Intestinal microbiota dynamics in piglets: the interplay with swine enteric coronavirus infections and implications for disease control

Infections of swine enteric coronavirus (SECoV), including porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and swine acute diarrhea syndrome coronavirus (SADS-CoV), cause severe diarrhea in piglets and result in substantial losses to the pig industry. The intestinal microbiota plays a crucial role in SECoV disease progression and outcomes, yet current research largely focuses on specific age groups or intestinal segments. This review provides a comprehensive analysis of the dynamic microbiota changes in piglets after SECoV infections across different ages and intestinal regions. It discusses differential microbiota analyses, functional changes, metabolic products, alongside their effects on immune responses. Additionally, we explore fecal bacterial transplantation as a potential intervention and highlight the role of the microbiota in either promoting or inhibiting SECoV infections. The development of advanced research tools, including culturomics, sequencing technologies, and multi-omics approaches, is pivotal in understanding the intricate relationship between the porcine intestinal microbiota and SECoV infections, offering potential strategies for preventing and controlling SECoV-related diseases.