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Tan N, Zhao M, Luo Z, Li Z, Zhang X, Xu J, Gu X, Wang Q, Ding S, Ying M, Xu Y. Linalool as a key component in strawberry volatile organic compounds (VOCs) modulates gut microbiota, systemic inflammation, and glucolipid metabolism. Food Chem 2024; 460:140361. [PMID: 39098193 DOI: 10.1016/j.foodchem.2024.140361] [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: 05/05/2024] [Revised: 06/14/2024] [Accepted: 07/03/2024] [Indexed: 08/06/2024]
Abstract
Strawberries are rich in volatile organic compounds (VOCs), which are increasingly recognized as potential health-promoting factors. This study explored the health effects of intaking strawberry VOC extract and its dominant terpene, linalool. The results indicated that linalool and strawberry VOC extract significantly increased the abundance of beneficial bacteria like Lactobacillus, Bacillus, and Alistipes in mice. Moreover, mice treated with linalool and strawberry VOC extract exhibited notable reductions in serum pro-inflammatory cytokines; interleukin IL-6 decreased by 14.5% and 21.8%, respectively, while IL-1β levels decreased by 9.6% and 13.4%, respectively. Triglyceride levels in the treated groups were reduced by 38.3% and 58.1%, respectively. Spearman's correlation analysis revealed that Bacillus negatively correlated with glucolipid indices, and Bifidobacterium and Dubosiella negatively correlated with inflammatory factors, indicating that alterations in glucolipid metabolism might be associated with the regulation of gut microbiota and systemic inflammation.
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Affiliation(s)
- Nanfeng Tan
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Minjie Zhao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China
| | - Zhenbiao Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Xuenan Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jiayi Xu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Xinya Gu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Qingqing Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Shenghua Ding
- Hunan Agricultural Product Processing Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Miaomiao Ying
- College of Landscape and Hydraulic Engineering, Wenzhou Vocational College of Science and Technology, Wenzhou, China
| | - Yanqun Xu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Ningbo Research Institute, Zhejiang University, Ningbo, 315100, China; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, 02138, USA.
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Paone P, Latousakis D, Terrasi R, Vertommen D, Jian C, Borlandelli V, Suriano F, Johansson MEV, Puel A, Bouzin C, Delzenne NM, Salonen A, Juge N, Florea BI, Muccioli GG, Overkleeft H, Van Hul M, Cani PD. Human milk oligosaccharide 2'-fucosyllactose protects against high-fat diet-induced obesity by changing intestinal mucus production, composition and degradation linked to changes in gut microbiota and faecal proteome profiles in mice. Gut 2024; 73:1632-1649. [PMID: 38740509 DOI: 10.1136/gutjnl-2023-330301] [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: 05/17/2023] [Accepted: 04/27/2024] [Indexed: 05/16/2024]
Abstract
OBJECTIVE To decipher the mechanisms by which the major human milk oligosaccharide (HMO), 2'-fucosyllactose (2'FL), can affect body weight and fat mass gain on high-fat diet (HFD) feeding in mice. We wanted to elucidate whether 2'FL metabolic effects are linked with changes in intestinal mucus production and secretion, mucin glycosylation and degradation, as well as with the modulation of the gut microbiota, faecal proteome and endocannabinoid (eCB) system. RESULTS 2'FL supplementation reduced HFD-induced obesity and glucose intolerance. These effects were accompanied by several changes in the intestinal mucus layer, including mucus production and composition, and gene expression of secreted and transmembrane mucins, glycosyltransferases and genes involved in mucus secretion. In addition, 2'FL increased bacterial glycosyl hydrolases involved in mucin glycan degradation. These changes were linked to a significant increase and predominance of bacterial genera Akkermansia and Bacteroides, different faecal proteome profile (with an upregulation of proteins involved in carbon, amino acids and fat metabolism and a downregulation of proteins involved in protein digestion and absorption) and, finally, to changes in the eCB system. We also investigated faecal proteomes from lean and obese humans and found similar changes observed comparing lean and obese mice. CONCLUSION Our results show that the HMO 2'FL influences host metabolism by modulating the mucus layer, gut microbiota and eCB system and propose the mucus layer as a new potential target for the prevention of obesity and related disorders.
