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Isokääntä H, Pinto da Silva L, Karu N, Kallonen T, Aatsinki AK, Hankemeier T, Schimmel L, Diaz E, Hyötyläinen T, Dorrestein PC, Knight R, Orešič M, Kaddurah-Daouk R, Dickens AM, Lamichhane S. Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization. Anal Chem 2024; 96:8893-8904. [PMID: 38782403 PMCID: PMC11154662 DOI: 10.1021/acs.analchem.3c04436] [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: 10/02/2023] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
Metabolites from feces provide important insights into the functionality of the gut microbiome. As immediate freezing is not always feasible in gut microbiome studies, there is a need for sampling protocols that provide the stability of the fecal metabolome and microbiome at room temperature (RT). Here, we investigated the stability of various metabolites and the microbiome (16S rRNA) in feces collected in 95% ethanol (EtOH) and commercially available sample collection kits with specific preservatives OMNImet•GUT/OMNIgene•GUT. To simulate field-collection scenarios, the samples were stored at different temperatures at varying durations (24 h + 4 °C, 24 h RT, 36 h RT, 48 h RT, and 7 days RT) and compared to aliquots immediately frozen at -80 °C. We applied several targeted and untargeted metabolomics platforms to measure lipids, polar metabolites, endocannabinoids, short-chain fatty acids (SCFAs), and bile acids (BAs). We found that SCFAs in the nonstabilized samples increased over time, while a stable profile was recorded in sample aliquots stored in 95% EtOH and OMNImet•GUT. When comparing the metabolite levels between aliquots stored at room temperature and at +4 °C, we detected several changes in microbial metabolites, including multiple BAs and SCFAs. Taken together, we found that storing samples at RT and stabilizing them in 95% EtOH yielded metabolomic results comparable to those from flash freezing. We also found that the overall composition of the microbiome did not vary significantly between different storage types. However, notable differences were observed in the α diversity. Altogether, the stability of the metabolome and microbiome in 95% EtOH provided results similar to those of the validated commercial collection kits OMNImet•GUT and OMNIgene•GUT, respectively.
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Affiliation(s)
- Heidi Isokääntä
- Research
Center for Infections and Immunity, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Lucas Pinto da Silva
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
| | - Naama Karu
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Teemu Kallonen
- Department
of Clinical Microbiology, Laboratory Division, Turku University Hospital, Kiinamyllynkatu 10 D, 20520 Turku, Finland
- Clinical
Microbiome Bank, Microbe Center, University
Hospital and University of Turku, 20520 Turku, Finland
| | - Anna-Katariina Aatsinki
- Centre
for
Population Health Research, University of
Turku, Kiinamyllynkatu
10A, 20520 Turku, Finland
| | - Thomas Hankemeier
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Leyla Schimmel
- Department
of Psychiatry and Behavioral Sciences, Duke
University, Durham, North Carolina 27708-0187, United States
| | - Edgar Diaz
- Department
of Psychiatry and Behavioral Sciences, Duke
University, Durham, North Carolina 27708-0187, United States
| | - Tuulia Hyötyläinen
- School
of Science and Technology, Örebro
University, 70281 Örebro, Sweden
| | - Pieter C. Dorrestein
- Center
for Microbiome Innovation, University of
California, San Diego, La Jolla, California 92093-6607, United States
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California,
San Diego, 9500 Gilman, La Jolla, California 92093-0657, United States
| | - Rob Knight
- Center
for Microbiome Innovation, University of
California, San Diego, La Jolla, California 92093-6607, United States
| | - Matej Orešič
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden
| | - Rima Kaddurah-Daouk
- Department
of Psychiatry and Behavioral Sciences, Duke
University, Durham, North Carolina 27708-0187, United States
| | - Alex M. Dickens
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
- Department of Chemistry, University of
Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Santosh Lamichhane
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
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2
