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Microbiota biobanking using ice recrystalization inhibitor

ABSTRACT: This study use different ice recrystalization inhibitors (IRIs) for better storing live microbiota. We evaluated whether the addition of IRIs can improve the cultivibility of microbiome and maintain their resposnes to prebiotic kestose. Frozen or fresh microbiota were cultured with or without kestose for 24 hours, and microbiota samples were collected for metaproteomics analysis.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Human Feces Metagenome

SUBMITTER: Xu Zhang

LAB HEAD: Xu Zhang

PROVIDER: PXD034979 | Pride | 2023-02-07

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	IRI_sample_specific_db.fasta	Fasta
	Microbiome_IRIstudy.zip	Other
	Xu_20210512_IRIstudy_Concentration_TMT_Plate1_A.raw	Raw
	Xu_20210512_IRIstudy_Concentration_TMT_Plate1_B.raw	Raw
	Xu_20210512_IRIstudy_Concentration_TMT_Plate1_C.raw	Raw

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Publications

An economic and robust TMT labeling approach for high throughput proteomic and metaproteomic analysis.

Creskey Marybeth M Li Leyuan L Ning Zhibin Z Fekete Emily Ef EE Mayne Janice J Walker Krystal K Ampaw Anna A Ben Robert R Zhang Xu X Figeys Daniel D

Proteomics 20230113 21-22

Multiplexed quantitative proteomics using tandem mass tag (TMT) is increasingly used in -omic study of complex samples. While TMT-based proteomics has the advantages of the higher quantitative accuracy, fewer missing values, and reduced instrument analysis time, it is limited by the additional reagent cost. In addition, current TMT labeling workflows involve repeated small volume pipetting of reagents in volatile solvents, which may increase the sample-to-sample variations and is not readily sui ...[more]

PMID: 36528842

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In-vitro human gut microbiota culture with added sugars

Project description:Three human gut microbiome samples from different individuals were cultured in an optimized culture medium with or without the presence of different sugars (10 mM glucose, 20 mM fructose, 10 mM glucose + 20 mM fructose, or 10 mM kestose). Samples were cultured in technical triplicates, and were taken at 0 hr, 1hr, 5 hr, 12 hr and 24 hr of culturing for optical density and metaproteomic analyses. Cultured microbiota cells were subjected to metaproteomics analysis using LC-MS/MS and a TMT approach.

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Effects of 5 drugs on the human gut microbiome.

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Functional effects of sweeteners on ex vivo human gut microbiome

Project description:We systematically investigated the responses of five human gut microbiomes to 21 common sweeteners, using an approach combining high-throughput ex vivo microbiome culturing and metaproteomics to quantify functional changes in different taxa. Hierarchical clustering based on metaproteomic responses of individual microbiomes resulted in two clusters. The first cluster was composed of non-caloric artificial sweeteners (NAS) and two sugar alcohols with shorter carbon backbones (4-5 carbon atoms), and the second cluster was composed of sugar alcohols with longer carbon backbones. The metaproteomic functional responses of the second cluster were similar to the prebiotic fructooligosaccharides and kestose, indicating that these sugar alcohol-type sweeteners have potential prebiotic functions.

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Evaluation of different protein extraction protocols to study human gut microbiota.

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