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Nebauer DJ, Pearson LA, Neilan BA. Critical steps in an environmental metaproteomics workflow. Environ Microbiol 2024; 26:e16637. [PMID: 38760994 DOI: 10.1111/1462-2920.16637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/30/2024] [Indexed: 05/20/2024]
Abstract
Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As the field is still maturing, it lacks consistent workflows, making it challenging for non-expert researchers to navigate. This review aims to introduce the workflow of environmental metaproteomics. It outlines the standard practices for sample collection, processing, and analysis, and offers strategies to overcome the unique challenges presented by common environmental matrices such as soil, freshwater, marine environments, biofilms, sludge, and symbionts. The review also highlights the bottlenecks in data analysis that are specific to metaproteomics samples and provides suggestions for researchers to obtain high-quality datasets. It includes recent benchmarking studies and descriptions of software packages specifically built for metaproteomics analysis. The article is written without assuming the reader's familiarity with single-organism proteomic workflows, making it accessible to those new to proteomics or mass spectrometry in general. This primer for environmental metaproteomics aims to improve accessibility to this exciting technology and empower researchers to tackle challenging and ambitious research questions. While it is primarily a resource for those new to the field, it should also be useful for established researchers looking to streamline or troubleshoot their metaproteomics experiments.
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Affiliation(s)
- Daniel J Nebauer
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
- Centre of Excellence in Synthetic Biology, Australian Research Council, Sydney, New South Wales, Australia
| | - Leanne A Pearson
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
- Centre of Excellence in Synthetic Biology, Australian Research Council, Sydney, New South Wales, Australia
| | - Brett A Neilan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
- Centre of Excellence in Synthetic Biology, Australian Research Council, Sydney, New South Wales, Australia
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2
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Li L, Mayne J, Beltran A, Zhang X, Ning Z, Figeys D. RapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics. MICROBIOME RESEARCH REPORTS 2024; 3:26. [PMID: 38841404 PMCID: PMC11149095 DOI: 10.20517/mrr.2023.57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/03/2024] [Accepted: 03/25/2024] [Indexed: 06/07/2024]
Abstract
Aim: Our gut microbiome has its own functionalities which can be modulated by various xenobiotic and biotic components. The development and application of a high-throughput functional screening approach of individual gut microbiomes accelerates drug discovery and our understanding of microbiome-drug interactions. We previously developed the rapid assay of individual microbiome (RapidAIM), which combined an optimized culturing model with metaproteomics to study gut microbiome responses to xenobiotics. In this study, we aim to incorporate automation and multiplexing techniques into RapidAIM to develop a high-throughput protocol. Methods: To develop a 2.0 version of RapidAIM, we automated the protein analysis protocol, and introduced a tandem mass tag (TMT) multiplexing technique. To demonstrate the typical outcome of the protocol, we used RapidAIM 2.0 to evaluate the effect of prebiotic kestose on ex vivo individual human gut microbiomes biobanked with five different workflows. Results: We describe the protocol of RapidAIM 2.0 with extensive details on stool sample collection, biobanking, in vitro culturing and stimulation, sample processing, metaproteomics measurement, and data analysis. The analysis depth of 5,014 ± 142 protein groups per multiplexed sample was achieved. A test on five biobanking methods using RapidAIM 2.0 showed the minimal effect of sample processing on live microbiota functional responses to kestose. Conclusions: Depth and reproducibility of RapidAIM 2.0 are comparable to previous manual label-free metaproteomic analyses. In the meantime, the protocol realizes culturing and sample preparation of 320 samples in six days, opening the door to extensively understanding the effects of xenobiotic and biotic factors on our internal ecology.
