Article
Gastroenterology & Hepatology
Nicolas Nalpas, Lesley Hoyles, Viktoria Anselm, Tariq Ganief, Laura Martinez-Gili, Cristina Grau, Irina Droste-Borel, Laetitia Davidovic, Xavier Altafaj, Marc-Emmanuel Dumas, Boris Macek
Summary: Intestinal microbiota plays a crucial role in maintaining host homeostasis, and its dysregulation has been linked to various disorders. Metaproteomics analysis of fecal samples presents challenges due to sample complexity, lack of consensus in preparation methods, and the need for specialized bioinformatic analyses. Despite these challenges, comparing protein and gene abundances can provide valuable insights and highlights the importance of metaproteomics in studying complex microbiome samples.
Article
Biochemical Research Methods
Kai Cheng, Zhibin Ning, Leyuan Li, Xu Zhang, Joeselle M. Serrana, Janice Mayne, Daniel Figeys
Summary: The studies of microbial communities have become increasingly important in various fields, and metaproteomics is a powerful tool for interpreting the roles of community members. However, analyzing metaproteomic data sets at the genome resolution is still challenging. In this study, a specially designed tool called MetaLab-MAG was developed for characterizing microbiomes from metagenome-assembled genome databases.
JOURNAL OF PROTEOME RESEARCH
(2022)
Letter
Microbiology
Tim van den Bossche, Magnus O. Arntzen, Dorte Becher, Dirk Benndorf, Vincent G. H. Eijsink, Celine Henry, Pratik D. Jagtap, Nico Jehmlich, Catherine Juste, Benoit J. Kunath, Bart Mesuere, Thilo Muth, Phillip B. Pope, Jana Seifert, Alessandro Tanca, Sergio Uzzau, Paul Wilmes, Robert L. Hettich, Jean Armengaud
Summary: Metaproteomics is a crucial approach for understanding microbiome function through genomic and metabolic connections. The international metaproteomics community has launched the Metaproteomics Initiative to promote dissemination of fundamentals, advancements, and applications, while also serving as a central information hub and meeting place for collaboration in microbiome research.
Editorial Material
Multidisciplinary Sciences
Jack Leeming, Gregorio Iraola
Summary: Computational microbiologist Gregorio Iraola leads a consortium that focuses on customizing public-health interventions according to local needs.
Article
Biochemical Research Methods
Kay Schallert, Pieter Verschaffelt, Bart Mesuere, Dirk Benndorf, Lennart Martens, Tim Van den Bossche
Summary: In metaproteomics, the protein inference problem is more challenging than in single-species proteomics. To address this issue, we developed a tool called Pout2Prot, which converts Percolator output files into protein group output files that can be used with Prophane.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Microbiology
Nathanael D. Arnold, Daniel Garbe, Thomas B. Brueck
Summary: Several newly discovered chitinolytic bacteria have potential applications in crop protection, cosmetics, medical, textile, and wastewater industries. Comparative analysis suggests that these strains may belong to a novel genus and could be used for environmentally friendly N-acetylglucosamine production from crustacean shell or fungal biomass waste.
Article
Microbiology
Hannes Petruschke, Christian Schori, Sebastian Canzler, Sarah Riesbeck, Anja Poehlein, Rolf Daniel, Daniel Frei, Tina Segessemann, Johannes Zimmerman, Georgios Marinos, Christoph Kaleta, Nico Jehmlich, Christian H. Ahrens, Martin von Bergen
Summary: Researchers identified 31 novel sProteins, with two potentially having antimicrobial functions, in a simplified human intestinal microbiota model. These new proteins may have a significant impact on understanding microbial community function and organization within the microbiota.
Article
Biochemical Research Methods
Pieter Verschaffelt, Tim Van den Bossche, Lennart Martens, Peter Dawyndt, Bart Mesuere
Summary: Metaproteomics has become an important research tool for studying microbial systems, leading to increased data generation. However, tools for processing this data have not kept pace. Unipept is a widely used tool for data interpretation, but its web-based implementation has limitations on data analysis. To address this, Unipept Desktop has been introduced to increase throughput and capacity for metaproteomics data analysis.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Microbiology
Angie Mordant, Manuel Kleiner
Summary: This study evaluated methods to preserve fecal microbiome samples for metaproteomics analyses when flash-freezing is not possible. Results suggest that preservation at room temperature in RNAlater or an RNAlater-like solution performs as well as freezing for the preservation of intestinal microbiome samples before metaproteomics analyses.
