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Zhao Z, Amano C, Reinthaler T, Baltar F, Orellana MV, Herndl GJ. Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean. Nat Commun 2024; 15:6411. [PMID: 39080340 PMCID: PMC11289388 DOI: 10.1038/s41467-024-50867-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 07/24/2024] [Indexed: 08/02/2024] Open
Abstract
Proteins in the open ocean represent a significant source of organic matter, and their profiles reflect the metabolic activities of marine microorganisms. Here, by analyzing metaproteomic samples collected from the Pacific, Atlantic and Southern Ocean, we reveal size-fractionated patterns of the structure and function of the marine microbiota protein pool in the water column, particularly in the dark ocean (>200 m). Zooplankton proteins contributed three times more than algal proteins to the deep-sea community metaproteome. Gammaproteobacteria exhibited high metabolic activity in the deep-sea, contributing up to 30% of bacterial proteins. Close virus-host interactions of this taxon might explain the dominance of gammaproteobacterial proteins in the dissolved fraction. A high urease expression in nitrifiers suggested links between their dark carbon fixation and zooplankton urea production. In summary, our results uncover the taxonomic contribution of the microbiota to the oceanic protein pool, revealing protein fluxes from particles to the dissolved organic matter pool.
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Affiliation(s)
- Zihao Zhao
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria.
| | - Chie Amano
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Mónica V Orellana
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria.
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands.
- Environmental & Climate Research Hub, University of Vienna, Vienna, Austria.
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2
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Sampara P, Lawson CE, Scarborough MJ, Ziels RM. Advancing environmental biotechnology with microbial community modeling rooted in functional 'omics. Curr Opin Biotechnol 2024; 88:103165. [PMID: 39033648 DOI: 10.1016/j.copbio.2024.103165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/21/2024] [Accepted: 06/04/2024] [Indexed: 07/23/2024]
Abstract
Emerging biotechnologies that solve pressing environmental and climate emergencies will require harnessing the vast functional diversity of the underlying microbiomes driving such engineered processes. Modeling is a critical aspect of process engineering that informs system design as well as aids diagnostic optimization of performance. 'Conventional' bioprocess models assume homogenous biomass within functional guilds and thus fail to predict emergent properties of diverse microbial physiologies, such as product specificity and community interactions. Yet, recent advances in functional 'omics-based approaches can provide a 'lens' through which we can probe and measure in situ ecophysiologies of environmental microbiomes. Here, we overview microbial community modeling approaches that incorporate functional 'omics data, which we posit can advance our ability to design and control new environmental biotechnologies going forward.
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Affiliation(s)
- Pranav Sampara
- Department of Civil Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher E Lawson
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Matthew J Scarborough
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Ryan M Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, British Columbia, Canada.
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3
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Manoil D, Parga A, Bostanci N, Belibasakis GN. Microbial diagnostics in periodontal diseases. Periodontol 2000 2024. [PMID: 38797888 DOI: 10.1111/prd.12571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 05/29/2024]
Abstract
Microbial analytical methods have been instrumental in elucidating the complex microbial etiology of periodontal diseases, by shaping our understanding of subgingival community dynamics. Certain pathobionts can orchestrate the establishment of dysbiotic communities that can subvert the host immune system, triggering inflammation and tissue destruction. Yet, diagnosis and management of periodontal conditions still rely on clinical and radiographic examinations, overlooking the well-established microbial etiology. This review summarizes the chronological emergence of periodontal etiological models and the co-evolution with technological advances in microbial detection. We additionally review the microbial analytical approaches currently accessible to clinicians, highlighting their value in broadening the periodontal assessment. The epidemiological importance of obtaining culture-based antimicrobial susceptibility profiles of periodontal taxa for antibiotic resistance surveillance is also underscored, together with clinically relevant analytical approaches to guide antibiotherapy choices, when necessary. Furthermore, the importance of 16S-based community and shotgun metagenomic profiling is discussed in outlining dysbiotic microbial signatures. Because dysbiosis precedes periodontal damage, biomarker identification offers early diagnostic possibilities to forestall disease relapses during maintenance. Altogether, this review highlights the underutilized potential of clinical microbiology in periodontology, spotlighting the clinical areas most conductive to its diagnostic implementation for enhancing prevention, treatment predictability, and addressing global antibiotic resistance.
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Affiliation(s)
- Daniel Manoil
- Division of Cariology and Endodontics, University Clinics of Dental Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Ana Parga
- Division of Cariology and Endodontics, University Clinics of Dental Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Nagihan Bostanci
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Georgios N Belibasakis
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
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4
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Sheriff EK, Salvato F, Andersen SE, Chatterjee A, Kleiner M, Duerkop BA. Enterococcal quorum-controlled protease alters phage infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593607. [PMID: 38766208 PMCID: PMC11100838 DOI: 10.1101/2024.05.10.593607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Increased prevalence of multidrug resistant bacterial infections has sparked interest in alternative antimicrobials, including bacteriophages (phages). Limited understanding of the phage infection process hampers our ability to utilize phages to their full therapeutic potential. To understand phage infection dynamics we performed proteomics on Enterococcus faecalis infected with the phage VPE25. We discovered numerous uncharacterized phage proteins are produced during phage infection of Enterococcus faecalis. Additionally, we identified hundreds of changes in bacterial protein abundances during infection. One such protein, enterococcal gelatinase (GelE), an fsr quorum sensing regulated protease involved in biofilm formation and virulence, was reduced during VPE25 infection. Plaque assays showed that mutation of either the fsrA or gelE resulted in plaques with a "halo" morphology and significantly larger diameters, suggesting decreased protection from phage infection. GelE-associated protection during phage infection is dependent on the murein hydrolase regulator LrgA and antiholin-like protein LrgB, whose expression have been shown to be regulated by GelE. Our work may be leveraged in the development of phage therapies that can modulate the production of GelE thereby altering biofilm formation and decreasing E. faecalis virulence.
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Affiliation(s)
- Emma K. Sheriff
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Fernanda Salvato
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
| | - Shelby E. Andersen
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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5
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Sun Z, Ning Z, Figeys D. The Landscape and Perspectives of the Human Gut Metaproteomics. Mol Cell Proteomics 2024; 23:100763. [PMID: 38608842 PMCID: PMC11098955 DOI: 10.1016/j.mcpro.2024.100763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/26/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024] Open
Abstract
The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics. In this article, we present the current landscape of human gut metaproteomics studies by re-analyzing the identification results from 15 published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.
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Affiliation(s)
- Zhongzhi Sun
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Zhibin Ning
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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6
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Petrone BL, Bartlett A, Jiang S, Korenek A, Vintila S, Tenekjian C, Yancy WS, David LA, Kleiner M. Metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588275. [PMID: 38645092 PMCID: PMC11030321 DOI: 10.1101/2024.04.09.588275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Objective biomarkers of food intake are a sought-after goal in nutrition research. Most biomarker development to date has focused on metabolites detected in blood, urine, skin or hair, but detection of consumed foods in stool has also been shown to be possible via DNA sequencing. An additional food macromolecule in stool that harbors sequence information is protein. However, the use of protein as an intake biomarker has only been explored to a very limited extent. Here, we evaluate and compare measurement of residual food-derived DNA and protein in stool as potential biomarkers of intake. We performed a pilot study of DNA sequencing-based metabarcoding (FoodSeq) and mass spectrometry-based metaproteomics in five individuals' stool sampled in short, longitudinal bursts accompanied by detailed diet records (n=27 total samples). Dietary data provided by stool DNA, stool protein, and written diet record independently identified a strong within-person dietary signature, identified similar food taxa, and had significantly similar global structure in two of the three pairwise comparisons between measurement techniques (DNA-to-protein and DNA-to-diet record). Metaproteomics identified proteins including myosin, ovalbumin, and beta-lactoglobulin that differentiated food tissue types like beef from dairy and chicken from egg, distinctions that were not possible by DNA alone. Overall, our results lay the groundwork for development of targeted metaproteomic assays for dietary assessment and demonstrate that diverse molecular components of food can be leveraged to study food intake using stool samples.
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Affiliation(s)
- Brianna L Petrone
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
- Medical Scientist Training Program, Duke University School of Medicine, Durham, NC, United States
| | - Alexandria Bartlett
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Abigail Korenek
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | | | - William S Yancy
- Duke Lifestyle and Weight Management Center, Durham, NC, United States
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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7
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Wu E, Mallawaarachchi V, Zhao J, Yang Y, Liu H, Wang X, Shen C, Lin Y, Qiao L. Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics. MICROBIOME 2024; 12:58. [PMID: 38504332 PMCID: PMC10949615 DOI: 10.1186/s40168-024-01775-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/05/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Microbiota are closely associated with human health and disease. Metaproteomics can provide a direct means to identify microbial proteins in microbiota for compositional and functional characterization. However, in-depth and accurate metaproteomics is still limited due to the extreme complexity and high diversity of microbiota samples. It is generally recommended to use metagenomic data from the same samples to construct the protein sequence database for metaproteomic data analysis. Although different metagenomics-based database construction strategies have been developed, an optimization of gene taxonomic annotation has not been reported, which, however, is extremely important for accurate metaproteomic analysis. RESULTS Herein, we proposed an accurate taxonomic annotation pipeline for genes from metagenomic data, namely contigs directed gene annotation (ConDiGA), and used the method to build a protein sequence database for metaproteomic analysis. We compared our pipeline (ConDiGA or MD3) with two other popular annotation pipelines (MD1 and MD2). In MD1, genes were directly annotated against the whole bacterial genome database; in MD2, contigs were annotated against the whole bacterial genome database and the taxonomic information of contigs was assigned to the genes; in MD3, the most confident species from the contigs annotation results were taken as reference to annotate genes. Annotation tools, including BLAST, Kaiju, and Kraken2, were compared. Based on a synthetic microbial community of 12 species, it was found that Kaiju with the MD3 pipeline outperformed the others in the construction of protein sequence database from metagenomic data. Similar performance was also observed with a fecal sample, as well as in silico mixed datasets of the simulated microbial community and the fecal sample. CONCLUSIONS Overall, we developed an optimized pipeline for gene taxonomic annotation to construct protein sequence databases. Our study can tackle the current taxonomic annotation reliability problem in metagenomics-derived protein sequence database and can promote the in-depth metaproteomic analysis of microbiome. The unique metagenomic and metaproteomic datasets of the 12 bacterial species are publicly available as a standard benchmarking sample for evaluating various analysis pipelines. The code of ConDiGA is open access at GitHub for the analysis of microbiota samples. Video Abstract.
