GC-MS-Based Metabolome and Metabolite Regulation in Serum-Resistant Streptococcus agalactiae

Proteomics and metabolomics analyses of Streptococcus agalactiae isolates from human and animal sources

Streptococcus agalactiae (S. agalactiae), group B Streptococcus (GBS), a major cause of infection in a wide variety of diseases, have been compared in different human and animal sources. We aimed to compare the bacterial proteome and metabolome profiles of human and animal S. agalactiae strains to delineate biological interactions relevant to infection. With the innovative advancement in mass spectrometry, a comparative result between both strains provided a solid impression of different responses to the host. For instance, stress-related proteins (Asp23/Gls24 family envelope stress response protein and heat shock protein 70), which play a role in the survival of GBS under extreme environmental conditions or during treatment, are highly expressed in human and animal strains. One human strain contains ꞵ-lactamase (serine hydrolase) and biofilm regulatory protein (lytR), which are important virulence regulators and potential targets for the design of novel antimicrobials. Another human strain contains the aminoglycosides-resistance bifunctional AAC/APH (A0A0U2QMQ5) protein, which confers resistance to almost all clinically used aminoglycosides. Fifteen different metabolites were annotated between the two groups. L-aspartic acid, ureidopropionic acid, adenosine monophosphate, L-tryptophan, and guanosine monophosphate were annotated at higher levels in human strains. Butyric acid, fumaric acid, isoleucine, leucine, and hippuric acid have been found in both human and animal strains. Certain metabolites were uniquely expressed in animal strains, with fold changes greater than 2. For example, putrescine modulates biofilm formation. Overall, this study provides biological insights into the substantial possible bacterial response reflected in its macromolecular production, either at the proteomic or metabolomic level.

Aspartate metabolic flux promotes nitric oxide to eliminate both antibiotic-sensitive and -resistant Edwardsiella tarda in zebrafish

Introduction

Metabolic reprogramming potentiates host protection against antibiotic-sensitive or -resistant bacteria. However, it remains unclear whether a single reprogramming metabolite is effective enough to combat both antibiotic-sensitive and -resistant bacteria. This knowledge is key for implementing an antibiotic-free approach.

Methods

The reprogramming metabolome approach was adopted to characterize the metabolic state of zebrafish infected with tetracycline-sensitive and -resistant Edwardsiella tarda and to identify overlapping depressed metabolite in dying zebrafish as a reprogramming metabolite.

Results

Aspartate was identify overlapping depressed metabolite in dying zebrafish as a reprogramming metabolite. Exogenous aspartate protects zebrafish against infection caused by tetracycline-sensitive and -resistant E. tarda. Mechanistically, exogenous aspartate promotes nitric oxide (NO) biosynthesis. NO is a well-documented factor of promoting innate immunity against bacteria, but whether it can play a role in eliminating both tetracycline-sensitive and -resistant E. tarda is unknown. Thus, in this study, aspartate was replaced with sodium nitroprusside to provide NO, which led to similar aspartate-induced protection against tetracycline-sensitive and -resistant E. tarda.

Discussion

These findings support the conclusion that aspartate plays an important protective role through NO against both types of E. tarda. Importantly, we found that tetracycline-sensitive and -resistant E. tarda are sensitive to NO. Therefore, aspartate is an effective reprogramming metabolite that allows implementation of an antibiotic-free approach against bacterial pathogens.

Metabolism responses in the intestine of Oreochromis mossambicus exposed to salinity, alkalinity and salt-alkalinity stress using LC-MS/MS-based metabolomics

Multiple abiotic stresses are imposed on fish as a result of unprecedented changes in temperature and precipitation patterns in recent decades. It is unclear how teleosts respond to severe ambient salinity, alkalinity, and saline-alkalinity in terms of their metabolic and molecular osmoregulation processes. The metabolic reactions in the intestine of Oreochromis mossambicus under salinity (25 g/L, S_C), alkalinity (4 g/L, A_C), and saline-alkalinity (salinity: 25 g/L & alkalinity: 4 g/L, SA_C) stresses were examined in this research utilizing LC-MS/MS-based metabolomics. The findings demonstrated that the three osmotic-stressed groups' metabolic profiles were considerably different from those of the control group. Osmolytes, energy sources, free amino acids, and several intermediate metabolites were all synthetically adjusted as part of the osmoregulation associated with the salinity, alkalinity, and saline-alkalinity stress. Following osmotic stress, osmoregulation-related pathways, including the mTOR signaling pathway, TCA cycle, glycolysis/gluconeogenesis, etc., were also discovered in the intestine of O. mossambicus. Overall, our findings can assist in better comprehending the molecular regulatory mechanism in euryhaline fish under various osmotic pressures and can offer a preliminary profile of osmotic regulation.

