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Sun Z, Ning Z, Figeys D. The Landscape and Perspectives of the Human Gut Metaproteomics. Mol Cell Proteomics 2024; 23:100763. [PMID: 38608842 PMCID: PMC11098955 DOI: 10.1016/j.mcpro.2024.100763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/26/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024] Open
Abstract
The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics. In this article, we present the current landscape of human gut metaproteomics studies by re-analyzing the identification results from 15 published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.
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Affiliation(s)
- Zhongzhi Sun
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Zhibin Ning
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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Liu Z, Yue T, Zheng X, Luo S, Xu W, Yan J, Weng J, Yang D, Wang C. Microbial and metabolomic profiles of type 1 diabetes with depression: A case-control study. J Diabetes 2024; 16:e13542. [PMID: 38599848 PMCID: PMC11006619 DOI: 10.1111/1753-0407.13542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 12/17/2023] [Accepted: 01/31/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Depression is the most common psychological disorder in patients with type 1 diabetes (T1D). However, the characteristics of microbiota and metabolites in these patients remain unclear. This study aimed to investigate microbial and metabolomic profiles and identify novel biomarkers for T1D with depression. METHODS A case-control study was conducted in a total of 37 T1D patients with depression (TD+), 35 T1D patients without depression (TD-), and 29 healthy controls (HCs). 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS) metabolomics analysis were conducted to investigate the characteristics of microbiota and metabolites. The association between altered microbiota and metabolites was explored by Spearman's rank correlation and visualized by a heatmap. The microbial signatures to discriminate TD+ from TD- were identified by a random forest (RF) classifying model. RESULTS In microbiota, 15 genera enriched in TD- and 2 genera enriched in TD+, and in metabolites, 14 differential metabolites (11 upregulated and 3 downregulated) in TD+ versus TD- were identified. Additionally, 5 genera (including Phascolarctobacterium, Butyricimonas, and Alistipes from altered microbiota) demonstrated good diagnostic power (area under the curve [AUC] = 0.73; 95% CI, 0.58-0.87). In the correlation analysis, Butyricimonas was negatively correlated with glutaric acid (r = -0.28, p = 0.015) and malondialdehyde (r = -0.30, p = 0.012). Both Phascolarctobacterium (r = 0.27, p = 0.022) and Alistipes (r = 0.31, p = 0.009) were positively correlated with allopregnanolone. CONCLUSIONS T1D patients with depression were characterized by unique profiles of gut microbiota and serum metabolites. Phascolarctobacterium, Butyricimonas, and Alistipes could predict the risk of T1D with depression. These findings provide further evidence that the microbiota-gut-brain axis is involved in T1D with depression.
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Affiliation(s)
- Ziyu Liu
- Department of Endocrinology and MetabolismThe Third Affiliated Hospital of Sun Yat‐sen University, Guangdong Diabetes Prevention and Control Research Center, Guangdong Provincial Key Laboratory of DiabetologyGuangzhouChina
- Department of EndocrinologyThe Sixth Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | - Tong Yue
- Department of Endocrinology, Institute of Endocrine and Metabolic DiseasesThe First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of the Chinese Academy of Sciences (Hefei), University of Science and Technology of ChinaHefeiChina
| | - Xueying Zheng
- Department of Endocrinology, Institute of Endocrine and Metabolic DiseasesThe First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of the Chinese Academy of Sciences (Hefei), University of Science and Technology of ChinaHefeiChina
| | - Sihui Luo
- Department of Endocrinology, Institute of Endocrine and Metabolic DiseasesThe First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of the Chinese Academy of Sciences (Hefei), University of Science and Technology of ChinaHefeiChina
| | - Wen Xu
- Department of Endocrinology and MetabolismThe Third Affiliated Hospital of Sun Yat‐sen University, Guangdong Diabetes Prevention and Control Research Center, Guangdong Provincial Key Laboratory of DiabetologyGuangzhouChina
| | - Jinhua Yan
- Department of Endocrinology and MetabolismThe Third Affiliated Hospital of Sun Yat‐sen University, Guangdong Diabetes Prevention and Control Research Center, Guangdong Provincial Key Laboratory of DiabetologyGuangzhouChina
| | - Jianping Weng
- Department of Endocrinology and MetabolismThe Third Affiliated Hospital of Sun Yat‐sen University, Guangdong Diabetes Prevention and Control Research Center, Guangdong Provincial Key Laboratory of DiabetologyGuangzhouChina
- Department of Endocrinology, Institute of Endocrine and Metabolic DiseasesThe First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of the Chinese Academy of Sciences (Hefei), University of Science and Technology of ChinaHefeiChina
| | - Daizhi Yang
- Department of Endocrinology and MetabolismThe Third Affiliated Hospital of Sun Yat‐sen University, Guangdong Diabetes Prevention and Control Research Center, Guangdong Provincial Key Laboratory of DiabetologyGuangzhouChina
| | - Chaofan Wang
- Department of Endocrinology and MetabolismThe Third Affiliated Hospital of Sun Yat‐sen University, Guangdong Diabetes Prevention and Control Research Center, Guangdong Provincial Key Laboratory of DiabetologyGuangzhouChina
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Ullah H, Arbab S, Tian Y, Liu CQ, Chen Y, Qijie L, Khan MIU, Hassan IU, Li K. The gut microbiota-brain axis in neurological disorder. Front Neurosci 2023; 17:1225875. [PMID: 37600019 PMCID: PMC10436500 DOI: 10.3389/fnins.2023.1225875] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 07/07/2023] [Indexed: 08/22/2023] Open
Abstract
The gut microbiota (GM) plays an important role in the physiology and pathology of the host. Microbiota communicate with different organs of the organism by synthesizing hormones and regulating body activity. The interaction of the central nervous system (CNS) and gut signaling pathways includes chemical, neural immune and endocrine routes. Alteration or dysbiosis in the gut microbiota leads to different gastrointestinal tract disorders that ultimately impact host physiology because of the abnormal microbial metabolites that stimulate and trigger different physiologic reactions in the host body. Intestinal dysbiosis leads to a change in the bidirectional relationship between the CNS and GM, which is linked to the pathogenesis of neurodevelopmental and neurological disorders. Increasing preclinical and clinical studies/evidence indicate that gut microbes are a possible susceptibility factor for the progression of neurological disorders, including Alzheimer's disease (AD), Parkinson's disease (PD), multiple sclerosis (MS) and autism spectrum disorder (ASD). In this review, we discuss the crucial connection between the gut microbiota and the central nervous system, the signaling pathways of multiple biological systems and the contribution of gut microbiota-related neurological disorders.
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Affiliation(s)
- Hanif Ullah
- Department of Nursing, West China Hospital, West China School of Nursing, Sichuan University, Chengdu, China
| | - Safia Arbab
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yali Tian
- Department of Nursing, West China Hospital, West China School of Nursing, Sichuan University, Chengdu, China
| | - Chang-qing Liu
- Department of Nursing, West China Hospital, West China School of Nursing, Sichuan University, Chengdu, China
| | - Yuwen Chen
- Department of Nursing, West China Hospital, West China School of Nursing, Sichuan University, Chengdu, China
| | - Li Qijie
- Department of Nursing, West China Hospital, West China School of Nursing, Sichuan University, Chengdu, China
| | - Muhammad Inayat Ullah Khan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Inam Ul Hassan
- Department of Microbiology, Hazara University Mansehra, Mansehra, Pakistan
| | - Ka Li
- Department of Nursing, West China Hospital, West China School of Nursing, Sichuan University, Chengdu, China
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Cerquetella M, Mangiaterra S, Pinnella F, Rossi G, Marchegiani A, Gavazza A, Serri E, Di Cerbo A, Marini C, Cecconi D, Sorio D, Marchetti V, Vincenzetti S. Fecal Proteome Profile in Dogs Suffering from Different Hepatobiliary Disorders and Comparison with Controls. Animals (Basel) 2023; 13:2343. [PMID: 37508119 PMCID: PMC10376375 DOI: 10.3390/ani13142343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
In the present study, the fecal proteomes of clinically healthy dogs (HD = n. 10), of dogs showing clinical, ultrasonographic, and/or laboratory evidence of different hepatobiliary dysfunction (DHD = n. 10), and of dogs suffering from chronic hepatitis (CHD = n. 10) were investigated with an Ultimate 3000 nanoUPLC system, coupled to an Orbitrap Fusion Lumos Tribrid mass spectrometer. Fifty-two different proteins of canine origin were identified qualitatively in the three study groups, and quantitative differences were found in 55 proteins when comparing groups. Quantitatively, a total of 41 and 36 proteins were found differentially abundant in the DHD and CHD groups compared to the control HD, and 38 proteins resulted dysregulated in the CHD group as compared to the DHD group. Among the various proteins, differently abundant fecal fibronectin and haptoglobin were more present in the feces of healthy and DHD dogs than in chronic ones, leading us to hypothesize its possible diagnostic/monitoring role in canine chronic hepatitis. On the other hand, the trefoil factor 2 was increased in DHD dogs. Our results show that the analysis of the fecal proteome is a very promising field of study, and in the case of dogs suffering from different hepatobiliary disorders, it was able to highlight both qualitative and quantitative differences among the three groups included. Results need to be confirmed with western blotting and in further studies.
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Affiliation(s)
- Matteo Cerquetella
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
| | - Sara Mangiaterra
- Futuravet Veterinary Referral Center, 62029 Tolentino, MC, Italy
| | - Francesco Pinnella
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
| | - Giacomo Rossi
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
| | - Andrea Marchegiani
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
| | - Alessandra Gavazza
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
| | - Evelina Serri
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
| | - Alessandro Di Cerbo
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
| | - Carlotta Marini
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
| | - Daniela Cecconi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, VR, Italy
| | - Daniela Sorio
- Centre for Technological Platforms (CPT), University of Verona, Piazzale L.A. Scuro 10, 37134 Verona, VR, Italy
| | - Veronica Marchetti
- Department of Veterinary Sciences, University of Pisa, Via Livornese, San Piero a Grado, 56122 Pisa, PI, Italy
| | - Silvia Vincenzetti
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Circonvallazione 93/95, 62024 Matelica, MC, Italy
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Devi MB, Sarma HK, Mukherjee AK, Khan MR. Mechanistic Insights into Immune-Microbiota Interactions and Preventive Role of Probiotics Against Autoimmune Diabetes Mellitus. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10087-1. [PMID: 37171690 DOI: 10.1007/s12602-023-10087-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Recent studies on genetically susceptible individuals and animal models revealed the potential role of the intestinal microbiota in the pathogenesis of type 1 diabetes (T1D) through complex interactions with the immune system. T1D incidence has been increasing exponentially with modern lifestyle altering normal microbiota composition, causing dysbiosis characterized by an imbalance in the gut microbial community. Dysbiosis has been suggested to be a potential contributing factor in T1D. Moreover, several studies have shown the potential role of probiotics in regulating T1D through various mechanisms. Current T1D therapies target curative measures; however, preventive therapeutics are yet to be proven. This review highlights immune microbiota interaction and the immense role of probiotics and postbiotics as important immunological interventions for reducing the risk of T1D.
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Affiliation(s)
- M Bidyarani Devi
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
- Department of Biotechnology, Gauhati University, Guwahati, Assam, India
| | | | - Ashis K Mukherjee
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
| | - Mojibur R Khan
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India.
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Alsharairi NA. Exploring the Diet-Gut Microbiota-Epigenetics Crosstalk Relevant to Neonatal Diabetes. Genes (Basel) 2023; 14:genes14051017. [PMID: 37239377 DOI: 10.3390/genes14051017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Neonatal diabetes (NDM) is a rare monogenic disorder that presents as hyperglycemia during the first six months of life. The link between early-life gut microbiota dysbiosis and susceptibility to NDM remains uncertain. Experimental studies have demonstrated that gestational diabetes mellitus (GDM) could develop into meconium/gut microbiota dysbiosis in newborns, and thus, it is thought to be a mediator in the pathogenesis of NDM. Epigenetic modifications have been considered as potential mechanisms by which the gut microbiota and susceptibility genes interact with the neonatal immune system. Several epigenome-wide association studies have revealed that GDM is associated with neonatal cord blood and/or placental DNA methylation alterations. However, the mechanisms linking diet in GDM with gut microbiota alterations, which may in turn induce the expression of genes linked to NDM, are yet to be unraveled. Therefore, the focus of this review is to highlight the impacts of diet, gut microbiota, and epigenetic crosstalk on altered gene expression in NDM.
