51
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Muth T, Kohrs F, Heyer R, Benndorf D, Rapp E, Reichl U, Martens L, Renard BY. MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go. Anal Chem 2017; 90:685-689. [PMID: 29215871 PMCID: PMC5757220 DOI: 10.1021/acs.analchem.7b03544] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Metaproteomics,
the mass spectrometry-based analysis of proteins
from multispecies samples faces severe challenges concerning data
analysis and results interpretation. To overcome these shortcomings,
we here introduce the MetaProteomeAnalyzer (MPA) Portable software.
In contrast to the original server-based MPA application, this newly
developed tool no longer requires computational expertise for installation
and is now independent of any relational database system. In addition,
MPA Portable now supports state-of-the-art database search engines
and a convenient command line interface for high-performance data
processing tasks. While search engine results can easily be combined
to increase the protein identification yield, an additional two-step
workflow is implemented to provide sufficient analysis resolution
for further postprocessing steps, such as protein grouping as well
as taxonomic and functional annotation. Our new application has been
developed with a focus on intuitive usability, adherence to data standards,
and adaptation to Web-based workflow platforms. The open source software
package can be found at https://github.com/compomics/meta-proteome-analyzer.
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Affiliation(s)
- Thilo Muth
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute , 13353 Berlin, Germany
| | - Fabian Kohrs
- Bioprocess Engineering, Otto von Guericke University Magdeburg , 39106 Magdeburg, Germany
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University Magdeburg , 39106 Magdeburg, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University Magdeburg , 39106 Magdeburg, Germany.,Max Planck Institute for Dynamics of Complex Technical Systems , Bioprocess Engineering, 39106 Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems , Bioprocess Engineering, 39106 Magdeburg, Germany
| | - Udo Reichl
- Bioprocess Engineering, Otto von Guericke University Magdeburg , 39106 Magdeburg, Germany.,Max Planck Institute for Dynamics of Complex Technical Systems , Bioprocess Engineering, 39106 Magdeburg, Germany
| | - Lennart Martens
- Department of Biochemistry, Ghent University , 9000 Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB , 9000 Ghent, Belgium
| | - Bernhard Y Renard
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute , 13353 Berlin, Germany
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Multi-Omic Biogeography of the Gastrointestinal Microbiota of a Pre-Weaned Lamb. Proteomes 2017; 5:proteomes5040036. [PMID: 29258228 PMCID: PMC5748571 DOI: 10.3390/proteomes5040036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 01/23/2023] Open
Abstract
The digestive functions of the pre-weaned lamb gastrointestinal tracts (GITs) have been the subject of much research in recent years, but the microbial and host functions underlying these complex processes remain largely unknown. Here, we undertook a proof-of-principle metaproteogenomic investigation on luminal and mucosal samples collected from 10 GITs of a 30-day-old pre-weaned lamb. We demonstrate that the analysis of the diverse ecological niches along the GITs can reveal microbiota composition and metabolic functions, although low amounts of microbial proteins could be identified in the small intestinal and mucosal samples. Our data suggest that a 30-day lamb has already developed mature microbial functions in the forestomachs, while the effect of the milky diet appears to be more evident in the remaining GITs. We also report the distribution and the relative abundance of the host functions, active at the GIT level, with a special focus on those involved in digestive processes. In conclusion, this pilot study supports the suitability of a metaproteogenomic approach to the characterization of microbial and host functions of the lamb GITs, opening the way to further studies aimed at investigating the impact of early dietary interventions on the GIT microbiota of small ruminants.
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53
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Proteomics and the human microbiome: where we are today and where we would like to be. Emerg Top Life Sci 2017; 1:401-409. [DOI: 10.1042/etls20170051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 11/17/2022]
Abstract
What are all these hundreds of different bacterial species doing in and on us? What interactions occur between the host and the microbes, and between the microbes themselves? By studying proteins, metaproteomics tries to find preliminary answers to these questions. There is daunting complexity around this; in fact, many of these proteins have never been studied before. This article is an introduction to the field of metaproteomics in the context of the human microbiome. It summarizes where we are and what we have learnt so far. The focus will be on faecal proteomics as most metaproteomics research has been conducted on that sample type. Metaproteomics has made major advances in the past decade, but new sample preparation strategies, improved mass spectrometric analysis and, most importantly, data analysis and interpretation have the potential to pave the way for large-cohort metaproteomics.
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54
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Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M, Figeys D. Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions. Anal Chem 2017; 90:86-109. [DOI: 10.1021/acs.analchem.7b04340] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amanda E. Starr
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shelley A. Deeke
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rachid Daoud
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - James Ryan
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kai Cheng
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Linh V. H. Nguyen
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Elias Abou-Samra
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1M1, Canada
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55
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Pinto E, Anselmo M, Calha M, Bottrill A, Duarte I, Andrew PW, Faleiro ML. The intestinal proteome of diabetic and control children is enriched with different microbial and host proteins. MICROBIOLOGY-SGM 2017; 163:161-174. [PMID: 28270263 DOI: 10.1099/mic.0.000412] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this study, the intestinal microbial proteome of children with established type 1 diabetes (T1D) was compared with the proteome of healthy children (Control) with the aim to identify differences in the activity of the intestinal microbiota that not only will contribute to a deeper knowledge of the functionality of the gut in these children but also may provide new approaches to improve the control of the disease. Faecal protein extracts collected from three T1D children (aged 9.3±0.6 years) and three Control children (aged 9.3±1.5 years) were analysed using a combination of 2D gel electrophoresis and spectral counting. The results evidenced markedly differences between the intestinal proteome of T1D children and the Control. The T1D microbial intestinal proteome was enriched with proteins of clostridial cluster XVa and cluster IV and Bacteroides. In contrast, the Control proteome was enriched with bifidobacterial proteins. In both groups, proteins with moonlight function were observed. Human proteins also distinguished the two groups with T1D children depleted in exocrine pancreatic enzymes.
