched in Lachnospiraceae, Prevotella, and Lactobacillus on both sampling days (p < 0.05). Overall, each fecal phenotype exhibited a distinct bacterial signature, and the sample type influenced the composition of the captured community. Monitoring fecal phenotypes alongside selecting appropriate sample types may enhance the interpretation of microbiome data and offer a practical, non-invasive approach to assess gut health during the critical weaning period. PDFDocument eng 2026-10-20T09:14:43.118735107Z 2026 bacterial abundances fecal phenotype fecal sampling gut microbiome intestinal development weaning piglets 1735401 b application/pdf http://creativecommons.org/licenses/by/4.0/