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Affiliation(s)
- Naser A Alsharairi
- Heart, Mind & Body Research Group, Griffith University, Gold Coast, QLD P.O. Box 4222, Australia
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7
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Lo Conte M, Cosorich I, Ferrarese R, Antonini Cencicchio M, Nobili A, Palmieri V, Massimino L, Lamparelli LA, Liang W, Riba M, Devecchi E, Bolla AM, Pedone E, Scavini M, Bosi E, Fasano A, Ungaro F, Diana J, Mancini N, Falcone M. Alterations of the intestinal mucus layer correlate with dysbiosis and immune dysregulation in human Type 1 Diabetes. EBioMedicine 2023; 91:104567. [PMID: 37062177 PMCID: PMC10139895 DOI: 10.1016/j.ebiom.2023.104567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 03/09/2023] [Accepted: 03/30/2023] [Indexed: 04/18/2023] Open
Abstract
BACKGROUND In preclinical models of Type 1 Diabetes (T1D) the integrity of the gut barrier (GB) is instrumental to avoid dysregulated crosstalk between the commensal microbiota and immune cells and to prevent autoimmunity. The GB is composed of the intestinal epithelial barrier (IEB) and of the mucus layer containing mucins and antimicrobial peptides (AMPs) that are crucial to maintain immune tolerance. In preclinical models of T1D the alterations of the GB primarily affect the mucus layer. In human T1D increased gut permeability and IEB damage have been demonstrated but the integrity of the mucus layer was never assessed. METHODS We evaluated GB integrity by measuring serological markers of IEB damage (serological levels of zonulin) and bacterial translocation such as lipopolysaccharide binding protein (LBP) and myeloid differentiation protein 2 (MD2), and mRNA expression of tight junction proteins, mucins and AMPs in intestinal tissue of T1D patients and healthy controls (HC). Simultaneously, we performed immunological profiling on intestinal tissue and 16S rRNA analysis on the mucus-associated gut microbiota (MAGM). FINDINGS Our data show a GB damage with mucus layer alterations and reduced mRNA expression of several mucins (MUC2, MUC12, MUC13, MUC15, MUC20, MUC21) and AMPs (HD4 and HD5) in T1D patients. Mucus layer alterations correlated with reduced relative abundance of short chain fatty acids (SCFA)-producing bacteria such as Bifidobacterium dentium, Clostridium butyricum and Roseburia intestinalis that regulate mucin expression and intestinal immune homeostasis. In T1D patients we also found intestinal immune dysregulation with higher percentages of effector T cells such as T helper (Th) 1, Th17 and TNF-α+ T cells. INTERPRETATION Our data show that mucus layer alterations are present in T1D subjects and associated with dysbiosis and immune dysregulation. FUNDING Research Grants from the Juvenile Diabetes Foundation (Grant 1-INO-2018-640-A-N to MF and 2-SRA-2019-680-S-B to JD) and from the Italian Ministry of Health (Grant RF19-12370721 to MF).
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Affiliation(s)
- Marta Lo Conte
- Autoimmune Pathogenesis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ilaria Cosorich
- Autoimmune Pathogenesis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Roberto Ferrarese
- Virology and Microbiology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Martina Antonini Cencicchio
- Autoimmune Pathogenesis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angelica Nobili
- Autoimmune Pathogenesis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Vittoria Palmieri
- Autoimmune Pathogenesis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Massimino
- Experimental Gastroenterology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | - Michela Riba
- Center for OMICS Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisabetta Devecchi
- Clinical Nutrition Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Mario Bolla
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Erika Pedone
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marina Scavini
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Emanuele Bosi
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy; San Raffaele Vita Salute University, Milan, Italy
| | - Alessio Fasano
- Department of Pediatrics, Harvard Medical School, MA, USA
| | - Federica Ungaro
- Experimental Gastroenterology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Nicasio Mancini
- Virology and Microbiology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy; San Raffaele Vita Salute University, Milan, Italy
| | - Marika Falcone
- Autoimmune Pathogenesis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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Huang X, Huang X, Huang Y, Zheng J, Lu Y, Mai Z, Zhao X, Cui L, Huang S. The oral microbiome in autoimmune diseases: friend or foe? J Transl Med 2023; 21:211. [PMID: 36949458 PMCID: PMC10031900 DOI: 10.1186/s12967-023-03995-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/15/2023] [Indexed: 03/24/2023] Open
Abstract
The human body is colonized by abundant and diverse microorganisms, collectively known as the microbiome. The oral cavity has more than 700 species of bacteria and consists of unique microbiome niches on mucosal surfaces, on tooth hard tissue, and in saliva. The homeostatic balance between the oral microbiota and the immune system plays an indispensable role in maintaining the well-being and health status of the human host. Growing evidence has demonstrated that oral microbiota dysbiosis is actively involved in regulating the initiation and progression of an array of autoimmune diseases.Oral microbiota dysbiosis is driven by multiple factors, such as host genetic factors, dietary habits, stress, smoking, administration of antibiotics, tissue injury and infection. The dysregulation in the oral microbiome plays a crucial role in triggering and promoting autoimmune diseases via several mechanisms, including microbial translocation, molecular mimicry, autoantigen overproduction, and amplification of autoimmune responses by cytokines. Good oral hygiene behaviors, low carbohydrate diets, healthy lifestyles, usage of prebiotics, probiotics or synbiotics, oral microbiota transplantation and nanomedicine-based therapeutics are promising avenues for maintaining a balanced oral microbiome and treating oral microbiota-mediated autoimmune diseases. Thus, a comprehensive understanding of the relationship between oral microbiota dysbiosis and autoimmune diseases is critical for providing novel insights into the development of oral microbiota-based therapeutic approaches for combating these refractory diseases.
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Affiliation(s)
- Xiaoyan Huang
- Department of Preventive Dentistry, Stomatological Hospital, School of Stomatology, Southern Medical University, Haizhu District, No.366 Jiangnan Da Dao Nan, Guangzhou, 510280, China
| | - Xiangyu Huang
- Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Haizhu District, No.366 Jiangnan Da Dao Nan, Guangzhou, 510280, China
| | - Yi Huang
- Department of Preventive Dentistry, Stomatological Hospital, School of Stomatology, Southern Medical University, Haizhu District, No.366 Jiangnan Da Dao Nan, Guangzhou, 510280, China
| | - Jiarong Zheng
- Department of Dentistry, The First Affiliated Hospital, Sun Yat-Sen University, Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Ye Lu
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Haizhu District, Guangzhou, 510280, China
| | - Zizhao Mai
- Department of Dentistry, The First Affiliated Hospital, Sun Yat-Sen University, Zhongshan 2nd Road, Guangzhou, 510080, China
| | - Xinyuan Zhao
- Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Haizhu District, No.366 Jiangnan Da Dao Nan, Guangzhou, 510280, China.
| | - Li Cui
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital, School of Stomatology, Southern Medical University, Haizhu District, Guangzhou, 510280, China.
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, CA, 90095, USA.
| | - Shaohong Huang
- Department of Preventive Dentistry, Stomatological Hospital, School of Stomatology, Southern Medical University, Haizhu District, No.366 Jiangnan Da Dao Nan, Guangzhou, 510280, China.
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9
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Das S, Gnanasambandan R. Intestinal microbiome diversity of diabetic and non-diabetic kidney disease: Current status and future perspective. Life Sci 2023; 316:121414. [PMID: 36682521 DOI: 10.1016/j.lfs.2023.121414] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/09/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
A significant portion of the health burden of diabetic kidney disease (DKD) is caused by both type 1 and type 2 diabetes which leads to morbidity and mortality globally. It is one of the most common diabetic complications characterized by loss of renal function with high prevalence, often leading to acute kidney disease (AKD). Inflammation triggered by gut microbiota is commonly associated with the development of DKD. Interactions between the gut microbiota and the host are correlated in maintaining metabolic and inflammatory homeostasis. However, the fundamental processes through which the gut microbiota affects the onset and progression of DKD are mainly unknown. In this narrative review, we summarised the potential role of the gut microbiome, their pathogenicity between diabetic and non-diabetic kidney disease (NDKD), and their impact on host immunity. A well-established association has already been seen between gut microbiota, diabetes and kidney disease. The gut-kidney interrelationship is confirmed by mounting evidence linking gut dysbiosis to DKD, however, it is still unclear what is the real cause of gut dysbiosis, the development of DKD, and its progression. In addition, we also try to distinguish novel biomarkers for early detection of DKD and the possible therapies that can be used to regulate the gut microbiota and improve the host immune response. This early detection and new therapies will help clinicians for better management of the disease and help improve patient outcomes.
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Affiliation(s)
- Soumik Das
- School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014, India
| | - Ramanathan Gnanasambandan
- School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014, India.
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10
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Fujisaka S, Watanabe Y, Tobe K. The gut microbiome: a core regulator of metabolism. J Endocrinol 2023; 256:e220111. [PMID: 36458804 PMCID: PMC9874984 DOI: 10.1530/joe-22-0111] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/02/2022] [Indexed: 12/03/2022]
Abstract
The human body is inhabited by numerous bacteria, fungi, and viruses, and each part has a unique microbial community structure. The gastrointestinal tract harbors approximately 100 trillion strains comprising more than 1000 bacterial species that maintain symbiotic relationships with the host. The gut microbiota consists mainly of the phyla Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Of these, Firmicutes and Bacteroidetes constitute 70-90% of the total abundance. Gut microbiota utilize nutrients ingested by the host, interact with other bacterial species, and help maintain healthy homeostasis in the host. In recent years, it has become increasingly clear that a breakdown of the microbial structure and its functions, known as dysbiosis, is associated with the development of allergies, autoimmune diseases, cancers, and arteriosclerosis, among others. Metabolic diseases, such as obesity and diabetes, also have a causal relationship with dysbiosis. The present review provides a brief overview of the general roles of the gut microbiota and their relationship with metabolic disorders.
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Affiliation(s)
- Shiho Fujisaka
- First Department of Internal Medicine, Faculty of Medicine, University of Toyama, Sugitani, Toyama, Japan
| | - Yoshiyuki Watanabe
- First Department of Internal Medicine, Faculty of Medicine, University of Toyama, Sugitani, Toyama, Japan
| | - Kazuyuki Tobe
- First Department of Internal Medicine, Faculty of Medicine, University of Toyama, Sugitani, Toyama, Japan
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11
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Sarnoff RP, Bhatt RR, Osadchiy V, Dong T, Labus JS, Kilpatrick LA, Chen Z, Subramanyam V, Zhang Y, Ellingson BM, Naliboff B, Chang L, Mayer EA, Gupta A. A multi-omic brain gut microbiome signature differs between IBS subjects with different bowel habits. Neuropharmacology 2023; 225:109381. [PMID: 36539012 DOI: 10.1016/j.neuropharm.2022.109381] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/25/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Alterations of the brain-gut-microbiome system (BGM) have been implicated in the pathophysiology of irritable bowel syndrome (IBS), yet bowel habit-specific alterations have not been elucidated. In this cross-sectional study, we apply a systems biology approach to characterize BGM patterns related to predominant bowel habit. Fecal samples and resting state fMRI were obtained from 102 premenopausal women (36 constipation-predominant IBS (IBS-C), 27 diarrhea-predominant IBS (IBS-D), 39 healthy controls (HCs)). Data integration analysis using latent components (DIABLO) was used to integrate data from the phenome, microbiome, metabolome, and resting-state connectome to predict HCs vs IBS-C vs IBS-D. Bloating and visceral sensitivity, distinguishing IBS from HC, were negatively associated with beneficial microbes and connectivity involving the orbitofrontal cortex. This suggests that gut interactions may generate aberrant central autonomic and descending pain pathways in IBS. The connection between IBS symptom duration, key microbes, and caudate connectivity may provide mechanistic insight to the chronicity of pain in IBS. Compared to IBS-C and HCs, IBS-D had higher levels of many key metabolites including tryptophan and phenylalanine, and increased connectivity between the sensorimotor and default mode networks; thus, suggestingan influence on diarrhea, self-related thoughts, and pain perception in IBS-D ('bottom-up' mechanism). IBS-C's microbiome and metabolome resembled HCs, but IBS-C had increased connectivity in the default mode and salience networks compared to IBS-D, which may indicate importance of visceral signals, suggesting a more 'top-down' BGM pathophysiology. These BGM characteristics highlight possible mechanistic differences for variations in the IBS bowel habit phenome. This article is part of the Special Issue on 'Microbiome & the Brain: Mechanisms & Maladies'.
