BackgroundHuman gut microbes metabolize food and host secretions, consuming and producing small molecules that are important to health and homeostasis. Here, we present an atlas of diet- and microbiome-derived metabolites in the human gut, constructed from a controlled feeding experiment of adults on omnivore and enteral nutrition diets.ResultsBy comparing metabolite concentration before and after microbiome depletion with antibiotics and polyethylene glycol, we identified 2856 microbial products decreasing and 1057 microbial substrates increasing in concentration after depletion. We also identified 2496 diet-derived metabolites by comparing diet groups when the microbiome was depleted. Seven days after antibiotics, 98% of gut metabolites recovered to pre-antibiotic levels in the omnivore group. In plasma samples, only 93 microbiome-derived metabolites varied with gut microbiome depletion, indicating a limited impact on circulating metabolites. To demonstrate our metabolite atlas, we annotated metabolites associated with inflammatory bowel disease and identified the microbiome-derived metabolites altered in gut dysbiosis.ConclusionsWe identified metabolites associated with the metabolism of the human gut microbiome, mapping its overall metabolic potential. Furthermore, we measured the rate at which metabolites were recovered following gut microbiome disruption.

INTRODUCTION Spontaneous bacterial peritonitis (SBP) is a common complication of decompensated cirrhosis with high mortality, and patients may have evidence of concomitant infection in other sources, including the bloodstream and urinary tract.1 The most common isolates from ascitic fluid are gram-negative enteric organisms (primarily Escherichia coli and Klebsiella) due to gut bacterial translocation2,3; however, the microorganism profile of culture data in other sources has not been well studied. Delineating the epidemiology of SBP across infectious sources and patient characteristics is important in identifying high-risk patients, tailoring effective antibiotic regimens, and antibiotic stewardship. We aimed to (1) investigate the distribution of organisms among patients with positive cultures (peritoneal fluid, blood, and urine) in a national cohort of patients with cirrhosis hospitalized with SBP and (2) model the risk of 30-day mortality in patients with positive versus negative cultures. METHODS This was a retrospective cohort study of adult patients with cirrhosis in the Veterans Outcomes and Costs Associated With Liver Diseases cohort4–6 with index hospitalization for SBP between January 2008 and October 2023. SBP was defined by paracentesis-obtained ascites fluid polymorphonuclear leukocyte count >250/mm3 in the hospital or up to 7 days prior to hospitalization as per prior methods.7 Baseline demographic data, body mass index, etiology of cirrhosis, MELD-Na prior to hospitalization, and MELD-Na on hospital presentation were collected. We analyzed culture growth stratified by source (blood, peritoneal, and urine samples) and Child-Pugh-Turcotte (CTP) class. In preparation for modeling of 30-day mortality, culture sources and results were categorized as urine/blood/peritoneal culture−; isolated urine culture+; blood culture+/peritoneal culture−, blood culture−/peritoneal culture+; and blood culture+/peritoneal culture+. A logistic regression model was fit with this primary exposure adjusted for age, sex, body mass index, race, etiology, prehospital MELD-Na, and diabetes (Supplemental Methods, https://links.lww.com/HC9/B891). Data management and statistical analyses were performed using STATA/BE 18.0 (College Station, TX). RESULTS A total of 5176 patients were included from 125 Veterans Health Administration centers; SBP was diagnosed at median hospital day 1 (IQR 0, 3). Patients were predominantly male (98%) and White (62%) with alcohol-associated liver disease (43.7%). On average, there was an increase in median MELD-Na from 16 to 24 at the time of hospitalization (Supplemental Table S1, https://links.lww.com/HC9/B891). Culture data identified organisms in 1748 patients (33.8%), with the majority identified in peritoneal fluid followed by blood and urine. E. coli was the most common organism across all fluid sources (urine 21.2%, blood 22.3%, peritoneal fluid 24.3%; p<0.001). There were significant differences in organism