Next Article in Journal
Neuroendocrine Effects on the Risk of Metabolic Syndrome in Children
Previous Article in Journal
Eco-Physiological Responses of Avicennia marina (Forssk.) Vierh. to Trace Metals Pollution via Intensifying Antioxidant and Secondary Metabolite Contents
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Metabolites
Volume 13
Issue 7
10.3390/metabo13070809
metabolites-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Construction of a Bacterial Lipidomics Analytical Platform: Pilot Validation with Bovine Paratuberculosis Serum

by
Paul L. Wood
1,* and
Erdal Erol
2
1
Metabolomics Unit, College of Veterinary Medicine, Lincoln Memorial University, 6965 Cumberland Gap Pkwy, Harrogate, TN 37752, USA
2
Department of Veterinary Science, Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY 40546, USA
*
Author to whom correspondence should be addressed.
Metabolites 2023, 13(7), 809; https://doi.org/10.3390/metabo13070809
Submission received: 16 May 2023 / Revised: 23 June 2023 / Accepted: 27 June 2023 / Published: 29 June 2023
(This article belongs to the Section Lipid Metabolism)
Browse Figures
Versions Notes

Abstract

:
Lipidomics analyses of bacteria offer the potential to detect and monitor infections in a host since many bacterial lipids are not present in mammals. To evaluate this omics approach, we first built a database of bacterial lipids for representative Gram-positive and Gram-negative bacteria. Our lipidomics analysis of the reference bacteria involved high-resolution mass spectrometry and electrospray ionization with less than a 1.0 ppm mass error. The lipidomics profiles of bacterial cultures clearly distinguished between Gram-positive and Gram-negative bacteria. In the case of bovine paratuberculosis (PTB) serum, we monitored two unique bacterial lipids that we also monitored in Mycobacterium avian subspecies PTB. These were PDIM-B C82, a phthiodiolone dimycocerosate, and the trehalose monomycolate hTMM 28:1, constituents of the bacterial cell envelope in mycolic-containing bacteria. The next step will be to determine if lipidomics can detect subclinical PTB infections which can last 2-to-4 years in bovine PTB. Our data further suggest that it will be worthwhile to continue building our bacterial lipidomics database and investigate the further utility of this approach in other infections of veterinary and human clinical interest.

1. Introduction

Lipidomics is a rapidly evolving “omics” platform that provides valuable information regarding structural, energy source/reserve, and signal-transduction lipid pools. Bacteria possess a number of unique lipids that are not present in their mammalian hosts. This provides the opportunity of lipidomics to obtain valuable non-mammalian lipid data that can (i) detect bacterial infection in a host, (ii) monitor the progression of an infection, (iii) monitor the efficacy of treatments on an infection, and (iv) potentially define new targets in the design of targeted antimicrobial therapeutics.
While the individual lipids of a given lipid family for a bacterial strain will alter with development and with environmental stresses, lipid families will be preserved and can be monitored. Our first high-level overview is a comparison of our current knowledge base for Gram-positive vs. Gram-negative bacterial lipidomics.

1.1. Gram-Positive Bacteria

1.1.1. Gram-Positive Bacteria: Lipoteichoic Acids

Gram-positive bacteria possess a cytoplasmic membrane and a multilaminar cell wall [1]. Between the cell membrane and cell wall is a heteropolysaccharide meshwork of peptidoglycans and arabinogalactans. Teichoic acids, which anchor to peptidoglycans in the cell wall, and lipoteichoic acids (LTAs), which are found in the cell membrane, are lipids that are unique to Gram-positive bacteria, providing a strong negative charge to the cell wall [2]. Precursors to LTAs that have been monitored in Gram-positive bacteria include a number of glycolipids (Table 1).
The diversity of LTA precursor lipidomes between different bacterial species is demonstrated by the detection of DHMG in only 12 of 19 clostridia species examined [9]. The further modification of these lipids through the addition of phosphoethanolamine only was present in 4 of those 12 species [9].

1.1.2. Gram-Positive Bacteria: Modified Phosphatidylglycerols

Aminoacylation of phosphatidylglycerol (PG) is another unique feature in the lipidome of Gram-positive bacteria (Table 2). The pathway for these aminoacylations is phosphatidic acid → CDP-DG → phosphatidylglycerophosphate → PG → aminoacyl-PG.
The diversity of amino acyl lipidomes between different bacterial species is demonstrated by the detection of lysyl-PG in only 5 of 24 clostridia species examined [9] and the detection of alanyl-PG in only 3 of 24 clostridia species examined [9].

1.1.3. Gram-Positive Bacteria: Mycolic Acids

A very unique family of glycolipids is also present in the outer wall of a number of bacteria in the Actinomycetes taxonomic group. These are the mycolic acids present in mycolic-acid-containing bacteria (MACB) [1,27] which include Mycobacteria (M. tuberculosis, M. leprae, M. bovis, Tskamurella pulmonis, Rhodococcus erythropolis, R. opacus, and R. equi) and Corynebacteria (C. glutamicum) [27,28]. Long-chain mycolic acids are covalently bound in the inner layer of the cell wall but are present as free acids in the outer domain. Lipids in this lipid family are diverse (Table 3).

1.1.4. Gram-Positive Bacteria: Mannosyl Phosphoinositols (PIMs)

PIMs are unique to Mycobacteria (M. tuberculosis, M. leprae, M. bovis, Tskamurella pulmonis, Rhodococcus erythropolis, and R. opacus, R.equi) and Corynebacteria (C. glutamicum) [27,28,29] (Table 4). They are critical structural components of both the outer and inner membranes of the cell envelope.

1.1.5. Gram-Positive Bacteria: Aminoacyl Lipids

While bacteria possess low levels of choline (PC) and ethanolamine (PE) glycerophospholipids, a number of aminoacylated forms of these lipids are present in the membranes of Gram-positive bacteria (Table 5).

1.2. Gram-Negative Bacteria

1.2.1. Gram-Negative Bacteria: Glycosyl Hydroxy Fatty Acids (HFAs) and Glycosyl-FAHFAs

Gram-negative bacteria possess a cell envelope comprising an inner and outer membrane with an intermediate peptidoglycan layer. Lipid A is a major membrane lipid in Gram-negative bacteria. This complex lipid has a core scaffold of P-glucosamine-glucosamine with acyl or FAHFA substitutions of the nitrogen in each hexose and acyl substitution of the hydroxy group in P-glucosamine [46,47,48].
Fatty acyls of hydroxy fatty acids (FAHFAs) [49] are present at high concentrations in Gram-negative bacteria, and both the glycosylated and aminoacyl forms are critical membrane constituents. The glycosylation of hydroxy fatty acids yields rhamnolipids, which act as biosurfactant antimicrobials. Representative glycolipids in Gram-negative bacteria are presented in Table 6.

1.2.2. Gram-Negative Bacteria: Aminoacyl Hydroxy Fatty Acids (HFAs) and FAHFAs

Gram-negative bacteria possess a diverse array of aminoacyl HFAs and FAHFAs that serve as virulence factors (Table 7).

1.2.3. Gram-Negative Bacteria: Modified Ceramides

Gram-negative bacteria possess several unique modified ceramides which are considered to contribute to membrane charge (Table 8).

1.2.4. Gram-Negative Bacteria: Glycosyl-Glycerophosphoalkylamines

Several complex glycolipids have been identified as regulators of cell temperature in Thermus thermophilus [91,92]: PLGN (Diacyl-PA-Acyl-Alkylamine-Glucosamine) and PGL (Diacyl-PA-Acyl-Alkylamine-N-Acetyl-Glucosamine).

1.2.5. Gram-Negative Bacteria: Sterols

Gram-negative bacteria utilize several unique cholesteryl acyl-glycosides as immunostimulants and hopanoids which order membrane lipids and regulate membrane permeability [97] (Table 9).

1.2.6. Gram-Negative Bacteria: Secondary Metabolites

Gram-negative bacteria produce a number of secondary metabolites that they utilize to protect against other microbes (Table 10).
In summary, the wide diversity of bacterial lipids offers the potential to differentiate different bacterial species via lipidomics analyses. For example, previous studies of polar lipids in Clostridia spp. in four different groups of bacteria based on morphological and biochemical criteria demonstrated that three of the four groups possessed lipids that distinguished each group. All groups had high levels of PE and PG. However, Group I (C. sporogenes prototype) possessed PE-NAcGlu-DGs, Group II (C. butyricum prototype) possessed glycerol and PG acetals of ethanolamine plasmalogens, Group III (C. novyi prototype) possessed aminoacyl-PGs, and Group IV (C. subterminale prototype) had no distinguishing polar lipids [106,107]. Extending future lipidomics analyses across a broader scope than just polar lipids should further increase our ability to differentiate ongoing bacterial infections.
The objective of our study was to initiate building a bacterial lipidomics database that we could utilize to interrogate serum from cows infected with paratuberculosis and provide the groundwork required to continue building and expanding the database such that it will allow for the interrogation of other clinically relevant infections.

2. Materials and Methods

2.1. Bacterial Processing

Bacterial pellets purchased from the ATTC (Manassas, VA, USA) were sonicated (Thermo Fisher FB50) in 1 mL of methanol and 1 mL of water containing 2 nanomoles of [13C3]DG 36:2 (Larodan, Monroe, MI, USA). Next 2 mL of tert-butylmethylether was added, and the samples were shaken at room temperature for 30 min (Thermo Fisher Multitube Vortexer, Waltham, MS, USA). Next, the samples were centrifuged at 4000× g for 30 min at room temperature. From the upper organic layer of these centrifuged samples, 1 mL aliquots were transferred to a deep-well microplate. The microplate samples were dried via vacuum centrifugation (Eppendorf Vacfuge Plus, Hamburg, Germany).
The Gram-positive bacterial pellets which we evaluated were Mycobacterium avium, ss. Paratuberculosis (ATCC 700535), Staphylococcus aureus (ATCC 10832), Mycobacterium bovis (ATTC 35737), Mycobacterium smegmatis (ATCC 14468), Rhodococcus equi (ATCC 7699), Enterococcus faecalis (ATCC 19433), and Corynebacterium glutamicum (13032). The purchased Gram-negative bacterial pellets were Helicobacter pylori (ATCC 43504), Pseudomonas aeruginosa (ATCC 10145), Proteus mirabilis (ATCC 12453), Moraxella bovoculi (ATCC BBA-1259), and Escherichia coli (ATCC 12435).