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Affiliation(s)
- Elsa Pinto
- Faculdade de Ciências e Tecnologia, Centro de Investigação em Biomedicina, Universidade do Algarve Campus de Gambelas, 8005-139 Faro, Portugal
| | - Marisol Anselmo
- Núcleo de Diabetologia, Nutrição e Doenças Metabólicas (NDNDM) do Hospital de Faro, 8000-386 Faro, Portugal
| | - Manuela Calha
- Núcleo de Diabetologia, Nutrição e Doenças Metabólicas (NDNDM) do Hospital de Faro, 8000-386 Faro, Portugal
| | - Andrew Bottrill
- Protein and Nucleic Acid Chemistry Laboratory (PNACL), University of Leicester, Leicester LE1 7RH, UK
| | - Isabel Duarte
- Faculdade de Ciências e Tecnologia, Centro de Investigação em Biomedicina, Universidade do Algarve Campus de Gambelas, 8005-139 Faro, Portugal
| | - Peter W Andrew
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 7RH, UK
| | - Maria L Faleiro
- Faculdade de Ciências e Tecnologia, Centro de Investigação em Biomedicina, Universidade do Algarve Campus de Gambelas, 8005-139 Faro, Portugal
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Deusch S, Camarinha-Silva A, Conrad J, Beifuss U, Rodehutscord M, Seifert J. A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments. Front Microbiol 2017; 8:1605. [PMID: 28883813 PMCID: PMC5573736 DOI: 10.3389/fmicb.2017.01605] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/07/2017] [Indexed: 12/11/2022] Open
Abstract
The structure and function of the microbiome inhabiting the rumen are, amongst other factors, mainly shaped by the animal's feed intake. Describing the influence of different diets on the inherent community arrangement and associated metabolic activities of the most active ruminal fractions (bacteria and archaea) is of great interest for animal nutrition, biotechnology, and climatology. Samples were obtained from three fistulated Jersey cows rotationally fed with corn silage, grass silage or grass hay, each supplemented with a concentrate mixture. Samples were fractionated into ruminal fluid, particle-associated rumen liquid, and solid matter. DNA, proteins and metabolites were analyzed subsequently. DNA extracts were used for Illumina sequencing of the 16S rRNA gene and the metabolomes of rumen fluids were determined by 500 MHz-NMR spectroscopy. Tryptic peptides derived from protein extracts were measured by LC-ESI-MS/MS and spectra were processed by a two-step database search for quantitative metaproteome characterization. Data are available via ProteomeXchange with the identifier PXD006070. Protein- and DNA-based datasets revealed significant differences between sample fractions and diets and affirmed similar trends concerning shifts in phylogenetic composition. Ribosomal genes and proteins belonging to the phylum of Proteobacteria, particularly Succinivibrionaceae, exhibited a higher abundance in corn silage-based samples while fiber-degraders of the Lachnospiraceae family emerged in great quantities throughout the solid phase fractions. The analysis of 8163 quantified bacterial proteins revealed the presence of 166 carbohydrate active enzymes in varying abundance. Cellulosome affiliated proteins were less expressed in the grass silage, glycoside hydrolases appeared in slightest numbers in the corn silage. Most expressed glycoside hydrolases belonged to families 57 and 2. Enzymes analogous to ABC transporters for amino acids and monosaccharides were more abundant in the corn silage whereas oligosaccharide transporters showed a higher abundance in the fiber-rich diets. Proteins involved in carbon metabolism were detected in high numbers and identification of metabolites like short-chain fatty acids, methylamines and phenylpropionate by NMR enabled linkage between producers and products. This study forms a solid basis to retrieve deeper insight into the complex network of microbial adaptation in the rumen.
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Affiliation(s)
- Simon Deusch
- Department of Feed-Gut Microbiota Interaction, Institute of Animal Science, University of HohenheimStuttgart, Germany
| | - Amélia Camarinha-Silva
- Department of Feed-Gut Microbiota Interaction, Institute of Animal Science, University of HohenheimStuttgart, Germany
| | - Jürgen Conrad
- Department of Bioorganic Chemistry, Institute of Chemistry, University of HohenheimStuttgart, Germany
| | - Uwe Beifuss
- Department of Bioorganic Chemistry, Institute of Chemistry, University of HohenheimStuttgart, Germany
| | - Markus Rodehutscord
- Department of Feed-Gut Microbiota Interaction, Institute of Animal Science, University of HohenheimStuttgart, Germany
| | - Jana Seifert
- Department of Feed-Gut Microbiota Interaction, Institute of Animal Science, University of HohenheimStuttgart, Germany
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57
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Jia X, Xi BD, Li MX, Yang Y, Wang Y. Metaproteomics analysis of the functional insights into microbial communities of combined hydrogen and methane production by anaerobic fermentation from reed straw. PLoS One 2017; 12:e0183158. [PMID: 28817657 PMCID: PMC5560556 DOI: 10.1371/journal.pone.0183158] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/31/2017] [Indexed: 12/13/2022] Open
Abstract
A metaproteomic approach was used to analyse the proteins expressed and provide functional evidence of key metabolic pathways in the combined production of hydrogen and methane by anaerobic fermentation (CHMP-AF) for reed straw utilisation. The functions and structures of bacteria and archaea populations show significant succession in the CHMP-AF process. There are many kinds of bacterial functional proteins, mainly belonging to phyla Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes, that are involved in carbohydrate metabolism, energy metabolism, lipid metabolism, and amino acid metabolism. Ferredoxin-NADP reductase, present in bacteria in genus Azotobacter, is an important enzyme for NADH/NAD+ equilibrium regulation in hydrogen production. The archaeal functional proteins are mainly involved in methane metabolism in energy metabolism, such as acetyl-CoA decarboxylase, and methyl-coenzyme M reductase, and the acetic acid pathway exhibited the highest proportion of the total. The archaea of genus Methanosarcina in phylum Euryarchaeota can produce methane under the effect of multi-functional proteins through acetic acid, CO2 reduction, and methyl nutrient pathways. The study demonstrates metaproteomics as a new way of uncovering community functional and metabolic activity. The combined information was used to identify the metabolic pathways and organisms crucial for lignocellulosic biomass degradation and biogas production. This also regulates the process from its protein levels and improves the efficiency of biogas production using reed straw biomass.
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Affiliation(s)
- Xuan Jia
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, Beijing Technology and Business University, Beijing, China
| | - Bei-Dou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Ming-Xiao Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
- * E-mail:
| | - Yang Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Yong Wang
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, Beijing Technology and Business University, Beijing, China
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58
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Tanca A, Abbondio M, Palomba A, Fraumene C, Manghina V, Cucca F, Fiorillo E, Uzzau S. Potential and active functions in the gut microbiota of a healthy human cohort. MICROBIOME 2017; 5:79. [PMID: 28709472 PMCID: PMC5513205 DOI: 10.1186/s40168-017-0293-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/28/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND The study of the gut microbiota (GM) is rapidly moving towards its functional characterization by means of shotgun meta-omics. In this context, there is still no consensus on which microbial functions are consistently and constitutively expressed in the human gut in physiological conditions. Here, we selected a cohort of 15 healthy subjects from a native and highly monitored Sardinian population and analyzed their GMs using shotgun metaproteomics, with the aim of investigating GM functions actually expressed in a healthy human population. In addition, shotgun metagenomics was employed to reveal GM functional potential and to compare metagenome and metaproteome profiles in a combined taxonomic and functional fashion. RESULTS Metagenomic and metaproteomic data concerning the taxonomic structure of the GM under study were globally comparable. On the contrary, a considerable divergence between genetic potential and functional activity of the human healthy GM was observed, with the metaproteome displaying a higher plasticity, compared to the lower inter-individual variability of metagenome profiles. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several GM members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis, and short-chain fatty acid production). Noteworthy, Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the metabolic activity with the highest expression rate and the lowest inter-individual variability in the study cohort, in line with the previously reported importance of the biosynthesis of this microbial product for the gut homeostasis. CONCLUSIONS Our results provide detailed and taxon-specific information regarding functions and pathways actively working in a healthy GM. The reported discrepancy between expressed functions and functional potential suggests that caution should be used before drawing functional conclusions from metagenomic data, further supporting metaproteomics as a fundamental approach to characterize the human GM metabolic functions and activities.
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Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Antonio Palomba
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy
| | - Cristina Fraumene
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy
| | - Valeria Manghina
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Francesco Cucca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Sergio Uzzau
- Porto Conte Ricerche, Science and Technology Park of Sardinia, S.P. 55 Porto Conte - Capo Caccia km 8,400, Località Tramariglio, 07041, Alghero, SS, Italy.