distribution across CTP classes for blood, peritoneal, and urine cultures (each p<0.001; Figure 1A–C). E. coli prevalence increased with liver disease severity in these groups (CTP A 29.9% vs. C 38.8% in blood; 35.2% vs. 39.2% in peritoneal fluid; 28.5% vs. 37.5% in urine), as did Klebsiella (eg, CTP A 15.5% vs. C 28.6% in blood). By contrast, S. aureus prevalence declined with increasing severity of liver disease (CTP A 35.5% vs. C 10.2% in blood; 17.2% vs. 5.4% in peritoneal fluid; 6.9% vs. 0.0% in urine). Enterococcus species were highly prevalent in urine cultures across all CTP classes (range 34.0%–37.5%).FIGURE 1: Distribution of most common organisms by CTP class in (A) blood cultures (B) peritoneal fluid cultures, and (C) urine cultures. Abbreviation: CTP, Child-Pugh-Turcotte.In adjusted analysis, patients who were blood culture+/peritoneal culture+ had a 2.49-fold increased odds of 30-day mortality versus culture− patients (95% CI: 1.92–3.22; Supplemental Table S2, https://links.lww.com/HC9/B891). Patients who were blood culture−/peritoneal culture+ had 1.47-fold increased odds of 30-day mortality versus those who were culture− (95% CI: 1.23–1.77), and patients who were blood culture+/peritoneal culture− had a 1.38-fold increased odds of mortality versus culture− patients (95% CI: 1.12–1.66); all p<0.001. DISCUSSION In this large cohort, there were significant differences in the microbiology of organisms in the blood, peritoneal fluid, and urine of patients with SBP across CTP classes. Higher CTP class was associated with higher rates of E. coli and Klebsiella infections and less S. aureus across all culture sources. The observed differences may reflect microbiome changes and potential differences in susceptibility to infection by selected organisms. Additionally, medication effects may impact the risk of selected microorganism infections. Lactulose and rifaximin, which are used for the treatment of HE, are known to alter the microbiome and increase the colonization of organisms in the gut.8 Prior studies also report that antibiotic overuse, nosocomial infections, and an increase in invasive procedures may shift the infectious landscape of SBP.3,9,10 However, no prior studies have explored the changing epidemiology of microorganisms across liver disease severity and multiple culture data sources. Further studies are needed to build on our findings and investigate the microorganism profile of patients treated for SBP and other infections and to evaluate resistance patterns based on specific antimicrobial exposures. Our study also demonstrated higher odds of 30-day mortality in patients with positive cultures from both blood and peritoneal fluid, followed by positivity in one source or the other, relative to culture-negative patients. It is likely that multiple positive cultures indicate a more disseminated infection in an already vulnerable host with decompensated cirrhosis. This finding provides insight into patient prognosis and supports early identification and aggressive interventions with appropriate antimicrobial therapy for these higher-risk patients. Consistent with our findings, concurrent bacteremia has been associated with poor outcomes in SBP resulting in higher mortality.2 Finally, urine culture positivity did not impact the odds of mortality; asymptomatic bacteriuria is possible in many cases, though similar rates of E. coli and Klebsiella in urine cultures suggest a shared underlying source (ie, gut translocation). Several limitations exist in this study. First, there are external validity limitations given that the Veterans cohort is predominantly male, largely White, and skewed toward HCV and alcohol-associated liver disease. Second, given the retrospective nature of this study, residual confounding is possible. Third, we were not able to explore antibiotic resistance patterns in this cohort or the influence of prior antibiotic exposure on microorganism distributions. These mark important areas of future inquiry. In conclusion, we observed changing distributions of microorganisms from culture data across CTP classes in patients hospitalized with SBP. Patients with positive culture data in both blood and peritoneal cultures had the highest risk of 30-day mortality, underscoring the need for early detection and aggressive management in this high-risk population.