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Affiliation(s)
- Rachel P Sarnoff
- G. Oppenheimer Family Center for Neurobiology of Stress and Resilience, USA; David Geffen School of Medicine, USA; Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Ravi R Bhatt
- G. Oppenheimer Family Center for Neurobiology of Stress and Resilience, USA; Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, USA
| | - Vadim Osadchiy
- G. Oppenheimer Family Center for Neurobiology of Stress and Resilience, USA; David Geffen School of Medicine, USA; Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Tien Dong
- G. Oppenheimer Family Center for Neurobiology of Stress and Resilience, USA; David Geffen School of Medicine, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, USA; UCLA Microbiome Center, USA; Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Jennifer S Labus
- G. Oppenheimer Family Center for Neurobiology of Stress and Resilience, USA; David Geffen School of Medicine, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, USA
| | - Lisa A Kilpatrick
- G. Oppenheimer Family Center for Neurobiology of Stress and Resilience, USA; David Geffen School of Medicine, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, USA
| | - Zixi Chen
- G. Oppenheimer Family Center for Neurobiology of Stress and Resilience, USA
| | | | - Yurui Zhang
- G. Oppenheimer Family Center for Neurobiology of Stress and Resilience, USA
| | - Benjamin M Ellingson
- Departments of Radiological Sciences, Psychiatry, and Neurosurgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Bruce Naliboff
- G. Oppenheimer Family Center for Neurobiology of Stress and Resilience, USA; David Geffen School of Medicine, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, USA
| | - Lin Chang
- G. Oppenheimer Family Center for Neurobiology of Stress and Resilience, USA; David Geffen School of Medicine, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, USA
| | - Emeran A Mayer
- G. Oppenheimer Family Center for Neurobiology of Stress and Resilience, USA; David Geffen School of Medicine, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, USA; UCLA Microbiome Center, USA.
| | - Arpana Gupta
- G. Oppenheimer Family Center for Neurobiology of Stress and Resilience, USA; David Geffen School of Medicine, USA; Vatche and Tamar Manoukian Division of Digestive Diseases, USA; UCLA Microbiome Center, USA.
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12
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Miura N, Okuda S. Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics. Comput Struct Biotechnol J 2023; 21:1140-1150. [PMID: 36817962 PMCID: PMC9925844 DOI: 10.1016/j.csbj.2023.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/14/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
Metaproteomics is a relatively young field that has only been studied for approximately 15 years. Nevertheless, it has the potential to play a key role in disease research by elucidating the mechanisms of communication between the human host and the microbiome. Although it has been useful in developing an understanding of various diseases, its analytical strategies remain limited to the extended application of proteomics. The sequence databases in metaproteomics must be large because of the presence of thousands of species in a typical sample, which causes problems unique to large databases. In this review, we demonstrate the usefulness of metaproteomics in disease research through examples from several studies. Additionally, we discuss the challenges of applying metaproteomics to conventional proteomics analysis methods and introduce studies that may provide clues to the solutions. We also discuss the need for a standard false discovery rate control method for metaproteomics to replace common target-decoy search approaches in proteomics and a method to ensure the reliability of peptide spectrum match.
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Affiliation(s)
- Nobuaki Miura
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 2-5274 Gakkocho-dori, Chuo-ku, Niigata 951-8514, Japan
| | - Shujiro Okuda
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 2-5274 Gakkocho-dori, Chuo-ku, Niigata 951-8514, Japan,Medical AI Center, Niigata University School of Medicine, 2-5274 Gakkocho-dori, Chuo-ku, Niigata 951-8514, Japan,Corresponding author at: Medical AI Center, Niigata University School of Medicine, 2-5274 Gakkocho-dori, Chuo-ku, Niigata 951-8514, Japan.
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13
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Okada M, Zhang V, Loaiza Naranjo JD, Tillett BJ, Wong FS, Steptoe RJ, Bergot AS, Hamilton-Williams EE. Islet-specific CD8 + T cells gain effector function in the gut lymphoid tissues via bystander activation not molecular mimicry. Immunol Cell Biol 2023; 101:36-48. [PMID: 36214093 PMCID: PMC10092732 DOI: 10.1111/imcb.12593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/14/2022] [Accepted: 10/08/2022] [Indexed: 11/30/2022]
Abstract
Type 1 diabetes (T1D) is caused by aberrant activation of autoreactive T cells specific for the islet beta cells. How islet-specific T cells evade tolerance to become effector T cells is unknown, but it is believed that an altered gut microbiota plays a role. Possible mechanisms include bystander activation of autoreactive T cells in the gut or "molecular mimicry" from cross-reactivity between gut microbiota-derived peptides and islet-derived epitopes. To investigate these mechanisms, we use two islet-specific CD8+ T cell clones and the non-obese diabetic mouse model of type 1 diabetes. Both insulin-specific G9C8 cells and IGRP-specific 8.3 cells underwent early activation and proliferation in the pancreatic draining lymph nodes but not in the Peyer's patches or mesenteric lymph nodes. Mutation of the endogenous epitope for G9C8 cells abolished their CD69 upregulation and proliferation, ruling out G9C8 cell activation by a gut microbiota derived peptide and molecular mimicry. However, previously activated islet-specific effector memory cells but not naïve cells migrated into the Peyer's patches where they increased their cytotoxic function. Oral delivery of butyrate, a microbiota derived anti-inflammatory metabolite, reduced IGRP-specific cytotoxic function. Thus, while initial activation of islet-specific CD8+ T cells occurred in the pancreatic lymph nodes, activated cells trafficked through the gut lymphoid tissues where they gained additional effector function via non-specific bystander activation influenced by the gut microbiota.
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Affiliation(s)
- Mirei Okada
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Vivian Zhang
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Jeniffer D Loaiza Naranjo
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Bree J Tillett
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - F Susan Wong
- Division of Infection and Immunity and Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Raymond J Steptoe
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Anne-Sophie Bergot
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Emma E Hamilton-Williams
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
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14
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Abstract
The high-dimensional nature of proteomics data presents challenges for statistical analysis and biological interpretation. Multivariate analysis, combined with insightful visualization can help to reveal the underlying patterns in complex biological data. This chapter introduces the R package mixOmics which focuses on data exploration and integration. We first introduce methods for single data sets: both Principal Component Analysis, which can identify the patterns of variance present in data, and sparse Partial Least Squares Discriminant Analysis, which aims to identify variables that can classify samples into known groups. We then present integrative methods with Projection to Latent Structures and further extensions for discriminant analysis. We illustrate each technique on a breast cancer multi-omics study and provide the R code and data as online supplementary material for readers interested in reproducing these analyses.
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Affiliation(s)
- Zoe Welham
- Kolling Institute, St Leonards, NSW, Australia
| | - Sébastien Déjean
- Institut de Mathématiques de Toulouse, UMR 5219, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia.
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15
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Gavin PG, Kim KW, Craig ME, Hill MM, Hamilton-Williams EE. Multi-omic interactions in the gut of children at the onset of islet autoimmunity. MICROBIOME 2022; 10:230. [PMID: 36527134 PMCID: PMC9756488 DOI: 10.1186/s40168-022-01425-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The gastrointestinal ecosystem is a highly complex environment with a profound influence on human health. Inflammation in the gut, linked to an altered gut microbiome, has been associated with the development of multiple human conditions including type 1 diabetes (T1D). Viruses infecting the gastrointestinal tract, especially enteroviruses, are also thought to play an important role in T1D pathogenesis possibly via overlapping mechanisms. However, it is not known whether the microbiome and virome act together or which risk factor may be of greater importance at the time when islet autoimmunity is initiated. RESULTS Here, we apply an integrative approach to combine comprehensive fecal virome, microbiome, and metaproteome data sampled before and at the onset of islet autoimmunity in 40 children at increased risk of T1D. We show strong age-related effects, with microbial and metaproteome diversity increasing with age while host antibody number and abundance declined with age. Mastadenovirus, which has been associated with a reduced risk of T1D, was associated with profound changes in the metaproteome indicating a functional shift in the microbiota. Multi-omic factor analysis modeling revealed a cluster of proteins associated with carbohydrate transport from the genus Faecalibacterium were associated with islet autoimmunity. CONCLUSIONS These findings demonstrate the interrelatedness of the gut microbiota, metaproteome and virome in young children. We show a functional remodeling of the gut microbiota accompanies both islet autoimmunity and viral infection with a switch in function in Faecalibacterium occurring at the onset of islet autoimmunity. Video Abstract.
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Affiliation(s)
- Patrick G Gavin
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, Australia
- Present Address: Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Present Address: Harvard Medical School, Boston, MA, USA
| | - Ki Wook Kim
- Virology Research Laboratory, Prince of Wales Hospital Randwick, Sydney, Australia
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Maria E Craig
- Virology Research Laboratory, Prince of Wales Hospital Randwick, Sydney, Australia
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
- Institute of Endocrinology and Diabetes, Children's Hospital at Westmead, Sydney, Australia
- Discipline of Child and Adolescent Health, University of Sydney, Sydney, Australia
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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16
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Functional and Taxonomic Traits of the Gut Microbiota in Type 1 Diabetes Children at the Onset: A Metaproteomic Study. Int J Mol Sci 2022; 23:ijms232415982. [PMID: 36555624 PMCID: PMC9787575 DOI: 10.3390/ijms232415982] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/02/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Type 1 diabetes (T1D) is a chronic autoimmune metabolic disorder with onset in pediatric/adolescent age, characterized by insufficient insulin production, due to a progressive destruction of pancreatic β-cells. Evidence on the correlation between the human gut microbiota (GM) composition and T1D insurgence has been recently reported. In particular, 16S rRNA-based metagenomics has been intensively employed in the last decade in a number of investigations focused on GM representation in relation to a pre-disease state or to a response to clinical treatments. On the other hand, few works have been published using alternative functional omics, which is more suitable to provide a different interpretation of such a relationship. In this work, we pursued a comprehensive metaproteomic investigation on T1D children compared with a group of siblings (SIBL) and a reference control group (CTRL) composed of aged matched healthy subjects, with the aim of finding features in the T1D patients' GM to be related with the onset of the disease. Modulated metaproteins were found either by comparing T1D with CTRL and SIBL or by stratifying T1D by insulin need (IN), as a proxy of β-cells damage, showing some functional and taxonomic traits of the GM, possibly related to the disease onset at different stages of severity.
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17
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Dang G, Wang W, Zhong R, Wu W, Chen L, Zhang H. Pectin supplement alleviates gut injury potentially through improving gut microbiota community in piglets. Front Microbiol 2022; 13:1069694. [PMID: 36569061 PMCID: PMC9780600 DOI: 10.3389/fmicb.2022.1069694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
As pectin is widely used as a food and feed additive due to its tremendous prebiotic potentials for gut health. Yet, the underlying mechanisms associated with its protective effect remain unclear. Twenty-four piglets (Yorkshire × Landrace, 6.77 ± 0.92 kg) were randomly divided into three groups with eight replicates per treatment: (1) Control group (CON), (2) Lipopolysaccharide-challenged group (LPS), (3) Pectin-LPS group (PECL). Piglets were administrated with LPS or saline on d14 and 21 of the experiment. Piglets in each group were fed with corn-soybean meal diets containing 5% citrus pectin or 5% microcrystalline cellulose. Our result showed that pectin alleviated the morphological damage features by restoring the goblet numbers which the pig induced by LPS in the cecum. Besides, compared with the LPS group, pectin supplementation elevated the mRNA expression of tight junction protein [Claudin-1, Claudin-4, and zonula occludens-1 (ZO-1)], mucin (Muc-2), and anti-inflammatory cytokines [interleukin 10 (IL-10), and IL-22]. Whereas pectin downregulated the expression of proinflammatory cytokines (IL-1β, IL-6, IL-18), tumor necrosis factor-&alpha (TNF-α), and NF-κB. What is more, pectin supplementation also significantly increased the abundance of beneficial bacteria (Lactobacillus, Clostridium_sensu_stricto_1, Blautia, and Subdoligranulum), and significantly reduced the abundance of harmful bacteria, such as Streptococcus. Additionally, pectin restored the amount of short-chain fatty acids (SCFAs) after being decreased by LPS (mainly Acetic acid, Propionic acid, and Butyric acid) to alleviate gut injury and improve gut immunity via activating relative receptors (GPR43, GPR109, AhR). Mantel test and correlation analysis also revealed associations between intestinal microbiota and intestinal morphology, and intestinal inflammation in piglets. Taken together, dietary pectin supplementation enhances the gut barrier and improves immunity to ameliorate LPS-induced injury by optimizing gut microbiota and their metabolites.
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Affiliation(s)
- Guoqi Dang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China,Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, Liège University, Gembloux, Belgium
| | - Wenxing Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruqing Zhong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weida Wu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liang Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Liang Chen,
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China,Hongfu Zhang,
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18
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Zhang Z, Li J, Zhang M, Li B, Pan X, Dong X, Pan LL, Sun J. GPR109a Regulates Phenotypic and Functional Alterations in Macrophages and the Progression of Type 1 Diabetes. Mol Nutr Food Res 2022; 66:e2200300. [PMID: 36208084 DOI: 10.1002/mnfr.202200300] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 08/27/2022] [Indexed: 01/18/2023]
Abstract
SCOPE Dietary fibers can alter gut microbiota and microbial metabolite profiles. SCFAs are produced by bacterial fermentation of fiber, mediating immune homeostasis through G-protein-coupled receptors (GPCRs). GPR109a, a receptor for niacin and butyrate, expressed by immune cells and non-immune cells, is a key factor regulating immune responses. However, the role and underlying mechanisms of GPR109a in type 1 diabetes (T1D) remain unclear. METHODS AND RESULTS Experimental T1D was induced by streptozotocin in GPR109a-deficient (Gpr109a-/- ) and wild type mice. The study found that Gpr109a-/- mice were more susceptible to T1D with dysregulated immune responses, along with increased M1 macrophage polarization (from 10.55% to 21.48%). Further, an adoptive transfer experiment demonstrated that GPR109a-deficient macrophages promoted the homing of intestine-derived type 1 cytotoxic T cells to pancreas (from 18.91% to 24.24%), thus disturbing the pancreatic immune homeostasis in non-obese diabetic mice. Mechanistically, GPR109a deficiency promoted M1 macrophage polarization associated with the activation of suppressor of cytokine signaling 3-signal transducer and activator of transcription 1 signaling pathway. CONCLUSION The findings reveal that macrophage GPR109a deficiency accelerates the development of T1D. Activation of GPR109a on macrophage by dietary components may provide a new strategy for preventing or treating T1D.