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
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59
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Heyer R, Schallert K, Zoun R, Becher B, Saake G, Benndorf D. Challenges and perspectives of metaproteomic data analysis. J Biotechnol 2017; 261:24-36. [PMID: 28663049 DOI: 10.1016/j.jbiotec.2017.06.1201] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/20/2017] [Accepted: 06/23/2017] [Indexed: 02/07/2023]
Abstract
In nature microorganisms live in complex microbial communities. Comprehensive taxonomic and functional knowledge about microbial communities supports medical and technical application such as fecal diagnostics as well as operation of biogas plants or waste water treatment plants. Furthermore, microbial communities are crucial for the global carbon and nitrogen cycle in soil and in the ocean. Among the methods available for investigation of microbial communities, metaproteomics can approximate the activity of microorganisms by investigating the protein content of a sample. Although metaproteomics is a very powerful method, issues within the bioinformatic evaluation impede its success. In particular, construction of databases for protein identification, grouping of redundant proteins as well as taxonomic and functional annotation pose big challenges. Furthermore, growing amounts of data within a metaproteomics study require dedicated algorithms and software. This review summarizes recent metaproteomics software and addresses the introduced issues in detail.
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Affiliation(s)
- Robert Heyer
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Kay Schallert
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Roman Zoun
- Otto von Guericke University, Institute for Technical and Business Information Systems, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Beatrice Becher
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Gunter Saake
- Otto von Guericke University, Institute for Technical and Business Information Systems, Universitätsplatz 2, 39106 Magdeburg, Germany.
| | - Dirk Benndorf
- Otto von Guericke University, Bioprocess Engineering, Universitätsplatz 2, 39106 Magdeburg, Germany; Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstraße 1, 39106, Magdeburg, Germany.
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60
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Mesuere B, Van der Jeugt F, Willems T, Naessens T, Devreese B, Martens L, Dawyndt P. High-throughput metaproteomics data analysis with Unipept: A tutorial. J Proteomics 2017; 171:11-22. [PMID: 28552653 DOI: 10.1016/j.jprot.2017.05.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/15/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023]
Abstract
In recent years, shotgun metaproteomics has established itself as an important tool to study the composition of complex ecosystems and microbial communities. Two key steps in metaproteomics data analysis are the inference of proteins from the identified peptides, and the determination of the taxonomic origin and function of these proteins. This tutorial therefore introduces the Unipept command line interface (http://unipept.ugent.be/clidocs) as a platform-independent tool for such metaproteomics data analyses. First, a detailed overview is given of the available Unipept commands and their functions. Next, the power of the Unipept command line interface is illustrated using two case studies that analyze a single tryptic peptide, and a set of peptides retrieved from a shotgun metaproteomics experiment, respectively. Finally, the analysis results obtained using these command line tools are compared with the interactive taxonomic analysis that is available on the Unipept website.
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Affiliation(s)
- Bart Mesuere
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium.
| | - Felix Van der Jeugt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Toon Willems
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Tom Naessens
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Bart Devreese
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Peter Dawyndt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
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61
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Nakatsuji T, Chen TH, Narala S, Chun KA, Two AM, Yun T, Shafiq F, Kotol PF, Bouslimani A, Melnik AV, Latif H, Kim JN, Lockhart A, Artis K, David G, Taylor P, Streib J, Dorrestein PC, Grier A, Gill SR, Zengler K, Hata TR, Leung DYM, Gallo RL. Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis. Sci Transl Med 2017; 9:eaah4680. [PMID: 28228596 PMCID: PMC5600545 DOI: 10.1126/scitranslmed.aah4680] [Citation(s) in RCA: 648] [Impact Index Per Article: 92.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/08/2016] [Accepted: 01/17/2017] [Indexed: 12/21/2022]
Abstract
The microbiome can promote or disrupt human health by influencing both adaptive and innate immune functions. We tested whether bacteria that normally reside on human skin participate in host defense by killing Staphylococcus aureus, a pathogen commonly found in patients with atopic dermatitis (AD) and an important factor that exacerbates this disease. High-throughput screening for antimicrobial activity against S. aureus was performed on isolates of coagulase-negative Staphylococcus (CoNS) collected from the skin of healthy and AD subjects. CoNS strains with antimicrobial activity were common on the normal population but rare on AD subjects. A low frequency of strains with antimicrobial activity correlated with colonization by S. aureus The antimicrobial activity was identified as previously unknown antimicrobial peptides (AMPs) produced by CoNS species including Staphylococcus epidermidis and Staphylococcus hominis These AMPs were strain-specific, highly potent, selectively killed S. aureus, and synergized with the human AMP LL-37. Application of these CoNS strains to mice confirmed their defense function in vivo relative to application of nonactive strains. Strikingly, reintroduction of antimicrobial CoNS strains to human subjects with AD decreased colonization by S. aureus These findings show how commensal skin bacteria protect against pathogens and demonstrate how dysbiosis of the skin microbiome can lead to disease.
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Affiliation(s)
- Teruaki Nakatsuji
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Tiffany H Chen
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Saisindhu Narala
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Kimberly A Chun
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Aimee M Two
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Tong Yun
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Faiza Shafiq
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Paul F Kotol
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92092, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92092, USA
| | - Haythem Latif
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92092, USA
| | - Ji-Nu Kim
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92092, USA
| | | | - Keli Artis
- Rho Federal Systems Division Inc., Chapel Hill, NC 27517, USA
| | - Gloria David
- Rho Federal Systems Division Inc., Chapel Hill, NC 27517, USA
| | - Patricia Taylor
- Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO 80206, USA
| | - Joanne Streib
- Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO 80206, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92092, USA
- Departments of Chemistry, Biochemistry and Pharmacology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Alex Grier
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14611, USA
| | - Steven R Gill
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14611, USA
| | - Karsten Zengler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92092, USA
| | - Tissa R Hata
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA
| | - Donald Y M Leung
- Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO 80206, USA
| | - Richard L Gallo
- Department of Dermatology, University of California, San Diego, La Jolla, CA 92092, USA.
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62
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Petriz BA, Franco OL. Metaproteomics as a Complementary Approach to Gut Microbiota in Health and Disease. Front Chem 2017; 5:4. [PMID: 28184370 PMCID: PMC5266679 DOI: 10.3389/fchem.2017.00004] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/13/2017] [Indexed: 12/20/2022] Open
Abstract
Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota, such as the human gut. The advances in molecular separation methods coupled with mass spectrometry (e.g., LC-MS/MS) and proteome bioinformatics have been fundamental in these novel large-scale metaproteomic studies, which have further been performed in a wide range of samples including soil, plant and human environments. Metaproteomic studies will make major progress if a comprehensive database covering the genes and expresses proteins from all gut microbial species is developed. To this end, we here present some of the main limitations of metaproteomic studies in complex microbiota environments, such as the gut, also addressing the up-to-date pipelines in sample preparation prior to fractionation/separation and mass spectrometry analysis. In addition, a novel approach to the limitations of metagenomic databases is also discussed. Finally, prospects are addressed regarding the application of metaproteomic analysis using a unified host-microbiome gene database and other meta-OMICs platforms.
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Affiliation(s)
- Bernardo A Petriz
- Department of Health, Molecular and Physiologic Adaptations to Exercise, Centro Universitário do Distrito Federal Brasília, Brazil
| | - Octávio L Franco
- S-Inova Biotech, Universidade Católica Dom Bosco Campo Grande, Brazil
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63
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Khalilpour A, Kilic T, Khalilpour S, Álvarez MM, Yazdi IK. Proteomic-based biomarker discovery for development of next generation diagnostics. Appl Microbiol Biotechnol 2016; 101:475-491. [PMID: 28013407 DOI: 10.1007/s00253-016-8029-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 01/09/2023]
Abstract
In the post-genome age, proteomics is receiving significant attention because they provide an invaluable source of biological structures and functions at the protein level. The search for disease-specific biomarkers for diagnostic and/or therapeutic applications is one of the areas that proteomics is having a significant impact. Thus, the identification of a "good" biomarker enables a more accurate early diagnosis and prognosis of disease. Rapid advancements in mass spectrometry (MS) instrumentation, liquid chromatography MS (LCMS), protein microarray technology, and other protein profiling methodologies have a substantial expansion of our toolbox to identify disease-specific protein and peptide biomarkers. This review covers a selection of widely used proteomic technologies for biomarker discovery. In addition, we describe the most commonly used approaches for diagnosis based on proteomic biomarkers and further discuss trends and critical challenges during development of cost-effective rapid diagnostic tests and microfluidic diagnostic systems based on proteomic biomarkers.