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Affiliation(s)
- Enhui Wu
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China
| | - Vijini Mallawaarachchi
- School of Computing, College of Engineering, Computing and Cybernetics, The Australian National University, Canberra, ACT, 2600, Australia
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Jinzhi Zhao
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China
| | - Yi Yang
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China
| | - Hebin Liu
- Shanghai Omicsolution Co., Ltd, Shanghai, 200000, China
| | - Xiaoqing Wang
- Shanghai Omicsolution Co., Ltd, Shanghai, 200000, China
| | - Chengpin Shen
- Shanghai Omicsolution Co., Ltd, Shanghai, 200000, China
| | - Yu Lin
- School of Computing, College of Engineering, Computing and Cybernetics, The Australian National University, Canberra, ACT, 2600, Australia
| | - Liang Qiao
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China.
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8
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Ravi Kumar R, Ndiaye MM, Haddad I, Vinh J, Verdier Y. ChipFilter: Microfluidic-Based Comprehensive Sample Preparation Methodology for Microbial Consortia. J Proteome Res 2024; 23:869-880. [PMID: 38353246 PMCID: PMC10913871 DOI: 10.1021/acs.jproteome.3c00288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 01/04/2024] [Accepted: 01/19/2024] [Indexed: 03/02/2024]
Abstract
The metaproteomic approach is an attractive way to describe a microbiome at the functional level, allowing the identification and quantification of proteins across a broad dynamic range as well as the detection of post-translational modifications. However, it remains relatively underutilized, mainly due to technical challenges that should be addressed, including the complexity of extracting proteins from heterogeneous microbial communities. Here, we show that a ChipFilter microfluidic device coupled to a liquid chromatography tandem mass spectrometry (LC-MS/MS) setup can be successfully used for the identification of microbial proteins. Using cultures of Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae, we have shown that it is possible to directly lyse the cells and digest the proteins in the ChipFilter to allow the identification of a higher number of proteins and peptides than that by standard protocols, even at low cell density. The peptides produced are overall longer after ChipFilter digestion but show no change in their degree of hydrophobicity. Analysis of a more complex mixture of 17 species from the gut microbiome showed that the ChipFilter preparation was able to identify and estimate the amounts of 16 of these species. These results show that ChipFilter can be used for the proteomic study of microbiomes, particularly in the case of a low volume or cell density. The mass spectrometry data have been deposited on the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD039581.
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Affiliation(s)
- Ranjith
Kumar Ravi Kumar
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Massamba Mbacke Ndiaye
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Iman Haddad
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Joelle Vinh
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Yann Verdier
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
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9
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Shi M, Evans CA, McQuillan JL, Noirel J, Pandhal J. LFQRatio: A Normalization Method to Decipher Quantitative Proteome Changes in Microbial Coculture Systems. J Proteome Res 2024; 23:999-1013. [PMID: 38354288 PMCID: PMC10913063 DOI: 10.1021/acs.jproteome.3c00714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The value of synthetic microbial communities in biotechnology is gaining traction due to their ability to undertake more complex metabolic tasks than monocultures. However, a thorough understanding of strain interactions, productivity, and stability is often required to optimize growth and scale up cultivation. Quantitative proteomics can provide valuable insights into how microbial strains adapt to changing conditions in biomanufacturing. However, current workflows and methodologies are not suitable for simple artificial coculture systems where strain ratios are dynamic. Here, we established a workflow for coculture proteomics using an exemplar system containing two members, Azotobacter vinelandii and Synechococcus elongatus. Factors affecting the quantitative accuracy of coculture proteomics were investigated, including peptide physicochemical characteristics such as molecular weight, isoelectric point, hydrophobicity, and dynamic range as well as factors relating to protein identification such as varying proteome size and shared peptides between species. Different quantification methods based on spectral counts and intensity were evaluated at the protein and cell level. We propose a new normalization method, named "LFQRatio", to reflect the relative contributions of two distinct cell types emerging from cell ratio changes during cocultivation. LFQRatio can be applied to real coculture proteomics experiments, providing accurate insights into quantitative proteome changes in each strain.
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Affiliation(s)
- Mengxun Shi
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
| | - Caroline A Evans
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
| | - Josie L McQuillan
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
| | - Josselin Noirel
- GBCM Laboratory (EA7528), Conservatoire National des Arts et Métiers, HESAM Université, 2 rue Conté, Paris 75003, France
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
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10
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Owens LA, Friant S, Martorelli Di Genova B, Knoll LJ, Contreras M, Noya-Alarcon O, Dominguez-Bello MG, Goldberg TL. VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages. Nat Commun 2024; 15:402. [PMID: 38195557 PMCID: PMC10776621 DOI: 10.1038/s41467-023-44521-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Protocols for characterizing taxonomic assemblages by deep sequencing of short DNA barcode regions (metabarcoding) have revolutionized our understanding of microbial communities and are standardized for bacteria, archaea, and fungi. Unfortunately, comparable methods for host-associated eukaryotes have lagged due to technical challenges. Despite 54 published studies, issues remain with primer complementarity, off-target amplification, and lack of external validation. Here, we present VESPA (Vertebrate Eukaryotic endoSymbiont and Parasite Analysis) primers and optimized metabarcoding protocol for host-associated eukaryotic community analysis. Using in silico prediction, panel PCR, engineered mock community standards, and clinical samples, we demonstrate VESPA to be more effective at resolving host-associated eukaryotic assemblages than previously published methods and to minimize off-target amplification. When applied to human and non-human primate samples, VESPA enables reconstruction of host-associated eukaryotic endosymbiont communities more accurately and at finer taxonomic resolution than microscopy. VESPA has the potential to advance basic and translational science on vertebrate eukaryotic endosymbiont communities, similar to achievements made for bacterial, archaeal, and fungal microbiomes.
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Affiliation(s)
- Leah A Owens
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
| | - Sagan Friant
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Bruno Martorelli Di Genova
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, The University of Vermont, Burlington, VT, USA
| | - Laura J Knoll
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Monica Contreras
- Center for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, Venezuela
| | - Oscar Noya-Alarcon
- Centro Amazónico de Investigación y Control de Enfermedades Tropicales-CAICET, Puerto Ayacucho, Amazonas, Venezuela
| | - Maria G Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University-New Brunswick, New Brunswick, NJ, USA
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA
- Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA
- Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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11
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Roothans N, Gabriëls M, Abeel T, Pabst M, van Loosdrecht MCM, Laureni M. Aerobic denitrification as an N2O source from microbial communities. THE ISME JOURNAL 2024; 18:wrae116. [PMID: 38913498 PMCID: PMC11272060 DOI: 10.1093/ismejo/wrae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/26/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and heterotrophic denitrification, respectively. Beyond this established dichotomy, we quantitatively show that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed to frequent oxic/anoxic transitions. Two planktonic, nitrification-inhibited enrichment cultures were established under continuous organic carbon and nitrate feeding, and cyclic oxygen availability. Over a third of the influent organic substrate was respired with nitrate as electron acceptor at high oxygen concentrations (>6.5 mg/L). N2O accounted for up to one-quarter of the nitrate reduced under oxic conditions. The enriched microorganisms maintained a constitutive abundance of denitrifying enzymes due to the oxic/anoxic frequencies exceeding their protein turnover-a common scenario in natural and engineered ecosystems. The aerobic denitrification rates are ascribed primarily to the residual activity of anaerobically synthesised enzymes. From an ecological perspective, the selection of organisms capable of sustaining significant denitrifying activity during aeration shows their competitive advantage over other heterotrophs under varying oxygen availabilities. Ultimately, we propose that the contribution of heterotrophic denitrification to aerobic nitrogen turnover and N2O emissions is currently underestimated in dynamic environments.
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Affiliation(s)
- Nina Roothans
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Minke Gabriëls
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, van Mourik Broekmanweg 6, Delft 2628 XE, the Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, United States
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Michele Laureni
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
- Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
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12
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Salvato F, Kleiner M. A Complete Metaproteomic Workflow for Arabidopsis Roots Inoculated by Synthetic Bacteria. Methods Mol Biol 2024; 2820:57-65. [PMID: 38941015 DOI: 10.1007/978-1-0716-3910-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Root metaproteome analysis can reveal the functions that govern plant-microbe and microbe-microbe interactions under specific environmental conditions. Efficient protein extraction method from microbes associated with plant roots is crucial for the comprehensive analysis of the metaproteome. In this chapter, a straightforward protein extraction method for roots of Arabidopsis inoculated with a microbial community that uses only milligrams of tissue is outlined. In addition, the plant inoculation using a synthetic community (SynCom) and the methods for a nanoflow liquid chromatography coupled to a high-resolution/high-accuracy mass spectrometer (LC-MS/MS) are described.
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Affiliation(s)
- Fernanda Salvato
- North Carolina State University, Plant and Microbial Biology Department, Raleigh, NC, USA
- Thermo Fisher Scientific, San Jose, CA, USA
| | - Manuel Kleiner
- North Carolina State University, Plant and Microbial Biology Department, Raleigh, NC, USA
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13
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Ratinskaia L, Malavin S, Zvi-Kedem T, Vintila S, Kleiner M, Rubin-Blum M. Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani have the genetic potential to fix nitrogen. ISME COMMUNICATIONS 2024; 4:ycae076. [PMID: 38873029 PMCID: PMC11171427 DOI: 10.1093/ismeco/ycae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/06/2024] [Accepted: 05/31/2024] [Indexed: 06/15/2024]
Abstract
Lucinid clams are one of the most diverse and widespread symbiont-bearing animal groups in both shallow and deep-sea chemosynthetic habitats. Lucinids harbor Ca. Thiodiazotropha symbionts that can oxidize inorganic and organic substrates such as hydrogen sulfide and formate to gain energy. The interplay between these key metabolic functions, nutrient uptake and biotic interactions in Ca. Thiodiazotropha is not fully understood. We collected Lucinoma kazani individuals from next to a deep-sea brine pool in the eastern Mediterranean Sea, at a depth of 1150 m and used Oxford Nanopore and Illumina sequencing to obtain high-quality genomes of their Ca. Thiodiazotropha gloverae symbiont. The genomes served as the basis for transcriptomic and proteomic analyses to characterize the in situ gene expression, metabolism and physiology of the symbionts. We found genes needed for N2 fixation in the deep-sea symbiont's genome, which, to date, were only found in shallow-water Ca. Thiodiazotropha. However, we did not detect the expression of these genes and thus the potential role of nitrogen fixation in this symbiosis remains to be determined. We also found the high expression of carbon fixation and sulfur oxidation genes, which indicate chemolithoautotrophy as the key physiology of Ca. Thiodiazotropha. However, we also detected the expression of pathways for using methanol and formate as energy sources. Our findings highlight the key traits these microbes maintain to support the nutrition of their hosts and interact with them.
