The Experts below are selected from a list of 3513 Experts worldwide ranked by ideXlab platform
Daniel Figeys - One of the best experts on this subject based on the ideXlab platform.
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MetaLab 2.0 Enables Accurate Post-Translational Modifications Profiling in Metaproteomics.
Journal of the American Society for Mass Spectrometry, 2020Co-Authors: Kai Cheng, Xu Zhang, Zhibin Ning, Janice Mayne, Bo Liao, Daniel FigeysAbstract:Studying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains underexplored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed comprehensive software termed MetaLab for the data analysis of metaproteomic data sets. Here, we build an open search workflow within MetaLab for unbiased identification and quantification of unmodified peptides as well as peptides with various PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, Metaproteomics from mouse and human gut microbiomes, and modification-specific enriched data sets. Superior accuracy and sensitivity were obtained simultaneously by using our method compared with the traditional closed search strategy.
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Metaproteomics Reveals Growth Phase-Dependent Responses of an In Vitro Gut Microbiota to Metformin.
Journal of the American Society for Mass Spectrometry, 2020Co-Authors: Zikai Hao, Xu Zhang, Zhibin Ning, Janice Mayne, Kai Cheng, Krystal Walker, Hong Liu, Daniel FigeysAbstract:Metaproteomics has been used in combination with in vitro gut microbiota models to study drug-microbiome interactions. However, it remains unexplored whether the Metaproteomics profile of in vitro gut microbiota responds differently to a same stimulus added at different growth phases. In this study, we cultured a human gut microbiota in 96-deep well plates using a previously validated model. Metformin was added during the lag, log, and stationary phases. Microbiome samples, collected at different time points, were analyzed by optical density and function by metaproteomic. The in vitro gut microbiota growth curves, taxonomy, and functional responses were different depending whether metformin was added during the lag, log, or stationary phases. The addition of drugs at the log phase may lead to the greatest decline of bacterial growth. Metaproteomic analysis suggests that the strength of the metformin effect on the gut microbiome functional profile may be ranked as lag phase > log phase > stationary phase. Metformin added at the lag phase may result in a significantly reduced level of the Clostridiales order and an increased level of the Bacteroides genus, which is different from stimulations during the rest of the growth phases. Metformin may also result in alterations of several pathways, including energy production and conversion, lipid transport and metabolism, translation, ribosomal structure, and biogenesis. Our results indicate that the timing for drug stimulation should be considered when studying drug-microbiome interactions in vitro.
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Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics
Analytical chemistry, 2020Co-Authors: Jiaqin Wang, Xu Zhang, Zhibin Ning, Janice Mayne, Kai Cheng, Cian Schmitt-ulms, Krystal Walker, Daniel FigeysAbstract:Changes in microbiome composition and function have been linked to human health and diseases. Metaproteomics provides invaluable functional information on the state of a microbiome. However, lower-abundance bacteria in complex microbiomes are difficult to observe by Metaproteomics. In this study, stepwise differential lysis protocols were developed for human stool microbiomes to separate different microbial species and to increase the depth of metaproteomic measurements. We achieved differential lysis of Gram-positive (G+) and Gram-negative (G-) bacteria, selective enrichment of specific bacteria, and functional enrichment by our stepwise differential lysis protocols. Therefore, differential lysis can serve as a fractionation method to reduce sample complexity and selectively extract proteins from specific taxa for deep metaproteomic studies.
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metalab 2 0 enables accurate post translational modifications profiling in Metaproteomics
bioRxiv, 2020Co-Authors: Kai Cheng, Xu Zhang, Daniel Figeys, Zhibin Ning, Janice Mayne, Bo LiaoAbstract:Abstract Studying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains under-explored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed a comprehensive software termed MetaLab for the data analysis of metaproteomic datasets. Here we build an open search workflow within MetaLab for unbiased identification and quantification of PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, Metaproteomics from mouse and human gut microbiomes, and modification-specific enriched datasets. Superior accuracy and sensitivity were obtained simultaneously by using our method comparing with the traditional closed search strategy.
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Perspective and Guidelines for Metaproteomics in Microbiome Studies.
