Liquid chromatography time of flight mass spectrometry based environmental metabolomics for the analysis of Pseudomonas putida Bacteria in potable water

Multi-Costimulatory Pathways Drive the Antagonistic Pseudoalteromonas piscicida against the Dominant Pathogenic Vibrio harveyi in Mariculture: Insights from Proteomics and Metabolomics

Vibrio harveyi is the dominant pathogen in mariculture, and biocontrol of this pathogen using antagonistic probiotics is a long-standing biological challenge. Here, Pseudoalteromonas piscicida WCPW15003 as a probiotic effectively antagonized dominant pathogenic V. harveyi in a mariculture, with a growth-of-inhibition ratio of 6.3 h-1. The antagonistic activities of cells and intracellular components of WCPW15003 made a greater contribution to the antagonistic process than did extracellular metabolites and caused the dominance of WCPW15003 during the antagonistic process in vitro. WCPW15003 was safe for the pearl gentian grouper (♀ Epinephelus fuscoguttatus × ♂ Epinephelus lanceolatus) and, as a consequence of the antagonistic effect on V. harveyi, protected the fish from an immune response in vivo. A comprehensive combined proteomics and metabolomics analysis of antagonistic WCPW15003 and pathogenic V. harveyi in a coculture compared to a monoculture was performed to investigate the antagonistic molecular mechanisms. The results showed that during the antagonistic process, WCPW15003 in a coculture had significantly downregulated metabolic pathways for histidine metabolism, arginine biosynthesis, and phenylalanine metabolism, and upregulated glycerophospholipid metabolism, leading to a competitive advantage against the co-occurring species, V. harveyi. This defined a mechanism by which multi-costimulatory pathways drove P. piscicida WCPW15003 against V. harveyi. IMPORTANCE V. harveyi as a dominant pathogen has become a major hazard in mariculture development and seafood safety, and biocontrol of this pathogen using antagonistic probiotic agents is a long-standing biological challenge. P. piscicida WCPW15003 has promise as a novel, safe, and effective bioagent for specifically inhibiting dominant pathogenic V. harveyi and protects mariculture animals from infection by this pathogen by moderating the host immune response, which is heavily driven by multi-costimulatory pathways in a coculture of WCPW15003 and V. harveyi. This work identified a direction for comprehensively elucidating the molecular mechanism of WCPW15003 antagonism against the dominant pathogen in mariculture using modern molecular biology techniques and provided deep insights into the advantages and potential of this antagonistic probiotic against V. harveyi for the construction of an environmentally friendly, recirculating mariculture system.

Modern Analytical Techniques for Detection of Bacteria in Surface and Wastewaters

Contamination of surface waters with pathogens as well as all diseases associated with such events are a significant concern worldwide. In recent decades, there has been a growing interest in developing analytical methods with good performance for the detection of this category of contaminants. The most important analytical methods applied for the determination of bacteria in waters are traditional ones (such as bacterial culturing methods, enzyme-linked immunoassay, polymerase chain reaction, and loop-mediated isothermal amplification) and advanced alternative methods (such as spectrometry, chromatography, capillary electrophoresis, surface-enhanced Raman scattering, and magnetic field-assisted and hyphenated techniques). In addition, optical and electrochemical sensors have gained much attention as essential alternatives for the conventional detection of bacteria. The large number of available methods have been materialized by many publications in this field aimed to ensure the control of water quality in water resources. This study represents a critical synthesis of the literature regarding the latest analytical methods covering comparative aspects of pathogen contamination of water resources. All these aspects are presented as representative examples, focusing on two important bacteria with essential implications on the health of the population, namely Pseudomonas aeruginosa and Escherichia coli.

Metabolomic approach to measuring quality of chilled chicken meat during storage

The metabolites of stored, chilled chicken meat were analyzed using liquid chromatograph-mass spectrometry and metabolomics. The results showed significant differences in the metabolites of chicken meat stored at 4°C for 0 D and meat stored for longer periods of 2 D, 4 D, 6 D, and 10 D, when analyzed based on a variable of importance >2 and P < 0.05. These changed metabolites included amino acids, amines, nucleosides, nucleotides, carbohydrates, organic acids, and other substances. The data from this study provide a holistic understanding of food quality changes in chicken meat during deterioration in storage.