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Affiliation(s)
| | | | | | | | | | - Daniel Figeys
- Correspondence to: Prof. Daniel Figeys, School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa K1H 8M5, Ontario, Canada. E-mail:
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3
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Baptista NT, Dessalles R, Illner AK, Ville P, Ribet L, Anton PM, Durand-Dubief M. Harnessing the power of resistant starch: a narrative review of its health impact and processing challenges. Front Nutr 2024; 11:1369950. [PMID: 38571748 PMCID: PMC10987757 DOI: 10.3389/fnut.2024.1369950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/05/2024] [Indexed: 04/05/2024] Open
Abstract
Starch is a primary energy storage for plants, making it an essential component of many plant-based foods consumed today. Resistant starch (RS) refers to those starch fractions that escape digestion in the small intestine and reach the colon where they are fermented by the microflora. RS has been repeatedly reported as having benefits on health, but ensuring that its content remains in food processing may be challenging. The present work focuses on the impact RS on health and explores the different processes that may influence its presence in foods, thus potentially interfering with these effects. Clinical evidence published from 2010 to 2023 and studying the effect of RS on health parameters in adult populations, were identified, using PUBMED/Medline and Cochrane databases. The search focused as well on observational studies related to the effect of food processes on RS content. While processes such as milling, fermentation, cooking and heating seem to have a deleterious influence on RS content, other processes, such as cooling, cooking time, storage time, or water content, may positively impact its presence. Regarding the influence on health parameters, there is a body of evidence suggesting an overall significant beneficial effect of RS, especially type 1 and 2, on several health parameters such as glycemic response, insulin resistance index, bowel function or inflammatory markers. Effects are more substantiated in individuals suffering from metabolic diseases. The effects of RS may however be exerted differently depending on the type. A better understanding of the influence of food processes on RS can guide the development of dietary intake recommendations and contribute to the development of food products rich in RS.
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Affiliation(s)
| | | | - Anne-Kathrin Illner
- Transformations and Agroressources, Institut Polytechnique UniLaSalle, Université d’Artois, Beauvais, France
| | - Patrice Ville
- Department of Regulatory Department, University of Lesaffre International, Marcq-en-Baroeul, France
| | - Léa Ribet
- Transformations and Agroressources, Institut Polytechnique UniLaSalle, Université d’Artois, Beauvais, France
| | - Pauline M. Anton
- Transformations and Agroressources, Institut Polytechnique UniLaSalle, Université d’Artois, Beauvais, France
| | - Mickaël Durand-Dubief
- Discovery and Front-End Innovation, Lesaffre Institute of Science and Technology, Lille, France
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4
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Smith AD, Chen C, Cheung L, Ward RE, Jones BS, Pletsch EA, Dawson HD. A type 4 resistant potato starch alters the cecal microbiome and gene expression in mice fed a western diet based on NHANES data. Food Funct 2024; 15:3141-3157. [PMID: 38439638 DOI: 10.1039/d3fo04512a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Four major types of resistant starch (RS1-4) are present in foods, all of which can alter the microbiome and are fermented in the cecum and colon to produce short-chain fatty acids (SCFAs). Type 4 RSs are chemically modified starches, not normally found in foods, but have become a popular food additive as their addition increases fiber content. Multiple studies, in humans and rodents, have explored how different RS4 affect post-prandial glucose metabolism, but fewer studies have examined the effects of RS4 consumption on the microbiome. In addition, many RS studies conducted in rodents use high-fat diets that do not approximate what is typically consumed by humans. To address this, mice were fed a Total Western Diet (TWD), based on National Health and Nutrition Examination Survey (NHANES) data that mimics the macro and micronutrient composition of a typical American diet, for six weeks, and then supplemented with 0, 2, 5, or 10% of the RS4, Versafibe 1490™ (VF), a phosphorylated and cross-linked potato starch, for an additional three weeks. The cecal contents were analyzed for SCFA content and microbiota composition. Butyrate production was increased while branched chain SCFA production decreased. The alpha-diversity of the microbiome decreased in mice fed the TWD with 10% VF 1490 added while the beta-diversity plot showed that the 5% and 10% VF groups were distinct from mice fed the TWD. Similarly, the largest changes in relative abundance of various genera were greatest in mice fed the 10% VF diet. To examine the effect of VF consumption on tissue gene expression, cecal and distal colon tissue mRNA abundance were analyzed by RNASeq. Gene expression changes were more prevalent in the cecum than the colon and in mice fed the 10% VF diet, but the number of changes was substantially lower than we previously observed in mice fed the TWD supplemented with native potato starch (RPS). These results provide additional evidence that the structure of the RS is a major factor determining its effects on the microbiome and gene expression in the cecum and colon.