Functional proteomics identify mannitol metabolism in serum resistance and therapeutic implications in Vibrio alginolyticus

Serum resistance is recognized as one of the most important pathogenic traits of bacterial pathogens, and no control measure is available. Based on our previous discovery that pathogenic Escherichia coli represses glycine, serine, and threonine metabolism to confer serum resistance and that the reactivation of this pathway by exogenous glycine could restore serum sensitivity, we further investigate the mechanism underlying the action of glycine in Vibrio alginolyticus. Thus, V. alginolyticus is treated with glycine, and the proteomic change is profiled with tandem mass tag-based quantitative proteomics. Compared to the control group, glycine treatment influences the expression of a total of 291 proteins. Among them, a trap-type mannitol/chloroaromatic compound transport system with periplasmic component, encoded by N646_0992, is the most significantly increased protein. In combination with the pathway enrichment analysis showing the altered fructose and mannitol metabolism, mannitol has emerged as a possible metabolite in enhancing the serum killing activity. To demonstrate this, exogenous mannitol reduces bacterial viability. This synergistic effect is further confirmed in a V. alginolyticus-Danio rerio infection model. Furthermore, the mechanism underlying mannitol-enabled serum killing is dependent on glycolysis and the pyruvate cycle that increases the deposition of complement components C3b and C5b-9 on the bacterial surface, whereas inhibiting glycolysis or the pyruvate cycle significantly weakened the synergistic effects and complement deposition. These data together suggest that mannitol is a potent metabolite in reversing the serum resistance of V. alginolyticus and has promising use in aquaculture.

Exogenous glycine promotes oxidation of glutathione and restores sensitivity of bacterial pathogens to serum-induced cell death

Pathogenic strains of bacteria are often highly adept at evading serum-induced cell death, which is an essential complement-mediated component of the innate immune response. This phenomenon, known as serum-resistance, is poorly understood, and as a result, no effective clinical tools are available to restore serum-sensitivity to pathogenic bacteria. Here, we provide evidence that exogenous glycine reverses defects in glycine, serine and threonine metabolism associated with serum resistance, restores susceptibility to serum-induced cell death, and alters redox balance and glutathione (GSH) metabolism. More specifically, in Vibrio alginolyticus and Escherichia coli, exogenous glycine promotes oxidation of GSH to GSH disulfide (GSSG), disrupts redox balance, increases oxidative stress and reduces membrane integrity, leading to increased binding of complement. Antioxidant or ROS scavenging agents abrogate this effect and agents that generate or potentiate oxidation stimulate serum-mediated cell death. Analysis of several clinical isolates of E. coli demonstrates that glutathione metabolism is repressed in serum-resistant bacteria. These data suggest a novel mechanism underlying serum-resistance in pathogenic bacteria, characterized by an induced shift in the GSH/GSSG ratio impacting redox balance. The results could potentially lead to novel approaches to manage infections caused by serum-resistant bacteria both in aquaculture and human health.

Exogenous Alanine Reverses the Bacterial Resistance to Zhongshengmycin with the Promotion of the P Cycle in Xanthomonas oryzae

Microbial antibiotic resistance has become a worldwide concern, as it weakens the efficiency of the control of pathogenic microbes in both the fields of medicine and plant protection. A better understanding of antibiotic resistance mechanisms is helpful for the development of efficient approaches to settle this issue. In the present study, GC-MS-based metabolomic analysis was applied to explore the mechanisms of Zhongshengmycin (ZSM) resistance in Xanthomonas oryzae (Xoo), a bacterium that causes serious disease in rice. Our results show that the decline in the pyruvate cycle (the P cycle) was a feature for ZSM resistance in the metabolome of ZSM-resistant strain (Xoo-ZSM), which was further demonstrated as the expression level of genes involved in the P cycle and two enzyme activities were reduced. On the other hand, alanine was considered a crucial metabolite as it was significantly decreased in Xoo-ZSM. Exogenous alanine promoted the P cycle and enhanced the ZSM-mediated killing efficiency in Xoo-ZSM. Our study highlights that the depressed P cycle is a feature in Xoo-ZSM for the first time. Additionally, exogenous alanine is a candidate enhancer and can be applied with ZSM to improve the antibiotic-mediated killing efficiency in the control of infection caused by Xoo.

Serum Metabolomics of Tick-Borne Encephalitis Based on Orbitrap-Mass Spectrometry

Background

Tick-borne encephalitis virus (TBEV), the most prevalent arbovirus, causes potentially fatal encephalitis in humans. Prevalent in northeast China, tick-borne encephalitis (TBE) poses a major threat to public health, local economies and tourism. There are no biomarkers for TBE, which is classified serologically and clinically. Due to sample heterogeneity of samples and different detection platforms, obtaining stable markers is a great challenge for metabolomics. Accurate annotation is vital for data mining and interpretation.

Objective

To identify reliable biomarkers of TBEV infection.

Methods

An untargeted metabolomics analysis of serum from 30 TBE patients and 30 healthy controls was carried out. Liquid chromatography–mass spectrometry (LC-MS)-based metabolomics methods were used to characterize the subjects’ serum metabolic profiles and to screen and validate TBE biomarkers.

