Summary of Study ST003530
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 PR002172. The data can be accessed directly via it's Project DOI: 10.21228/M8VV6J 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 | ST003530 |
| Study Title | Microbiome and metabolome association network analysis identifies Clostridium_sensu_stricto_1 and Paraprevotella as putative keystone genera in the gut of common marmosets |
| Study Summary | The common marmoset (Callithrix jacchus), a nonhuman primate species, is a model organism that has garnered interest in recent years for its potential translational value in a variety of research settings including the field of microbiomics. While the composition of the marmoset’s gut microbiome has been described in captivity, little is known about how gut microbiota interact with each other over time and how they relate to metabolite productions. To help answer this, we characterized interactions in the gut microbiome of the common marmoset by calculating the Spearman correlation coefficient between 16S rDNA-derived relative genera abundance data and targeted metabolomics data collected longitudinally from 10 marmosets (6 males and 4 females). Association network graphs were used to visualize significant correlations and identify genera and metabolites that exhibit a high degree of associations, marking them as more influential within the microbiome. Clostridium_sensu_stricto_1, among the highest-degree genera for bacterial and metabololomic associations, also had a high relative betweenness centrality and negatively associated with high-degree Paraprevotella, indicating that it potentially plays a gatekeeping role within the bacteria-bacteria interaction and communication network. Corresponding metabolites with more numerous bacterial associations, including bile acids and taurine, are known regulators of bacterial growth that provide a potential mechanism through which Clostridium_sensu_stricto_1 and others exert their influence. To further characterize microbiome interactions, we performed hierarchical clustering on significant within-dataset associations and developed a new “Keystone Candidate Score” metric that identified Clostridium_sensu_stricto_1 and Paraprevotella as the most influential bacteria (so-called candidate keystone genera) in the marmoset gut microbiome. |
| Institute | University of Nebraska-Lincoln |
| Last Name | Alvarez |
| First Name | Sophie |
| Address | 2020 ryons st |
| salvarez@unl.edu | |
| Phone | 4024724575 |
| Submit Date | 2024-10-22 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf, mzML |
| Analysis Type Detail | GC-MS/LC-MS |
| Release Date | 2024-12-31 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002172 |
| Project DOI: | doi: 10.21228/M8VV6J |
| Project Title: | Microbiome and metabolome association network analysis identifies Clostridium_sensu_stricto_1 and Paraprevotella as putative keystone genera in the gut of common marmosets |
| Project Summary: | The common marmoset (Callithrix jacchus), a nonhuman primate species, is a model organism that has garnered interest in recent years for its potential translational value in a variety of research settings including the field of microbiomics. While the composition of the marmoset’s gut microbiome has been described in captivity, little is known about how gut microbiota interact with each other over time and how they relate to metabolite productions. To help answer this, we characterized interactions in the gut microbiome of the common marmoset by calculating the Spearman correlation coefficient between 16S rDNA-derived relative genera abundance data and targeted metabolomics data collected longitudinally from 10 marmosets (6 males and 4 females). Association network graphs were used to visualize significant correlations and identify genera and metabolites that exhibit a high degree of associations, marking them as more influential within the microbiome. Clostridium_sensu_stricto_1, among the highest-degree genera for bacterial and metabololomic associations, also had a high relative betweenness centrality and negatively associated with high-degree Paraprevotella, indicating that it potentially plays a gatekeeping role within the bacteria-bacteria interaction and communication network. Corresponding metabolites with more numerous bacterial associations, including bile acids and taurine, are known regulators of bacterial growth that provide a potential mechanism through which Clostridium_sensu_stricto_1 and others exert their influence. To further characterize microbiome interactions, we performed hierarchical clustering on significant within-dataset associations and developed a new “Keystone Candidate Score” metric that identified Clostridium_sensu_stricto_1 and Paraprevotella as the most influential bacteria (so-called candidate keystone genera) in the marmoset gut microbiome. |
| Institute: | University of Nebraska-Lincoln |
| Last Name: | Alvarez |
| First Name: | Sophie |
| Address: | 1901 Vine St |
| Email: | salvarez@unl.edu |
| Phone: | 4024724575 |
Subject:
| Subject ID: | SU003659 |
| Subject Type: | Mammal |
| Subject Species: | Callithrix jacchus |
| Taxonomy ID: | 9483 |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Callithrix jacchus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA387314 | 1223 | Control |
| SA387315 | 790 | Control |
| SA387316 | 970 | Control |
| SA387317 | 1022 | Control |
| SA387318 | 1024 | Control |
| SA387319 | 958 | Control |
| SA387320 | 920 | Control |
| SA387321 | 843 | Control |
| SA387322 | 680 | Control |
| SA387323 | 915 | Control |
| SA387324 | 794 | Post |
| SA387325 | 875 | Post |
| SA387326 | 716 | Post |
| SA387327 | 877 | Post |
| SA387328 | 1192 | Post |
| SA387329 | 1189 | Post |
| SA387330 | 745 | Post |
| SA387331 | 1075 | Post |
| SA387332 | 711 | Post |
| SA387333 | 1140 | Post |
| SA387334 | 1026 | Pre |
| SA387335 | 640 | Pre |
| SA387336 | 1087 | Pre |
| SA387337 | 677 | Pre |
| SA387338 | 751 | Pre |
| SA387339 | 940 | Pre |
| SA387340 | 764 | Pre |
| SA387341 | 641 | Pre |
| SA387342 | 1124 | Pre |
| SA387343 | 643 | Pre |
| SA387344 | 1097 | Stress |
| SA387345 | 1161 | Stress |
| SA387346 | 667 | Stress |
| SA387347 | 816 | Stress |
| SA387348 | 1160 | Stress |
| SA387349 | 671 | Stress |
| SA387350 | 1028 | Stress |
| SA387351 | 748 | Stress |
| SA387352 | 676 | Stress |
| SA387353 | 829 | Stress |
| Showing results 1 to 40 of 40 |
Collection:
| Collection ID: | CO003652 |
| Collection Summary: | Fecal samples were collected from captive marmosets approximately 2 days before the isolation challenge (Pre-Stress or Pre), 2 days into the challenge (Stress), 2 days after the end of the challenge (Post-Stress or Post), and 1 month afterward (Control). A total of 40 fecal samples collected (4 time points/marmoset × 10 marmosets) were used for metabolomics analysis. Collected fecal samples were aliquoted and frozen before being stored at -80°C. |
| Sample Type: | Feces |
Treatment:
| Treatment ID: | TR003668 |
| Treatment Summary: | The antibiotic regimen (vancomycin = 30 mg/kg, enrofloxacin = 10 mg/kg and neomycin = 20 mg/kg) was administered orally using marshmallows and marshmallow fluff once daily for 28 days. Fecal samples were collected from captive marmosets approximately 2 days before the isolation challenge (Pre-Stress or Pre), 2 days into the challenge (Stress), 2 days after the end of the challenge (Post-Stress or Post), and 1 month afterward (Control). |
Sample Preparation:
| Sampleprep ID: | SP003666 |
| Sampleprep Summary: | For SCFAs, an aliquot of 50 mg of fecal sample was extracted using 0.5% phosphoric acid spiked with 83.7 µg of D3-acetate as the internal standard. The samples were disrupted and homogenized by adding 2 stainless steel beads (SSB 32) using the TissueLyserII at 20 Hz for 2 min. The samples were additionally sonicated for 5 min. After centrifugation at 16,000 g for 10 min, the supernatants were transferred to a new tube. Butanol was added to the supernatant, and samples were extracted one more time using the TissueLyserII at 2 Hz for 2 min. The samples were centrifuged at 16,000 g for 10 min and the upper phase was transferred to a new tube. For Bile Acids, an aliquot of 50 mg of fecal samples was extracted by adding 2 stainless steel beads (SSB 32) and chilled methanol:acetonitrile (1:1) solution using the TissueLyserII at 20 Hz for 3 min. The internal standard used is a mixture of several isotope labelled bile acids (D4-taurochenodeoxycholic acid; D4-taurocholic acid; D4-glycocholic acid; D4-glycochenodeoxycholic acid; D4-chenodeoxycholic acid; D4-deoxycholic acid). Samples were centrifuged at 4°C at 16,000 g for 10 min, and supernatants were transferred to new tubes. Samples were extracted the same way a second time with supernatants combined to the first one and then dried down using a SAVANT speed-vac. Pellets were resuspended using 30% methanol and transferred to HPLC vials. |
Chromatography:
| Chromatography ID: | CH004403 |
| Chromatography Summary: | for SCFAs |
| Instrument Name: | Agilent 7890B |
| Column Name: | Agilent VF-WAXms (30m x 0.25mm, 0.25um) |
| Column Temperature: | 70 |
| Flow Gradient: | none |
| Flow Rate: | 1.2 mL/min |
| Solvent A: | none |
| Solvent B: | none |
| Chromatography Type: | GC |
| Chromatography ID: | CH004404 |
| Chromatography Summary: | for BAs |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters ACCQ-TAG ULTRA C18 (100 x 2.1mm, 1.7um) |
| Column Temperature: | 55 |
| Flow Gradient: | 30% B for 1.5 min, to 55% B in 0.2 min, to 98% B in 3.3 min, hold at 98% B for 5 min, to 30% B in 0.5 min |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% water; 2 mM ammonium formate; 0.5% formic acid |
| Solvent B: | 10% isopropanol/90% acetonitrile; 0.5% formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN005798 |
| Analysis Type: | MS |
| Chromatography ID: | CH004403 |
| Num Factors: | 4 |
| Num Metabolites: | 5 |
| Units: | concentration in ng/g wet feces |
| Analysis ID: | AN005799 |
| Analysis Type: | MS |
| Chromatography ID: | CH004404 |
| Num Factors: | 4 |
| Num Metabolites: | 14 |
| Units: | concentration in mg/g wet feces |
