From Gut to Blood: Spatial and Temporal Pathobiome Dynamics during Acute Abdominal Murine Sepsis

Abdominal sepsis triggers the transition of microorganisms from the gut to the peritoneum and bloodstream. Unfortunately, there is a limitation of methods and biomarkers to reliably study the emergence of pathobiomes and to monitor their respective dynamics. Three-month-old CD-1 female mice underwent cecal ligation and puncture (CLP) to induce abdominal sepsis. Serial and terminal endpoint specimens were collected for fecal, peritoneal lavage, and blood samples within 72 h. Microbial species compositions were determined by NGS of (cell-free) DNA and confirmed by microbiological cultivation. As a result, CLP induced rapid and early changes of gut microbial communities, with a transition of pathogenic species into the peritoneum and blood detected at 24 h post-CLP. NGS was able to identify pathogenic species in a time course-dependent manner in individual mice using cfDNA from as few as 30 microliters of blood. Absolute levels of cfDNA from pathogens changed rapidly during acute sepsis, demonstrating its short half-life. Pathogenic species and genera in CLP mice significantly overlapped with pathobiomes from septic patients. The study demonstrated that pathobiomes serve as reservoirs following CLP for the transition of pathogens into the bloodstream. Due to its short half-life, cfDNA can serve as a precise biomarker for pathogen identification in blood.

Automated summary

Abdominal sepsis leads to the migration of microorganisms from the gut to the peritoneum and bloodstream, but there are limited methods and biomarkers to study and monitor this process. In this study, cecal ligation and puncture (CLP) were used to induce abdominal sepsis in mice, and NGS was employed to analyze the microbial species composition in fecal, peritoneal lavage, and blood samples. The results showed rapid changes in gut microbial communities after CLP, with pathogenic species detected in the peritoneum and blood as early as 24 hours post-CLP. NGS of cfDNA from blood samples as small as 30 microliters was able to accurately identify pathogenic species in a time-dependent manner.