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Affiliation(s)
- Lina Ratinskaia
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa 3108000Israel
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838Israel
| | - Stas Malavin
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa 3108000Israel
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker 8499000, Israel
| | - Tal Zvi-Kedem
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa 3108000Israel
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838Israel
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, United States
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, United States
| | - Maxim Rubin-Blum
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa 3108000Israel
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838Israel
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14
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Sasi R, Suchithra TV. Wastewater microbial diversity versus molecular analysis at a glance: a mini-review. Braz J Microbiol 2023; 54:3033-3039. [PMID: 37723328 PMCID: PMC10689596 DOI: 10.1007/s42770-023-01130-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/10/2023] [Indexed: 09/20/2023] Open
Abstract
Microorganisms play a vital role in biological wastewater treatment by converting organic and toxic materials into harmless substances. Understanding microbial communities' structure, taxonomy, phylogeny, and metabolic activities is essential to improve these processes. Molecular microbial ecology employs molecular techniques to study community profiles and phylogenetic information since culture-dependent approaches have limitations in providing a comprehensive understanding of microbial diversity in a system. Genomic advancements such as DNA hybridization, microarray analysis, sequencing, and reverse sample genome probing have enabled the detailed characterization of microbial communities in wastewater treatment facilities. This mini-review summarizes the current state of knowledge on the diversity of microorganisms in wastewater treatment plants, emphasizing critical microbial processes such as nitrogen and phosphorus removal.
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Affiliation(s)
- R Sasi
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, Kerala, India, 673601
| | - T V Suchithra
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, Kerala, India, 673601.
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15
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Abbondio M, Tanca A, De Diego L, Sau R, Bibbò S, Pes GM, Dore MP, Uzzau S. Metaproteomic assessment of gut microbial and host functional perturbations in Helicobacter pylori-infected patients subjected to an antimicrobial protocol. Gut Microbes 2023; 15:2291170. [PMID: 38063474 PMCID: PMC10730194 DOI: 10.1080/19490976.2023.2291170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
The impact of therapeutic interventions on the human gut microbiota (GM) is a clinical issue of paramount interest given the strong interconnection between microbial dynamics and human health. Orally administered antibiotics are known to reduce GM biomass and modify GM taxonomic profile. However, the impact of antimicrobial therapies on GM functions and biochemical pathways has scarcely been studied. Here, we characterized the fecal metaproteome of 10 Helicobacter pylori-infected patients before (T0) and after 10 days (T1) of a successful quadruple therapy (bismuth, tetracycline, metronidazole, and rabeprazole) and 30 days after therapy cessation (T2), to investigate how GM and host functions change during the eradication and healing processes. At T1, the abundance ratio between microbial and host proteins was reversed compared with that at T0 and T2. Several pathobionts (including Klebsiella, Proteus, Enterococcus, Muribaculum, and Enterocloster) were increased at T1. Therapy reshaped the relative contributions of the functions required to produce acetate, propionate, and butyrate. Proteins related to the uptake and processing of complex glycans were increased. Microbial cross-feeding with sialic acid, fucose, and rhamnose was enhanced, whereas hydrogen sulfide production was reduced. Finally, microbial proteins involved in antibiotic resistance and inflammation were more abundant after therapy. Moreover, a reduction in host proteins with known roles in inflammation and H. pylori-mediated carcinogenesis was observed. In conclusion, our results support the use of metaproteomics to monitor drug-induced remodeling of GM and host functions, opening the way for investigating new antimicrobial therapies aimed at preserving gut environmental homeostasis.
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Affiliation(s)
- Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Laura De Diego
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Rosangela Sau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Stefano Bibbò
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Giovanni Mario Pes
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Maria Pina Dore
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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16
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Zorz J, Paquette AJ, Gillis T, Kouris A, Khot V, Demirkaya C, De La Hoz Siegler H, Strous M, Vadlamani A. Coordinated proteome change precedes cell lysis and death in a mat-forming cyanobacterium. THE ISME JOURNAL 2023; 17:2403-2414. [PMID: 37914776 PMCID: PMC10689466 DOI: 10.1038/s41396-023-01545-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
Cyanobacteria form dense multicellular communities that experience transient conditions in terms of access to light and oxygen. These systems are productive but also undergo substantial biomass turnover through cell death, supplementing heightened heterotrophic respiration. Here we use metagenomics and metaproteomics to survey the molecular response of a mat-forming cyanobacterium undergoing mass cell lysis after exposure to dark and anoxic conditions. A lack of evidence for viral, bacterial, or eukaryotic antagonism contradicts commonly held beliefs on the causative agent for cyanobacterial death during dense growth. Instead, proteogenomics data indicated that lysis likely resulted from a genetically programmed response triggered by a failure to maintain osmotic pressure in the wake of severe energy limitation. Cyanobacterial DNA was rapidly degraded, yet cyanobacterial proteins remained abundant. A subset of proteins, including enzymes involved in amino acid metabolism, peptidases, toxin-antitoxin systems, and a potentially self-targeting CRISPR-Cas system, were upregulated upon lysis, indicating possible involvement in the programmed cell death response. We propose this natural form of cell death could provide new pathways for controlling harmful algal blooms and for sustainable bioproduct production.
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Affiliation(s)
- Jackie Zorz
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada.
| | - Alexandre J Paquette
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Timber Gillis
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Angela Kouris
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
- Synergia Biotech Inc., Calgary, AB, Canada
| | - Varada Khot
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Cigdem Demirkaya
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, AB, Canada
| | | | - Marc Strous
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Agasteswar Vadlamani
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
- Synergia Biotech Inc., Calgary, AB, Canada
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17
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Timofeeva AM, Galyamova MR, Sedykh SE. Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production. Microorganisms 2023; 11:2864. [PMID: 38138008 PMCID: PMC10745983 DOI: 10.3390/microorganisms11122864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia are believed to be the most promising form of these bacteria. However, designing and modeling bacterial consortia to achieve desired phenotypic outcomes in plants is challenging. This review aims to address this challenge by exploring key antimicrobial interactions. Special attention is given to approaches for developing soil plant growth-promoting bacteria consortia. Additionally, advanced omics-based methods are analyzed that allow soil microbiomes to be characterized, providing an understanding of the molecular and functional aspects of these microbial communities. A comprehensive discussion explores the utilization of bacterial preparations in biofertilizers for agricultural applications, focusing on the intricate design of synthetic bacterial consortia with these preparations. Overall, the review provides valuable insights and strategies for intentionally designing bacterial consortia to enhance plant growth and development.
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Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Maria R. Galyamova
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
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18
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Creskey M, Li L, Ning Z, Fekete EE, Mayne J, Walker K, Ampaw A, Ben R, Zhang X, Figeys D. An economic and robust TMT labeling approach for high throughput proteomic and metaproteomic analysis. Proteomics 2023; 23:e2200116. [PMID: 36528842 DOI: 10.1002/pmic.202200116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Multiplexed quantitative proteomics using tandem mass tag (TMT) is increasingly used in -omic study of complex samples. While TMT-based proteomics has the advantages of the higher quantitative accuracy, fewer missing values, and reduced instrument analysis time, it is limited by the additional reagent cost. In addition, current TMT labeling workflows involve repeated small volume pipetting of reagents in volatile solvents, which may increase the sample-to-sample variations and is not readily suitable for high throughput applications. In this study, we demonstrated that the TMT labeling procedures could be streamlined by using pre-aliquoted dry TMT reagents in a 96 well plate or 12-tube strip. As little as 50 μg dry TMT per channel was used to label 6-12 μg peptides, yielding high TMT labeling efficiency (∼99%) in both microbiome and mammalian cell line samples. We applied this workflow to analyze 97 samples in a study to evaluate whether ice recrystallization inhibitors improve the cultivability and activity of frozen microbiota. The results demonstrated tight sample clustering corresponding to groups and consistent microbiome responses to prebiotic treatments. This study supports the use of TMT reagents that are pre-aliquoted, dried, and stored for robust quantitative proteomics and metaproteomics in high throughput applications.
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Affiliation(s)
- Marybeth Creskey
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Leyuan Li
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Zhibin Ning
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Emily Ef Fekete
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Janice Mayne
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Krystal Walker
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Anna Ampaw
- Department of Chemistry, Faculty of Science, University of Ottawa, Ottawa, Canada
| | - Robert Ben
- Department of Chemistry, Faculty of Science, University of Ottawa, Ottawa, Canada
| | - Xu Zhang
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
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19
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Kleikamp HBC, Grouzdev D, Schaasberg P, van Valderen R, van der Zwaan R, Wijgaart RVD, Lin Y, Abbas B, Pronk M, van Loosdrecht MCM, Pabst M. Metaproteomics, metagenomics and 16S rRNA sequencing provide different perspectives on the aerobic granular sludge microbiome. WATER RESEARCH 2023; 246:120700. [PMID: 37866247 DOI: 10.1016/j.watres.2023.120700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023]
Abstract
The tremendous progress in sequencing technologies has made DNA sequencing routine for microbiome studies. Additionally, advances in mass spectrometric techniques have extended conventional proteomics into the field of microbial ecology. However, systematic studies that provide a better understanding of the complementary nature of these 'omics' approaches, particularly for complex environments such as wastewater treatment sludge, are urgently needed. Here, we describe a comparative metaomics study on aerobic granular sludge from three different wastewater treatment plants. For this, we employed metaproteomics, whole metagenome, and 16S rRNA amplicon sequencing to study the same granule material with uniform size. We furthermore compare the taxonomic profiles using the Genome Taxonomy Database (GTDB) to enhance the comparability between the different approaches. Though the major taxonomies were consistently identified in the different aerobic granular sludge samples, the taxonomic composition obtained by the different omics techniques varied significantly at the lower taxonomic levels, which impacts the interpretation of the nutrient removal processes. Nevertheless, as demonstrated by metaproteomics, the genera that were consistently identified in all techniques cover the majority of the protein biomass. The established metaomics data and the contig classification pipeline are publicly available, which provides a valuable resource for further studies on metabolic processes in aerobic granular sludge.