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Affiliation(s)
- Paola Paone
- Louvain Drug Research Institute (LDRI), Metabolism and Nutrition research group (MNUT), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Dimitris Latousakis
- The Gut Microbiome and Health and Food Safety Institute Strategic Programme, Norwich Research Park, Quadram Institute Bioscience, Norwich, UK
| | - Romano Terrasi
- Louvain Drug Research Institute (LDRI), Bioanalysis and Pharmacology of Bioactive Lipids Research Group (BPBL), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Didier Vertommen
- de Duve Institute, MASSPROT platform, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Ching Jian
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Valentina Borlandelli
- Department Bio-organic Synthesis, Leids Instituut voor Chemisch Onderzoek, Leiden University, Leiden, The Netherlands
| | - Francesco Suriano
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Malin E V Johansson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Anthony Puel
- Louvain Drug Research Institute (LDRI), Metabolism and Nutrition research group (MNUT), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO) Department, WEL Research Institute, Wavre, Belgium
| | - Caroline Bouzin
- Institute of Experimental and Clinical Research (IREC), IREC Imaging Platform (2IP RRID:SCR_023378), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Nathalie M Delzenne
- Louvain Drug Research Institute (LDRI), Metabolism and Nutrition research group (MNUT), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Nathalie Juge
- The Gut Microbiome and Health and Food Safety Institute Strategic Programme, Norwich Research Park, Quadram Institute Bioscience, Norwich, UK
| | - Bogdan I Florea
- Department Bio-organic Synthesis, Leids Instituut voor Chemisch Onderzoek, Leiden University, Leiden, The Netherlands
| | - Giulio G Muccioli
- Louvain Drug Research Institute (LDRI), Bioanalysis and Pharmacology of Bioactive Lipids Research Group (BPBL), UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Herman Overkleeft
- Department Bio-organic Synthesis, Leids Instituut voor Chemisch Onderzoek, Leiden University, Leiden, The Netherlands
| | - Matthias Van Hul
- Louvain Drug Research Institute (LDRI), Metabolism and Nutrition research group (MNUT), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO) Department, WEL Research Institute, Wavre, Belgium
| | - Patrice D Cani
- Louvain Drug Research Institute (LDRI), Metabolism and Nutrition research group (MNUT), UCLouvain, Université catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO) Department, WEL Research Institute, Wavre, Belgium
- Institute of Experimental and Clinical Research (IREC), UCLouvain, Université catholique de Louvain, Brussels, Belgium
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3
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Do K, Mehta S, Wagner R, Bhuming D, Rajczewski AT, Skubitz APN, Johnson JE, Griffin TJ, Jagtap PD. A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease. mSphere 2024; 9:e0079323. [PMID: 38780289 PMCID: PMC11332332 DOI: 10.1128/msphere.00793-23] [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: 12/18/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
Clinical metaproteomics has the potential to offer insights into the host-microbiome interactions underlying diseases. However, the field faces challenges in characterizing microbial proteins found in clinical samples, usually present at low abundance relative to the host proteins. As a solution, we have developed an integrated workflow coupling mass spectrometry-based analysis with customized bioinformatic identification, quantification, and prioritization of microbial proteins, enabling targeted assay development to investigate host-microbe dynamics in disease. The bioinformatics tools are implemented in the Galaxy ecosystem, offering the development and dissemination of complex bioinformatic workflows. The modular workflow integrates MetaNovo (to generate a reduced protein database), SearchGUI/PeptideShaker and MaxQuant [to generate peptide-spectral matches (PSMs) and quantification], PepQuery2 (to verify the quality of PSMs), Unipept (for taxonomic and functional annotation), and MSstatsTMT (for statistical analysis). We have utilized this workflow in diverse clinical samples, from the characterization of nasopharyngeal swab samples to bronchoalveolar lavage fluid. Here, we demonstrate its effectiveness via analysis of residual fluid from cervical swabs. The complete workflow, including training data and documentation, is available via the Galaxy Training Network, empowering non-expert researchers to utilize these powerful tools in their clinical studies. IMPORTANCE Clinical metaproteomics has immense potential to offer functional insights into the microbiome and its contributions to human disease. However, there are numerous challenges in the metaproteomic analysis of clinical samples, including handling of very large protein sequence databases for sensitive and accurate peptide and protein identification from mass spectrometry data, as well as taxonomic and functional annotation of quantified peptides and proteins to enable interpretation of results. To address these challenges, we have developed a novel clinical metaproteomics workflow that provides customized bioinformatic identification, verification, quantification, and taxonomic and functional annotation. This bioinformatic workflow is implemented in the Galaxy ecosystem and has been used to characterize diverse clinical sample types, such as nasopharyngeal swabs and bronchoalveolar lavage fluid. Here, we demonstrate its effectiveness and availability for use by the research community via analysis of residual fluid from cervical swabs.
