Summary of Study ST002465
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 PR001468. The data can be accessed directly via it's Project DOI: 10.21228/M8ZT5R 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 | ST002465 |
| Study Title | Map of microbially induced metabolic changes across diverse body sites in mice - Mouse Data |
| Study Summary | Tissue samples from contents along the intestinal tract and systemic sites in mice that did not have any bacteria (germ free) or colonized with a simplified microbiota or more complex microbiota. |
| Institute | University of Calgary |
| Department | Physiology and Pharmacology |
| Laboratory | McCoy |
| Last Name | Brown |
| First Name | Kirsty |
| Address | 3330 Hospital Dr NW |
| kirsty.brown12@gmail.com; kathy.mccoy@ucalgary.ca | |
| Phone | 2508692232 |
| Submit Date | 2023-02-04 |
| Total Subjects | 72 |
| Num Males | 36 |
| Num Females | 36 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-02-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001468 |
| Project DOI: | doi: 10.21228/M8ZT5R |
| Project Title: | Microbiota alter the metabolome in an age and sex dependent manner in mice |
| Project Summary: | Tissue samples from contents along the intestinal tract and systemic sites in mice that did not have any bacteria (germ free) or colonized with a simplified microbiota or more complex microbiota. |
| Institute: | University of Calgary |
| Department: | Physiology and Pharmacology |
| Laboratory: | McCoy |
| Last Name: | BROWN |
| First Name: | KIRSTY |
| Address: | 2500 University Dr NW, CALGARY, AB, T2N 1N4, Canada |
| Email: | kirsty.brown1@ucalgary.ca; Kathy.mccoy@ucalgary.ca |
| Phone: | 2508692232 |
| Funding Source: | Canadian Institute of Health Research, Natural Science and Engineering Research Council of Canada, Alberta Innovates Health Solutions |
| Publications: | Microbiota alter the metabolome in an age and sex dependent manner in mice |
| Contributors: | Kirsty Brown, Carolyn A. Thomson, Ryan Groves, Vina Fan, Ian A. Lewis, Kathy D. McCoy |
Subject:
| Subject ID: | SU002555 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Age Or Age Range: | 3-12 weeks |
| Animal Animal Supplier: | In house breeding |
| Animal Housing: | Germ-free and gnotobiotic isolators for germ and gnotobiotic mice. Individually ventilated cages for specific pathogen free mice |
| Animal Light Cycle: | 12 hours |
| Animal Feed: | LabDiet (Cat# 5010; Laboratory Autoclavable Rodent Diet) |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Site | Microbiota | Age(weeks) | Sex |
|---|---|---|---|---|---|
| SA246529 | cec_gf_12_F_1 | Cecum_content | gf | 12 | F |
| SA246530 | cec_gf_12_F_4 | Cecum_content | gf | 12 | F |
| SA246531 | cec_gf_12_F_3 | Cecum_content | gf | 12 | F |
| SA246532 | cec_gf_12_F_2 | Cecum_content | gf | 12 | F |
| SA246533 | cec_gf_12_M_4 | Cecum_content | gf | 12 | M |
| SA246534 | cec_gf_12_M_1 | Cecum_content | gf | 12 | M |
| SA246535 | cec_gf_12_M_3 | Cecum_content | gf | 12 | M |
| SA246536 | cec_gf_12_M_2 | Cecum_content | gf | 12 | M |
| SA246537 | cec_gf_3_F_4 | Cecum_content | gf | 3 | F |
| SA246538 | cec_gf_3_F_1 | Cecum_content | gf | 3 | F |
| SA246539 | cec_gf_3_F_3 | Cecum_content | gf | 3 | F |
| SA246540 | cec_gf_3_F_2 | Cecum_content | gf | 3 | F |
| SA246541 | cec_gf_3_M_4 | Cecum_content | gf | 3 | M |
| SA246542 | cec_gf_3_M_3 | Cecum_content | gf | 3 | M |
| SA246543 | cec_gf_3_M_2 | Cecum_content | gf | 3 | M |
| SA246544 | cec_gf_3_M_1 | Cecum_content | gf | 3 | M |
| SA246545 | cec_gf_8_F_4 | Cecum_content | gf | 8 | F |
| SA246546 | cec_gf_8_F_3 | Cecum_content | gf | 8 | F |
| SA246547 | cec_gf_8_F_2 | Cecum_content | gf | 8 | F |
| SA246548 | cec_gf_8_F_1 | Cecum_content | gf | 8 | F |
| SA246549 | cec_gf_8_M_4 | Cecum_content | gf | 8 | M |
| SA246550 | cec_gf_8_M_3 | Cecum_content | gf | 8 | M |
