Applications of cellular fatty acid analysis

In vitro alternative for reactogenicity assessment of outer membrane vesicle based vaccines

Intrinsic or added immune activating molecules are key for most vaccines to provide desired immunity profiles but may increase systemic reactogenicity. Regulatory agencies require rabbit pyrogen testing (RPT) for demonstration of vaccine reactogenicity. Recently, the monocyte activation test (MAT) gained popularity as in vitro alternative, yet this assay was primarily designed to test pyrogen-free products. The aim was to adjust the MAT to enable testing of pyrogen containing vaccines in an early stage of development where no reference batch is yet available. The MAT and RPT were compared for assessing unknown safety profiles of pertussis outer membrane vesicle (OMV) vaccine candidates to those of Bexsero as surrogate reference vaccine. Pertussis OMVs with wild-type LPS predominantly activated TLR2 and TLR4 and were more reactogenic than Bexsero. However, this reactogenicity profile for pertussis OMVs could be equalized or drastically reduced compared to Bexsero or a whole-cell pertussis vaccine, respectively by dose changing, modifying the LPS, intranasal administration, or a combination of these. Importantly, except for LPS modified products, reactogenicity profiles obtained with the RPT and MAT were comparable. Overall, we demonstrated that this pertussis OMV vaccine candidate has an acceptable safety profile. Furthermore, the MAT proved its applicability to assess reactogenicity levels of pyrogen containing vaccines at multiple stages of vaccine development and could eventually replace rabbit pyrogen testing.

Fusarium oxysporum & Fusarium solani: Identification, Characterization, and Differentiation the Fungal Phenolic Profiles by HPLC and the Fungal Lipid Profiles by GC-MS

Fusarium is a famous genus including a numerous species of endophytic fungi as it is known as a productive source of secondary metabolites which had various bioactivities. Fungal secondary metabolites are defined as chemical compounds produced by fungus and not essential for it. The common secondary metabolites of Fusarium sp. (e.g., phenols, flavonoids, alkaloids, saponins, and terpenes) had a wide range of biological properties comprising antioxidant, antidiabetic, antibacterial, antifungal, and cytotoxic activities. In this way, the present study was performed to evaluate the phenolic compounds and flavonoids of Fusarium oxysporum and Fusarium solani qualitatively and quantitatively via high-performance liquid chromatography (HPLC). Moreover, lipid criteria of Fusarium oxysporum and Fusarium solani extracts had been displayed by gas chromatography-mass spectrometry (GC-MS) and their fatty acids had been identified to define the prolific species of the most biological and valuable fatty acids. In discrimination between phenols and flavonoids of Fusarium oxysporum and Fusarium solani as natural biological constituents analyzed by HPLC, the methanolic extracts of Fusarium species revealed that phenols level was elevated in F. oxysporum than its level in F. solani as well flavonoids level was advanced in F. oxysporum compared to F. solani. Furthermore, the HPLC chromatograph showed significant detection for some phenols in F. oxysporum extract were disappeared in F. solani extract and also some flavonoids were detected in F. oxysporum extract were vanished in F. solani extract. On the other side, the quantitative lipid analysis of Fusarium species chloroform extracts showed significant elevation in F. oxysporum lipid amount compared to F. solani, as the qualitative lipid analysis by GC-MS indicated that the concentration of saturated fatty acids was receded in F. oxysporum (29.18%) than its concentration in F. solani (40.11%) and the ratio of oxidation was 3.73% in F. oxysoporum while in F. solani was 4.23%. These displayed data illustrated conclusively that Fusarium oxysporum had a wide medicinal effectiveness as antioxidant, anticancer, anti-inflammation, and cardioprotective action due to its plentiful content from valuable phenols, flavonoids, and fatty acids in comparison with F. solani, as it may be elected as an alternative natural drug for some pharmaceutical applications.

The Fatty Acid Methyl Ester (FAME) profile of Phytophthora agathidicida and its potential use as diagnostic tool

Phytophthora diseases cause devastation to crops and native ecosystems worldwide. In New Zealand, Phytophthora agathidicida is threatening the survival of kauri, an endemic, culturally and ecologically important tree species. The current method for detecting P. agathidicida is a soil bating assay that is time-consuming and requires high levels of expertise to assess, thus limiting the analytical sample throughput. Here, we characterized the fatty acid methyl ester (FAME) profile of P. agathidicida. We also compared it with the FAME profile of P. cinnamomi and assessed the efficacy of FAME analysis as a diagnostic tool for detecting the pathogen in soil samples. In FAME analysis, the total fatty acid content is isolated from a sample and converted to FAMEs for analysis, a process that takes less than a day. Unique fatty acid acyl chains can serve as biomarkers for specific organisms. We detected 12 fatty acids in P. agathidicida, two of which (20:4ω6 and 20:5ω3) show promise as potential Phytophthora specific biomarkers. Collectively, these findings advance our fundamental understanding of P. agathidicida biology and provide a promising technique to increase the rate of sample processing and the speed of pathogen detection for P. agathidicida in soil.

Detection of Species-Specific Lipids by Routine MALDI TOF Mass Spectrometry to Unlock the Challenges of Microbial Identification and Antimicrobial Susceptibility Testing

MALDI-TOF mass spectrometry has revolutionized clinical microbiology diagnostics by delivering accurate, fast, and reliable identification of microorganisms. It is conventionally based on the detection of intracellular molecules, mainly ribosomal proteins, for identification at the species-level and/or genus-level. Nevertheless, for some microorganisms (e.g., for mycobacteria) extensive protocols are necessary in order to extract intracellular proteins, and in some cases a protein-based approach cannot provide sufficient evidence to accurately identify the microorganisms within the same genus (e.g., Shigella sp. vs E. coli and the species of the M. tuberculosis complex). Consequently lipids, along with proteins are also molecules of interest. Lipids are ubiquitous, but their structural diversity delivers complementary information to the conventional protein-based clinical microbiology matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) based approaches currently used. Lipid modifications, such as the ones found on lipid A related to polymyxin resistance in Gram-negative pathogens (e.g., phosphoethanolamine and aminoarabinose), not only play a role in the detection of microorganisms by routine MALDI-TOF mass spectrometry but can also be used as a read-out of drug susceptibility. In this review, we will demonstrate that in combination with proteins, lipids are a game-changer in both the rapid detection of pathogens and the determination of their drug susceptibility using routine MALDI-TOF mass spectrometry systems.

