Summary of Study ST002807

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001754. The data can be accessed directly via it's Project DOI: 10.21228/M8071P This work is supported by NIH grant, U2C- DK119886.


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.

Show all samples  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST002807
Study TitleMetabolomic response of river biofilm to cobalt
Study SummaryMetabolites are low molecular-weight molecules produced during cellular metabolism. The global expression of the (meta-)metabolome could thus potentially be used to characterize the exposure of an organism or a community to a specific stressor. Here, the meta-metabolomic fingerprints of mature biofilms were examined after 1, 3 and 7 days of exposure to five concentrations of cobalt (0, 10-7, 10-6, 5 x 10-6 and 10-5 M) in aquatic microcosms. The global changes in meta-metabolomic fingerprints were in plain agreement with those of the other biological parameters studied (cobalt bioaccumulation, biomass, chlorophyll). To better understand the dose-responses of the biofilm meta-metabolome, the untargeted LC-HRMS metabolomic data were further processed using DRomics to build dose-response model curves and to calculate benchmark doses to be aggregated into an empirical cumulative density function. A trend analysis of the dose-response curves suggests the presence of homeostasis (0 - 4.7 x 10-7 M), defense (4.7 x 10-7 – 2.7 x 10-6 M) and damage (higher than 2.7 x 10-6 M) response ranges in biofilms exposed to various cobalt concentrations. The present study demonstrates that the use of untargerted meta-metabolomics represents a promising approach for environmental risk assessment of metals by relating molecular defense and damage mechanisms to contaminant concentration.
Muséum Nationale d'Histoire Naturelle
Last NameMarie
First NameBenjamin
Address12 rue Buffon 75005 Paris
Submit Date2023-08-02
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2023-08-27
Release Version1
Benjamin Marie Benjamin Marie application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR001754
Project DOI:doi: 10.21228/M8071P
Project Title:Metabolomic response of river biofilm to cobalt
Project Summary:The metabolomic fingerprints of mature biofilms maintained in aquatic microcosms.
Institute:Muséum Nationale d'Histoire Naturelle
Last Name:Marie
First Name:Benjamin
Address:12 rue Buffon 75005 Paris


Subject ID:SU002914
Subject Type:Other organism
Subject Species:Biofilm microbial community


Subject type: Other organism; Subject species: Biofilm microbial community (Factor headings shown in green)