Results

A total of 3370 molecular features were extracted from each sample, and the peak intensity of each feature was obtained. Pattern analysis, principal component analysis, partial least squares discriminant analysis were used to screen for potential metabolites. Bilirubin, LysoPC (18:1[9Z]), palmitic acid, and CL (8:0/8:0/8:0/8:0) were significantly different. Pathway enrichment analysis showed that these metabolites were in the fatty acid biosynthesis and glycerophospholipid metabolism pathways. The phospholipid family had a significant difference in both the difference ratio and the abundance.

Conclusion

Phospholipids may be used to distinguish TBEV patients from healthy controls. TBEV infection affects the normal metabolic activity of host cells, providing insight into the pathogenesis of TBE.

Elevation of Fatty Acid Biosynthesis Metabolism Contributes to Zhongshengmycin Resistance in Xanthomonas oryzae

Xanthomonas oryzae severely impacts the yield and quality of rice. Antibiotics are the most common control measure for this pathogen; however, the overuse of antibiotics in past decades has caused bacterial resistance to these antibiotics. The agricultural context is of particular importance as antibiotic-resistant bacteria are prevalent, but the resistance mechanism largely remains unexplored. Herein, using gas chromatography-mass spectrometry (GC-MS), we demonstrated that zhongshengmycin-resistant X. oryzae (Xoo-Rzs) and zhongshengmycin-sensitive X. oryzae (Xoo-S) have distinct metabolic profiles. We found that the resistance to zhongshengmycin (ZS) in X. oryzae is related to increased fatty acid biosynthesis. This was demonstrated by measuring the Acetyl-CoA carboxylase (ACC) activity, the expression levels of enzyme genes involved in the fatty acid biosynthesis and degradation pathways, and adding exogenous materials, i.e., triclosan and fatty acids. Our work provides a basis for the subsequent control of the production of antibiotic-resistant strains of X. oryzae and the development of coping strategies.

Serum metabolomic profiling based on GC/MS helped to discriminate Diffuse Large B-cell Lymphoma patients with different prognosis

BACKGROUND

The varied clinical outcomes of patients with Diffuse Large B Cell Lymphoma (DLBCL) are attributed to the different genetic and phenotypic subtypes. The purpose of this study was to determine whether metabolic alterations were related to cell-of-origin subtypes of DLBCL and find some metabolites which are associated with the clinical outcomes.

METHODS

Pre-treatment serum samples from eighty (80) newly diagnosed DLBCL patients, including twenty-eight (28) patients with Germinal Center B cell-like (GCB) subtypes and fifty-two (52) patients with non-GCB subtypes, were tested by the Gas Chromatography-Mass Spectrometry (GC-MS) technique. Univariate and multivariate analysis methods, principal component analysis (PCA), and partial least square discriminant analysis (PLS-DA) were conducted to examine the potential differential metabolites. Overall survival (OS) was calculated.

RESULTS

Overall, 65 out of 1472 entities were identified for subsequent analysis. Unfortunately, the initial PLS-DA analysis failed to discriminate GCB from non-GCB samples. Intriguingly, further PLS-DA analysis identified two subgroups of DLBCL (named as group A and group B) and the metabolic subgroups were significantly associated with overall survival. Valine, hexadecenoic acid, and pyroglutamic acid were identified and verified as the most important altered metabolites and could be candidate biomarkers for the prognosis of DLBCL.

CONCLUSIONS

Our results demonstrated that metabolic alterations in serum could be helpful to predict different clinical outcomes of DLBCL patients. Further studies are warranted to understand whether the altered metabolites might serve as prognostic factors for DLBCL.

Na+-NQR Confers Aminoglycoside Resistance via the Regulation of l-Alanine Metabolism

The Na⁺-NQR complex functions as a unique redox-driven sodium pump, generating membrane potential directly. However, whether it mediates generation of membrane potential indirectly is unknown. The present study shows that the Na⁺-NQR complex impacts membrane potential through other antiporter families Atp and Mnh. It proceeds by ATP and then cAMP/CRP regulon, which inhibits l-alanine catabolism and promotes l-alanine anabolism. When the Na⁺-NQR complex is reduced as in antibiotic-resistant bacteria, l-alanine is depressed, which is related to the antibiotic resistance phenotypes. However, exogenous l-alanine reverts the phenotype and promotes antibiotic-mediated killing. These findings suggest a novel mechanism by which the Na⁺-NQR system regulates antibiotic resistance via l-alanine metabolism in a cAMP/CRP complex-dependent manner.

Sodium-translocating NADH:quinone oxidoreductase (Na⁺-NQR) functions as a unique redox-driven sodium pump, generating membrane potential, which is related to aminoglycoside antibiotic resistance. However, whether it modulates other metabolisms to confer antibiotic resistance is unknown. The present study showed that loss of nqrA or nqrF led to differential metabolomes with elevated resistance to aminoglycoside antibiotics. Decreased alanine, aspartate, and glutamate metabolism and depressed abundance of alanine were characterized as the most impacted pathway and crucial biomarker, respectively. Further data showed that higher viability was detected in ΔnqrA and ΔnqrF mutant strains than their parent strain ATCC 33787 in the presence of gentamicin but recovered by exogenous l-alanine. It proceeds by the following events. The loss of nqrA or nqrF led to the decrease of membrane potential, ATPase activity, and then ATP and cyclic AMP (cAMP), which reduced the cAMP/CRP (cAMP receptor protein) complex. The reduced cAMP/CRP complex promoted l-alanine catabolism and inhibited l-alanine anabolism, causing reduced levels of alanine. Reduced alanine affected the expression of antiporter families Atp and Mnh genes. Our results suggest a novel mechanism by which the Na⁺-NQR system regulates antibiotic resistance via l-alanine metabolism in a cAMP/CRP complex-dependent manner.

