Dataset Information

Proteomics for Newport Estuary Samples

ABSTRACT: Microorganisms are key contributors to biogeochemical flux in estuarine ecosystems. In this study, we conducted proteogenomic characterization of microbial communities from estuarine ecosystems.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Escherichia Coli

SUBMITTER: Zhou Li

LAB HEAD: Chongle Pan

PROVIDER: PXD008093 | Pride | 2018-07-04

REPOSITORIES: Pride

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Publications

Microbial Community Structure-Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities.

Kieft Brandon B Li Zhou Z Bryson Samuel S Crump Byron C BC Hettich Robert R Pan Chongle C Mayali Xavier X Mueller Ryan S RS

Frontiers in microbiology 20180614

Linking microbial community structure to ecological processes requires understanding of the functional roles among individual populations and the factors that influence their distributions. These structure-function relationships are particularly difficult to disentangle in estuaries, due to highly variable physico-chemical conditions. Yet, examining microbe-mediated turnover of resources in these "bioreactor" ecosystems is critical for understanding estuarine ecology. In this study, a combined m ...[more]

PMID: 29963029

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Project description:The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, in modulating immunity and in regulating metabolic processes. We use the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species to study potential synergistic effects with a particular focus on detecting novel proteins with less than 100 amino acids (= sProteins), some of which may contribute to regulate the simplified human intestinal microbiota. Although several studies have shown that sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. In this study, we created a multi-species integrated proteogenomics search database (multi-species iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were first sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied prior to mass spectrometric analysis to specifically increase the chances for novel sProtein discovery. Searching the MS/MS data against the multi-species iPtgxDB enabled us to identify 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. Importantly, when comparing the expression of these novel sProteins in single strain cultivations to the multi-species community grown in a bioreactor, we found that six of them were only identified in the SIHUMIx community, indicating a possible important role of sProteins in the organization of microbial communities. Furthermore, in silico prediction suggested that two of these novel sProteins have a potential antimicrobial function. We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in microbial communities that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the multi-species community is expected to enable new insights into the structure, regulation and function of bacterial communities such as those of the human intestinal tract.

Dataset Information

Proteomics for Newport Estuary Samples

Publications

Microbial Community Structure-Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities.

Similar Datasets

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