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Indira Chandran V, Wernberg CW, Lauridsen MM, Skytthe MK, Bendixen SM, Larsen FT, Hansen CD, Grønkjær LL, Siersbæk MS, Caterino TD, Detlefsen S, Møller HJ, Grøntved L, Ravnskjaer K, Moestrup SK, Thiele MS, Krag A, Graversen JH. Circulating TREM2 as a noninvasive diagnostic biomarker for NASH in patients with elevated liver stiffness. Hepatology 2023; 77:558-572. [PMID: 35712786 PMCID: PMC9869959 DOI: 10.1002/hep.32620] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/24/2022] [Accepted: 06/12/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND AND AIMS Reliable noninvasive biomarkers are an unmet clinical need for the diagnosis of NASH. This study investigates the diagnostic accuracy of the circulating triggering receptor expressed on myeloid cells 2 (plasma TREM2) as a biomarker for NASH in patients with NAFLD and elevated liver stiffness. APPROACH AND RESULTS We collected cross-sectional, clinical data including liver biopsies from a derivation ( n = 48) and a validation cohort ( n = 170) of patients with elevated liver stiffness measurement (LSM ≥ 8.0 kPa). Patients with NAFLD activity scores (NAS) ≥4 were defined as having NASH. Plasma TREM2 levels were significantly elevated in patients with NASH of the derivation cohort, with an area under the receiver operating characteristics curve (AUROC) of 0.92 (95% confidence interval [CI], 0.84-0.99). In the validation cohort, plasma TREM2 level increased approximately two-fold in patients with NASH, and a strong diagnostic accuracy was confirmed (AUROC, 0.83; 95% CI, 0.77-0.89; p < 0.0001). Plasma TREM2 levels were associated with the individual histologic features of NAS: steatosis, lobular inflammation, and ballooning ( p < 0.0001), but only weakly with fibrosis stages. Dual cutoffs for rule-in and rule-out were explored: a plasma TREM2 level of ≤38 ng/ml was found to be an optimal NASH rule-out cutoff (sensitivity 90%; specificity 52%), whereas a plasma TREM2 level of ≥65 ng/ml was an optimal NASH rule-in cutoff (specificity 89%; sensitivity 54%). CONCLUSIONS Plasma TREM2 is a plausible individual biomarker that can rule-in or rule-out the presence of NASH with high accuracy and thus has the potential to reduce the need for liver biopsies and to identify patients who are eligible for clinical trials in NASH.
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Affiliation(s)
| | - Charlotte Wilhelmina Wernberg
- Liver Research Group, Department of Gastroenterology and Hepatology, University Hospital of South Denmark, Esbjerg, Denmark,Centre for Liver Research, Department of Gastroenterology and Hepatology, Odense University Hospital, Odense, Denmark
| | - Mette Munk Lauridsen
- Liver Research Group, Department of Gastroenterology and Hepatology, University Hospital of South Denmark, Esbjerg, Denmark
| | | | | | - Frederik Tibert Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Camilla Dalby Hansen
- Centre for Liver Research, Department of Gastroenterology and Hepatology, Odense University Hospital, Odense, Denmark
| | - Lea Ladegaard Grønkjær
- Liver Research Group, Department of Gastroenterology and Hepatology, University Hospital of South Denmark, Esbjerg, Denmark
| | - Majken Storm Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Tina Di Caterino
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Sönke Detlefsen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Holger Jon Møller
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Kim Ravnskjaer
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Søren Kragh Moestrup
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Maja Sofie Thiele
- Centre for Liver Research, Department of Gastroenterology and Hepatology, Odense University Hospital, Odense, Denmark
| | - Aleksander Krag
- Centre for Liver Research, Department of Gastroenterology and Hepatology, Odense University Hospital, Odense, Denmark
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3
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de Zawadzki A, Thiele M, Suvitaival T, Wretlind A, Kim M, Ali M, Bjerre AF, Stahr K, Mattila I, Hansen T, Krag A, Legido-Quigley C. High-Throughput UHPLC-MS to Screen Metabolites in Feces for Gut Metabolic Health. Metabolites 2022; 12:metabo12030211. [PMID: 35323654 PMCID: PMC8950041 DOI: 10.3390/metabo12030211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 02/01/2023] Open
Abstract
Feces are the product of our diets and have been linked to diseases of the gut, including Chron’s disease and metabolic diseases such as diabetes. For screening metabolites in heterogeneous samples such as feces, it is necessary to use fast and reproducible analytical methods that maximize metabolite detection. As sample preparation is crucial to obtain high quality data in MS-based clinical metabolomics, we developed a novel, efficient and robust method for preparing fecal samples for analysis with a focus in reducing aliquoting and detecting both polar and non-polar metabolites. Fecal samples (n = 475) from patients with alcohol-related liver disease and healthy controls were prepared according to the proposed method and analyzed in an UHPLC-QQQ targeted platform in order to obtain a quantitative profile of compounds that impact liver-gut axis metabolism. MS analyses of the prepared fecal samples have shown reproducibility and coverage of n = 28 metabolites, mostly comprising bile acids and amino acids. We report metabolite-wise relative standard deviation (RSD) in quality control samples, inter-day repeatability, LOD (limit of detection), LOQ (limit of quantification), range of linearity and method recovery. The average concentrations for 135 healthy participants are reported here for clinical applications. Our high-throughput method provides a novel tool for investigating gut-liver axis metabolism in liver-related diseases using a noninvasive collected sample.