MICROBIOLOGY SPECTRUM
(2021)
Article
Biochemical Research Methods
Weiliang Huang, Maureen A. Kane
Summary: Metaproteomics by mass spectrometry is a powerful method for analyzing proteins in complex samples, providing insights into the functional composition of microbiota. Human gastrointestinal microbiota plays important roles in human health, and metaproteomics reveals novel associations between microbiota and diseases. The MAPLE microbiome analysis pipeline offers a user-friendly solution for optimal proteome inference and comprehensive comparison of microbiota composition.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Microbiology
Anthony Duncan, Kerrie Barry, Chris Daum, Emiley Eloe-Fadrosh, Simon Roux, Katrin Schmidt, Susannah G. Tringe, Klaus U. Valentin, Neha Varghese, Asaf Salamov, Igor Grigoriev, Richard M. Leggett, Vincent Moulton, Thomas Mock
Summary: This study assembled 143 high-quality MAGs from chlorophyll a maximum layers in the surface of the Arctic and Atlantic Oceans. The results revealed strict demarcation between Arctic and Atlantic MAGs, but high similarity between adjacent sampling stations in each ocean. Eukaryotic MAGs were more diverse in the Arctic, while prokaryotic MAGs were more diverse in the Atlantic.
Article
Biochemistry & Molecular Biology
Daniel Walke, Kay Schallert, Prasanna Ramesh, Dirk Benndorf, Emanuel Lange, Udo Reichl, Robert Heyer
Summary: The taxonomic and functional characterization of microbial communities from diverse environments is increasingly important, with researchers using multi-omics methods to assign genes, transcripts, or proteins to biological pathways. The MPA_Pathway_Tool is a new web application that helps users create and map microbial community data onto specific pathways for better understanding of their functions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ruirui Hu, Fulin Li, Yifan Chen, Chuyang Liu, Jiawei Li, Zhongchen Ma, Yue Wang, Chaowen Cui, Chengfang Luo, Ping Zhou, Wei Ni, Qing-Yong Yang, Shengwei Hu
Summary: The Animal Meta-omics landscape database is a comprehensive and freely available resource that includes metagenomic, metatranscriptomic, and metaproteomic data from various non-human animal species. It provides abundant information on animal microbiomes and allows researchers to efficiently access and acquire cross-host microbiota information through a user-friendly interface. These resources are of great importance for exploring animal microbiota.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Laurin Christopher Gierse, Alexander Meene, Sebastian Skorka, Fabian Cuypers, Surabhi Surabhi, Borja Ferrero-Bordera, Bernd Kreikemeyer, Doerte Becher, Sven Hammerschmidt, Nikolai Siemens, Tim Urich, Katharina Riedel
Summary: Pneumonia is one of the leading causes of death worldwide. This study investigated the impact of Streptococcus pneumoniae and influenza A virus on the structure and function of the respiratory and gastrointestinal microbiomes of mice. Specific differences were identified between bacterial and viral infections using a meta-omics approach.
MICROBIOLOGY SPECTRUM
(2023)
Article
Genetics & Heredity
Valerie C. Schiml, Francesco Delogu, Praveen Kumar, Benoit Kunath, Berenice Batut, Subina Mehta, James E. Johnson, Bjoern Gruening, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin, Magnus O. Arntzen
Summary: This study presents three integrative meta-omics workflows developed in Galaxy for enhanced analysis and integration of metagenomics, metatranscriptomics, and metaproteomics, combined with a newly developed web-application ViMO to analyze metabolisms in complex microbial communities. The workflows were applied on a cellulose-degrading consortium to analyze the roles of uncultured microorganisms in biomass degradation processes. The workflows allowed for reconstruction of metagenome-assembled genomes (MAGs) and analysis of the functional potential of the microbiome using metatranscriptomics and metaproteomics.
ENVIRONMENTAL MICROBIOME
(2023)
Article
Biochemical Research Methods
Clement Lozano, Lucia Grenga, Fabrice Gallais, Guylaine Miotello, Laurent Bellanger, Jean Armengaud
Summary: The recent outbreak of monkeypox in non-endemic countries has led to the urgent need for expanded surveillance and understanding of its origin and spread. This study presents experimental data on the proteome of the monkeypox virus, using state-of-the-art shotgun proteomics techniques. The findings highlight potential candidate markers for virus detection and could contribute to the development of mass spectrometry-based tests.