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Affiliation(s)
- Akbar Khalilpour
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA. .,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Tugba Kilic
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Biomedical Engineering, Faculty of Engineering and Architecture, Izmir Katip Celebi University, 35620, Izmir, Turkey.,Department of Biotechnology, Institute of Science, Ege University, 35100, Izmir, Turkey
| | - Saba Khalilpour
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - Mario Moisés Álvarez
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Iman K Yazdi
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 65 Landsdowne Street, Rm. 265, Cambridge, MA, 02139, USA.,Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, 02139, USA
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64
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Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns. ISME JOURNAL 2016; 11:309-314. [PMID: 27824341 PMCID: PMC5270573 DOI: 10.1038/ismej.2016.132] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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65
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Keiblinger KM, Fuchs S, Zechmeister-Boltenstern S, Riedel K. Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding. FEMS Microbiol Ecol 2016; 92:fiw180. [PMID: 27549116 PMCID: PMC5026301 DOI: 10.1093/femsec/fiw180] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/31/2016] [Accepted: 08/18/2016] [Indexed: 11/14/2022] Open
Abstract
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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Affiliation(s)
- Katharina M Keiblinger
- Institute for Soil Research, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), Peter Jordan-Strasse 82, 1190 Vienna, Austria
| | - Stephan Fuchs
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17489 Greifswald, Germany
| | - Sophie Zechmeister-Boltenstern
- Institute for Soil Research, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), Peter Jordan-Strasse 82, 1190 Vienna, Austria
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahnstrasse 15, 17489 Greifswald, Germany
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66
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Franco Cairo JPL, Carazzolle MF, Leonardo FC, Mofatto LS, Brenelli LB, Gonçalves TA, Uchima CA, Domingues RR, Alvarez TM, Tramontina R, Vidal RO, Costa FF, Costa-Leonardo AM, Paes Leme AF, Pereira GAG, Squina FM. Expanding the Knowledge on Lignocellulolytic and Redox Enzymes of Worker and Soldier Castes from the Lower Termite Coptotermes gestroi. Front Microbiol 2016; 7:1518. [PMID: 27790186 PMCID: PMC5061848 DOI: 10.3389/fmicb.2016.01518] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/12/2016] [Indexed: 11/13/2022] Open
Abstract
Termites are considered one of the most efficient decomposers of lignocelluloses on Earth due to their ability to produce, along with its microbial symbionts, a repertoire of carbohydrate-active enzymes (CAZymes). Recently, a set of Pro-oxidant, Antioxidant, and Detoxification enzymes (PAD) were also correlated with the metabolism of carbohydrates and lignin in termites. The lower termite Coptotermes gestroi is considered the main urban pest in Brazil, causing damage to wood constructions. Recently, analysis of the enzymatic repertoire of C. gestroi unveiled the presence of different CAZymes. Because the gene profile of CAZy/PAD enzymes endogenously synthesized by C. gestroi and also by their symbiotic protists remains unclear, the aim of this study was to explore the eukaryotic repertoire of these enzymes in worker and soldier castes of C. gestroi. Our findings showed that worker and soldier castes present similar repertoires of CAZy/PAD enzymes, and also confirmed that endo-glucanases (GH9) and beta-glucosidases (GH1) were the most important glycoside hydrolase families related to lignocellulose degradation in both castes. Classical cellulases such as exo-glucanases (GH7) and endo-glucanases (GH5 and GH45), as well as classical xylanases (GH10 and GH11), were found in both castes only taxonomically related to protists, highlighting the importance of symbiosis in C. gestroi. Moreover, our analysis revealed the presence of Auxiliary Activity enzyme families (AAs), which could be related to lignin modifications in termite digestomes. In conclusion, this report expanded the knowledge on genes and proteins related to CAZy/PAD enzymes from worker and soldier castes of lower termites, revealing new potential enzyme candidates for second-generation biofuel processes.
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Affiliation(s)
- João P L Franco Cairo
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM)Campinas, Brazil; Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Marcelo F Carazzolle
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP) Campinas, Brazil
| | - Flávia C Leonardo
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil; Centro de Hematologia e Hemoterapia (Hemocentro), Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Luciana S Mofatto
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil; Centro de Hematologia e Hemoterapia (Hemocentro), Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Lívia B Brenelli
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM)Campinas, Brazil; Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Thiago A Gonçalves
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM)Campinas, Brazil; Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Cristiane A Uchima
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
| | - Romênia R Domingues
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBIO), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
| | - Thabata M Alvarez
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
| | - Robson Tramontina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM)Campinas, Brazil; Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Ramon O Vidal
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP) Campinas, Brazil
| | - Fernando F Costa
- Centro de Hematologia e Hemoterapia (Hemocentro), Universidade Estadual de Campinas (UNICAMP) Campinas, Brazil
| | - Ana M Costa-Leonardo
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP) Rio Claro, Brazil
| | - Adriana F Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBIO), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
| | - Gonçalo A G Pereira
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP) Campinas, Brazil
| | - Fabio M Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
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67
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Tanca A, Palomba A, Fraumene C, Pagnozzi D, Manghina V, Deligios M, Muth T, Rapp E, Martens L, Addis MF, Uzzau S. The impact of sequence database choice on metaproteomic results in gut microbiota studies. MICROBIOME 2016; 4:51. [PMID: 27671352 PMCID: PMC5037606 DOI: 10.1186/s40168-016-0196-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/12/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics, the study of the whole protein complement of a microbial community, can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. RESULTS Here, we present a systematic investigation of variables concerning database construction and annotation and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. In particular, the contribution of experimental metagenomic databases was revealed to be mandatory when dealing with mouse samples. Moreover, the use of a "merged" database, containing all metagenomic sequences from the population under study, was found to be generally preferable over the use of sample-matched databases. We also observed that taxonomic and functional results are strongly database-dependent, in particular when analyzing the mouse gut microbiota. As a striking example, the Firmicutes/Bacteroidetes ratio varied up to tenfold depending on the database used. Finally, assembling reads into longer contigs provided significant advantages in terms of functional annotation yields. CONCLUSIONS This study contributes to identify host- and database-specific biases which need to be taken into account in a metaproteomic experiment, providing meaningful insights on how to design gut microbiota studies and to perform metaproteomic data analysis. In particular, the use of multiple databases and annotation tools has to be encouraged, even though this requires appropriate bioinformatic resources.
