Summary of Study ST003511
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002156. The data can be accessed directly via it's Project DOI: 10.21228/M8XR64 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003511 |
| Study Title | Lipidomic analysis of Malassezia globosa at different growth stages and the dynamics of uptake and secreted lipids with growth media |
| Study Summary | Malassezia is one of the most abundant genera found on human skin; specifically, M. globosa is one of the yeast species dominant in this organ as it has been associated with several skin diseases. Malassezia cannot synthesize fatty acids. In response, the yeast cell intakes external fatty acids from the host or the growth media for survival. Several studies have focused on investigating the identity of lipids and enzymes in M. globosa to understand its lipid metabolism and the biology of the yeast cell-host interaction. In this work, we performed a supernatant lipidomic analysis on the mDixon media and the supernatant and on the M. globosa at early and late stationary phase (72h and 90h, respectively) to determine the lipid dynamics (lipids consumed vs. lipids secreted) between the growth media and the two stages of growth. We were able to identify 87 lipids within 17 classes of lipids; during the analysis, the increment of several lipids increased throughout time concerning the growth media, suggesting a secretion pattern from the cell to the media; some lipids found in this group were conjugated Sterols (ST) such as Glycochenodeoxycholic acid (GCDCA), Glycerophospholipids (GP), specifically phosphocholine's (PCs), Cardiolipins (CL), in particular those with chains of (47 to 54 carbons) and Sphingolipids (SP) such as Cer-PI which might have some role in pathogenicity. Likewise, the increment of some lipids decreased, but some only reduced at the late stationary phase (90h) only when the nutrients available was minimal. Finally, we observed a third pattern in which the amount of some lipids decreased throughout time (starting in the early stationary phase and finishing in the late stationary phase), hinting at a distinctive consumption pattern. The principal lipids consumed wereSterols (ST) bile acids, cholic acid, and its derivates, some phosphocholines (PCs), Fatty acyls (FA), and cardiolipins (CL). The consumption of these lipids was associated with different metabolic roles of the lipids in the cell as it lacks production of these lipids in M. globosa. |
| Institute | Universidad de los Andes, Colombia |
| Last Name | Cala |
| First Name | Mónica |
| Address | CALLE 46 N 3 35 |
| mp.cala10@uniandes.edu.co | |
| Phone | +573164316037 |
| Submit Date | 2024-09-30 |
| Num Groups | 6 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-10-21 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002156 |
| Project DOI: | doi: 10.21228/M8XR64 |
| Project Title: | Lipidomic analysis of Malassezia globosa at different growth stages and the dynamics of uptake and secreted lipids with growth media |
| Project Type: | Lipidomics |
| Project Summary: | Malassezia is one of the most abundant genera found on human skin; specifically, M. globosa is one of the yeast species dominant in this organ as it has been associated with several skin diseases. Malassezia cannot synthesize fatty acids. In response, the yeast cell intakes external fatty acids from the host or the growth media for survival. Several studies have focused on investigating the identity of lipids and enzymes in M. globosa to understand its lipid metabolism and the biology of the yeast cell-host interaction. In this work, we performed a supernatant lipidomic analysis on the mDixon media and the supernatant and on the M. globosa at early and late stationary phase (72h and 90h, respectively) to determine the lipid dynamics (lipids consumed vs. lipids secreted) between the growth media and the two stages of