Staphylococcus borealis sp. nov., isolated from human skin and blood

When analysing a large cohort of Staphylococcus haemolyticus, using whole-genome sequencing, five human isolates (four from the skin and one from a blood culture) with aberrant phenotypic and genotypic traits were identified. They were phenotypically similar with yellow colonies, nearly identical 16S rRNA gene sequences and initially speciated as S. haemolyticus based on 16S rRNA gene sequence and MALDI-TOF MS. However, compared to S. haemolyticus, these five strains demonstrate: (i) considerable phylogenetic distance with an average nucleotide identity <95 % and inferred DNA-DNA hybridization <70  %; (ii) a pigmented phenotype; (iii) urease production; and (iv) different fatty acid composition. Based on the phenotypic and genotypic results, we conclude that these strains represent a novel species, for which the name Staphylococcus borealis sp. nov. is proposed. The novel species belong to the genus Staphylococcus and is coagulase- and oxidase-negative and catalase-positive. The type strain, 51-48^T, is deposited in the Culture Collection University of Gothenburg (CCUG 73747^T) and in the Spanish Type Culture Collection (CECT 30011^T).

Spontaneously released Neisseria meningitidis outer membrane vesicles as vaccine platform: production and purification

Outer membrane vesicles (OMVs) are nanoparticles produced by Gram-negative bacteria that can be used as vaccines. The application of OMVs as vaccine component can be expanded by expressing heterologous antigens on OMVs, creating an OMV-based antigen presenting platform. This study aims to develop a production process for such OMV-based vaccines and studies a production method based on meningococcal OMVs that express heterologous antigens on their surface. As a proof of concept, the Borrelia burgdorferi antigens OspA and OspC were expressed on Neisseria meningitidis OMVs to create a concept anti-Lyme disease vaccine. Production of OMVs released in the culture supernatant was induced by high dissolved oxygen concentrations and purification was based on scalable unit operations. A crude recovery of 90 mg OMV protein could be obtained per liter culture. Expressing heterologous antigens on the OMVs did result in minor reduction of bacterial growth, while OMV production remained constant. The antigen expression did not alter the OMV characteristics. This study shows that production of well characterized OMVs containing heterologous antigens is possible with high yields by combining high oxygen concentrations with an optimized purification process. It is concluded that heterologous OMVs show potential as a vaccine platform.

Conversion of rainforest to oil palm and rubber plantations alters energy channels in soil food webs

In the last decades, lowland tropical rainforest has been converted in large into plantation systems. Despite the evident changes above ground, the effect of rainforest conversion on the channeling of energy in soil food webs was not studied. Here, we investigated community-level neutral lipid fatty acid profiles in dominant soil fauna to track energy channels in rainforest, rubber, and oil palm plantations in Sumatra, Indonesia. Abundant macrofauna including Araneae, Chilopoda, and Diplopoda contained high amounts of plant and fungal biomarker fatty acids (FAs). Lumbricina had the lowest amount of plant, but the highest amount of animal-synthesized C20 polyunsaturated FAs as compared to other soil taxa. Mesofauna detritivores (Collembola and Oribatida) contained high amounts of algal biomarker FAs. The differences in FA profiles between taxa were evident if data were analyzed across land-use systems, suggesting that soil fauna of different size (macro- and mesofauna) are associated with different energy channels. Despite that, rainforest conversion changed the biomarker FA composition of soil fauna at the community level. Conversion of rainforest into oil palm plantations enhanced the plant energy channel in soil food webs and reduced the bacterial energy channel; conversion into rubber plantations reduced the AMF-based energy channel. The changes in energy distribution within soil food webs may have significant implications for the functioning of tropical ecosystems and their response to environmental changes. At present, these responses are hard to predict considering the poor knowledge on structure and functioning of tropical soil food webs.

Utilisation of Ambient Laser Desorption Ionisation Mass Spectrometry (ALDI-MS) Improves Lipid-Based Microbial Species Level Identification

The accurate and timely identification of the causative organism of infection is important in ensuring the optimum treatment regimen is prescribed for a patient. Rapid evaporative ionisation mass spectrometry (REIMS), using electrical diathermy for the thermal disruption of a sample, has been shown to provide fast and accurate identification of microorganisms directly from culture. However, this method requires contact to be made between the REIMS probe and microbial biomass; resulting in the necessity to clean or replace the probes between analyses. Here, optimisation and utilisation of ambient laser desorption ionisation (ALDI) for improved speciation accuracy and analytical throughput is shown. Optimisation was completed on 15 isolates of Escherichia coli, showing 5 W in pulsatile mode produced the highest signal-to-noise ratio. These parameters were used in the analysis of 150 clinical isolates from ten microbial species, resulting in a speciation accuracy of 99.4% - higher than all previously reported REIMS modalities. Comparison of spectral data showed high levels of similarity between previously published electrical diathermy REIMS data. ALDI does not require contact to be made with the sample during analysis, meaning analytical throughput can be substantially improved, and further, increases the range of sample types which can be analysed in potential direct-from-sample pathogen detection.

Taxonomy and evolution of Aspergillus, Penicillium and Talaromyces in the omics era - Past, present and future

Aspergillus, Penicillium and Talaromyces are diverse, phenotypically polythetic genera encompassing species important to the environment, economy, biotechnology and medicine, causing significant social impacts. Taxonomic studies on these fungi are essential since they could provide invaluable information on their evolutionary relationships and define criteria for species recognition. With the advancement of various biological, biochemical and computational technologies, different approaches have been adopted for the taxonomy of Aspergillus, Penicillium and Talaromyces; for example, from traditional morphotyping, phenotyping to chemotyping (e.g. lipotyping, proteotypingand metabolotyping) and then mitogenotyping and/or phylotyping. Since different taxonomic approaches focus on different sets of characters of the organisms, various classification and identification schemes would result. In view of this, the consolidated species concept, which takes into account different types of characters, is recently accepted for taxonomic purposes and, together with the lately implemented 'One Fungus - One Name' policy, is expected to bring a more stable taxonomy for Aspergillus, Penicillium and Talaromyces, which could facilitate their evolutionary studies. The most significant taxonomic change for the three genera was the transfer of Penicillium subgenus Biverticillium to Talaromyces (e.g. the medically important thermally dimorphic 'P. marneffei' endemic in Southeast Asia is now named T. marneffei), leaving both Penicillium and Talaromyces as monophyletic genera. Several distantly related Aspergillus-like fungi were also segregated from Aspergillus, making this genus, containing members of both sexual and asexual morphs, monophyletic as well. In the current omics era, application of various state-of-the-art omics technologies is likely to provide comprehensive information on the evolution of Aspergillus, Penicillium and Talaromyces and a stable taxonomy will hopefully be achieved.