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Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Antonio Palomba
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Cristina Fraumene
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Daniela Pagnozzi
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Valeria Manghina
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Massimo Deligios
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Thilo Muth
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Research Group Bioinformatics (NG 4), Robert Koch Institute, Berlin, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Lennart Martens
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Medical Biotechnology Center, VIB, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Zwijnaarde, Ghent, Belgium
| | - Maria Filippa Addis
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Sergio Uzzau
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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68
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Muth T, Renard BY, Martens L. Metaproteomic data analysis at a glance: advances in computational microbial community proteomics. Expert Rev Proteomics 2016; 13:757-69. [DOI: 10.1080/14789450.2016.1209418] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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69
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An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. J Biotechnol 2016; 231:268-279. [PMID: 27312700 DOI: 10.1016/j.jbiotec.2016.06.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/08/2016] [Accepted: 06/12/2016] [Indexed: 12/29/2022]
Abstract
To study the metaproteome of a biogas-producing microbial community, fermentation samples were taken from an agricultural biogas plant for microbial cell and protein extraction and corresponding metagenome analyses. Based on metagenome sequence data, taxonomic community profiling was performed to elucidate the composition of bacterial and archaeal sub-communities. The community's cytosolic metaproteome was represented in a 2D-PAGE approach. Metaproteome databases for protein identification were compiled based on the assembled metagenome sequence dataset for the biogas plant analyzed and non-corresponding biogas metagenomes. Protein identification results revealed that the corresponding biogas protein database facilitated the highest identification rate followed by other biogas-specific databases, whereas common public databases yielded insufficient identification rates. Proteins of the biogas microbiome identified as highly abundant were assigned to the pathways involved in methanogenesis, transport and carbon metabolism. Moreover, the integrated metagenome/-proteome approach enabled the examination of genetic-context information for genes encoding identified proteins by studying neighboring genes on the corresponding contig. Exemplarily, this approach led to the identification of a Methanoculleus sp. contig encoding 16 methanogenesis-related gene products, three of which were also detected as abundant proteins within the community's metaproteome. Thus, metagenome contigs provide additional information on the genetic environment of identified abundant proteins.
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70
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Addis MF, Tanca A, Landolfo S, Abbondio M, Cutzu R, Biosa G, Pagnozzi D, Uzzau S, Mannazzu I. Proteomic analysis ofRhodotorula mucilaginosa: dealing with the issues of a non-conventional yeast. Yeast 2016; 33:433-49. [DOI: 10.1002/yea.3162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 02/16/2016] [Accepted: 03/09/2016] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - Sara Landolfo
- Dipartimento di Agraria; Università di Sassari; Italy
| | | | | | | | | | - Sergio Uzzau
- Porto Conte Ricerche; Tramariglio Alghero Italy
- Dipartimento di Scienze Biomediche; Università di Sassari; Italy
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71
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Herbst FA, Lünsmann V, Kjeldal H, Jehmlich N, Tholey A, von Bergen M, Nielsen JL, Hettich RL, Seifert J, Nielsen PH. Enhancing metaproteomics--The value of models and defined environmental microbial systems. Proteomics 2016; 16:783-98. [PMID: 26621789 DOI: 10.1002/pmic.201500305] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/03/2015] [Accepted: 11/26/2015] [Indexed: 12/24/2022]
Abstract
Metaproteomics--the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time--has provided new features to study complex microbial communities in order to unravel these "black boxes." New technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. Following a short introduction to microbial communities and metaproteomics, we introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.
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Affiliation(s)
- Florian-Alexander Herbst
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Vanessa Lünsmann
- Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Henrik Kjeldal
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Nico Jehmlich
- Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Martin von Bergen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.,Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, TN, USA
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Per Halkjaer Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
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72
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Addis MF, Tanca A, Uzzau S, Oikonomou G, Bicalho RC, Moroni P. The bovine milk microbiota: insights and perspectives from -omics studies. MOLECULAR BIOSYSTEMS 2016; 12:2359-72. [DOI: 10.1039/c6mb00217j] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recent findings and future perspectives of -omics studies on the bovine milk microbiota, focusing on its impact on animal health.
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Affiliation(s)
- M. F. Addis
- Porto Conte Ricerche
- SP 55 Porto Conte/Capo Caccia
- 07041 Alghero
- Italy
| | - A. Tanca
- Porto Conte Ricerche
- SP 55 Porto Conte/Capo Caccia
- 07041 Alghero
- Italy
| | - S. Uzzau
- Porto Conte Ricerche
- SP 55 Porto Conte/Capo Caccia
- 07041 Alghero
- Italy
- Università degli Studi di Sassari
| | - G. Oikonomou
- Epidemiology and Population Health
- Institute of Infection and Global Health
- University of Liverpool
- Liverpool
- UK
| | - R. C. Bicalho
- Cornell University
- Department of Population Medicine and Diagnostic Sciences
- College of Veterinary Medicine
- Ithaca
- USA
| | - P. Moroni
- Cornell University
- Department of Population Medicine and Diagnostic Sciences
- College of Veterinary Medicine
- Ithaca
- USA
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73
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Mayne J, Ning Z, Zhang X, Starr AE, Chen R, Deeke S, Chiang CK, Xu B, Wen M, Cheng K, Seebun D, Star A, Moore JI, Figeys D. Bottom-Up Proteomics (2013-2015): Keeping up in the Era of Systems Biology. Anal Chem 2015; 88:95-121. [PMID: 26558748 DOI: 10.1021/acs.analchem.5b04230] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Janice Mayne
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Zhibin Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Xu Zhang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Amanda E Starr
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Rui Chen
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Shelley Deeke
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Cheng-Kang Chiang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Bo Xu
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Ming Wen
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Kai Cheng
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Deeptee Seebun
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Alexandra Star
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Jasmine I Moore
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
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74
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Jia RZ, Zhang RJ, Wei Q, Chen WF, Cho IK, Chen WX, Li QX. Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry. ACTA ACUST UNITED AC 2015; 8:98-107. [PMID: 26500417 PMCID: PMC4616259 DOI: 10.4172/jpb.1000357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mass spectrometry (MS) has been widely used for specific, sensitive and rapid analysis of proteins and has shown a high potential for bacterial identification and characterization. Type strains of four species of rhizobia and Escherichia coli DH5α were employed as reference bacteria to optimize various parameters for identification and classification of species of rhizobia by matrix-assisted laser desorption/ionization time-of-flight MS (MALDI TOF MS). The parameters optimized included culture medium states (liquid or solid), bacterial growth phases, colony storage temperature and duration, and protein data processing to enhance the bacterial identification resolution, accuracy and reliability. The medium state had little effects on the mass spectra of protein profiles. A suitable sampling time was between the exponential phase and the stationary phase. Consistent protein mass spectral profiles were observed for E. coli colonies pre-grown for 14 days and rhizobia for 21 days at 4°C or 21°C. A dendrogram of 75 rhizobial strains of 4 genera was constructed based on MALDI TOF mass spectra and the topological patterns agreed well with those in the 16S rDNA phylogenetic tree. The potential of developing a mass spectral database for all rhizobia species was assessed with blind samples. The entire process from sample preparation to accurate identification and classification of species required approximately one hour.
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Affiliation(s)
- Rui Zong Jia
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA ; State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China ; State Key Biotechnology Laboratory for Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, Hainan, 571101, China
| | - Rong Juan Zhang
- State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China ; Dongying Municipal Bureau of Agriculture, Dongying, Shandong, 257091, China
| | - Qing Wei
- State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China ; State Key Biotechnology Laboratory for Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, Hainan, 571101, China
| | - Wen Feng Chen
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA ; State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Il Kyu Cho
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Wen Xin Chen
- State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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75
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Tanca A, Palomba A, Pisanu S, Addis MF, Uzzau S. A human gut metaproteomic dataset from stool samples pretreated or not by differential centrifugation. Data Brief 2015; 4:559-62. [PMID: 26306325 PMCID: PMC4536287 DOI: 10.1016/j.dib.2015.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/15/2015] [Accepted: 07/15/2015] [Indexed: 01/01/2023] Open
Abstract
We present a human gut metaproteomic dataset deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001573. Ten aliquots of a single stool sample collected from a healthy human volunteer were either pretreated by differential centrifugation (DC; N=5) or not centrifuged (NC; N=5). Protein extracts were then processed by filter-aided sample preparation, single-run liquid chromatography and high-resolution mass spectrometry, and peptide identification was carried out using Sequest-HT as search engine within the Proteome Discoverer informatic platform. The dataset described here is also related to the research article entitled "Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota" published in Proteomics (Tanca et al., 2015), [1].
