Development of a chemically defined medium for the production of enterolysin A from Enterococcus faecalis B9510

Study of sulfoglycolysis in Enterococcus gilvus reveals a widespread bifurcated pathway for dihydroxypropanesulfonate degradation

Sulfoquinovose (SQ), the polar head group of sulfolipids essential for photosynthesis, is naturally abundant. Anaerobic Firmicutes degrade SQ through a transaldolase-dependent (sulfo-TAL) pathway, producing dihydroxypropanesulfonate (DHPS). Some bacteria extend this pathway by the sequential action of HpfG and HpfD converting DHPS to 3-hydroxypropanesulfonate (3-HPS) via 3-sulfopropionaldehyde (3-SPA). Here, we report a variant sulfo-TAL pathway in Enterococcus gilvus, involving additional enzymes, a NAD+-dependent 3-SPA dehydrogenase HpfX, and a 3-sulfopropionyl-CoA synthetase HpfYZ, which oxidize 3-SPA to 3-sulfopropionate (3-SP) coupled with ATP formation. E. gilvus grown on SQ or DHPS produced a mixture of 3-HPS and 3-SP, indicating the bifurcated pathway. Similar genes are found in various Firmicutes, including gut bacteria. Importantly, 3-SP, but not 3-HPS, can serve as a respiratory terminal electron acceptor for Bilophila wadsworthia, a common intestinal pathobiont, resulting in the production of toxic H2S. This research expands our understanding of sulfonate metabolism and reveals cross-feeding in the anaerobic microbiome.

Function and contribution of two putative Enterococcus faecalis glycosaminoglycan degrading enzymes to bacteremia and catheter-associated urinary tract infection

Enterococcus faecalis is a common cause of healthcare-acquired bloodstream infections and catheter-associated urinary tract infections (CAUTIs) in both adults and children. Treatment of E. faecalis infection is frequently complicated by multi-drug resistance. Based on protein homology, E. faecalis encodes two putative hyaluronidases, EF3023 (HylA) and EF0818 (HylB). In other Gram-positive pathogens, hyaluronidases have been shown to contribute to tissue damage and immune evasion, but the function in E. faecalis has yet to be explored. Here, we show that both hylA and hylB contribute to E. faecalis pathogenesis. In a CAUTI model, ΔhylA exhibited defects in bladder colonization and dissemination to the bloodstream, and ΔhylB exhibited a defect in kidney colonization. Furthermore, a ΔhylAΔhylB double mutant exhibited a severe colonization defect in a model of bacteremia while the single mutants colonized to a similar level as the wild-type strain, suggesting potential functional redundancy within the bloodstream. We next examined enzymatic activity, and demonstrate that HylB is capable of digesting both hyaluronic acid (HA) and chondroitin sulfate in vitro, while HylA exhibits only a very modest activity against heparin. Importantly, HA degradation by HylB provided a modest increase in cell density during the stationary phase and also contributed to dampening of lipopolysaccharide-mediated NF-κB activation. Overall, these data demonstrate that glycosaminoglycan degradation is important for E. faecalis pathogenesis in the urinary tract and during bloodstream infection.

Function and contribution of two putative Enterococcus faecalis glycosaminoglycan degrading enzymes to bacteremia and catheter-associated urinary tract infection

Enterococcus faecalis is a common cause of healthcare acquired bloodstream infections and catheter associated urinary tract infections (CAUTI) in both adults and children. Treatment of E. faecalis infection is frequently complicated by multi-drug resistance. Based on protein homology, E. faecalis encodes two putative hyaluronidases, EF3023 (HylA) and EF0818 (HylB). In other Gram-positive pathogens, hyaluronidases have been shown to contribute to tissue damage and immune evasion, but function in E. faecalis has yet to be explored. Here, we show that both hylA and hylB contribute to E. faecalis pathogenesis. In a CAUTI model, Δ hylA exhibited defects in bladder colonization and dissemination to the bloodstream, and Δ hylB exhibited a defect in kidney colonization. Furthermore, a Δ hylA Δ hylB double mutant exhibited a severe colonization defect in a model of bacteremia while the single mutants colonized to a similar level as the wild-type strain, suggesting potential functional redundancy within the bloodstream. We next examined enzymatic activity, and demonstrate that HylB is capable of digesting both HA and CS in vitro while HylA exhibits only a very modest activity against heparin. Importantly, HA degradation by HylB provided a modest increase in cell density during stationary phase and also contributed to dampening of LPS-mediated NF-Bκ activation. Overall, these data demonstrate that glycosaminoglycan degradation is important for E. faecalis pathogenesis in the urinary tract and during bloodstream infection.

