Although it has long been recognized that the enteric community of bacteria that inhabit the human distal intestinal track broadly impacts human health, the biochemical details that underlie these effects remain largely undefined. Here, we report a broad MS-based metabolomics study that demonstrates a surprisingly large effect of the gut ''microbiome'' on mammalian blood metabolites. Plasma extracts from germ-free mice were compared with samples from conventional (conv) animals by using various MS-based methods. Hundreds of features were detected in only 1 sample set, with the majority of these being unique to the conv animals, whereas Ϸ10% of all features observed in both sample sets showed significant changes in their relative signal intensity. Amino acid metabolites were particularly affected. For example, the bacterial-mediated production of bioactive indole-containing metabolites derived from tryptophan such as indoxyl sulfate and the antioxidant indole-3-propionic acid (IPA) was impacted. Production of IPA was shown to be completely dependent on the presence of gut microflora and could be established by colonization with the bacterium Clostridium sporogenes. Multiple organic acids containing phenyl groups were also greatly increased in the presence of gut microbes. A broad, drug-like phase II metabolic response of the host to metabolites generated by the microbiome was observed, suggesting that the gut microflora has a direct impact on the drug metabolism capacity of the host. Together, these results suggest a significant interplay between bacterial and mammalian metabolism.

Translocation of bacteria and their products across the intestinal barrier is common in patients with liver disease, and there is evidence that experimental liver fibrosis depends on bacterial translocation. The purpose of our study was to investigate liver fibrosis in conventional and germ‐free (GF) C57BL/6 mice. Chronic liver injury was induced by administration of thioacetamide (TAA) in the drinking water for 21 wk or by repeated intraperitoneal injections of carbon tetrachloride (CCl4). Increased liver fibrosis was observed in GF mice compared with conventional mice. Hepatocytes showed more toxin‐induced oxidative stress and cell death. This was accompanied by increased activation of hepatic stellate cells, but hepatic mediators of inflammation were not significantly different. Similarly, a genetic model using Myd88/Trif‐deficient mice, which lack downstream innate immunity signaling, had more severe fibrosis than wild‐type mice. Isolated Myd88/Trif‐deficient hepatocytes were more susceptible to toxin‐induced cell death in culture. In conclusion, the commensal microbiota prevents fibrosis upon chronic liver injury in mice. This is the first study describing a beneficial role of the commensal microbiota in maintaining liver homeostasis and preventing liver fibrosis.—Mazagova, M., Wang, L., Anfora, A. T., Wissmueller, M., Lesley, S. A., Miyamoto, Y., Eckmann, L., Dhungana, S., Pathmasiri, W., Sumner, S., Westwater, C., Brenner, D. A., Schnabl, B., Commensal microbiota is hepatoprotective and prevents liver fibrosis in mice. FASEB J. 29, 1043–1055 (2015). http://www.fasebj.org

In this study we show that deletion of the genes encoding L-serine deaminases SdaA and SdaB resulted in a mutant that accumulates higher intracellular levels of L-serine than CFT073. CFT073 sdaA sdaB has a mild competitive colonization defect whereas a CFT073 dsdA sdaA sdaB triple mutant shows a greater loss in competitive colonization ability. Thus, the inability to generate serine-specific catabolic products does not result in hypercolonization and the ability to catabolize serine represents a positive physiological trait during murine UTI. CFT073 dsdC and CFT073 dsdC dsdA mutants continue to outcompete the wild type in the UTI model. These results confirm that loss of DsdA activity results in the hypercolonization phenotype and that DsdC does not play a direct role in the elevated-colonization phenotype. Interestingly, a CFT073 dsdA mutant with deletions of D-serine transporter genes dsdX and cycA shows wild-type colonization levels of the bladder but is attenuated for kidney colonization. Thus, D-serine acts as a signal for hypercolonization and virulence gene expression by CFT073 dsdA, whereas overall catabolism of serine represents a positive Escherichia coli fitness trait during UTI.Urinary tract infections (UTIs) in adult women impose an estimated cost of $2.4 billion per year in the United States (12). Most women will experience at least one UTI in their lifetime, resulting in an estimated 6.8 million physician visits, 1.2 million emergency room visits, and nearly a quarter million hospitalizations each year. Escherichia coli remains by far the primary causative agent of community-acquired UTIs (11).The urinary tract is a normally sterile environment, and it poses daunting challenges to colonization by E. coli and other microorganisms. In addition to the cleansing flow of urine, numerous innate and acquired immune factors challenge the growth of uropathogenic Escherichia coli (UPEC) in the urinary tract. The host defense involves phagocytic attack, antimicrobial peptides, complement lytic and opsonizing factors, and reactive oxygen and nitrogen species. In addition, the urinary tract offers high-salt and high-osmolarity conditions while limiting E. coli nutrients common to the intestinal tract, especially neutral sugars and iron (4). Thus, we hypothesize that the ability of UPEC to import and metabolize the available carbon and nitrogen sources present in the urinary tract plays a special role in its ability to colonize and cause disease at that site.From a bacterial nutritional standpoint, urine is a dilute mixture of amino acids and small peptides, quite similar to tryptone broth, with the notable exception of the abundance of urea in urine (4). The growth of E. coli in tryptone broth is well characterized, where growing cells preferentially and sequentially utilize serine and then aspartate while secreting acetate. Once these amino acids are depleted, cells then import and use tryptophan and acetate, followed by alanine, glutamine, and threonine (31). This order of nutrient preference holds true for ...