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Affiliation(s)
- Hugo B C Kleikamp
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
| | | | - Pim Schaasberg
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Ramon van Valderen
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Ramon van der Zwaan
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Roel van de Wijgaart
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Ben Abbas
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Mario Pronk
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | | | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
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20
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Li S, Mosier D, Dong X, Kouris A, Ji G, Strous M, Diao M. Frequency of change determines effectiveness of microbial response strategies. THE ISME JOURNAL 2023; 17:2047-2057. [PMID: 37723339 PMCID: PMC10579261 DOI: 10.1038/s41396-023-01515-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023]
Abstract
Nature challenges microbes with change at different frequencies and demands an effective response for survival. Here, we used controlled laboratory experiments to investigate the effectiveness of different response strategies, such as post-translational modification, transcriptional regulation, and specialized versus adaptable metabolisms. For this, we inoculated replicated chemostats with an enrichment culture obtained from sulfidic stream microbiomes 16 weeks prior. The chemostats were submitted to alternatingly oxic and anoxic conditions at three frequencies, with periods of 1, 4 and 16 days. The microbial response was recorded with 16S rRNA gene amplicon sequencing, shotgun metagenomics, transcriptomics and proteomics. Metagenomics resolved provisional genomes of all abundant bacterial populations, mainly affiliated with Proteobacteria and Bacteroidetes. Almost all these populations maintained a steady growth rate under both redox conditions at all three frequencies of change. Our results supported three conclusions: (1) Oscillating oxic/anoxic conditions selected for generalistic species, rather than species specializing in only a single condition. (2) A high frequency of change selected for strong codon usage bias. (3) Alignment of transcriptomes and proteomes required multiple generations and was dependent on a low frequency of change.
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Affiliation(s)
- Shengjie Li
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, 100871, Beijing, China
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Damon Mosier
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, 100871, Beijing, China
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Muhe Diao
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada.
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21
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Klaes S, Madan S, Deobald D, Cooper M, Adrian L. GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry. Int J Mol Sci 2023; 24:15692. [PMID: 37958676 PMCID: PMC10649880 DOI: 10.3390/ijms242115692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Profiling bacterial populations in mixed communities is a common task in microbiology. Sequencing of 16S small subunit ribosomal-RNA (16S rRNA) gene amplicons is a widely accepted and functional approach but relies on amplification primers and cannot quantify isotope incorporation. Tandem mass spectrometry proteotyping is an effective alternative for taxonomically profiling microorganisms. We suggest that targeted proteotyping approaches can complement traditional population analyses. Therefore, we describe an approach to assess bacterial community compositions at the family level using the taxonomic marker protein GroEL, which is ubiquitously found in bacteria, except a few obligate intracellular species. We refer to our method as GroEL-proteotyping. GroEL-proteotyping is based on high-resolution tandem mass spectrometry of GroEL peptides and identification of GroEL-derived taxa via a Galaxy workflow and a subsequent Python-based analysis script. Its advantage is that it can be performed with a curated and extendable sample-independent database and that GroEL can be pre-separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to reduce sample complexity, improving GroEL identification while simultaneously decreasing the instrument time. GroEL-proteotyping was validated by employing it on a comprehensive raw dataset obtained through a metaproteome approach from synthetic microbial communities as well as real human gut samples. Our data show that GroEL-proteotyping enables fast and straightforward profiling of highly abundant taxa in bacterial communities at reasonable taxonomic resolution.
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Affiliation(s)
- Simon Klaes
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty III Process Sciences, Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Shobhit Madan
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty of Engineering, Ansbach University of Applied Sciences, 91522 Ansbach, Germany
| | - Darja Deobald
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
| | - Myriel Cooper
- Faculty III Process Sciences, Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, 10587 Berlin, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty III Process Sciences, Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, 13355 Berlin, Germany
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22
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Jagtap PD, Hoopmann MR, Neely BA, Harvey A, Käll L, Perez-Riverol Y, Abajorga MK, Thomas JA, Weintraub ST, Palmblad M. The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020). J Biomol Tech 2023; 34:3fc1f5fe.a058bad4. [PMID: 37969874 PMCID: PMC10644979 DOI: 10.7171/3fc1f5fe.a058bad4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Metaproteomics research using mass spectrometry data has emerged as a powerful strategy to understand the mechanisms underlying microbiome dynamics and the interaction of microbiomes with their immediate environment. Recent advances in sample preparation, data acquisition, and bioinformatics workflows have greatly contributed to progress in this field. In 2020, the Association of Biomolecular Research Facilities Proteome Informatics Research Group launched a collaborative study to assess the bioinformatics options available for metaproteomics research. The study was conducted in 2 phases. In the first phase, participants were provided with mass spectrometry data files and were asked to identify the taxonomic composition and relative taxa abundances in the samples without supplying any protein sequence databases. The most challenging question asked of the participants was to postulate the nature of any biological phenomena that may have taken place in the samples, such as interactions among taxonomic species. In the second phase, participants were provided a protein sequence database composed of the species present in the sample and were asked to answer the same set of questions as for phase 1. In this report, we summarize the data processing methods and tools used by participants, including database searching and software tools used for taxonomic and functional analysis. This study provides insights into the status of metaproteomics bioinformatics in participating laboratories and core facilities.
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Affiliation(s)
| | | | - Benjamin A. Neely
- National Institute of Standards and TechnologyCharlestonSouth Carolina29412USA
| | | | - Lukas Käll
- Royal Institute of Technology114 28StockholmSweden
| | - Yasset Perez-Riverol
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteWellcome Trust Genome CampusHinxtonCambridgeCB10 1SDUnited Kingdom
| | | | | | | | - Magnus Palmblad
- Center for Proteomics and MetabolomicsLeiden University Medical Center2000 RC LeidenThe Netherlands
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23
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Wuyts S, Alves R, Zimmermann‐Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, Müller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P. Consistency across multi-omics layers in a drug-perturbed gut microbial community. Mol Syst Biol 2023; 19:e11525. [PMID: 37485738 PMCID: PMC10495815 DOI: 10.15252/msb.202311525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023] Open
Abstract
Multi-omics analyses are used in microbiome studies to understand molecular changes in microbial communities exposed to different conditions. However, it is not always clear how much each omics data type contributes to our understanding and whether they are concordant with each other. Here, we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics and metabolomics). We find that all the omics methods with species resolution are highly consistent in estimating relative species abundances. Furthermore, different omics methods complement each other for capturing functional changes. For example, while nearly all the omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control. Metabolomics revealed a decrease in oligosaccharide uptake, likely caused by Bacteroidota depletion. Our study highlights how multi-omics datasets can be utilized to reveal complex molecular responses to external perturbations in microbial communities.
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Affiliation(s)
- Sander Wuyts
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Renato Alves
- European Molecular Biology LaboratoryHeidelbergGermany
| | | | | | - Sonja Blasche
- European Molecular Biology LaboratoryHeidelbergGermany
- Medical Research Council Toxicology UnitCambridgeUK
| | | | - Philipp E Geyer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Rajna Hercog
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Ece Kartal
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Lisa Maier
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Johannes B Müller
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Sarela Garcia Santamarina
- European Molecular Biology LaboratoryHeidelbergGermany
- Present address:
MOSTMICRO Unit, Instituto de Tecnologia Quimica e BiologicaUniversidade Nova de LisboaOeirasPortugal
| | | | | | - Anja Telzerow
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Peter V Treit
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Tobias Wenzel
- European Molecular Biology LaboratoryHeidelbergGermany
- Present address:
Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Catolica de ChileSantiagoChile
| | | | - Kiran R Patil
- European Molecular Biology LaboratoryHeidelbergGermany
- Medical Research Council Toxicology UnitCambridgeUK
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Proteomics Program, NNF Center for Protein Research, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Michael Kuhn
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Peer Bork
- European Molecular Biology LaboratoryHeidelbergGermany
- Max Delbrück Centre for Molecular MedicineBerlinGermany
- Yonsei Frontier Lab (YFL)Yonsei UniversitySeoulSouth Korea
- Department of Bioinformatics, BiocenterUniversity of WürzburgWürzburgGermany
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24
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Lin TY, Liu WT. Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor. WATER RESEARCH 2023; 243:120358. [PMID: 37481999 DOI: 10.1016/j.watres.2023.120358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/09/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.
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Affiliation(s)
- Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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25
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Quitón-Tapia S, Trueba-Santiso A, Garrido JM, Suárez S, Omil F. Metalloenzymes play major roles to achieve high-rate nitrogen removal in N-damo communities: Lessons from metaproteomics. BIORESOURCE TECHNOLOGY 2023:129476. [PMID: 37429551 DOI: 10.1016/j.biortech.2023.129476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/12/2023]
Abstract
Nitrite-driven anaerobic methane oxidation (N-damo) is a promising biological process to achieve carbon-neutral wastewater treatment solutions, aligned with the sustainable development goals. Here, the enzymatic activities in a membrane bioreactor highly enriched in N-damo bacteria operated at high nitrogen removal rates were investigated. Metaproteomic analyses, with a special focus on metalloenzymes, revealed the complete enzymatic route of N-damo including their unique nitric oxide dismutases. The relative protein abundance evidenced that "Ca. Methylomirabilis lanthanidiphila" was the predominant N-damo species, attributed to the induction of its lanthanide-binding methanol dehydrogenase in the presence of cerium. Metaproteomics also disclosed the activity of the accompanying taxa in denitrification, methylotrophy and methanotrophy. The most abundant functional metalloenzymes from this community require copper, iron, and cerium as cofactors which was correlated with the metal consumptions in the bioreactor. This study highlights the usefulness of metaproteomics for evaluating the enzymatic activities in engineering systems to optimize microbial management.