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Affiliation(s)
- Andressa de Zawadzki
- Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark; (A.d.Z.); (T.S.); (A.W.); (M.K.); (M.A.); (A.F.B.); (K.S.); (I.M.)
| | - Maja Thiele
- Department of Gastroenterology and Hepatology, Odense University Hospital, 5000 Odense, Denmark; (M.T.); (A.K.)
- Department of Clinical Medicine, University of Southern Denmark, 5230 Odense, Denmark
| | - Tommi Suvitaival
- Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark; (A.d.Z.); (T.S.); (A.W.); (M.K.); (M.A.); (A.F.B.); (K.S.); (I.M.)
| | - Asger Wretlind
- Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark; (A.d.Z.); (T.S.); (A.W.); (M.K.); (M.A.); (A.F.B.); (K.S.); (I.M.)
| | - Min Kim
- Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark; (A.d.Z.); (T.S.); (A.W.); (M.K.); (M.A.); (A.F.B.); (K.S.); (I.M.)
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, 2730 Herlev, Denmark
| | - Mina Ali
- Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark; (A.d.Z.); (T.S.); (A.W.); (M.K.); (M.A.); (A.F.B.); (K.S.); (I.M.)
| | - Annette F. Bjerre
- Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark; (A.d.Z.); (T.S.); (A.W.); (M.K.); (M.A.); (A.F.B.); (K.S.); (I.M.)
| | - Karin Stahr
- Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark; (A.d.Z.); (T.S.); (A.W.); (M.K.); (M.A.); (A.F.B.); (K.S.); (I.M.)
| | - Ismo Mattila
- Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark; (A.d.Z.); (T.S.); (A.W.); (M.K.); (M.A.); (A.F.B.); (K.S.); (I.M.)
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 1165 Copenhagen, Denmark;
| | - Aleksander Krag
- Department of Gastroenterology and Hepatology, Odense University Hospital, 5000 Odense, Denmark; (M.T.); (A.K.)
- Department of Clinical Medicine, University of Southern Denmark, 5230 Odense, Denmark
| | - Cristina Legido-Quigley
- Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark; (A.d.Z.); (T.S.); (A.W.); (M.K.); (M.A.); (A.F.B.); (K.S.); (I.M.)
- Institute of Pharmaceutical Science, King’s College London, London SE19NH, UK
- Correspondence:
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4
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Zhang X, Xu T, Wang X, Geng Y, Zhao N, Hu L, Liu H, Kang S, Xu S. Effect of Dietary Protein Levels on Dynamic Changes and Interactions of Ruminal Microbiota and Metabolites in Yaks on the Qinghai-Tibetan Plateau. Front Microbiol 2021; 12:684340. [PMID: 34434174 PMCID: PMC8381366 DOI: 10.3389/fmicb.2021.684340] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/30/2021] [Indexed: 12/26/2022] Open
Abstract
To improve performance and optimize rumen function in yaks (Bos grunniens), further knowledge on the appropriate dietary protein levels for ruminal microbiota and the metabolite profiles of yaks in feedlot feeding is necessary. Current understanding of dietary protein requirements, ruminal microbiota, and metabolites is limited. In this study, yaks were fed a low-protein diet (L; 9.64%), middle low-protein diet (ML; 11.25%), middle high-protein diet (MH; 12.48%), or a high-protein diet (H; 13.87%), and the effects of those diets on changes and interactions in ruminal microbiota and metabolites were investigated. Twenty-four female yaks were selected, and the effects on ruminal microbiota and metabolites were investigated using 16s rRNA gene sequencing and gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS). Diets containing different protein levels changed the composition of the rumen bacterial community, the H group significantly reduced the diversity of ruminal microbiota (p < 0.05), and the number of shared amplicon sequence variants (ASVs) between the H group and the other three groups was lower, suggesting that the ruminal microbiota community fluctuated more with a high-protein diet. In rumen, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant bacteria at the phylum level, and Bacteroidetes was significantly less abundant in the MH group than in the L and ML groups (p < 0.05). Prevotella_1, Rikenellaceae_RC9_gut_group, and Christensenellaceae_R-7_group had the highest abundance at the genus level. Prevotellaceae was enriched in the low-protein groups, whereas Bacteroidales_BS11_gut_group was enriched in the high-protein groups. Rumen metabolite concentrations and metabolic patterns were altered by dietary protein levels: organic acid metabolites, antioxidant-related metabolites, and some plant-derived metabolites showed variation between the groups. Enrichment analysis revealed that significant changes were concentrated in six pathways, including the citrate cycle (TCA cycle), glyoxylate and dicarboxylate metabolism, and butanoate metabolism. Network analysis showed promotion or restraint relationships between different rumen microbiota and metabolites. Overall, the rumen function was higher in the MH group. This study provides a reference for appropriate dietary protein levels and improves understanding of rumen microbes and metabolites.