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Affiliation(s)
| | | | | | | | - Sergio Uzzau
- Porto Conte Ricerche, Tramariglio, Alghero, Italy ; Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
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76
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Jagtap PD, Blakely A, Murray K, Stewart S, Kooren J, Johnson JE, Rhodus NL, Rudney J, Griffin TJ. Metaproteomic analysis using the Galaxy framework. Proteomics 2015; 15:3553-65. [DOI: 10.1002/pmic.201500074] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/25/2015] [Accepted: 06/04/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Pratik D. Jagtap
- Center for Mass Spectrometry and Proteomics; University of Minnesota; Minneapolis MN USA
- Department of Biochemistry; Molecular Biology and Biophysics; University of Minnesota; Minneapolis MN USA
| | | | - Kevin Murray
- Department of Biochemistry; Molecular Biology and Biophysics; University of Minnesota; Minneapolis MN USA
| | | | - Joel Kooren
- Department of Biochemistry; Molecular Biology and Biophysics; University of Minnesota; Minneapolis MN USA
| | | | - Nelson L. Rhodus
- School of Dentistry; University of Minnesota; Minneapolis MN USA
| | - Joel Rudney
- School of Dentistry; University of Minnesota; Minneapolis MN USA
| | - Timothy J. Griffin
- Center for Mass Spectrometry and Proteomics; University of Minnesota; Minneapolis MN USA
- Department of Biochemistry; Molecular Biology and Biophysics; University of Minnesota; Minneapolis MN USA
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77
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Pisanu S, Cubeddu T, Pagnozzi D, Rocca S, Cacciotto C, Alberti A, Marogna G, Uzzau S, Addis MF. Neutrophil extracellular traps in sheep mastitis. Vet Res 2015; 46:59. [PMID: 26088507 PMCID: PMC4471908 DOI: 10.1186/s13567-015-0196-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 04/30/2015] [Indexed: 01/21/2023] Open
Abstract
Neutrophil extracellular traps (NETs) are structures composed of DNA, histones, and antimicrobial proteins that are released extracellularly by neutrophils and other immune cells as a means for trapping and killing invading pathogens. Here, we describe NET formation in milk and in mammary alveoli of mastitic sheep, and provide a dataset of proteins found in association to these structures. Nucleic acid staining, immunomicroscopy and fluorescent in-situ hybridization of mastitic mammary tissue from sheep infected with Streptococcus uberis demonstrated the presence of extranuclear DNA colocalizing with antimicrobial proteins, histones, and bacteria. Then, proteomic analysis by LTQ-Orbitrap Velos mass spectrometry provided detailed information on protein abundance changes occurring in milk upon infection. As a result, 1095 unique proteins were identified, of which 287 being significantly more abundant in mastitic milk. Upon protein ontology classification, the most represented localization classes for upregulated proteins were the cytoplasmic granule, the nucleus, and the mitochondrion, while function classes were mostly related to immune defence and inflammation pathways. All known NET markers were massively increased, including histones, granule proteases, and antimicrobial proteins. Of note was the detection of protein arginine deiminases (PAD3 and PAD4). These enzymes are responsible for citrullination, the post-translational modification that is known to trigger NET formation by inducing chromatin decondensation and extracellular release of NETs. As a further observation, citrullinated residues were detected by tandem mass spectrometry in histones of samples from mastitic animals. In conclusion, this work provides novel microscopic and proteomic information on NETs formed in vivo in the mammary gland, and reports the most complete database of proteins increased in milk upon bacterial mastitis.
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Affiliation(s)
| | - Tiziana Cubeddu
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy.
| | | | - Stefano Rocca
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy.
| | - Carla Cacciotto
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy.
| | - Alberto Alberti
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy.
| | - Gavino Marogna
- Istituto Zooprofilattico Sperimentale G, Pegreffi, Sassari, Italy.
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78
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McNair K, Edwards RA. GenomePeek-an online tool for prokaryotic genome and metagenome analysis. PeerJ 2015; 3:e1025. [PMID: 26157610 PMCID: PMC4476108 DOI: 10.7717/peerj.1025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 05/25/2015] [Indexed: 12/23/2022] Open
Abstract
As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.
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Affiliation(s)
- Katelyn McNair
- Department of Computer Science, San Diego State University , San Diego, CA , USA ; Department of Biology, San Diego State University , San Diego, CA , USA
| | - Robert A Edwards
- Department of Computer Science, San Diego State University , San Diego, CA , USA ; Department of Biology, San Diego State University , San Diego, CA , USA ; Computational Sciences Research Center, San Diego State University , San Diego, CA , USA ; Mathematics and Computer Science Division, Argonne National Laboratory , Argonne, IL , USA
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79
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Liu D, Li M, Xi B, Zhao Y, Wei Z, Song C, Zhu C. Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant. Microb Biotechnol 2015; 8:950-60. [PMID: 25989417 PMCID: PMC4621448 DOI: 10.1111/1751-7915.12290] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 03/31/2015] [Accepted: 04/06/2015] [Indexed: 01/14/2023] Open
Abstract
Composting is an appropriate management alternative for municipal solid waste; however, our knowledge about the microbial regulation of this process is still scare. We employed metaproteomics to elucidate the main biodegradation pathways in municipal solid waste composting system across the main phases in a large-scale composting plant. The investigation of microbial succession revealed that Bacillales, Actinobacteria and Saccharomyces increased significantly with respect to abundance in composting process. The key microbiologic population for cellulose degradation in different composting stages was different. Fungi were found to be the main producers of cellulase in earlier phase. However, the cellulolytic fungal communities were gradually replaced by a purely bacterial one in active phase, which did not support the concept that the thermophilic fungi are active through the thermophilic phase. The effective decomposition of cellulose required the synergy between bacteria and fungi in the curing phase.
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Affiliation(s)
- Dongming Liu
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.,Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
| | - Mingxiao Li
- Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
| | - Beidou Xi
- Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
| | - Yue Zhao
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Zimin Wei
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Caihong Song
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.,Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
| | - Chaowei Zhu
- Innovation Base of Groundwater and Environmental System Engineering, Chinese Research Academy of Environmental Science, Beijing, 100012, China
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80
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Muth T, Kolmeder CA, Salojärvi J, Keskitalo S, Varjosalo M, Verdam FJ, Rensen SS, Reichl U, de Vos WM, Rapp E, Martens L. Navigating through metaproteomics data: a logbook of database searching. Proteomics 2015; 15:3439-53. [PMID: 25778831 DOI: 10.1002/pmic.201400560] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/13/2015] [Accepted: 03/06/2015] [Indexed: 11/12/2022]
Abstract
Metaproteomic research involves various computational challenges during the identification of fragmentation spectra acquired from the proteome of a complex microbiome. These issues are manifold and range from the construction of customized sequence databases, the optimal setting of search parameters to limitations in the identification search algorithms themselves. In order to assess the importance of these individual factors, we studied the effect of strategies to combine different search algorithms, explored the influence of chosen database search settings, and investigated the impact of the size of the protein sequence database used for identification. Furthermore, we applied de novo sequencing as a complementary approach to classic database searching. All evaluations were performed on a human intestinal metaproteome dataset. Pyrococcus furiosus proteome data were used to contrast database searching of metaproteomic data to a classic proteomic experiment. Searching against subsets of metaproteome databases and the use of multiple search engines increased the number of identifications. The integration of P. furiosus sequences in a metaproteomic sequence database showcased the limitation of the target-decoy-controlled false discovery rate approach in combination with large sequence databases. The selection of varying search engine parameters and the application of de novo sequencing represented useful methods to increase the reliability of the results. Based on our findings, we provide recommendations for the data analysis that help researchers to establish or improve analysis workflows in metaproteomics.