2.2. Lipidomics Analysis

We utilized published data and lipid databases for bacterial lipids and then incorporated them into our established lipidomics analytical platform [106,108,109,110,111,112] such that now we can interrogate approximately 11,000 individual lipids. As a pilot to evaluate the utility of this platform to detect active bacterial infections, we utilized the platform to examine the lipidome of a number of representative Gram-positive and Gram-negative bacteria and plasma samples from cows with paratuberculosis [112].
Specifically, to the dried samples, we added 200 μL of 2-propanol:methanol:chloroform (8:4:4), containing 5 mM ammonium chloride [108,111]. Lipids were characterized by flow infusion analysis (FIA) with electrospray ionization (ESI). FIA at 20 µL/minute was performed utilizing high-resolution (140,000 at 200 amu) data acquisition with an orbitrap mass spectrometer (Thermo Q Exactive) [106,108,109,110,111,112]. The FIA included a 30 s scan in the positive ESI mode (300–1500 amu), followed by a 30 s scan in the negative ESI mode (290–1500 amu). Between sample injections, the syringe and tubing were flushed with 1 mL of methanol, followed by 1 mL of hexane: ethyl acetate: chloroform: water (3:2:1:0.1). FIA has the advantages of high sample throughput with a short analysis time for each sample and data acquisition with a constant concentration of the lipid matrix.
For MS/MS analyses, parent ions were selected with a 0.4 amu window and collision energies of 15, 30, and 50 arbitrary units. Product ions were monitored with a resolution of 240,000. Product ions with a <1.0 ppm mass error are listed in Supplementary Table S3. We utilized Lincoln Memorial University, Metabolomics Unit, Flow Infusion Lipidomics Analytical Platform (Version 1.0).

2.3. Bovine PTB Serum Samples

Serum samples (100 μL) from our previous research [112] were used for this study and processed as described above. The cattle (n = 10) were 2-to-2.5-year-old angus. PTB infection was confirmed utilizing enzyme-linked immunosorbent assay (ELISA) (IDEXX MAP ELISA Ab Test kit, Westbrood, ME, USA). All testing was performed at the University of Kentucky Veterinary Diagnostic Laboratory (UKVDL), a fully accredited laboratory of the American Association of Veterinary Laboratory Diagnosticians (AAVLD).

2.4. Data Reduction

To our established in-house lipid database in Excel (Microsoft 365), we added the exact masses for a large number of individual bacterial lipids. Exact masses were obtained from online databases and the published literature. The databases we used included LipidMaps [PMID 33037133], E. coli Metabolome Database (ECMDB) [PMID 26481353], Yeast Metabolome Database (YMDB) [PMID 27899612], Mycobacterium tuberculosis Database (Mtb LipidDB) [PMID 21285232], Chemical Entities of Biological Interest (ChEBI) [PMID 26467479], Human Metabolome Database (HMDB) [PMID 34986597], Seaweed Metabolite Database (SWMD) [PMID 21423723], PubChem [PMID 33151290], and PubMed [PMID 33085945].
Mass spectrometric data were imported into this spreadsheet. This included individual scanned masses and their associated peak intensities. Based on the infusion solvent, the predominant ions were [M+H]+ or [M+NH4]+ in positive electrospray ionization (PESI), and they were [M-H]− or [M+Cl]− in NESI [108,111]. To define which ions were optimal for different lipid families, along with defining MS/MS criteria for structural validation, we purchased a number of microbial lipid standards. This included mycolic acids (Cat. 791280 and 791282), acyl-ceramides (Cat. 860626), lysyl-PG (Cat. 840521), sulfogalactosyl-ceramides (Cat. 860571), monogalactosyl-DG (Cat. 840523), and digalactosyl-DG (Cat. 840524) from Avanti Polar Lipids (Alabaster, AL, USA) and lipid A variants (Cat. SML-2430, Cat, L6895, and L5399), acyl trehalose (Cat. 30564), trehalose dimycolates (Cat. T3034), and rhamnolipids (Cat. R95MD and R95DD) from Sigma-Aldrich (St. Louis, MO, USA) to gain practical experience. In the case of lipid classes for which analytical standards were not available, we utilized the experiences from the prior literature and our in-house experience with our infusion solvent.
For each lipid in the Excel mass list, the imported data were searched for a matching mass with <1.0 ppm mass error. For positive hits, the extracted mass and the associated peak intensity were imported into a new active spreadsheet. The specific details for each lipid class, along with the associated ionization modes and MS/MS products, are presented in Supplementary Table S3, which details all the lipid classes included in our lipidomics analytical platform, along with citations for representative publications.

3. Results

3.1. Gram-Positive Bacteria

3.1.1. M. avium Specific Lipids: Phthiodiolone Dimycocerosates and Diacyltrehaloses

M. avium was unique in that it was the only Gram-positive species we examined that possessed phthiodiolone dimycocerosates and diacyltrehaloses (Figure 1 and Supplementary Table S1). The phthiodiolone dimycocerosates (PDIMs) are long-chain β-diols esterified at the hydroxy groups with multimethyl-branched fatty acids (mycocerosic acids). We specifically monitored PDIM-B forms in which a position 2 of the diol is a keto group. The dominant member of this lipid family was PDIM-B C82 in the ATCC bacterial pellets and was detected in the serum of cattle with paratuberculosis but not in control cows (Figure 1 and Supplementary Table S1). In contrast, while we detected diacyltrehaloses in the M. avium bacterial pellet (Supplementary Table S1), these lipids were undetectable in the serum of infected cows. The diacyltrehaloses were in the DAT2 family which have a fatty acid (16:0 to 19:0) and a mycolipanolic fatty acid substituent. The mycolipanolic fatty acids were 3-hydroxy-2,4,6-methyl fatty acids of 24 to 28 carbons.

3.1.2. Trehalose Mycolates

Hydroxy-trehalose monomycolates (hTMMs) were monitored in all of the examined bacteria except for S. aureus and E. faecalis (Supplementary Table S1). Each bacterial strain had a different dominant hTMM. In the case of M. avium, hTMM 28:1 was the dominant member of the lipid family and was also detected in the serum of PTB-positive cattle (Figure 2). While acetylTMMs were monitored in M. avium and a number of other Gram-positive bacteria (Supplementary Table S1), we did not detect any of this lipid family in the serum of infected cows.

3.1.3. Lipoteichoic Acid Precursors

Lipoteichoic acid precursors (LTAPs; dihexosyldiacylglycerol-glycerol phosphate), along with the mono-alanine and di-alanine analogs, were not detected in the M. avium bacterial pellet (Supplementary Table S1). LTAP 32:0 was monitored in S. aureus, while LTAPs and Ala-LTAPs were monitored in the bacterial pellets from R. equi, E. faecalis, and C. glutamicum. As with other lipids, the dominant LTAP lipid family member was different for each bacterial strain. Di-Ala-LTAPs were detected only in R. equi bacterial pellets.

3.1.4. Mannosyl Phosphoinositols (PIM1)

Acyl-PIM1 family members were only monitored in the C. glutamicum bacterial pellets (Supplementary Table S1), consistent with prior studies [16]. The acyl-PIM1 family has also been reported for a number of Mycobacteria [41]; however, we did not detect any acyl-PIM1 in the Mycobacteria we studied. This may have resulted from low levels and/or ion suppression.

3.1.5. Mycolic Acids

All of the Gram-positive bacteria that we studied were found to contain mycolic acids (Figure 3 and Figure 4; Supplementary Table S1). A diverse array of mycolic acids was monitored in the bacterial pellets. Most mycolic acids are tethered in the outer membrane, but there are small membrane levels of free mycolic acids [31,32,33,34,113], as demonstrated in Figure 3 and Figure 4. For the unsaturated lipids, our data do not distinguish between a double bond or a cyclopropyl substitution [113]. Both M. bovis and M. smegmatis mycolic acids were skewed to a distribution of longer-chain fatty acyl substituents (Figure 4). Interestingly, only these two bacterial strains had measurable levels of epoxymycolic acids (Supplementary Table S1). It also needs to be noted that our analyses do not distinguish between the isobars of oxygenated lipids [113]. For example, epoxymycolic acid 77:1 = ketomycolic acid 77:1 = methoxymycolic acid 77:2.
Dicarboxylic mycolic acids were only detected in M. avium and M. bovis (Supplementary Table S1).
The complexity of mycolic acids in bacteria was reflected in our analysis of the serum from cows infected with PTB. Four of the ten cows had levels of mycolic acid 50:2 (0.0011 ± 0.00064), five cows had dicarboxylic acid 82:1 (0.0053 ± 0.00065), two cows had dicarboxylic mycolic acid 84:1, one cow had dicarboxylic mycolic acid 82:2, and one cow had dicarboxylic mycolic acid 84:2. These lipids were not detected in the 10 control cows. This heterogeneity of detectable mycolic acids in the serum of infected cows may be reflective of different stages of the PTB infection, which is known to progress slowly over time [114].

3.1.6. Glycopeptidolipids (GPLs)

The cell walls of a number of Mycobacteria contain a family of unique GPLs that consist of a hydroxy fatty acid coupled to a peptide which in turn is coupled to rhamnose [115,116,117]. The hydroxy fatty acid has a deoxytalose (dTal) glycation which has 0-to-2 possible acetylations. The peptide is Phe-Thr-Ala-Alaninol, and the terminal rhamnose has 0-to-3 possible O-methylations. This lipid family serves as cell-surface antigens.
We monitored an array of GPLs with the rank order of prevalence C. glutamicum > M. smegmatis > R. equi > M. bovis (Supplementary Table S1).

3.1.7. Sulfonolipids

Sulfonolipids are characterized by the replacement of serine in the sphingolipid base by the sulfonic acid capnine generating sulfobacins (monohydroxy) and sulfocristamides (di-hydroxy) [118]. These lipids are required for gliding motility and demonstrate pro-inflammatory and cytotoxic activities [118]. Both C. glutamicum and M. bovis were found to possess these highly charged sphingolipids (Supplementary Table S1).