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Affiliation(s)
- Katherine Do
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Reid Wagner
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Dechen Bhuming
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew T. Rajczewski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Amy P. N. Skubitz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - James E. Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Pratik D. Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
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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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Chen X, Hou Y, Liao A, Pan L, Yang S, Liu Y, Wang J, Xue Y, Zhang M, Zhu Z, Huang J. Integrated Analysis of Gut Microbiome and Adipose Transcriptome Reveals Beneficial Effects of Resistant Dextrin from Wheat Starch on Insulin Resistance in Kunming Mice. Biomolecules 2024; 14:186. [PMID: 38397423 PMCID: PMC10886926 DOI: 10.3390/biom14020186] [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: 12/03/2023] [Revised: 01/14/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Systemic chronic inflammation is recognized as a significant contributor to the development of obesity-related insulin resistance. Previous studies have revealed the physiological benefits of resistant dextrin (RD), including obesity reduction, lower fasting glucose levels, and anti-inflammation. The present study investigated the effects of RD intervention on insulin resistance (IR) in Kunming mice, expounding the mechanisms through the gut microbiome and transcriptome of white adipose. In this eight-week study, we investigated changes in tissue weight, glucose-lipid metabolism levels, serum inflammation levels, and lesions of epididymal white adipose tissue (eWAT) evaluated via Hematoxylin and Eosin (H&E) staining. Moreover, we analyzed the gut microbiota composition and transcriptome of eWAT to assess the potential protective effects of RD intervention. Compared with a high-fat, high-sugar diet (HFHSD) group, the RD intervention significantly enhanced glucose homeostasis (e.g., AUC-OGTT, HOMA-IR, p < 0.001), and reduced lipid metabolism (e.g., TG, LDL-C, p < 0.001) and serum inflammation levels (e.g., IL-1β, IL-6, p < 0.001). The RD intervention also led to changes in the gut microbiota composition, with an increase in the abundance of probiotics (e.g., Parabacteroides, Faecalibaculum, and Muribaculum, p < 0.05) and a decrease in harmful bacteria (Colidextribacter, p < 0.05). Moreover, the RD intervention had a noticeable effect on the gene transcription profile of eWAT, and KEGG enrichment analysis revealed that differential genes were enriched in PI3K/AKT, AMPK, in glucose-lipid metabolism, and in the regulation of lipolysis in adipocytes signaling pathways. The findings demonstrated that RD not only ameliorated IR, but also remodeled the gut microbiota and modified the transcriptome profile of eWAT.