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Affiliation(s)
- XiaoLing Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - TianWei Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - XunGang Wang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - YuanYue Geng
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Na Zhao
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - LinYong Hu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - HongJin Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - ShengPing Kang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - ShiXiao Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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5
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Renwick S, Ganobis CM, Elder RA, Gianetto-Hill C, Higgins G, Robinson AV, Vancuren SJ, Wilde J, Allen-Vercoe E. Culturing Human Gut Microbiomes in the Laboratory. Annu Rev Microbiol 2021; 75:49-69. [PMID: 34038159 DOI: 10.1146/annurev-micro-031021-084116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human gut microbiota is a complex community of prokaryotic and eukaryotic microbes and viral particles that is increasingly associated with many aspects of host physiology and health. However, the classical microbiology approach of axenic culture cannot provide a complete picture of the complex interactions between microbes and their hosts in vivo. As such, recently there has been much interest in the culture of gut microbial ecosystems in the laboratory as a strategy to better understand their compositions and functions. In this review, we discuss the model platforms and methods available in the contemporary microbiology laboratory to study human gut microbiomes, as well as current knowledge surrounding the isolation of human gut microbes for the potential construction of defined communities for use in model systems. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Simone Renwick
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Caroline M Ganobis
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Riley A Elder
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Connor Gianetto-Hill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Gregory Higgins
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Avery V Robinson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Sarah J Vancuren
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Jacob Wilde
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
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6
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Le Barz M, Vors C, Combe E, Joumard-Cubizolles L, Lecomte M, Joffre F, Trauchessec M, Pesenti S, Loizon E, Breyton AE, Meugnier E, Bertrand K, Drai J, Robert C, Durand A, Cuerq C, Gaborit P, Leconte N, Bernalier-Donadille A, Cotte E, Laville M, Lambert-Porcheron S, Ouchchane L, Vidal H, Malpuech-Brugère C, Cheillan D, Michalski MC. Milk polar lipids favorably alter circulating and intestinal ceramide and sphingomyelin species in postmenopausal women. JCI Insight 2021; 6:146161. [PMID: 33857018 PMCID: PMC8262315 DOI: 10.1172/jci.insight.146161] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/09/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND High circulating levels of ceramides (Cer) and sphingomyelins (SM) are associated with cardiometabolic diseases. The consumption of whole fat dairy products, naturally containing such polar lipids (PL), is associated with health benefits, but the impact on sphingolipidome remains unknown. METHODS In a 4-week randomized controlled trial, 58 postmenopausal women daily consumed milk PL-enriched cream cheese (0, 3, or 5 g of milk PL). Postprandial metabolic explorations were performed before and after supplementation. Analyses included SM and Cer species in serum, chylomicrons, and feces. The ileal contents of 4 ileostomy patients were also explored after acute milk PL intake. RESULTS Milk PL decreased serum atherogenic C24:1 Cer, C16:1 SM, and C18:1 SM species (Pgroup < 0.05). Changes in serum C16+18 SM species were positively correlated with the reduction of cholesterol (r = 0.706), LDL-C (r = 0.666), and ApoB (r = 0.705) (P < 0.001). Milk PL decreased chylomicron content in total SM and C24:1 Cer (Pgroup < 0.001), parallel to a marked increase in total Cer in feces (Pgroup < 0.001). Milk PL modulated some specific SM and Cer species in both ileal efflux and feces, suggesting differential absorption and metabolization processes in the gut. CONCLUSION Milk PL supplementation decreased atherogenic SM and Cer species associated with the improvement of cardiovascular risk markers. Our findings bring insights on sphingolipid metabolism in the gut, especially Cer, as signaling molecules potentially participating in the beneficial effects of milk PL. TRIAL REGISTRATION ClinicalTrials.gov, NCT02099032, NCT02146339. FUNDING ANR-11-ALID-007-01; PHRCI-2014: VALOBAB, no. 14-007; CNIEL; GLN 2018-11-07; HCL (sponsor).