3.1.8. Alpha-Acyl Hydroxy Fatty Acids (AAHFAs)

AAHFAs are a unique family of FAHFA lipids in which case the acylation is at a hydroxy group on carbon 2, with the acyl substitution being butyric acid [119]. The functions of these newly discovered lipids remain to be elaborated. In our analyses, we found high levels of AAHFAs in M. avium and moderate levels in S. aureus and M. bovis (Supplementary Table S1).

3.2. Gram-Negative Bacteria

Gram-negative bacteria lack the cell wall characteristic of Gram-positive bacteria. Lipid A is a major membrane lipid in the cell envelope, comprising an inner and outer membrane with an intermediate peptidoglycan layer. While intact lipid A molecules are large and tethered, a number of lipid A precursors are easily analyzed via conventional lipid-extraction procedures. Modified fatty acyls of hydroxy fatty acids (FAHFAs) are one example of these lipid A constituents that are absent from Gram-positive bacteria.

3.2.1. Aminoacyl FAHFAs

FAHFAs are present in mammals, but the aminoacyl forms of these lipids are not [49]. Aminoacyl FAHFAs are unique to Gram-negative bacteria. In our study, we monitored glycyl-, lysyl-, hydroxylysyl-, glutaminyl-, and ornithinyl-FAHFAs in the Gram-negative bacteria we evaluated. Orn-FAHFA (Figure 5) and Gly-FAHFA were monitored in all bacteria examined, while Ala-FAHFA was absent from H. pylori (Supplementary Table S2).
Gly-Ser-FAHFAs are characteristic of some Gram-negative bacteria [73,77]. We monitored these unique dipeptide lipids in P. mirabilis and M. bovoculi (Supplementary Table S2). Gly-Ser-hydroxy-fatty acids were also monitored in these two bacterial strains, as well as in H. pylori.
Aminoacyl FAHFAs have long been conjectured to play a role in replacing glycerophospholipids in membranes, where they regulate membrane charge. Other studies have also demonstrated their roles in signal transduction. For example, ornithine lipids act at GPCRs involved in immune activation [65]. Similarly, Gly-Ser lipids act at Toll-like 2 receptors involved in immunostimulation [69,70].

3.2.2. Modified Ceramides

The addition of a polar phosphoethanolamine or phosphoglycerol group to ceramides has been shown to be another unique feature of a number of Gram-negative bacteria [64,67,73,74,75,76,77,79]. We monitored a diverse array of these lipids in H. pylori, P. mirabilis, and M. bovocali but not in E. coli or P. aeruginosa (Supplementary Table S2).

3.2.3. Unique Sterols

Cholesteryl-acylphosphoglycosides (CPGs) have been detected in H. pylori [93,94] and Borella burgdorferi [95,96]. We confirm that H. pylori has these unique lipids and report for the first time that P. mirabilis also has these membrane lipids (Supplementary Table S2).

3.2.4. Phosphatidyltrehalose (PT)

Phosphatidyltrehaloses have been reported for Salmonella paratyphi and S. typhi [120]. We report for the first time that these immunostimulant lipids are also present in P. mirabilis and E. coli (Supplementary Table S2).

4. Discussion

Our data support previous studies demonstrating the stark contrast of the lipidomes of Gram-positive and Gram-negative bacteria. Furthermore, by utilizing a standard lipid-extraction procedure, we were able to demonstrate the presence of both PDIM-B C82, a phthiodiolone dimycocerosate, and the trehalose monomycolate hTMM 28:1 in the plasma of cows with PTB. These specific constituents of the bacterial cell envelope in M. avium are the dominant family members we extracted from commercial bacterial pellets. Serum mycolic acids were also detected, but the levels were much more variable. Our data demonstrate the power and specificity of lipidomics to detect bacterial infections. Presumably, targeted assays to provide absolute lipid levels will provide even more specificity and sensitivity.
Lipid biomarkers have been utilized previously to demonstrate the presence of tuberculosis in archaeological samples [121,122,123,124,125] and to monitor Gram-negative bacterial infections in carotid atheroma (Gly-Ser-lipids) [73] and in oral samples from patients with periodontitis [77]. These and our current data support the idea of building a database of microbial lipids of interest to human and veterinary clinical medicine. Such a database will, in turn, yield the data required to determine which lipids might be of value to establish absolute quantitation clinical assays.

5. Study Limitations

This is the first step in building a comprehensive bacterial lipidomics database that will be expanded as we add the profiles of other bacteria to increase its applicability to bacterial research. Our FIA methodology has the strengths of covering a broader range of lipids and providing a stable and constant background, compared to hybrid chromatographic methods. However, issues with isobars are more prevalent with FIA. To reduce this risk, we utilized HRMS and only accepted lipids that were <1.0 ppm mass error. We also utilized MS2 to validate the lipid identities. The MS2 parameters for each lipid class are presented in Supplementary Table S3: Lincoln Memorial University, Metabolomics Unit, Flow Infusion Lipidomics Analytical Platform (Version 1.0).

Supplementary Materials

The following supporting information, in a single file, can be downloaded at https://www.mdpi.com/article/10.3390/metabo13070809/s1. Table S1: Rank order of lipid families in Gram-positive bacteria. Table S2: Rank order of lipid families in Gram-negative bacteria. Table S3: Lincoln Memorial University, Metabolomics Unit, Flow Infusion Lipidomics Analytical Platform (Version 1.0).

Author Contributions

Both authors were responsible for the conceptualization and conduct of the study. P.L.W. was responsible for the methodology, data reduction software, validation and formal analysis, investigation, resources, data curation, and the original draft preparation. Both authors were responsible for the manuscript review and editing. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by Lincoln Memorial University.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