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Affiliation(s)
- Allen D Smith
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Rm. 228, Bldg. 307C, BARC-East, 10, 300 Baltimore Ave., Beltsville, MD, 20705, USA.
| | - Celine Chen
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Rm. 228, Bldg. 307C, BARC-East, 10, 300 Baltimore Ave., Beltsville, MD, 20705, USA.
| | - Lumei Cheung
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Rm. 228, Bldg. 307C, BARC-East, 10, 300 Baltimore Ave., Beltsville, MD, 20705, USA.
| | - Robert E Ward
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, USA
| | - B Sky Jones
- Department of Nutrition, Dietetics and Food Sciences, Utah State University, USA
| | - Elizabeth A Pletsch
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Rm. 228, Bldg. 307C, BARC-East, 10, 300 Baltimore Ave., Beltsville, MD, 20705, USA.
| | - Harry D Dawson
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Agricultural Research Service, United States Department of Agriculture, Rm. 228, Bldg. 307C, BARC-East, 10, 300 Baltimore Ave., Beltsville, MD, 20705, USA.
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5
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Catassi G, Aloi M, Giorgio V, Gasbarrini A, Cammarota G, Ianiro G. The Role of Diet and Nutritional Interventions for the Infant Gut Microbiome. Nutrients 2024; 16:400. [PMID: 38337684 PMCID: PMC10857663 DOI: 10.3390/nu16030400] [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: 12/14/2023] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
The infant gut microbiome plays a key role in the healthy development of the human organism and appears to be influenced by dietary practices through multiple pathways. First, maternal diet during pregnancy and infant nutrition significantly influence the infant gut microbiota. Moreover, breastfeeding fosters the proliferation of beneficial bacteria, while formula feeding increases microbial diversity. The timing of introducing solid foods also influences gut microbiota composition. In preterm infants the gut microbiota development is influenced by multiple factors, including the time since birth and the intake of breast milk, and interventions such as probiotics and prebiotics supplementation show promising results in reducing morbidity and mortality in this population. These findings underscore the need for future research to understand the long-term health impacts of these interventions and for further strategies to enrich the gut microbiome of formula-fed and preterm infants.
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Affiliation(s)
- Giulia Catassi
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Pediatric Gastroenterology and Liver Unit, Sapienza University of Rome, Umberto I Hospital, 00161 Rome, Italy;
| | - Marina Aloi
- Pediatric Gastroenterology and Liver Unit, Sapienza University of Rome, Umberto I Hospital, 00161 Rome, Italy;
| | - Valentina Giorgio
- Department of Woman and Child Health and Public Health, UOC Pediatria, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy;
| | - Antonio Gasbarrini
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Giovanni Cammarota
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Gianluca Ianiro
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
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Song YC, Das D, Zhang Y, Chen MX, Fernie AR, Zhu FY, Han J. Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants. Trends Biotechnol 2023; 41:1532-1548. [PMID: 37365082 DOI: 10.1016/j.tibtech.2023.05.010] [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: 03/17/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023]
Abstract
Proteogenomics (PG) integrates the proteome with the genome and transcriptome to refine gene models and annotation. Coupled with single-cell (SC) assays, PG effectively distinguishes heterogeneity among cell groups. Affiliating spatial information to PG reveals the high-resolution circuitry within SC atlases. Additionally, PG can investigate dynamic changes in protein-coding genes in plants across growth and development as well as stress and external stimulation, significantly contributing to the functional genome. Here we summarize existing PG research in plants and introduce the technical features of various methods. Combining PG with other omics, such as metabolomics and peptidomics, can offer even deeper insights into gene functions. We argue that the application of PG will represent an important font of foundational knowledge for plants.
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Affiliation(s)
- Yu-Chen Song
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences and Technology, 52 Agricultural Building, University of Missouri-Columbia, MO 65201, USA
| | - Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Mo-Xian Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.
| | - Fu-Yuan Zhu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Jiangang Han
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China.