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Affiliation(s)
- Mélanie Le Barz
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France
| | - Cécile Vors
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France.,TCentre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, CENS, FCRIN/FORCE Network, 69310, Pierre-Bénite, France
| | - Emmanuel Combe
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France
| | - Laurie Joumard-Cubizolles
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000, Clermont-Ferrand, France
| | - Manon Lecomte
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France.,TCentre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, CENS, FCRIN/FORCE Network, 69310, Pierre-Bénite, France
| | - Florent Joffre
- ITERG, ZA Pessac-Canéjan, 11 Rue Gaspard Monge, 33610, Canéjan, France
| | - Michèle Trauchessec
- Hospices Civils de Lyon, 69000, Lyon, France.,Unité Maladies Héréditaires du Métabolisme, Service de Biochimie et Biologie Moléculaire Grand Est, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, 69677, Bron, France
| | - Sandra Pesenti
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France
| | - Emmanuelle Loizon
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France
| | - Anne-Esther Breyton
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France.,TCentre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, CENS, FCRIN/FORCE Network, 69310, Pierre-Bénite, France
| | - Emmanuelle Meugnier
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France
| | - Karène Bertrand
- ITERG, ZA Pessac-Canéjan, 11 Rue Gaspard Monge, 33610, Canéjan, France
| | - Jocelyne Drai
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France.,Hospices Civils de Lyon, 69000, Lyon, France.,Unité de Nutrition Endocrinologie Métabolisme, Service de Biochimie, Centre de Biologie et de Pathologie Sud, Hospices Civils de Lyon, 69495, Pierre-Bénite, France
| | - Chloé Robert
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France.,TCentre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, CENS, FCRIN/FORCE Network, 69310, Pierre-Bénite, France
| | - Annie Durand
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France
| | - Charlotte Cuerq
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France.,Hospices Civils de Lyon, 69000, Lyon, France.,Unité de Nutrition Endocrinologie Métabolisme, Service de Biochimie, Centre de Biologie et de Pathologie Sud, Hospices Civils de Lyon, 69495, Pierre-Bénite, France
| | - Patrice Gaborit
- ACTALIA Dairy Products and Technologies, Avenue François Mitterrand, BP49, 17700, Surgères, France.,ENILIA ENSMIC, Avenue François Mitterrand, 17700, Surgères, France
| | - Nadine Leconte
- INRAE, Institut Agro, STLO (Science et Technologie du Lait et de l'Œuf), 35042, Rennes, France
| | | | - Eddy Cotte
- Hospices Civils de Lyon, 69000, Lyon, France.,Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, Service de chirurgie digestive, 69310, Pierre-Bénite, France.,Université Claude Bernard Lyon 1, Faculté de médecine Lyon-Sud-Charles Mérieux, EMR 3738, 69600, Oullins, France
| | - Martine Laville
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France.,TCentre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, CENS, FCRIN/FORCE Network, 69310, Pierre-Bénite, France.,Hospices Civils de Lyon, 69000, Lyon, France.,Université Claude Bernard Lyon 1, Faculté de médecine Lyon-Sud-Charles Mérieux, EMR 3738, 69600, Oullins, France
| | - Stéphanie Lambert-Porcheron
- TCentre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, CENS, FCRIN/FORCE Network, 69310, Pierre-Bénite, France.,Hospices Civils de Lyon, 69000, Lyon, France
| | - Lemlih Ouchchane
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut Pascal, 63000, Clermont-Ferrand, France.,CHU Clermont-Ferrand, Unité de Biostatistique-Informatique Médicale, 63000, Clermont-Ferrand, France
| | - Hubert Vidal
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France
| | - Corinne Malpuech-Brugère
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000, Clermont-Ferrand, France
| | - David Cheillan
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France.,Hospices Civils de Lyon, 69000, Lyon, France.,Unité Maladies Héréditaires du Métabolisme, Service de Biochimie et Biologie Moléculaire Grand Est, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, 69677, Bron, France
| | - Marie-Caroline Michalski
- Univ Lyon, CarMeN laboratory, INSERM, INRAE, INSA Lyon, Université Claude Bernard Lyon 1, Charles Mérieux Medical School, 69310, Pierre-Bénite, France.,TCentre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Université Claude Bernard Lyon1, Hospices Civils de Lyon, CENS, FCRIN/FORCE Network, 69310, Pierre-Bénite, France
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7
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Lamichhane S, Sen P, Alves MA, Ribeiro HC, Raunioniemi P, Hyötyläinen T, Orešič M. Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations. Metabolites 2021; 11:55. [PMID: 33467644 PMCID: PMC7830997 DOI: 10.3390/metabo11010055] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/09/2021] [Accepted: 01/12/2021] [Indexed: 02/08/2023] Open
Abstract
Various studies aiming to elucidate the role of the gut microbiome-metabolome co-axis in health and disease have primarily focused on water-soluble polar metabolites, whilst non-polar microbial lipids have received less attention. The concept of microbiota-dependent lipid biotransformation is over a century old. However, only recently, several studies have shown how microbial lipids alter intestinal and circulating lipid concentrations in the host, thus impacting human lipid homeostasis. There is emerging evidence that gut microbial communities play a particularly significant role in the regulation of host cholesterol and sphingolipid homeostasis. Here, we review and discuss recent research focusing on microbe-host-lipid co-metabolism. We also discuss the interplay of human gut microbiota and molecular lipids entering host systemic circulation, and its role in health and disease.