Exogenous maltose enhances Zebrafish immunity to levofloxacin-resistant Vibrio alginolyticus

Understanding the interplay between bacterial fitness, antibiotic resistance, host immunity and host metabolism could guide treatment and improve immunity against antibiotic-resistant pathogens. The acquisition of levofloxacin (Lev) resistance affects the fitness of Vibrio alginolyticus in vitro and in vivo. Lev-resistant (Lev-R) V. alginolyticus exhibits slow growth, reduced pathogenicity and greater resistance to killing by the host, Danio rerio (zebrafish), than Lev-sensitive (Lev-S) V. alginolyticus, suggesting that Lev-R V. alginolyticus triggers a weaker innate immune response in D. rerio than Lev-S V. alginolyticus. Differences were detected in the metabolome of D. rerio infected with Lev-S or Lev-R V. alginolyticus. Maltose, a crucial metabolite, is significantly downregulated in D. rerio infected with Lev-R V. alginolyticus, and exogenous maltose enhances the immune response of D. rerio to Lev-R V. alginolyticus, leading to better clearance of the infection. Furthermore, we demonstrate that exogenous maltose stimulates the host production of lysozyme and its binding to Lev-R V. alginolyticus, which depends on bacterial membrane potential. We suggest that exogenous exposure to crucial metabolites could be an effective strategy for treating and/or managing infections with antibiotic-resistant bacteria.

Biochar mediates microbial communities and their metabolic characteristics under continuous monoculture

Biochar amendment has been extensively used to improve plant performance and suppress disease in monoculture systems; however, few studies have focused on the underlying control mechanisms of replanting disease. In this study, we assessed the effects of biochar application on Radix pseudostellariae plant growth, rhizosphere soil microbial communities, and the physiological properties of microorganisms in a consecutive monoculture system. We found that biochar addition had little impact on the physiological parameters of tissue cultures of R. pseudostellaria but did significantly mediate microbial abundance in the rhizosphere soil of different consecutive monoculture years, leading to decreases in the abundance of pathogenic Fusarium oxysporum, Talaromyces helicus, and Kosakonia sacchari. Furthermore, biochar amendment had negative effects on the growth of beneficial bacteria, such as Burkholderia ambifaria, Pseudomonas chlororaphis, and Bacillus pumilus. Metabolomic analysis indicated that biochar significantly influenced the metabolic processes of F. oxysporum while inhibiting the mycelial growth and abating the virulence on plants. In summary, this study details the potential mechanisms responsible for the biochar-stimulated changes in the abundances and metabolism of rhizosphere bacteria and fungi, decreases in the contents of pathogens, and therefore improvements in the environmental conditions for plants growth. Further research is needed to evaluate the effects of biochar in long-term field trials.

Aeromonas hydrophila suppresses complement pathways via degradation of complement C3 in bony fish by metalloprotease

Aeromonas hydrophila is a pathogen that causes high mortality in the grass carp. The complement system, as a frontline defence of innate immunity, plays an important role in the immune response against pathogens. However, the immunity evasion mechanism of A. hydrophila against the complement system of grass carp remains unclear. In this study, we described an additional mechanism used by A. hydrophila GD18 to evade the complement system and survive in grass carp serum. First, A. hydrophila evaded the bactericidal activity of grass carp serum. Second, the haemolytic activity assays showed that A. hydrophila obviously suppressed the alternative pathway, which depended on preventing the formation or disabling the function of the membrane-attack complex (MAC). Further research indicated that A. hydrophila targeted complement C3, the central component of the three complement pathways, and degraded it in the grass carp serum, leading to the inhibition of the complement pathways, which resulted in the serum-resistance of A. hydrophila. Furthermore, cleavage analyses showed that extracellular proteases (ECPases) of A. hydrophila efficiently cleaved purified C3 as well as C3 in grass carp serum. Finally, protease inhibitor studies and mass spectrum analysis identified the secreted metalloprotease elastase (AhE), which was present in large amounts in crude ECPases, as the central molecule responsible for C3 cleavage. Compared to wild strain GD18, the AhE knockout, Δahe was dramatically reduced in the ability of serum resistance. Our findings suggested that A. hydrophila escaped serum-killing by suppressing the complement pathways via the degradation of complement C3 in bony fish, which was related to secreted metalloproteases.