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Affiliation(s)
- Thilo Muth
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Carolin A Kolmeder
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jarkko Salojärvi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Salla Keskitalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Froukje J Verdam
- Department of General Surgery, NUTRIM, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sander S Rensen
- Department of General Surgery, NUTRIM, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Otto-von-Guericke University, Bioprocess Engineering, Magdeburg, Germany
| | - Willem M de Vos
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland.,Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Lennart Martens
- Department of Biochemistry, Ghent University, Ghent, Belgium.,Department of Medical Protein Research, VIB, Ghent, Belgium
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81
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Lassek C, Burghartz M, Chaves-Moreno D, Otto A, Hentschker C, Fuchs S, Bernhardt J, Jauregui R, Neubauer R, Becher D, Pieper DH, Jahn M, Jahn D, Riedel K. A metaproteomics approach to elucidate host and pathogen protein expression during catheter-associated urinary tract infections (CAUTIs). Mol Cell Proteomics 2015; 14:989-1008. [PMID: 25673765 PMCID: PMC4390275 DOI: 10.1074/mcp.m114.043463] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 01/20/2015] [Indexed: 12/11/2022] Open
Abstract
Long-term catheterization inevitably leads to a catheter-associated bacteriuria caused by multispecies bacterial biofilms growing on and in the catheters. The overall goal of the presented study was (1) to unravel bacterial community structure and function of such a uropathogenic biofilm and (2) to elucidate the interplay between bacterial virulence and the human immune system within the urine. To this end, a metaproteomics approach combined with in vitro proteomics analyses was employed to investigate both, the pro- and eukaryotic protein inventory. Our proteome analyses demonstrated that the biofilm of the investigated catheter is dominated by three bacterial species, that is, Pseudomonas aeruginosa, Morganella morganii, and Bacteroides sp., and identified iron limitation as one of the major challenges in the bladder environment. In vitro proteome analysis of P. aeruginosa and M. morganii isolated from the biofilm revealed that these opportunistic pathogens are able to overcome iron restriction via the production of siderophores and high expression of corresponding receptors. Notably, a comparison of in vivo and in vitro protein profiles of P. aeruginosa and M. morganii also indicated that the bacteria employ different strategies to adapt to the urinary tract. Although P. aeruginosa seems to express secreted and surface-exposed proteases to escape the human innate immune system and metabolizes amino acids, M. morganii is able to take up sugars and to degrade urea. Most interestingly, a comparison of urine protein profiles of three long-term catheterized patients and three healthy control persons demonstrated the elevated level of proteins associated with neutrophils, macrophages, and the complement system in the patient's urine, which might point to a specific activation of the innate immune system in response to biofilm-associated urinary tract infections. We thus hypothesize that the often asymptomatic nature of catheter-associated urinary tract infections might be based on a fine-tuned balance between the expression of bacterial virulence factors and the human immune system.
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Affiliation(s)
- Christian Lassek
- From the ‡Institute of Microbiology, University of Greifswald, 17489 Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, Germany; §Institute of Microbiology, Technische Universität Braunschweig, 38106 Braunschweig, Spielmannstrasse 7, Germany
| | - Melanie Burghartz
- §Institute of Microbiology, Technische Universität Braunschweig, 38106 Braunschweig, Spielmannstrasse 7, Germany
| | - Diego Chaves-Moreno
- ¶Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Inhoffenstrasse 7, Germany
| | - Andreas Otto
- From the ‡Institute of Microbiology, University of Greifswald, 17489 Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, Germany
| | - Christian Hentschker
- From the ‡Institute of Microbiology, University of Greifswald, 17489 Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, Germany
| | - Stephan Fuchs
- From the ‡Institute of Microbiology, University of Greifswald, 17489 Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, Germany
| | - Jörg Bernhardt
- From the ‡Institute of Microbiology, University of Greifswald, 17489 Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, Germany
| | - Ruy Jauregui
- ¶Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Inhoffenstrasse 7, Germany
| | | | - Dörte Becher
- From the ‡Institute of Microbiology, University of Greifswald, 17489 Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, Germany
| | - Dietmar H Pieper
- ¶Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Inhoffenstrasse 7, Germany
| | - Martina Jahn
- §Institute of Microbiology, Technische Universität Braunschweig, 38106 Braunschweig, Spielmannstrasse 7, Germany
| | - Dieter Jahn
- §Institute of Microbiology, Technische Universität Braunschweig, 38106 Braunschweig, Spielmannstrasse 7, Germany
| | - Katharina Riedel
- From the ‡Institute of Microbiology, University of Greifswald, 17489 Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, Germany; ¶Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Inhoffenstrasse 7, Germany;
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82
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Tanca A, Palomba A, Pisanu S, Addis MF, Uzzau S. Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota. Proteomics 2015; 15:3474-85. [PMID: 25677681 DOI: 10.1002/pmic.201400573] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/15/2015] [Accepted: 02/05/2015] [Indexed: 02/03/2023]
Abstract
To date, most metaproteomic studies of the gut microbiota employ stool sample pretreatment methods to enrich for microbial components. However, a specific investigation aimed at assessing if, how, and to what extent this may impact on the final taxonomic and functional results is still lacking. Here, stool replicates were either pretreated by differential centrifugation (DC) or not centrifuged. Protein extracts were then processed by filter-aided sample preparation, single-run LC, and high-resolution MS, and the metaproteomic data were compared by spectral counting. DC led to a higher number of identifications, a significantly richer microbial diversity, as well as to reduced information on the nonmicrobial components (host and food) when compared to not centrifuged. Nevertheless, dramatic differences in the relative abundance of several gut microbial taxa were also observed, including a significant change in the Firmicutes/Bacteroidetes ratio. Furthermore, some important microbial functional categories, including cell surface enzymes, membrane-associated proteins, extracellular proteins, and flagella, were significantly reduced after DC. In conclusion, this work underlines that a critical evaluation is needed when selecting the appropriate stool sample processing protocol in the context of a metaproteomic study, depending on the specific target to which the research is aimed. All MS data have been deposited in the ProteomeXchange with identifier PXD001573 (http://proteomecentral.proteomexchange.org/dataset/PXD001573).
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Affiliation(s)
| | | | | | | | - Sergio Uzzau
- Porto Conte Ricerche, Tramariglio, Alghero, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
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83
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Nesvizhskii AI. Proteogenomics: concepts, applications and computational strategies. Nat Methods 2015; 11:1114-25. [PMID: 25357241 DOI: 10.1038/nmeth.3144] [Citation(s) in RCA: 505] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 09/22/2014] [Indexed: 12/19/2022]
Abstract
Proteogenomics is an area of research at the interface of proteomics and genomics. In this approach, customized protein sequence databases generated using genomic and transcriptomic information are used to help identify novel peptides (not present in reference protein sequence databases) from mass spectrometry-based proteomic data; in turn, the proteomic data can be used to provide protein-level evidence of gene expression and to help refine gene models. In recent years, owing to the emergence of new sequencing technologies such as RNA-seq and dramatic improvements in the depth and throughput of mass spectrometry-based proteomics, the pace of proteogenomic research has greatly accelerated. Here I review the current state of proteogenomic methods and applications, including computational strategies for building and using customized protein sequence databases. I also draw attention to the challenge of false positive identifications in proteogenomics and provide guidelines for analyzing the data and reporting the results of proteogenomic studies.