Seasonal metabolic analysis of marine sediments collected from Moreton Bay in South East Queensland, Australia, using a multi-omics-based approach

Anthropogenic effects of urban density have altered natural ecosystems. Such changes include eutrophication of freshwater and adjoining coastal habitats, and increased levels of inorganic nutrients and pollutants into waterways. In Australia, these changes are intensified by large-scale ocean-atmospheric events, leading to considerable abiotic stress on the natural flora and fauna. Bacterial communities in marine sediments from Moreton Bay (South East Queensland, Australia) were examined in order to assess the impact of rainfall changes, chemical pollution, and subsequent abiotic stress on living organisms within a marine ecosystem. Sediments were collected during the wet and dry seasons and analyzed using bacterial metagenomics and community metabolomics techniques. Physicochemical data were also analyzed to account for biological variance that may be due to non-rainfall-based abiotic stresses. Wet-dry seasonality was the dominant control on bacterial community structure and metabolic function. Changes in the availability of nutrients, organic matter and light appeared to be the major seasonal stressors. In contrast, urban and industrial pollutants appeared to be minor stressors at the sites sampled. During the wet season, the bacterial community composition reflected organisms that utilize biogeochemical pathways with fast kinetics, such as aerobic metabolism, direct assimilation of inorganic compounds, and primary production. The transition to the dry season saw the bacterial community composition shift towards organisms that utilize more complex organic energy sources, such as carbohydrates and fatty acids, and anaerobic redox processes.

Infectious helminth ova in wastewater and sludge: A review on public health issues and current quantification practices

Raw and partially treated wastewater has been widely used to maintain the global water demand. Presence of viable helminth ova and larvae in the wastewater raised significant public health concern especially when used for agriculture and aquaculture. Depending on the prevalence of helminth infections in communities, up to 1.0 × 10³ ova/larvae can be presented per litre of wastewater and 4 gm (dry weight) of sludge. Multi-barrier approaches including pathogen reduction, risk assessment, and exposure reduction have been suggested by health regulators to minimise the potential health risk. However, with a lack of a sensitive and specific method for the quantitative detection of viable helminth ova from wastewater, an accurate health risk assessment is difficult to achieve. As a result, helminth infections are difficult to control from the communities despite two decades of global effort (mass drug administration). Molecular methods can be more sensitive and specific than currently adapted culture-based and vital stain methods. The molecular methods, however, required more and thorough investigation for its ability with accurate quantification of viable helminth ova/larvae from wastewater and sludge samples. Understanding different cell stages and corresponding gene copy numbers is pivotal for accurate quantification of helminth ova/larvae in wastewater samples. Identifying specific genetic markers including protein, lipid, and metabolites using multiomics approach could be utilized for cheap, rapid, sensitive, specific and point of care detection tools for helminth ova and larva in the wastewater.

Metabolomic analysis of low and high biofilm-forming Helicobacter pylori strains

The biofilm-forming-capability of Helicobacter pylori has been suggested to be among factors influencing treatment outcome. However, H. pylori exhibit strain-to-strain differences in biofilm-forming-capability. Metabolomics enables the inference of spatial and temporal changes of metabolic activities during biofilm formation. Our study seeks to examine the differences in metabolome of low and high biofilm-formers using the metabolomic approach. Eight H. pylori clinical strains with different biofilm-forming-capability were chosen for metabolomic analysis. Bacterial metabolites were extracted using Bligh and Dyer method and analyzed by Liquid Chromatography/Quadrupole Time-of-Flight mass spectrometry. The data was processed and analyzed using the MassHunter Qualitative Analysis and the Mass Profiler Professional programs. Based on global metabolomic profiles, low and high biofilm-formers presented as two distinctly different groups. Interestingly, low-biofilm-formers produced more metabolites than high-biofilm-formers. Further analysis was performed to identify metabolites that differed significantly (p-value < 0.005) between low and high biofilm-formers. These metabolites include major categories of lipids and metabolites involve in prostaglandin and folate metabolism. Our findings suggest that biofilm formation in H. pylori is complex and probably driven by the bacterium’ endogenous metabolism. Understanding the underlying metabolic differences between low and high biofilm-formers may enhance our current understanding of pathogenesis, extragastric survival and transmission of H. pylori infections.