Fatty Acid 13C Isotopologue Profiling Provides Insight into Trophic Carbon Transfer and Lipid Metabolism of Invertebrate Consumers

Fatty acids (FAs) are useful biomarkers in food web ecology because they are typically assimilated as a complete molecule and transferred into consumer tissue with minor or no modification, allowing the dietary routing between different trophic levels. However, the FA trophic marker approach is still hampered by the limited knowledge in lipid metabolism of the soil fauna. This study used entirely labelled palmitic acid (¹³C16:0, 99 atom%) as a tracer in fatty acid metabolism pathways of two widespread soil Collembola, Protaphorura fimata and Heteromurus nitidus. In order to investigate the fate and metabolic modifications of this precursor, a method of isotopologue profiling is presented, performed by mass spectrometry using single ion monitoring. Moreover, the upstream laboratory feeding experiment is described, as well as the extraction and methylation of dominant lipid fractions (neutral lipids, phospholipids) and the related formula and calculations. Isotopologue profiling does not only yield the overall ¹³C enrichment in fatty acids derived from the ¹³C labeled precursor but also produces the pattern of isotopologues exceeding the mass of the parent ion (i.e., the FA molecular ion M⁺) of each labeled FA by one or more mass units (M⁺¹, M⁺², M⁺³, etc.). This knowledge allows conclusions on the ratio of dietary routing of an entirely consumed FA in comparison to de novo biosynthesis. The isotopologue profiling is suggested as a useful tool for evaluation of fatty acid metabolism in soil animals to disentangle trophic interactions.

Analysis of Chemical Signatures of Alkaliphiles using Fatty Acid Methyl Ester Analysis

BACKGROUND

Fatty acids occur in nearly all living organisms as the important predominant constituents of lipids. While all fatty acids have essentially the same chemical nature, they are an extremely diverse group of compounds.

MATERIALS AND METHODS

To test the hypothesis, fatty acids of alkaliphiles isolates, Bacillus subtilis SVUNM4, Bacillus licheniformis SVUNM8, Bacillus methylotrohicus SVUNM9, and Paenibacillus dendritiformis SVUNM11, were characterized compared using gas chromatography-mass spectrometry (GC-MS) analysis.

RESULTS

The content of investigated ten fatty acids, 1, 2-benzenedicarboxylic acid butyl 2-methylpropyl ester, phthalic acid, isobutyl 2-pentyl ester, dibutyl phthalate, cyclotrisiloxane, hexamethyl, cyclotetrasiloxane, octamethyl, dodecamethyl, heptasiloxane 1,1,3,3,5,5,7,7,9,9,11,11,13,13-etradecamethyl, 7,15-dihydroxydehydroabietic acid, methyl ester, di (trimethylsilyl) ether, hentriacontane, 2-thiopheneacetic acid, undec-2-enyl ester, obviously varied among four species, suggesting each species has its own fatty acid pattern.

CONCLUSIONS

These findings demonstrated that GC-MS-based fatty acid profiling analysis provides the reliable platform to classify these four species, which is helpful for ensuring their biotechnological interest and novel chemotaxonomic.

Omental adipocytes enhance the invasiveness of gastric cancer cells by oleic acid-induced activation of the PI3K-Akt signaling pathway

A considerable number of patients with advanced gastric cancer have a clear predilection for metastasis to the great omentum, an organ mainly composed of adipose tissue. However, it remains unclear why tumor cells preferentially spread to and progress in the omentum. Here, we used a two-dimensional co-culture system to simulate the crosstalk between adipocytes and gastric cancer cells and showed that after co-culture with isolated omental adipocytes, gastric cancer cells exhibited a significant increase in lipid uptake and enhanced invasiveness. A lipidomic study showed that gastric cancer cells accumulated higher levels of oleic acid during the co-culture. By performing an assay of key enzymes in lipid synthesis, we demonstrated that the increased amount of oleic acid in gastric cancer cells mainly came from the adjacent adipocytes in the co-culture system. Furthermore, our data showed that at a certain concentration range, oleic acid treatment enhanced the invasiveness of gastric cancer cells in vitro and in a CAM assay, through the PI3K/Akt pathway, with the associated increased expression of the key pro-invasion factor MMP-2. Taken together, our results demonstrated that adipocytes may serve as an exogenous source of oleic acid that promotes gastric cancer cell invasion through the PI3K/Akt signaling pathway.

Regulated covalent modifications of lipid A

Regulated covalent modifications of lipid A are implicated in virulence of pathogenic Gram-negative bacteria. The Salmonella PhoP/PhoQ-activated gene pagP is required for resistance to cationic antimicrobial peptides and for biosynthesis of hepta-acylated lipid A species containing palmitate. Interestingly, pagP encodes an unusual enzyme of lipid A biosynthesis localized in the outer membrane, whereas all previously characterized lipid A enzymes are cytoplasmic or associated with the inner membrane. PagP is not unique, however, as pagL encodes another outer membrane enzyme in Salmonella that deacylates the 3 position of lipid A.

