Summary of Study ST001945
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 PR001232. The data can be accessed directly via it's Project DOI: 10.21228/M8G11Z 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 | ST001945 |
| Study Title | Capybara gut microbiome |
| Study Summary | The largest living rodent dwelling Pantanal wetlands and Amazon basin, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive. Herein, combining multi-meta-omics approaches, carbohydrate enzymology and X-ray crystallography, we elucidated the microbial community composition and structure, enzymatic systems and metabolic pathways involved in the conversion of recalcitrant dietary fibers into short-chain fatty acids, a main energy source for the host. The high efficiency of this microbiota in the deconstruction of plant polysaccharides is underpinned on the combination of unique enzymatic mechanisms from Fibrobacteres to degrade cellulose with a broad arsenal of Carbohydrate-Active enZymes (CAZymes) organized in polysaccharide utilization loci (PULs) from Bacteroidetes, to tackle with complex hemicelluloses typically found in gramineous and aquatic plants. Exploring the genomic dark matter of this community, two novel CAZy families were unveiled including a glycoside hydrolase family of β-galactosidases and a carbohydrate-binding module family involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to CAZymes. Together, these results demonstrate at community and molecular levels how the capybara gut microbiota orchestrates the deconstruction and utilization of dietary fibers, representing an untapped reservoir of new and intricate enzymatic mechanisms to overcome the lignocellulose recalcitrance, a central challenge toward a bio-based and sustainable economy. |
| Institute | Brazilian Center for Research in Energy and Materials (CNPEM) |
| Last Name | Persinoti |
| First Name | Gabriela |
| Address | Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, Sao Paulo, 13083-100, Brazil |
| gabriela.persinoti@lnbr.cnpem.br | |
| Phone | +55 19 35175165 |
| Submit Date | 2021-09-18 |
| Num Groups | 2 |
| Total Subjects | 6 |
| Num Females | 6 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2021-11-04 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001232 |
| Project DOI: | doi: 10.21228/M8G11Z |
| Project Title: | Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to break down complex plant polysaccharides |
| Project Summary: | The largest living rodent dwelling Pantanal wetlands and Amazon basin, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive. Herein, combining multi-meta-omics approaches, carbohydrate enzymology and X-ray crystallography, we elucidated the microbial community composition and structure, enzymatic systems and metabolic pathways involved in the conversion of recalcitrant dietary fibers into short-chain fatty acids, a main energy source for the host. The high efficiency of this microbiota in the deconstruction of plant polysaccharides is underpinned on the combination of unique enzymatic mechanisms from Fibrobacteres to degrade cellulose with a broad arsenal of Carbohydrate-Active enZymes (CAZymes) organized in polysaccharide utilization loci (PULs) from Bacteroidetes, to tackle with complex hemicelluloses typically found in gramineous and aquatic plants. Exploring the genomic dark matter of this community, two novel CAZy families were unveiled including a glycoside hydrolase family of β-galactosidases and a carbohydrate-binding module family involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to CAZymes. Together, these results demonstrate at community and molecular levels how the capybara gut microbiota orchestrates the deconstruction and utilization of dietary fibers, representing an untapped reservoir of new and intricate enzymatic mechanisms to overcome the lignocellulose recalcitrance, a central challenge toward a bio-based and sustainable economy. |
| Institute: | Brazilian Center for Research in Energy and Materials (CNPEM) |
| Last Name: | Persinoti |
| First Name: | Gabriela |
