Metabolomic profiles of human fecal samples in different storage conditions
Ontology highlight
ABSTRACT:
INSTRUMENT(S): maXis 4G
ORGANISM(S): Homo Sapiens
SUBMITTER: 
Pieter Dorrestein
PROVIDER: MSV000084554 | MassIVE | Thu Nov 07 14:42:00 GMT 2019
REPOSITORIES: MassIVE
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Project description:Data was collected on a LC-MS/MS system (c-18 column) positive mode. Data analyzing storage conditions of different storage collection devices for human fecal samples.
2019-11-07 | MSV000084554 | GNPS
Project description:We performed a mass spectrometry-based metaproteomic study to assess the impact of storage media on human gut microbiome in fecal samples. We evaluated FDA-authorized OMNIgene·GUT (OG), phosphate-buffered saline (PBS), and RNALater (RNAL) buffers.
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Project description:This study aimed to analyze changes in gut microbiota composition in mice after transplantation of fecal microbiota (FMT, N = 6) from the feces of NSCLC patients by analyzing fecal content using 16S rRNA sequencing, 10 days after transplantation. Specific-pathogen-free (SPF) mice were used for each experiments (N=4) as controls.
2023-07-01 | E-MTAB-12812 | biostudies-arrayexpress
Project description:Changes in Microbiota Profiles After Prolonged Frozen Storage of Stool Suspensions
| PRJEB33794 | ENA
Project description:The aim of this study was to develop a suitable method to preserve fecal samples for metaproteomics analyses when flash-freezing is not an option. Fecal samples were collected from conventional adult C57BL/6 mice and combined into a fecal master mix. The fecal master mix was then split into 48 subsamples that were subjected to different preservation treatments. The following six preservation methods were tested: flash-freezing in liquid nitrogen followed by storage at -80°C, immersion in RNAlater® and storage at room temperature, immersion in RNAlater® and immediate storage at -80°C, immersion in 95% ethanol and storage at room temperature, immersion in a RNAlater-like buffer “NAP buffer” and storage at room temperature, and immersion in an autoclaved RNAlater-like buffer “Autoclaved NAP buffer” and storage at room temperature. Proteins were extracted from the samples after being stored for 1 and 4 weeks. There were 4 replicates per treatment and time-point. Samples were analyzed by LC-MS/MS and the data were analyzed with Proteome Discoverer against a large database of mouse microbiota protein sequences.
2021-11-25 | PXD024115 | Pride
Project description:Due to ease of acquisition, fecal samples are often used in studies investigating gut microbiota. Improper handling of these samples can lead to bacterial growth and alter bacterial composition. While freezing samples at -80 °C is considered gold standard, this is not suitable for studies utilizing self-sampling by lay participants or field studies. Thus to effectively prevent bacterial growth, techniques that allow efficient fecal storage outside laboratory facilities are needed. Fecal samples were collected from three donors. From each donor feces, 45 samples were collected and stored either freshly frozen at -80 or -20 °C, or in three separate storage buffers at room temperature or 4 °C for 24 or 72 hours. Bacterial composition was analyzed using Illumina amplicon sequencing of the V4 region of the 16 S rRNA gene. While storage conditions did affect bacterial composition and diversity compared to storage at -80 °C, the variation between donors superseded the variations introduced by storage. Samples stored at -20 °C most closely resembled those stored at -80 °C. When investigating variations in bacterial composition between separate study populations, fecal samples can efficiently be stored in -20 °C freezers or in one of the presented storage buffers, without severe alterations in bacterial composition.
