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Dehghan Manshadi M, Setoodeh P, Zare H. Systematic analysis of microorganisms' metabolism for selective targeting. Sci Rep 2024; 14:16446. [PMID: 39014020 PMCID: PMC11252421 DOI: 10.1038/s41598-024-65936-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/25/2024] [Indexed: 07/18/2024] Open
Abstract
Selective drugs with a relatively narrow spectrum can reduce the side effects of treatments compared to broad-spectrum antibiotics by specifically targeting the pathogens responsible for infection. Furthermore, combating an infectious pathogen, especially a drug-resistant microorganism, is more efficient by attacking multiple targets. Here, we combined synthetic lethality with selective drug targeting to identify multi-target and organism-specific potential drug candidates by systematically analyzing the genome-scale metabolic models of six different microorganisms. By considering microorganisms as targeted or conserved in groups ranging from one to six members, we designed 665 individual case studies. For each case, we identified single essential reactions as well as double, triple, and quadruple synthetic lethal reaction sets that are lethal for targeted microorganisms and neutral for conserved ones. As expected, the number of obtained solutions for each case depends on the genomic similarity between the studied microorganisms. Mapping the identified potential drug targets to their corresponding pathways highlighted the importance of key subsystems such as cell envelope biosynthesis, glycerophospholipid metabolism, membrane lipid metabolism, and the nucleotide salvage pathway. To assist in the validation and further investigation of our proposed potential drug targets, we introduced two sets of targets that can theoretically address a substantial portion of the 665 cases. We expect that the obtained solutions provide valuable insights into designing narrow-spectrum drugs that selectively cause system-wide damage only to the target microorganisms.
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Affiliation(s)
- Mehdi Dehghan Manshadi
- Department of Chemical Engineering, School of Chemical, Petroleum and Gas Engineering, Shiraz University, Shiraz, Iran
| | - Payam Setoodeh
- Department of Chemical Engineering, School of Chemical, Petroleum and Gas Engineering, Shiraz University, Shiraz, Iran.
- W Booth School of Engineering Practice and Technology, McMaster University, Hamilton, ON, Canada.
| | - Habil Zare
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX, USA.
- Department of Cell Systems and Anatomy, University of Texas Health Science Center, San Antonio, TX, USA.
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2
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Zaidan N, Wang C, Chen Z, Lieske JC, Milliner D, Seide B, Ho M, Li H, Ruggles KV, Modersitzki F, Goldfarb DS, Blaser M, Nazzal L. Multiomics Assessment of the Gut Microbiome in Rare Hyperoxaluric Conditions. Kidney Int Rep 2024; 9:1836-1848. [PMID: 38899198 PMCID: PMC11184406 DOI: 10.1016/j.ekir.2024.03.004] [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] [Received: 12/11/2023] [Revised: 02/14/2024] [Accepted: 03/04/2024] [Indexed: 06/21/2024] Open
Abstract
Introduction Hyperoxaluria is a risk factor for kidney stone formation and chronic kidney disease progression. The microbiome is an important protective factor against oxalate accumulation through the activity of its oxalate-degrading enzymes (ODEs). In this cross-sectional study, we leverage multiomics to characterize the microbial community of participants with primary and enteric hyperoxaluria, as well as idiopathic calcium oxalate kidney stone (CKS) formers, focusing on the relationship between oxalate degrading functions of the microbiome. Methods Patients diagnosed with type 1 primary hyperoxaluria (PH), enteric hyperoxaluria (EH), and CKS were screened for inclusion in the study. Participants completed a food frequency questionnaire recording their dietary oxalate content while fecal oxalate levels were ascertained. DNA and RNA were extracted from stool samples and sequenced. Metagenomic (MTG) and metatranscriptomic (MTT) data were processed through our bioinformatics pipelines, and microbiome diversity, differential abundance, and networks were subject to statistical analysis in relationship with oxalate levels. Results A total of 38 subjects were recruited, including 13 healthy participants, 12 patients with recurrent CKS, 8 with PH, and 5 with EH. Urinary and fecal oxalate were significantly higher in the PH and the EH population compared to healthy controls. At the community level, alpha-diversity and beta-diversity indices were similar across all populations. The respective contributions of single bacterial species to the total oxalate degradative potential were similar in healthy and PH subjects. MTT-based network analysis identified the most interactive bacterial network in patients with PH. Patients with EH had a decreased abundance of multiple major oxalate degraders. Conclusion The composition and inferred activity of oxalate-degrading microbiota were differentially associated with host clinical conditions. Identifying these changes improves our understanding of the relationships between dietary constituents, microbiota, and oxalate homeostasis, and suggests new therapeutic approaches protecting against hyperoxaluria.