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Affiliation(s)
- Silvana Quitón-Tapia
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Alba Trueba-Santiso
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain.
| | - Juan M Garrido
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Sonia Suárez
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Francisco Omil
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
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26
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Chen Y, Gin JW, Wang Y, de Raad M, Tan S, Hillson NJ, Northen TR, Adams PD, Petzold CJ. Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format. PLoS One 2023; 18:e0288102. [PMID: 37418444 DOI: 10.1371/journal.pone.0288102] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/20/2023] [Indexed: 07/09/2023] Open
Abstract
Plate-based proteomic sample preparation offers a solution to the large sample throughput demands in the biotechnology field where hundreds or thousands of engineered microbes are constructed for testing is routine. Meanwhile, sample preparation methods that work efficiently on broader microbial groups are desirable for new applications of proteomics in other fields, such as microbial communities. Here, we detail a step-by-step protocol that consists of cell lysis in an alkaline chemical buffer (NaOH/SDS) followed by protein precipitation with high-ionic strength acetone in 96-well format. The protocol works for a broad range of microbes (e.g., Gram-negative bacteria, Gram-positive bacteria, non-filamentous fungi) and the resulting proteins are ready for tryptic digestion for bottom-up quantitative proteomic analysis without the need for desalting column cleanup. The yield of protein using this protocol increases linearly with respect to the amount of starting biomass from 0.5-2.0 OD*mL of cells. By using a bench-top automated liquid dispenser, a cost-effective and environmentally-friendly option to eliminating pipette tips and reducing reagent waste, the protocol takes approximately 30 minutes to extract protein from 96 samples. Tests on mock mixtures showed expected results that the biomass composition structure is in close agreement with the experimental design. Lastly, we applied the protocol for the composition analysis of a synthetic community of environmental isolates grown on two different media. This protocol has been developed to facilitate rapid, low-variance sample preparation of hundreds of samples and allow flexibility for future protocol development.
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Affiliation(s)
- Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Jennifer W Gin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Ying Wang
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Markus de Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Stephen Tan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Nathan J Hillson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Trent R Northen
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Paul D Adams
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America
- Molecular Biophysics and Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
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27
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Li L, Wang T, Ning Z, Zhang X, Butcher J, Serrana JM, Simopoulos CMA, Mayne J, Stintzi A, Mack DR, Liu YY, Figeys D. Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics. Nat Commun 2023; 14:3428. [PMID: 37301875 PMCID: PMC10257714 DOI: 10.1038/s41467-023-39149-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Functional redundancy is a key ecosystem property representing the fact that different taxa contribute to an ecosystem in similar ways through the expression of redundant functions. The redundancy of potential functions (or genome-level functional redundancy [Formula: see text]) of human microbiomes has been recently quantified using metagenomics data. Yet, the redundancy of expressed functions in the human microbiome has never been quantitatively explored. Here, we present an approach to quantify the proteome-level functional redundancy [Formula: see text] in the human gut microbiome using metaproteomics. Ultra-deep metaproteomics reveals high proteome-level functional redundancy and high nestedness in the human gut proteomic content networks (i.e., the bipartite graphs connecting taxa to functions). We find that the nested topology of proteomic content networks and relatively small functional distances between proteomes of certain pairs of taxa together contribute to high [Formula: see text] in the human gut microbiome. As a metric comprehensively incorporating the factors of presence/absence of each function, protein abundances of each function and biomass of each taxon, [Formula: see text] outcompetes diversity indices in detecting significant microbiome responses to environmental factors, including individuality, biogeography, xenobiotics, and disease. We show that gut inflammation and exposure to specific xenobiotics can significantly diminish the [Formula: see text] with no significant change in taxonomic diversity.
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Affiliation(s)
- Leyuan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 102206, Beijing, China
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Tong Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Zhibin Ning
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Xu Zhang
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - James Butcher
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Joeselle M Serrana
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Caitlin M A Simopoulos
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Janice Mayne
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - David R Mack
- Department of Paediatrics, Faculty of Medicine, University of Ottawa and Children's Hospital of Eastern Ontario Inflammatory Bowel Disease Centre and Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Daniel Figeys
- School of Pharmaceutical Sciences and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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28
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Kwoji ID, Aiyegoro OA, Okpeku M, Adeleke MA. 'Multi-omics' data integration: applications in probiotics studies. NPJ Sci Food 2023; 7:25. [PMID: 37277356 DOI: 10.1038/s41538-023-00199-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
The concept of probiotics is witnessing increasing attention due to its benefits in influencing the host microbiome and the modulation of host immunity through the strengthening of the gut barrier and stimulation of antibodies. These benefits, combined with the need for improved nutraceuticals, have resulted in the extensive characterization of probiotics leading to an outburst of data generated using several 'omics' technologies. The recent development in system biology approaches to microbial science is paving the way for integrating data generated from different omics techniques for understanding the flow of molecular information from one 'omics' level to the other with clear information on regulatory features and phenotypes. The limitations and tendencies of a 'single omics' application to ignore the influence of other molecular processes justify the need for 'multi-omics' application in probiotics selections and understanding its action on the host. Different omics techniques, including genomics, transcriptomics, proteomics, metabolomics and lipidomics, used for studying probiotics and their influence on the host and the microbiome are discussed in this review. Furthermore, the rationale for 'multi-omics' and multi-omics data integration platforms supporting probiotics and microbiome analyses was also elucidated. This review showed that multi-omics application is useful in selecting probiotics and understanding their functions on the host microbiome. Hence, recommend a multi-omics approach for holistically understanding probiotics and the microbiome.
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Affiliation(s)
- Iliya Dauda Kwoji
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa
| | - Olayinka Ayobami Aiyegoro
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, Northwest, South Africa
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa
| | - Matthew Adekunle Adeleke
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa.
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29
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Correia GD, Marchesi JR, MacIntyre DA. Moving beyond DNA: towards functional analysis of the vaginal microbiome by non-sequencing-based methods. Curr Opin Microbiol 2023; 73:102292. [PMID: 36931094 DOI: 10.1016/j.mib.2023.102292] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 03/17/2023]
Abstract
Over the last two decades, sequencing-based methods have revolutionised our understanding of niche-specific microbial complexity. In the lower female reproductive tract, these approaches have enabled identification of bacterial compositional structures associated with health and disease. Application of metagenomics and metatranscriptomics strategies have provided insight into the putative function of these communities but it is increasingly clear that direct measures of microbial and host cell function are required to understand the contribution of microbe-host interactions to pathophysiology. Here we explore and discuss current methods and approaches, many of which rely upon mass-spectrometry, being used to capture functional insight into the vaginal mucosal interface. In addition to improving mechanistic understanding, these methods offer innovative solutions for the development of diagnostic and therapeutic strategies designed to improve women's health.
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Affiliation(s)
- Gonçalo Ds Correia
- Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Julian R Marchesi
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK; Centre for Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, Imperial College London, London W2 1NY, UK
| | - David A MacIntyre
- Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK.
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30
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Zvi-Kedem T, Vintila S, Kleiner M, Tchernov D, Rubin-Blum M. Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels. ISME COMMUNICATIONS 2023; 3:48. [PMID: 37210404 PMCID: PMC10199937 DOI: 10.1038/s43705-023-00254-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 04/25/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
Abstract
Bathymodioline mussels rely on thiotrophic and/or methanotrophic chemosynthetic symbionts for nutrition, yet, secondary heterotrophic symbionts are often present and play an unknown role in the fitness of the organism. The bathymodioline Idas mussels that thrive in gas seeps and on sunken wood in the Mediterranean Sea and the Atlantic Ocean, host at least six symbiont lineages that often co-occur. These lineages include the primary symbionts chemosynthetic methane- and sulfur-oxidizing gammaproteobacteria, and the secondary symbionts, Methylophagaceae, Nitrincolaceae and Flavobacteriaceae, whose physiology and metabolism are obscure. Little is known about if and how these symbionts interact or exchange metabolites. Here we curated metagenome-assembled genomes of Idas modiolaeformis symbionts and used genome-centered metatranscriptomics and metaproteomics to assess key symbiont functions. The Methylophagaceae symbiont is a methylotrophic autotroph, as it encoded and expressed the ribulose monophosphate and Calvin-Benson-Bassham cycle enzymes, particularly RuBisCO. The Nitrincolaceae ASP10-02a symbiont likely fuels its metabolism with nitrogen-rich macromolecules and may provide the holobiont with vitamin B12. The Urechidicola (Flavobacteriaceae) symbionts likely degrade glycans and may remove NO. Our findings indicate that these flexible associations allow for expanding the range of substrates and environmental niches, via new metabolic functions and handoffs.
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Affiliation(s)
- Tal Zvi-Kedem
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa, 3108000, Israel
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Dan Tchernov
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Maxim Rubin-Blum
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa, 3108000, Israel.
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31
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Mappa C, Alpha-Bazin B, Pible O, Armengaud J. Mix24X, a Lab-Assembled Reference to Evaluate Interpretation Procedures for Tandem Mass Spectrometry Proteotyping of Complex Samples. Int J Mol Sci 2023; 24:ijms24108634. [PMID: 37239979 DOI: 10.3390/ijms24108634] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Correct identification of the microorganisms present in a complex sample is a crucial issue. Proteotyping based on tandem mass spectrometry can help establish an inventory of organisms present in a sample. Evaluation of bioinformatics strategies and tools for mining the recorded datasets is essential to establish confidence in the results obtained and to improve these pipelines in terms of sensitivity and accuracy. Here, we propose several tandem mass spectrometry datasets recorded on an artificial reference consortium comprising 24 bacterial species. This assemblage of environmental and pathogenic bacteria covers 20 different genera and 5 bacterial phyla. The dataset comprises difficult cases, such as the Shigella flexneri species, which is closely related to Escherichia coli, and several highly sequenced clades. Different acquisition strategies simulate real-life scenarios: from rapid survey sampling to exhaustive analysis. We provide access to individual proteomes of each bacterium separately to provide a rational basis for evaluating the assignment strategy of MS/MS spectra when recorded from complex mixtures. This resource should provide an interesting common reference for developers who wish to compare their proteotyping tools and for those interested in evaluating protein assignment when dealing with complex samples, such as microbiomes.