S. typhimurium also synthesizes S-2-hydroxymyristate modified lipid A in a PhoP/PhoQ-dependent manner. We postulated that 2-hydroxylation might be catalyzed by a novel dioxygenase. Using well-characterized dioxygenase sequences as probes, tBLASTn searches revealed unassigned open reading frame(s) with similarity to mammalian aspartyl β-hydroxylases in bacteria known to make 2-hydroxyacylated lipid A. The S. typhimurium aspartyl β-hydroxylase homologue ( lpxO) was cloned and expressed in Escherichia coli K-12, which does not contain lpxO. Analysis of the resulting construct revealed that lpxO expression induces O2-dependent formation of 2-hydroxymyristate-modified lipid A in E. coli. LpxO may be an inner membrane enzyme that catalyzes Fe2+/ascorbate/α-ketoglutarate dependent hydroxylation of lipid A. We propose that 2-hydroxymyristate released from LPS inside infected animal cells might be converted to 2-hydroxymyristoyl coenzyme A, a potent inhibitor of protein N-myristoyl transferase.

Immunoproteomic Profiling of Bordetella pertussis Outer Membrane Vesicle Vaccine Reveals Broad and Balanced Humoral Immunogenicity

The current resurgence of whooping cough is alarming, and improved pertussis vaccines are thought to offer a solution. Outer membrane vesicle vaccines (omvPV) are potential vaccine candidates, but omvPV-induced humoral responses have not yet been characterized in detail. The purpose of this study was to determine the antigen composition of omvPV and to elucidate the immunogenicity of the individual antigens. Quantitative proteome analysis revealed the complex composition of omvPV. The omvPV immunogenicity profile in mice was compared to those of classic whole cell vaccine (wPV), acellular vaccine (aPV), and pertussis infection. Pertussis-specific antibody levels, antibody isotypes, IgG subclasses, and antigen specificity were determined after vaccination or infection by using a combination of multiplex immunoassays, two-dimensional immunoblotting, and mass spectrometry. The vaccines and infection raised strong antibody responses, but large quantitative and qualitative differences were measured. The highest antibody levels were obtained by omvPV. All IgG subclasses (IgG1/IgG2a/IgG2b/IgG3) were elicited by omvPV and in a lower magnitude by wPV, but not by aPV (IgG1) or infection (IgG2a/b). The majority of omvPV-induced antibodies were directed against Vag8, BrkA, and LPS. The broad and balanced humoral response makes omvPV a promising pertussis vaccine candidate.

Postharvest application of organic and inorganic salts to control potato (Solanum tuberosum L.) storage soft rot: plant tissue-salt physicochemical interactions

Soft rot caused by Pectobacterium sp. is a devastating disease affecting stored potato tubers, and there is a lack of effective means of controlling this disease. In this study, 21 organic and inorganic salts were tested for their ability to control soft rot in potato tubers. In the preventive treatment, significant control of soft rot was observed with AlCl3 (≥66%) and Na2S2O3 (≥57%) and to a lesser extent with Al lactate and Na benzoate (≥34%) and K sorbate and Na propionate (≥27%). However, only a moderate control was achieved by curative treatment with AlCl3 and Na2S2O3 (42%) and sodium benzoate (≥33%). Overall, the in vitro inhibitory activity of salts was attenuated in the presence of plant tissue (in vivo) to different degrees. The inhibitory action of the salts in the preventive treatment, whether effective or otherwise, showed an inverse linear relationship with water ionization capacity (pK') of the salt ions, whereas in the curative treatment, only the effective salts showed this inverse linear relationship. Salt-plant tissue interactions appear to play a central role in the attenuated inhibitory activity of salts in potato tuber through reduction in the availability of the inhibitory ions for salt-bacteria interactions. This study demonstrates that AlCl3, Na2S2O3, and Na benzoate have potential in controlling potato tuber soft rot and provides a general basis for understanding of specific salt-tissue interactions.

Improved production process for native outer membrane vesicle vaccine against Neisseria meningitidis

An improved detergent-free process has been developed to produce vaccine based on native outer membrane vesicles (NOMV) against Neisseria meningitidis serogroup B. Performance was evaluated with the NonaMen vaccine concept, which provides broad coverage based on nine distinct PorA antigens. Scalable aseptic equipment was implemented, replacing undesirable steps like ultracentrifugation, inactivation with phenol, and the use of preservatives. The resulting process is more consistent and gives a higher yield than published reference processes, enabling NOMV production at commercial scale. Product quality met preliminary specifications for 9 consecutive batches, and an ongoing study confirmed real-time stability up to 12 months after production. As the NOMV had low endotoxic activity and induced high bactericidal titres in mice, they are expected to be safe and effective in humans. The production process is not limited to NonaMen and may be applicable for other N. meningitidis serogroups and other gram-negative pathogens. The current results therefore facilitate the late-stage development and clinical evaluation of NOMV vaccines.

Chemotaxonomy of heterocystous cyanobacteria using FAME profiling as species markers

The fatty acid methyl ester (FAME) analysis of the 12 heterocystous cyanobacterial strains showed different fatty acid profiling based on the presence/absence and the percentage of 13 different types of fatty acids. The major fatty acids viz. palmitic acid (16:0), hexadecadienoic acid (16:2), stearic acid (18:0), oleic acid (18:1), linoleic (18:2), and linolenic acid (18:3) were present among all the strains except Cylindrospermum musicola where oleic acid (18:1) was absent. All the strains showed high levels of polyunsaturated fatty acid (PUFAs; 41-68.35%) followed by saturated fatty acid (SAFAs; 1.82-40.66%) and monounsaturated fatty acid (0.85-24.98%). Highest percentage of PUFAs and essential fatty acid (linolenic acid; 18:3) was reported in Scytonema bohnerii which can be used as fatty acid supplement in medical and biotechnological purpose. The cluster analysis based on FAME profiling suggests the presence of two distinct clusters with Euclidean distance ranging from 0 to 25. S. bohnerii of cluster I was distantly related to the other strains of cluster II. The genotypes of cluster II were further divided into two subclusters, i.e., IIa with C. musicola showing great divergence with the other genotypes of IIb which was further subdivided into two groups. Subsubcluster IIb(1) was represented by a genotype, Anabaena sp. whereas subsubcluster IIb(2) was distinguished by two groups, i.e., one group having significant similarity among their three genotypes showed distant relation with the other group having closely related six genotypes. To test the validity of the fatty acid profiles as a marker, cluster analysis has also been generated on the basis of morphological attributes. Our results suggest that FAME profiling might be used as species markers in the study of polyphasic approach based taxonomy and phylogenetic relationship.