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Affiliation(s)
- Nadim Zaidan
- Department of Medicine, Division of Nephrology, NYU Langone Medical Center, New York, New York, USA
| | - Chan Wang
- Department of Population Health, New York University School of Medicine, NYU Langone Health, New York, New York, USA
| | - Ze Chen
- Department of Population Health, New York University School of Medicine, NYU Langone Health, New York, New York, USA
| | - John C. Lieske
- Department of Internal Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
- Department of Laboratory Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Dawn Milliner
- Department of Internal Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Barbara Seide
- Department of Internal Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Melody Ho
- Department of Medicine, Division of Nephrology, NYU Langone Medical Center, New York, New York, USA
| | - Huilin Li
- Department of Population Health, New York University School of Medicine, NYU Langone Health, New York, New York, USA
| | - Kelly V. Ruggles
- Department of Medicine, Division of Precision Medicine, New York University School of Medicine, NYU Langone Health, New York, New York, USA
| | - Frank Modersitzki
- Department of Medicine, Division of Nephrology, NYU Langone Medical Center, New York, New York, USA
| | - David S. Goldfarb
- Department of Medicine, Division of Nephrology, NYU Langone Medical Center, New York, New York, USA
| | - Martin Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - Lama Nazzal
- Department of Medicine, Division of Nephrology, NYU Langone Medical Center, New York, New York, USA
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Lee J, Lee J, Kim K, Lee J, Jung Y, Hyeon JS, Seo A, Jin W, Weon B, Shin N, Kim S, Lim CS, Kim YS, Lee JP, Hwang GS, Yang SH. Antibiotic-induced intestinal microbiota depletion can attenuate the acute kidney injury to chronic kidney disease transition via NADPH oxidase 2 and trimethylamine-N-oxide inhibition. Kidney Int 2024; 105:1239-1253. [PMID: 38431216 DOI: 10.1016/j.kint.2024.01.040] [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: 03/12/2023] [Revised: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 03/05/2024]
Abstract
Intestinal microbiota and their metabolites affect systemic inflammation and kidney disease outcomes. Here, we investigated the key metabolites associated with the acute kidney injury (AKI)-to chronic kidney disease (CKD) transition and the effect of antibiotic-induced microbiota depletion (AIMD) on this transition. In 61 patients with AKI, 59 plasma metabolites were assessed to determine the risk of AKI-to-CKD transition. An AKI-to-CKD transition murine model was established four weeks after unilateral ischemia-reperfusion injury (IRI) to determine the effects of AIMD on the gut microbiome, metabolites, and pathological responses related to CKD transition. Human proximal tubular epithelial cells were challenged with CKD transition-related metabolites, and inhibitory effects of NADPH oxidase 2 (NOX2) signals were tested. Based on clinical metabolomics, plasma trimethylamine N-oxide (TMAO) was associated with a significantly increased risk for AKI-to-CKD transition [adjusted odds ratio 4.389 (95% confidence interval 1.106-17.416)]. In vivo, AIMD inhibited a unilateral IRI-induced increase in TMAO, along with a decrease in apoptosis, inflammation, and fibrosis. The expression of NOX2 and oxidative stress decreased after AIMD. In vitro, TMAO induced fibrosis with NOX2 activation and oxidative stress. NOX2 inhibition successfully attenuated apoptosis, inflammation, and fibrosis with suppression of G2/M arrest. NOX2 inhibition (in vivo) showed improvement in pathological changes with a decrease in oxidative stress without changes in TMAO levels. Thus, TMAO is a key metabolite associated with the AKI-to-CKD transition, and NOX2 activation was identified as a key regulator of TMAO-related AKI-to-CKD transition both in vivo and in vitro.
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Affiliation(s)
- Jeonghwan Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Jinhaeng Lee
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
| | - Kyuhong Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jiwon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Youngae Jung
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
| | - Jin Seong Hyeon
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
| | - Areum Seo
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Wencheng Jin
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Boram Weon
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea; Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Nayeon Shin
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Sejoong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Chun Soo Lim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Yon Su Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jung Pyo Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea.
| | - Geum-Sook Hwang
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea; College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea.
| | - Seung Hee Yang
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea; Kidney Research Institute, Seoul National University, Seoul, Republic of Korea.