Journal of proteome research, 2019Co-Authors: Xu Zhang, Daniel FigeysAbstract:The microbiome is emerging as a prominent factor affecting human health, and its dysbiosis is associated with various diseases. Compositional profiling of microbiome is increasingly being supplemented with functional characterization. Metaproteomics is intrinsically focused on functional changes and therefore will be an important tool in those studies of the human microbiome. In the past decade, development of new experimental and bioinformatic approaches for Metaproteomics has enabled large-scale human metaproteomic studies. However, challenges still exist, and there remains a lack of standardizations and guidelines for properly performing metaproteomic studies on human microbiome. Herein, we provide a perspective of recent developments, the challenges faced, and the future directions of Metaproteomics and its applications. In addition, we propose a set of guidelines/recommendations for performing and reporting the results from metaproteomic experiments for the study of human microbiomes. We anticipate that these guidelines will be optimized further as more metaproteomic questions are raised and addressed, and metaproteomic applications are published, so that they are eventually recognized and applied in the field.
Xu Zhang - One of the best experts on this subject based on the ideXlab platform.
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MetaLab 2.0 Enables Accurate Post-Translational Modifications Profiling in Metaproteomics.
Journal of the American Society for Mass Spectrometry, 2020Co-Authors: Kai Cheng, Xu Zhang, Zhibin Ning, Janice Mayne, Bo Liao, Daniel FigeysAbstract:Studying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains underexplored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed comprehensive software termed MetaLab for the data analysis of metaproteomic data sets. Here, we build an open search workflow within MetaLab for unbiased identification and quantification of unmodified peptides as well as peptides with various PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, Metaproteomics from mouse and human gut microbiomes, and modification-specific enriched data sets. Superior accuracy and sensitivity were obtained simultaneously by using our method compared with the traditional closed search strategy.
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Metaproteomics Reveals Growth Phase-Dependent Responses of an In Vitro Gut Microbiota to Metformin.
Journal of the American Society for Mass Spectrometry, 2020Co-Authors: Zikai Hao, Xu Zhang, Zhibin Ning, Janice Mayne, Kai Cheng, Krystal Walker, Hong Liu, Daniel FigeysAbstract:Metaproteomics has been used in combination with in vitro gut microbiota models to study drug-microbiome interactions. However, it remains unexplored whether the Metaproteomics profile of in vitro gut microbiota responds differently to a same stimulus added at different growth phases. In this study, we cultured a human gut microbiota in 96-deep well plates using a previously validated model. Metformin was added during the lag, log, and stationary phases. Microbiome samples, collected at different time points, were analyzed by optical density and function by metaproteomic. The in vitro gut microbiota growth curves, taxonomy, and functional responses were different depending whether metformin was added during the lag, log, or stationary phases. The addition of drugs at the log phase may lead to the greatest decline of bacterial growth. Metaproteomic analysis suggests that the strength of the metformin effect on the gut microbiome functional profile may be ranked as lag phase > log phase > stationary phase. Metformin added at the lag phase may result in a significantly reduced level of the Clostridiales order and an increased level of the Bacteroides genus, which is different from stimulations during the rest of the growth phases. Metformin may also result in alterations of several pathways, including energy production and conversion, lipid transport and metabolism, translation, ribosomal structure, and biogenesis. Our results indicate that the timing for drug stimulation should be considered when studying drug-microbiome interactions in vitro.
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Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics
Analytical chemistry, 2020Co-Authors: Jiaqin Wang, Xu Zhang, Zhibin Ning, Janice Mayne, Kai Cheng, Cian Schmitt-ulms, Krystal Walker, Daniel FigeysAbstract:Changes in microbiome composition and function have been linked to human health and diseases. Metaproteomics provides invaluable functional information on the state of a microbiome. However, lower-abundance bacteria in complex microbiomes are difficult to observe by Metaproteomics. In this study, stepwise differential lysis protocols were developed for human stool microbiomes to separate different microbial species and to increase the depth of metaproteomic measurements. We achieved differential lysis of Gram-positive (G+) and Gram-negative (G-) bacteria, selective enrichment of specific bacteria, and functional enrichment by our stepwise differential lysis protocols. Therefore, differential lysis can serve as a fractionation method to reduce sample complexity and selectively extract proteins from specific taxa for deep metaproteomic studies.