Simple procedure for fatty acid analysis of glycerophospholipids in Escherichia coli and Saccharomyces cerevisiae

Rapid, convenient methods have been developed for fatty acid analysis of membrane glycerophospholipids in microorganisms. Fatty acid methyl esters derived from glycerophospholipids have been prepared directly from wet pellets of Escherichia coli cells or Saccharomyces cerevisiae spheroplasts without lipid extraction and fractionation in high yields under mild temperature conditions for analysis by gas chromatography.

Lipid profiling of the soybean pathogen Phytophthora sojae using Fatty Acid Methyl Esters (FAMEs)

Phytophthora sojae is a destructive soilborne pathogen of soybean, but currently there is no rapid or commercially available testing for its infestation level in soil. For growers, such information would greatly improve their ability to make management decisions to minimize disease damage to soybean crops. Fatty acid profiling of P. sojae holds potential for determining the prevalence of this pathogen in soil. In this study, the Fatty Acid Methyl Ester (FAME) profile of P. sojae was determined in pure culture, and the profile was subsequently evaluated for its potential use in detecting the pathogen in soil. The predominant fatty acids in the FAME profile of P. sojae are the unsaturated 18C fatty acids (18:1ω9 and 18:2ω6) followed by the saturated and unsaturated 16C fatty acids (16:0 and 16:1ω7). FAME analysis of P. sojae zoospores showed two additional long-chain saturated fatty acids (20:0 and 22:0) that were not detected in the mycelium of this organism. Addition of a known number of zoospores of P. sojae to soil demonstrated that fatty acids such as 18:1ω9, 18:2ω6, 20:1ω9, 20:4ω6, and 22:1ω9 could be detected and quantified against the background levels of fatty acids present in soil. These results show the potential for using selected FAMEs of P. sojae as a marker for detecting this pathogen in soybean fields.

Isolation, characterization of Rhodococcus sp. P14 capable of degrading high-molecular-weight polycyclic aromatic hydrocarbons and aliphatic hydrocarbons

Rhodococcus sp. P14 was isolated from crude oil-contaminated sediments. This strain was capable of utilizing three to five rings polycyclic aromatic hydrocarbons (PAHs) including phenanthrene (Phe), pyrene (Pyr), and benzo[a]pyrene (BaP) as a sole carbon and energy source. After cultivated with 50mg/L of each PAH, strain P14 removed 43% Phe, 34% Pyr and 30% BaP in 30 d. Four different hydroxyphenanthrene products derived from Phe by strain P14 (1,2,3,4-hydroxyphenanthrene) were detected using SPME-GC-MS. Strain P14 also was capable of degrading mineral oil with n-alkanes of C17 to C21 carbon chain length. Compared with glucose-grown cells, PAHs-grown cells had decreased contents of shorter-chain length fatty acids (≤ C16:0), increased contents of C18:0, Me-C19:0 and disappeared odd-number carbon chain fatty acids. The contents of unsaturated C19:1, Me-C19:0 increased and C18:0 decreased in mineral oil-grown cells. At the same time, the strain P14 tended to float when cultivated in mineral oil-supplemented liquid medium. The degradation capability of P14 to alkane and PAHs and its floating characteristics will be very helpful for future's application in oil-spill bioremediation.

Metabolic footprinting of the anaerobic bacterium Fusobacterium varium using 1H NMR spectroscopy

Metabolic footprinting of the anaerobic bacterium Fusobacterium varium demonstrated the accumulation of six carboxylic acids as metabolic end-products and revealed specific growth requirements and utilization capabilities towards amino acids. Guided by (1)H NMR determinations of residual amino acids in spent medium, a modified chemically defined minimal medium (CDMM*) was developed by minimizing the amino acid composition while satisfying nutritional requirements to support abundant growth of F. varium. Quantitative determinations of carboxylate salts and residual substrates were readily performed by (1)H NMR analysis of lyophilized residues from CDMM* cultures without interference from initial medium components. Only small concentrations of alanine, arginine, glycine, isoleucine, leucine, methionine, proline and valine were required to support growth of F. varium, whereas larger quantities of aspartate, asparagine, cysteine, glutamine, glutamate, histidine, lysine, serine and threonine were utilized, most likely as energy sources. Both bacterial growth and the distribution of carboxylate end-products depended on the composition of the chemically defined medium. In cultures provided with glucose as the primary energy source, the accumulation of butyrate and lactate correlated with growth, consistent with the regeneration of reduced coenzyme formed by the oxidative steps of glucose catabolism.

Study of human microecology by mass spectrometry of microbial markers

This review shows that mass spectrometry of microbial markers (MSMM) permits simultaneous in situ determination of more than one hundred microbial fatty acids in clinical, biotechnological or environmental samples, without precultivation and use of biochemical test materials and primers. Unprecedented information about the quantity of anaerobes and uncultivated aerobes, as well as actinobacteria, yeasts, viruses and microscopic fungi in one sample has provided a full understanding of microbial etiology in clinical conditions of patients. The study of intestine dysbiosis has confirmed the hypothesis about the nosological specificity of changes in the intestinal microbiota. It has been proven that infectious processes are polymicrobial. Measurements have shown that anaerobes dominate in number and functional activities in inflammation. The division of microbes into pathogenic and non- pathogenic is artificial. All microbes living in a human body simultaneously stay in both forms. Lactobacilli and bifidobacteria appear as agents of septic conditions and endocarditis. МSММ data confirm that anaerobes of Clostridium, Eubacterium, Propionibacterium, as well as actinobacteria of Streptomyces, Nocardia, Rhodococcus are mixed infection dominants. The data testify translocation of these microbes in inflammation loci from the intestine. Quantitative comparison of concentration of markers in the inflamed organ and blood proves reproduction of microorganisms in this locus. The current hypothesis is confirmed that the goal of translocation is not only infection, but also a biofilm formation similar to intestines, which stimulate local immunity, protection from local pathogens and restoration of the damaged tissues. Quantification using GC-MS revealed that the influence of antibiotics on the normal intestine’s microbiota are not as dramatic as believed. Growth-promoting effects are the most important benefits of probiotic applications. The probiotic essence is not the microbial biomass itself, but growth factors, alarm molecules, and other factors of intestinal microbes. There are new possibilities in improving probiotics by using microbial 'consortia', modelling real gut microbiota.