Glycine, serine and threonine metabolism confounds efficacy of complement-mediated killing

Serum resistance is a poorly understood but common trait of some difficult-to-treat pathogenic strains of bacteria. Here, we report that glycine, serine and threonine catabolic pathway is down-regulated in serum-resistant Escherichia coli, whereas exogenous glycine reverts the serum resistance and effectively potentiates serum to eliminate clinically-relevant bacterial pathogens in vitro and in vivo. We find that exogenous glycine increases the formation of membrane attack complex on bacterial membrane through two previously unrecognized regulations: 1) glycine negatively and positively regulates metabolic flux to purine biosynthesis and Krebs cycle, respectively. 2) α-Ketoglutarate inhibits adenosine triphosphate synthase, which in together promote the formation of cAMP/CRP regulon to increase the expression of complement-binding proteins HtrE, NfrA, and YhcD. The results could lead to effective strategies for managing the infection with serum-resistant bacteria, an especially valuable approach for treating individuals with weak acquired immunity but a normal complement system.

Serum-resistant bacteria can escape complement killing in the bloodstream. Here, using metabolomics and metabolite perturbations, the authors describe an altered metabolic state in serum-resistant Escherichia coli and show that exogenous glycine potentiates elimination of pathogenic bacteria in vivo.

Analysis of serum metabolite profiles in syphilis patients by untargeted metabolomics

BACKGROUND

Global metabolomics analysis can provide substantial information on energy metabolism, physiology, possible diagnostic biomarkers and intervention strategies for pathogens.

OBJECTIVE

To gain a better understanding of the mechanisms of syphilis and analysis of serum metabolite profiles in syphilis patients.

METHODS

We conducted an untargeted metabolomics analysis of serum from 20 syphilis patients and 20 healthy controls.

RESULTS

A total of 2890 molecular features were extracted from each sample, and the peak intensity of each feature was obtained. Distinct differential metabolites were identified by principal component analysis, partial least squares-discriminant analysis and hierarchical clustering analysis. Furthermore, five metabolites were identified as significantly different by Student's t-test, including trimethylamine N-oxide, l-arginine, lysoPC(18:0), betaine and acetylcarnitine. KEGG analysis showed that these differential metabolites were in various pathways, including Chagas disease, fatty acid biosynthesis, primary bile acid biosynthesis, Salmonella infection, ABC transporters, glycerophospholipid metabolism and choline metabolism. Among them, trimethylamine N-oxide was 3.922 times in patients with syphilis than healthy controls.

CONCLUSION

Trimethylamine N-oxide may be used as an indicator to distinguish between syphilis patients and healthy controls. The changes in these metabolites suggest that Treponema pallidum affects the normal metabolic activity of host cells, providing some clues for elucidating the pathogenesis of T. pallidum.

A metabolomic investigation into the temperature-dependent virulence of Pseudomonas plecoglossicida from large yellow croaker (Pseudosciaena crocea)

Pseudomonas plecoglossicida is associated with multiple fish diseases, and temperature is one of the most important environmental factors related to its outbreak. To elucidate the influence of temperature variation on the pathogen, the global metabolomics of P. plecoglossicida (NZBD9) were analysed at the virulent (18°C) and avirulent (12°C and 28°C) temperatures. The result showed that the levels of Phosphoric acid, Tyrosine, Spermidine and Sucrose were significantly reduced，while Itaconic acid, Glucaric acid and Isomaltose were increased in P. plecoglossicida at 18°C. These metabolic adjustments assist P. plecoglossicida to survive in adverse environments, proliferate in the host, colonize and resist host immune clearance during the initial steps of infection. The results suggested that L321_03626 and L321_18122 genes played a key role in the regulation of these metabolic adaptions and thus regulated P. plecoglossicida virulence at virulent temperature, which was proved by further gene silencing and artificial infection. The present study, for the first time, determines the P. plecoglossicida metabolomic responses to temperature variation, which is helpful to explore its pathogenic mechanism and provides reference for disease control.

Metabolite Profiles of the Cerebrospinal Fluid in Neurosyphilis Patients Determined by Untargeted Metabolomics Analysis

The mechanism underlying the stealth property of neurosyphilis is still unclear. Global metabolomics analysis can provide substantial information on energy metabolism, physiology and possible diagnostic biomarkers and intervention strategies for pathogens. To gain better understanding of the metabolic mechanism of neurosyphilis, we conducted an untargeted metabolomics analysis of cerebrospinal fluid (CSF) from 18 neurosyphilis patients and an identical number of syphilis/non-neurosyphilis patients and syphilis-free patients using the Agilent, 1290 Infinity LC system. The raw data were normalized and subjected to subsequent statistical analysis by MetaboAnalyst 4.0. Metabolites with a variable importance in projection (VIP) greater than one were validated by Student’s T-test. A total of 1,808 molecular features were extracted from each sample using XCMS software, and the peak intensity of each feature was obtained. Partial-least squares discrimination analysis provided satisfactory separation by comparing neurosyphilis, syphilis/non-neurosyphilis and syphilis-free patients. A similar trend was obtained in the hierarchical clustering analysis. Furthermore, several metabolites were identified as significantly different by Student’s T-test, including L-gulono-gamma-lactone, D-mannose, N-acetyl-L-tyrosine, hypoxanthine, and S-methyl-5′-thioadenosine. Notably, 87.369-fold and 7.492-fold changes of N-acetyl-L-tyrosine were observed in neurosyphilis patients compared with syphilis/non-neurosyphilis patients and syphilis-free patients. These differential metabolites are involved in overlapping pathways, including fructose and mannose metabolism, lysosomes, ABC transporters, and galactose metabolism. Several significantly expressed metabolites were identified in CSF from neurosyphilis patients, including L-gulono-gamma-lactone, D-mannose, N-acetyl-L-tyrosine, and hypoxanthine. These differential metabolites could potentially improve neurosyphilis diagnostics in the future. The role of these differential metabolites in the development of neurosyphilis deserves further exploration.