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Affiliation(s)
- Zhaodi Zhang
- Key Laboratory of Food Science and Technology, Department of Food Science and Engineering, Jiangnan University, Wuxi, 214122, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Jiahong Li
- Key Laboratory of Food Science and Technology, Department of Food Science and Engineering, Jiangnan University, Wuxi, 214122, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Ming Zhang
- Key Laboratory of Food Science and Technology, Department of Food Science and Engineering, Jiangnan University, Wuxi, 214122, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Binbin Li
- Key Laboratory of Food Science and Technology, Department of Food Science and Engineering, Jiangnan University, Wuxi, 214122, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - XiaoHua Pan
- Key Laboratory of Food Science and Technology, Department of Food Science and Engineering, Jiangnan University, Wuxi, 214122, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoliang Dong
- Key Laboratory of Food Science and Technology, Department of Food Science and Engineering, Jiangnan University, Wuxi, 214122, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Li-Long Pan
- Wuxi School of Medicine, Jiangnan University, Wuxi, 214122, China
| | - Jia Sun
- Key Laboratory of Food Science and Technology, Department of Food Science and Engineering, Jiangnan University, Wuxi, 214122, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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19
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Functional and metabolic alterations of gut microbiota in children with new-onset type 1 diabetes. Nat Commun 2022; 13:6356. [PMID: 36289225 PMCID: PMC9606127 DOI: 10.1038/s41467-022-33656-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/23/2022] [Indexed: 12/25/2022] Open
Abstract
Gut dysbiosis has been linked to type 1 diabetes (T1D); however, microbial capacity in T1D remains unclear. Here, we integratively profiled gut microbial functional and metabolic alterations in children with new-onset T1D in independent cohorts and investigated the underlying mechanisms. In T1D, the microbiota was characterized by decreased butyrate production and bile acid metabolism and increased lipopolysaccharide biosynthesis at the species, gene, and metabolite levels. The combination of 18 bacterial species and fecal metabolites provided excellently discriminatory power for T1D. Gut microbiota from children with T1D induced elevated fasting glucose levels and declined insulin sensitivity in antibiotic-treated mice. In streptozotocin-induced T1D mice, butyrate and lipopolysaccharide exerted protective and destructive effects on islet structure and function, respectively. Lipopolysaccharide aggravated the pancreatic inflammatory response, while butyrate activated Insulin1 and Insulin2 gene expression. Our study revealed perturbed microbial functional and metabolic traits in T1D, providing potential avenues for microbiome-based prevention and intervention for T1D.
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20
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Elsherbiny NM, Ramadan M, Abu Faddan NH, Hassan EA, Ali ME, Abd El-Rehim ASED, Abbas WA, Abozaid MAA, Hassanin E, Mohamed GA, Hetta HF, Salah M. Impact of Geographical Location on the Gut Microbiota Profile in Egyptian Children with Type 1 Diabetes Mellitus: A Pilot Study. Int J Gen Med 2022; 15:6173-6187. [PMID: 35864993 PMCID: PMC9296103 DOI: 10.2147/ijgm.s361169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 06/10/2022] [Indexed: 12/11/2022] Open
Abstract
Purpose To investigate the compositional and functional characteristics of T1DM-associated gut microbiota in two Egyptian cities and to study the geographical locality effects. Patients and Methods This case-control study included 32 children with controlled T1DM and 16 controls, selected from two different regions of Egypt. The gut microbiota of both diabetic and control children was analyzed through 16S rRNA gene sequencing; this was done using the Illumina MiSeq platform. Results Consistent findings among the diabetic children included significantly lower alpha diversity than the control children, as well as a lower mean Firmicutes/Bacteroidetes (F/B) ratio, and reduced proportions of Firmicutes and the genera Prevotella and Ruminococcus. In the diabetic children, there were also significantly enriched representations of Actinobacteria, Bacteroidetes, and Proteobacteria and the genera Lactobacilli, Bacteroides, and Faecalibacterium. When comparing the two diabetic groups, the Ismailia group (IsDM) was found to have a significantly higher F/B ratio and diversity indices, with resultant differences at the functional level. Conclusion There are a number of consistent changes in the microbiota profile characterizing the diabetic groups irrespective of the geographical location including significantly lower alpha diversity, mean Firmicutes/ Bacteroidetes (F/B) ratio, and reduced proportions of Firmicutes and genera Prevotella and Ruminococcus. There are also significantly enriched representations of Actinobacteria, Bacteroidetes, and Proteobacteria and genera Lactobacilli, Bacteroides, and Faecalibacterium pointing to the greater driving power of the disease.
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Affiliation(s)
- Nahla M Elsherbiny
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Mohammed Ramadan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut, Egypt
| | - Nagla H Abu Faddan
- Department of Pediatrics, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Elham Ahmed Hassan
- Department of Gastroenterology and Tropical Medicine, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Mohamed E Ali
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut, Egypt
| | | | - Wael A Abbas
- Department of Internal Medicine, Gastroenterology and Hepatology Unit, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Mohamed A A Abozaid
- Department of Internal Medicine, Gastroenterology and Hepatology Unit, Faculty of Medicine, Assiut University, Assiut, Egypt
| | | | - Ghada A Mohamed
- Department of Internal Medicine, Endocrine Unit, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Helal F Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Mohammed Salah
- Department of Microbiology and Immunology, Faculty of pharmacy, Port Said University, Port Said, Egypt
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21
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Yang L, Gao Y, Gong J, Wang H, Farag MA, Simal‐Gandara J, Zhao Y, Nie S, Xiao J. Myricetin ameliorated prediabetes via immunomodulation and gut microbiota interaction. FOOD FRONTIERS 2022. [DOI: 10.1002/fft2.152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Li Yang
- Institute of Chinese Medical Sciences State Key Laboratory of Quality Research in Chinese Medicine University of Macau Macau China
| | - Yongchao Gao
- Department of Clinical Pharmacology Xiangya Hospital Central South University Changsha China
| | - Jupeng Gong
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety College of Food Science and Technology Guangdong Ocean University Zhanjiang China
| | - Hui Wang
- State Key Laboratory of Food Science and Technology China‐Canada Joint Lab of Food Science and Technology (Nanchang) Nanchang University Nanchang China
| | - Mohamed A. Farag
- Pharmacognosy Department College of Pharmacy Cairo University Cairo Egypt
| | - Jesus Simal‐Gandara
- Nutrition and Bromatology Group Department of Analytical and Food Chemistry Faculty of Sciences Universidade de Vigo Ourense Spain
| | - Yonghua Zhao
- Institute of Chinese Medical Sciences State Key Laboratory of Quality Research in Chinese Medicine University of Macau Macau China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology China‐Canada Joint Lab of Food Science and Technology (Nanchang) Nanchang University Nanchang China
| | - Jianbo Xiao
- Nutrition and Bromatology Group Department of Analytical and Food Chemistry Faculty of Sciences Universidade de Vigo Ourense Spain
- Institute of Food Safety and Nutrition Jinan University Guangzhou China
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22
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Tiwari N, Bansal M, Santhiya D, Sharma JG. Insights into microbial diversity on plastisphere by multi-omics. Arch Microbiol 2022; 204:216. [PMID: 35316402 DOI: 10.1007/s00203-022-02806-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 12/20/2022]
Abstract
Plastic pollution is a major concern in marine environment as it takes many years to degrade and is one of the greatest threats to marine life. Plastic surface, referred to as plastisphere, provides habitat for growth and proliferation of various microorganisms. The discovery of these microbes is necessary to identify significant genes, enzymes and bioactive compounds that could help in bioremediation and other commercial applications. Conventional culture techniques have been successful in identifying few microbes from these habitats, leaving majority of them yet to be explored. As such, to recognize the vivid genetic diversity of microbes residing in plastisphere, their structure and corresponding ecological roles within the ecosystem, an emerging technique, called metagenomics has been explored. The technique is expected to provide hitherto unknown information on microbes from the plastisphere. Metagenomics along with next generation sequencing provides comprehensive knowledge on microbes residing in plastisphere that identifies novel microbes for plastic bioremediation, bioactive compounds and other potential benefits. The following review summarizes the efficiency of metagenomics and next generation sequencing technology over conventionally used methods for culturing microbes. It attempts to illustrate the workflow mechanism of metagenomics to elucidate diverse microbial profiles. Further, importance of integrated multi-omics techniques has been highlighted in discovering microbial ecology residing on plastisphere for wider applications.
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Affiliation(s)
- Neha Tiwari
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Megha Bansal
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Deenan Santhiya
- Department of Applied Chemistry, Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, Delhi, 110042, India.
| | - Jai Gopal Sharma
- Department of Biotechnology, Delhi Technological University, Delhi, India
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23
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Identification of antimicrobial peptides from the human gut microbiome using deep learning. Nat Biotechnol 2022; 40:921-931. [PMID: 35241840 DOI: 10.1038/s41587-022-01226-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/19/2022] [Indexed: 02/07/2023]
Abstract
The human gut microbiome encodes a large variety of antimicrobial peptides (AMPs), but the short lengths of AMPs pose a challenge for computational prediction. Here we combined multiple natural language processing neural network models, including LSTM, Attention and BERT, to form a unified pipeline for candidate AMP identification from human gut microbiome data. Of 2,349 sequences identified as candidate AMPs, 216 were chemically synthesized, with 181 showing antimicrobial activity (a positive rate of >83%). Most of these peptides have less than 40% sequence homology to AMPs in the training set. Further characterization of the 11 most potent AMPs showed high efficacy against antibiotic-resistant, Gram-negative pathogens and demonstrated significant efficacy in lowering bacterial load by more than tenfold against a mouse model of bacterial lung infection. Our study showcases the potential of machine learning approaches for mining functional peptides from metagenome data and accelerating the discovery of promising AMP candidate molecules for in-depth investigations.
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24
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Stamboulian M, Canderan J, Ye Y. Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species. PLoS Comput Biol 2022; 18:e1009397. [PMID: 35302987 PMCID: PMC8967034 DOI: 10.1371/journal.pcbi.1009397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/30/2022] [Accepted: 02/15/2022] [Indexed: 12/26/2022] Open
Abstract
Host-microbiome interactions and the microbial community have broad impact in human health and diseases. Most microbiome based studies are performed at the genome level based on next-generation sequencing techniques, but metaproteomics is emerging as a powerful technique to study microbiome functional activity by characterizing the complex and dynamic composition of microbial proteins. We conducted a large-scale survey of human gut microbiome metaproteomic data to identify generalist species that are ubiquitously expressed across all samples and specialists that are highly expressed in a small subset of samples associated with a certain phenotype. We were able to utilize the metaproteomic mass spectrometry data to reveal the protein landscapes of these species, which enables the characterization of the expression levels of proteins of different functions and underlying regulatory mechanisms, such as operons. Finally, we were able to recover a large number of open reading frames (ORFs) with spectral support, which were missed by de novo protein-coding gene predictors. We showed that a majority of the rescued ORFs overlapped with de novo predicted protein-coding genes, but on opposite strands or in different frames. Together, these demonstrate applications of metaproteomics for the characterization of important gut bacterial species. Many reference genomes for studying human gut microbiome are available, but knowledge about how microbial organisms work is limited. Identification of proteins at individual species or community level provides direct insight into the functionality of microbial organisms. By analyzing more than a thousand metaproteomics datasets, we examined protein landscapes of more than two thousands of microbial species that may be important to human health and diseases. This work demonstrated new applications of metaproteomic datasets for studying individual genomes. We made the analysis results available through a website (called GutBac), which we believe will become a resource for studying microbial species important for human health and diseases.