BACKGROUND & AIMS:Crohn's disease is associated with alterations in the gut microbiome and metabolome described as dysbiosis. We characterized the microbial and metabolic consequences of ileal resection, the most common Crohn's disease surgery. METHODS:Patients with and without intestinal resection were identified from the Diet to Induce Remission in Crohn's Disease and Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease studies. Stool samples were analyzed with shotgun metagenomics sequencing. Fecal butyrate was measured with 1H nuclear magnetic resonance spectroscopy. Fecal bile acids and plasma 7α-hydroxy-4-cholesten-3-one (C4) was measured with mass spectrometry. RESULTS:Intestinal resection was associated with reduced alpha diversity and altered beta diversity with increased Proteobacteria and reduced Bacteroidetes and Firmicutes. Surgery was associated with higher representation of genes in the KEGG pathway for ABC transporters and reduction in genes related to bacterial metabolism. Surgery was associated with reduced concentration of the But gene but this did not translate to reduced fecal butyrate concentration. Surgery was associated with decreased abundance of bai operon genes, with increased plasma C4 concentration, increased primary bile acids and reduced secondary bile acids, including isoLCA. Additionally, Egerthella lenta, Adlercreutzia equalofaciens, and Gordonibacter pamelaeae were lower in abundance among patients with prior surgery in both cohorts. CONCLUSIONS:In 2 different populations, prior surgery in Crohn's disease is associated with altered fecal microbiome. Patients who had undergone ileal resection had reduction in the potentially beneficial bacteria E lenta and related actinobacteria and secondary bile acids, including isoLCA, suggesting that these could be biomarkers of patients at higher risk for disease progression.

Bacterial translocation from the gut microbiota is a source of sepsis in susceptible patients. Previous work suggests that overgrowth of gut pathobionts, including Klebsiella pneumoniae, increases the risk of disseminated infection. Our data from a human dietary intervention study found that, in the absence of fiber, K. pneumoniae bloomed during microbiota recovery from antibiotic treatment. We thus hypothesized that dietary nutrients directly support or suppress colonization of this gut pathobiont in the microbiota. Consistent with our study in humans, complex carbohydrates in dietary fiber suppressed the colonization of K. pneumoniae and allowed for recovery of competing commensals in mouse models. In contrast, through ex vivo and in vivo modeling, we identified simple carbohydrates as a limiting resource for K. pneumoniae in the gut. As proof of principle, supplementation with lactulose, a nonabsorbed simple carbohydrate and an FDA-approved therapy, increased colonization of K. pneumoniae. Disruption of the intestinal epithelium led to dissemination of K. pneumoniae into the bloodstream and liver, which was prevented by dietary fiber. Our results show that dietary simple and complex carbohydrates were critical not only in the regulation of pathobiont colonization but also disseminated infection, suggesting that targeted dietary interventions may offer a preventative strategy in high-risk patients.

BACKGROUND & AIMS: Altered plasma acylcarnitine levels are well-known biomarkers for a variety of mitochondrial fatty acid oxidation disorders and can be used as an alternative energy source for the intestinal epithelium when short-chain fatty acids are low. These membrane-permeable fatty acid in-termediates are excreted into the gut lumen via bile and are increased in the feces of patients with inflammatory bowel disease (IBD). METHODS: Herein, based on studies in human subjects, ani-mal models, and bacterial cultures, we show a strong positive correlation between fecal carnitine and acylcarnitines and the abundance of Enterobacteriaceae in IBD where they can be consumed by bacteria both in vitro and in vivo. RESULTS: Carnitine metabolism promotes the growth of Escherichia coli via anaerobic respiration dependent on the cai operon, and acetylcarnitine dietary supplementation increases fecal carnitine levels with enhanced intestinal colonization of the enteric pathogen Citrobacter rodentium. CONCLUSIONS: In total, these results indicate that the increased luminal concentrations of carnitine and acylcarni-tines in patients with IBD may promote the expansion of pathobionts belonging to the Enterobacteriaceae family, thereby contributing to disease pathogenesis.

Dysbiosis of the gut microbiota is increasingly appreciated as both a consequence and precipitant of human disease. The outgrowth of the bacterial family Enterobacteriaceae is a common feature of dysbiosis, including the human pathogen Klebsiella pneumoniae. Dietary interventions have proven efficacious in the resolution of dysbiosis, though the specific dietary components involved remain poorly defined. Based on a previous human diet study, we hypothesized that dietary nutrients serve as a key resource for the growth of bacteria found in dysbiosis. Through human sample testing, and ex-vivo, and in vivo modeling, we find that nitrogen is not a limiting resource for the growth of Enterobacteriaceae in the gut, contrary to previous studies. Instead, we identify dietary simple carbohydrates as critical in colonization of K. pneumoniae. We additionally find that dietary fiber is necessary for colonization resistance against K. pneumoniae, mediated by recovery of the commensal microbiota, and protecting the host against dissemination from the gut microbiota during colitis. Targeted dietary therapies based on these findings may offer a therapeutic strategy in susceptible patients with dysbiosis.