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metalab 2 0 enables accurate post translational modifications profiling in Metaproteomics
bioRxiv, 2020Co-Authors: Kai Cheng, Xu Zhang, Daniel Figeys, Zhibin Ning, Janice Mayne, Bo LiaoAbstract:Abstract Studying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains under-explored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed a comprehensive software termed MetaLab for the data analysis of metaproteomic datasets. Here we build an open search workflow within MetaLab for unbiased identification and quantification of PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, Metaproteomics from mouse and human gut microbiomes, and modification-specific enriched datasets. Superior accuracy and sensitivity were obtained simultaneously by using our method comparing with the traditional closed search strategy.
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Perspective and Guidelines for Metaproteomics in Microbiome Studies.
Journal of proteome research, 2019Co-Authors: Xu Zhang, Daniel FigeysAbstract:The microbiome is emerging as a prominent factor affecting human health, and its dysbiosis is associated with various diseases. Compositional profiling of microbiome is increasingly being supplemented with functional characterization. Metaproteomics is intrinsically focused on functional changes and therefore will be an important tool in those studies of the human microbiome. In the past decade, development of new experimental and bioinformatic approaches for Metaproteomics has enabled large-scale human metaproteomic studies. However, challenges still exist, and there remains a lack of standardizations and guidelines for properly performing metaproteomic studies on human microbiome. Herein, we provide a perspective of recent developments, the challenges faced, and the future directions of Metaproteomics and its applications. In addition, we propose a set of guidelines/recommendations for performing and reporting the results from metaproteomic experiments for the study of human microbiomes. We anticipate that these guidelines will be optimized further as more metaproteomic questions are raised and addressed, and metaproteomic applications are published, so that they are eventually recognized and applied in the field.
Zhibin Ning - One of the best experts on this subject based on the ideXlab platform.
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MetaLab 2.0 Enables Accurate Post-Translational Modifications Profiling in Metaproteomics.
Journal of the American Society for Mass Spectrometry, 2020Co-Authors: Kai Cheng, Xu Zhang, Zhibin Ning, Janice Mayne, Bo Liao, Daniel FigeysAbstract:Studying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains underexplored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed comprehensive software termed MetaLab for the data analysis of metaproteomic data sets. Here, we build an open search workflow within MetaLab for unbiased identification and quantification of unmodified peptides as well as peptides with various PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, Metaproteomics from mouse and human gut microbiomes, and modification-specific enriched data sets. Superior accuracy and sensitivity were obtained simultaneously by using our method compared with the traditional closed search strategy.
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Metaproteomics Reveals Growth Phase-Dependent Responses of an In Vitro Gut Microbiota to Metformin.
Journal of the American Society for Mass Spectrometry, 2020Co-Authors: Zikai Hao, Xu Zhang, Zhibin Ning, Janice Mayne, Kai Cheng, Krystal Walker, Hong Liu, Daniel FigeysAbstract:Metaproteomics has been used in combination with in vitro gut microbiota models to study drug-microbiome interactions. However, it remains unexplored whether the Metaproteomics profile of in vitro gut microbiota responds differently to a same stimulus added at different growth phases. In this study, we cultured a human gut microbiota in 96-deep well plates using a previously validated model. Metformin was added during the lag, log, and stationary phases. Microbiome samples, collected at different time points, were analyzed by optical density and function by metaproteomic. The in vitro gut microbiota growth curves, taxonomy, and functional responses were different depending whether metformin was added during the lag, log, or stationary phases. The addition of drugs at the log phase may lead to the greatest decline of bacterial growth. Metaproteomic analysis suggests that the strength of the metformin effect on the gut microbiome functional profile may be ranked as lag phase > log phase > stationary phase. Metformin added at the lag phase may result in a significantly reduced level of the Clostridiales order and an increased level of the Bacteroides genus, which is different from stimulations during the rest of the growth phases. Metformin may also result in alterations of several pathways, including energy production and conversion, lipid transport and metabolism, translation, ribosomal structure, and biogenesis. Our results indicate that the timing for drug stimulation should be considered when studying drug-microbiome interactions in vitro.