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Vandecruys M, De Smet S, De Beir J, Renier M, Leunis S, Van Criekinge H, Glorieux G, Raes J, Vanden Wyngaert K, Nagler E, Calders P, Monbaliu D, Cornelissen V, Evenepoel P, Van Craenenbroeck AH. Revitalizing the Gut Microbiome in Chronic Kidney Disease: A Comprehensive Exploration of the Therapeutic Potential of Physical Activity. Toxins (Basel) 2024; 16:242. [PMID: 38922137 PMCID: PMC11209503 DOI: 10.3390/toxins16060242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024] Open
Abstract
Both physical inactivity and disruptions in the gut microbiome appear to be prevalent in patients with chronic kidney disease (CKD). Engaging in physical activity could present a novel nonpharmacological strategy for enhancing the gut microbiome and mitigating the adverse effects associated with microbial dysbiosis in individuals with CKD. This narrative review explores the underlying mechanisms through which physical activity may favorably modulate microbial health, either through direct impact on the gut or through interorgan crosstalk. Also, the development of microbial dysbiosis and its interplay with physical inactivity in patients with CKD are discussed. Mechanisms and interventions through which physical activity may restore gut homeostasis in individuals with CKD are explored.
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Affiliation(s)
- Marieke Vandecruys
- Nephrology and Renal Transplantation Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium; (M.V.); or (P.E.)
| | - Stefan De Smet
- Exercise Physiology Research Group, Department of Movement Sciences, KU Leuven, 3000 Leuven, Belgium;
| | - Jasmine De Beir
- Department of Rehabilitation Sciences, Ghent University, 9000 Ghent, Belgium; (J.D.B.); (P.C.)
| | - Marie Renier
- Group Rehabilitation for Internal Disorders, Department of Rehabilitation Sciences, KU Leuven, 3000 Leuven, Belgium; (M.R.); (V.C.)
| | - Sofie Leunis
- Department of Microbiology, Immunology and Transplantation, Abdominal Transplantation, KU Leuven, 3000 Leuven, Belgium; (S.L.); (H.V.C.); (D.M.)
| | - Hanne Van Criekinge
- Department of Microbiology, Immunology and Transplantation, Abdominal Transplantation, KU Leuven, 3000 Leuven, Belgium; (S.L.); (H.V.C.); (D.M.)
| | - Griet Glorieux
- Department of Internal Medicine and Pediatrics, Nephrology Section, Ghent University Hospital, 9000 Ghent, Belgium; (G.G.); (K.V.W.); (E.N.)
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute for Medical Research, 3000 Leuven, Belgium;
- VIB-KU Leuven Center for Microbiology, 3000 Leuven, Belgium
| | - Karsten Vanden Wyngaert
- Department of Internal Medicine and Pediatrics, Nephrology Section, Ghent University Hospital, 9000 Ghent, Belgium; (G.G.); (K.V.W.); (E.N.)
| | - Evi Nagler
- Department of Internal Medicine and Pediatrics, Nephrology Section, Ghent University Hospital, 9000 Ghent, Belgium; (G.G.); (K.V.W.); (E.N.)
| | - Patrick Calders
- Department of Rehabilitation Sciences, Ghent University, 9000 Ghent, Belgium; (J.D.B.); (P.C.)
| | - Diethard Monbaliu
- Department of Microbiology, Immunology and Transplantation, Abdominal Transplantation, KU Leuven, 3000 Leuven, Belgium; (S.L.); (H.V.C.); (D.M.)
- Transplantoux Foundation, 3000 Leuven, Belgium
| | - Véronique Cornelissen
- Group Rehabilitation for Internal Disorders, Department of Rehabilitation Sciences, KU Leuven, 3000 Leuven, Belgium; (M.R.); (V.C.)
| | - Pieter Evenepoel
- Nephrology and Renal Transplantation Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium; (M.V.); or (P.E.)
- Department of Nephrology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Amaryllis H. Van Craenenbroeck
- Nephrology and Renal Transplantation Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium; (M.V.); or (P.E.)
- Department of Nephrology, University Hospitals Leuven, 3000 Leuven, Belgium
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Lambert K, Rinninella E, Biruete A, Sumida K, Stanford J, Raoul P, Mele MC, Wang AYM, Mafra D. Targeting the Gut Microbiota in Kidney Disease: The Future in Renal Nutrition and Metabolism. J Ren Nutr 2023; 33:S30-S39. [PMID: 37632511 PMCID: PMC10872791 DOI: 10.1053/j.jrn.2022.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/05/2022] [Accepted: 12/10/2022] [Indexed: 08/28/2023] Open
Abstract
There is increasing interest in the therapeutic potential of manipulating the gut microbiome of patients with chronic kidney disease (CKD). This is because there is a substantial deviation from a balanced gut microbiota profile in CKD, with many deleterious downstream effects. Nutritional interventions such as plant-based diets with reduced animal protein intake and the use of probiotics, prebiotics, and synbiotics may alter the microbiome. This article aims to briefly describe what is known about the gut microbiome in patients with CKD, factors contributing to gut dysbiosis, and outline important evidence gaps. Future potential therapies, including restoring the microbiota with food and microbiota-based and metabolomic-based therapies, are also discussed.