A Review on Enterocin DD14, the Leaderless Two-Peptide Bacteriocin with Multiple Biological Functions and Unusual Transport Pathway

Enterocin DD14 (EntDD14) is a two-peptide leaderless bacteriocin (LLB) produced by Enterococcus faecalis 14, a human strain isolated from meconium. Studies performed on EntDD14 enabled it to show its activity against Gram-positive bacteria such as Listeria monocytogenes, Clostridium perfringens, Enterococcus faecalis, and Staphylococcus aureus. EntDD14 was also shown to potentiate the activity of different antibiotics such as erythromycin, kanamycin, and methicillin when assessed against methicillin-resistant Staphylococcus aureus (MRSA) in vitro and in vivo in the NMRI-F holoxenic mouse model. Additionally, EntDD14 has an antiviral activity and decreased the secretion of pro-inflammatory IL-6 and IL-8 in inflamed human intestinal Caco-2 cells. The genome of E. faecalis 14 was sequenced and annotated. Molecular tools such as Bagel4 software enabled us to locate a 6.7kb-EntDD14 cluster. Transport of EntDD14 outside of the cytoplasm was shown to be performed synergistically by a channel composed of two pleckstrin-homology-domain-containing proteins, namely DdE/DdF and the ABC transporter DdGHIJ. This latter could also protect the bacteriocinogenic strain against extracellular EntDD14. Here, we focus on academic data and potential therapeutic issues of EntDD14, as a model of two-peptide LLB.

Intermediate role of gut microbiota in vitamin B nutrition and its influences on human health

Vitamin B consists of a group of water-soluble micronutrients that are mainly derived from the daily diet. They serve as cofactors, mediating multiple metabolic pathways in humans. As an integrated part of human health, gut microbiota could produce, consume, and even compete for vitamin B with the host. The interplay between gut microbiota and the host might be a crucial factor affecting the absorbing processes of vitamin B. On the other hand, vitamin B supplementation or deficiency might impact the growth of specific bacteria, resulting in changes in the composition and function of gut microbiota. Together, the interplay between vitamin B and gut microbiota might systemically contribute to human health. In this review, we summarized the interactions between vitamin B and gut microbiota and tried to reveal the underlying mechanism so that we can have a better understanding of its role in human health.

Biomarker enrichment medium: A defined medium for metabolomic analysis of microbial pathogens

Microbes have diverse metabolic capabilities and differences in these phenotypes are critical for differentiating strains, species, and broader taxa of microorganisms. Recent advances in liquid chromatography-mass spectrometry (LC-MS) allow researchers to track the complex combinations of molecules that are taken up by each cell type and to quantify the rates that individual metabolites enter or exit the cells. This metabolomics-based approach allows complex metabolic phenotypes to be captured in a single assay, enables computational models of microbial metabolism to be constructed, and can serve as a diagnostic approach for clinical microbiology. Unfortunately, metabolic phenotypes are directly affected by the molecular composition of the culture medium and many traditional media are subject to molecular-level heterogeneity. Herein, we show that commercially sourced Mueller Hinton (MH) medium, a Clinical and Laboratory Standards Institute (CLSI) approved medium for clinical microbiology, has significant lot-to-lot and supplier-to-supplier variability in the concentrations of individual nutrients. We show that this variability does not affect microbial growth rates but does affect the metabolic phenotypes observed in vitro—including metabolic phenotypes that distinguish six common pathogens. To address this, we used a combination of isotope-labeling, substrate exclusion, and nutritional supplementation experiments using Roswell Park Memorial Institute (RPMI) medium to identify the specific nutrients used by the microbes to produce diagnostic biomarkers, and to formulate a Biomarker Enrichment Medium (BEM) as an alternative to complex undefined media for metabolomics research, clinical diagnostics, antibiotic susceptibility testing, and other applications where the analysis of stable microbial metabolic phenotypes is important.

Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition

Gut colonization with multidrug-resistant (MDR) bacteria enhances the risk of bloodstream infections in susceptible individuals. We demonstrate highly variable degrees of ex vivo colonization resistance against a carbapenem-resistant Klebsiella pneumoniae strain in human feces samples and subsequently isolate diverse K. oxytoca strains from protected donors. Several of these K. oxytoca strains reduce gut colonization of MDR K. pneumoniae strains in antibiotic-treated and gnotobiotic mouse models. Comparative analysis of K. oxytoca strains coupled with CRISPR-Cas9-mediated deletion of casA, a protein essential for utilization of selected beta-glucosides, identified competition for specific carbohydrates as key in promoting colonization resistance. In addition to direct competition between K. oxytoca and K. pneumoniae, cooperation with additional commensals is required to reestablish full colonization resistance and gut decolonization. Finally, humanized microbiota mice generated from K. pneumoniae-susceptible donors are protected by K. oxytoca administration, demonstrating the potential of commensal K. oxytoca strains as next-generation probiotics.