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Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics
Analytical chemistry, 2020Co-Authors: Jiaqin Wang, Xu Zhang, Zhibin Ning, Janice Mayne, Kai Cheng, Cian Schmitt-ulms, Krystal Walker, Daniel FigeysAbstract:Changes in microbiome composition and function have been linked to human health and diseases. Metaproteomics provides invaluable functional information on the state of a microbiome. However, lower-abundance bacteria in complex microbiomes are difficult to observe by Metaproteomics. In this study, stepwise differential lysis protocols were developed for human stool microbiomes to separate different microbial species and to increase the depth of metaproteomic measurements. We achieved differential lysis of Gram-positive (G+) and Gram-negative (G-) bacteria, selective enrichment of specific bacteria, and functional enrichment by our stepwise differential lysis protocols. Therefore, differential lysis can serve as a fractionation method to reduce sample complexity and selectively extract proteins from specific taxa for deep metaproteomic studies.
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metalab 2 0 enables accurate post translational modifications profiling in Metaproteomics
bioRxiv, 2020Co-Authors: Kai Cheng, Xu Zhang, Daniel Figeys, Zhibin Ning, Janice Mayne, Bo LiaoAbstract:Abstract Studying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains under-explored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed a comprehensive software termed MetaLab for the data analysis of metaproteomic datasets. Here we build an open search workflow within MetaLab for unbiased identification and quantification of PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, Metaproteomics from mouse and human gut microbiomes, and modification-specific enriched datasets. Superior accuracy and sensitivity were obtained simultaneously by using our method comparing with the traditional closed search strategy.
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iMetaLab 1.0: a web platform for Metaproteomics data analysis
Bioinformatics (Oxford England), 2018Co-Authors: Bo Liao, Xu Zhang, Zhibin Ning, Janice Mayne, Kai Cheng, Daniel FigeysAbstract:Summary The human gut microbiota, a complex, dynamic and biodiverse community, has been increasingly shown to influence many aspects of health and disease. Metaproteomic analysis has proven to be a powerful approach to study the functionality of the microbiota. However, the processing and analyses of metaproteomic mass spectrometry data remains a daunting task in Metaproteomics data analysis. We developed iMetaLab, a web based platform to provide a user-friendly and comprehensive data analysis pipeline with a focus on lowering the technical barrier for Metaproteomics data analysis. Availability and implementation iMetaLab is freely available through at http://imetalab.ca. Supplementary information Supplementary data are available at Bioinformatics online.
Janice Mayne - One of the best experts on this subject based on the ideXlab platform.
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MetaLab 2.0 Enables Accurate Post-Translational Modifications Profiling in Metaproteomics.
Journal of the American Society for Mass Spectrometry, 2020Co-Authors: Kai Cheng, Xu Zhang, Zhibin Ning, Janice Mayne, Bo Liao, Daniel FigeysAbstract:Studying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains underexplored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed comprehensive software termed MetaLab for the data analysis of metaproteomic data sets. Here, we build an open search workflow within MetaLab for unbiased identification and quantification of unmodified peptides as well as peptides with various PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, Metaproteomics from mouse and human gut microbiomes, and modification-specific enriched data sets. Superior accuracy and sensitivity were obtained simultaneously by using our method compared with the traditional closed search strategy.
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Metaproteomics Reveals Growth Phase-Dependent Responses of an In Vitro Gut Microbiota to Metformin.
Journal of the American Society for Mass Spectrometry, 2020Co-Authors: Zikai Hao, Xu Zhang, Zhibin Ning, Janice Mayne, Kai Cheng, Krystal Walker, Hong Liu, Daniel FigeysAbstract:Metaproteomics has been used in combination with in vitro gut microbiota models to study drug-microbiome interactions. However, it remains unexplored whether the Metaproteomics profile of in vitro gut microbiota responds differently to a same stimulus added at different growth phases. In this study, we cultured a human gut microbiota in 96-deep well plates using a previously validated model. Metformin was added during the lag, log, and stationary phases. Microbiome samples, collected at different time points, were analyzed by optical density and function by metaproteomic. The in vitro gut microbiota growth curves, taxonomy, and functional responses were different depending whether metformin was added during the lag, log, or stationary phases. The addition of drugs at the log phase may lead to the greatest decline of bacterial growth. Metaproteomic analysis suggests that the strength of the metformin effect on the gut microbiome functional profile may be ranked as lag phase > log phase > stationary phase. Metformin added at the lag phase may result in a significantly reduced level of the Clostridiales order and an increased level of the Bacteroides genus, which is different from stimulations during the rest of the growth phases. Metformin may also result in alterations of several pathways, including energy production and conversion, lipid transport and metabolism, translation, ribosomal structure, and biogenesis. Our results indicate that the timing for drug stimulation should be considered when studying drug-microbiome interactions in vitro.