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7
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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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8
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Chen R, Zhang C, Xu F, Yu L, Tian F, Chen W, Zhai Q. Meta-analysis reveals gut microbiome and functional pathway alterations in response to resistant starch. Food Funct 2023. [PMID: 37194392 DOI: 10.1039/d3fo00845b] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Resistant starch (RS) has the ability to improve the structure of the gut microbiota, regulate glucolipid metabolism and maintain the health of the human body, and has been extensively studied by many scholars in recent years. However, previous studies have provided a wide range of results on the differences in the gut microbiota after RS intake. In this article, we performed a meta-analysis of a total of 955 samples of 248 individuals from the seven studies included to compare the gut microbiota of the baseline and the end-point of RS intake. At the end-point, RS intake was related to a lower gut microbial α-diversity and higher relative abundance of Ruminococcus, Agathobacter, Faecalibacterium and Bifidobacterium, and the functional pathways of the gut microbiota related to the carbohydrate metabolism, lipid metabolism, amino acid metabolism and genetic information processing were higher. Different types of resistant starch and different populations led to varied responses on the gut microbiome. The altered gut microbiome may contribute to improve the blood glucose level and insulin resistance, which may be a potential treatment route for diabetes, obesity and other metabolic diseases.
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Affiliation(s)
- Ruimin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Chengcheng Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Fusheng Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
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9
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Effect of resistant starch types as a prebiotic. Appl Microbiol Biotechnol 2023; 107:491-515. [PMID: 36512032 DOI: 10.1007/s00253-022-12325-y] [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: 06/16/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
Abstract
Since the role of intestinal microbiota in metabolism was understood, the importance of dietary components such as fibres and prebiotics, which affect the modulation of microbiota, has been increasing day by day. While all prebiotic components are considered dietary fibre, not every dietary fibre is considered a prebiotic. While fructooligosaccharides, galactooligosaccharides, inulin, and galactans are considered prebiotics, other fermentable carbohydrates are considered candidate prebiotic components based on in vitro and preclinical studies. Resistant starch, one of such carbohydrates, is considered a potential prebiotic component when it is made resistant to digestion naturally or chemically. In this review, both in vitro and in vivo studies in which the prebiotic capacity of type II, type III, and type IV resistant starch isolated from food and produced commercially was assessed were analyzed. According to the results of current studies, certain types of resistant starch are thought to have a high prebiotic capacity, and they may be candidate prebiotic components although positive results have not been achieved in all studies. KEY POINTS: • Resistant starch is undigested in the small intestine and is fermented in the large intestine. • Resistant starch fermentation positively affects the growth of Bifidobacterium and Lactobacillus. • Resistant starch can be considered a prebiotic ingredient.
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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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11
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MetaProClust-MS1: an MS1 Profiling Approach for Large-Scale Microbiome Screening. mSystems 2022; 7:e0038122. [PMID: 35950762 PMCID: PMC9426440 DOI: 10.1128/msystems.00381-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Metaproteomics is used to explore the functional dynamics of microbial communities. However, acquiring metaproteomic data by tandem mass spectrometry (MS/MS) is time-consuming and resource-intensive, and there is a demand for computational methods that can be used to reduce these resource requirements. We present MetaProClust-MS1, a computational framework for microbiome feature screening developed to prioritize samples for follow-up MS/MS. In this proof-of-concept study, we tested and compared MetaProClust-MS1 results on gut microbiome data, from fecal samples, acquired using short 15-min MS1-only chromatographic gradients and MS1 spectra from longer 60-min gradients to MS/MS-acquired data. We found that MetaProClust-MS1 identified robust gut microbiome responses caused by xenobiotics with significantly correlated cluster topologies of comparable data sets. We also used MetaProClust-MS1 to reanalyze data from both a clinical MS/MS diagnostic study of pediatric patients with inflammatory bowel disease and an experiment evaluating the therapeutic effects of a small molecule on the brain tissue of Alzheimer's disease mouse models. MetaProClust-MS1 clusters could distinguish between inflammatory bowel disease diagnoses (ulcerative colitis and Crohn's disease) using samples from mucosal luminal interface samples and identified hippocampal proteome shifts of Alzheimer's disease mouse models after small-molecule treatment. Therefore, we demonstrate that MetaProClust-MS1 can screen both microbiomes and single-species proteomes using only MS1 profiles, and our results suggest that this approach may be generalizable to any proteomics experiment. MetaProClust-MS1 may be especially useful for large-scale metaproteomic screening for the prioritization of samples for further metaproteomic characterization, using MS/MS, for instance, in addition to being a promising novel approach for clinical diagnostic screening. IMPORTANCE Growing evidence suggests that human gut microbiome composition and function are highly associated with health and disease. As such, high-throughput metaproteomic studies are becoming more common in gut microbiome research. However, using a conventional long liquid chromatography (LC)-MS/MS gradient metaproteomics approach as an initial screen in large-scale microbiome experiments can be slow and expensive. To combat this challenge, we introduce MetaProClust-MS1, a computational framework for microbiome screening using MS1-only profiles. In this proof-of-concept study, we show that MetaProClust-MS1 identifies clusters of gut microbiome treatments using MS1-only profiles similar to those identified using MS/MS. Our approach allows researchers to prioritize samples and treatments of interest for further metaproteomic analyses and may be generally applicable to any proteomic analysis. In particular, this approach may be especially useful for large-scale metaproteomic screening or in clinical settings where rapid diagnostic evidence is required.