Article
Microbiology
Jean Armengaud
Summary: Microbial communities have attracted much attention due to their roles and numerous applications in the medical, environmental, and biotechnological fields. However, studying these communities is challenging due to their diversity and complexity. Metaproteomics, a method based on protein identification and quantification, is gaining momentum in microbiome and holobiont research, and holds great potential in providing a comprehensive understanding of microbial communities.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Benjamin A. R. N. Durand, Catherine Dunyach-Remy, Oumayma El Kaddouri, Riham Daher, Jean-Philippe Lavigne, Jean Armengaud, Lucia Grenga
Summary: This study investigates the production and secretion of bacterial virulence interacting proteins in Helcococcus kunzii, a skin commensal bacterium found in chronic wounds. The cellular proteome and exoproteome of H. kunzii were analyzed, revealing differences between growth stages and discussing metabolic variations. This research provides important insights for understanding this opportunistic pathogen and developing innovative wound management approaches.
PROTEOMICS CLINICAL APPLICATIONS
(2023)
Article
Environmental Sciences
Jennifer Laurent, Iwan Le Berre, Jean Armengaud, Senthilkumar Kailasam, Jerome Couteau, Matthieu Waeles, Jean Laroche, Vianney Pichereau
Summary: This study aimed to develop a multidisciplinary approach to assess the ecological status of six moderate-sized French estuaries. By gathering geographical information, hydrobiological data, chemistry of pollutants, and fish biology, including integration of proteomics and transcriptomics data, the researchers were able to characterize and identify the main stressors impacting each estuary's hydrological system.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Immunology
Melanie Gonzales, Laure Plener, Jean Armengaud, Nicholas Armstrong, Eric Chabriere, David Daude
Summary: This study demonstrates the importance of Quorum sensing in Burkholderia thailandensis using an enzyme-based quorum quenching strategy. The disruption of quorum sensing greatly affects bacterial behavior, including motility, proteolytic activity, and antimicrobial molecule production. Furthermore, the study shows that quorum sensing disruption significantly enhances the bactericidal activity against fungi and yeast. These findings are of prime interest for understanding the virulence of Burkholderia species and developing alternative treatments.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Editorial Material
Microbiology
Rosa Maria Martinez-Espinosa, Jean Armengaud, Sabine Matallana-Surget, Alfonso Olaya-Abril
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Olivier Pible, Pauline Petit, Gerard Steinmetz, Corinne Rivasseau, Jean Armengaud
Summary: Sampling small amounts of biofilm from harsh environments such as the biofilm present on the walls of a radioactive material storage pool offers limited analytical options for taxonomic characterization and estimation of biomass contributions. This study proposes a tandem-mass spectrometry proteotyping approach that transforms peptide sequence information into useful taxonomical information to determine biomass contributions at different taxonomical ranks. This new methodology is applied for the first time to analyze the composition of biofilms from minute quantities of material collected from a pool used to store radioactive sources in a nuclear facility.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Neurosciences
Aloise Mabondzo, Rania Harati, Lea Broca-Brisson, Anne-Cecile Guyot, Narciso Costa, Francesco Cacciante, Elena Putignano, Laura Baroncelli, Matthew R. Skelton, Cathy Saab, Emmanuelle Martini, Henri Benech, Thomas Joudinaud, Jean-Charles Gaillard, Jean Armengaud, Rifat Hamoudi
Summary: Creatine transporter deficiency (CTD) is a genetic disorder that impairs the uptake of creatine into the brain, leading to intellectual disability. This study investigated the therapeutic potential of dodecyl creatine ester (DCE) in a mouse model of CTD and identified biomarkers associated with cognitive improvement. The findings shed light on the pathogenesis of CTD and provide insights for potential treatments.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2023)
Article
Chemistry, Analytical
Madisson Chabas, Olivier Pible, Jean Armengaud, Beatrice Alpha-Bazin
Summary: To accurately and rapidly identify microorganisms from complex microbiota for clinical diagnostic purposes, an innovative label-free multiplexing method for the identification of microorganisms using tandem mass spectrometry is proposed in this paper. The method involves offline reversed-phase fractionation of individual peptidomes and achieves multiplexing by mixing fractions of staged hydrophobicity. This approach enables the identification of up to 21 microorganisms in a single 60-minute run without the use of labeling reagents, providing new perspectives for high-throughput proteotyping of bacteria in large culturomics projects.