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Affiliation(s)
- Xinyang Chen
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yinchen Hou
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- College of Food and Biological Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China;
| | - Aimei Liao
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Long Pan
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Shengru Yang
- College of Food and Biological Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China;
| | - Yingying Liu
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Jingjing Wang
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yingchun Xue
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Mingyi Zhang
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Zhitong Zhu
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Jihong Huang
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng 475004, China
- School of Food and Pharmacy, Xuchang University, Xuchang 461000, China
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Do K, Mehta S, Wagner R, Bhuming D, Rajczewski AT, Skubitz APN, Johnson JE, Griffin TJ, Jagtap PD. A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568121. [PMID: 38045370 PMCID: PMC10690215 DOI: 10.1101/2023.11.21.568121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Clinical metaproteomics has the potential to offer insights into the host-microbiome interactions underlying diseases. However, the field faces challenges in characterizing microbial proteins found in clinical samples, which are usually present at low abundance relative to the host proteins. As a solution, we have developed an integrated workflow coupling mass spectrometry-based analysis with customized bioinformatic identification, quantification and prioritization of microbial and host proteins, enabling targeted assay development to investigate host-microbe dynamics in disease. The bioinformatics tools are implemented in the Galaxy ecosystem, offering the development and dissemination of complex bioinformatic workflows. The modular workflow integrates MetaNovo (to generate a reduced protein database), SearchGUI/PeptideShaker and MaxQuant (to generate peptide-spectral matches (PSMs) and quantification), PepQuery2 (to verify the quality of PSMs), and Unipept and MSstatsTMT (for taxonomy and functional annotation). We have utilized this workflow in diverse clinical samples, from the characterization of nasopharyngeal swab samples to bronchoalveolar lavage fluid. Here, we demonstrate its effectiveness via analysis of residual fluid from cervical swabs. The complete workflow, including training data and documentation, is available via the Galaxy Training Network, empowering non-expert researchers to utilize these powerful tools in their clinical studies.
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7
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Dassoff E, Shireen A, Wright A. Lipid emulsion structure, digestion behavior, physiology, and health: a scoping review and future directions. Crit Rev Food Sci Nutr 2023:1-33. [PMID: 37947287 DOI: 10.1080/10408398.2023.2273448] [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: 11/12/2023]
Abstract
Research investigating the effects of the food matrix on health is needed to untangle many unresolved questions in nutritional science. Emulsion structure plays a fundamental role in this inquiry; however, the effects of oil-in-water emulsion structure on broad metabolic, physiological, and health-related outcomes have not been comprehensively reviewed. This systematic scoping review targets this gap and examines methodological considerations for the field of relating food structure and health. MEDLINE, Web of Science, and CAB Direct were searched from inception to December 2022, returning 3106 articles, 52 of which were eligible for inclusion. Many investigated emulsion lipid droplet size and/or gastric colloidal stability and their relation to postprandial weight-loss-related outcomes. The present review also identifies numerous novel relationships between emulsion structures and health-related outcomes. "Omics" endpoints present an exciting avenue for more comprehensive analysis in this area, yet interpretation remains difficult. Identifying valid surrogate biomarkers for long-term outcomes and disease risk will be a turning point for food structure research, leading to breakthroughs in the pace and utility of research that generates advancements in health. The review's findings and recommendations aim to support new hypotheses, future trial design, and evidence-based emulsion design for improved health and well-being.
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Affiliation(s)
- Erik Dassoff
- Human Health and Nutritional Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Arshia Shireen
- Human Health and Nutritional Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Amanda Wright
- Human Health and Nutritional Sciences, University of Guelph, Guelph, Ontario, Canada
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Ascandari A, Aminu S, Safdi NEH, El Allali A, Daoud R. A bibliometric analysis of the global impact of metaproteomics research. Front Microbiol 2023; 14:1217727. [PMID: 37476667 PMCID: PMC10354264 DOI: 10.3389/fmicb.2023.1217727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023] Open
Abstract
Background Metaproteomics is a subfield in meta-omics that is used to characterize the proteome of a microbial community. Despite its importance and the plethora of publications in different research area, scientists struggle to fully comprehend its functional impact on the study of microbiomes. In this study, bibliometric analyses are used to evaluate the current state of metaproteomic research globally as well as evaluate the specific contribution of Africa to this burgeoning research area. In this study, we use bibliometric analyses to evaluate the current state of metaproteomic research globally, identify research frontiers and hotspots, and further predict future trends in metaproteomics. The specific contribution of Africa to this research area was evaluated. Methods Relevant documents from 2004 to 2022 were extracted from the Scopus database. The documents were subjected to bibliometric analyses and visualization using VOS viewer and Biblioshiny package in R. Factors such as the trends in publication, country and institutional cooperation networks, leading scientific journals, author's productivity, and keywords analyses were conducted. The African publications were ranked using Field-Weighted Citation Impact (FWCI) scores. Results A total of 1,138 documents were included and the number of publications increased drastically from 2004 to 2022 with more publications (170) reported in 2021. In terms of publishers, Frontiers in Microbiology had the highest number of total publications (62). The United States of America (USA), Germany, China, and Canada, together with other European countries were the most productive. Institution-wise, the Helmholtz Zentrum für Umweltforschung, Germany had more publications while Max Plank Institute had the highest total collaborative link strength. Jehmlich N. was the most productive author whereas Hettich RL had the highest h-index of 63. Regarding Africa, only 2.2% of the overall publications were from the continent with more publication outputs from South Africa. More than half of the publications from the continent had an FWCI score ≥ 1. Conclusion The scientific outputs of metaproteomics are rapidly evolving with developed countries leading the way. Although Africa showed prospects for future progress, this could only be accelerated by providing funding, increased collaborations, and mentorship programs.