| Address: | Rua Giuseppe Máximo Scolfaro, 10.000, Polo II de Alta Tecnologia de Campinas, Campinas, Sao Paulo, 13083-100, Brazil |
| Email: | gabriela.persinoti@lnbr.cnpem.br |
| Phone: | +55 19 35175165 |
Subject:
| Subject ID: | SU002023 |
| Subject Type: | Mammal |
| Subject Species: | Hydrochoerus hydrochaeris |
| Gender: | Female |
Factors:
Subject type: Mammal; Subject species: Hydrochoerus hydrochaeris (Factor headings shown in green)
| mb_sample_id | local_sample_id | group |
|---|---|---|
| SA183471 | 1_1H_12Abril2018 | Cecal 2.1 |
| SA183472 | R3_1H_20Abril2018 | Cecal 2.1 |
| SA183473 | R2_1H_20Abril2018 | Cecal 2.1 |
| SA183474 | 2_1H_12Abril2018 | Cecal 2.1 |
| SA183475 | 3_1H_12Abril2018 | Cecal 2.1 |
| SA183476 | R1_1H_20Abril2018 | Cecal 2.1 |
| SA183477 | R6.1_1H_19Abril2018 | Cecal 3.1 |
| SA183478 | R6_1H_19Abril2018 | Cecal 3.1 |
| SA183479 | 5_1H_12Abril2018 | Cecal 3.1 |
| SA183480 | R4_1H_20Abril2018 | Cecal 3.1 |
| SA183481 | 6_1H_13Abril2018 | Cecal 3.1 |
| SA183482 | 4_1H_12Abril2018 | Cecal 3.1 |
| SA183483 | R8_1H_20Abril2018 | Cecal 4.1 |
| SA183484 | R9.1_1H_20Abril2018 | Cecal 4.1 |
| SA183485 | R9_1H_20Abril2018 | Cecal 4.1 |
| SA183486 | R7_1H_19Abril2018 | Cecal 4.1 |
| SA183487 | 7_1H_13Abril2018 | Cecal 4.1 |
| SA183488 | 9_1H_13Abril2018 | Cecal 4.1 |
| SA183489 | 12.1_1H_10Abril2018 | Rectal 2.1 |
| SA183490 | 12_1H_10Abril2018 | Rectal 2.1 |
| SA183491 | 11_1H_09Abril2018 | Rectal 2.1 |
| SA183492 | 10R_1H_10Abril2018 | Rectal 2.1 |
| SA183493 | 11R_1H_10Abril2018 | Rectal 2.1 |
| SA183494 | 10_1H_09Abril2018 | Rectal 2.1 |
| SA183495 | 15.1_1H_11Abril2018 | Rectal 3.1 |
| SA183496 | 13_1H_11Abril2018 | Rectal 3.1 |
| SA183497 | 15_1H_11Abril2018 | Rectal 3.1 |
| SA183498 | 14_1H_11Abril2018 | Rectal 3.1 |
| SA183499 | 18.1_1H_12Abril2018 | Rectal 4.1 |
| SA183500 | 17_1H_11Abril2018 | Rectal 4.1 |
| SA183501 | 16_1H_11Abril2018 | Rectal 4.1 |
| SA183502 | 18_1H_11Abril2018 | Rectal 4.1 |
| Showing results 1 to 32 of 32 |
Collection:
| Collection ID: | CO002016 |
| Collection Summary: | This study was carried out in strict accordance with the Animal Management Rule of the Brazilian Ministry of Environment (Sisbio 59826-1). The samples were obtained from three euthanized female animals in Tatuí/São Paulo State, Brazil (September 2017) as a measure of management of Rocky Mountain Spotted Fever (RMSF) hosts. After euthanasia, 20 g of intestinal contents were collected from the cecum and recto of each animal. All samples were placed in sterile containers and immediately frozen in liquid nitrogen. Samples were kept at −80 °C until processing. |
| Sample Type: | Cecum |
Treatment:
| Treatment ID: | TR002035 |
| Treatment Summary: | Approximately 30 mg of dry cecal and rectal contents from three female animals were used for NRM-based metabolomics analysis |
Sample Preparation:
| Sampleprep ID: | SP002029 |
| Sampleprep Summary: | Approximately 30 mg of dry cecal and rectal contents, and 300 μL of solution 2:1 (methanol: chloroform) were mixed and sonicated for 1 min (4 cycles of 15 sec with intervals of 10 sec) and placed at 4 °C for 15 min. Next, 300 μL of solution 1:1 (methanol: ultrapure water) was added, followed by centrifugation at 16,000 g and 4 °C for 20 min. The supernatant was transferred to a new tube and were dried in CentriVap Solvent System (Labconco Corporation). Samples were diluted to 630 μL by addition of D2O, 70 μL of sodium phosphate buffer (final concentration 0.1 M) containing dimethyl-silapentane-sulfonate (final concentration 0.5 mM) for NMR chemical shift reference and concentration calibration. The samples were filtrated in a syringe filter with a 0.22 µm pore size hydrophilic polyethersulfone (PES) membrane. |
Analysis:
| Analysis ID: | AN003167 |
| Laboratory Name: | Brazilian Center for Research in Energy and Materials (CNPEM) |
| Analysis Type: | NMR |
| Num Factors: | 6 |
| Num Metabolites: | 49 |
| Units: | μM |
NMR:
| NMR ID: | NM000217 |
| Analysis ID: | AN003167 |
| Instrument Name: | Varian Inova NMR spectrometer (Agilent Technologies Inc.) |
| Instrument Type: | Other |
| NMR Experiment Type: | 1D-1H |
| Spectrometer Frequency: | 599.84 MHz |