| SA246551 | cec_gf_8_M_1 | Cecum_content | gf | 8 | M |
| SA246552 | cec_gf_8_M_2 | Cecum_content | gf | 8 | M |
| SA246553 | cec_sdm_12_F_4 | Cecum_content | sdm | 12 | F |
| SA246554 | cec_sdm_12_F_1 | Cecum_content | sdm | 12 | F |
| SA246555 | cec_sdm_12_F_3 | Cecum_content | sdm | 12 | F |
| SA246556 | cec_sdm_12_F_2 | Cecum_content | sdm | 12 | F |
| SA246557 | cec_sdm_12_M_4 | Cecum_content | sdm | 12 | M |
| SA246558 | cec_sdm_12_M_1 | Cecum_content | sdm | 12 | M |
| SA246559 | cec_sdm_12_M_3 | Cecum_content | sdm | 12 | M |
| SA246560 | cec_sdm_12_M_2 | Cecum_content | sdm | 12 | M |
| SA246561 | cec_sdm_3_F_4 | Cecum_content | sdm | 3 | F |
| SA246562 | cec_sdm_3_F_3 | Cecum_content | sdm | 3 | F |
| SA246563 | cec_sdm_3_F_2 | Cecum_content | sdm | 3 | F |
| SA246564 | cec_sdm_3_F_1 | Cecum_content | sdm | 3 | F |
| SA246565 | cec_sdm_3_M_4 | Cecum_content | sdm | 3 | M |
| SA246566 | cec_sdm_3_M_3 | Cecum_content | sdm | 3 | M |
| SA246567 | cec_sdm_3_M_2 | Cecum_content | sdm | 3 | M |
| SA246568 | cec_sdm_3_M_1 | Cecum_content | sdm | 3 | M |
| SA246569 | cec_sdm_8_F_4 | Cecum_content | sdm | 8 | F |
| SA246570 | cec_sdm_8_F_3 | Cecum_content | sdm | 8 | F |
| SA246571 | cec_sdm_8_F_1 | Cecum_content | sdm | 8 | F |
| SA246572 | cec_sdm_8_F_2 | Cecum_content | sdm | 8 | F |
| SA246573 | cec_sdm_8_M_3 | Cecum_content | sdm | 8 | M |
| SA246574 | cec_sdm_8_M_4 | Cecum_content | sdm | 8 | M |
| SA246575 | cec_sdm_8_M_2 | Cecum_content | sdm | 8 | M |
| SA246576 | cec_sdm_8_M_1 | Cecum_content | sdm | 8 | M |
| SA246577 | cec_spf_12_F_3 | Cecum_content | spf | 12 | F |
| SA246578 | cec_spf_12_F_4 | Cecum_content | spf | 12 | F |
| SA246579 | cec_spf_12_F_2 | Cecum_content | spf | 12 | F |
| SA246580 | cec_spf_12_F_1 | Cecum_content | spf | 12 | F |
| SA246581 | cec_spf_12_M_4 | Cecum_content | spf | 12 | M |
| SA246582 | cec_spf_12_M_3 | Cecum_content | spf | 12 | M |
| SA246583 | cec_spf_12_M_2 | Cecum_content | spf | 12 | M |
| SA246584 | cec_spf_3_F_4 | Cecum_content | spf | 3 | F |
| SA246585 | cec_spf_3_F_3 | Cecum_content | spf | 3 | F |
| SA246586 | cec_spf_3_F_2 | Cecum_content | spf | 3 | F |
| SA246587 | cec_spf_3_F_1 | Cecum_content | spf | 3 | F |
| SA246588 | cec_spf_3_M_4 | Cecum_content | spf | 3 | M |
| SA246589 | cec_spf_3_M_3 | Cecum_content | spf | 3 | M |
| SA246590 | cec_spf_3_M_1 | Cecum_content | spf | 3 | M |
| SA246591 | cec_spf_3_M_2 | Cecum_content | spf | 3 | M |
| SA246592 | cec_spf_8_F_4 | Cecum_content | spf | 8 | F |
| SA246593 | cec_spf_8_F_1 | Cecum_content | spf | 8 | F |
| SA246594 | cec_spf_8_F_3 | Cecum_content | spf | 8 | F |
| SA246595 | cec_spf_8_F_2 | Cecum_content | spf | 8 | F |
| SA246596 | cec_spf_8_M_4 | Cecum_content | spf | 8 | M |
| SA246597 | cec_spf_8_M_1 | Cecum_content | spf | 8 | M |
| SA246598 | cec_spf_8_M_3 | Cecum_content | spf | 8 | M |
| SA246599 | cec_spf_8_M_2 | Cecum_content | spf | 8 | M |
| SA246600 | col_gf_12_F_4 | Colon_content | gf | 12 | F |
| SA246601 | col_gf_12_F_3 | Colon_content | gf | 12 | F |
| SA246602 | col_gf_12_F_2 | Colon_content | gf | 12 | F |
| SA246603 | col_gf_12_F_1 | Colon_content | gf | 12 | F |
| SA246604 | col_gf_12_M_4 | Colon_content | gf | 12 | M |
| SA246605 | col_gf_12_M_2 | Colon_content | gf | 12 | M |
| SA246606 | col_gf_12_M_3 | Colon_content | gf | 12 | M |
| SA246607 | col_gf_12_M_1 | Colon_content | gf | 12 | M |
| SA246608 | col_gf_3_F_4 | Colon_content | gf | 3 | F |
| SA246609 | col_gf_3_F_3 | Colon_content | gf | 3 | F |
| SA246610 | col_gf_3_F_1 | Colon_content | gf | 3 | F |
| SA246611 | col_gf_3_F_2 | Colon_content | gf | 3 | F |
| SA246612 | col_gf_3_M_4 | Colon_content | gf | 3 | M |
| SA246613 | col_gf_3_M_1 | Colon_content | gf | 3 | M |
| SA246614 | col_gf_3_M_3 | Colon_content | gf | 3 | M |
| SA246615 | col_gf_3_M_2 | Colon_content | gf | 3 | M |