Acid stress-mediated metabolic shift in Lactobacillus sanfranciscensis LSCE1

Lactobacillus sanfranciscensis LSCE1 was selected as a target organism originating from recurrently refreshed sourdough to study the metabolic rerouting associated with the acid stress exposure during sourdough fermentation. In particular, the acid stress induced a metabolic shift toward overproduction of 3-methylbutanoic and 2-methylbutanoic acids accompanied by reduced sugar consumption and primary carbohydrate metabolite production. The fate of labeled leucine, the role of different nutrients and precursors, and the expression of the genes involved in branched-chain amino acid (BCAA) catabolism were evaluated at pH 3.6 and 5.8. The novel application of the program XCMS to the solid-phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS) data allowed accurate separation and quantification of 2-methylbutanoic and 3-methylbutanoic acids, generally reported as a cumulative datum. The metabolites coming from BCAA catabolism increased up to seven times under acid stress. The gene expression analysis confirmed that some genes associated with BCAA catabolism were overexpressed under acid conditions. The experiment with labeled leucine showed that 2-methylbutanoic acid originated also from leucine. While the overproduction of 3-methylbutanoic acid under acid stress can be attributed to the need to maintain redox balance, the rationale for the production of 2-methylbutanoic acid from leucine can be found in a newly proposed biosynthesis pathway leading to 2-methylbutanoic acid and 3 mol of ATP per mol of leucine. Leucine catabolism to 3-methylbutanoic and 2-methylbutanoic acids suggests that the switch from sugar to amino acid catabolism supports growth in L. sanfranciscensis in restricted environments such as sourdough characterized by acid stress and recurrent carbon starvation.

Description of Gibbsiella quercinecans gen. nov., sp. nov., associated with Acute Oak Decline

Gram-negative, facultatively anaerobic bacterial strains were consistently isolated from oak trees displaying symptoms of extensive stem bleeding. In Britain, this disorder is called Acute Oak Decline (AOD). A similar condition has been noted on species of Mediterranean oak in Spain. The identity of bacterial isolates from symptomatic trees in both countries was investigated using molecular techniques and phenotypic assays. 16S rRNA gene sequencing indicated that the strains were most closely related to the genera Serratia, Kluyvera, Klebsiella and Raoultella (all>97%). Phylogenetic analysis revealed that the strains formed a distinct lineage within the family Enterobacteriaceae, which was confirmed by both gyrB- and rpoB-gene sequencing. DNA-DNA hybridization confirmed that the strains belonged to a single taxon which could also be differentiated phenotypically from its closest phylogenetic neighbours. The phylogenetic and phenotypic data both demonstrated that the strains isolated from oak represented a novel genus and species within the family Enterobacteriaceae for which the name Gibbsiella quercinecans gen. nov., sp. nov. (type strain=FRB 97(T)=LMG 25500(T)=NCPPB 4470(T)) is proposed.

Fatty Acid methyl ester profiles for characterization of glomalean fungi and their endomycorrhizae

Arbuscule-forming fungi in the order Glomales form obligate endomycorrhizal associations with plants that make them difficult to quantify, and taxonomy of the group is only beginning to be objectively understood. Fatty acid methyl ester (FAME) profiles were analyzed to assess the diversity and quantity of fatty acids in 53 isolates of 24 glomalean species. Spores and endomycorrhizal roots of sudan grass (Sorghum sudanense) and the citrus rootstock Carrizo citrange (Poncirus trifoliata x Citrus sinensis) were examined. Spores yielded reproducible FAME profiles from replicate spore collections extracted from soil pot cultures despite being grown in association with a host plant and with contaminating microorganisms present. Unweighted pair group analysis revealed relatively tight clusters of groups at the intraspecific, specific, and generic levels; however, lipid profiles at the family level were convergent. Thus, FAME profile comparisons provided a robust measure of similarity below the family level. FAME profiles in sudan grass roots containing vesicles and/or spores of Glomus intraradices were more similar to spore profiles than to profiles from nonmycorrhizal roots. The FAME profiles for Gigaspora species, which do not form vesicles or spores in roots, were less distinct from nonmycorrhizal roots. G. intraradices and G. rosea produced fatty acids in roots that were distinguishable from each other as well as from the host root. Production in citrus roots of the fatty acid 16:1(inf(omega)5) cis by two Glomus species was correlated with the development of mycorrhizal colonization as measured by clearing and staining procedures and by estimates of total incidence and vesicle intensity. FAME analysis of roots not only provided a measure of colonization development but also served as an index of carbon allocated to intraradical fungal growth and lipid storage.

Use of fatty acid methyl ester profiles for discrimination of Bacillus cereus T-strain spores grown on different media

The goal of this study was to determine if cellular fatty acid methyl ester (FAME) profiling could be used to distinguish among spore samples from a single species (Bacillus cereus T strain) that were prepared on 10 different medium formulations. To analyze profile differences and identify FAME biomarkers diagnostic for the chemical constituents in each sporulation medium, a variety of statistical techniques were used, including nonmetric multidimensional scaling (nMDS), analysis of similarities (ANOSIM), and discriminant function analysis (DFA). The results showed that one FAME biomarker, oleic acid (18:1 omega9c), was exclusively associated with spores grown on Columbia agar supplemented with sheep blood and was indicative of blood supplements that were present in the sporulation medium. For spores grown in other formulations, multivariate comparisons across several FAME biomarkers were required to discern profile differences. Clustering patterns in nMDS plots and R values from ANOSIM revealed that dissimilarities among FAME profiles were most pronounced when spores grown with disparate sources of complex additives or protein supplements were compared (R > 0.8), although other factors also contributed to FAME differences. DFA indicated that differentiation could be maximized with a targeted subset of FAME variables, and the relative contributions of branched FAME biomarkers to group dissimilarities changed when different media were compared. When taken together, these analyses indicate that B. cereus spore samples grown in different media can be resolved with FAME profiling and that this may be a useful technique for providing intelligence about the production methods of Bacillus organisms in a forensic investigation.