A protein-free chemically defined medium for the cultivation of various micro-organisms with food safety significance

AIMS

To develop a broadly applicable medium free of proteins with well-defined and reproducible chemical composition for the cultivation of various micro-organisms with food safety significance.

METHODS AND RESULTS

The defined medium was designed as a buffered minimal salt medium supplemented with amino acids, vitamins, trace metals and other nutrients. Various strains commonly used for food safety research were selected to test the new defined medium. We investigated single growth factors needed by different strains and the growth performance of each strain cultivated in the defined medium. Results showed that the tested strains initially grew slower in the defined medium compared to tryptic soy broth, but after an overnight incubation cultures from the defined medium reached adequately high cell densities.

CONCLUSIONS

The newly designed defined medium can be widely applied in food safety studies that require media with well-defined chemical constituents.

SIGNIFICANCE AND IMPACT OF THE STUDY

Defined media are important in studies of microbial metabolites and physiological properties. A defined medium capable of cultivating different strains simultaneously is needed in the food safety area. The new defined medium has broader applications in comparing different strains directly and provides more reproducible results.

Statistical optimization of culture conditions of mesophillic gamma-glutamyl transpeptidase from Bacillus altitudinis IHB B1644

Microbial gamma-glutamyl transpeptidase (GGT) is a key enzyme in production of several γ-glutamyl compounds with food and pharmaceutical applications. Bacterial GGTs are not commercially available in the market owing to their low production from various sources. Thus, the study was focused on achieving the higher GGT production from B. altitudinis IHB B1644 by optimizing the culture conditions using one-variable-at-a-time (OVAT) strategy. A mesophillic temperature of 28 °C, agitation 200 rpm and neutral pH 7 were found to be optimal for higher GGT titre. Among the medium components, the monosaccharide glucose served as the best carbon source over disaccharides, and yeast extract was the preferred organic nitrogen source over inorganic nitrogen sources. The statistical approaches (Plakett-Burman and response surface methodology) were further employed for the optimization of medium components. Medium composition: 0.1% w/v glucose, 0.3% w/v yeast extract, 0.03% w/v magnesium sulphate, 0.20% w/v potassium dihydrogen phosphate and 2.5% w/v sodium chloride with inoculum size (1% v/v) was suitable for higher GGT titres (449 U ml^-1). Time kinetics showed the stability of enzyme up to 96 h of incubation suggesting its application in the industrial use. The proposed strategy resulted in 2.6-fold increase in the GGT production compared to that obtained in the unoptimized medium. The results demonstrated that RSM was fitting to identify the optimum production conditions and this finding should be of great importance for commercial GGT production.

d-Serine Degradation by Proteus mirabilis Contributes to Fitness during Single-Species and Polymicrobial Catheter-Associated Urinary Tract Infection

Urinary tract infections are among the most common health care-associated infections worldwide, the majority of which involve a urinary catheter (CAUTI). Our recent investigation of CAUTIs in nursing home residents identified Proteus mirabilis, Enterococcus species, and Escherichia coli as the three most common organisms. These infections are also often polymicrobial, and we identified Morganella morganii, Enterococcus species, and Providencia stuartii as being more prevalent during polymicrobial CAUTI than single-species infection. Our research therefore focuses on identifying “core” fitness factors that are highly conserved in P. mirabilis and that contribute to infection regardless of the presence of these other organisms. In this study, we determined that the ability to degrade d-serine, the most abundant d-amino acid in urine and serum, strongly contributes to P. mirabilis fitness within the urinary tract, even when competing for nutrients with another organism. d-Serine uptake and degradation therefore represent potential targets for disruption of P. mirabilis infections.