| SA246616 | col_gf_8_F_4 | Colon_content | gf | 8 | F |
| SA246617 | col_gf_8_F_1 | Colon_content | gf | 8 | F |
| SA246618 | col_gf_8_F_3 | Colon_content | gf | 8 | F |
| SA246619 | col_gf_8_F_2 | Colon_content | gf | 8 | F |
| SA246620 | col_gf_8_M_4 | Colon_content | gf | 8 | M |
| SA246621 | col_gf_8_M_3 | Colon_content | gf | 8 | M |
| SA246622 | col_gf_8_M_2 | Colon_content | gf | 8 | M |
| SA246623 | col_gf_8_M_1 | Colon_content | gf | 8 | M |
| SA246624 | col_sdm_12_F_3 | Colon_content | sdm | 12 | F |
| SA246625 | col_sdm_12_F_1 | Colon_content | sdm | 12 | F |
| SA246626 | col_sdm_12_F_2 | Colon_content | sdm | 12 | F |
| SA246627 | col_sdm_12_M_1 | Colon_content | sdm | 12 | M |
| SA246628 | col_sdm_12_M_4 | Colon_content | sdm | 12 | M |
Collection:
| Collection ID: | CO002548 |
| Collection Summary: | Mice were anaesthetized with isoflurane and blood was collected by retro-orbital bleed to serum separation collection tubes (BD, NJ, USA). Urine was collected from the mouse either before it was euthanized, immediately following euthanization or directly from the bladder following euthanization. Mice were euthanized by cervical dislocation. 1.5mL of ice-cold sterile PBS was injected into the peritoneal cavity, massaged for 20 seconds then removed and collected. The spleen and a segment of left lobe of the liver was collected. The intestine was excised and content from the entire length of the jejunum, ileum, cecum, and colon were collected. For the purposes of these experiments, the first 10cm of the small intestine was considered duodenum, and the remaining length was split in half with the proximal segment considered jejunum and the distal segment considered ileum. Following collection, blood was centrifuged (10,000 xg, 10 minutes, 4°C) and serum transferred into a 1.5mL Eppendorf tube. All collected samples were placed in liquid nitrogen immediately after collection and stored at -80°C until processing. For processing liver tissue, spleen, and intestinal content, ~50mg of tissue or content was added to a pre-weighed 2mL safe-lock tube containing a steel bead (3mm, Qiagen, Hilden, Germany). Tubes were reweighed and 5X v/w of ice-cold 50% methanol was added. Samples were homogenized (2 minutes, 30Hz), beads were removed, and samples stored at -20°C for 1 hour. Samples were centrifuged (max. speed, 15 minutes, 4֯C), supernatant was recovered and combined 1:4 with 50% methanol to obtain a final dilution of D20. For serum and urine, sample was combined 1:1 with 100% methanol and stored and -20°C for 1 hour. Samples were centrifuged (max. speed, 15 minutes, 4°C), supernatant was recovered and combined 1:25 with 50% methanol to obtain a final dilution of D50. Samples were centrifuged (max. speed, 15 minutes, 4°C) and supernatants were recovered and stored at -80°C until further processing. |
| Sample Type: | intestine content / liver / spleen / urine / peritoneal fluid / serum |
| Storage Conditions: | Described in summary |
Treatment:
| Treatment ID: | TR002567 |
| Treatment Summary: | GF and OMM12-colonized gnotobiotic mice were housed in flexible-film isolators within the International Microbiome Centre (IMC) and SPF mice were maintained in the Mouse Barrier Unit (MBU) at the University of Calgary. GF mice were routinely tested for the absence of bacteria by aerobic and anaerobic culture, gram staining, and vital dye (DNA-dye Sytox green) staining of caecal contents and all mice were routinely screened for the presence of pathogens. For SPF colonization by co-housing, 8-week-old GF animals were exported, transferred into sterile individually ventilated cages and transported from the IMC to the MBU where a colonizer SPF mouse was transferred into each cage. For OMM12 colonization by co-housing, 8-week-old GF animals were transferred into isolators containing OMM12-colonized mice and an OMM12-colonized mouse was added to each cage. All animals were fed identical autoclaved diets and maintained with 12-hour light-dark cycle. |