All data are in the manuscript.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Sohlenkamp, C.; Geiger, O. Bacterial membrane lipids: Diversity in structures and pathways. FEMS Microbiol. Rev. 2016, 40, 133–159. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  2. Shiraishi, T.; Yokota, S.; Fukiya, S.; Yokota, A. Structural diversity and biological significance of lipoteichoic acid in Gram-positive bacteria: Focusing on beneficial probiotic lactic acid bacteria. Biosci. Microbiota Food Health 2016, 35, 147–161. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  3. Adams, H.M.; Joyce, L.R.; Guan, Z.; Akins, R.L.; Palmer, K.L. Streptococcus mitis and S. oralis Lack a Requirement for CdsA, the Enzyme Required for Synthesis of Major Membrane Phospholipids in Bacteria. Antimicrob. Agents Chemother. 2017, 61, e02552-16. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  4. Wei, Y.; Joyce, L.R.; Wall, A.M.; Guan, Z.; Palmer, K.L. Streptococcus pneumoniae, S. mitis, and S. oralis Produce a Phosphatidylglycerol-Dependent, ltaS-Independent Glycerophosphate-Linked Glycolipid. mSphere 2021, 6, e01099-20. [Google Scholar] [CrossRef] [PubMed]
  5. Guan, Z.; Garrett, T.A.; Goldfine, H. Lipidomic Analysis of Clostridium cadaveris and Clostridium fallax. Lipids 2019, 54, 423–431. [Google Scholar] [CrossRef] [PubMed]
  6. Sallans, L.; Giner, J.L.; Kiemle, D.J.; Custer, J.E.; Kaneshiro, E.S. Structural identities of four glycosylated lipids in the oral bacterium Streptococcus mutans UA159. Biochim. Biophys. Acta 2013, 1831, 1239–1249. [Google Scholar] [CrossRef] [PubMed]
  7. Guan, Z.; Chen, L.; Gerritsen, J.; Smidt, H.; Goldfine, H. The cellular lipids of Romboutsia. Biochim. Biophys. Acta 2016, 1861 Pt A, 1076–1082. [Google Scholar] [CrossRef] [PubMed]
  8. Lopes, C.; Barbosa, J.; Maciel, E.; da Costa, E.; Alves, E.; Domingues, P.; Mendo, S.; Domingues, M.R.M. Lipidomic signature of Bacillus licheniformis I89 during the different growth phases unravelled by high-resolution liquid chromatography-mass spectrometry. Arch. Biochem. Biophys. 2019, 663, 83–94. [Google Scholar] [CrossRef] [PubMed]
  9. Guan, Z.; Goldfine, H. Lipid diversity in clostridia. Biochim. Biophys. Acta Mol. Cell Biol. Lipids 2021, 1866, 158966. [Google Scholar] [CrossRef] [PubMed]
  10. Harrison, N.A.; Gardner, C.L.; da Silva, D.R.; Gonzalez, C.F.; Lorca, G.L. Identification of Biomarkers for Systemic Distribution of Nanovesicles from Lactobacillus johnsonii N6.2. Front. Immunol. 2021, 12, 723433. [Google Scholar] [CrossRef] [PubMed]
  11. Webb, A.J.; Karatsa-Dodgson, M.; Gründling, A. Two-enzyme systems for glycolipid and polyglycerolphosphate lipoteichoic acid synthesis in Listeria monocytogenes. Mol. Microbiol. 2009, 74, 299–314. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  12. Luo, Y. Alanylated lipoteichoic acid primer in Bacillus subtilis. F1000Research 2016, 5, 155. [Google Scholar] [CrossRef] [PubMed]
  13. Atila, M.; Luo, Y. Profiling and tandem mass spectrometry analysis of aminoacylated phospholipids in Bacillus subtilis. F1000Research 2016, 5, 121. [Google Scholar] [CrossRef] [PubMed]
  14. Percy, M.G.; Karinou, E.; Webb, A.J.; Gründling, A. Identification of a Lipoteichoic Acid Glycosyltransferase Enzyme Reveals that GW-Domain-Containing Proteins Can Be Retained in the Cell Wall of Listeria monocytogenes in the Ab-sence of Lipoteichoic Acid or Its Modifications. J. Bacteriol. 2016, 198, 2029–2042. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  15. Smith, A.M.; Harrison, J.S.; Grube, C.D.; Sheppe, A.E.; Sahara, N.; Ishii, R.; Nureki, O.; Roy, H. tRNA-dependent alanylation of diacylglycerol and phosphatidylglycerol in Corynebacterium glutamicum. Mol. Microbiol. 2015, 98, 681–693. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  16. Klatt, S.; Brammananth, R.; O’Callaghan, S.; Kouremenos, K.A.; Tull, D.; Crellin, P.K.; Coppel, R.L.; McConville, M.J. Identification of novel lipid modifications and intermembrane dynamics in Corynebacterium glutamicum using high-resolution mass spectrometry. J. Lipid Res. 2018, 59, 1190–1204, Outstanding publication. A must read. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  17. Tatituri, R.V.V.; Hsu, F.F. Characterization of the Uncommon Lipid Families in Corynebacterium glutamicum by Mass Spectrometry. Methods Mol. Biol. 2021, 306, 227–238. [Google Scholar] [PubMed]
  18. Wang, H.J.; Tatituri, R.V.V.; Goldner, N.K.; Dantas, G.; Hsu, F.F. Unveiling the biodiversity of lipid species in Corynebacteria- characterization of the uncommon lipid families in C. glutamicum and pathogen C. striatum by mass spectrometry. Biochimie 2020, 178, 158–169, Outstanding publication. A must read. [Google Scholar] [CrossRef] [PubMed]
  19. Luo, Y.; Javed, M.A.; Deneer, H. Comparative study on nutrient depletion-induced lipidome adaptations in Staphylococcus haemolyticus and Staphylococcus epidermidis. Sci. Rep. 2018, 8, 2356. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  20. Joyce, L.R.; Manzer, H.S.; da CMendonça, J.; Villarreal, R.; Nagao, P.E.; Doran, K.S.; Palmer, K.L.; Guan, Z. Identification of a novel cationic glycolipid in Streptococcus agalactiae that contributes to brain entry and meningitis. PLoS Biol. 2022, 20, e3001555. [Google Scholar] [CrossRef] [PubMed]
  21. Johnston, N.C.; Aygun-Sunar, S.; Guan, Z.; Ribeiro, A.A.; Daldal, F.; Raetz, C.R.; Goldfine, H. A phosphoethanolamine-modified glycosyl diradylglycerol in the polar lipids of Clostridium tetani. J. Lipid Res. 2010, 51, 1953–1961. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  22. Guan, Z.; Johnston, N.C.; Aygun-Sunar, S.; Daldal, F.; Raetz, C.R.; Goldfine, H. Structural characterization of the polar lipids of Clostridium novyi NT. Further evidence for a novel anaerobic biosynthetic pathway to plasmalogens. Biochim. Biophys. Acta 2011, 1811, 186–193. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  23. Slavetinsky, C.; Kuhn, S.; Peschel, A. Bacterial aminoacyl phospholipids-Biosynthesis and role in basic cellular processes and pathogenicity. Biochim. Biophys. Acta Mol. Cell Biol. Lipids 2017, 1862, 1310–1318. [Google Scholar] [CrossRef] [PubMed]
  24. Roy, H. Tuning the properties of the bacterial membrane with aminoacylated phosphatidylglycerol. IUBMB Life 2009, 61, 940–953. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  25. Atila, M.; Katselis, G.; Chumala, P.; Luo, Y. Characterization of N-Succinylation of L-Lysylphosphatidylglycerol in Bacillus subtilis Using Tandem Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2016, 27, 1606–1613. [Google Scholar] [CrossRef] [PubMed]
  26. Khuller, G.K.; Subrahmanyam, D. On the ornithinyl ester of phosphatidylglycerol of Mycobacterium 607. J. Bacteriol. 1970, 101, 654–656. [Google Scholar] [CrossRef] [PubMed]
  27. Kato, M.; Asamizu, S.; Onaka, H. Intimate relationships among actinomycetes and mycolic acid-containing bacteria. Sci. Rep. 2022, 12, 7222. [Google Scholar] [CrossRef] [PubMed]
  28. Rahlwes, K.C.; Sparks, I.L.; Morita, Y.S. Cell Walls and Membranes of Actinobacteria. Subcell Biochem. 2019, 92, 417–469. [Google Scholar] [PubMed]
  29. Blevins, M.S.; Klein, D.R.; Brodbelt, J.S. Localization of Cyclopropane Modifications in Bacterial Lipids via 213 nm Ultraviolet Photodissociation Mass Spectrometry. Anal. Chem. 2019, 91, 6820–6828. [Google Scholar] [CrossRef] [PubMed]
  30. Madacki, J.; Laval, F.; Grzegorzewicz, A.; Lemassu, A.; Záhorszká, M.; Arand, M.; McNeil, M.; Daffé, M.; Jackson, M.; Lanéelle, M.A.; et al. Impact of the epoxide hydrolase EphD on the metabolism of mycolic acids in mycobacteria. J. Biol. Chem. 2018, 293, 5172–5184. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  31. Hsu, F.F.; Soehl, K.; Turk, J.; Haas, A. Characterization of mycolic acids from the pathogen Rhodococcus equi by tandem mass spectrometry with electrospray ionization. Anal. Biochem. 2011, 409, 112–122. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  32. Hsu, F.F.; Wohlmann, J.; Turk, J.; Haas, A. Structural definition of trehalose 6-monomycolates and trehalose 6,6′-dimycolates from the pathogen Rhodococcus equi by multiple-stage linear ion-trap mass spectrometry with electrospray ionization. J. Am. Soc. Mass Spectrom. 2011, 22, 2160–2170. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  33. Gein, S.V.; Kochina, O.A.; Kuyukina, M.S.; Klimenko, D.P.; Ivshina, I.B. Effects of Monoacyltrehalose Fraction of Rhodococcus Biosurfactant on the Innate and Adaptive Immunity Parameters In Vivo. Bull. Exp. Biol. Med. 2020, 169, 474–477. [Google Scholar] [CrossRef] [PubMed]
  34. Purdy, G.E.; Hsu, F.F. Complete Characterization of Polyacyltrehaloses from Mycobacterium tuberculosis H37Rv Biofilm Cultures by Multiple-Stage Linear Ion-Trap Mass Spectrometry Reveals a New Tetraacyltrehalose Family. Biochemistry 2021, 60, 381–397. [Google Scholar] [CrossRef] [PubMed]