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Affiliation(s)
- Moses Stamboulian
- Computer Science Department, Indiana University, Bloomington, Indiana, United States of America
| | - Jamie Canderan
- Computer Science Department, Indiana University, Bloomington, Indiana, United States of America
| | - Yuzhen Ye
- Computer Science Department, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
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25
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Zhang T, Gao G, Sakandar HA, Kwok LY, Sun Z. Gut Dysbiosis in Pancreatic Diseases: A Causative Factor and a Novel Therapeutic Target. Front Nutr 2022; 9:814269. [PMID: 35242797 PMCID: PMC8885515 DOI: 10.3389/fnut.2022.814269] [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: 11/25/2021] [Accepted: 01/21/2022] [Indexed: 12/12/2022] Open
Abstract
Pancreatic-related disorders such as pancreatitis, pancreatic cancer, and type 1 diabetes mellitus (T1DM) impose a substantial challenge to human health and wellbeing. Even though our understanding of the initiation and progression of pancreatic diseases has broadened over time, no effective therapeutics is yet available for these disorders. Mounting evidence suggests that gut dysbiosis is closely related to human health and disease, and pancreatic diseases are no exception. Now much effort is under way to explore the correlation and eventually potential causation between the gut microbiome and the course of pancreatic diseases, as well as to develop novel preventive and/or therapeutic strategies of targeted microbiome modulation by probiotics, prebiotics, synbiotics, postbiotics, and fecal microbiota transplantation (FMT) for these multifactorial disorders. Attempts to dissect the intestinal microbial landscape and its metabolic profile might enable deep insight into a holistic picture of these complex conditions. This article aims to review the subtle yet intimate nexus loop between the gut microbiome and pancreatic diseases, with a particular focus on current evidence supporting the feasibility of preventing and controlling pancreatic diseases via microbiome-based therapeutics and therapies.
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Affiliation(s)
- Tao Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Guangqi Gao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Hafiz Arbab Sakandar
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
- *Correspondence: Zhihong Sun
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Bandala-Sanchez E, Roth-Schulze AJ, Oakey H, Penno MAS, Bediaga NG, Naselli G, Ngui KM, Smith AD, Huang D, Zozaya-Valdes E, Thomson RL, Brown JD, Vuillermin PJ, Barry SC, Craig ME, Rawlinson WD, Davis EA, Harris M, Soldatos G, Colman PG, Wentworth JM, Haynes A, Morahan G, Sinnott RO, Papenfuss AT, Couper JJ, Harrison LC. Women with type 1 diabetes exhibit a progressive increase in gut Saccharomyces cerevisiae in pregnancy associated with evidence of gut inflammation. Diabetes Res Clin Pract 2022; 184:109189. [PMID: 35051423 DOI: 10.1016/j.diabres.2022.109189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 12/26/2022]
Abstract
AIMS Studies of the gut microbiome have focused on its bacterial composition. We aimed to characterize the gut fungal microbiome (mycobiome) across pregnancy in women with and without type 1 diabetes. METHODS Faecal samples (n = 162) were collected from 70 pregnant women (45 with and 25 without type 1 diabetes) across all trimesters. Fungi were analysed by internal transcribed spacer 1 amplicon sequencing. Markers of intestinal inflammation (faecal calprotectin) and intestinal epithelial integrity (serum intestinal fatty acid binding protein; I-FABP), and serum antibodies to Saccharomyces cerevisiae (ASCA) were measured. RESULTS Women with type 1 diabetes had decreased fungal alpha diversity by the third trimester, associated with an increased abundance of Saccharomyces cerevisiae that was inversely related to the abundance of the anti-inflammatory butyrate-producing bacterium Faecalibacterium prausnitzii. Women with type 1 diabetes had higher concentrations of calprotectin, I-FABP and ASCA. CONCLUSIONS Women with type 1 diabetes exhibit a shift in the gut mycobiome across pregnancy associated with evidence of gut inflammation and impaired intestinal barrier function. The relevance of these findings to the higher rate of pregnancy complications in type 1 diabetes warrants further study.
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Affiliation(s)
- Esther Bandala-Sanchez
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Alexandra J Roth-Schulze
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Helena Oakey
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Megan A S Penno
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Naiara G Bediaga
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Gaetano Naselli
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Katrina M Ngui
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Alannah D Smith
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Dexing Huang
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Enrique Zozaya-Valdes
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Rebecca L Thomson
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - James D Brown
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Peter J Vuillermin
- Faculty of School of Medicine, Deakin University and Child Health Research Unit, Barwon Health, Geelong, VIC, Australia
| | - Simon C Barry
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Maria E Craig
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division, South Eastern Area Laboratory Services Microbiology, NSW Health Pathology, Sydney, NSW, Australia; School of Medical Sciences, Biotechnology and Biomolecular Sciences, Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - Elizabeth A Davis
- Telethon Institute for Child Health Research, Centre for Child Health Research, University of Western Australia, Perth, WA, Australia
| | - Mark Harris
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia; Queensland Children's Hospital, South Brisbane, QLD, Australia
| | - Georgia Soldatos
- Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne and Diabetes and Vascular Medicine Unit, Monash Health, Melbourne, VIC, Australia
| | - Peter G Colman
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - John M Wentworth
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia; Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Aveni Haynes
- Telethon Institute for Child Health Research, Centre for Child Health Research, University of Western Australia, Perth, WA, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, WA, Australia
| | - Richard O Sinnott
- Melbourne eResearch Group, School of Computing and Information Services, University of Melbourne, Melbourne, VIC, Australia
| | - Anthony T Papenfuss
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology and School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia; Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Jennifer J Couper
- The University of Adelaide, Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Women's and Children's Hospital, Adelaide, SA, Australia
| | - Leonard C Harrison
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
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Bell KJ, Saad S, Tillett BJ, McGuire HM, Bordbar S, Yap YA, Nguyen LT, Wilkins MR, Corley S, Brodie S, Duong S, Wright CJ, Twigg S, de St Groth BF, Harrison LC, Mackay CR, Gurzov EN, Hamilton-Williams EE, Mariño E. Metabolite-based dietary supplementation in human type 1 diabetes is associated with microbiota and immune modulation. MICROBIOME 2022; 10:9. [PMID: 35045871 PMCID: PMC8772108 DOI: 10.1186/s40168-021-01193-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Short-chain fatty acids (SCFAs) produced by the gut microbiota have beneficial anti-inflammatory and gut homeostasis effects and prevent type 1 diabetes (T1D) in mice. Reduced SCFA production indicates a loss of beneficial bacteria, commonly associated with chronic autoimmune and inflammatory diseases, including T1D and type 2 diabetes. Here, we addressed whether a metabolite-based dietary supplement has an impact on humans with T1D. We conducted a single-arm pilot-and-feasibility trial with high-amylose maize-resistant starch modified with acetate and butyrate (HAMSAB) to assess safety, while monitoring changes in the gut microbiota in alignment with modulation of the immune system status. RESULTS HAMSAB supplement was administered for 6 weeks with follow-up at 12 weeks in adults with long-standing T1D. Increased concentrations of SCFA acetate, propionate, and butyrate in stools and plasma were in concert with a shift in the composition and function of the gut microbiota. While glucose control and insulin requirements did not change, subjects with the highest SCFA concentrations exhibited the best glycemic control. Bifidobacterium longum, Bifidobacterium adolescentis, and vitamin B7 production correlated with lower HbA1c and basal insulin requirements. Circulating B and T cells developed a more regulatory phenotype post-intervention. CONCLUSION Changes in gut microbiota composition, function, and immune profile following 6 weeks of HAMSAB supplementation were associated with increased SCFAs in stools and plasma. The persistence of these effects suggests that targeting dietary SCFAs may be a mechanism to alter immune profiles, promote immune tolerance, and improve glycemic control for the treatment of T1D. TRIAL REGISTRATION ACTRN12618001391268. Registered 20 August 2018, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=375792 Video Abstract.
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Affiliation(s)
- Kirstine J Bell
- Charles Perkins Centre, University of Sydney, Camperdown, Sydney, New South Wales, 2050, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Sonia Saad
- Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney Medical School, University of Sydney, St Leonards, Sydney, New South Wales, Australia
| | - Bree J Tillett
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Brisbane, Queensland, 4102, Australia
| | - Helen M McGuire
- Charles Perkins Centre, University of Sydney, Camperdown, Sydney, New South Wales, 2050, Australia
- Discipline of Pathology, Faculty of Medicine and Health, The University of Sydney, Camperdown, Sydney, New South Wales, 2050, Australia
- Ramaciotti Facility for Human Systems Biology, The University of Sydney, Camperdown, Sydney, New South Wales, 2050, Australia
| | - Sara Bordbar
- Infection and Immunity Program, Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Melbourne, Victoria, 3800, Australia
| | - Yu Anne Yap
- Infection and Immunity Program, Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Melbourne, Victoria, 3800, Australia
| | - Long T Nguyen
- Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney Medical School, University of Sydney, St Leonards, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Susan Corley
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Shannon Brodie
- Charles Perkins Centre, University of Sydney, Camperdown, Sydney, New South Wales, 2050, Australia
| | - Sussan Duong
- Charles Perkins Centre, University of Sydney, Camperdown, Sydney, New South Wales, 2050, Australia
| | - Courtney J Wright
- Charles Perkins Centre, University of Sydney, Camperdown, Sydney, New South Wales, 2050, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Stephen Twigg
- Charles Perkins Centre, University of Sydney, Camperdown, Sydney, New South Wales, 2050, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Barbara Fazekas de St Groth
- Charles Perkins Centre, University of Sydney, Camperdown, Sydney, New South Wales, 2050, Australia
- Discipline of Pathology, Faculty of Medicine and Health, The University of Sydney, Camperdown, Sydney, New South Wales, 2050, Australia
- Ramaciotti Facility for Human Systems Biology, The University of Sydney, Camperdown, Sydney, New South Wales, 2050, Australia
| | - Leonard C Harrison
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Charles R Mackay
- Infection and Immunity Program, Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Melbourne, Victoria, 3800, Australia
| | - Esteban N Gurzov
- Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070, Brussels, Belgium
| | - Emma E Hamilton-Williams
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Brisbane, Queensland, 4102, Australia.
| | - Eliana Mariño
- Infection and Immunity Program, Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Melbourne, Victoria, 3800, Australia.
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Bielka W, Przezak A, Pawlik A. The Role of the Gut Microbiota in the Pathogenesis of Diabetes. Int J Mol Sci 2022; 23:ijms23010480. [PMID: 35008906 PMCID: PMC8745411 DOI: 10.3390/ijms23010480] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 02/06/2023] Open
Abstract
Diabetes mellitus is a significant clinical and therapeutic problem because it can lead to serious long-term complications. Its pathogenesis is not fully understood, but there are indications that dysbiosis can play a role in the development of diabetes, or that it appears during the course of the disease. Changes in microbiota composition are observed in both type 1 diabetes (T1D) and type 2 diabetes (T2D) patients. These modifications are associated with pro-inflammation, increased intestinal permeability, endotoxemia, impaired β-cell function and development of insulin resistance. This review summarizes the role of the gut microbiota in healthy individuals and the changes in bacterial composition that can be associated with T1D or T2D. It also presents new developments in diabetes therapy based on influencing the gut microbiota as a promising method to alter the course of diabetes. Moreover, it highlights the lacking data and suggests future directions needed to prove the causal relationship between dysbiosis and diabetes, both T1D and T2D.
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29
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Metaproteomics Approach and Pathway Modulation in Obesity and Diabetes: A Narrative Review. Nutrients 2021; 14:nu14010047. [PMID: 35010920 PMCID: PMC8746330 DOI: 10.3390/nu14010047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022] Open
Abstract
Low-grade inflammatory diseases revealed metabolic perturbations that have been linked to various phenotypes, including gut microbiota dysbiosis. In the last decade, metaproteomics has been used to investigate protein composition profiles at specific steps and in specific healthy/pathologic conditions. We applied a rigorous protocol that relied on PRISMA guidelines and filtering criteria to obtain an exhaustive study selection that finally resulted in a group of 10 studies, based on metaproteomics and that aim at investigating obesity and diabetes. This batch of studies was used to discuss specific microbial and human metaproteome alterations and metabolic patterns in subjects affected by diabetes (T1D and T2D) and obesity. We provided the main up- and down-regulated protein patterns in the inspected pathologies. Despite the available results, the evident paucity of metaproteomic data is to be considered as a limiting factor in drawing objective considerations. To date, ad hoc prepared metaproteomic databases collecting pathologic data and related metadata, together with standardized analysis protocols, are required to increase our knowledge on these widespread pathologies.
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30
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Yu D, Meng X, de Vos WM, Wu H, Fang X, Maiti AK. Implications of Gut Microbiota in Complex Human Diseases. Int J Mol Sci 2021; 22:12661. [PMID: 34884466 PMCID: PMC8657718 DOI: 10.3390/ijms222312661] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/30/2021] [Accepted: 11/17/2021] [Indexed: 02/07/2023] Open
Abstract
Humans, throughout the life cycle, from birth to death, are accompanied by the presence of gut microbes. Environmental factors, lifestyle, age and other factors can affect the balance of intestinal microbiota and their impact on human health. A large amount of data show that dietary, prebiotics, antibiotics can regulate various diseases through gut microbes. In this review, we focus on the role of gut microbes in the development of metabolic, gastrointestinal, neurological, immune diseases and, cancer. We also discuss the interaction between gut microbes and the host with respect to their beneficial and harmful effects, including their metabolites, microbial enzymes, small molecules and inflammatory molecules. More specifically, we evaluate the potential ability of gut microbes to cure diseases through Fecal Microbial Transplantation (FMT), which is expected to become a new type of clinical strategy for the treatment of various diseases.