mb_sample_id local_sample_id Sampling day Experimental group Cobalt concentration
SA30095120220202_C_M1a_1_1_5820 a control
SA30095220220202_C_M3b_6_1_5870 a control
SA30095320220202_C_M3a_5_1_5860 a control
SA30095420220202_C_M1b_2_1_5830 a control
SA30095520220202_C_M2a_3_1_5840 a control
SA30095620220202_C_M2b_4_1_5850 a control
SA30095720220202_B3_1j_M2_12_1_5941 b 0
SA30095820220202_B3_1j_M1_11_1_5931 b 0
SA30095920220202_B2_1j_M1_9_1_5911 b 0
SA30096020220202_B2_1j_M2_10_1_5921 b 0
SA30096120220202_B1_1j_M1_7_1_5891 b 0
SA30096220220202_B1_1j_M2_8_1_5901 b 0
SA30096320220202_B4_1j_M1_13_1_5961 e 1 x 10-7
SA30096420220202_B5_1j_M1_15_1_5981 e 1 x 10-7
SA30096520220202_B6_1j_M2_18_1_6011 e 1 x 10-7
SA30096620220202_B6_1j_M1_17_1_6001 e 1 x 10-7
SA30096720220202_B5_1j_M2_16_1_5991 e 1 x 10-7
SA30096820220202_B4_1j_M2_14_1_5971 e 1 x 10-7
SA30096920220202_B7_1j_M1_19_1_6031 h 1 x 10-6
SA30097020220202_B7_1j_M2_20_1_6041 h 1 x 10-6
SA30097120220202_B9_1j_M2_24_1_6081 h 1 x 10-6
SA30097220220202_B9_1j_M1_23_1_6071 h 1 x 10-6
SA30097320220202_B8_1j_M1_21_1_6051 h 1 x 10-6
SA30097420220202_B8_1j_M2_22_1_6061 h 1 x 10-6
SA30097520220202_B12_1j_M1_29_1_6141 k 5 x 10-6
SA30097620220202_B11_1j_M2_28_1_6131 k 5 x 10-6
SA30097720220202_B11_1j_M1_27_1_6121 k 5 x 10-6
SA30097820220202_B12_1j_M2_30_1_6151 k 5 x 10-6
SA30097920220202_B10_1j_M1_25_1_6101 k 5 x 10-6
SA30098020220202_B10_1j_M2_26_1_6111 k 5 x 10-6
SA30098120220202_B15_1j_M1_35_1_6211 n 1 x 10-5
SA30098220220202_B13_1j_M1_31_1_6171 n 1 x 10-5
SA30098320220202_B15_1j_M2_36_1_6221 n 1 x 10-5
SA30098420220202_B14_1j_M1_33_1_6191 n 1 x 10-5
SA30098520220202_B13_1j_M2_32_1_6181 n 1 x 10-5
SA30098620220202_B14_1j_M2_34_1_6201 n 1 x 10-5
SA30098720220202_B1_3j_M1_37_1_6243 c 0
SA30098820220202_B3_3j_M2_42_1_6293 c 0
SA30098920220202_B3_3j_M1_41_1_6283 c 0
SA30099020220202_B2_3j_M2_40_1_6273 c 0
SA30099120220202_B2_3j_M1_39_1_6263 c 0
SA30099220220202_B1_3j_M2_38_1_6253 c 0
SA30099320220202_B6_3j_M1_47_1_6353 f 1 x 10-7
SA30099420220202_B4_3j_M1_43_1_6313 f 1 x 10-7
SA30099520220202_B6_3j_M2_48_1_6363 f 1 x 10-7
SA30099620220202_B4_3j_M2_44_1_6323 f 1 x 10-7
SA30099720220202_B5_3j_M1_45_1_6333 f 1 x 10-7
SA30099820220202_B5_3j_M2_46_1_6343 f 1 x 10-7
SA30099920220202_B9_3j_M2_54_1_6433 i 1 x 10-6
SA30100020220202_B9_3j_M1_53_1_6423 i 1 x 10-6
SA30100120220202_B7_3j_M1_49_1_6383 i 1 x 10-6
SA30100220220202_B7_3j_M2_50_1_6393 i 1 x 10-6
SA30100320220202_B8_3j_M2_52_1_6413 i 1 x 10-6
SA30100420220202_B8_3j_M1_51_1_6403 i 1 x 10-6
SA30100520220202_B10_3j_M1_55_1_6453 l 5 x 10-6
SA30100620220202_B10_3j_M2_56_1_6463 l 5 x 10-6
SA30100720220202_B12_3j_M2_60_1_6503 l 5 x 10-6
SA30100820220202_B12_3j_M1_59_1_6493 l 5 x 10-6
SA30100920220202_B11_3j_M2_58_1_6483 l 5 x 10-6
SA30101020220202_B11_3j_M1_57_1_6473 l 5 x 10-6
SA30101120220202_B14_3j_M1_63_1_6543 o 1 x 10-5
SA30101220220202_B15_3j_M2_66_1_6573 o 1 x 10-5
SA30101320220202_B14_3j_M2_64_1_6553 o 1 x 10-5
SA30101420220202_B15_3j_M1_65_1_6563 o 1 x 10-5
SA30101520220202_B13_3j_M1_61_1_6523 o 1 x 10-5
SA30101620220202_B13_3j_M2_62_1_6533 o 1 x 10-5
SA30101720220202_B3_7j_M1_71_1_6637 d 0
SA30101820220202_B1_7j_M2_68_1_6607 d 0
SA30101920220202_B2_7j_M1_69_1_6617 d 0
SA30102020220202_B2_7j_M2_70_1_6627 d 0
SA30102120220202_B3_7j_M2_72_1_6647 d 0
SA30102220220202_B1_7j_M1_67_1_6597 d 0
SA30102320220202_B4_7j_M2_74_1_6677 g 1 x 10-7
SA30102420220202_B5_7j_M1_75_1_6687 g 1 x 10-7
SA30102520220202_B5_7j_M2_76_1_6697 g 1 x 10-7
SA30102620220202_B6_7j_M1_77_1_6707 g 1 x 10-7
SA30102720220202_B6_7j_M2_78_1_6717 g 1 x 10-7
SA30102820220202_B4_7j_M1_73_1_6667 g 1 x 10-7
SA30102920220202_B7_7j_M2_80_1_6747 j 1 x 10-6
SA30103020220202_B7_7j_M1_79_1_6737 j 1 x 10-6
SA30103120220202_B8_7j_M1_81_1_6757 j 1 x 10-6
SA30103220220202_B8_7j_M2_82_1_6767 j 1 x 10-6
SA30103320220202_B9_7j_M2_84_1_6787 j 1 x 10-6
SA30103420220202_B9_7j_M1_83_1_6777 j 1 x 10-6
SA30103520220202_B11_7j_M1_87_1_6827 m 5 x 10-6
SA30103620220202_B12_7j_M2_90_1_6857 m 5 x 10-6
SA30103720220202_B10_7j_M1_85_1_6807 m 5 x 10-6
SA30103820220202_B10_7j_M2_86_1_6817 m 5 x 10-6
SA30103920220202_B12_7j_M1_89_1_6847 m 5 x 10-6
SA30104020220202_B11_7j_M2_88_1_6837 m 5 x 10-6
SA30104120220202_B15_7j_M2_96_1_6927 p 1 x 10-5
SA30104220220202_B15_7j_M1_95_1_6917 p 1 x 10-5
SA30104320220202_B13_7j_M2_92_1_6887 p 1 x 10-5
SA30104420220202_B13_7j_M1_91_1_6877 p 1 x 10-5
SA30104520220202_B14_7j_M1_93_1_6897 p 1 x 10-5
SA30104620220202_B14_7j_M2_94_1_6907 p 1 x 10-5
Showing results 1 to 96 of 96