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Affiliation(s)
- AbdulAziz Ascandari
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Suleiman Aminu
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Nour El Houda Safdi
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Rachid Daoud
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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Discovering Biomarkers for Non-Alcoholic Steatohepatitis Patients with and without Hepatocellular Carcinoma Using Fecal Metaproteomics. Int J Mol Sci 2022; 23:ijms23168841. [PMID: 36012106 PMCID: PMC9408600 DOI: 10.3390/ijms23168841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022] Open
Abstract
High-calorie diets lead to hepatic steatosis and to the development of non-alcoholic fatty liver disease (NAFLD), which can evolve over many years into the inflammatory form of non-alcoholic steatohepatitis (NASH), posing a risk for the development of hepatocellular carcinoma (HCC). Due to diet and liver alteration, the axis between liver and gut is disturbed, resulting in gut microbiome alterations. Consequently, detecting these gut microbiome alterations represents a promising strategy for early NASH and HCC detection. We analyzed medical parameters and the fecal metaproteome of 19 healthy controls, 32 NASH patients, and 29 HCC patients, targeting the discovery of diagnostic biomarkers. Here, NASH and HCC resulted in increased inflammation status and shifts within the composition of the gut microbiome. An increased abundance of kielin/chordin, E3 ubiquitin ligase, and nucleophosmin 1 represented valuable fecal biomarkers, indicating disease-related changes in the liver. Although a single biomarker failed to separate NASH and HCC, machine learning-based classification algorithms provided an 86% accuracy in distinguishing between controls, NASH, and HCC. Fecal metaproteomics enables early detection of NASH and HCC by providing single biomarkers and machine learning-based metaprotein panels.
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Si YC, Ren CC, Zhang EW, Kang ZX, Mo XY, Li QQ, Chen B. Integrative Analysis of the Gut Microbiota and Metabolome in Obese Mice with Electroacupuncture by 16S rRNA Gene Sequencing and HPLC-MS-based Metabolic Profiling. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2022; 50:673-690. [PMID: 35282806 DOI: 10.1142/s0192415x22500276] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Acupuncture has been used to treat numerous diseases such as obesity in China for thousands of years. Several mechanisms of acupuncture on obesity have been surveyed based on metabolomics, but the effects of acupuncture on the alterations in the gut flora are still unclear. In this study, an integrated approach based on 16S rRNA gene sequencing combined with high-performance liquid chromatography-mass spectrometry (HPLC-MS) metabolic profiling was conducted to investigate the effects of acupuncture on high-fat-diet-induced obesity through the regulation of the relative abundances of gut microbiota and their relationships with biomarker candidates. A total of 10 significantly altered bacterial genera and 11 metabolites were recognized, which recovered to normal levels after electroacupuncture treatment. The relative abundances of the bacterial families Muribaculaceae,Lachnospiraceae,Desulfovibrionaceae,Helicobacteraceae, Prevotellaceae,Ruminococcaceae,Rikenellaceae,Deferribacteraceae,Bacteroidaceae andTannerellaceaewere remarkedly changed among the three groups. Potential biomarkers, including LysoPC(0:0/16:0) ([Formula: see text]1),PC(0:0/18:0) ([Formula: see text]2),Cholic acid([Formula: see text]3),LysoPC(16:0) ([Formula: see text]4), 3[Formula: see text],6[Formula: see text],7[Formula: see text]-Trihydroxy-5[Formula: see text]-cholanoic acid([Formula: see text]5), 5beta-Cyprinolsulfate([Formula: see text]6),PC(18:0/0:0) ([Formula: see text]7), 1-Nitro-5-hydroxy-6-glutathionyl-5,6-dihydronaphthalene([Formula: see text]8),Glycocholic acid([Formula: see text]9),[Formula: see text]-Arginine([Formula: see text]10) andGulonic acid([Formula: see text]11), were involved in several metabolic pathways, such as the glycerophospholipid metabolism and primary bile acid biosynthesis. Interestingly, there was a strong correlation between the perturbed gut flora in Bilophila and Bifidobacterium and the altered intestinal metabolite of 3[Formula: see text],6[Formula: see text],7[Formula: see text]-Trihydroxy-5[Formula: see text]-cholanoic acid and Cholanoic acid and [Formula: see text]-Arginine. This finding suggested that the effects of electroacupuncture might change the proportions of Bilophila and Bifidobacterium by regulating the constituents of the functional metabolite of 3[Formula: see text],6[Formula: see text],7[Formula: see text]-Trihydroxy-5[Formula: see text]-cholanoic acid and Cholanoic acid and [Formula: see text]-Arginine. These results indicated that the effects of electroacupuncture focused on custom metabolic pathways as well as depend on the changes in the gut microbiota in obesity. These findings suggest that the 16S rRNA gene sequencing and HPLC-MS-based metabolomics approach can be applied to comprehensively assess the effects of traditional Chinese medicines.
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Affiliation(s)
- Yuan-Cheng Si
- College of Acupuncture and Tuina, Guizhou University of Traditional Chinese Medicine, Dongqing South Road, Guiyang, Guizhou 550025, P. R. China
| | - Chen-Chen Ren
- College of Acupuncture and Tuina, Guizhou University of Traditional Chinese Medicine, Dongqing South Road, Guiyang, Guizhou 550025, P. R. China
| | - Er-Wei Zhang
- College of Acupuncture and Tuina, Guizhou University of Traditional Chinese Medicine, Dongqing South Road, Guiyang, Guizhou 550025, P. R. China
| | - Zhao-Xia Kang
- College of Acupuncture and Tuina, Guizhou University of Traditional Chinese Medicine, Dongqing South Road, Guiyang, Guizhou 550025, P. R. China
| | - Xi-Ya Mo
- College of Acupuncture and Tuina, Guizhou University of Traditional Chinese Medicine, Dongqing South Road, Guiyang, Guizhou 550025, P. R. China
| | - Qing-Qing Li
- College of Acupuncture and Tuina, Guizhou University of Traditional Chinese Medicine, Dongqing South Road, Guiyang, Guizhou 550025, P. R. China
| | - Bo Chen
- College of Acupuncture and Tuina, Guizhou University of Traditional Chinese Medicine, Dongqing South Road, Guiyang, Guizhou 550025, P. R. China
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11
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Dysbiotic Gut Bacteria in Obesity: An Overview of the Metabolic Mechanisms and Therapeutic Perspectives of Next-Generation Probiotics. Microorganisms 2022; 10:microorganisms10020452. [PMID: 35208906 PMCID: PMC8877435 DOI: 10.3390/microorganisms10020452] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
Obesity, a worldwide health concern with a constantly rising prevalence, is a multifactorial chronic disease associated with a wide range of physiological disruptions, including energy imbalance, central appetite and food reward dysregulation, and hormonal alterations and gut dysbiosis. The gut microbiome is a well-recognized factor in the pathophysiology of obesity, and its influence on host physiology has been extensively investigated over the last decade. This review highlights the mechanisms by which gut dysbiosis can contribute to the pathophysiology of obesity. In particular, we discuss gut microbiota’s contribution to host energy homeostatic changes, low-grade inflammation, and regulation of fat deposition and bile acid metabolism via bacterial metabolites, such as short-chain fatty acids, and bacterial components, such as lipopolysaccharides, among others. Finally, therapeutic strategies based on next-generation probiotics aiming to re-shape the intestinal microbiota and reverse metabolic alterations associated with obesity are described.
