Proteomics

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Free-Flow Isoelectric Focusing Based Metaproteomics Workflow Facilitates the Identification and Characterization of Human Salivary Microbiome for Lung Cancer


ABSTRACT: We developed a free-flow isoelectric focusing (FFIEF) based metaproteomics workflow to reduce the host interferences and enrich the low-abundant bacteria for better interpretation of salivary microbiome. We firstly tested the pretreatment module that could significantly reduce the host interferences by differential centrifugation and filtration. Then the FFIEF module was applied to separate the microbes and enrich the low-abundant bacteria, which showed a significant improvement in the identification efficiency of microbiome sample. Applying our method to lung cancer, we successfully identified Fusobacterium, Neisseriaceae, Actinomycetaceae, Burkholderiales, and Spirochaetia were associated with lung cancer as previous sequencing studies did, along with other 16 significantly different species. The dysregulated functions in lung cancer microbiome were also explained in details. Our workflow provides improved efficiency in identification and characterization of the salivary microbiome with great reproducibility. The ability of enriching low-abundant bacteria and functions enables in-deep analysis of previously underestimated information.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Human Saliva Metagenome

TISSUE(S): Saliva

DISEASE(S): Lung Cancer

SUBMITTER: xiaoteng Jiang  

LAB HEAD: Hua Xiao

PROVIDER: PXD026727 | Pride | 2022-11-17

REPOSITORIES: Pride

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Publications

In-Depth Metaproteomics Analysis of Oral Microbiome for Lung Cancer.

Jiang Xiaoteng X   Zhang Yan Y   Wang Huiyu H   Wang Zeyuan Z   Hu Shen S   Cao Chengxi C   Xiao Hua H  

Research (Washington, D.C.) 20221013


The human oral microbiome correlates with numerous diseases, including lung cancer. Identifying the functional changes by metaproteomics helps understand the disease-related dysbiosis, yet characterizing low-abundant bacteria is challenging. Here, we developed a free-flow isoelectric focusing electrophoresis-mass spectrometry- (FFIEF-MS-) based metaproteomics strategy to reduce host interferences and enrich low-abundant bacteria for in-depth interpretation of the oral microbiome. With our method  ...[more]

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