Delineation of the pan-proteome of fish-pathogenic Streptococcus agalactiae strains using a label-free shotgun approach

BACKGROUND

Streptococcus agalactiae (GBS) is a major pathogen of Nile tilapia, a global commodity of the aquaculture sector. The aims of this study were to evaluate protein expression in the main genotypes of GBS isolated from diseased fishes in Brazil using a label-free shotgun nano-liquid chromatography-ultra definition mass spectrometry (nanoLC-UDMS^E) approach and to compare the differential abundance of proteins identified in strains isolated from GBS-infected fishes and humans.

RESULTS

A total of 1070 protein clusters were identified by nanoLC-UDMS^E in 5 fish-adapted GBS strains belonging to sequence types ST-260 and ST-927 and the non-typeable (NT) lineage and 1 human GBS strain (ST-23). A total of 1065 protein clusters corresponded to the pan-proteome of fish-adapted GBS strains; 989 of these were identified in all fish-adapted GBS strains (core proteome), and 62 were shared by at least two strains (accessory proteome). Proteins involved in the stress response and in the regulation of gene expression, metabolism and virulence were detected, reflecting the adaptive ability of fish-adapted GBS strains in response to stressor factors that affect bacterial survival in the aquatic environment and bacterial survival and multiplication inside the host cell. Measurement of protein abundance among different hosts showed that 5 and 26 proteins were exclusively found in the human- and fish-adapted GBS strains, respectively; the proteins exclusively identified in fish isolates were mainly related to virulence factors. Furthermore, 215 and 269 proteins were up- and down-regulated, respectively, in the fish-adapted GBS strains in comparison to the human isolate.

CONCLUSIONS

Our study showed that the core proteome of fish-adapted GBS strains is conserved and demonstrated high similarity of the proteins expressed by fish-adapted strains to the proteome of the human GBS strain. This high degree of proteome conservation of different STs suggests that, a monovalent vaccine may be effective against these variants.

Metabolic regulation protects mice against Klebsiella pneumoniae lung infection

PURPOSE

Klebsiella pneumoniae-caused pneumonia is a risk factor for development of lung injury. However, the current clinical isolates of K. pneumoniae are mostly multidrug-resistance and thus must be addressed with new treatments. One ideal approach is to enhance the innate immunity of the infected host through metabolic modulators.

MATERIALS AND METHODS

We used GC/MS-based metabolomics to profile the metabolomes among Control, Dead and Survival groups. The key metabolites were administrated in mice, and the bacterial loads in lung and survival were measured. The effect of the key metabolites on macrophage phagocytosis was determined by flow cytometry.

RESULTS

Compared with the mice that compromised from K. pneumoniae lung infection, mice that survived the infection displayed the varied metabolomic profile. The differential analysis of metabolome showed D-Glucose, Glutamine, L-Serine, Myo-inositol, Ethanedioic acid and Lactic acid related to the host surviving a K. pneumoniae lung infection. Further pathway enrichment analysis proposed that valine, leucine and isoleucine biosynthesis involved in outcome of lung infection. The follow-up data showed that exogenous L-Serine, L-Valine and L-Leucine could decline the load of K. pneumoniae in infected lung and increases the mouse survival. More interestingly, L-Serine, L-Valine and L-Leucine also were able to promote macrophage phagocytosis that is the natural way to promote hosts to clear lung pathogens.

CONCLUSIONS

Our study establishes a novel strategy of identifying metabolic modulator from surviving host and emphasizes the feasibility of employing the metabolic modulator as a therapy for K. pneumoniae lung infection.

Boosted TCA cycle enhances survival of zebrafish to Vibrio alginolyticus infection

Vibrio alginolyticus is a waterborne pathogen that infects a wide variety of hosts including fish and human, and the outbreak of this pathogen can cause a huge economic loss in aquaculture. Thus, enhancing host's capability to survive from V. alginolyticus infection is key to fighting infection and this remains still unexplored. In the present study, we established a V. alginolyticus-zebrafish interaction model by which we explored how zebrafish survived from V. alginolyticus infection. We used GC-MS based metabolomic approaches to characterize differential metabolomes between survival and dying zebrafish upon infection. Pattern recognition analysis identified the TCA cycle as the most impacted pathway. The metabolites in the TCA cycle were decreased in the dying host, whereas the metabolites were increased in the survival host. Furthermore, the enzymatic activities of the TCA cycle including pyruvate dehydrogenase (PDH), α-ketoglutaric dehydrogenase (KGDH) and succinate dehydrogenase (SDH) also supported this conclusion. Among the increased metabolites in the TCA cycle, malic acid was the most crucial biomarker for fish survival. Indeed, exogenous malate promoted zebrafish survival in a dose-dependent manner. The corresponding activities of KGDH and SDH were also increased. These results indicate that the TCA cycle is a key pathway responsible for the survival or death in response to infection caused by V. alginolyticus, and highlight the way on development of metabolic modulation to control the infection.