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Affiliation(s)
- Charlotte Mappa
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
- Laboratoire Innovations Technologiques Pour la Détection et le Diagnostic (Li2D), Université de Montpellier, 30207 Bagnols sur Cèze, France
| | - Béatrice Alpha-Bazin
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
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32
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Andersen TO, Altshuler I, Vera-Ponce de León A, Walter JM, McGovern E, Keogh K, Martin C, Bernard L, Morgavi DP, Park T, Li Z, Jiang Y, Firkins JL, Yu Z, Hvidsten TR, Waters SM, Popova M, Arntzen MØ, Hagen LH, Pope PB. Metabolic influence of core ciliates within the rumen microbiome. THE ISME JOURNAL 2023:10.1038/s41396-023-01407-y. [PMID: 37169869 DOI: 10.1038/s41396-023-01407-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/13/2023]
Abstract
Protozoa comprise a major fraction of the microbial biomass in the rumen microbiome, of which the entodiniomorphs (order: Entodiniomorphida) and holotrichs (order: Vestibuliferida) are consistently observed to be dominant across a diverse genetic and geographical range of ruminant hosts. Despite the apparent core role that protozoal species exert, their major biological and metabolic contributions to rumen function remain largely undescribed in vivo. Here, we have leveraged (meta)genome-centric metaproteomes from rumen fluid samples originating from both cattle and goats fed diets with varying inclusion levels of lipids and starch, to detail the specific metabolic niches that protozoa occupy in the context of their microbial co-habitants. Initial proteome estimations via total protein counts and label-free quantification highlight that entodiniomorph species Entodinium and Epidinium as well as the holotrichs Dasytricha and Isotricha comprise an extensive fraction of the total rumen metaproteome. Proteomic detection of protozoal metabolism such as hydrogenases (Dasytricha, Isotricha, Epidinium, Enoploplastron), carbohydrate-active enzymes (Epidinium, Diplodinium, Enoploplastron, Polyplastron), microbial predation (Entodinium) and volatile fatty acid production (Entodinium and Epidinium) was observed at increased levels in high methane-emitting animals. Despite certain protozoal species having well-established reputations for digesting starch, they were unexpectedly less detectable in low methane emitting-animals fed high starch diets, which were instead dominated by propionate/succinate-producing bacterial populations suspected of being resistant to predation irrespective of host. Finally, we reaffirmed our abovementioned observations in geographically independent datasets, thus illuminating the substantial metabolic influence that under-explored eukaryotic populations have in the rumen, with greater implications for both digestion and methane metabolism.
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Affiliation(s)
- Thea O Andersen
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Ianina Altshuler
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Arturo Vera-Ponce de León
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Juline M Walter
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Emily McGovern
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County, Meath, Ireland
| | - Kate Keogh
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County, Meath, Ireland
| | - Cécile Martin
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, Saint-Genes-Champanelle, France
| | - Laurence Bernard
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, Saint-Genes-Champanelle, France
| | - Diego P Morgavi
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, Saint-Genes-Champanelle, France
| | - Tansol Park
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
| | - Zongjun Li
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Yu Jiang
- Center for Ruminant Genetics and Evolution, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Jeffrey L Firkins
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Sinead M Waters
- Teagasc, Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County, Meath, Ireland
| | - Milka Popova
- INRAE, VetAgro Sup, UMR Herbivores, Université Clermont Auvergne, Saint-Genes-Champanelle, France
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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Mappa C, Alpha-Bazin B, Pible O, Armengaud J. Evaluation of the Limit of Detection of Bacteria by Tandem Mass Spectrometry Proteotyping and Phylopeptidomics. Microorganisms 2023; 11:1170. [PMCID: PMC10223342 DOI: 10.3390/microorganisms11051170] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 06/01/2023] Open
Abstract
Shotgun proteomics has proven to be an attractive alternative for identifying a pathogen and characterizing the antimicrobial resistance genes it produces. Because of its performance, proteotyping of microorganisms by tandem mass spectrometry is expected to become an essential tool in modern healthcare. Proteotyping microorganisms that have been isolated from the environment by culturomics is also a cornerstone for the development of new biotechnological applications. Phylopeptidomics is a new strategy that estimates the phylogenetic distances between the organisms present in the sample and calculates the ratio of their shared peptides, thus improving the quantification of their contributions to the biomass. Here, we established the limit of detection of tandem mass spectrometry proteotyping based on MS/MS data recorded for several bacteria. The limit of detection for Salmonella bongori with our experimental set-up is 4 × 104 colony-forming units from a sample volume of 1 mL. This limit of detection is directly related to the amount of protein per cell and therefore depends on the shape and size of the microorganism. We have demonstrated that identification of bacteria by phylopeptidomics is independent of their growth stage and that the limit of detection of the method is not degraded in presence of additional bacteria in the same proportion.
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Affiliation(s)
- Charlotte Mappa
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Université de Montpellier, 30207 Bagnols-sur-Cèze, France
| | - Béatrice Alpha-Bazin
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Olivier Pible
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
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Ho SFS, Wheeler NE, Millard AD, van Schaik W. Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data. MICROBIOME 2023; 11:84. [PMID: 37085924 PMCID: PMC10120246 DOI: 10.1186/s40168-023-01533-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND The prediction of bacteriophage sequences in metagenomic datasets has become a topic of considerable interest, leading to the development of many novel bioinformatic tools. A comparative analysis of ten state-of-the-art phage identification tools was performed to inform their usage in microbiome research. METHODS Artificial contigs generated from complete RefSeq genomes representing phages, plasmids, and chromosomes, and a previously sequenced mock community containing four phage species, were used to evaluate the precision, recall, and F1 scores of the tools. We also generated a dataset of randomly shuffled sequences to quantify false-positive calls. In addition, a set of previously simulated viromes was used to assess diversity bias in each tool's output. RESULTS VIBRANT and VirSorter2 achieved the highest F1 scores (0.93) in the RefSeq artificial contigs dataset, with several other tools also performing well. Kraken2 had the highest F1 score (0.86) in the mock community benchmark by a large margin (0.3 higher than DeepVirFinder in second place), mainly due to its high precision (0.96). Generally, k-mer-based tools performed better than reference similarity tools and gene-based methods. Several tools, most notably PPR-Meta, called a high number of false positives in the randomly shuffled sequences. When analysing the diversity of the genomes that each tool predicted from a virome set, most tools produced a viral genome set that had similar alpha- and beta-diversity patterns to the original population, with Seeker being a notable exception. CONCLUSIONS This study provides key metrics used to assess performance of phage detection tools, offers a framework for further comparison of additional viral discovery tools, and discusses optimal strategies for using these tools. We highlight that the choice of tool for identification of phages in metagenomic datasets, as well as their parameters, can bias the results and provide pointers for different use case scenarios. We have also made our benchmarking dataset available for download in order to facilitate future comparisons of phage identification tools. Video Abstract.
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Affiliation(s)
- Siu Fung Stanley Ho
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nicole E. Wheeler
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Andrew D. Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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Corbera-Rubio F, Laureni M, Koudijs N, Müller S, van Alen T, Schoonenberg F, Lücker S, Pabst M, van Loosdrecht MCM, van Halem D. Meta-omics profiling of full-scale groundwater rapid sand filters explains stratification of iron, ammonium and manganese removals. WATER RESEARCH 2023; 233:119805. [PMID: 36868119 DOI: 10.1016/j.watres.2023.119805] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/30/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Rapid sand filters (RSF) are an established and widely applied technology for groundwater treatment. Yet, the underlying interwoven biological and physical-chemical reactions controlling the sequential removal of iron, ammonia and manganese remain poorly understood. To resolve the contribution and interactions between the individual reactions, we studied two full-scale drinking water treatment plant configurations, namely (i) one dual-media (anthracite and quartz sand) filter and (ii) two single-media (quartz sand) filters in series. In situ and ex situ activity tests were combined with mineral coating characterization and metagenome-guided metaproteomics along the depth of each filter. Both plants exhibited comparable performances and process compartmentalization, with most of ammonium and manganese removal occurring only after complete iron depletion. The homogeneity of the media coating and genome-based microbial composition within each compartment highlighted the effect of backwashing, namely the complete vertical mixing of the filter media. In stark contrast to this homogeneity, the removal of the contaminants was strongly stratified within each compartment, and decreased along the filter height. This apparent and longstanding conflict was resolved by quantifying the expressed proteome at different filter heights, revealing a consistent stratification of proteins catalysing ammonia oxidation and protein-based relative abundances of nitrifying genera (up to 2 orders of magnitude difference between top and bottom samples). This implies that microorganisms adapt their protein pool to the available nutrient load at a faster rate than the backwash mixing frequency. Ultimately, these results show the unique and complementary potential of metaproteomics to understand metabolic adaptations and interactions in highly dynamic ecosystems.
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Affiliation(s)
| | - Michele Laureni
- Delft University of Technology, van der Maasweg 9, HZ Delft 2629, The Netherlands.
| | - Nienke Koudijs
- Delft University of Technology, van der Maasweg 9, HZ Delft 2629, The Netherlands
| | - Simon Müller
- Delft University of Technology, van der Maasweg 9, HZ Delft 2629, The Netherlands
| | - Theo van Alen
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, AJ Nijmegen 6525, The Netherlands
| | | | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, AJ Nijmegen 6525, The Netherlands
| | - Martin Pabst
- Delft University of Technology, van der Maasweg 9, HZ Delft 2629, The Netherlands
| | | | - Doris van Halem
- Delft University of Technology, van der Maasweg 9, HZ Delft 2629, The Netherlands
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36
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Kronen M, Vázquez-Campos X, Wilkins MR, Lee M, Manefield MJ. Evidence for a Putative Isoprene Reductase in Acetobacterium wieringae. mSystems 2023; 8:e0011923. [PMID: 36943133 PMCID: PMC10134865 DOI: 10.1128/msystems.00119-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Recent discoveries of isoprene-metabolizing microorganisms suggest they might play an important role in the global isoprene budget. Under anoxic conditions, isoprene can be used as an electron acceptor and is reduced to methylbutene. This study describes the proteogenomic profiling of an isoprene-reducing bacterial culture to identify organisms and genes responsible for the isoprene hydrogenation reaction. A metagenome-assembled genome (MAG) of the most abundant (89% relative abundance) lineage in the enrichment, Acetobacterium wieringae, was obtained. Comparative proteogenomics and reverse transcription-PCR (RT-PCR) identified a putative five-gene operon from the A. wieringae MAG upregulated during isoprene reduction. The operon encodes a putative oxidoreductase, three pleiotropic nickel chaperones (2 × HypA, HypB), and one 4Fe-4S ferredoxin. The oxidoreductase is proposed as the putative isoprene reductase with a binding site for NADH, flavin adenine dinucleotide (FAD), two pairs of canonical [4Fe-4S] clusters, and a putative iron-sulfur cluster site in a Cys6-bonding environment. Well-studied Acetobacterium strains, such as A. woodii DSM 1030, A. wieringae DSM 1911, or A. malicum DSM 4132, do not encode the isoprene-regulated operon but encode, like many other bacteria, a homolog of the putative isoprene reductase (~47 to 49% amino acid sequence identity). Uncharacterized homologs of the putative isoprene reductase are observed across the Firmicutes, Spirochaetes, Tenericutes, Actinobacteria, Chloroflexi, Bacteroidetes, and Proteobacteria, suggesting the ability of biohydrogenation of unfunctionalized conjugated doubled bonds in other unsaturated hydrocarbons. IMPORTANCE Isoprene was recently shown to act as an electron acceptor for a homoacetogenic bacterium. The focus of this study is the molecular basis for isoprene reduction. By comparing a genome from our isoprene-reducing enrichment culture, dominated by Acetobacterium wieringae, with genomes of other Acetobacterium lineages that do not reduce isoprene, we shortlisted candidate genes for isoprene reduction. Using comparative proteogenomics and reverse transcription-PCR we have identified a putative five-gene operon encoding an oxidoreductase referred to as putative isoprene reductase.