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Affiliation(s)
- Santosh Lamichhane
- Turku Bioscience Centre, University of Turku and Abo Akademi University, FI-20520 Turku, Finland; (P.S.); (M.A.A.); (H.C.R.); (P.R.); (M.O.)
| | - Partho Sen
- Turku Bioscience Centre, University of Turku and Abo Akademi University, FI-20520 Turku, Finland; (P.S.); (M.A.A.); (H.C.R.); (P.R.); (M.O.)
- School of Medical Sciences, Orebro University, 702 81 Orebro, Sweden
| | - Marina Amaral Alves
- Turku Bioscience Centre, University of Turku and Abo Akademi University, FI-20520 Turku, Finland; (P.S.); (M.A.A.); (H.C.R.); (P.R.); (M.O.)
| | - Henrique C. Ribeiro
- Turku Bioscience Centre, University of Turku and Abo Akademi University, FI-20520 Turku, Finland; (P.S.); (M.A.A.); (H.C.R.); (P.R.); (M.O.)
| | - Peppi Raunioniemi
- Turku Bioscience Centre, University of Turku and Abo Akademi University, FI-20520 Turku, Finland; (P.S.); (M.A.A.); (H.C.R.); (P.R.); (M.O.)
| | | | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Abo Akademi University, FI-20520 Turku, Finland; (P.S.); (M.A.A.); (H.C.R.); (P.R.); (M.O.)
- School of Medical Sciences, Orebro University, 702 81 Orebro, Sweden
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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8
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Mojsak P, Rey-Stolle F, Parfieniuk E, Kretowski A, Ciborowski M. The role of gut microbiota (GM) and GM-related metabolites in diabetes and obesity. A review of analytical methods used to measure GM-related metabolites in fecal samples with a focus on metabolites' derivatization step. J Pharm Biomed Anal 2020; 191:113617. [PMID: 32971497 DOI: 10.1016/j.jpba.2020.113617] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 12/12/2022]
Abstract
Disruption of gut microbiota (GM) composition is increasingly related to the pathogenesis of various metabolic diseases. Additionally, GM is responsible for the production and transformation of metabolites involved in the development of metabolic disorders, such as obesity and type 2 diabetes mellitus (T2DM). The current state of knowledge regarding the composition of GM and GM-related metabolites in relation to the progress and development of obesity and T2DM is presented in this review. To understand the relationships between GM-related metabolites and the development of metabolic disorders, their accurate qualitative and quantitative measurement in biological samples is needed. Feces represent a valuable biological matrix which composition may reflect the health status of the lower gastrointestinal tract and the whole organism. Mass spectrometry (MS), mainly in combination with gas chromatography (GC) or liquid chromatography (LC), is commonly used to measure fecal metabolites. However, profiling metabolites in such a complex matrix as feces is challenging from both analytical chemistry and biochemistry standpoints. Chemical derivatization is one of the most effective methods used to overcome these problems. In this review, we provide a comprehensive summary of the derivatization methods of GM-related metabolites prior to GC-MS or LC-MS analysis, which have been published in the last five years (2015-2020). Additionally, analytical methods used for the analysis of GM-related metabolites without the derivatization step are also presented.
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Affiliation(s)
- Patrycja Mojsak
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Fernanda Rey-Stolle
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Ewa Parfieniuk
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Adam Kretowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland; Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Michal Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland.
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