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Affiliation(s)
- Dahai Yu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China; (X.M.); (X.F.)
| | - Xin Meng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China; (X.M.); (X.F.)
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands;
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Hao Wu
- Vascular Biology Program, Department of Surgery, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA;
| | - Xuexun Fang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun 130012, China; (X.M.); (X.F.)
| | - Amit K. Maiti
- Department of Genetics and Genomics, Mydnavar, 2645 Somerset Boulevard, Troy, MI 48084, USA
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31
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Xue W, Li JJ, Zou Y, Zou B, Wei L. Microbiota and Ocular Diseases. Front Cell Infect Microbiol 2021; 11:759333. [PMID: 34746029 PMCID: PMC8566696 DOI: 10.3389/fcimb.2021.759333] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/06/2021] [Indexed: 12/12/2022] Open
Abstract
Recent advances have identified significant associations between the composition and function of the gut microbiota and various disorders in organ systems other than the digestive tract. Utilizing next-generation sequencing and multiomics approaches, the microbial community that possibly impacts ocular disease has been identified. This review provides an overview of the literature on approaches to microbiota analysis and the roles of commensal microbes in ophthalmic diseases, including autoimmune uveitis, age-related macular degeneration, glaucoma, and other ocular disorders. In addition, this review discusses the hypothesis of the "gut-eye axis" and evaluates the therapeutic potential of targeting commensal microbiota to alleviate ocular inflammation.
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Affiliation(s)
- Wei Xue
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Jing Jing Li
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Yanli Zou
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China.,Department of Ophthalmology, Affiliated Foshan Hospital, Southern Medical University, Foshan, China
| | - Bin Zou
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
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Morse ZJ, Horwitz MS. Virus Infection Is an Instigator of Intestinal Dysbiosis Leading to Type 1 Diabetes. Front Immunol 2021; 12:751337. [PMID: 34721424 PMCID: PMC8554326 DOI: 10.3389/fimmu.2021.751337] [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: 07/31/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022] Open
Abstract
In addition to genetic predisposition, environmental determinants contribute to a complex etiology leading to onset of type 1 diabetes (T1D). Multiple studies have established the gut as an important site for immune modulation that can directly impact development of autoreactive cell populations against pancreatic self-antigens. Significant efforts have been made to unravel how changes in the microbiome function as a contributor to autoimmune responses and can serve as a biomarker for diabetes development. Large-scale longitudinal studies reveal that common environmental exposures precede diabetes pathology. Virus infections, particularly those associated with the gut, have been prominently identified as risk factors for T1D development. Evidence suggests recent-onset T1D patients experience pre-existing subclinical enteropathy and dysbiosis leading up to development of diabetes. The start of these dysbiotic events coincide with detection of virus infections. Thus viral infection may be a contributing driver for microbiome dysbiosis and disruption of intestinal homeostasis prior to T1D onset. Ultimately, understanding the cross-talk between viral infection, the microbiome, and the immune system is key for the development of preventative measures against T1D.
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Affiliation(s)
| | - Marc S. Horwitz
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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33
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Jia LL, Zhang M, Liu H, Sun J, Pan LL. Early-life fingolimod treatment improves intestinal homeostasis and pancreatic immune tolerance in non-obese diabetic mice. Acta Pharmacol Sin 2021; 42:1620-1629. [PMID: 33473182 PMCID: PMC8463616 DOI: 10.1038/s41401-020-00590-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 09/26/2020] [Indexed: 02/06/2023] Open
Abstract
Fingolimod has beneficial effects on multiple diseases, including type 1 diabetes (T1D) and numerous preclinical models of colitis. Intestinal dysbiosis and intestinal immune dysfunction contribute to disease pathogenesis of T1D. Thus, the beneficial effect of fingolimod on T1D may occur via the maintenance of intestinal homeostasis to some extent. Herein, we investigated the role of fingolimod in intestinal dysfunction in non-obese diabetic (NOD) mice and possible mechanisms. NOD mice were treated with fingolimod (1 mg · kg-1 per day, i.g.) from weaning (3-week-old) to 31 weeks of age. We found that fingolimod administration significantly enhanced the gut barrier (evidenced by enhanced expression of tight junction proteins and reduced intestinal permeability), attenuated intestinal microbial dysbiosis (evidenced by the reduction of enteric pathogenic Proteobacteria clusters), as well as intestinal immune dysfunction (evidenced by inhibition of CD4+ cells activation, reduction of T helper type 1 cells and macrophages, and the expansion of regulatory T cells). We further revealed that fingolimod administration suppressed the activation of CD4+ cells and the differentiation of T helper type 1 cells, promoted the expansion of regulatory T cells in the pancreas, which might contribute to the maintenance of pancreatic immune tolerance and the reduction of T1D incidence. The protection might be due to fingolimod inhibiting the toll-like receptor 2/4/nuclear factor-κB/NOD-like receptor protein 3 inflammasome pathway in the colon. Collectively, early-life fingolimod treatment attenuates intestinal microbial dysbiosis and intestinal immune dysfunction in the T1D setting, which might contribute to its anti-diabetic effect.
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Affiliation(s)
- Ling-Ling Jia
- Wuxi School of Medicine, Jiangnan University, Wuxi, 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Ming Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - He Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Jia Sun
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
| | - Li-Long Pan
- Wuxi School of Medicine, Jiangnan University, Wuxi, 214122, China.
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34
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Uchida A, Yasuma T, Takeshita A, Toda M, Okano Y, Nishihama K, D'Alessandro-Gabazza CN, Fridman D'Alessandro V, Inoue C, Takagi T, Mukaiyama H, Takagi N, Shimizu K, Yano Y, Gabazza EC. Oral Limonite Supplement Ameliorates Glucose Intolerance in Diabetic and Obese Mice. J Inflamm Res 2021; 14:3089-3105. [PMID: 34276223 PMCID: PMC8277451 DOI: 10.2147/jir.s320451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/18/2021] [Indexed: 12/20/2022] Open
Abstract
Introduction Diabetes mellitus is a serious threat to public health worldwide. It causes a substantial economic burden, mental and physical disabilities, poor quality of life, and high mortality. Limonite is formed when iron-rich materials from the underground emerge and oxidized on the ground surface. It is currently used to purify contaminated water, absorption of irritant gases, and improve livestock breeding. Limonite can change the composition of environmental microbial communities. In the present study, we evaluated whether limonite can ameliorate glucose metabolism abnormalities by remodeling the gut microbiome. Methods The investigation was performed using mouse models of streptozotocin-induced diabetes mellitus and high-calorie diet-induced metabolic syndrome. Results Oral limonite supplement was associated with significant body weight recovery, reduced glycemia with improved insulin secretion, increased number of regulatory T cells, and abundant beneficial gut microbial populations in mice with diabetes mellitus compared to control. Similarly, mice with obesity fed with limonite supplements had significantly reduced body weight, insulin resistance, steatohepatitis, and systemic inflammatory response with significant gut microbiome remodeling. Conclusion This study demonstrates that limonite supplement ameliorates abnormal glucose metabolism in diabetes mellitus and obesity. Gut microbiome remodeling, inhibition of inflammatory cytokines, and the host immune response regulation may explain the limonite’s beneficial activity under pathological conditions in vivo.
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Affiliation(s)
- Akihiro Uchida
- Department of Diabetes and Endocrinology, Mie University Faculty and Graduate School of Medicine, Tsu, Mie, Japan
| | - Taro Yasuma
- Department of Diabetes and Endocrinology, Mie University Faculty and Graduate School of Medicine, Tsu, Mie, Japan.,Department of Immunology, Mie University Faculty and Graduate School of Medicine, Tsu, Mie, Japan
| | - Atsuro Takeshita
- Department of Diabetes and Endocrinology, Mie University Faculty and Graduate School of Medicine, Tsu, Mie, Japan.,Department of Immunology, Mie University Faculty and Graduate School of Medicine, Tsu, Mie, Japan
| | - Masaaki Toda
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Tsu, Mie, Japan
| | - Yuko Okano
- Department of Diabetes and Endocrinology, Mie University Faculty and Graduate School of Medicine, Tsu, Mie, Japan.,Department of Immunology, Mie University Faculty and Graduate School of Medicine, Tsu, Mie, Japan
| | - Kota Nishihama
- Department of Diabetes and Endocrinology, Mie University Faculty and Graduate School of Medicine, Tsu, Mie, Japan
| | | | | | - Chisa Inoue
- Department of Diabetes and Endocrinology, Mie University Faculty and Graduate School of Medicine, Tsu, Mie, Japan
| | | | | | | | | | - Yutaka Yano
- Department of Diabetes and Endocrinology, Mie University Faculty and Graduate School of Medicine, Tsu, Mie, Japan
| | - Esteban C Gabazza
- Department of Immunology, Mie University Faculty and Graduate School of Medicine, Tsu, Mie, Japan
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35
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Biemann R, Buß E, Benndorf D, Lehmann T, Schallert K, Püttker S, Reichl U, Isermann B, Schneider JG, Saake G, Heyer R. Fecal Metaproteomics Reveals Reduced Gut Inflammation and Changed Microbial Metabolism Following Lifestyle-Induced Weight Loss. Biomolecules 2021; 11:biom11050726. [PMID: 34066026 PMCID: PMC8150863 DOI: 10.3390/biom11050726] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/30/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
Gut microbiota-mediated inflammation promotes obesity-associated low-grade inflammation, which represents a hallmark of metabolic syndrome. To investigate if lifestyle-induced weight loss (WL) may modulate the gut microbiome composition and its interaction with the host on a functional level, we analyzed the fecal metaproteome of 33 individuals with metabolic syndrome in a longitudinal study before and after lifestyle-induced WL in a well-defined cohort. The 6-month WL intervention resulted in reduced BMI (-13.7%), improved insulin sensitivity (HOMA-IR, -46.1%), and reduced levels of circulating hsCRP (-39.9%), indicating metabolic syndrome reversal. The metaprotein spectra revealed a decrease of human proteins associated with gut inflammation. Taxonomic analysis revealed only minor changes in the bacterial composition with an increase of the families Desulfovibrionaceae, Leptospiraceae, Syntrophomonadaceae, Thermotogaceae and Verrucomicrobiaceae. Yet we detected an increased abundance of microbial metaprotein spectra that suggest an enhanced hydrolysis of complex carbohydrates. Hence, lifestyle-induced WL was associated with reduced gut inflammation and functional changes of human and microbial enzymes for carbohydrate hydrolysis while the taxonomic composition of the gut microbiome remained almost stable. The metaproteomics workflow has proven to be a suitable method for monitoring inflammatory changes in the fecal metaproteome.
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Affiliation(s)
- Ronald Biemann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Paul-List-Str. 13/15, 04103 Leipzig, Germany;
- Correspondence: (R.B.); (D.B.); (R.H.)
| | - Enrico Buß
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
- Microbiology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06354 Köthen, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- Correspondence: (R.B.); (D.B.); (R.H.)
| | - Theresa Lehmann
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
| | - Kay Schallert
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
| | - Sebastian Püttker
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
| | - Udo Reichl
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Paul-List-Str. 13/15, 04103 Leipzig, Germany;
- Institute of Clinical Chemistry and Pathobiochemistry, Otto von Guericke University, Leipziger Straße 44, 39120 Magdeburg, Germany
| | - Jochen G. Schneider
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg;
- Department of Internal Medicine II, Saarland University Medical Center, Kirrberger Str., 66424 Homburg Saar, Germany
| | - Gunter Saake
- Database and Software Engineering Group, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany;
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany; (E.B.); (T.L.); (K.S.); (S.P.); (U.R.)
- Database and Software Engineering Group, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany;
- Correspondence: (R.B.); (D.B.); (R.H.)
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36
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FFAR from the Gut Microbiome Crowd: SCFA Receptors in T1D Pathology. Metabolites 2021; 11:metabo11050302. [PMID: 34064625 PMCID: PMC8151283 DOI: 10.3390/metabo11050302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/14/2022] Open
Abstract
The gut microbiome has emerged as a novel determinant of type 1 diabetes (T1D), but the underlying mechanisms are unknown. In this context, major gut microbial metabolites, short-chain fatty acids (SCFAs), are considered to be an important link between the host and gut microbiome. We, along with other laboratories, have explored how SCFAs and their cognate receptors affect various metabolic conditions, including obesity, type 2 diabetes, and metabolic syndrome. Though gut microbiome and SCFA-level changes have been reported in T1D and in mouse models of the disease, the role of SCFA receptors in T1D remains under explored. In this review article, we will highlight the existing and possible roles of these receptors in T1D pathology. We conclude with a discussion of SCFA receptors as therapeutic targets for T1D, exploring an exciting new potential for novel treatments of glucometabolic disorders.