Proteus mirabilis is a common cause of catheter-associated urinary tract infection (CAUTI) and secondary bacteremia, which are frequently polymicrobial. We previously utilized transposon insertion-site sequencing (Tn-Seq) to identify novel fitness factors for colonization of the catheterized urinary tract during single-species and polymicrobial infection, revealing numerous metabolic pathways that may contribute to P. mirabilis fitness regardless of the presence of other cocolonizing organisms. One such “core” fitness factor was d-serine utilization. In this study, we generated isogenic mutants in d-serine dehydratase (dsdA), d-serine permease (dsdX), and the divergently transcribed activator of the operon (dsdC) to characterize d-serine utilization in P. mirabilis and explore the contribution of this pathway to fitness during single-species and polymicrobial infection. P. mirabilis was capable of utilizing either d- or l-serine as a sole carbon or nitrogen source, and dsdA, dsdX, and dsdC were each specifically required for d-serine degradation. This capability was highly conserved among P. mirabilis isolates, although not universal among uropathogens: Escherichia coli and Morganella morganii utilized d-serine, while Providencia stuartii and Enterococcus faecalis did not. d-Serine utilization did not contribute to P. mirabilis growth in urine ex vivo during a 6-h time course but significantly contributed to fitness during single-species and polymicrobial CAUTI during a 96-h time course, regardless of d-serine utilization by the coinfecting isolate. d-Serine utilization also contributed to secondary bacteremia during CAUTI as well as survival in a direct bacteremia model. Thus, we propose d-serine utilization as a core fitness factor in P. mirabilis and a possible target for disruption of infection.

IMPORTANCE Urinary tract infections are among the most common health care-associated infections worldwide, the majority of which involve a urinary catheter (CAUTI). Our recent investigation of CAUTIs in nursing home residents identified Proteus mirabilis, Enterococcus species, and Escherichia coli as the three most common organisms. These infections are also often polymicrobial, and we identified Morganella morganii, Enterococcus species, and Providencia stuartii as being more prevalent during polymicrobial CAUTI than single-species infection. Our research therefore focuses on identifying “core” fitness factors that are highly conserved in P. mirabilis and that contribute to infection regardless of the presence of these other organisms. In this study, we determined that the ability to degrade d-serine, the most abundant d-amino acid in urine and serum, strongly contributes to P. mirabilis fitness within the urinary tract, even when competing for nutrients with another organism. d-Serine uptake and degradation therefore represent potential targets for disruption of P. mirabilis infections.

Development of a Chemically Defined Medium for Better Yield and Purification of Enterocin Y31 fromEnterococcus faeciumY31

The macro- and micronutrients in traditional medium, such as MRS, used for cultivating lactic acid bacteria, especially for bacteriocin production, have not been defined, preventing the quantitative monitoring of metabolic flux during bacteriocin biosynthesis. To enhance Enterocin Y31 production and simplify steps of separation and purification, we developed a simplified chemically defined medium (SDM) for the growth ofEnterococcus faeciumY31 and production of its bacteriocin, Enterocin Y31. We found that the bacterial growth was unrelated to Enterocin Y31 production in MRS; therefore, both the growth rate and the Enterocin Y31 production were set as the index for investigation. Single omission experiments revealed that 5 g/L NaCl, five vitamins, two nucleic acid bases, MgSO4·7H2O, MnSO4·4H2O, KH2PO4, K2HPO4, CH3COONa, fourteen amino acids, and glucose were essential for the strain’s growth and Enterocin Y31 production. Thus, a novel simplified and defined medium (SDM) was formulated with 30 components in total. Consequently, Enterocin Y31 production yield was higher in SDM as compared to either MRS or CDM. SDM improved the Enterocin Y31 production and simplified the steps of purification (only two steps), which has broad potential applications.

Determination of the mode of action of enterolysin A, produced by Enterococcus faecalis B9510

AIM

The current study aimed to visualize the damage caused by enterolysin A to the cells of sensitive strains and to find out cleavage site within the peptidoglycan moiety of bacterial cell walls.

METHODS AND RESULTS

Enterolysin A produced by a local isolate, Enterococcus faecalis B9510 was found to rapidly kill cells of the sensitive strain Lactococcus lactis ssp. cremoris 2144 during 120 min of treatment as compared to the untreated control where no such effect was observed. Transmission electron microscopy of the enterolysin A-treated cells revealed leaking of the cytoplasmic contents ultimately resulting in complete lysis of cell walls. To find the cleavage site, purified cell walls of L. lactis ssp. cremoris 2144, Pediococcus pentosaceus 43201 and Lactobacillus delbrueckii ssp. bulgaricus ATCC 11842 were treated with enterolysin A, and liberated amino acids were derivatized for N and C terminals and analysed using thin layer chromatography on silica gel with isopropanol as solvent. The results showed that enterolysin A cleaves the peptide bonds at two locations within peptidoglycan subunits. The first location is between L-alanine and D-glutamic acid of the stem peptide and the other location is between L-lysine of the stem peptide and D-aspartic acid of the interpeptide bridge.

CONCLUSIONS

Enterolysin A cleaves the peptide bonds within the stem peptide as well as in the interpeptide bridge of Gram-positive bacterial cell walls. This gives a possible reason for the broad spectrum of enterolysin A activity.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report identifying the cleavage site of enterolysin A within the cell walls of sensitive bacteria. This will help in identifying potential applications for enterolysin A.