  35. Gilleron, M.; Stenger, S.; Mazorra, Z.; Wittke, F.; Mariotti, S.; Böhmer, G.; Prandi, J.; Mori, L.; Puzo, G.; De Libero, G. Diacylated sulfoglycolipids are novel mycobacterial antigens stimulating CD1-restricted T cells during infection with Mycobacterium tuberculosis. J. Exp. Med. 2004, 199, 649–659. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  36. Layre, E.; Cala-De Paepe, D.; Larrouy-Maumus, G.; Vaubourgeix, J.; Mundayoor, S.; Lindner, B.; Puzo, G.; Gilleron, M. Deciphering sulfoglycolipids of Mycobacterium tuberculosis. J. Lipid Res. 2011, 52, 1098–1110. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  37. Seeliger, J.C.; Holsclaw, C.M.; Schelle, M.W.; Botyanszki, Z.; Gilmore, S.A.; Tully, S.E.; Niederweis, M.; Cravatt, B.F.; Leary, J.A.; Bertozzi, C.R. Elucidation and chemical modulation of sulfolipid-1 biosynthesis in Mycobacterium tuberculosis. J. Biol. Chem. 2012, 287, 7990–8000. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  38. Rens, C.; Chao, J.D.; Sexton, D.L.; Tocheva, E.I.; Av-Gay, Y. Roles for phthiocerol dimycocerosate lipids in Mycobacterium tuberculosis pathogenesis. Microbiology 2021, 167, 001042. [Google Scholar] [CrossRef] [PubMed]
  39. Flentie, K.N.; Stallings, C.L.; Turk, J.; Minnaard, A.J.; Hsu, F.F. Characterization of phthiocerol and phthiodiolone dimycocerosate esters of M. tuberculosis by multiple-stage linear ion-trap MS. J. Lipid Res. 2016, 57, 142–155. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  40. Hayashi, J.M.; Luo, C.Y.; Mayfield, J.A.; Hsu, T.; Fukuda, T.; Walfield, A.L.; Giffen, S.R.; Leszyk, J.D.; Baer, C.E.; Bennion, O.T.; et al. Spatially distinct and metabolically active membrane domain in mycobacteria. Proc. Natl. Acad. Sci. USA 2016, 113, 5400–5405. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  41. Toyonaga, K.; Torigoe, S.; Motomura, Y.; Kamichi, T.; Hayashi, J.M.; Morita, Y.S.; Noguchi, N.; Chuma, Y.; Kiyohara, H.; Matsuo, K.; et al. C-Type Lectin Receptor DCAR Recognizes Mycobacterial Phosphatidyl-Inositol Mannosides to Promote a Th1 Response during Infection. Immunity 2016, 45, 1245–1257. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  42. Zhang, J.; Liang, Q.; Xu, Z.; Cui, M.; Zhang, Q.; Abreu, S.; David, M.; Lejeune, C.; Chaminade, P.; Virolle, M.J.; et al. The Inhibition of Antibiotic Production in Streptomyces coelicolor Over-Expressing the TetR Regulator SCO3201 IS Correlated with Changes in the Lipidome of the Strain. Front. Microbiol. 2020, 11, 1399. [Google Scholar] [CrossRef] [PubMed]
  43. Bieberich, E.; Kawaguchi, T.; Yu, R.K. N-acylated serinol is a novel ceramide mimic inducing apoptosis in neuroblastoma cells. J. Biol. Chem. 2000, 275, 177–181. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  44. Wen, S.; Ye, L.; Liu, D.; Yang, B.; Man, M.Q. Topical N-palmitoyl serinol, a commensal bacterial metabolite, prevents the development of epidermal permeability barrier dysfunction in a murine model of atopic dermatitis-like skin. Can. J. Vet. Res. 2021, 85, 201–204. [Google Scholar] [PubMed]
  45. Cohen, L.J.; Esterhazy, D.; Kim, S.H.; Lemetre, C.; Aguilar, R.R.; Gordon, E.A.; Pickard, A.J.; Cross, J.R.; Emiliano, A.B.; Han, S.M.; et al. Commensal bacteria make GPCR ligands that mimic human signalling molecules. Nature 2017, 549, 48–53. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  46. Buré, C.; Le Sénéchal, C.; Macias, L.; Tokarski, C.; Vilain, S.; Brodbelt, J.S. Characterization of Isomers of Lipid A from Pseudomonas aeruginosa PAO1 by Liquid Chromatography with Tandem Mass Spectrometry with Higher-Energy Collisional Dissociation and Ultraviolet Photodissociation. Anal. Chem. 2021, 93, 4255–4262. [Google Scholar] [CrossRef] [PubMed]
  47. Froning, M.; Helmer, P.O.; Hayen, H. Identification and structural characterization of lipid A from Escherichia coli, Pseudomonas putida and Pseudomonas taiwanensis using liquid chromatography coupled to high-resolution tandem mass spectrometry. Rapid Commun. Mass Spectrom. 2020, 34, e8897. [Google Scholar] [CrossRef] [PubMed]
  48. Larrouy-Maumus, G. Shotgun Bacterial Lipid A Analysis Using Routine MALDI-TOF Mass Spectrometry. Methods Mol. Biol. 2021, 2306, 275–283. [Google Scholar] [PubMed]
  49. Wood, P.L. Fatty Acyl Esters of Hydroxy Fatty Acid (FAHFA) Lipid Families. Metabolites 2020, 10, 512. [Google Scholar] [CrossRef] [PubMed]
  50. Behrens, B.; Engelen, J.; Tiso, T.; Blank, L.M.; Hayen, H. Characterization of rhamnolipids by liquid chromatography/mass spectrometry after solid-phase extraction. Anal. Bioanal. Chem. 2016, 408, 2505–2514. [Google Scholar] [CrossRef] [PubMed]
  51. Zhao, F.; Shi, R.; Ma, F.; Han, S.; Zhang, Y. Oxygen effects on rhamnolipids production by Pseudomonas aeruginosa. Microb. Cell Factories 2018, 17, 39. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  52. El-Housseiny, G.S.; Aboshanab, K.M.; Aboulwafa, M.M.; Hassouna, N.A. Structural and Physicochemical Characterization of Rhamnolipids produced by Pseudomonas aeruginosa P6. AMB Express 2020, 10, 201. [Google Scholar] [CrossRef] [PubMed]
  53. Hošková, M.; Ježdík, R.; Schreiberová, O.; Chudoba, J.; Šír, M.; Čejková, A.; Masák, J.; Jirků, V.; Řezanka, T. Structural and physiochemical characterization of rhamnolipids produced by Acinetobacter calcoaceticus, Enterobacter asburiae and Pseudomonas aeruginosa in single strain and mixed cultures. J. Biotechnol. 2015, 193, 45–51. [Google Scholar] [CrossRef] [PubMed]
  54. Lybbert, A.C.; Williams, J.L.; Raghuvanshi, R.; Jones, A.D.; Quinn, R.A. Mining Public Mass Spectrometry Data to Characterize the Diversity and Ubiquity of P. aeruginosa Specialized Metabolites. Metabolites 2020, 10, 445. [Google Scholar] [CrossRef] [PubMed]
  55. Kawakami, N.; Fujisaki, S. Undecaprenyl phosphate metabolism in Gram-negative and Gram-positive bacteria. Biosci. Biotechnol. Biochem. 2018, 82, 940–946. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  56. Wang, X.; Ribeiro, A.A.; Guan, Z.; Raetz, C.R. Identification of undecaprenyl phosphate-beta-D-galactosamine in Francisella novicida and its function in lipid A modification. Biochemistry 2009, 48, 1162–1172. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  57. Collins, M.D.; Goodfellow, M.; Minnikin, D.E.; Alderson, G. Menaquinone composition of mycolic acid-containing actinomycetes and some sporoactinomycetes. J. Appl. Bacteriol. 1985, 58, 77–86. [Google Scholar] [CrossRef] [PubMed]
  58. Lynch, A.; Tammireddy, S.R.; Doherty, M.K.; Whitfield, P.D.; Clarke, D.J. The Glycine Lipids of Bacteroides thetaiotaomicron Are Important for Fitness during Growth In Vivo and In Vitro. Appl. Environ. Microbiol. 2019, 85, e02157-18. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  59. Lynch, A.; Crowley, E.; Casey, E.; Cano, R.; Shanahan, R.; McGlacken, G.; Marchesi, J.R.; Clarke, D.J. The Bacteroidales produce an N-acylated derivative of glycine with both cholesterol-solubilising and hemolytic activity. Sci. Rep. 2017, 7, 13270. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  60. Kawazoe, R.; Okuyama, H.; Reichardt, W.; Sasaki, S. Phospholipids and a novel glycine-containing lipoamino acid in Cytophaga johnsonae Stanier strain C21. J. Bacteriol. 1991, 173, 5470–5475. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  61. Moore, E.K.; Hopmans, E.C.; Rijpstra, W.I.; Sánchez-Andrea, I.; Villanueva, L.; Wienk, H.; Schoutsen, F.; Stams, A.J.; Sinninghe Damsté, J.S. Lysine and novel hydroxylysine lipids in soil bacteria: Amino acid membrane lipid response to temperature and pH in Pseudopedobacter saltans. Front. Microbiol. 2015, 6, 637. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  62. Geiger, O.; González-Silva, N.; López-Lara, I.M.; Sohlenkamp, C. Amino acid-containing membrane lipids in bacteria. Prog. Lipid Res. 2010, 49, 46–60. [Google Scholar] [CrossRef] [PubMed]
  63. Vences-Guzmán, M.Á.; Guan, Z.; Ormeño-Orrillo, E.; González-Silva, N.; López-Lara, I.M.; Martínez-Romero, E.; Geiger, O.; Sohlenkamp, C. Hydroxylated ornithine lipids increase stress tolerance in Rhizobium tropici CIAT899. Mol. Microbiol. 2011, 79, 1496–1514. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  64. Vences-Guzmán, M.Á.; Guan, Z.; Bermúdez-Barrientos, J.R.; Geiger, O.; Sohlenkamp, C. Agrobacteria lacking ornithine lipids induce more rapid tumour formation. Environ. Microbiol. 2013, 15, 895–906. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  65. Córdoba-Castro, L.A.; Salgado-Morales, R.; Torres, M.; Martínez-Aguilar, L.; Lozano, L.; Vences-Guzmán, M.Á.; Guan, Z.; Dantán-González, E.; Serrano, M.; Sohlenkamp, C. Ornithine Lipids in Burkholderia spp. Pathogenicity. Front. Mol. Biosci. 2021, 7, 610932. [Google Scholar] [CrossRef] [PubMed]
  66. González-Silva, N.; López-Lara, I.M.; Reyes-Lamothe, R.; Taylor, A.M.; Sumpton, D.; Thomas-Oates, J.; Geiger, O. The dioxygenase-encoding olsD gene from Burkholderia cenocepacia causes the hydroxylation of the amide-linked fatty acyl moiety of ornithine-containing membrane lipids. Biochemistry 2011, 50, 6396–6408. [Google Scholar] [CrossRef] [PubMed]
  67. Batrakov, S.G.; Mosezhnyi, A.E.; Ruzhitsky, A.O.; Sheichenko, V.I.; Nikitin, D.I. The polar-lipid composition of the sphingolipid-producing bacterium Flectobacillus major. Biochim. Biophys. Acta 2000, 1484, 225–240. [Google Scholar] [CrossRef] [PubMed]