| S-EPMC6255890 | biostudies-literature
Project description:IntroductionFew studies have investigated the influence of storage conditions on urine samples and none of them used targeted mass spectrometry (MS).ObjectivesWe investigated the stability of metabolite profiles in urine samples under different storage conditions using targeted metabolomics.MethodsPooled, fasting urine samples were collected and stored at -80 °C (biobank standard), -20 °C (freezer), 4 °C (fridge), ~9 °C (cool pack), and ~20 °C (room temperature) for 0, 2, 8 and 24 h. Metabolite concentrations were quantified with MS using the AbsoluteIDQ™ p150 assay. We used the Welch-Satterthwaite-test to compare the concentrations of each metabolite. Mixed effects linear regression was used to assess the influence of the interaction of storage time and temperature.ResultsThe concentrations of 63 investigated metabolites were stable at -20 and 4 °C for up to 24 h when compared to samples immediately stored at -80 °C. When stored at ~9 °C for 24 h, few amino acids (Arg, Val and Leu/Ile) significantly decreased by 40% in concentration (P < 7.9E-04); for an additional three metabolites (Ser, Met, Hexose H1) when stored at ~20 °C reduced up to 60% in concentrations. The concentrations of four more metabolites (Glu, Phe, Pro, and Thr) were found to be significantly influenced when considering the interaction between exposure time and temperature.ConclusionOur findings indicate that 78% of quantified metabolites were stable for all examined storage conditions. Particularly, some amino acid concentrations were sensitive to changes after prolonged storage at room temperature. Shipping or storing urine samples on cool packs or at room temperature for more than 8 h and multiple numbers of freeze and thaw cycles should be avoided.
| S-EPMC5126183 | biostudies-literature
Project description:Fresh-frozen stool banks intended for humans with gastrointestinal and metabolic disorders have been recently established and there are ongoing efforts to establish the first veterinary fresh-frozen stool bank. Fresh frozen stored feces provide an advantage of increased availability and accessibility to high-quality optimal donor fecal material. The stability of frozen canine feces regarding fecal microbiome composition and diversity has not been reported in dogs, providing the basis for this study. We hypothesized that fecal microbial composition and diversity of healthy dogs would remain stable when stored at -20°C and -80°C for up to 12 months compared to baseline samples evaluated before freezing. Stool samples were collected from 20 apparently healthy dogs, manually homogenized, cryopreserved in 20% glycerol and aliquoted, frozen in liquid nitrogen and stored at -20°C or -80°C for 3, 6, 9, and 12 months. At baseline and after period of storage, aliquots were thawed and treated with propidium monoazide before fecal DNA extraction. Following long-read 16S-rRNA amplicon sequencing, bacterial community composition and diversity were compared among treatment groups. We demonstrated that fresh-frozen canine stools collected from 20 apparently healthy dogs could be stored for up to 12 months at -80°C with minimal change in microbial community composition and diversity and that storage at -80°C is superior to storage at -20°C. We also found that differences between dogs had the largest effect on community composition and diversity. Relative abundances of certain bacterial taxa, including those known to be short-chain fatty acid producers, varied significantly with specific storage temperatures and duration. Further work is required to ascertain whether fecal donor material that differs in bacterial community composition and diversity across storage conditions and duration could lead to differences in clinical efficacy for specific clinical indications of fecal microbiota transplantation.
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Project description:We examined fecal proteins from normal subjects (n=6), patients with inflammatory bowel disease (n=8), patients with colorectal adenoma (n=8), and patients with colorectal cancer (n=14) in the hope of identifying novel fecal protein markers that could be used to identify colorectal diseases.
2022-12-22 | PXD039089 |
Project description:Three storage conditions were compared in 293T cells: (1) 37C (control), (2) 4C overnight, and (3) -80C storage followed by liquid nitrogen preservation. Either cold storage induced significant alterations in cell diameter, circularity, and proteome composition. This study highlights the importance of preserving cells under viable conditions to maintain the integrity of the proteome and underscore the necessity of optimizing cell storage protocols to ensure accurate representation of the cellular proteome, particularly in the context of SCP studies. By elucidating the intricate interplay between storage conditions, cellular morphology, and protein expression, this study contributes valuable insights towards advancing SCP methodologies and enhancing our understanding of cellular heterogeneity.
2024-06-26 | MSV000095162 | MassIVE