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Affiliation(s)
- Kelly Lambert
- School of Medical, Indigenous, and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Emanuele Rinninella
- Clinical Nutrition Unit, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, Rome, Italy
| | - Annabel Biruete
- Department of Nutrition Science, Purdue University, West Lafayette, Indiana, USA, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Keiichi Sumida
- Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Tennessee
| | - Jordan Stanford
- School of Medical, Indigenous, and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales, Australia
| | - Pauline Raoul
- Clinical Nutrition Unit, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Maria Cristina Mele
- Clinical Nutrition Unit, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Angela Yee-Moon Wang
- Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong SAR, China
| | - Denise Mafra
- Professor, Graduate Program in Nutrition Sciences, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil
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Faerber V, Kuhn KS, Garneata L, Kalantar-Zadeh K, Kalim S, Raj DS, Westphal M. The Microbiome and Protein Carbamylation: Potential Targets for Protein-Restricted Diets Supplemented with Ketoanalogues in Predialysis Chronic Kidney Disease. Nutrients 2023; 15:3503. [PMID: 37630693 PMCID: PMC10459041 DOI: 10.3390/nu15163503] [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: 07/12/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
In chronic kidney disease (CKD), metabolic derangements resulting from the interplay between decreasing renal excretory capacity and impaired gut function contribute to accelerating disease progression and enhancing the risk of complications. To protect residual kidney function and improve quality of life in conservatively managed predialysis CKD patients, current guidelines recommend protein-restricted diets supplemented with essential amino acids (EAAs) and their ketoanalogues (KAs). In clinical studies, such an approach improved nitrogen balance and other secondary metabolic disturbances, translating to clinical benefits, mainly the delayed initiation of dialysis. There is also increasing evidence that a protein-restricted diet supplemented with KAs slows down disease progression. In the present review article, recent insights into the role of KA/EAA-supplemented protein-restricted diets in delaying CKD progression are summarized, and possible mechanistic underpinnings, such as protein carbamylation and gut dysbiosis, are elucidated. Emerging evidence suggests that lowering urea levels may reduce protein carbamylation, which might contribute to decreased morbidity and mortality. Protein restriction, alone or in combination with KA/EAA supplementation, modulates gut dysbiosis and decreases the generation of gut-derived uremic toxins associated, e.g., with cardiovascular disease, inflammation, protein energy wasting, and disease progression. Future studies are warranted to assess the effects on the gut microbiome, the generation of uremic toxins, as well as markers of carbamylation.
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Affiliation(s)
- Valentin Faerber
- Department of Medical Scientific Affairs, Pharma and Nutrition, Fresenius Kabi Deutschland GmbH, 61352 Bad Homburg, Germany; (K.S.K.); (M.W.)
| | - Katharina S. Kuhn
- Department of Medical Scientific Affairs, Pharma and Nutrition, Fresenius Kabi Deutschland GmbH, 61352 Bad Homburg, Germany; (K.S.K.); (M.W.)
| | - Liliana Garneata
- “Dr. Carol Davila” Teaching Hospital of Nephrology, 4 Calea Grivitei, Sector 1, 010731 Bucharest, Romania;
| | - Kamyar Kalantar-Zadeh
- Division of Nephrology Hypertension and Kidney Transplantation, Department of Medicine, University of California Irvine (UCI), Orange, CA 90286, USA;
| | - Sahir Kalim
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA;
| | - Dominic S. Raj
- Division of Kidney Diseases and Hypertension, George Washington University School of Medicine, Washington, DC 20037, USA;
| | - Martin Westphal
- Department of Medical Scientific Affairs, Pharma and Nutrition, Fresenius Kabi Deutschland GmbH, 61352 Bad Homburg, Germany; (K.S.K.); (M.W.)