Functional metabolomics approach reveals the reduced biosynthesis of fatty acids and TCA cycle is required for pectinase activity in Bacillus licheniformis

Increase of pectinase activity is especially important in fermentation industry. Understanding of the metabolic mechanisms can find metabolic modulation approach to promote high yield of pectinase. Higher activity of pectinase was detected in DY1 than DY2, two strains of Bacillus licheniformis. GC-MS-based metabolomics identified differential metabolome of DY2 compared with DY1, characterizing the increased TCA cycle and biosynthesis of fatty acids. Elevated activity of pyruvate dehydrogenase (PDH), α-ketoglutaric dehydrogenase (KGDH) and succinate dehydrogenase (SDH) showed global elevation of carbon metabolism, which is consistent with the result that lowers glucose in DY2 than DY1. Inhibitors malonate, furfural and triclosan, of PDH, SDH and biosynthesis of fatty acids, promoted pectinase activity, where triclosan increased pectinase activity by 179%. These results indicate that functional metabolomics is an effective approach to understand metabolic mechanisms of fermentation production and provides clues to develop new methods for changing bacterial physiology and production.

Edwardsiella tarda Sip2: A Serum-Induced Protein That Is Essential to Serum Survival, Acid Resistance, Intracellular Replication, and Host Infection

Edwardsiella tarda is a broad-host pathogen that can infect mammals, reptiles, and fish. E. tarda exhibits a remarkable ability to survive in host serum and replicate in host phagocytes, but the underlining mechanism is unclear. In this study, in order to identify E. tarda proteins involved in serum resistance, iTRAQ proteomic analysis was performed to examine the whole-cell protein profiles of TX01, a pathogenic E. tarda isolate, in response to serum treatment. Of the differentially expressed proteins identified, one (named Sip2) possesses a conserved hydrogenase domain and is homologous to the putative hydrogenase accessory protein HypB. When Sip2 was expressed in Escherichia coli, it significantly enhanced the survival of the host cells in serum. Compared to TX01, the sip2 knockout, TX01Δsip2, was dramatically reduced in the ability of hydrogenase activity, serum resistance, intracellular replication, dissemination in fish tissues, and causing mortality in infected fish. The lost virulence capacities of TX01Δsip2 were restored by complementation with the sip2 gene. Furthermore, TX01Δsip2 was significantly reduced in the capacity to grow under low pHs and iron-depleted conditions, and was unable to maintain its internal pH in acidic environment. Taken together, these results indicate that Sip2 is a novel serum-induced protein that is essential to serum resistance, cellular and tissue infection, and coping with acidic stress via its ability to modulate intracellular pH.

Edwardsiella tarda Tunes Tricarboxylic Acid Cycle to Evade Complement-Mediated Killing

Evasion of complement-mediated killing is a common phenotype for many different types of pathogens, but the mechanism is still poorly understood. Most of the clinic isolates of Edwardsiella tarda, an important pathogen infecting both of human and fish, are commonly found serum-resistant. To explore the potential mechanisms, we applied gas chromatography-mass spectrometry (GC-MS)-based metabolomics approaches to profile the metabolomes of E. tarda EIB202 in the presence or absence of serum stress. We found that tricarboxylic acid (TCA) cycle was greatly enhanced in the presence of serum. The quantitative real-time PCR (qRT-PCR) and enzyme activity assays validated this result. Furthermore, exogenous succinate that promotes the TCA cycle increased serum resistance, while TCA cycle inhibitors (bromopyruvate and propanedioic acid) that inhibit TCA cycle, attenuated serum resistance. Moreover, the enhanced TCA cycle increased membrane potential, thus decreased the formation of membrane attack complex at cell surface, resulting serum resistance. These evidences suggested a previously unknown membrane potential-dependent mechanism of serum resistance. Therefore, our findings reveal that pathogen mounts a metabolic trick to cope with the serum complement-mediated killing.