ANALYTICAL CHEMISTRY
(2023)
Article
Biology
Clement Car, Andre Gilles, Elen Goujon, Marie-Laure Delignette Muller, Luc Camoin, Sandrine Frelon, Pablo Burraco, Samuel Granjeaud, Emilie Baudelet, Stephane Audebert, German Orizaola, Jean Armengaud, Arthur Tenenhaus, Imene Garali, Jean-Marc Bonzom, Olivier Armant
Summary: By analyzing the radar observation data from the Urumqi Satellite Receiving Station, researchers have found that the mass balance of the Yabulangsha Glacier has undergone significant changes over time. The results of the study indicate a trend of increasing mass balance of the glacier, which may be attributed to factors such as increased precipitation and decreased temperature.
Article
Environmental Sciences
Maxime Lepretre, Arnaud Chaumot, Rayan Aboud, Nicolas Delorme, Anabelle Espeyte, Arnaud Salvador, Sophie Ayciriex, Jean Armengaud, Marina Coquery, Olivier Geffard, Davide Degli-Esposti
Summary: Mass spectrometry in multiple reaction monitoring (MRM) mode enables selective and multiplexed quantification of peptides derived from proteins. This study evaluates the feasibility of using dynamic MRM (dMRM) tools to investigate proteomes in sentinel species and demonstrates their potential for discovering new protein biomarkers. A dMRM assay was developed to capture the functional proteome of a freshwater crustacean and assess the effects of metal exposure. Metal-specific signatures were identified as potential biomarkers for tracking metal levels in freshwater ecosystems. This study highlights the potential of dMRM for identifying and developing biomarkers in sentinel species.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Clement Baratange, Hugo Baali, Veronique Gaillet, Isabelle Bonnard, Laurence Delahaut, Jean-Charles Gaillard, Dominique Grandjean, Stephanie Sayen, Andrea Gallorini, Nathalie Le Bris, David Renault, Florian Breider, Jean-Luc Loizeau, Jean Armengaud, Claudia Cosio
Summary: Dreissena polymorpha is a bivalve species with potential for biomonitoring in freshwater ecosystems due to its abundance and high filtration activity. This study aimed to investigate the molecular responses of D. polymorpha to stress caused by carbamazepine (CBZ) and mercury (Hg) individually and in combination. The results showed that the co-exposure of CBZ and Hg caused more alterations in the bivalve compared to single exposures. Specifically, neurotransmission-related proteins and metabolites were modulated by the co-exposure, while calcium signaling pathways and amino acids were specifically affected by CBZ, and cytoskeleton remodeling and hypoxia-induced factor 1 pathway were specifically affected by Hg. The study highlighted the importance of characterizing the molecular toxicity pathways of multi-contamination to improve risk assessment and anticipate adverse effects in biota.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Jean-Lou Reyre, Sacha Grisel, Mireille Haon, Ruite Xiang, Jean-Charles Gaillard, Jean Armengaud, Victor Guallar, Antoine Margeot, Simon Arragain, Jean-Guy Berrin, Bastien Bissaro
Summary: Lytic polysaccharide monooxygenases (LPMOs) are enzymes that promote the conversion of biopolymers such as cellulose and chitin in Nature. The functional relevance of the multiple LPMO-encoding genes in Polyporales fungi remains unclear. This study characterized six AA9-X282s, which are AA9 proteins with unique features, and found that they have weak binding properties to cellulose and low cellulolytic oxidative activity. The presence of phosphorylated residues, including a conserved residue near the copper site, and a glycine-rich C-terminal extension with potential phosphate-binding properties were also identified. These findings question the involvement of these AA9 proteins in plant cell wall degradation and provide new insights into their functional divergence.
SCIENTIFIC REPORTS
(2023)
Meeting Abstract
Orthopedics
A. Defois, N. Bon, A. Charpentier, M. Georget, F. Blanchard, A. Hamel, D. Waast, J. Armengaud, O. Renoult, C. Pecqueur, Y. Maugars, M. -A. Boutet, J. Guicheux, C. Vinatier
OSTEOARTHRITIS AND CARTILAGE
(2023)
Article
Biochemical Research Methods
Imed Dorbani, Jean Armengaud, Frederic Carlin, Catherine Duport
Summary: This study compared the spore proteomes of Bacillus atrophaeus and Bacillus pumilus using a shotgun proteomic approach. It identified several differentially expressed proteins and provided a molecular signature to elucidate the resistance differences between the two strains.