Temporal Microbial Dynamics in Feces Discriminate by Nutrition, Fecal Color, Consistency and Sample Type in Suckling and Newly Weaned Piglets

SIMPLE SUMMARY: The collection of feces has several advantages when studying the development of the gut microbiome in piglets as feces are easy to collect and can be collected from the same animal several times. Sow milk is the major food for the piglet and microbes during the suckling phase. The introduction of creep feed during the suckling phase may modify age-related microbial development. Moreover, feces from healthy piglets can differ in consistency and color. Moreover, it can be difficult to always collect feces from very young piglets, in which cases rectal swab samples are often collected. These factors may be behind the variation in microbiome composition and total abundances among animals. We followed the developing microbiome in feces from day 2 to 34 of life in piglets that drank only sow milk or had additional access to creep feed during the suckling phase. Weaning took place on day 28. Results supported that age and nutrition during the suckling phase were major factors influencing total and relative microbial abundances. However, results also indicated that color, consistency and sample type should be considered as additional factors when studying the fecal microbiome in suckling and newly weaned piglets. ABSTRACT: Feces enable frequent samplings for the same animal, which is valuable in studies investigating the development of the gut microbiome in piglets. Creep feed should prepare the piglet’s gut for the postweaning period and shape the microbiome accordingly. Little is known about the variation that is caused by differences in fecal color and consistency and different sample types (feces versus swab samples). Therefore, this study evaluated the age-related alterations in the microbiome composition (16S rRNA gene) in feces of suckling and newly weaned piglets in the context of nutrition and fecal consistency, color and sample type from day 2 to 34 of life. Feces from 40 healthy piglets (2 each from 20 litters) were collected on days 2, 6, 13, 20, 27, 30 and 34. Weaning occurred on day 28. Half of the litters only drank sow milk during the suckling phase, whereas the other half had access to creep feed from day 10. Creep feeding during the suckling phase influenced the age-related total bacterial and archaeal abundances but had less of an influence on the relative bacterial composition. Results further showed different taxonomic compositions in feces of different consistency, color and sample type, emphasizing the need to consider these characteristics in comprehensive microbiome studies.