A metabolomic investigation into the effects of temperature on Streptococcus agalactiae from Nile tilapia (Oreochromis niloticus) based on UPLC-MS/MS

Streptococcosis caused by Streptococcus agalactiae is one of the most serious diseases in farmed tilapia, and temperature is one of the most important environmental factors related to its outbreak. To elucidate the influence of temperature variation on the pathogen from a metabolic perspective, the global metabolomics of 2 pathogenic strains of S. agalactiae from sick tilapia were analyzed at 35°C and 25°C using ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) combined with pattern recognition approaches and pathway analysis. The result showed that the metabolic status of S. agalactiae was extensively affected by its culture temperature. Based on the results of metabolites contributing to these differences, a large number of nucleotides and their ramifications were markedly elevated at 35°C. Various energy substances, components of the cell wall and substances associated with stress regulation such as glyceraldehyde 3-phosphate, pyroglutamic acid, glutamate, d-Alanyl-d-alanine, glycerophosphocholine, dephospho-CoA, and oxidized glutathione increased when the strains were cultured at 35°C. Additionally, a general decrease in various precursors of capsule, antigen, and virulence protein formation were detected including mannose, maltotriose, N-acetyl-d-glucosamine 6-phosphate, uracil, proline, and citrulline. These metabolic changes indicated that metabolic activity decreased, while adaptive ability to environment and pathogenicity to host increased at high temperature. This study is the first to determine the metabolomic responses of S. agalactiae to temperature, and the results are useful to reveal its pathogenic mechanism and find effective disease control.

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions

Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation. The metagenomic analysis of viromes without exogenous DNA contamination and microbiomes of vent samples indicated that viruses had compensation effects on the metabolisms of their host microorganisms. Viral genes not only participated in most of the microbial metabolic pathways but also formed branched pathways in microbial metabolisms, including pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; nitrogen metabolism and assimilation pathways of the two-component system; selenocompound metabolism; aminoacyl-tRNA biosynthesis; and amino sugar and nucleotide sugar metabolism. As is well known, deep-sea hydrothermal vent ecosystems exist in relatively isolated environments which are barely influenced by other ecosystems. The metabolic compensation of hosts mediated by viruses might represent a very important aspect of virus-host interactions.

Viruses are the most abundant biological entities in the oceans and have very important roles in regulating microbial community structure and biogeochemical cycles. The relationship between virus and host microbes is broadly thought to be that of predator and prey. Viruses can lyse host cells to control microbial population sizes and affect community structures of hosts by killing specific microbes. However, viruses also influence their hosts through manipulation of bacterial metabolism. We found that viral genes not only participated in most microbial metabolic pathways but also formed branched pathways in microbial metabolisms. The metabolic compensation of hosts mediated by viruses may help hosts to adapt to extreme environments and may be essential for host survival.

Metabolic Mechanism for l-Leucine-Induced Metabolome To Eliminate Streptococcus iniae

Crucial metabolites that modulate hosts' metabolome to eliminate bacterial pathogens have been documented, but the metabolic mechanisms are largely unknown. The present study explores the metabolic mechanism for l-leucine-induced metabolome to eliminate Streptococcus iniae in tilapia. GC-MS-based metabolomics was used to investigate the tilapia liver metabolic profile in the presence of exogenous l-leucine. Thirty-seven metabolites of differential abundance were determined, and 11 metabolic pathways were enriched. Pattern recognition analysis identified serine and proline as crucial metabolites, which are the two metabolites identified in survived tilapias during S. iniae infection, suggesting that the two metabolites play crucial roles in l-leucine-induced elimination of the pathogen by the host. Exogenous l-serine reduces the mortality of tilapias infected by S. iniae, providing a robust proof supporting the conclusion. Furthermore, exogenous l-serine elevates expression of genes IL-1β and IL-8 in tilapia spleen, but not TNFα, CXCR4 and Mx, suggesting that the metabolite promotes a phagocytosis role of macrophages, which is consistent with the finding that l-leucine promotes macrophages to kill both Gram-positive and Gram-negative bacterial pathogens. Therefore, the ability of phagocytosis enhanced by exogenous l-leucine is partly attributed to elevation of l-serine. These results demonstrate a metabolic mechanism by which exogenous l-leucine modulates tilapias' metabolome to enhance innate immunity and eliminate pathogens.

Exogenous l-Valine Promotes Phagocytosis to Kill Multidrug-Resistant Bacterial Pathogens

The emergence of multidrug-resistant bacteria presents a severe threat to public health and causes extensive losses in livestock husbandry and aquaculture. Effective strategies to control such infections are in high demand. Enhancing host immunity is an ideal strategy with fewer side effects than antibiotics. To explore metabolite candidates, we applied a metabolomics approach to investigate the metabolic profiles of mice after Klebsiella pneumoniae infection. Compared with the mice that died from K. pneumoniae infection, mice that survived the infection displayed elevated levels of l-valine. Our analysis showed that l-valine increased macrophage phagocytosis, thereby reducing the load of pathogens; this effect was not only limited to K. pneumoniae but also included Escherichia coli clinical isolates in infected tissues. Two mechanisms are involved in this process: l-valine activating the PI3K/Akt1 pathway and promoting NO production through the inhibition of arginase activity. The NO precursor l-arginine is necessary for l-valine-stimulated macrophage phagocytosis. The valine-arginine combination therapy effectively killed K. pneumoniae and exerted similar effects in other Gram-negative (E. coli and Pseudomonas aeruginosa) and Gram-positive (Staphylococcus aureus) bacteria. Our study extends the role of metabolism in innate immunity and develops the possibility of employing the metabolic modulator-mediated innate immunity as a therapy for bacterial infections.