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Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics
Analytical chemistry, 2020Co-Authors: Jiaqin Wang, Xu Zhang, Zhibin Ning, Janice Mayne, Kai Cheng, Cian Schmitt-ulms, Krystal Walker, Daniel FigeysAbstract:Changes in microbiome composition and function have been linked to human health and diseases. Metaproteomics provides invaluable functional information on the state of a microbiome. However, lower-abundance bacteria in complex microbiomes are difficult to observe by Metaproteomics. In this study, stepwise differential lysis protocols were developed for human stool microbiomes to separate different microbial species and to increase the depth of metaproteomic measurements. We achieved differential lysis of Gram-positive (G+) and Gram-negative (G-) bacteria, selective enrichment of specific bacteria, and functional enrichment by our stepwise differential lysis protocols. Therefore, differential lysis can serve as a fractionation method to reduce sample complexity and selectively extract proteins from specific taxa for deep metaproteomic studies.
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metalab 2 0 enables accurate post translational modifications profiling in Metaproteomics
bioRxiv, 2020Co-Authors: Kai Cheng, Xu Zhang, Daniel Figeys, Zhibin Ning, Janice Mayne, Bo LiaoAbstract:Abstract Studying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains under-explored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed a comprehensive software termed MetaLab for the data analysis of metaproteomic datasets. Here we build an open search workflow within MetaLab for unbiased identification and quantification of PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, Metaproteomics from mouse and human gut microbiomes, and modification-specific enriched datasets. Superior accuracy and sensitivity were obtained simultaneously by using our method comparing with the traditional closed search strategy.
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iMetaLab 1.0: a web platform for Metaproteomics data analysis
Bioinformatics (Oxford England), 2018Co-Authors: Bo Liao, Xu Zhang, Zhibin Ning, Janice Mayne, Kai Cheng, Daniel FigeysAbstract:Summary The human gut microbiota, a complex, dynamic and biodiverse community, has been increasingly shown to influence many aspects of health and disease. Metaproteomic analysis has proven to be a powerful approach to study the functionality of the microbiota. However, the processing and analyses of metaproteomic mass spectrometry data remains a daunting task in Metaproteomics data analysis. We developed iMetaLab, a web based platform to provide a user-friendly and comprehensive data analysis pipeline with a focus on lowering the technical barrier for Metaproteomics data analysis. Availability and implementation iMetaLab is freely available through at http://imetalab.ca. Supplementary information Supplementary data are available at Bioinformatics online.
Katharina Riedel - One of the best experts on this subject based on the ideXlab platform.
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A complete and flexible workflow for Metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane
Nature Protocols, 2020Co-Authors: Henning Schiebenhoefer, Dirk Benndorf, Kay Schallert, Thilo Muth, Katharina Riedel, Bernhard Y. Renard, Kathrin Trappe, Emanuel Schmid, Stephan FuchsAbstract:Metaproteomics, the study of the collective protein composition of multi-organism systems, provides deep insights into the biodiversity of microbial communities and the complex functional interplay between microbes and their hosts or environment. Thus, Metaproteomics has become an indispensable tool in various fields such as microbiology and related medical applications. The computational challenges in the analysis of corresponding datasets differ from those of pure-culture proteomics, e.g., due to the higher complexity of the samples and the larger reference databases demanding specific computing pipelines. Corresponding data analyses usually consist of numerous manual steps that must be closely synchronized. With MetaProteomeAnalyzer and Prophane, we have established two open-source software solutions specifically developed and optimized for Metaproteomics. Among other features, peptide-spectrum matching is improved by combining different search engines and, compared to similar tools, metaproteome annotation benefits from the most comprehensive set of available databases (such as NCBI, UniProt, EggNOG, PFAM, and CAZy). The workflow described in this protocol combines both tools and leads the user through the entire data analysis process, including protein database creation, database search, protein grouping and annotation, and results visualization. To the best of our knowledge, this protocol presents the most comprehensive, detailed and flexible guide to Metaproteomics data analysis to date. While beginners are provided with robust, easy-to-use, state-of-the-art data analysis in a reasonable time (a few hours, depending on, among other factors, the protein database size and the number of identified peptides and inferred proteins), advanced users benefit from the flexibility and adaptability of the workflow. This protocol provides a detailed guide to Metaproteomics data analysis and visualization. The modular and customizable workflow is based on two open-source tools (MetaProteomeAnalyzer and Prophane) and is illustrated with example datasets.