Development of Untargeted Metabolomics Methods for the Rapid Detection of Pathogenic Naegleria fowleri

Despite comparatively low levels of infection, primary amoebic meningoencephalitis (PAM) induced by Naegleria fowleri is extremely lethal, with mortality rates above 95%. As a thermophile, this organism is often found in moderate-to-warm climates and has the potential to colonize drinking water distribution systems (DWDSs). Current detection approaches require days to obtain results, whereas swift corrective action can maximize the benefit of public health. Presently, there is little information regarding the underlying in situ metabolism for this amoeba but the potential exists to exploit differentially expressed metabolic signatures as a rapid detection technique. This research outlines the biochemical profiles of selected pathogenic and nonpathogenic Naegleria in vitro using an untargeted metabolomics approach to identify a panel of diagnostically meaningful compounds that may enable rapid detection of viable pathogenic N. fowleri and augment results from traditional monitoring approaches.

Metabolic dynamics of Desulfovibrio vulgaris biofilm grown on a steel surface

In this study, a comparative metabolomics approach combining gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) was applied first between planktonic cells and biofilms and then between pure cultures and biofilms of Desulfovibrio vulgaris. The results revealed that the overall metabolic level of the biofilm cells was down-regulated, especially for metabolites related to the central carbon metabolism, compared to the planktonic cells and the pure culture of D. vulgaris. In addition, pathway enrichment analysis of the 58 metabolites identified by GC-MS showed that fatty acid biosynthesis in the biofilm cells was up-regulated, suggesting that fatty acids may be important for the formation, maintenance and function of D. vulgaris biofilm. This study offers a valuable perspective on the metabolic dynamics of the D. vulgaris biofilm.

Determination of Ancylostoma caninum ova viability using metabolic profiling

Differentiation between viable and non-viable hookworm ova in environmental samples is necessary in order to implement strategies to mitigate re-infections in endemic regions. In this study, an untargeted metabolic profiling method was developed that utilised gas chromatography-mass spectrometry (GC-MS) in order to investigate hookworm ova viability. Ancylostoma caninum was used to investigate the metabolites within viable and non-viable ova. Univariate and multivariate statistical analyses of the data resulted in the identification of 53 significant metabolites across all hookworm ova samples. The major compounds observed in viable and non-viable hookworm ova were tetradecanoic acid, commonly known as myristic acid [fold change (FC) = 0.4], and dodecanoic acid, commonly known as lauric acid (FC = 0.388). Additionally, the viable ova had self-protecting metabolites such as prostaglandins, a typical feature absent in non-viable ova. The results of this study demonstrate that metabolic profiling using GC-MS methods can be used to determine the viability of canine hookworm ova. Further studies are needed to assess the applicability of metabolic profiling using GC-MS to detect viable hookworm ova in the mixed (viable and non-viable) populations from environmental samples and identify the metabolites specific to human hookworm species.

New Technologies for Studying Biofilms

Bacteria have traditionally been studied as single-cell organisms. In laboratory settings, aerobic bacteria are usually cultured in aerated flasks, where the cells are considered essentially homogenous. However, in many natural environments, bacteria and other microorganisms grow in mixed communities, often associated with surfaces. Biofilms are comprised of surface-associated microorganisms, their extracellular matrix material, and environmental chemicals that have adsorbed to the bacteria or their matrix material. While this definition of a biofilm is fairly simple, biofilms are complex and dynamic. Our understanding of the activities of individual biofilm cells and whole biofilm systems has developed rapidly, due in part to advances in molecular, analytical, and imaging tools and the miniaturization of tools designed to characterize biofilms at the enzyme level, cellular level, and systems level.

The use of metabolomics in the study of metals in biological systems

Metabolomics and systems biology/toxicology can elucidate novel pathways and mechanistic networks of metals and metalloids in biological systems, as well as providing useful biomarkers of the metal status of organisms.