Collection ID:CO002907
Collection Summary:Four weeks before the start of the experiment, the mature biofilms were collected by natural colonisation of glass slides (5 x 10 cm).
Sample Type:Microbial biofilm


Treatment ID:TR002923
Treatment Summary:A total of 15 microcosms were filled with 15 L of the Gave de Pau water; three for each of the five exposure conditions: 2 x 10-9 M (background concentration used as control), 1 x 10-7, 1 x 10-6, 5 x 10-6 and 1 x10-5 M Co. Cobalt (Cobalt Standard for ICP, 1000 mg·L-1, Supelco, Germany) was added in each microcosm and let equilibrating for 24 h (D-1). The microcosms were placed in one of the artificial streams of the facility in order to maintain the water temperature at 13.5 ± 1.0°C (Table S2). After one, three and seven days of exposure (D1, D3 and D7), slides were collected from each microcosm for metabolomics.

Sample Preparation:

Sampleprep ID:SP002920
Sampleprep Summary:Briefly, freeze-dried biofilms (1 mg) were diluted in 10 µL of cold 75% methanol acidified with 0.1% formic acid and sonicated on ice during 30 s, at 80 % of the maximum intensity (SONICS Vibra Cell, Newton, CT, USA; 130 Watts, 20 kHz). The homogenates were then centrifuged at 4°C (12,000 g: 10 min). The supernatants were then collected and stored in the dark at -20°C.
Processing Storage Conditions:-20℃

Combined analysis:

Analysis ID AN004564
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters Acquity
Column Thermo Acclaim Polar Advantage II (150 x 3mm,3um)
MS instrument type QTOF
MS instrument name Bruker maXis Impact qTOF
Units Dalton


Chromatography ID:CH003429
Instrument Name:Waters Acquity
Column Name:Thermo Acclaim Polar Advantage II (150 x 3mm,3um)
Column Temperature:40
Flow Gradient:5-90%
Flow Rate:300 microliter per minute
Solvent A:Water
Solvent B:ACN
Chromatography Type:Reversed phase


MS ID:MS004310
Analysis ID:AN004564
Instrument Name:Bruker maXis Impact qTOF
Instrument Type:QTOF
MS Comments:Metabolites were subsequently ionised and analysed using an electrospray ionization hybrid quadrupole time-of-flight high-resolution mass spectrometer (ESI-Qq-TOF Compact, Bruker) at 2 Hz speed on the 50–1500 m/z range on positive autoMS/MS mode between 2 and 8 Hz speed on the 50–1500 m/z range with information-dependent acquisition (IDA).