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Zhang X, Walker K, Mayne J, Li L, Ning Z, Stintzi A, Figeys D. Evaluating live microbiota biobanking using an ex vivo microbiome assay and metaproteomics. Gut Microbes 2022; 14:2035658. [PMID: 35130123 PMCID: PMC8824213 DOI: 10.1080/19490976.2022.2035658] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Biobanking of live microbiota is becoming indispensable for mechanistic and clinical investigations of drug-microbiome interactions and fecal microbiota transplantation. However, there is a lack of methods to rapidly and systematically evaluate whether the biobanked microbiota maintains their cultivability and functional activity. In this study, we use a rapid ex vivo microbiome assay and metaproteomics to evaluate the cultivability and the functional responses of biobanked microbiota to treatment with a prebiotic (fructo-oligosaccharide, FOS). Our results indicate that the microbiota cultivability and their functional responses to FOS treatment were well maintained by freezing in a deoxygenated glycerol buffer at -80°C for 12 months. We also demonstrate that the fecal microbiota is functionally stable for 48 hours on ice in a deoxygenated glycerol buffer, allowing off-site fecal sample collection and shipping to laboratory for live microbiota biobanking. This study provides a method for rapid evaluation of the cultivability of biobanked live microbiota. Our results show minimal detrimental influences of long-term freezing in deoxygenated glycerol buffer on the cultivability of fecal microbiota.
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Affiliation(s)
- Xu Zhang
- School of Pharmaceutical Sciences, 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, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Janice Mayne
- School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Leyuan Li
- School of Pharmaceutical Sciences, 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, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Alain Stintzi
- School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada,CONTACT Daniel Figeys School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Room 4510D, 451 Smyth Road, Ottawa, ONK1H 8M5, Canada
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Simopoulos CMA, Figeys D, Lavallée-Adam M. Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies. Methods Mol Biol 2022; 2456:319-338. [PMID: 35612752 DOI: 10.1007/978-1-0716-2124-0_22] [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: 10/18/2022]
Abstract
Constant improvements in mass spectrometry technologies and laboratory workflows have enabled the proteomics investigation of biological samples of growing complexity. Microbiomes represent such complex samples for which metaproteomics analyses are becoming increasingly popular. Metaproteomics experimental procedures create large amounts of data from which biologically relevant signal must be efficiently extracted to draw meaningful conclusions. Such a data processing requires appropriate bioinformatics tools specifically developed for, or capable of handling metaproteomics data. In this chapter, we outline current and novel tools that can perform the most commonly used steps in the analysis of cutting-edge metaproteomics data, such as peptide and protein identification and quantification, as well as data normalization, imputation, mining, and visualization. We also provide details about the experimental setups in which these tools should be used.
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Affiliation(s)
- Caitlin M A Simopoulos
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
- School of Pharmaceutical Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Mathieu Lavallée-Adam
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.
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Abstract
Resistant starch, microbiome, and precision modulation. Mounting evidence has positioned the gut microbiome as a nexus of health. Modulating its phylogenetic composition and function has become an attractive therapeutic prospect. Resistant starches (granular amylase-resistant α-glycans) are available as physicochemically and morphologically distinguishable products. Attempts to leverage resistant starch as microbiome-modifying interventions in clinical studies have yielded remarkable inter-individual variation. Consequently, their utility as a potential therapy likely depends predominantly on the selected resistant starch and the subject's baseline microbiome. The purpose of this review is to detail i) the heterogeneity of resistant starches, ii) how resistant starch is sequentially degraded and fermented by specialized gut microbes, and iii) how resistant starch interventions yield variable effects on the gut microbiome.
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Affiliation(s)
- Peter A. Dobranowski
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
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