  68. Nemati, R.; Dietz, C.; Anstadt, E.; Clark, R.; Smith, M.; Nichols, F.; Yao, X. Simultaneous Determination of Absolute Configuration and Quantity of Lipopeptides Using Chiral Liquid Chromatography/Mass Spectrometry and Diastereomeric Internal Standards. Anal. Chem. 2017, 89, 3583–3589. [Google Scholar] [CrossRef] [PubMed]
  69. Clark, R.B.; Cervantes, J.L.; Maciejewski, M.W.; Farrokhi, V.; Nemati, R.; Yao, X.; Anstadt, E.; Fujiwara, M.; Wright, K.T.; Riddle, C.; et al. Serine lipids of Porphyromonas gingivalis are human and mouse Toll-like receptor 2 ligands. Infect. Immun. 2013, 81, 3479–3489. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  70. Nichols, F.C.; Clark, R.B.; Maciejewski, M.W.; Provatas, A.A.; Balsbaugh, J.L.; Dewhirst, F.E.; Smith, M.B.; Rahmlow, A. A novel phosphoglycerol serine-glycine lipodipeptide of Porphyromonas gingivalis is a TLR2 ligand. J. Lipid Res. 2020, 61, 1645–1657. [Google Scholar] [CrossRef] [PubMed]
  71. Bill, M.K.; Brinkmann, S.; Oberpaul, M.; Patras, M.A.; Leis, B.; Marner, M.; Maitre, M.P.; Hammann, P.E.; Vilcinskas, A.; Schuler, S.M.M.; et al. Novel Glycerophospholipid, Lipo- and N-acyl Amino Acids from Bacteroidetes: Isolation, Structure Elucidation and Bioactivity. Molecules 2021, 26, 5195. [Google Scholar] [CrossRef] [PubMed]
  72. Sartorio, M.G.; Valguarnera, E.; Hsu, F.F.; Feldman, M.F. Lipidomics Analysis of Outer Membrane Vesicles and Elucidation of the Inositol Phosphoceramide Biosynthetic Pathway in Bacteroides thetaiotaomicron. Microbiol. Spectr. 2022, 10, e0063421. [Google Scholar] [CrossRef] [PubMed]
  73. Nemati, R.; Dietz, C.; Anstadt, E.J.; Cervantes, J.; Liu, Y.; Dewhirst, F.E.; Clark, R.B.; Finegold, S.; Gallagher, J.J.; Smith, M.B.; et al. Deposition and hydrolysis of serine dipeptide lipids of Bacteroidetes bacteria in human arteries: Relationship to atherosclerosis. J. Lipid Res. 2017, 58, 1999–2007. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  74. Panevska, A.; Skočaj, M.; Križaj, I.; Maček, P.; Sepčić, K. Ceramide phosphoethanolamine, an enigmatic cellular membrane sphingolipid. Biochim. Biophys. Acta Biomembr. 2019, 1861, 1284–1292. [Google Scholar] [CrossRef] [PubMed]
  75. Brown, E.M.; Ke, X.; Hitchcock, D.; Jeanfavre, S.; Avila-Pacheco, J.; Nakata, T.; Arthur, T.D.; Fornelos, N.; Heim, C.; Franzosa, E.A.; et al. Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis. Cell Host Microbe 2019, 25, 668–680.e7. [Google Scholar] [CrossRef] [PubMed]
  76. Nichols, F.C.; Riep, B.; Mun, J.; Morton, M.D.; Bojarski, M.T.; Dewhirst, F.E.; Smith, M.B. Structures and biological activity of phosphorylated dihydroceramides of Porphyromonas gingivalis. J. Lipid Res. 2004, 45, 2317–2330. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  77. Nichols, F.C.; Bhuse, K.; Clark, R.B.; Provatas, A.A.; Carrington, E.; Wang, Y.H.; Zhu, Q.; Davey, M.E.; Dewhirst, F.E. Serine/Glycine Lipid Recovery in Lipid Extracts from Healthy and Diseased Dental Samples: Relationship to Chronic Periodontitis. Front. Oral Health 2021, 2, 698481. [Google Scholar] [CrossRef] [PubMed]
  78. Bickert, A.; Ginkel, C.; Kol, M.; vom Dorp, K.; Jastrow, H.; Degen, J.; Jacobs, R.L.; Vance, D.E.; Winterhager, E.; Jiang, X.C.; et al. Functional characterization of enzymes catalyzing ceramide phosphoethanolamine biosynthesis in mice. J. Lipid Res. 2015, 56, 821–835. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  79. Nichols, F.C.; Yao, X.; Bajrami, B.; Downes, J.; Finegold, S.M.; Knee, E.; Gallagher, J.J.; Housley, W.J.; Clark, R.B. Phosphorylated dihydroceramides from common human bacteria are recovered in human tissues. PLoS ONE 2011, 6, e16771. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  80. Mileykovskaya, E.; Ryan, A.C.; Mo, X.; Lin, C.C.; Khalaf, K.I.; Dowhan, W.; Garrett, T.A. Phosphatidic acid and N-acylphosphatidylethanolamine form membrane domains in Escherichia coli mutant lacking cardiolipin and phosphatidylglycerol. J. Biol. Chem. 2009, 284, 2990–3000. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  81. Hines, K.M.; Xu, L. Lipidomic consequences of phospholipid synthesis defects in Escherichia coli revealed by HILIC-ion mobility-mass spectrometry. Chem. Phys. Lipids 2019, 219, 15–22. [Google Scholar] [CrossRef] [PubMed]
  82. Palyzová, A.; Marešová, H.; Novák, J.; Zahradník, J.; Řezanka, T. Effect of the anti-inflammatory drug diclofenac on lipid composition of bacterial strain Raoultella sp. KDF8. Folia Microbiol. 2020, 65, 763–773. [Google Scholar] [CrossRef] [PubMed]
  83. Nguyen, N.A.; Sallans, L.; Kaneshiro, E.S. The major glycerophospholipids of the predatory and parasitic bacterium Bdellovibrio bacteriovorus HID5. Lipids 2008, 43, 1053–1063. [Google Scholar] [CrossRef] [PubMed]
  84. Kobayashi, T.; Nishijima, M.; Tamori, Y.; Nojima, S.; Seyama, Y.; Yamakawa, T. Acyl phosphatidylglycerol of Escherichia coli. Biochim. Biophys. Acta 1980, 620, 356–363. [Google Scholar] [PubMed]
  85. Nishijima, M.; Sa-Eki, T.; Tamori, Y.; Doi, O.; Nojima, S. Synthesis of acyl phosphatidylglycerol from phosphatidylglycerol in Escherichia coli K-12. Evidence for the participation of detergent-resistant phospholipase A and heat-labile membrane-bound factor(s). Biochim. Biophys. Acta 1978, 528, 107–118. [Google Scholar] [PubMed]
  86. Appala, K.; Bimpeh, K.; Freeman, C.; Hines, K.M. Recent applications of mass spectrometry in bacterial lipidomics. Anal. Bioanal. Chem. 2020, 412, 5935–5943. [Google Scholar] [CrossRef] [PubMed]
  87. Hsu, F.F.; Turk, J.; Shi, Y.; Groisman, E.A. Characterization of acylphosphatidylglycerols from Salmonella typhimurium by tandem mass spectrometry with electrospray ionization. J. Am. Soc. Mass Spectrom. 2004, 15, 1–11. [Google Scholar] [PubMed] [Green Version]
  88. Dalebroux, Z.D.; Matamouros, S.; Whittington, D.; Bishop, R.E.; Miller, S.I. PhoPQ regulates acidic glycerophospholipid content of the Salmonella typhimurium outer membrane. Proc. Natl. Acad. Sci. USA 2014, 111, 1963–1968. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  89. Sun, L.; Zhang, Y.; Cai, T.; Li, X.; Li, N.; Xie, Z.; Yang, F.; You, X. CrrAB regulates PagP-mediated glycerophosphoglycerol palmitoylation in the outer membrane of Klebsiella pneumoniae. J. Lipid Res. 2022, 63, 100251. [Google Scholar] [CrossRef] [PubMed]
  90. Inoue, M.; Tsuboi, K.; Okamoto, Y.; Hidaka, M.; Uyama, T.; Tsutsumi, T.; Tanaka, T.; Ueda, N.; Tokumura, A. Peripheral tissue levels and molecular species compositions of N-acyl-phosphatidylethanolamine and its metabolites in mice lacking N-acyl-phosphatidylethanolamine-specific phospholipase D. J. Biochem. 2017, 162, 449–458. [Google Scholar] [CrossRef] [PubMed]
  91. Suda, Y.; Okazaki, F.; Hasegawa, Y.; Adachi, S.; Fukase, K.; Kokubo, S.; Kuramitsu, S.; Kusumoto, S. Structural characterization of neutral and acidic glycolipids from Thermus thermophilus HB8. PLoS ONE 2012, 7, e35067. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  92. Nemoto, N.; Kawaguchi, M.; Yura, K.; Shimada, H.; Bessho, Y. PGLN: A newly identified amino phosphoglycolipid species in Thermus thermophilus HB8. Biochem. Biophys. Rep. 2022, 32, 101377. [Google Scholar] [CrossRef] [PubMed]
  93. Hirai, Y.; Haque, M.; Yoshida, T.; Yokota, K.; Yasuda, T.; Oguma, K. Unique cholesteryl glucosides in Helicobacter pylori: Composition and structural analysis. J. Bacteriol. 1995, 177, 5327–5333. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  94. Nagata, M.; Toyonaga, K.; Ishikawa, E.; Haji, S.; Okahashi, N.; Takahashi, M.; Izumi, Y.; Imamura, A.; Takato, K.; Ishida, H.; et al. Helicobacter pylori metabolites exacerbate gastritis through C-type lectin receptors. J. Exp. Med. 2021, 218, e20200815. [Google Scholar] [CrossRef] [PubMed]
  95. Stübs, G.; Fingerle, V.; Zähringer, U.; Schumann, R.R.; Rademann, J.; Schröder, N.W. Acylated cholesteryl galactosides are ubiquitous glycolipid antigens among Borrelia burgdorferi sensu lato. FEMS Immunol. Med. Microbiol. 2011, 63, 140–143. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  96. Hove, P.R.; Magunda, F.; de Mello Marques, M.A.; Islam, M.N.; Harton, M.R.; Jackson, M.; Belisle, J.T. Dentification and functional analysis of a galactosyltransferase capable of cholesterol glycolipid formation in the Lyme disease spirochete Borrelia burgdorferi. PLoS ONE 2021, 16, e0252214. [Google Scholar] [CrossRef] [PubMed]
  97. Mangiarotti, A.; Genovese, D.M.; Naumann, C.A.; Monti, M.R.; Wilke, N. Hopanoids, like sterols, modulate dynamics, compaction, phase segregation and permeability of membranes. Biochim. Biophys. Acta Biomembr. 2019, 1861, 183060. [Google Scholar] [CrossRef] [PubMed]