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37
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Harbison JE, Thomson RL, Wentworth JM, Louise J, Roth-Schulze A, Battersby RJ, Ngui KM, Penno MAS, Colman PG, Craig ME, Barry SC, Tran CD, Makrides M, Harrison LC, Couper JJ. Associations between diet, the gut microbiome and short chain fatty acids in youth with islet autoimmunity and type 1 diabetes. Pediatr Diabetes 2021; 22:425-433. [PMID: 33470492 DOI: 10.1111/pedi.13178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/24/2020] [Accepted: 12/28/2020] [Indexed: 12/20/2022] Open
Abstract
AIM We aimed to characterize associations between diet and the gut microbiome and short chain fatty acid (SCFA) products in youth with islet autoimmunity or type 1 diabetes (IA/T1D) in comparison with controls. RESEARCH DESIGN AND METHODS Eighty participants (25 diagnosed with T1D, 17 with confirmed IA, 38 sibling or unrelated controls) from the Australian T1D Gut Study cohort were studied (median [IQR] age 11.7 [8.9, 14.0] years, 43% female). A Food Frequency Questionnaire characterized daily macronutrient intake over the preceding 6 months. Plasma and fecal SCFA were measured by gas chromatography; gut microbiome composition and diversity by 16S rRNA gene sequencing. RESULTS A 10 g increase in daily carbohydrate intake associated with higher plasma acetate in IA/T1D (adjusted estimate +5.2 (95% CI 1.1, 9.2) μmol/L p = 0.01) and controls (adjusted estimate +4.1 [95% CI 1.7, 8.5] μmol/L p = 0.04). A 5 g increase in total fat intake associated with lower plasma acetate in IA/T1D and controls. A 5% increase in noncore (junk) food intake associated with reduced richness (adjusted estimate -4.09 [95%CI -7.83, -0.35] p = .03) and evenness (-1.25 [95% CI -2.00, -0.49] p < 0.01) of the gut microbiome in IA/T1D. Fiber intake associated with community structure of the microbiome in IA/T1D. CONCLUSIONS Modest increments in carbohydrate and fat intake associated with plasma acetate in all youth. Increased junk food intake associated with reduced diversity of the gut microbiome in IA/T1D alone. These associations with the gut microbiome in IA/T1D support future efforts to promote SCFA by using dietary interventions.
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Affiliation(s)
- Jessica E Harbison
- Women's and Children's Hospital, Adelaide, South Australia, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Rebecca L Thomson
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - John M Wentworth
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Jennie Louise
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | | | | | - Katrina M Ngui
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Megan A S Penno
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Peter G Colman
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Maria E Craig
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Simon C Barry
- Women's and Children's Hospital, Adelaide, South Australia, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Cuong D Tran
- CSIRO, Health and Biosecurity, Adelaide, South Australia, Australia
| | - Maria Makrides
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia.,SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Leonard C Harrison
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Jennifer J Couper
- Women's and Children's Hospital, Adelaide, South Australia, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
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38
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Huang W, Kane MA. MAPLE: A Microbiome Analysis Pipeline Enabling Optimal Peptide Search and Comparative Taxonomic and Functional Analysis. J Proteome Res 2021; 20:2882-2894. [PMID: 33848166 DOI: 10.1021/acs.jproteome.1c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metaproteomics by mass spectrometry (MS) is a powerful approach to profile a large number of proteins expressed by all organisms in a highly complex biological or ecological sample, which is able to provide a direct and quantitative assessment of the functional makeup of a microbiota. The human gastrointestinal microbiota has been found playing important roles in human physiology and health, and metaproteomics has been shown to shed light on multiple novel associations between microbiota and diseases. MS-powered proteomics generally relies on genome data to define search space. However, metaproteomics, which simultaneously analyzes all proteins from hundreds to thousands of species, faces significant challenges regarding database search and interpretation of results. To overcome these obstacles, we have developed a user-friendly microbiome analysis pipeline (MAPLE, freely downloadable at http://maple.rx.umaryland.edu/), which is able to define an optimal search space by inferring proteomes specific to samples following the principle of parsimony. MAPLE facilitates highly comparable or better peptide identification compared to a sample-specific metagenome-guided search. In addition, we implemented an automated peptide-centric enrichment analysis function in MAPLE to address issues of traditional protein-centric comparison, enabling straightforward and comprehensive comparison of taxonomic and functional makeup between microbiota.
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Affiliation(s)
- Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland 21201, United States
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39
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Gavin PG, Wong J, Loo D, Zipris D, Hill MM, Hamilton-Williams EE. Metaproteomic sample preparation methods bias the recovery of host and microbial proteins according to taxa and cellular compartment. J Proteomics 2021; 240:104219. [PMID: 33831598 DOI: 10.1016/j.jprot.2021.104219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 02/07/2023]
Abstract
Faecal proteomics studies have focussed on identification of microbial proteins, however; stool represents a valuable resource to interrogate the host interactions with the microbiota without the need for invasive intestinal biopsies. As the widely used enrichment method (differential centrifugation, DC) enriches for microbial proteins, we compared two other methods for enrichment of host proteins, termed 'host enriched' (HE) and ALL (all proteins). The HE and ALL protocols identified 1.8-fold more host proteins than DC while detecting a similar number of microbial proteins, but the methods had limited overlap in the specific microbial proteins detected. To maximize identification of both host and microbial proteins, samples were subjected to HE and the remaining material was used to perform DC. These two fractions displayed large differences in relative taxonomic abundance and cellular compartmentalization, with proteins from Bacteroidales and extracellular vesicles were enriched in the soluble HE component. The combination of data generated from these two fractions may allow identification of more distinct proteins than simply performing samples in duplicate or more complex fractionation techniques, or a single fraction could be chosen to suit the experimental hypothesis. SIGNIFICANCE: We compared how different stool protein preparation methods influenced the taxonomic and functional characteristics of microbial and host proteins identified. Surprisingly, a method designed to enrich for host proteins recovered a similar number of microbial protein groups to the method that specifically enriched intact bacterial cells. However, the taxonomic and subcellular origin of the microbial proteins differed considerably between the methods. By implementing a two-step method, we could maximize recovery of both host and microbial proteins derived from different cellular compartments and taxa.
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Affiliation(s)
- Patrick G Gavin
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Justin Wong
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Dorothy Loo
- Translational Research Institute, Woolloongabba, QLD, Australia
| | - Danny Zipris
- Innate Biotechnologies, LLC, Denver, CO 80231, United States of America
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Emma E Hamilton-Williams
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia; Correspondence should be addressed to A/Prof Emma Hamilton-Williams, The University of Queensland Diamantina Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia.
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40
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Hamilton-Williams EE, Lorca GL, Norris JM, Dunne JL. A Triple Threat? The Role of Diet, Nutrition, and the Microbiota in T1D Pathogenesis. Front Nutr 2021; 8:600756. [PMID: 33869260 PMCID: PMC8046917 DOI: 10.3389/fnut.2021.600756] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
In recent years the role of the intestinal microbiota in health and disease has come to the forefront of medical research. Alterations in the intestinal microbiota and several of its features have been linked to numerous diseases, including type 1 diabetes (T1D). To date, studies in animal models of T1D, as well as studies in human subjects, have linked several intestinal microbiota alterations with T1D pathogenesis. Features that are most often linked with T1D pathogenesis include decreased microbial diversity, the relative abundance of specific strains of individual microbes, and altered metabolite production. Alterations in these features as well as others have provided insight into T1D pathogenesis and shed light on the potential mechanism by which the microbiota plays a role in T1D pathogenesis, yet the underlying factors leading to these alterations remains unknown. One potential mechanism for alteration of the microbiota is through diet and nutrition. Previous studies have shown associations of diet with islet autoimmunity, but a direct contributing factor has yet to be identified. Diet, through introduction of antigens and alteration of the composition and function of the microbiota, may elicit the immune system to produce autoreactive responses that result in the destruction of the beta cells. Here, we review the evidence associating diet induced changes in the intestinal microbiota and their contribution to T1D pathogenesis. We further provide a roadmap for determining the effect of diet and other modifiable factors on the entire microbiota ecosystem, including its impact on both immune and beta cell function, as it relates to T1D. A greater understanding of the complex interactions between the intestinal microbiota and several interacting systems in the body (immune, intestinal integrity and function, metabolism, beta cell function, etc.) may provide scientifically rational approaches to prevent development of T1D and other childhood immune and allergic diseases and biomarkers to evaluate the efficacy of interventions.
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Affiliation(s)
- Emma E. Hamilton-Williams
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Graciela L. Lorca
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, United States
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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41
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George AK, Behera J, Homme RP, Tyagi N, Tyagi SC, Singh M. Rebuilding Microbiome for Mitigating Traumatic Brain Injury: Importance of Restructuring the Gut-Microbiome-Brain Axis. Mol Neurobiol 2021; 58:3614-3627. [PMID: 33774742 PMCID: PMC8003896 DOI: 10.1007/s12035-021-02357-2] [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: 12/15/2020] [Accepted: 03/10/2021] [Indexed: 12/20/2022]
Abstract
Traumatic brain injury (TBI) is a damage to the brain from an external force that results in temporary or permanent impairment in brain functions. Unfortunately, not many treatment options are available to TBI patients. Therefore, knowledge of the complex interplay between gut microbiome (GM) and brain health may shed novel insights as it is a rapidly expanding field of research around the world. Recent studies show that GM plays important roles in shaping neurogenerative processes such as blood-brain-barrier (BBB), myelination, neurogenesis, and microglial maturation. In addition, GM is also known to modulate many aspects of neurological behavior and cognition; however, not much is known about the role of GM in brain injuries. Since GM has been shown to improve cellular and molecular functions via mitigating TBI-induced pathologies such as BBB permeability, neuroinflammation, astroglia activation, and mitochondrial dysfunction, herein we discuss how a dysbiotic gut environment, which in fact, contributes to central nervous system (CNS) disorders during brain injury and how to potentially ward off these harmful effects. We further opine that a better understanding of GM-brain (GMB) axis could help assist in designing better treatment and management strategies in future for the patients who are faced with limited options.
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Affiliation(s)
- Akash K George
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA.,Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA
| | - Jyotirmaya Behera
- Bone Biology Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA
| | - Rubens P Homme
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA.,Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA
| | - Neetu Tyagi
- Bone Biology Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA
| | - Suresh C Tyagi
- Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA
| | - Mahavir Singh
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA. .,Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky, 40202, USA.
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Nilsen M, Lokmic A, Angell IL, Lødrup Carlsen KC, Carlsen KH, Haugen G, Hedlin G, Jonassen CM, Marsland BJ, Nordlund B, Rehbinder EM, Saunders CM, Skjerven HO, Snipen L, Staff AC, Söderhäll C, Vettukattil R, Rudi K. Fecal Microbiota Nutrient Utilization Potential Suggests Mucins as Drivers for Initial Gut Colonization of Mother-Child-Shared Bacteria. Appl Environ Microbiol 2021; 87:e02201-20. [PMID: 33452029 PMCID: PMC8105027 DOI: 10.1128/aem.02201-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/04/2021] [Indexed: 01/04/2023] Open
Abstract
The nutritional drivers for mother-child sharing of bacteria and the corresponding longitudinal trajectory of the infant gut microbiota development are not yet completely settled. We therefore aimed to characterize the mother-child sharing and the inferred nutritional utilization potential for the gut microbiota from a large unselected cohort. We analyzed in depth gut microbiota in 100 mother-child pairs enrolled antenatally from the general population-based Preventing Atopic Dermatitis and Allergies in Children (PreventADALL) cohort. Fecal samples collected at gestational week 18 for mothers and at birth (meconium), 3, 6, and 12 months for infants were analyzed by reduced metagenome sequencing to determine metagenome size and taxonomic composition. The nutrient utilization potential was determined based on the Virtual Metabolic Human (VMH, www.vmh.life) database. The estimated median metagenome size was ∼150 million base pairs (bp) for mothers and ∼20 million bp at birth for the children. Longitudinal analyses revealed mother-child sharing (P < 0.05, chi-square test) from birth up to 6 months for 3 prevalent Bacteroides species (prevalence, >25% for all age groups). In a multivariate analysis of variance (ANOVA), the mother-child-shared Bacteroides were associated with vaginal delivery (1.7% explained variance, P = 0.0001). Both vaginal delivery and mother-child sharing were associated with host-derived mucins as nutrient sources. The age-related increase in metagenome size corresponded to an increased diversity in nutrient utilization, with dietary polysaccharides as the main age-related factor. Our results support host-derived mucins as potential selection means for mother-child sharing of initial colonizers, while the age-related increase in diversity was associated with dietary polysaccharides.IMPORTANCE The initial bacterial colonization of human infants is crucial for lifelong health. Understanding the factors driving this colonization will therefore be of great importance. Here, we used a novel high-taxonomic-resolution approach to deduce the nutrient utilization potential of the infant gut microbiota in a large longitudinal mother-child cohort. We found mucins as potential selection means for the initial colonization of mother-child-shared bacteria, while the transition to a more adult-like microbiota was associated with dietary polysaccharide utilization potential. This knowledge will be important for a future understanding of the importance of diet in shaping the gut microbiota composition and development during infancy.
