Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic

Quantitative metaproteomics is a relatively new research field that applies proteomics techniques to study microbial proteins of the microbiome and holds great potential in truly quantifying the functional proteins actually expressed by microbes in the biological environment, such as the gastrointestinal tract. The significant association between arsenic exposure and gut microbiome perturbations has been reported; however, metaproteomics has not yet been applied to study arsenic-induced proteome changes of the microbiome. Most importantly, to our knowledge, isobaric-labeling-based large-scale metaproteomics has not been reported using the advanced database-search approaches such as MetaPro-IQ and matched metagenome database-search strategies to provide high quantification accuracy and fewer missing quantification values. In the present study, a new experimental workflow coupled to isobaric labeling and MetaPro-IQ was demonstrated for the metaproteomics study of arsenic-induced gut microbiome perturbations. The advantages of this workflow were also discussed. For all 18 fecal samples analyzed, 7611 protein groups were quantified without any missing values. The consistent results of expression profiles were observed between 16S rRNA gene sequencing and metaproteomics. This isobaric-labeling-based workflow demonstrated the significant improvement of quantitative metaproteomics for gut microbiome study.