  98. Malott, R.J.; Wu, C.H.; Lee, T.D.; Hird, T.J.; Dalleska, N.F.; Zlosnik, J.E.; Newman, D.K.; Speert, D.P. Fosmidomycin decreases membrane hopanoids and potentiates the effects of colistin on Burkholderia multivorans clinical isolates. Antimicrob. Agents Chemother. 2014, 58, 5211–5219. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  99. Schmerk, C.L.; Welander, P.V.; Hamad, M.A.; Bain, K.L.; Bernards, M.A.; Summons, R.E.; Valvano, M.A. Elucidation of the Burkholderia cenocepacia hopanoid biosynthesis pathway uncovers functions for conserved proteins in hopanoid-producing bacteria. Environ. Microbiol. 2015, 17, 735–750. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  100. Renoux, J.M.; Rohmer, M. Prokaryotic triterpenoids. New bacteriohopanetetrol cyclitol ethers from the methylotrophic bacterium Methylobacterium organophilum. Eur. J. Biochem. 1985, 151, 405–410. [Google Scholar] [CrossRef] [PubMed]
  101. Garcia Costas, A.M.; Tsukatani, Y.; Rijpstra, W.I.; Schouten, S.; Welander, P.V.; Summons, R.E.; Bryant, D.A. Identification of the bacteriochlorophylls, carotenoids, quinones, lipids, and hopanoids of “Candidatus Chloracidobacterium thermophilum”. J. Bacteriol. 2012, 194, 1158–1168. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  102. Araújo, R.G.; Zavala, N.R.; Castillo-Zacarías, C.; Barocio, M.E.; Hidalgo-Vázquez, E.; Parra-Arroyo, L.; Rodríguez-Hernández, J.A.; Martínez-Prado, M.A.; Sosa-Hernández, J.E.; Martínez-Ruiz, M.; et al. Recent Advances in Prodigiosin as a Bioactive Compound in Nanocomposite Applications. Molecules 2022, 27, 4982. [Google Scholar] [CrossRef] [PubMed]
  103. Stankovic, N.; Radulovic, V.; Petkovic, M.; Vuckovic, I.; Jadranin, M.; Vasiljevic, B.; Nikodinovic-Runic, J. Streptomyces sp. JS520 produces exceptionally high quantities of undecylprodigiosin with antibacterial, antioxidative, and UV-protective properties. Appl. Microbiol. Biotechnol. 2012, 96, 1217–1231. [Google Scholar] [CrossRef] [PubMed]
  104. Koyun, M.T.; Sirin, S.; Aslim, B.; Taner, G.; Dolanbay, S.N. Characterization of prodigiosin pigment by Serratia marcescens and the evaluation of its bioactivities. Toxicol. Vitr. 2022, 82, 105368. [Google Scholar] [CrossRef] [PubMed]
  105. Klaus, J.R.; Coulon, P.M.L.; Koirala, P.; Seyedsayamdost, M.R.; Déziel, E.; Chandler, J.R. Secondary metabolites from the Burkholderia pseudomallei complex: Structure, ecology, and evolution. J. Ind. Microbiol. Biotechnol. 2020, 47, 877–887. [Google Scholar] [CrossRef] [PubMed]
  106. Wood, P.L. Non-targeted lipidomics utilizing constant infusion high resolution ESI mass spectrometry. In Springer Protocols, Neuromethods: Lipidomics; Wood, P.L., Ed.; Humana Press: New York, NY, USA, 2017; Volume 125, pp. 13–19. ISBN 978-1-0716-0863-0. [Google Scholar]
  107. Guan, Z.; Johnston, N.C.; Raetz, C.R.H.; Johnson, E.A.; Goldfine, H. Lipid diversity among botulinum neurotoxin-producing clostridia. Microbiology 2012, 158, 2577–2584. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  108. Wood, P.L.; Woltjer, R.L. Electrospray Ionization High Resolution Mass Spectrometry of the Chloride Adducts of Steroids, Mono- and Oligo-saccharides, Xyloglucans, Ceramides, Gangliosides, and Phenols. In Springer Protocols, Neuromethods: Metabolomics; Wood, P.L., Ed.; Humana Press: New York, NY, USA, 2021; Volume 159, pp. 69–76. ISBN 978-1-0716-0863-0. [Google Scholar]
  109. Wood, P.L.; Scoggin, K.; Ball, B.A.; Lawrence, L.; Troedsson, M.H.; Squires, E.L. Lipidomics of equine sperm and seminal plasma: Identification of amphiphilic (O-acyl)-ω-hydroxy- fatty acids. Theriogenology 2016, 86, 1212–1225. [Google Scholar] [CrossRef] [PubMed]
  110. Wood, P.L.; Muir, W.; Christmann, U.; Gibbons, P.; Hancock, C.L.; Poole, C.M.; Emery, A.L.; Poovey, J.R.; Scarborough, J.J.; Christopher, J.S.; et al. Lipidomics of chicken egg yolk: High resolution mass spectrometric characterization of nutritional lipid families. Poult. Sci. 2021, 100, 887–899. [Google Scholar] [CrossRef] [PubMed]
  111. Wood, P.L.; Hauther, K.A.; Scarborough, J.H.; Craney, D.J.; Dudzik, B.; Cebak, J.E.; Woltjer, R.L. Human brain lipidomics: Utilities of chloride adducts in flow injection analyses (FIA). Life 2021, 11, 403. [Google Scholar] [CrossRef] [PubMed]
  112. Wood, P.L.; Erol EHoffsis, G.F.; DeBuck, J. Serum Lipidomics of Bovine Paratuberculosis: Disruption of Choline-Containing Glycerophospholipids and Sphingolipids. Sage Open Med. 2018, 6, 2050312118775302. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  113. Laval, F.; Laneelle, M.-A.; Deon, C.; Monsarrat, B.; Daffe, M. Accurate molecular mass detreremination of mycolic acids by MALD-TOF mass spectrometry. Anal. Chem. 2001, 73, 4537–4544. [Google Scholar] [CrossRef] [PubMed]
  114. Schukken, Y.H.; Whitlock, R.H.; Wolfgang, D.; Grohn, Y.; Beaver, A.; VanKessel, J.; Zurakowski, M.; Mitchell, R. Longitudinal data collection of Mycobacterium avium subspecies Paratuberculosis infections in dairy herds: The value of precise field data. Vet. Res. 2015, 46, 65. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  115. Aspinall, G.O.; Chatterjee, D.; Brennan, P.J. The variable surface glycolipids of mycobacteria: Structures, synthesis of epitopes, and biological properties. Adv. Carbohydr. Chem. Biochem. 1995, 51, 169–242. [Google Scholar] [PubMed]
  116. Hsu, F.F.; Pacheco, S.; Turk, J.; Purdy, G. Structural determination of glycopeptidolipids of Mycobacterium smegmatis by high-resolution multiple-stage linear ion-trap mass spectrometry with electrospray ionization. J. Mass Spectrom. 2012, 47, 1269–1281. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  117. Schorey, J.S.; Sweet, L. The mycobacterial glycopeptidolipids: Structure, function, and their role in pathogenesis. Glycobiology 2008, 18, 832–841. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  118. Ryan, E.; Joyce, S.A.; Clarke, D.J. Membrane lipids from gut microbiome-associated bacteria as structural and signalling molecules. Microbiology 2023, 169, micro001315. [Google Scholar] [CrossRef] [PubMed]
  119. Yasuda, S.; Okahashi, N.; Tsugawa, H.; Ogata, Y.; Ikeda, K.; Suda, W.; Arai, H.; Hattori, M.; Arita, M. Elucidation of Gut Microbiota-Associated Lipids Using LC-MS/MS and 16S rRNA Sequence Analyses. iScience 2020, 23, 101841. [Google Scholar] [CrossRef] [PubMed]
  120. Reinink, P.; Buter, J.; Mishra, V.K.; Ishikawa, E.; Cheng, T.Y.; Willemsen, P.T.J.; Porwollik, S.; Brennan, P.J.; Heinz, E.; Mayfield, J.A.; et al. Discovery of Salmonella trehalose phospholipids reveals functional convergence with mycobacteria. J. Exp. Med. 2019, 216, 757–771. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  121. Lee, O.Y.; Wu, H.H.; Besra, G.S.; Rothschild, B.M.; Spigelman, M.; Hershkovitz, I.; Bar-Gal, G.K.; Donoghue, H.D.; Minnikin, D.E. Lipid biomarkers provide evolutionary signposts for the oldest known cases of tuberculosis. Tuberculosis 2015, 95 (Suppl. S1), S127–S132. [Google Scholar] [CrossRef] [PubMed]
  122. Lee, O.Y.; Wu, H.H.; Donoghue, H.D.; Spigelman, M.; Greenblatt, C.L.; Bull, I.D.; Rothschild, B.M.; Martin, L.D.; Minnikin, D.E.; Besra, G.S. Mycobacterium tuberculosis complex lipid virulence factors preserved in the 17,000-year-old skeleton of an extinct bison, Bison antiquus. PLoS ONE 2012, 7, e41923. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  123. Masson, M.; Molnár, E.; Donoghue, H.D.; Besra, G.S.; Minnikin, D.E.; Wu, H.H.; Lee, O.Y.; Bull, I.D.; Pálfi, G. Osteological and biomolecular evidence of a 7000-year-old case of hypertrophic pulmonary osteopathy secondary to tuberculosis from neolithic hungary. PLoS ONE 2013, 8, e78252. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  124. Váradi, O.A.; Rakk, D.; Spekker, O.; Terhes, G.; Urbán, E.; Berthon, W.; Pap, I.; Szikossy, I.; Maixner, F.; Zink, A.; et al. Verification of tuberculosis infection among Vác mummies (18th century CE, Hungary) based on lipid biomarker profiling with a new HPLC-HESI-MS approach. Tuberculosis 2021, 126, 102037. [Google Scholar] [CrossRef] [PubMed]
  125. Spekker, O.; Váradi, O.A.; Szekeres, A.; Jäger, H.Y.; Zink, A.; Berner, M.; Pany-Kucera, D.; Strondl, L.; Klostermann, P.; Samu, L.; et al. A rare case of calvarial tuberculosis from the Avar Age (8th century CE) cemetery of Kaba-Bitózug (Hajdú-Bihar county, Hungary)-Pathogenesis and differential diagnostic aspects. Tuberculosis 2022, 135, 102226. [Google Scholar] [CrossRef] [PubMed]
Metabolites 13 00809 g001 550
Figure 1. Relative PDIM-B levels in the bacterial pellet of M. avium (Red bars) and in the serum of 10 cows infected with PTB (blue bar; mean ± SD).
Figure 1. Relative PDIM-B levels in the bacterial pellet of M. avium (Red bars) and in the serum of 10 cows infected with PTB (blue bar; mean ± SD).
Metabolites 13 00809 g001
Metabolites 13 00809 g002 550
Figure 2. Relative hTMM levels in the bacterial pellet of M. avium (Red bars) and in the serum of 10 cows infected with PTB (blue bar; mean ± SD).
Figure 2. Relative hTMM levels in the bacterial pellet of M. avium (Red bars) and in the serum of 10 cows infected with PTB (blue bar; mean ± SD).
Metabolites 13 00809 g002
Metabolites 13 00809 g003 550
Figure 3. Bacterial mycolic acid levels presented as a rank order for M. avium, S. aureus, R. equi, E. faecalis, and C. glutamicum. The data are presented in Supplementary Table S1. With FIA, we cannot distinguish between double bonds and cyclopropane groups in the mycolic acids designated as unsaturated.