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Affiliation(s)
- Alexey I Nesvizhskii
- 1] Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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84
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Muth T, Behne A, Heyer R, Kohrs F, Benndorf D, Hoffmann M, Lehtevä M, Reichl U, Martens L, Rapp E. The MetaProteomeAnalyzer: A Powerful Open-Source Software Suite for Metaproteomics Data Analysis and Interpretation. J Proteome Res 2015; 14:1557-65. [DOI: 10.1021/pr501246w] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Thilo Muth
- Max Planck Institute
for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Alexander Behne
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Robert Heyer
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Fabian Kohrs
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Dirk Benndorf
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Marcus Hoffmann
- Max Planck Institute
for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Miro Lehtevä
- Department
of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Udo Reichl
- Max Planck Institute
for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
- Chair
of Bioprocess Engineering, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Lennart Martens
- Department
of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Erdmann Rapp
- Max Planck Institute
for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
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85
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Mesuere B, Debyser G, Aerts M, Devreese B, Vandamme P, Dawyndt P. The Unipept metaproteomics analysis pipeline. Proteomics 2015; 15:1437-42. [DOI: 10.1002/pmic.201400361] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/10/2014] [Accepted: 11/26/2014] [Indexed: 02/06/2023]
Affiliation(s)
- Bart Mesuere
- Faculty of Sciences; Department of Applied Mathematics; Computer Science and Statistics; Ghent University; Ghent Belgium
| | - Griet Debyser
- Faculty of Sciences; Laboratory for Protein Biochemistry and Biomolecular Engineering; Ghent University; Ghent Belgium
| | - Maarten Aerts
- Faculty of Sciences; Laboratory for Microbiology; Ghent University; Ghent Belgium
| | - Bart Devreese
- Faculty of Sciences; Laboratory for Protein Biochemistry and Biomolecular Engineering; Ghent University; Ghent Belgium
| | - Peter Vandamme
- Faculty of Sciences; Laboratory for Microbiology; Ghent University; Ghent Belgium
| | - Peter Dawyndt
- Faculty of Sciences; Department of Applied Mathematics; Computer Science and Statistics; Ghent University; Ghent Belgium
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86
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Sauer S, Luge T. Nutriproteomics: Facts, concepts, and perspectives. Proteomics 2015; 15:997-1013. [DOI: 10.1002/pmic.201400383] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/03/2014] [Accepted: 11/27/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Sascha Sauer
- Otto Warburg Laboratory; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Toni Luge
- Otto Warburg Laboratory; Max Planck Institute for Molecular Genetics; Berlin Germany
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87
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Mao L, Franke J. Symbiosis, dysbiosis, and rebiosis-The value of metaproteomics in human microbiome monitoring. Proteomics 2014; 15:1142-51. [DOI: 10.1002/pmic.201400329] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/02/2014] [Accepted: 10/08/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Lei Mao
- Department of Life Science Engineering; HTW Berlin - University of Applied Sciences; Germany
| | - Jacqueline Franke
- Department of Life Science Engineering; HTW Berlin - University of Applied Sciences; Germany
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Tanca A, Palomba A, Pisanu S, Deligios M, Fraumene C, Manghina V, Pagnozzi D, Addis MF, Uzzau S. A straightforward and efficient analytical pipeline for metaproteome characterization. MICROBIOME 2014; 2:49. [PMID: 25516796 PMCID: PMC4266899 DOI: 10.1186/s40168-014-0049-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/11/2014] [Indexed: 05/27/2023]
Abstract
BACKGROUND The massive characterization of host-associated and environmental microbial communities has represented a real breakthrough in the life sciences in the last years. In this context, metaproteomics specifically enables the transition from assessing the genomic potential to actually measuring the functional expression of a microbiome. However, significant research efforts are still required to develop analysis pipelines optimized for metaproteome characterization. RESULTS This work presents an efficient analytical pipeline for shotgun metaproteomic analysis, combining bead-beating/freeze-thawing for protein extraction, filter-aided sample preparation for cleanup and digestion, and single-run liquid chromatography-tandem mass spectrometry for peptide separation and identification. The overall procedure is more time-effective and less labor-intensive when compared to state-of-the-art metaproteomic techniques. The pipeline was first evaluated using mock microbial mixtures containing different types of bacteria and yeasts, enabling the identification of up to over 15,000 non-redundant peptide sequences per run with a linear dynamic range from 10(4) to 10(8) colony-forming units. The pipeline was then applied to the mouse fecal metaproteome, leading to the overall identification of over 13,000 non-redundant microbial peptides with a false discovery rate of <1%, belonging to over 600 different microbial species and 250 functionally relevant protein families. An extensive mapping of the main microbial metabolic pathways actively functioning in the gut microbiome was also achieved. CONCLUSIONS The analytical pipeline presented here may be successfully used for the in-depth and time-effective characterization of complex microbial communities, such as the gut microbiome, and represents a useful tool for the microbiome research community.
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Affiliation(s)
- Alessandro Tanca
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Antonio Palomba
- />Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
| | - Salvatore Pisanu
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Massimo Deligios
- />Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
| | - Cristina Fraumene
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Valeria Manghina
- />Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
| | - Daniela Pagnozzi
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Maria Filippa Addis
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
| | - Sergio Uzzau
- />Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio 07041 Alghero, Italy
- />Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
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Ghisaura S, Anedda R, Pagnozzi D, Biosa G, Spada S, Bonaglini E, Cappuccinelli R, Roggio T, Uzzau S, Addis MF. Impact of three commercial feed formulations on farmed gilthead sea bream (Sparus aurata, L.) metabolism as inferred from liver and blood serum proteomics. Proteome Sci 2014; 12:44. [PMID: 25342931 PMCID: PMC4200174 DOI: 10.1186/s12953-014-0044-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/31/2014] [Indexed: 11/10/2022] Open
Abstract
Background The zootechnical performance of three different commercial feeds and their impact on liver and serum proteins of gilthead sea bream (Sparus aurata, L.) were assessed in a 12 week feeding trial. The three feeds, named A, B, and C, were subjected to lipid and protein characterization by gas chromatography (GC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. Results Feed B was higher in fish-derived lipids and proteins, while feeds C and A were higher in vegetable components, although the largest proportion of feed C proteins was represented by pig hemoglobin. According to biometric measurements, the feeds had significantly different impacts on fish growth, producing a higher average weight gain and a lower liver somatic index in feed B over feeds A and C, respectively. 2D DIGE/MS analysis of liver tissue and Ingenuity pathways analysis (IPA) highlighted differential changes in proteins involved in key metabolic pathways of liver, spanning carbohydrate, lipid, protein, and oxidative metabolism. In addition, serum proteomics revealed interesting changes in apolipoproteins, transferrin, warm temperature acclimation-related 65 kDa protein (Wap65), fibrinogen, F-type lectin, and alpha-1-antitrypsin. Conclusions This study highlights the contribution of proteomics for understanding and improving the metabolic compatibility of feeds for marine aquaculture, and opens new perspectives for its monitoring with serological tests. Electronic supplementary material The online version of this article (doi:10.1186/s12953-014-0044-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefania Ghisaura
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Roberto Anedda
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Daniela Pagnozzi
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Grazia Biosa
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Simona Spada
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Elia Bonaglini
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Roberto Cappuccinelli
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Tonina Roggio
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Sergio Uzzau
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Maria Filippa Addis
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
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