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12
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Van Den Bossche T, Arntzen MØ, Becher D, Benndorf D, Eijsink VGH, Henry C, Jagtap PD, Jehmlich N, Juste C, Kunath BJ, Mesuere B, Muth T, Pope PB, Seifert J, Tanca A, Uzzau S, Wilmes P, Hettich RL, Armengaud J. The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. MICROBIOME 2021; 9:243. [PMID: 34930457 PMCID: PMC8690404 DOI: 10.1186/s40168-021-01176-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/10/2021] [Indexed: 05/04/2023]
Abstract
Through connecting genomic and metabolic information, metaproteomics is an essential approach for understanding how microbiomes function in space and time. The international metaproteomics community is delighted to announce the launch of the Metaproteomics Initiative (www.metaproteomics.org), the goal of which is to promote dissemination of metaproteomics fundamentals, advancements, and applications through collaborative networking in microbiome research. The Initiative aims to be the central information hub and open meeting place where newcomers and experts interact to communicate, standardize, and accelerate experimental and bioinformatic methodologies in this field. We invite the entire microbiome community to join and discuss potential synergies at the interfaces with other disciplines, and to collectively promote innovative approaches to gain deeper insights into microbiome functions and dynamics. Video Abstract.
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Affiliation(s)
- Tim Van Den Bossche
- VIB-UGent Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000, Ghent, Belgium
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Dörte Becher
- Institute for Microbiology, Department for Microbial Proteomics, University of Greifswald, 17498, Greifswald, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, 39106, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
- Microbiology, Anhalt University of Applied Sciences, 06354, Köthen, Germany
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Céline Henry
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research GmbH-UFZ, Department of Molecular Systems Biology, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Catherine Juste
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Benoit J Kunath
- Luxembourg Centre for Systems Biomedicine and Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bart Mesuere
- VIB-UGent Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Thilo Muth
- Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, 1432, Ås, Norway
- Faculty of Biosciences, NMBU - Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Jana Seifert
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70599, Stuttgart, Germany
| | - Alessandro Tanca
- Center for Research and Education on the Microbiota, Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Sergio Uzzau
- Center for Research and Education on the Microbiota, Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine and Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - 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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13
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Walke D, Schallert K, Ramesh P, Benndorf D, Lange E, Reichl U, Heyer R. MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways. Int J Mol Sci 2021; 22:ijms222010992. [PMID: 34681649 PMCID: PMC8539661 DOI: 10.3390/ijms222010992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/02/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Taxonomic and functional characterization of microbial communities from diverse environments such as the human gut or biogas plants by multi-omics methods plays an ever more important role. Researchers assign all identified genes, transcripts, or proteins to biological pathways to better understand the function of single species and microbial communities. However, due to the versality of microbial metabolism and a still-increasing number of newly biological pathways, linkage to standard pathway maps such as the KEGG central carbon metabolism is often problematic. We successfully implemented and validated a new user-friendly, stand-alone web application, the MPA_Pathway_Tool. It consists of two parts, called 'Pathway-Creator' and 'Pathway-Calculator'. The 'Pathway-Creator' enables an easy set-up of user-defined pathways with specific taxonomic constraints. The 'Pathway-Calculator' automatically maps microbial community data from multiple measurements on selected pathways and visualizes the results. The MPA_Pathway_Tool is implemented in Java and ReactJS.
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Affiliation(s)
- Daniel Walke
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
- Correspondence: (D.W.); (R.H.)
| | - Kay Schallert
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
| | - Prasanna Ramesh
- Database and Software Engineering Group, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany;
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
- Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Microbiology, Bernburger Straße 55, 06354 Köthen, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Emanuel Lange
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
| | - Udo Reichl
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (K.S.); (D.B.); (E.L.); (U.R.)
- Database and Software Engineering Group, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany;
- Correspondence: (D.W.); (R.H.)
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