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Affiliation(s)
- Miriam Kronen
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Michael J Manefield
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
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Proteomics as a New-Generation Tool for Studying Moulds Related to Food Safety and Quality. Int J Mol Sci 2023; 24:ijms24054709. [PMID: 36902140 PMCID: PMC10003330 DOI: 10.3390/ijms24054709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Mould development in foodstuffs is linked to both spoilage and the production of mycotoxins, provoking food quality and food safety concerns, respectively. The high-throughput technology proteomics applied to foodborne moulds is of great interest to address such issues. This review presents proteomics approaches useful for boosting strategies to minimise the mould spoilage and the hazard related to mycotoxins in food. Metaproteomics seems to be the most effective method for mould identification despite the current problems related to the bioinformatics tool. More interestingly, different high resolution mass spectrometry tools are suitable for evaluating the proteome of foodborne moulds able to unveil the mould's response under certain environmental conditions and the presence of biocontrol agents or antifungals, being sometimes combined with a method with limited ability to separate proteins, the two-dimensional gel electrophoresis. However, the matrix complexity, the high ranges of protein concentrations needed and the performing of multiple steps are some of the proteomics limitations for the application to foodborne moulds. To overcome some of these limitations, model systems have been developed and proteomics applied to other scientific fields, such as library-free data independent acquisition analyses, the implementation of ion mobility, and the evaluation of post-translational modifications, are expected to be gradually implemented in this field for avoiding undesirable moulds in foodstuffs.
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38
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Kleiner M, Kouris A, Violette M, D'Angelo G, Liu Y, Korenek A, Tolić N, Sachsenberg T, McCalder J, Lipton MS, Strous M. Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. MICROBIOME 2023; 11:24. [PMID: 36755313 PMCID: PMC9909930 DOI: 10.1186/s40168-022-01454-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. RESULTS Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50-99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC-MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. CONCLUSIONS We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.
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Affiliation(s)
- Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Marlene Violette
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Grace D'Angelo
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Yihua Liu
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
- Max Planck Institute for Biology, Tübingen, Germany
| | - Abigail Korenek
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Nikola Tolić
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Timo Sachsenberg
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Janine McCalder
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Mary S Lipton
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada.
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Canderan J, Stamboulian M, Ye Y. MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data. J Proteome Res 2023; 22:442-453. [PMID: 36688801 PMCID: PMC9903327 DOI: 10.1021/acs.jproteome.2c00614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Indexed: 01/24/2023]
Abstract
The microbiome has been shown to be important for human health because of its influence on disease and the immune response. Mass spectrometry is an important tool for evaluating protein expression and species composition in the microbiome but is technically challenging and time-consuming. Multiplexing has emerged as a way to make spectrometry workflows faster while improving results. Here, we present MetaProD (MetaProteomics in Django) as a highly configurable metaproteomic data analysis pipeline supporting label-free and multiplexed mass spectrometry. The pipeline is open-source, uses fully open-source tools, and is integrated with Django to offer a web-based interface for configuration and data access. Benchmarking of MetaProD using multiple metaproteomics data sets showed that MetaProD achieved fast and efficient identification of peptides and proteins. Application of MetaProD to a multiplexed cancer data set resulted in identification of more differentially expressed human proteins in cancer tissues versus healthy tissues as compared to previous studies; in addition, MetaProD identified bacterial proteins in those samples, some of which are differentially abundant.
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Affiliation(s)
- Jamie Canderan
- Informatics
Department, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, United States
| | - Moses Stamboulian
- Informatics
Department, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, United States
| | - Yuzhen Ye
- Computer
Science Department, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, United States
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40
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Couvillion SP, Mostoller KE, Williams JE, Pace RM, Stohel IL, Peterson HK, Nicora CD, Nakayasu ES, Webb-Robertson BJM, McGuire MA, McGuire MK, Metz TO. Interrogating the role of the milk microbiome in mastitis in the multi-omics era. Front Microbiol 2023; 14:1105675. [PMID: 36819069 PMCID: PMC9932517 DOI: 10.3389/fmicb.2023.1105675] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
There is growing interest in a functional understanding of milk-associated microbiota as there is ample evidence that host-associated microbial communities play an active role in host health and phenotype. Mastitis, characterized by painful inflammation of the mammary gland, is prevalent among lactating humans and agricultural animals and is associated with significant clinical and economic consequences. The etiology of mastitis is complex and polymicrobial and correlative studies have indicated alterations in milk microbial community composition. Recent evidence is beginning to suggest that a causal relationship may exist between the milk microbiota and host phenotype in mastitis. Multi-omic approaches can be leveraged to gain a mechanistic, molecular level understanding of how the milk microbiome might modulate host physiology, thereby informing strategies to prevent and ameliorate mastitis. In this paper, we review existing studies that have utilized omics approaches to investigate the role of the milk microbiome in mastitis. We also summarize the strengths and challenges associated with the different omics techniques including metagenomics, metatranscriptomics, metaproteomics, metabolomics and lipidomics and provide perspective on the integration of multiple omics technologies for a better functional understanding of the milk microbiome.
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Affiliation(s)
- Sneha P. Couvillion
- Pacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, WA, United States,*Correspondence: Sneha P. Couvillion, ✉
| | - Katie E. Mostoller
- Pacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, WA, United States
| | - Janet E. Williams
- Department of Animal, Veterinary, and Food Sciences, University of Idaho, Moscow, ID, United States
| | - Ryan M. Pace
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, United States
| | - Izabel L. Stohel
- Pacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, WA, United States
| | - Haley K. Peterson
- Department of Animal, Veterinary, and Food Sciences, University of Idaho, Moscow, ID, United States
| | - Carrie D. Nicora
- Pacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, WA, United States
| | - Ernesto S. Nakayasu
- Pacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, WA, United States
| | - Bobbie-Jo M. Webb-Robertson
- Pacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, WA, United States
| | - Mark A. McGuire
- Department of Animal, Veterinary, and Food Sciences, University of Idaho, Moscow, ID, United States
| | - Michelle K. McGuire
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, ID, United States
| | - Thomas O. Metz
- Pacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, WA, United States,Thomas O. Metz, ✉
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41
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Fekete EE, Figeys D, Zhang X. Microbiota-directed biotherapeutics: considerations for quality and functional assessment. Gut Microbes 2023; 15:2186671. [PMID: 36896938 PMCID: PMC10012963 DOI: 10.1080/19490976.2023.2186671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Mounting evidence points to causative or correlative roles of gut microbiome in the development of a myriad of diseases ranging from gastrointestinal diseases, metabolic diseases to neurological disorders and cancers. Consequently, efforts have been made to develop and apply therapeutics targeting the human microbiome, in particular the gut microbiota, for treating diseases and maintaining wellness. Here we summarize the current development of gut microbiota-directed therapeutics with a focus on novel biotherapeutics, elaborate the need of advanced -omics approaches for evaluating the microbiota-type biotherapeutics, and discuss the clinical and regulatory challenges. We also discuss the development and potential application of ex vivo microbiome assays and in vitro intestinal cellular models in this context. Altogether, this review aims to provide a broad view of promises and challenges of the emerging field of microbiome-directed human healthcare.
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Affiliation(s)
- Emily Ef Fekete
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada.,Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Xu Zhang
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada.,School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
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42
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Pible O, Petit P, Steinmetz G, Rivasseau C, Armengaud J. Taxonomical composition and functional analysis of biofilms sampled from a nuclear storage pool. Front Microbiol 2023; 14:1148976. [PMID: 37125163 PMCID: PMC10133526 DOI: 10.3389/fmicb.2023.1148976] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Sampling small amounts of biofilm from harsh environments such as the biofilm present on the walls of a radioactive material storage pool offers few analytical options if taxonomic characterization and estimation of the different biomass contributions are the objectives. Although 16S/18S rRNA amplification on extracted DNA and sequencing is the most widely applied method, its reliability in terms of quantitation has been questioned as yields can be species-dependent. Here, we propose a tandem-mass spectrometry proteotyping approach consisting of acquiring peptide data and interpreting then against a generalist database without any a priori. The peptide sequence information is transformed into useful taxonomical information that allows to obtain the different 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. For these biofilms, we report the identification of three genera, namely Sphingomonas, Caulobacter, and Acidovorax, and their functional characterization by metaproteomics which shows that these organisms are metabolic active. Differential expression of Gene Ontology GOslim terms between the two main microorganisms highlights their metabolic specialization.