D-ornithine has previously been suggested to enhance the expression of pyrrolysine-containing proteins. We unexpectedly discovered that uptake of D-ornithine results in the insertion of a new amino acid, pyrroline-carboxy-lysine (Pcl) instead of the anticipated pyrrolysine (Pyl). Our feeding and biochemical studies point to specific roles of the poorly understood Pyl biosynthetic enzymes PylC and PylD in converting L-lysine and D-ornithine to Pcl and confirm intermediates in the biosynthesis of Pyl.

In vivo accumulation of D-serine by Escherichia coli CFT073 leads to elevated expression of PAP fimbriae and hemolysin by an unknown mechanism. Loss of D-serine catabolism by CFT073 leads to a competitive advantage during murine urinary tract infection (UTI), but loss of both D-and L-serine catabolism results in attenuation. Serine is the first amino acid to be consumed in closed tryptone broth cultures and precedes the production of acetyl phosphate, a high-energy molecule involved in intracellular signaling, and the eventual secretion of acetate. We propose that the colonization defect associated with the loss of serine catabolism is due to perturbations of acetate metabolism. CFT073 grows more rapidly on acetogenic substrates than does E. coli K-12 isolate MG1655. As shown by transcription microarray results, D-serine is catabolized into acetate via the phosphotransacetylase (pta) and acetate kinase (ackA) genes while downregulating expression of acetyl coenzyme A synthase (acs). CFT073 acs, which is unable to reclaim secreted acetate, colonized mouse bladders and kidneys in the murine model of UTI indistinguishably from the wild type. Both pta and ackA are involved in the maintenance of intracellular acetyl phosphate. CFT073 pta and ackA mutants were screened to investigate the role of acetyl phosphate in UTI pathogenesis. Both single mutants are at a competitive disadvantage relative to the wild type in the kidneys but normally colonize the bladder. CFT073 ackA pta was attenuated in both the bladder and the kidneys. Thus, we demonstrate that CFT073 is adapted to acetate metabolism as a result of requiring a proper cycling of the acetyl phosphate pathway for colonization of the upper urinary tract.Urinary tract infections (UTIs) place a significant burden on the United States healthcare system, costing upwards of $2.4 billion per year (28). The majority of women will experience a UTI in their lifetime, and every year there are approximately 6.8 million physician visits, 1.2 million emergency room visits, a quarter million hospitalizations, and thousands of deaths due to complications of UTIs, most often sepsis (10,18,28,47). Escherichia coli is the most commonly isolated causative agent of community-acquired UTIs (10).The transition from residence in the gastrointestinal tract, where uropathogenic Escherichia coli (UPEC) transiently resides, to the urinary tract represents a significant change in environment. While the gastrointestinal tract is densely populated with many different species of bacteria, the bladder is normally a sterile environment yet one that presents significant challenges to bacterial growth. In addition to the cleansing flow of urine, numerous innate and acquired immune factors challenge the growth of UPEC in the urinary tract. The host defense involves phagocytic attack, antimicrobial peptides, complement lytic and opsonizing factors, and reactive oxygen and nitrogen species. In addition, the urinary tract as reflected in urine is limited in nutrients common to the intestinal tract, esp...