growth. We were able to identify 87 lipids within 17 classes of lipids; during the analysis, the increment of several lipids increased throughout time concerning the growth media, suggesting a secretion pattern from the cell to the media; some lipids found in this group were conjugated Sterols (ST) such as Glycochenodeoxycholic acid (GCDCA), Glycerophospholipids (GP), specifically phosphocholine's (PCs), Cardiolipins (CL), in particular those with chains of (47 to 54 carbons) and Sphingolipids (SP) such as Cer-PI which might have some role in pathogenicity. Likewise, the increment of some lipids decreased, but some only reduced at the late stationary phase (90h) only when the nutrients available was minimal. Finally, we observed a third pattern in which the amount of some lipids decreased throughout time (starting in the early stationary phase and finishing in the late stationary phase), hinting at a distinctive consumption pattern. The principal lipids consumed wereSterols (ST) bile acids, cholic acid, and its derivates, some phosphocholines (PCs), Fatty acyls (FA), and cardiolipins (CL). The consumption of these lipids was associated with different metabolic roles of the lipids in the cell as it lacks production of these lipids in M. globosa. |
| Institute: | Universidad de los Andes |
| Last Name: | Cala |
| First Name: | Monica |
| Address: | CALLE 46 N 3 35 Bogota-Colombia |
| Email: | mp.cala10@uniandes.edu.co |
| Phone: | +573164316037 |
Subject:
| Subject ID: | SU003640 |
| Subject Type: | Fungi |
| Subject Species: | Malassezia globosa |
| Taxonomy ID: | 76773 |
Factors:
Subject type: Fungi; Subject species: Malassezia globosa (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Sample_type | Time of collection |
|---|---|---|---|---|
| SA386089 | Sg1_2 | mDixon(media) | mDixon | na |
| SA386090 | Sg1_3 | mDixon(media) | mDixon | na |
| SA386091 | Sg1_1 | mDixon(media) | mDixon | na |
| SA386066 | Sg2_4 | Yeast | Mglobosa | 72h |
| SA386067 | Sg2_5 | Yeast | Mglobosa | 72h |
| SA386068 | Sg2_6 | Yeast | Mglobosa | 72h |
| SA386069 | Sg3_7 | Yeast | Mglobosa | 90h |
| SA386070 | Sg3_8 | Yeast | Mglobosa | 90h |
| SA386071 | Sg3_9 | Yeast | Mglobosa | 90h |
| SA386072 | QC_14 | Yeast | Quality control | na |
| SA386073 | QC_13 | Yeast | Quality control | na |
| SA386074 | QC_12 | Yeast | Quality control | na |
| SA386075 | QC_11 | Yeast | Quality control | na |
| SA386076 | QC_10 | Yeast | Quality control | na |
| SA386077 | Sg4_15 | Yeast | Supernatant | 72h |
| SA386078 | Sg4_14 | Yeast | Supernatant | 72h |
| SA386079 | Sg4_12 | Yeast | Supernatant | 72h |
| SA386080 | Sg4_13 | Yeast | Supernatant | 72h |
| SA386081 | Sg4_11 | Yeast | Supernatant | 72h |
| SA386082 | Sg4_10 | Yeast | Supernatant | 72h |
| SA386083 | Sg5_16 | Yeast | Supernatant | 90h |
| SA386084 | Sg5_17 | Yeast | Supernatant | 90h |
| SA386085 | Sg5_18 | Yeast | Supernatant | 90h |
| SA386086 | Sg5_19 | Yeast | Supernatant | 90h |
| SA386087 | Sg5_20 | Yeast | Supernatant | 90h |
| SA386088 | Sg5_21 | Yeast | Supernatant | 90h |
| Showing results 1 to 26 of 26 |
Collection:
| Collection ID: | CO003633 |
| Collection Summary: | The reference strain Malassezia globosa CBS 7966 (Westerdijk Institute, Utrecht, The Netherlands) was used for the whole study. A frozen stock was reactivated and precultured at 33°C for seven days in modified Dixon (mDixon) agar [36 g L-1 mycosel agar [BD, USA], 20 g L-1 Ox Bile [Sigma Aldrich, USA], 36 g L-1 malt extract [Oxoid, UK], 0.02% glycerol [Sigma Aldrich, USA], 0.02% oleic acid [Sigma Aldrich, USA], and 0.1% Tween 40 [Sigma Aldrich, USA]]. Then, one colony was transferred to a new mDixon agar plate and was incubated for five days at 33°C. From this plate, yeasts were suspended in 3 mL inoculum in water plus 0.1% Tween 80 [Sigma Aldrich, USA] to a top standard of 2 on the McFarland scale and were used to inoculate 27 mL of mDixon broth [36 g L-1 malt extract [Oxoid, UK], 6 g L-1 peptone [BD, USA], 20 g L-1 Ox bile [Sigma Aldrich, USA, 0.02% glycerol [Sigma Aldrich, USA], 0.02% oleic acid [Sigma Aldrich, USA], and 0.1% Tween 40 [Sigma Aldrich, USA] for 96 hours at 33°C and 180 rpm. An aliquot of 300 mL was used to inoculate 29.7 mL of fresh mDixon broth and incubated at 33°C and 180 rpm for 72 h and 90 h to reach the early stationary and stationary phase. (doi:10.1007/978-3-642-03616-3_2; doi:10.3389/fcimb.2020.00338). |