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Serrano M, Srivastava A, Buck G, Zhu B, Edupuganti L, Adegbulugbe E, Shankaranarayanan D, Kopp JB, Raj DS. Dietary Protein and Fiber Affect Gut Microbiome and Treg/Th17 Commitment in Chronic Kidney Disease Mice. Am J Nephrol 2022; 53:646-651. [PMID: 36349783 PMCID: PMC10367184 DOI: 10.1159/000526957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/19/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Patients with chronic kidney disease (CKD) have dysbiosis, dysmetabolism, and immune dysregulation. Gut microbiome plays an important role shaping the immune system which is an important modulator of CKD progression. METHODS We compared the effect of a diet low in protein and high in fiber (LP-HF; n = 7) to that of diet rich in protein, but low in fiber (HP-LF; n = 7) on gut microbiome and T-cell commitment in male CKD (Alb/TGF-β1) mice. The gut microbiomes of these mice were subjected to 16S rRNA taxonomic profiling at baseline, 6 weeks and 12 weeks of the study. RESULTS The LP-HF diet was associated with an increase in Butyricicoccus pullicaecorum BT, a taxon whose functions include those closely related to butyric acid synthesis (Kendall's W statistic = 180 in analysis of microbiome composition). HP-LF diet was associated with increased abundance of two predominantly proteolytic bacterial strains related to Parabacteroides distasonis (W statistic = 173), Mucispirillum schaedleri, and Bacteroides dorei (W statistic = 192). Pathway analysis suggested that the LP-HF diet induced carbohydrate, lipid, and butyrate metabolism. As compared with HP-LF mice, LP-HF mice had 1.7-fold increase in CD4+Foxp3+Treg cells in spleen and 2.4-fold increase of these cells in peripheral blood. There was an 87% decrease in percentage of CD4+ Th17 + cells in spleen and an 85% decrease in peripheral blood, respectively, in LP-HF mice compared to the HP-LF mice. CONCLUSION The LP-HF diet promotes the proliferation of saccharolytic bacteria and favors T-cell commitment toward Treg cells in a CKD mouse of model. Clinical significance of the finding needs to be further investigated.
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Affiliation(s)
- Myrna Serrano
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Anvesha Srivastava
- Division of Kidney Diseases and Hypertension, George Washington University School of Medicine, Washington, District of Columbia, USA,
| | - Gregory Buck
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Bin Zhu
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Laahirie Edupuganti
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Esther Adegbulugbe
- Division of Kidney Diseases and Hypertension, George Washington University School of Medicine, Washington, District of Columbia, USA
| | - Divya Shankaranarayanan
- Division of Kidney Diseases and Hypertension, George Washington University School of Medicine, Washington, District of Columbia, USA
| | - Jeffrey B Kopp
- Kidney Disease Section, NIDDK, NIH, Bethesda, Maryland, USA
| | - Dominic S Raj
- Division of Kidney Diseases and Hypertension, George Washington University School of Medicine, Washington, District of Columbia, USA
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Favero C, Giordano L, Mihaila SM, Masereeuw R, Ortiz A, Sanchez-Niño MD. Postbiotics and Kidney Disease. Toxins (Basel) 2022; 14:toxins14090623. [PMID: 36136562 PMCID: PMC9501217 DOI: 10.3390/toxins14090623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Chronic kidney disease (CKD) is projected to become the fifth global cause of death by 2040 as a result of key shortcomings in the current methods available to diagnose and treat kidney diseases. In this regard, the novel holobiont concept, used to describe an individual host and its microbial community, may pave the way towards a better understanding of kidney disease pathogenesis and progression. Microbiota-modulating or -derived interventions include probiotics, prebiotics, synbiotics and postbiotics. As of 2019, the concept of postbiotics was updated by the International Scientific Association of Probiotics and Prebiotics (ISAPP) to refer to preparations of inanimate microorganisms and/or their components that confer a health benefit to the host. By explicitly excluding purified metabolites without a cellular biomass, any literature making use of such term is potentially rendered obsolete. We now review the revised concept of postbiotics concerning their potential clinical applications and research in kidney disease, by discussing in detail several formulations that are undergoing preclinical development such as GABA-salt for diet-induced hypertension and kidney injury, sonicated Lactobacillus paracasei in high fat diet-induced kidney injury, GABA-salt, lacto-GABA-salt and postbiotic-GABA-salt in acute kidney injury, and O. formigenes lysates for hyperoxaluria. Furthermore, we provide a roadmap for postbiotics research in kidney disease to expedite clinical translation.
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Affiliation(s)
- Chiara Favero
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, 28049 Madrid, Spain
| | - Laura Giordano
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Silvia Maria Mihaila
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Rosalinde Masereeuw
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Alberto Ortiz
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, 28049 Madrid, Spain
- Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORS) 2040, 28049 Madrid, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Correspondence: (A.O.); (M.D.S.-N.)
| | - Maria Dolores Sanchez-Niño
- Department of Nephrology and Hypertension, IIS-Fundacion Jimenez Diaz UAM, 28049 Madrid, Spain
- Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORS) 2040, 28049 Madrid, Spain
- Departamento de Farmacología, Facultad de Medicina, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Correspondence: (A.O.); (M.D.S.-N.)
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