Synthesis of cyclopropane fatty acids in Lactobacillus helveticus and Lactobacillus sanfranciscensis and their cellular fatty acids changes following short term acid and cold stresses

An implemented GC method to separate and quantify the cell cyclopropane fatty acids lactobacillic (C19cyc11) and dehydrosterculic (C19cyc9) was used to study the adaptive response to sublethal acid and cold stresses in Lactobacillus helveticus and Lactobacillus sanfranciscensis. The comparison of the composition of cellular fatty acids of the two strains and their changes after 2 h of stress exposure under micro-aerobic and anaerobic conditions indicated that the aerobic biosynthetic pathway for unsaturated fatty acids is prevalent in L. sanfranciscensis, while the anaerobic pathway is prevalent in L. helveticus. Indeed in the latter strain, in the presence of a source of oleic acid and under micro-aerobic conditions, C18:1n11 and its post-synthetic derivative C19cyc11 accounted for overall proportion ranging from 52 to 28% of the total FAs. On the other hand L. sanfranciscensis synthesizes by aerobic pathway C18:1n9 and transforms it to C19cyc9. However in this species the cumulative level of these two FAs did not exceed 30%. The relevant proportion of dodecanoic acid in the latter species suggests that carbon chain shortening is the principal strategy of L. sanfranciscensis to modulate fluidity or chemico-physical properties of the membranes.

Identification and characterization of Streptococcus agalactiae isolates using 16S rRNA sequencing and cellular fatty acid composition analysis

This study was undertaken to apply 16S rRNA sequence and Cellular Fatty Acid (CFA) composition analysis techniques for the identification and characterization of seven individual bacteria isolates obtained from seven infected fish samples. All samples were cultured on brain heart infusion agar. All the seven isolates were Gram positive and were identified as Streptococcus sp. The 16S rRNA sequencing method yielded about 1500 bps for each strain where upon the sequence was compared to nucleotide data in Gene Bank using BLASTN 2.2.1 sequence alignment from NCBI for the nucleotide comparison. The 16S rRNA gene sequence for all the seven samples had no sequence variation between the isolates and gave a 100% similarity to plus, plus strand with Streptococcus agalactiae strain A909 Accession number NC_007432.1 and S. agalactiae strain H36B (Accession number AAJS01000007). Also the 16S rRNA sequence showed a high (92-93%) similarity between S. agalactiae and S. equi, S. suis and S. uberis. All strains appeared to be nearly identical to each other after CFA analysis using Library Generation System (LGS) software (MIDI) and were consistent to that of S. agalactiae ATCC 12386, the CFA analysis not only confirmed the results of 16S rRNA sequence but also indicated a possibility of single source of infection. Despite their accuracy to identify the poorly described, rarely isolated, or phenotypically aberrant strains, 16S rRNA gene sequence analysis and CFA analysis lacks widespread use beyond the large and reference laboratories because of technical and cost considerations.

Characterization of Aspergillus species based on fatty acid profiles

Cellular fatty acid (FA) composition was utilized as a taxonomic tool to discriminate between different Aspergillus species. Several of the tested species had the same FA composition and different relative FA concentrations. The most important FAs were palmitic acid (C16:0), estearic acid (C18:0), oleic acid (C18:1) and linoleic acid (C18:2), which represented 95% of Aspergillus FAs. Multivariate data analysis demonstrated that FA analysis is a useful tool for differentiating species belonging to genus Aspergillus. All the species analyzed showed significantly FA acid profiles (p < 0.001). Furthermore, it will be possible to distinguish among Aspergillus spp. in the Flavi Section. FA composition can serve as a useful tool for the identification of filamentous fungi.

Towards large-scale FAME-based bacterial species identification using machine learning techniques

In the last decade, bacterial taxonomy witnessed a huge expansion. The swift pace of bacterial species (re-)definitions has a serious impact on the accuracy and completeness of first-line identification methods. Consequently, back-end identification libraries need to be synchronized with the List of Prokaryotic names with Standing in Nomenclature. In this study, we focus on bacterial fatty acid methyl ester (FAME) profiling as a broadly used first-line identification method. From the BAME@LMG database, we have selected FAME profiles of individual strains belonging to the genera Bacillus, Paenibacillus and Pseudomonas. Only those profiles resulting from standard growth conditions have been retained. The corresponding data set covers 74, 44 and 95 validly published bacterial species, respectively, represented by 961, 378 and 1673 standard FAME profiles. Through the application of machine learning techniques in a supervised strategy, different computational models have been built for genus and species identification. Three techniques have been considered: artificial neural networks, random forests and support vector machines. Nearly perfect identification has been achieved at genus level. Notwithstanding the known limited discriminative power of FAME analysis for species identification, the computational models have resulted in good species identification results for the three genera. For Bacillus, Paenibacillus and Pseudomonas, random forests have resulted in sensitivity values, respectively, 0.847, 0.901 and 0.708. The random forests models outperform those of the other machine learning techniques. Moreover, our machine learning approach also outperformed the Sherlock MIS (MIDI Inc., Newark, DE, USA). These results show that machine learning proves very useful for FAME-based bacterial species identification. Besides good bacterial identification at species level, speed and ease of taxonomic synchronization are major advantages of this computational species identification strategy.

