Summary of Study ST004347

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 PR002738. The data can be accessed directly via it's Project DOI: 10.21228/M8R54Z This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST004347
Study TitleHomarine Catabolism: In situ metabolomics from KM1906, surface samples along a transect in the North Pacific
Study SummaryAcross stations in the North Pacific, homarine concentrations (sum of dissolved and particulate measurements) were significantly correlated with hom gene transcript abundance (R² = 0.518, p = 0.0052, Spearman’s correlation), supporting coupling between substrate availability and gene expression.
Institute
University of Washington
DepartmentOceanography
Last NameCarlson
First NameLaura
Address1501 NE Boat Street
Emailtruxal@uw.edu
Phone2062216732
Submit Date2025-11-03
Study CommentsPart 3 of 6 datasets in project
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2026-01-02
Release Version1
Laura Carlson Laura Carlson
https://dx.doi.org/10.21228/M8R54Z
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002738
Project DOI:doi: 10.21228/M8R54Z
Project Title:Conserved pathway for homarine catabolism in environmental bacteria
Project Summary:Homarine (N-methylpicolinic acid) is a ubiquitous marine metabolite produced by phytoplankton and noted for its bioactivity in marine animals, yet its microbial degradation pathways are uncharacterized. Here, we identify a conserved operon (homABCDER) that mediates homarine catabolism in bacteria using comparative transcriptomics, mutagenesis, and targeted knockouts. Phylogenetic and genomic analyses show this operon distributed across abundant bacterial clades, including coastal copiotrophs (e.g., Rhodobacterales) and open-ocean oligotrophs (e.g., SAR11, SAR116). High-resolution mass spectrometry revealed N-methylglutamic acid and glutamic acid as key metabolic products of homarine in both model and natural systems, with N-methylglutamate dehydrogenase catalyzing their conversion. Metatranscriptomics showed responsive and in situ expression of hom genes aligned with homarine availability. These findings uncover the genetic and metabolic basis of homarine degradation, establish its ecological relevance, and highlight homarine as a versatile growth substrate that feeds into central metabolism via glutamic acid in diverse marine bacteria.
Institute:University of Washington, School of Oceanography
Last Name:Heal
First Name:Katherine
Address:1501 NE Boat Street, Marine Science Building, Room G, Seattle
Email:katherine.heal@pnnl.gov
Phone:612-616-4840

Subject:

Subject ID:SU004506
Subject Type:Water sample

Factors:

Subject type: Water sample; Subject species: - (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Lat Long
SA516084220623_Smp_MQBlk_5Dissolved_Blank NA NA
SA516085220623_Smp_MQBlk_1Dissolved_Blank NA NA
SA516086220623_Smp_MQBlk_2Dissolved_Blank NA NA
SA516087220623_Smp_MQBlk_4Dissolved_Blank NA NA
SA516088220623_Smp_MQBlk_3Dissolved_Blank NA NA
SA516089220623_Smp_MQBlk_6Dissolved_Blank NA NA
SA516097220623_Smp_MU1_ADissolved 22.24 -158
SA516098220623_Smp_MU1_CDissolved 22.24 -158
SA516099220623_Smp_MU1_BDissolved 22.24 -158
SA516100220623_Smp_MU2_CDissolved 24.1 -158
SA516101220623_Smp_MU2_ADissolved 24.1 -158
SA516102220623_Smp_MU2_BDissolved 24.1 -158
SA516103220623_Smp_MU3_CDissolved 25.55 -158
SA516104220623_Smp_MU3_BDissolved 25.55 -158
SA516105220623_Smp_MU3_ADissolved 25.55 -158
SA516106220623_Smp_MU4_ADissolved 27.47 -158
SA516107220623_Smp_MU4_BDissolved 27.47 -158
SA516108220623_Smp_MU4_CDissolved 27.47 -158
SA516109220623_Smp_MU5_ADissolved 29.28 -158
SA516110220623_Smp_MU5_BDissolved 29.28 -158
SA516111220623_Smp_MU5_CDissolved 29.28 -158
SA516112220623_Smp_MU6_ADissolved 31.1 -158
SA516113220623_Smp_MU6_BDissolved 31.1 -158
SA516114220623_Smp_MU6_CDissolved 31.1 -158
SA516115220623_Smp_MU7_CDissolved 32.18 -158
SA516116220623_Smp_MU7_ADissolved 32.18 -158
SA516117220623_Smp_MU7_BDissolved 32.18 -158
SA516118220623_Smp_MU13_CDissolved 33 -158
SA516119220623_Smp_MU13_BDissolved 33 -158
SA516120220623_Smp_MU13_ADissolved 33 -158
SA516121220623_Smp_MU8_CDissolved 34.16 -158
SA516122220623_Smp_MU8_ADissolved 34.16 -158
SA516123220623_Smp_MU8_BDissolved 34.16 -158
SA516124220623_Smp_MU9_CDissolved 35.59 -158
SA516125220623_Smp_MU9_BDissolved 35.59 -158
SA516126220623_Smp_MU9_ADissolved 35.59 -158
SA516127220623_Smp_MU10_CDissolved 36.57 -158
SA516128220623_Smp_MU10_BDissolved 36.57 -158
SA516129220623_Smp_MU10_ADissolved 36.57 -158
SA516130220623_Smp_MU14_BDissolved 37.38 -158
SA516131220623_Smp_MU14_ADissolved 37.38 -158
SA516132220623_Smp_MU14_CDissolved 37.38 -158
SA516133220623_Smp_MU12_ADissolved 37 -158
SA516134220623_Smp_MU12_BDissolved 37 -158
SA516135220623_Smp_MU12_CDissolved 37 -158
SA516136220623_Smp_MU15_BDissolved 38.45 -158
SA516137220623_Smp_MU15_ADissolved 38.45 -158
SA516138220623_Smp_MU15_CDissolved 38.45 -158
SA516139220623_Smp_MU11_BDissolved 38.58 -158
SA516140220623_Smp_MU11_ADissolved 38.58 -158
SA516141220623_Smp_MU11_CDissolved 38.58 -158
SA516142220623_Smp_MU16_ADissolved 40.53 -158
SA516143220623_Smp_MU16_BDissolved 40.53 -158
SA516144220623_Smp_MU16_CDissolved 40.53 -158
SA516145220623_Smp_MU17_BDissolved 42.334 -158
SA516146220623_Smp_MU17_ADissolved 42.334 -158
SA516090220623_Poo_TruePooG3-CXSPE_Full3Dissolved_QC NA NA
SA516091220623_Poo_TruePooG3-CXSPE_Full2Dissolved_QC NA NA
SA516092220623_Poo_TruePooG3-CXSPE_Full1Dissolved_QC NA NA
SA516093220623_Std_4uMStdsMix1InH2O_1Dissolved_Standard NA NA
SA516094220623_Std_4uMStdsMix1InH2O_2Dissolved_Standard NA NA
SA516095220623_Std_4uMStdsMix2InH2O_1Dissolved_Standard NA NA
SA516096220623_Std_4uMStdsMix2InH2O_2Dissolved_Standard NA NA
SA516147220628_Smp_MMQBlk1_BParticulate_Blank NA NA
SA516148220628_Smp_MBlk1_BParticulate_Blank NA NA
SA516149220628_Smp_MBlk1_AParticulate_Blank NA NA
SA516150220628_Smp_MMQBlk1_AParticulate_Blank NA NA
SA516158220628_Smp_MU1_CParticulate 22.24 -158
SA516159220628_Smp_MU1_AParticulate 22.24 -158
SA516160220628_Smp_MU1_BParticulate 22.24 -158
SA516161220628_Smp_MU2_AParticulate 24.1 -158
SA516162220628_Smp_MU2_BParticulate 24.1 -158
SA516163220628_Smp_MU2_CParticulate 24.1 -158
SA516164220628_Smp_MU3_AParticulate 25.55 -158
SA516165220628_Smp_MU3_BParticulate 25.55 -158
SA516166220628_Smp_MU3_CParticulate 25.55 -158
SA516167220628_Smp_MU4_AParticulate 27.47 -158
SA516168220628_Smp_MU4_CParticulate 27.47 -158
SA516169220628_Smp_MU4_BParticulate 27.47 -158
SA516170220628_Smp_MU5_CParticulate 29.28 -158
SA516171220628_Smp_MU5_BParticulate 29.28 -158
SA516172220628_Smp_MU5_AParticulate 29.28 -158
SA516173220628_Smp_MU6_AParticulate 31.1 -158
SA516174220628_Smp_MU6_CParticulate 31.1 -158
SA516175220628_Smp_MU6_BParticulate 31.1 -158
SA516176220628_Smp_MU24_BParticulate 31.24 -158
SA516177220628_Smp_MU24_CParticulate 31.24 -158
SA516178220628_Smp_MU24_AParticulate 31.24 -158
SA516179220628_Smp_MU7_CParticulate 32.18 -158
SA516180220628_Smp_MU7_AParticulate 32.18 -158
SA516181220628_Smp_MU7_BParticulate 32.18 -158
SA516182220628_Smp_MU23_CParticulate 33.34 -158
SA516183220628_Smp_MU23_BParticulate 33.34 -158
SA516184220628_Smp_MU23_AParticulate 33.34 -158
SA516185220628_Smp_MU8_CParticulate 34.16 -158
SA516186220628_Smp_MU8_BParticulate 34.16 -158
SA516187220628_Smp_MU8_AParticulate 34.16 -158
SA516188220628_Smp_MU22_AParticulate 34.39 -158
SA516189220628_Smp_MU22_CParticulate 34.39 -158
SA516190220628_Smp_MU22_BParticulate 34.39 -158
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Collection:

Collection ID:CO004499
Collection Summary:Metabolite samples were collected during the Gradients 3 cruise (KM1906) in the North Pacific in 2019. Briefly, 10L of water was collected from the shipboard flow-through underway sampling system and particulate metabolites were sampled by filtering the seawater using peristaltic pumps onto 142 mm diameter, 0.2 um pore size PTFE Omnipore filters, flash frozen in liquid nitrogen, and stored at -80 C until analysis. Dissolved metabolites were sampled by collecting the filtrate in 50 mL acid washed polypropylene Falcon tubes.
Sample Type:Marine particulate and dissolved matter
Storage Conditions:-80℃

Treatment:

Treatment ID:TR004515
Treatment Summary:No treatment - this was a study of the natural marine microbial population of a transect in the North Pacific.

Sample Preparation:

Sampleprep ID:SP004512
Sampleprep Summary:For particulate metabolites, cell pellets were extracted using a combination of mechanical and chemical disruption techniques as described in previous work (https://doi.org/10.1021/acs.analchem.7b04400). Dissolved metabolites were extracted using a cation-exchange-based solid phase extraction technique as described previously (https://doi.org/10.1002/lom3.10513). Following extraction, metabolites were dried down under N2 gas, reconstituted in water with isotope labeled internal standards, and analyzed using liquid chromatography mass spectrometry. Homarine concentrations were quantified by comparison to a 2H3-homarine internal standard.

Combined analysis:

Analysis ID AN007257
Chromatography ID CH005508
MS ID MS006951
Analysis type MS
Chromatography type HILIC
Chromatography system Waters Acquity I-Class
Column SeQuant ZIC- pHILIC (150 x 2.1mm,5um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE
Units nM

Chromatography:

Chromatography ID:CH005508
Chromatography Summary:For HILIC chromatography, a SeQuant ZIC-pHILIC column (5 um particle size, 2.1 mm x 150 mm, from Millipore) was used with 10 mM ammonium carbonate in 85:15 acetonitrile to water (Solvent A) and 10 mM ammonium carbonate in 85:15 water to acetonitrile (Solvent B) at a flow rate of 0.15 mL/min. This column was compared with a Waters UPLC BEH amide and a Millipore cHILIC column; the pHILIC showed superior reproducibility and peak shapes. The column was held at 100% A for 2 minutes, ramped to 64% B over 18 minutes, ramped to 100% B over 1 minute, held at 100% B for 5 minutes, and equilibrated at 100% A for 25 minutes (50 minutes total). The column was maintained at 30 C. The injection volume was 2 µL for samples and standard mixes. When starting a batch, the column was equilibrated at the starting conditions for at least 30 minutes. To improve the performance of the HILIC column, we maintained the same injection volume, kept the instrument running water blanks between samples as necessary, and injected standards in a representative matrix in addition to standards in water. After each batch, the column was flushed with 10 mM ammonium carbonate in 85:15 water to acetonitrile for 20 to 30 minutes.
Instrument Name:Waters Acquity I-Class
Column Name:SeQuant ZIC- pHILIC (150 x 2.1mm,5um)
Column Temperature:30
Flow Gradient:The column was held at 100% A for 2 minutes, ramped to 64% B over 18 minutes, ramped to 100% B over 1 minute, held at 100% B for 5 minutes, and equilibrated at 100% A for 25 minutes
Flow Rate:0.15 mL/min
Solvent A:85% acetonitrile/15% water; 10 mM ammonium carbonate
Solvent B:15% acetonitrile/85% water; 10 mM ammonium carbonate
Chromatography Type:HILIC

MS:

MS ID:MS006951
Analysis ID:AN007257
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS acquisition Comments: A full scan polarity switching method was used with a scan range of 60 to 900 m/z and a resolution of 60,000. MS parameters were as follows: capillary temperature was 320 ∞C, the H-ESI spray voltage was 3.5 kV, and the auxiliary gas heater temperature was 90 ∞C. The S-lens RF level was 65. Sheath gas, auxiliary gas, and sweep gas flow rates were maintained at 16, 3, and 1, respectively.
Ion Mode:POSITIVE
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