| Sample Type: | Yeast cells |
Treatment:
| Treatment ID: | TR003649 |
| Treatment Summary: | No treatments were applied to the samples. |
Sample Preparation:
| Sampleprep ID: | SP003647 |
| Sampleprep Summary: | Samples of M. globosa were collected at different growth stages, then centrifuged at 4,500 rpm for 10 minutes, and the supernatants were collected. Subsequently, 5 mL of isopropanol was added to the supernatant, followed by centrifugation at 4,500 rpm for another 10 minutes. Lipid extraction was performed according to Bligh and Dyer lipid extraction with some modifications (doi:10.1038/nprot.2016.040; doi:10.1016/j.jchromb.2017.06.045; doi:10.1021/acs.analchem.8b02839). 2mL of a citric acid buffer [0.1 M sodium citrate tribasic dihydrate, 1 M sodium chloride, pH 3.6], 2 mL of MeOH, and 4 mL of chloroform were added to 8 mL of supernatant collected previously. The mixture was homogenized with vortex for 15 min and sonicated for 30 min. The extracted lipids' organic phase was collected and dried on a Speed Vac. Then, the dry extract was re-dissolved in 1 mL of ACN containing 0.1% NH3·H2O (v/v), followed by strong anion-exchange solid-phase extraction using Strata SAX SPE-cartridge (55 uM, 70 A, 100 mg, 1 mL Phenomenex) which was pre-conditioned with 3 mL ACN. After sampling 1 mL of the lipid extract, the cartridge was washed with 3 mL acetone/H2O (1/9, v/v), 3mL acetone, and eluted with 3 mL formic acid/acetone (1/99, v/v) followed by evaporation using a Speed Vac. Samples were stored at -80°C for one week and dissolved in 1 mL of MeOH for further analysis (doi:10.1038/nprot.2016.040; doi:10.1016/j.jchromb.2017.06.045; doi:10.1021/acs.analchem.8b02839). |
Combined analysis:
| Analysis ID | AN005765 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1260 Infinity LC System |
| Column | Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6545 QTOF |
| Ion Mode | NEGATIVE |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH004374 |
| Chromatography Summary: | Chromatographic analysis was carried out at 65°C and constant flow 0.6 mL/min using gradient elution with phase A (60:40 ACN: type I water with 10 mM of ammonium formate and 0.1% v/v of formic acid) and mobile phase B (90:10 Isopropanol: Acetonitrile with 10 mM of ammonium formate and 0.1% v/v of formic acid). The elution gradient was 0 min 15% (B), 0–4 min 30% (B), 4–5 min 48% (B), 5–22 min 82% (B), 22–23 min 95% (B), 23–25 min 95% (B), 25–26 min 15% (B), and 26–31 min 15% (B). |
| Instrument Name: | Agilent 1260 Infinity LC System |
| Column Name: | Agilent InfinityLab Poroshell 120 EC-C18 (100 x 3mm,2.7um) |
| Column Temperature: | 65 °C |
| Flow Gradient: | The elution gradient was 0 min 15% (B), 0–4 min 30% (B), 4–5 min 48% (B), 5–22 min 82% (B), 22–23 min 95% (B), 23–25 min 95% (B), 25–26 min 15% (B), and 26–31 min 15% (B) |
| Flow Rate: | 0.6 mL/min |
| Solvent A: | 60% acetonitrile/40% water; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10 mM ammonium formate; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005485 |
| Analysis ID: | AN005765 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Mass spectrometry detection was performed in negative ionization mode in a full scan from 100 m/z to 1200 m/z. The mass correction was performed during the analysis with reference masses: m/z 121.0509 (C5H4N4) y m/z 922.0098 (C18H18O6N3P3F24). |
| Ion Mode: | NEGATIVE |