Modeling Neisseria meningitidis B metabolism at different specific growth rates

Neisseria meningitidis is a human pathogen that can infect diverse sites within the human host. The major diseases caused by N. meningitidis are responsible for death and disability, especially in young infants. At the Netherlands Vaccine Institute (NVI) a vaccine against serogroup B organisms is currently being developed. This study describes the influence of the growth rate of N. meningitidis on its macro-molecular composition and its metabolic activity and was determined in chemostat cultures. In the applied range of growth rates, no significant changes in RNA content and protein content with growth rate were observed in N. meningitidis. The DNA content in N. meningitidis was somewhat higher at the highest applied growth rate. The phospholipid and lipopolysaccharide content in N. meningitidis changed with growth rate but no specific trends were observed. The cellular fatty acid composition and the amino acid composition did not change significantly with growth rate. Additionally, it was found that the PorA content in outer membrane vesicles was significantly lower at the highest growth rate. The metabolic fluxes at various growth rates were calculated using flux balance analysis. Errors in fluxes were calculated using Monte Carlo Simulation and the reliability of the calculated flux distribution could be indicated, which has not been reported for this type of analysis. The yield of biomass on substrate (Y(x/s)) and the maintenance coefficient (m(s)) were determined as 0.44 (+/-0.04) g g(-1) and 0.04 (+/-0.02) g g(-1) h(-1), respectively. The growth associated energy requirement (Y(x/ATP)) and the non-growth associated ATP requirement for maintenance (m(ATP)) were estimated as 0.13 (+/-0.04) mol mol(-1) and 0.43 (+/-0.14) mol mol(-1) h(-1), respectively. It was found that the split ratio between the Entner-Doudoroff and the pentose phosphate pathway, the sole glucose utilizing pathways in N. meningitidis, had a minor effect on ATP formation rate but a major effect on the fluxes going through for instance the citric-acid cycle. For this reason, we presented flux ranges for underdetermined parts of metabolic network rather than presenting single flux values, which is more commonly done in literature.

Direct quantitation of fatty acids present in bacteria and fungi: stability of the cyclopropane ring to chlorotrimethylsilane

The stability of the cyclopropane ring and the fatty acid composition of microbial cells were determined using chlorotrimethylsilane as reagent with three different conditions 80 degrees C for 1 h, 60 degrees C for 1 h, and 60 degrees C for 2 h. Chlorotrimethylsilane permits a simultaneous extraction and derivatization of fatty acids. A basic method was used as reference. The bacteria, Escherichia coli, Burkholderia cepacia, and Lactobacillus brevis, and fungi Aspergillus niger and Gibberella fujikuroi were used. The stability of the cyclopropane ring on acidic conditions was tested using the cyclopropanecarboxylic acid and a commercial mixture of bacteria fatty acid methyl esters (BAME). Fisher's least significant difference test showed significant differences among the methods. The method using chlorotrimethylsilane and 1-pentanol for 1 h at 80 degrees C gave the best results in cyclopropane, hydroxyl, and total fatty acid recoveries. This procedure allows the fast and easy one-step direct extraction derivatization.

Phospholipid fatty acid analysis to monitor the co-composting process of olive oil mill wastes and organic household refuse

The co-composting of olive oil mill wastes and household refuse was followed for 5 months. During the thermophilic phase of composting, the aerobic heterotrophic bacteria (AHB) count, showed a significant rise with a slight regression of fungal biomass. In the same way, phospholipid fatty acids PLFAs common in bacteria, showed a significant increase of hydroxyl and branched PLFAs. The evaluation of the ratio of octadecenoic PLFAs to stearic acid (C18:1omega/C18:0) revealed a significant reduction while a significant rise in the length of aliphatic chains evaluated by the stearic acid to palmitic acid ratio (C18:0/C16:0) was noted during the stabilization phase. The follow-up of PLFAs, indicates the degree of biodegradation that occurs during composting, it can be regarded an indicator of the stability and maturity of the end product.

Fatty acid analysis as a chemotaxonomic tool for taxonomic and epidemiological characterization of four fish pathogenic Tenacibaculum species

AIMS

In this work, fatty acid content and profiles were analysed in order to differentiate the species Tenacibaculum maritimum, Tenacibaculum gallaicum, Tenacibaculum discolor and Tenacibaculum ovolyticum that are pathogenic for cultured marine fish and to assess the potential of fatty acid profiles as a tool for epizootiological typing.

METHODS AND RESULTS

The fatty acid methylesters (FAMEs) were extracted from cells grown on marine agar for 48 h at 25 degrees C and were prepared and analysed according to the standard protocol of the MIDI/Hewlett Packard Microbial Identification System. The cellular fatty acid profiles of Tenacibaculum strains tested were characterized by the presence of large amounts of branched (36.1-40.2%) and hydroxylated (29.6-31.7%) fatty acids. The FAME products from the four species significantly (P < 0.05) differed in the content of iso-C(15:0)3-OH, iso-C(16:0)3-OH, iso-C(15:1)G, summed feature 3 (a component that contains C(16:1)omega7c and/or iso-C(15:0) 2-OH), iso-C(16:0), C(17:1)omega6c, C(15:0)3-OH, iso-C(17:0)3-OH.

CONCLUSIONS

Results of present study demonstrated the existence of differences in the fatty acids content between the T. maritimum isolates from different marine fish/geographical origin and between strains of T. maritimum, T. discolor, T. gallaicum and T. ovolyticum.

SIGNIFICANCE AND IMPACT OF THE STUDY

Profiling of fatty acids may be a useful tool to distinguish T. maritimum from other Tenacibaculum species pathogenic for fish as well as for epizootiological differentiation of T. maritimum isolates.

Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes

A genome-scale flux model for primary metabolism of Neisseria meningitidis was constructed; a minimal medium for growth of N. meningitidis was designed using the model and tested successfully in batch and chemostat cultures.

Background

Neisseria meningitidis is a human pathogen that can infect diverse sites within the human host. The major diseases caused by N. meningitidis are responsible for death and disability, especially in young infants. In general, most of the recent work on N. meningitidis focuses on potential antigens and their functions, immunogenicity, and pathogenicity mechanisms. Very little work has been carried out on Neisseria primary metabolism over the past 25 years.

Results

Using the genomic database of N. meningitidis serogroup B together with biochemical and physiological information in the literature we constructed a genome-scale flux model for the primary metabolism of N. meningitidis. The validity of a simplified metabolic network derived from the genome-scale metabolic network was checked using flux-balance analysis in chemostat cultures. Several useful predictions were obtained from in silico experiments, including substrate preference. A minimal medium for growth of N. meningitidis was designed and tested succesfully in batch and chemostat cultures.

Conclusion

The verified metabolic model describes the primary metabolism of N. meningitidis in a chemostat in steady state. The genome-scale model is valuable because it offers a framework to study N. meningitidis metabolism as a whole, or certain aspects of it, and it can also be used for the purpose of vaccine process development (for example, the design of growth media). The flux distribution of the main metabolic pathways (that is, the pentose phosphate pathway and the Entner-Douderoff pathway) indicates that the major part of pyruvate (69%) is synthesized through the ED-cleavage, a finding that is in good agreement with literature.