phaidra.vetmeduni.ac.at o:5615 DOI 10.3389/fvets.2026.1815748 Characterization of fecal bacterial microbiomes according to fecal color, consistency, and sample type in piglets before and after weaning 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. eng bacterial abundances fecal phenotype fecal sampling gut microbiome intestinal development weaning piglets 2026-10-20T09:14:43.435Z LOMv1.0 Author BEGIN:VCARD VERSION:3.0 N:Vaggi;Chiara; FN:Chiara Vaggi END:VCARD BEGIN:VCARD VERSION:3.0 N:Vötterl;Julia; FN:Julia Vötterl X-ORCID:https://orcid.org/0000-0001-5079-0440 END:VCARD BEGIN:VCARD VERSION:3.0 N:Lerch;Frederike; FN:Frederike Lerch END:VCARD BEGIN:VCARD VERSION:3.0 N:Yosi;Fitra; FN:Fitra Yosi X-ORCID:https://orcid.org/0000-0001-9550-6474 END:VCARD BEGIN:VCARD VERSION:3.0 N:Koger;Simone; FN:Simone Koger END:VCARD BEGIN:VCARD VERSION:3.0 N:Ricci;Sara; FN:Sara Ricci X-ORCID:https://orcid.org/0000-0002-0117-9407 END:VCARD BEGIN:VCARD VERSION:3.0 N:Verhovsek;Doris; FN:Doris Verhovsek END:VCARD BEGIN:VCARD VERSION:3.0 N:Metzler-Zebeli;Barbara; FN:Barbara Metzler-Zebeli END:VCARD https://w3id.org/kim/hcrt/scheme https://w3id.org/kim/hcrt/text Textdokument Text LOMv1.0 yes https://creativecommons.org/licenses/by/4.0 application/pdf 1735401 https://phaidra.vetmeduni.ac.at/o:5615 https://phaidra.vetmeduni.ac.at/api/object/o:5615/thumbnail LOMv1.0 discipline