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Affiliation(s)
- Olivier Pible
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Pauline Petit
- Université Grenoble Alpes, CEA, CNRS, IRIG, Grenoble, France
| | - Gérard Steinmetz
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Corinne Rivasseau
- Université Grenoble Alpes, CEA, CNRS, IRIG, Grenoble, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
- *Correspondence: Jean Armengaud,
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43
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Wang S, Feng S, Pan C, Guo X. FineFDR: Fine-grained Taxonomy-specific False Discovery Rates Control in Metaproteomics. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE 2022; 2022:287-292. [PMID: 36910011 PMCID: PMC9998077 DOI: 10.1109/bibm55620.2022.9995401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Microbial community proteomics, also termed metaproteomics, investigates all proteins expressed by a microbiota. Tandem mass spectrometry (MS/MS) is the typical method for identifying proteins in metaproteomics, which involves searching the mass spectra against a protein sequence database. A major post-analysis step is controlling the false discovery rate (FDR), i.e., the ratio of false positives to the total number of annotations. The current popular target-decoy FDR estimation method treats all the peptides and proteins equally and overlooks that they could have varied probabilities of being identified. In this study, we report FineFDR, a framework for FDR assessment at fine-grained levels with taxonomy information considered. FineFDR groups the identified peptide-spectrum matches, peptides, and proteins from different taxonomic units and estimates the FDR in each group separately. Empirical experiments on the simulated and real-world data sets demonstrate that our FineFDR achieved higher precision and more peptide and protein identifications when compared to the state-of-the-art methods, such as Comet, Percolator, TIDD, and Tailor. FineFDR is freely available under the GNU GPL license at https://github.com/Biocomputing-Research-Group/FDR.
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Affiliation(s)
- Shengze Wang
- Department of Computer Science and Engineering University of North Texas, Denton, TX 76207, United States
| | - Shichao Feng
- Department of Computer Science and Engineering University of North Texas, Denton, TX 76207, United States
| | - Chongle Pan
- School of Computer Science Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Xuan Guo
- Department of Computer Science and Engineering University of North Texas, Denton, TX 76207, United States
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Duan H, Cheng K, Ning Z, Li L, Mayne J, Sun Z, Figeys D. Assessing the Dark Field of Metaproteome. Anal Chem 2022; 94:15648-15654. [DOI: 10.1021/acs.analchem.2c02452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Haonan Duan
- Daniel Figeys - School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
| | - Kai Cheng
- Daniel Figeys - School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
| | - Zhibin Ning
- Daniel Figeys - School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
| | - Leyuan Li
- Daniel Figeys - School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
| | - Janice Mayne
- Daniel Figeys - School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
| | - Zhongzhi Sun
- Daniel Figeys - School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
| | - Daniel Figeys
- Daniel Figeys - School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
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Abstract
Diet has a profound impact on the microbial community in the gastrointestinal tract, the intestinal microbiota, to the benefit or detriment of human health. To understand the influence of diet on the intestinal microbiota, research has focused on individual macronutrients. Some macronutrients (e.g. fiber) have been studied in great detail and have been found to strongly influence the intestinal microbiota. The relationship between dietary protein, a vital macronutrient, and the intestinal microbiota has gone largely unexplored. Emerging evidence suggests that dietary protein strongly impacts intestinal microbiota composition and function and that protein-microbiota interactions can have critical impacts on host health. In this review, we focus on recent studies investigating the impact of dietary protein quantity and source on the intestinal microbiota and resulting host health consequences. We highlight major open questions critical to understanding health outcomes mediated by interactions between dietary protein and the microbiota.
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Affiliation(s)
- Alexandria Bartlett
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham NC, USA
- Corresponding author
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC, USA
- Corresponding author
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46
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Salvato F, Vintila S, Finkel OM, Dangl JL, Kleiner M. Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:977-988. [PMID: 35876747 DOI: 10.1094/mpmi-05-22-0116-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species (Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry-based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Fernanda Salvato
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
| | - Omri M Finkel
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, U.S.A
| | - Jeffery L Dangl
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, U.S.A
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, U.S.A
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47
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Carper DL, Appidi MR, Mudbhari S, Shrestha HK, Hettich RL, Abraham PE. The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont. Microorganisms 2022; 10:microorganisms10102013. [PMID: 36296289 PMCID: PMC9609723 DOI: 10.3390/microorganisms10102013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Microorganisms are critical drivers of biological processes that contribute significantly to plant sustainability and productivity. In recent years, emerging research on plant holobiont theory and microbial invasion ecology has radically transformed how we study plant–microbe interactions. Over the last few years, we have witnessed an accelerating pace of advancements and breadth of questions answered using omic technologies. Herein, we discuss how current state-of-the-art genomics, transcriptomics, proteomics, and metabolomics techniques reliably transcend the task of studying plant–microbe interactions while acknowledging existing limitations impeding our understanding of plant holobionts.
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Affiliation(s)
- Dana L. Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Manasa R. Appidi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Sameer Mudbhari
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Him K. Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Correspondence:
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48
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Feng S, Ji HL, Wang H, Zhang B, Sterzenbach R, Pan C, Guo X. MetaLP: An integrative linear programming method for protein inference in metaproteomics. PLoS Comput Biol 2022; 18:e1010603. [PMID: 36269761 PMCID: PMC9629623 DOI: 10.1371/journal.pcbi.1010603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/02/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022] Open
Abstract
Metaproteomics based on high-throughput tandem mass spectrometry (MS/MS) plays a crucial role in characterizing microbiome functions. The acquired MS/MS data is searched against a protein sequence database to identify peptides, which are then used to infer a list of proteins present in a metaproteome sample. While the problem of protein inference has been well-studied for proteomics of single organisms, it remains a major challenge for metaproteomics of complex microbial communities because of the large number of degenerate peptides shared among homologous proteins in different organisms. This challenge calls for improved discrimination of true protein identifications from false protein identifications given a set of unique and degenerate peptides identified in metaproteomics. MetaLP was developed here for protein inference in metaproteomics using an integrative linear programming method. Taxonomic abundance information extracted from metagenomics shotgun sequencing or 16s rRNA gene amplicon sequencing, was incorporated as prior information in MetaLP. Benchmarking with mock, human gut, soil, and marine microbial communities demonstrated significantly higher numbers of protein identifications by MetaLP than ProteinLP, PeptideProphet, DeepPep, PIPQ, and Sipros Ensemble. In conclusion, MetaLP could substantially improve protein inference for complex metaproteomes by incorporating taxonomic abundance information in a linear programming model.
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Affiliation(s)
- Shichao Feng
- Department of Computer Science and Engineering, University of North Texas, Denton, Texas, United States of America
| | - Hong-Long Ji
- Department of Cellular and Molecular Biology, University of Texas at Tyler, Tyler, Texas, United States of America
- Texas Lung Injury Institute, University of Texas at Tyler, Tyler, Texas, United States of America
| | - Huan Wang
- College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, CHINA
| | - Bailu Zhang
- Department of Computer Science and Engineering, University of North Texas, Denton, Texas, United States of America
| | - Ryan Sterzenbach
- Department of Computer Science and Engineering, University of North Texas, Denton, Texas, United States of America
- Department of Biomedical Engineering, University of North Texas, Denton, Texas, United States of America
| | - Chongle Pan
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Xuan Guo
- Department of Computer Science and Engineering, University of North Texas, Denton, Texas, United States of America
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49
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Kennes-Veiga D, Trueba-Santiso A, Gallardo-Garay V, Balboa S, Carballa M, Lema JM. Sulfamethoxazole Enhances Specific Enzymatic Activities under Aerobic Heterotrophic Conditions: A Metaproteomic Approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13152-13159. [PMID: 36073795 PMCID: PMC9686132 DOI: 10.1021/acs.est.2c05001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
The growing concern about antibiotic-resistant microorganisms has focused on the sludge from wastewater treatment plants (WWTPs) as a potential hotspot for their development and spread. To this end, it seems relevant to analyze the changes on the microbiota as a consequence of the antibiotics that wastewater may contain. This study aims at determining whether the presence of sulfamethoxazole (SMX), even in relatively low concentrations, modifies the microbial activities and the enzymatic expression of an activated sludge under aerobic heterotrophic conditions. For that purpose, we applied a metaproteomic approach in combination with genomic and transformation product analyses. SMX was biotransformed, and the metabolite 2,4(1H,3H)-pteridinedione-SMX (PtO-SMX) from the pterin-conjugation pathway was detected at all concentrations tested. Metaproteomics showed that SMX at 50-2000 μg/L slightly affected the microbial community structure, which was confirmed by DNA metabarcoding. Interestingly, an enhanced activity of the genus Corynebacterium and specifically of five enzymes involved in its central carbon metabolism was found at increased SMX concentrations. Our results suggest a role of Corynebacterium genus on SMX risks mitigation in our bioreactors.
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Affiliation(s)
- David
M. Kennes-Veiga
- CRETUS,
Department of Chemical Engineering, University
of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Alba Trueba-Santiso
- CRETUS,
Department of Chemical Engineering, University
of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Valentina Gallardo-Garay
- CRETUS,
Department of Chemical Engineering, University
of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Sabela Balboa
- CRETUS,
Department of Microbiology, University of
Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Marta Carballa
- CRETUS,
Department of Chemical Engineering, University
of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Juan M. Lema
- CRETUS,
Department of Chemical Engineering, University
of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
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50
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Sampara P, Luo Y, Lin X, Ziels RM. Integrating Genome-Resolved Metagenomics with Trait-Based Process Modeling to Determine Biokinetics of Distinct Nitrifying Communities within Activated Sludge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11670-11682. [PMID: 35929783 PMCID: PMC9387530 DOI: 10.1021/acs.est.2c02081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Conventional bioprocess models for wastewater treatment are based on aggregated bulk biomass concentrations and do not incorporate microbial physiological diversity. Such a broad aggregation of microbial functional groups can fail to predict ecosystem dynamics when high levels of physiological diversity exist within trophic guilds. For instance, functional diversity among nitrite-oxidizing bacteria (NOB) can obfuscate engineering strategies for their out-selection in activated sludge (AS), which is desirable to promote energy-efficient nitrogen removal. Here, we hypothesized that different NOB populations within AS can have different physiological traits that drive process performance, which we tested by estimating biokinetic growth parameters using a combination of highly replicated respirometry, genome-resolved metagenomics, and process modeling. A lab-scale AS reactor subjected to a selective pressure for over 90 days experienced resilience of NOB activity. We recovered three coexisting Nitrospira population genomes belonging to two sublineages, which exhibited distinct growth strategies and underwent a compositional shift following the selective pressure. A trait-based process model calibrated at the NOB genus level better predicted nitrite accumulation than a conventional process model calibrated at the NOB guild level. This work demonstrates that trait-based modeling can be leveraged to improve our prediction, control, and design of functionally diverse microbiomes driving key environmental biotechnologies.
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