Sample Preparation:
| Sampleprep ID: | SP002561 |
| Sampleprep Summary: | Mice were anaesthetized with isoflurane and blood was collected by retro-orbital bleed to serum separation collection tubes (BD, NJ, USA). Urine was collected from the mouse either before it was euthanized, immediately following euthanization or directly from the bladder following euthanization. Mice were euthanized by cervical dislocation. 1.5mL of ice-cold sterile PBS was injected into the peritoneal cavity, massaged for 20 seconds then removed and collected. The spleen and a segment of left lobe of the liver was collected. The intestine was excised and content from the entire length of the jejunum, ileum, cecum, and colon were collected. For the purposes of these experiments, the first 10cm of the small intestine was considered duodenum, and the remaining length was split in half with the proximal segment considered jejunum and the distal segment considered ileum. Following collection, blood was centrifuged (10,000 xg, 10 minutes, 4°C) and serum transferred into a 1.5mL Eppendorf tube. All collected samples were placed in liquid nitrogen immediately after collection and stored at -80°C until processing. |
Combined analysis:
| Analysis ID | AN004021 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | Thermo Syncronis HILIC (100 x 2.1mm, 1.7um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | NEGATIVE |
| Units | AUC |
Chromatography:
| Chromatography ID: | CH002971 |
| Chromatography Summary: | All metabolomics data were collected at the Calgary Metabolomics Research Facility (CMRF). Briefly, samples were centrifuged (20,817 xg, 15 minutes, 4°C), then 200µL was transferred to a deep-well 96-well plate (Thermo FisherF) for LC-MS analysis. Data were collected on a Q Exactive™ HF Hybrid Quadrupole-Orbitrap™ Mass Spectrometer (Thermo-Fisher) coupled to a Vanquish™ UHPLC System (Thermo-Fisher). Metabolites were chromatographically separated on Syncronis HILIC UHPLC column (2.1mm x 100mm x 1.7um, Thermo-Fisher) at the flow rate of 600uL/min using a binary solvent system (solvent A, 20mM ammonium formate pH 3.0 in MS grade H20 and solvent B, MS grade acetonitrile with 0.1% formic acid (%v/v)) and the following gradient: 0-2 mins, 100 %B; 2-7 mins, 100-80 %B; 7-10 mins, 80-5 %B; 10-12 mins, 5% B; 12-13 mins, 5-100 %B; 13-15 mins, 100 %B. The samples injection volume was 2uL. MassM data were acquired in MS1, negative full scan mode at a resolution of 240,000 scanning from 50-750m/z. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Syncronis HILIC (100 x 2.1mm, 1.7um) |
| Column Temperature: | 30C |
| Flow Gradient: | 2 stage linear gradient |
| Flow Rate: | 600uL/min |
| Sample Injection: | 2uL |
| Solvent A: | 100% water; 20mM ammonium formate (pH3) |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Analytical Time: | 15 minutes |
| Washing Buffer: | 10% MeOH in H2O + 0.1% formic acid |
| Target Sample Temperature: | 4 |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003768 |
| Analysis ID: | AN004021 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolomics data files were processed with ms-mint (version 0.1.8.3; mint.resistancedb.org) Python package for targeted metabolomics and verified using El-Maven software package. For targeted analysis, metabolites were identified by matching observed m/z signals and chromatographic retention times to those observed from commercial metabolite standards library (MSMLSTM Sigma-Aldrich) containing 639 standards, 397 of which were detectable using our LC-MS and sample preparation methods and 140 of which were observed a detectable levels in the biological samples. |
| Ion Mode: | NEGATIVE |
