Biology subjects

Thuy-Boun, P. S.

Publications and source records attributed to Thuy-Boun, P. S..

3 recordsLinked to original sources

bioRxiv2020

Quantitative metaproteomics of patient fecal microbiota identifies host and microbial proteins associated with ulcerative colitis

Mass spectrometry-based metaproteomics technologies enable the direct observation of proteins within complex multi-organism environments. A major hurdle in mapping metaproteomic fragmentation spectra to their corresponding peptides is the need for large peptide databases encompassing all anticipated species contained within a biological sample. As we cannot predict the taxonomic composition of microbiomes a priori, we developed the ComPIL database which contains a comprehensive collection of 4.8 billion unique peptides from public sequencing repositories to enable our proteomics analyses. We analyzed fecal samples from ulcerative colitis (UC) patients using a tandem mass spectrometry (LC-MS/MS) workflow coupled to ComPIL in search of aberrant UC-associated proteins. We found 176 host and microbial protein groups differentially enriched between the healthy (control) or UC volunteer groups. Notably, gene ontology (GO) enrichment analysis revealed that serine-type endopeptidases are overrepresented in UC compared to healthy volunteers. Additionally, we demonstrate the feasibility of serine hydrolase chemical enrichment from fecal samples using a biotinylated fluorophosphate (FP) probe. Our findings illustrate that probe-susceptible hydrolases from hosts and microbes are likely active in the distal gut. Finally, we applied de novo peptide sequencing methods to our metaproteomics data to estimate the size of the "dark peptidome," the complement of peptides unidentified using ComPIL. We posit that our metaproteomics methods are generally applicable to future microbiota analyses and that our list of FP probe-enriched hydrolases may represent an important functionality to understanding the etiology of UC.

microbiology↗

bioRxiv2020

Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a healthy human microbiome

N-acetylneuraminic acid is the most abundant sialic acid in humans and is generally expressed as the terminal sugar on intestinal mucus glycans. Several pathogenic bacterial species harvest sialic acid from the mucus, diet, as well as other intestinal sources and display this sugar on their own surface to evade sialic acid-binding immunoglobulin-type lectin (Siglec)-mediated host immune surveillance. While previous studies have identified bacterial enzymes associated with sialic acid catabolism, no reported methods permit the selective labeling, tracking, and quantitation of sialic acid-presenting microbes within complex multi-microbial systems. Here, we apply an interdisciplinary approach combining metabolic labeling, click chemistry, metagenomic, and whole-genome sequencing to selectively track and identify sialic acid-presenting microbes from a cultured healthy human fecal microbiome. We isolated and identified a new strain of Escherichia coli that incorporates sialic acid onto its own surface. Analysis of the sequence data reveals that this E. coli strain encodes for the NanT, NeuA, and NeuS genes necessary for harvesting environmental sialic acid and generating the capsular polysialic acid. We envision that this method is applicable to the detection and quantitation of sialic acid-presenting bacteria from human, animal, and environmental microbiomes, as well as investigating the importance of other carbohydrates to commensal and pathogenic bacteria.

microbiology↗

bioRxiv2018

Triflic acid treatment enables LC-MS/MS analysis of insoluble bacterial biomass

The lysis and extraction of soluble bacterial proteins from cells is a common practice for proteomics analyses, but insoluble bacterial biomasses are often left behind. Here, we show that with triflic acid treatment, the insoluble bacterial biomass of Gram- and Gram+ bacteria can be rendered soluble. We use LC-MS/MS shotgun proteomics to show that bacterial proteins in the soluble and insoluble post-lysis fractions differ significantly. Additionally, in the case of Gram- Pseudomonas aeruginosa, triflic acid treatment enables the enrichment of cell envelope-associated proteins. Finally, we apply triflic acid to a human microbiome sample to show that this treatment is robust and enables the identification of a new, complementary subset of proteins from a complex microbial mixture.

systems biology↗