Figure 3. Bacterial mycolic acid levels presented as a rank order for M. avium, S. aureus, R. equi, E. faecalis, and C. glutamicum. The data are presented in Supplementary Table S1. With FIA, we cannot distinguish between double bonds and cyclopropane groups in the mycolic acids designated as unsaturated.
Metabolites 13 00809 g003
Metabolites 13 00809 g004 550
Figure 4. Bacterial mycolic acid levels presented as a rank order for M. bovis and M. smegmatis. The data are presented in Supplementary Table S1. With FIA, we cannot distinguish between double bonds and cyclopropane groups in the mycolic acids designated as unsaturated.
Figure 4. Bacterial mycolic acid levels presented as a rank order for M. bovis and M. smegmatis. The data are presented in Supplementary Table S1. With FIA, we cannot distinguish between double bonds and cyclopropane groups in the mycolic acids designated as unsaturated.
Metabolites 13 00809 g004
Metabolites 13 00809 g005 550
Figure 5. Bacterial ornithinyl-FAHFA levels presented as a rank order for each Gram-negative bacterial strain. The data are presented in Supplementary Table S1.
Figure 5. Bacterial ornithinyl-FAHFA levels presented as a rank order for each Gram-negative bacterial strain. The data are presented in Supplementary Table S1.
Metabolites 13 00809 g005
Table
Table 1. Gram-positive bacterial lipoteichoic-acid-associated lipids.
Table 1. Gram-positive bacterial lipoteichoic-acid-associated lipids.
Lipid ClassBacterial StrainsReferences
Monohexosyl-monoacylglycerol (MHMG)S. mitis and S. oralis C. cadaveris, C. fallax[3,4,5]
Dihexosyl-MG (DHMG)S. pneumoniae, S. mitis, S. oralis, S. mutans[4,6]
Monohexosyl-diacylglycerol (MHDG)S. pneumoniae, S. mitis, S. oralis, C. fallax, S. mutans, Rhomboutsia spp., B. licheniformis, Clostridia spp., L. johnsonii[4,5,6,7,8,9,10]
DHDGS. mitis and S. oralis, C. fallax, S. mutans, Rhomboutsia spp., B. licheniformis, Clostridia spp., L. johnsonii[4,5,6,7,8,9,10]
Lipoteichoic Acid Primer (LTAP; DHDG-GroP)Streptococcus spp., B. licheniformis, Clostridia spp., Listeria spp., Bacillus subtilis[4,5,6,8,9,11]
Alanylated-LTAP (LTAP-Ala) and Di-Alanylated-LTAPBacillus licheniformis, Bacillus subtilis[8,12,13]
Diglycerophosphate-DHDG (LTAdiP)S. pneumoniae, S. mitis, S. oralis, Listeria spp.[4,14]
Tri- and Tetra-Hexosyl-DGRhomboutsia spp., Clostridia spp.[7,9]
Ala-DGBacillus subtilis, Corynebacterium glutamicum[12,15,16,17]
Glucuronosyl-DG (GlcA-DG)Corynebacterium glutamicum[16,17,18]
Lysyl-DG and Lysyl-Galactosyl-DGStaphlococcus spp.[19,20]
Mannosyl-Glucuronosyl-DG (Man-GlcA-DG)Corynebacterium glutamicum, C. striatum[16,17,18]
N-Acetylglucosamine-DG (GlcNAc-DG)Clostridia spp.[9,19]
Phosphoethanolamine-GlcNAc-DG (PE-GlcNAc-DG)Clostridia spp.[9,21]
PE-MHDG and PE-DHDGClostridia spp.[9,21]
Type IV LTA intermediatesOral commensal bacteria[4]
Table
Table 2. Gram-positive bacterial aminoacyl phosphatidylglycerols (PGs).
Table 2. Gram-positive bacterial aminoacyl phosphatidylglycerols (PGs).
Lipid ClassBacterial StrainsReferences
Precursor CDP-DGCorynebacterium glutamicum, C. striatum, Clostridia spp.[16,17,18,22]
Lysyl-PGBacillus spp., Clostridium spp., Lactobacillus spp., Staphylococcus spp.[23,24]
Alanyl-PGP. aeruginosa, Clostridia spp., Bifidobacteria spp., Staphylococci spp., Listeria spp., Bacillus spp., C. Corynebacterium, B. subtilis[12,13,15,16,23,24]
Leucyl-PGB. subtilis[12,13]
Succinyl-Lysyl-PGB. subtilis[12,25]
Arginyl-PGEnterococcus spp., Staphylococci spp., Listeria spp., Bacillus spp.[23,24]
Ornithinyl-PGBacillus, Mycobacteria spp[23,24,26]
Aspartyl-PGB. subtilis[12,13]
Table
Table 3. Gram-positive bacterial mycolic acids.
Table 3. Gram-positive bacterial mycolic acids.
Lipid ClassBacterial StrainsReferences
Mycolic acids (C76–C88; ᾳ-, keto-, and methoxyM. tuberculosis[29,30]
Mycolic acids (C30-46)R. equi[31]
TMM (Trehalose MonoMycolates: hydroxy, keto, acetyl)Corynebacterium glutamicum, C. striatum, R. equi[16,17,18,32]
Acyl-TMM (Mycolic-Acyl-Trehalose)Corynebacterium glutamicum, C. striatum[18]
TDM (Trehalose dimycolate)Corynebacterium glutamicum, C. striatum[18]
Acyltrehalose (MAT) and Diacyltrehalose (DAT)Rhodococcus ruber, M. tuberculosis[33,34]
Acyl- and Diacyl-SulfotrehaloseRhodococcus ruber, M. tuberculosis[33,35,36,37]
Mycolic acid-PG (1-Mycolic-2-16:0 PG)Corynebacterium glutamicum, C. striatum[18]
Phthiocerol (methoxy, DIMA) / Phthiodiolone (keto, DIMB) DimycocerosatesMycobacteria spp.[38,39]
Table
Table 4. Gram-positive bacterial mannosyl phosphoinositols (PIs).
Table 4. Gram-positive bacterial mannosyl phosphoinositols (PIs).
Lipid ClassBacterial StrainsReferences
PIM1 (mannosyl-PI), PIM2 (dimannosyl-PI)Mycobacteria spp., Streptomyces coelicolor, Nocardia spp., Corynebacteria spp.[1,38,39,40,41,42]
Acyl-PIM2Mycobacteria, Corynebacteria[16,35,36,37,38,39,40,41]
Table
Table 5. Gram-positive bacterial aminoacyl phosphatidylethanolamines (PEs).
Table 5. Gram-positive bacterial aminoacyl phosphatidylethanolamines (PEs).
Lipid ClassBacterial StrainsReferences
Alanyl-PEBacillus subtilis[13]
Lysyl-PEBacillus subtilis[13]
PE Glycerol AcetalsClostridium fallax but not C. cadaveris[43,44,45]
GPCR LigandsOral Commensal bacteria[5,9]
Table
Table 6. Gram-negative bacterial glycosyl hydroxy fatty acids (HFAs) and fatty acyls of hydroxy fatty acids (FAHFAs).
Table 6. Gram-negative bacterial glycosyl hydroxy fatty acids (HFAs) and fatty acyls of hydroxy fatty acids (FAHFAs).
Lipid ClassBacterial StrainsReferences
Lipid A variantsP. aeruginosa, E. coli[45,46,47,48]
Rhamnosyl- and Di-Rhamnosyl-3-HFAPseudomonas spp., Actinetobacter calcoaceticus, Enterobacter asburiae[50,51,52,53,54]
Isopentyl metabolitesFrancisella novicida[55,56]
Menaquinones (MK-7, MK-8, and MK-9)Rhodococcus spp., Mycobacterium spp., Nocardia spp.[57]
Table
Table 7. Gram-negative bacterial aminoacyl hydroxy fatty acids (HFAs) and fatty acyls of hydroxy fatty acids (FAHFAs).
Table 7. Gram-negative bacterial aminoacyl hydroxy fatty acids (HFAs) and fatty acyls of hydroxy fatty acids (FAHFAs).
Lipid ClassBacterial StrainsReferences
Gly-FAHFABacteroidetes spp., Cytophaga johnsonae[58,59,60]
Lys-, Hydroxy-Lys-FAHFAPseudobacter saltans, Flavobacterium johsoniae, Rhizobium tropici[61,62,63]
Orn-FAHFAPlantomycetes spp., Burkholderia spp., Rhizobium spp., Agrobacteriumtume faciens[1,64,65,66]
Gln-FAHFA, Gln-FAHFA(OH)E. coli[45]
Gly-Ser-FAHFAFlectobacillus major, Bacteroidetes spp. including P. gingivalis[67,68,69,70,71,72]
Gly-Ser-Orn-FAHFA, Gly-Ser-Orn-FAHFA(OH)Bacteroidetes spp.[71]
Gly-Ser-FAHFA-P-DGP. gingivalis[70,71]
Gly-Ser-HFABacteroidetes spp., Cryptophaga johnsonae[60,71,72,73]
Gly-Ser-Orn-HFABateroidetes spp.[71]
Table
Table 8. Gram-negative-bacterial-modified ceramides.
Table 8. Gram-negative-bacterial-modified ceramides.
Lipid ClassBacterial StrainsReferences
Ceramide-Phosphoethanolamine (Cer-PE)Bacteroidetes spp., including P. gingivalis. Trace levels have been monitored in mammals.[67,74,75,76,77,78]
Cer-Phosphoinositol (Cer-PI)Bacteroidetes spp.[72,75]
Cer-Phosphoglycerol (Cer-PG)Bacteroidetes spp.[67,73,76,79]
NAPE (N-acyl-phosphatidylethanolamine)E. coli, Bdellovibrio spp. and Raoultella spp.[80,81,82,83]
Acyl-PGE. coli; Salmonella spp., Klebsiella pneumoniae. Additionally, C. glutamicum Gram-positive bacteria and mammals.[16,80,81,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99]
Table
Table 9. Gram-negative bacterial sterols.
Table 9. Gram-negative bacterial sterols.
Lipid ClassBacterial StrainsReferences
Cholesteryl Acyl ᾳ-Glycoside (CAG)Helicobacter pylori, Borrelia burgdorferi[93,94,95,96]
Cholesteryl Acyl ᾳ-Phospho-Glycoside (CPG)Helicobacter pylori, Borrelia burgdorferi[93,94,95,96]
Cholesteryl Phosphoethanolamine-Glycoside (CEPG)Helicobacter pylori[94]
Bacteriohopanetetrol cyclitol ethers (BHT-CE)Burkholderia spp., Methylobacterium organophilum, Chloracidobacteria spp.[98,99,100,101]
Table
Table 10. Gram-Negative Bacterial Secondary Metabolites.
Table 10. Gram-Negative Bacterial Secondary Metabolites.
Lipid ClassBacterial StrainsReferences
Undecylprodigiosin metabolitesStreptomyces spp., Serratia marcescens[102,103,104]
MalleilactoneBurkholderia pseudomallei[105]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Wood, P.L.; Erol, E. Construction of a Bacterial Lipidomics Analytical Platform: Pilot Validation with Bovine Paratuberculosis Serum. Metabolites 2023, 13, 809. https://doi.org/10.3390/metabo13070809

AMA Style

Wood PL, Erol E. Construction of a Bacterial Lipidomics Analytical Platform: Pilot Validation with Bovine Paratuberculosis Serum. Metabolites. 2023; 13(7):809. https://doi.org/10.3390/metabo13070809

Chicago/Turabian Style

Wood, Paul L., and Erdal Erol. 2023. "Construction of a Bacterial Lipidomics Analytical Platform: Pilot Validation with Bovine Paratuberculosis Serum" Metabolites 13, no. 7: 809. https://doi.org/10.3390/metabo13070809

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop