A recent report by the National Institutes of Health on sepsis research has implied that there is a trend to move away from mouse models of sepsis. The most commonly used animal model to study the pathogenesis of human sepsis is cecal ligation and puncture (CLP) in mice. The model has been the mainstay of sepsis research for decades and continues to be considered the gold standard to inform novel pathways of sepsis physiology and its therapeutic direction. Although there have been many criticism of the model, particularly regarding its relevance to human disease, how this model might be repurposed to be more reflective of the human condition begs discussion. In this piece, we compare and contrast the mouse microbiome of the CLP model to the emerging science of the microbiome of human sepsis and discuss the relevance for mice to harbor the very pathogens present in the human microbiome during sepsis as well as an underlying disease process to mimic the characteristics of those patients with undesirable outcomes. How to repurpose this model to incorporate these “human factors” is discussed in detail and suggestions offered.

Objectives: Determine whether preoperative dietary prehabilitation with a low-fat, high-fiber diet reverses the impact of Western diet (WD) on the intestinal microbiota and improves postoperative survival Background: We have previously demonstrated that WD fed mice subjected to an otherwise recoverable surgical injury (30% hepatectomy), antibiotics, and a short period of starvation demonstrate reduced survival (29%) compared to mice fed a low-fat, high-fiber standard chow (SD) (100%). Methods: Mice were subjected to 6 weeks of a WD and underwent dietary pre-habilitation (3 days vs 7 days) with a SD prior to exposure to antibiotics, starvation, and surgery. 16S rRNA gene sequencing was utilized to determine microbiota composition. Mass spectrometry measured short chain fatty acids and functional prediction from 16S gene amplicons were utilized to determine microbiota function. Results: As early as 24 hours, dietary prehabilitation of WD mice resulted in restoration of bacterial composition of the stool microbiota, transitioning from Firmicutes dominant to Bacteroidetes dominant. However, during this early pre-habilitation (ie, 3 days), stool butyrate per microbial biomass remained low and postoperative mortality remained unchanged from WD. Microbiota function demonstrated reduced butyrate contributing taxa as potentially responsible for failed recovery. In contrast, after 7 days of prehabilitation (7DP), there was greater restoration of butyrate producing taxa and survival after surgery improved (29% vs 79% vs 100%: WD vs 7DP vs SD, P < 0.001). Conclusions:The deleterious effects of WD on the gut microbiota can be restored after 7 days of dietary prehabilitation. Moreover, stool markers may define the readiness of the microbiome to withstand the process of surgery including exposure to antibiotics and short periods of starvation.

The intestinal microbiota are known to influence the host immune system and may play an important role in the pathobiology of sepsis. We have previously shown that fecal microbiota transplant (FMT) is protective in mice subjected to polymicrobial peritonitis. The aim of this study was to determine if the beneficial effect of FMT is associated with engraftment of specific taxa or functional characteristics induced by FMT. Methods: C57BL/6 mice were injected intra-peritoneally with Serratia marcescens, a gram-negative pathobiont, and simultaneously administered a fecal microbiota transplant (FMT), prepared from healthy littermates, via enema. Mice were allowed to recover and sacrificed when moribund. At sacrifice, stool, cecal contents, and FMT underwent 16S rRNA sequencing for compositional analysis. Cecal short-chain fatty acids (SCFAs) butyrate, propionate, and acetate were quantified via GC-MS. Cecal SCFA concentrations and microbiota composition (DESeq package in R, Vienna, Austria) were compared between surviving mice treated with FMT and nonsurviving mice treated with FMT . Results: Similar to previous experiments, FMT improved survival (56% for mice treated with FMT, n = 43, versus 29% for non-treated mice, n = 38, p = 0.03). Survival following FMT was associated with enrichment in 2 short-chain fatty acid-producing taxa from the class Clostridia, one from family Lachnospiraceae (mean abundance 24.7% versus 19.9%, p<0.001) and one from genus Pseudoflavonifractor (mean abundance 1.1% versus 0.7%, p<0.001). When compared to the mice that did not survive following FMT, surviving mice had higher concentrations of cecal propionate (mean [SD], 8.05 [2.98]mM vs 4.04 [0.75] mM), butyrate (16.40 [10.06] mM vs 2.37 [0.77] mM), and acetate (50.49 [12.52] mM vs 27.88 [7.99] mM). Conclusions: In mice infected with S. marcescens, administration of FMT may confer a survival benefit. Significant within-group differences for short-chain fatty acid concentrations were observed among mice treated with FMT, and these differences were associated with survival. Taken together, these results indicate that survival induced by FMT may be a function of its ability to enrich the gut with key metabolites known to be involved in enhancing immune function.