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microbial functionality as affected by experimental warming of a temperate mountain forest soil a Metaproteomics survey
Applied Soil Ecology, 2017Co-Authors: Stephan Fuchs, Dong Liu, Katharina M Keiblinger, Andreas Schindlbacher, Uwe Wegner, Hanyin Sun, Christian Lassek, Katharina Riedel, Sophie ZechmeisterboltensternAbstract:Abstract Soil microbes play an important role in terrestrial carbon (C) cycling, but their functional response to global warming remains yet unclear. Soil Metaproteomics has the potential to contribute to a better understanding of warming effects on soil microbes as proteins specifically represent active microbes and their physiological functioning. To quantify warming effects on microbial proteins and their distribution among different functional and phylogenetic groups, we sampled forest soil that had been artificially warmed (+4 °C) during seven consecutive growing seasons and analyzed its metaproteomic fingerprint and linked to soil respiration as a fundamental ecosystem service. Bacterial protein abundances largely exceeded fungal abundances at the study site but protein abundances showed only subtle differences among control and warmed soil at the phylum and class level, i.e. a temperature-induced decrease in Firmicutes , an increase in Agaricomycetes and Actinobacteria , and a decrease in the Asco/Basidiomycota ratio. Community function in warmed soil showed a clear trend towards increased proteins involved in microbial energy production and conversion, related to the increased CO 2 efflux from warmed soil as a result of stress environmental conditions. The differences in community function could be related to specific phyla using Metaproteomics, indicating that microbial adaptation to long-term soil warming mainly changed microbial functions, which is related to enhanced soil respiration. The response of soil respiration to warming (+35% soil CO 2 efflux during sampling) has not changed over time. Accordingly, potential long-term microbial adaptations to soil warming were too subtle to affect soil respiration rates or, were overlaid by other co-varying factors (e.g. substrate availability).
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Soil and leaf litter Metaproteomics-a brief guideline from sampling to understanding.
FEMS microbiology ecology, 2016Co-Authors: Katharina M Keiblinger, Stephan Fuchs, Sophie Zechmeister-boltenstern, Katharina RiedelAbstract:The increasing application of soil Metaproteomics is providing unprecedented, in-depth characterization of the composition and functionality of in situ microbial communities. Despite recent advances in high-resolution mass spectrometry, soil Metaproteomics still suffers from a lack of effective and reproducible protein extraction protocols and standardized data analyses. This review discusses the opportunities and limitations of selected techniques in soil-, and leaf litter Metaproteomics, and presents a step-by-step guideline on their application, covering sampling, sample preparation, extraction and data evaluation strategies. In addition, we present recent applications of soil Metaproteomics and discuss how such approaches, linking phylogenetics and functionality, can help gain deeper insights into terrestrial microbial ecology. Finally, we strongly recommend that to maximize the insights environmental Metaproteomics may provide, such methods should be employed within a holistic experimental approach considering relevant aboveground and belowground ecosystem parameters.
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Metaproteomics to unravel major microbial players in leaf litter and soil environments: Challenges and perspectives
Proteomics, 2013Co-Authors: Dörte Becher, Stephan Fuchs, Jörg Bernhardt, Katharina RiedelAbstract:Soil- and litter-borne microorganisms vitally contribute to biogeochemical cycles. However, changes in environmental parameters but also human interferences may alter species composition and elicit alterations in microbial activities. Soil and litter Metaproteomics, implying the assignment of soil and litter proteins to specific phylogenetic and functional groups, has a great potential to provide essential new insights into the impact of microbial diversity on soil ecosystem functioning. This article will illuminate challenges and perspectives of current soil and litter Metaproteomics research, starting with an introduction to an appropriate experimental design and state-of-the-art proteomics methodologies. This will be followed by a summary of important studies aimed at (i) the discovery of the major biotic drivers of leaf litter decomposition, (ii) Metaproteomics analyses of rhizosphere-inhabiting microbes, and (iii) global approaches to study bioremediation processes. The review will be closed by a brief outlook on future developments and some concluding remarks, which should assist the reader to develop successful concepts for soil and litter Metaproteomics studies.