Comparative analysis of fecal microbiota between diarrhea and non-diarrhea piglets reveals biomarkers of gut microbiota associated with diarrhea

Diarrhea poses a significant threat to the health and well-being of weaned piglets, leading to substantial morbidity and mortality and economic loss in the pig industry. However, the structural characteristics of the gut microbiota and the key genera associated with early diarrhea in piglets within large-scale production systems are poorly understood. This study aimed to investigate the differences in the microbial community structure and the specific genera alteration between the healthy piglets and diarrhea piglets, and to identify the biomarkers of gut microbiota associated with diarrhea in piglets. A total of 250 fecal samples, including 130 healthy piglets (Duroc × Landrace × Large Yorkshire) in the Control group and 120 from diarrhea piglets in Diarrhea group, were collected from three large-scale farms as discovery cohorts and were used for 16S rRNA gene sequencing. Additionally, 150 fecal samples from another large-scale pig farm were collected for the validation trail. The Chao1 and ACE indices were obviously lower (<i>P</i> < 0.01) in the diarrhea piglets compared to the healthy ones. Principal coordinate analysis showed significant differences in the distance matrix of gut microbiota between the healthy and diarrhea piglets (Bray-Curtis: <i>P</i> = 0.001, Jaccard: <i>P</i> = 0.001). Eighty-five genera were differentially enriched (<i>P</i> < 0.001) between healthy and diarrhea piglets. Notably, <i>Treponema</i>, <i>Sphaerochaeta</i>, <i>Escherichia-Shigella</i>, <i>Slackia</i>, and <i>Staphylococcus</i> were identified as potential biomarkers of diarrhea susceptibility; <i>Clostridium sensu stricto 1</i>, <i>Prevotella_9</i>, <i>Olsenella</i>, <i>Dorea</i>, and <i>Lachnospiraceae NK4A136 group</i> were found to be beneficial for maintaining intestinal homeostasis. These differentially enriched genera of healthy and diarrhea piglets were further confirmed in the validation cohort. In conclusion, this study identified the diarrhea-associated and beneficial genera in the faces of piglet, providing a theoretical basis for the diagnosis and intervention of diarrhea in weaned piglets.