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Affiliation(s)
- Morten Nilsen
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Asima Lokmic
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Inga Leena Angell
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Karin C Lødrup Carlsen
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
| | - Kai-Håkon Carlsen
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
| | - Guttorm Haugen
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
- Division of Obstetrics and Gynaecology, Oslo University Hospital, Oslo, Norway
| | - Gunilla Hedlin
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Christine Monceyron Jonassen
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Genetic Unit, Centre for Laboratory Medicine, Østfold Hospital Trust, Kalnes, Norway
| | - Benjamin J Marsland
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Björn Nordlund
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Eva Maria Rehbinder
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
- Division of Obstetrics and Gynaecology, Oslo University Hospital, Oslo, Norway
| | - Carina Madelen Saunders
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
| | - Håvard O Skjerven
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
| | - Lars Snipen
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Anne Cathrine Staff
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
- Division of Obstetrics and Gynaecology, Oslo University Hospital, Oslo, Norway
| | - Cilla Söderhäll
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Riyas Vettukattil
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
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Salvato F, Hettich RL, Kleiner M. Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes. PLoS Pathog 2021; 17:e1009245. [PMID: 33630960 PMCID: PMC7906368 DOI: 10.1371/journal.ppat.1009245] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Fernanda Salvato
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (FS); (MK)
| | - Robert L. Hettich
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, Tennessee, United States of America
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (FS); (MK)
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44
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Daliri EBM, Ofosu FK, Chelliah R, Lee BH, Oh DH. Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies. Biomolecules 2021; 11:300. [PMID: 33671370 PMCID: PMC7922017 DOI: 10.3390/biom11020300] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/10/2021] [Accepted: 02/14/2021] [Indexed: 12/14/2022] Open
Abstract
The advent of omic technology has made it possible to identify viable but unculturable micro-organisms in the gut. Therefore, application of multi-omic technologies in gut microbiome studies has become invaluable for unveiling a comprehensive interaction between these commensals in health and disease. Meanwhile, despite the successful identification of many microbial and host-microbial cometabolites that have been reported so far, it remains difficult to clearly identify the origin and function of some proteins and metabolites that are detected in gut samples. However, the application of single omic techniques for studying the gut microbiome comes with its own challenges which may be overcome if a number of different omics techniques are combined. In this review, we discuss our current knowledge about multi-omic techniques, their challenges and future perspective in this field of gut microbiome studies.
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Affiliation(s)
- Eric Banan-Mwine Daliri
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea; (E.B.-M.D.); (F.K.O.); (R.C.)
| | - Fred Kwame Ofosu
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea; (E.B.-M.D.); (F.K.O.); (R.C.)
| | - Ramachandran Chelliah
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea; (E.B.-M.D.); (F.K.O.); (R.C.)
| | - Byong H. Lee
- SportBiomics, Sacramento Inc., California, CA 95660, USA;
| | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea; (E.B.-M.D.); (F.K.O.); (R.C.)
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45
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Fu J, Luo Y, Mou M, Zhang H, Tang J, Wang Y, Zhu F. Advances in Current Diabetes Proteomics: From the Perspectives of Label- free Quantification and Biomarker Selection. Curr Drug Targets 2021; 21:34-54. [PMID: 31433754 DOI: 10.2174/1389450120666190821160207] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Due to its prevalence and negative impacts on both the economy and society, the diabetes mellitus (DM) has emerged as a worldwide concern. In light of this, the label-free quantification (LFQ) proteomics and diabetic marker selection methods have been applied to elucidate the underlying mechanisms associated with insulin resistance, explore novel protein biomarkers, and discover innovative therapeutic protein targets. OBJECTIVE The purpose of this manuscript is to review and analyze the recent computational advances and development of label-free quantification and diabetic marker selection in diabetes proteomics. METHODS Web of Science database, PubMed database and Google Scholar were utilized for searching label-free quantification, computational advances, feature selection and diabetes proteomics. RESULTS In this study, we systematically review the computational advances of label-free quantification and diabetic marker selection methods which were applied to get the understanding of DM pathological mechanisms. Firstly, different popular quantification measurements and proteomic quantification software tools which have been applied to the diabetes studies are comprehensively discussed. Secondly, a number of popular manipulation methods including transformation, pretreatment (centering, scaling, and normalization), missing value imputation methods and a variety of popular feature selection techniques applied to diabetes proteomic data are overviewed with objective evaluation on their advantages and disadvantages. Finally, the guidelines for the efficient use of the computationbased LFQ technology and feature selection methods in diabetes proteomics are proposed. CONCLUSION In summary, this review provides guidelines for researchers who will engage in proteomics biomarker discovery and by properly applying these proteomic computational advances, more reliable therapeutic targets will be found in the field of diabetes mellitus.
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Affiliation(s)
- Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University, Chongqing 401331, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University, Chongqing 401331, China
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46
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Yap YA, Mariño E. Dietary SCFAs Immunotherapy: Reshaping the Gut Microbiota in Diabetes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1307:499-519. [PMID: 32193865 DOI: 10.1007/5584_2020_515] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Diet-microbiota related inflammatory conditions such as obesity, autoimmune type 1 diabetes (T1D), type 2 diabetes (T2D), cardiovascular disease (CVD) and gut infections have become a stigma in Western societies and developing nations. This book chapter examines the most relevant pre-clinical and clinical studies about diet-gut microbiota approaches as an alternative therapy for diabetes. We also discuss what we and others have extensively investigated- the power of dietary short-chain fatty acids (SCFAs) technology that naturally targets the gut microbiota as an alternative method to prevent and treat diabetes and its related complications.
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Affiliation(s)
- Yu Anne Yap
- Infection and Immunity Program, Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Melbourne, VIC, Australia
| | - Eliana Mariño
- Infection and Immunity Program, Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Melbourne, VIC, Australia.
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47
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Yap YA, McLeod KH, McKenzie CI, Gavin PG, Davalos-Salas M, Richards JL, Moore RJ, Lockett TJ, Clarke JM, Eng VV, Pearson JS, Hamilton-Williams EE, Mackay CR, Mariño E. An acetate-yielding diet imprints an immune and anti-microbial programme against enteric infection. Clin Transl Immunology 2021; 10:e1233. [PMID: 33489123 PMCID: PMC7809703 DOI: 10.1002/cti2.1233] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 11/16/2020] [Accepted: 12/09/2020] [Indexed: 12/19/2022] Open
Abstract
Objectives During gastrointestinal infection, dysbiosis can result in decreased production of microbially derived short‐chain fatty acids (SCFAs). In response to the presence of intestinal pathogens, we examined whether an engineered acetate‐ or butyrate‐releasing diet can rectify the deficiency of SCFAs and lead to the resolution of enteric infection. Methods We tested whether a high acetate‐ or butyrate‐producing diet (HAMSA or HAMSB, respectively) condition Citrobacterrodentium infection in mice and assess its impact on host‐microbiota interactions. We analysed the adaptive and innate immune responses, changes in gut microbiome function, epithelial barrier function and the molecular mechanism via metabolite sensing G protein‐coupled receptor 43 (GPR43) and IL‐22 expression. Results HAMSA diet rectified the deficiency in acetate production and protected against enteric infection. Increased SCFAs affect the expression of pathogen virulence genes. HAMSA diet promoted compositional and functional changes in the gut microbiota during infection similar to healthy microbiota from non‐infected mice. Bacterial changes were evidenced by the production of proteins involved in acetate utilisation, starch and sugar degradation, amino acid biosynthesis, carbohydrate transport and metabolism. HAMSA diet also induced changes in host proteins critical in glycolysis, wound healing such as GPX1 and epithelial architecture such as EZR1 and PFN1. Dietary acetate assisted in rapid epithelial repair, as shown by increased colonic Muc‐2, Il‐22, and anti‐microbial peptides. We found that acetate increased numbers of colonic IL‐22 producing TCRαβ+CD8αβ+ and TCRγδ+CD8αα+ intraepithelial lymphocytes expressing GPR43. Conclusion HAMSA diet may be an effective therapeutic approach for fighting inflammation and enteric infections and offer a safe alternative that may impact on human health.
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Affiliation(s)
- Yu Anne Yap
- Department of Biochemistry and Molecular Biology Infection and Immunity Program Biomedicine Discovery Institute Monash University Clayton, Melbourne VIC Australia
| | - Keiran H McLeod
- Department of Biochemistry and Molecular Biology Infection and Immunity Program Biomedicine Discovery Institute Monash University Clayton, Melbourne VIC Australia
| | - Craig I McKenzie
- Department of Biochemistry and Molecular Biology Infection and Immunity Program Biomedicine Discovery Institute Monash University Clayton, Melbourne VIC Australia
| | - Patrick G Gavin
- The University of Queensland Diamantina Institute The University of Queensland Brisbane QLD Australia
| | - Mercedes Davalos-Salas
- Department of Biochemistry and Molecular Biology Infection and Immunity Program Biomedicine Discovery Institute Monash University Clayton, Melbourne VIC Australia
| | - James L Richards
- Department of Biochemistry and Molecular Biology Infection and Immunity Program Biomedicine Discovery Institute Monash University Clayton, Melbourne VIC Australia
| | - Robert J Moore
- Department of Microbiology Infection and Immunity Program Biomedicine Discovery Institute Monash University Clayton, Melbourne VIC Australia.,School of Science RMIT University Bundoora VIC Australia
| | | | | | - Vik Ven Eng
- Department of Microbiology Infection and Immunity Program Biomedicine Discovery Institute Monash University Clayton, Melbourne VIC Australia.,Centre for Innate Immunity and Infectious Diseases Hudson Institute of Medical Research Clayton, Melbourne VIC Australia
| | - Jaclyn S Pearson
- Department of Microbiology Infection and Immunity Program Biomedicine Discovery Institute Monash University Clayton, Melbourne VIC Australia.,Centre for Innate Immunity and Infectious Diseases Hudson Institute of Medical Research Clayton, Melbourne VIC Australia.,Department of Molecular and Translational Research Monash University Clayton, Melbourne VIC Australia
| | - Emma E Hamilton-Williams
- The University of Queensland Diamantina Institute The University of Queensland Brisbane QLD Australia
| | - Charles R Mackay
- Department of Microbiology Infection and Immunity Program Biomedicine Discovery Institute Monash University Clayton, Melbourne VIC Australia
| | - Eliana Mariño
- Department of Biochemistry and Molecular Biology Infection and Immunity Program Biomedicine Discovery Institute Monash University Clayton, Melbourne VIC Australia
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48
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Gathercole JL, Grosvenor AJ, Lee E, Thomas A, Mitchell CJ, Zeng N, D'Souza RF, Ramzan F, Sharma P, Knowles SO, Roy NC, Sjödin A, Wagner KH, Milan AM, Mitchell SM, Cameron-Smith D. Analysis of Human Faecal Host Proteins: Responsiveness to 10-Week Dietary Intervention Modifying Dietary Protein Intake in Elderly Males. Front Nutr 2021; 7:595905. [PMID: 33521034 PMCID: PMC7838370 DOI: 10.3389/fnut.2020.595905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022] Open
Abstract
Faecal proteomics targeting biomarkers of immunity and inflammation have demonstrated clinical application for the identification of changes in gastrointestinal function. However, there are limited comprehensive analyses of the host faecal proteome and how it may be influenced by dietary factors. To examine this, the Homo sapiens post-diet proteome of older males was analysed at the completion of a 10-week dietary intervention, either meeting the minimum dietary protein recommendations (RDA; n = 9) or twice the recommended dietary allowance (2RDA, n = 10). The host faecal proteome differed markedly between individuals, with only a small subset of proteins present in ≥ 60% of subjects (14 and 44 proteins, RDA and 2RDA, respectively, with only 7 common to both groups). No differences were observed between the diet groups on the profiles of host faecal proteins. Faecal proteins were detected from a wide range of protein classes, with high inter-individual variation and absence of obvious impact in response to diets with markedly different protein intake. This suggests that well-matched whole food diets with two-fold variation in protein intake maintained for 10 weeks have minimal impact on human faecal host proteins.
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Affiliation(s)
| | - Anita J Grosvenor
- Proteins and Metabolites Team, AgResearch, Lincoln, Christchurch, New Zealand
| | - Erin Lee
- Proteins and Metabolites Team, AgResearch, Lincoln, Christchurch, New Zealand
| | - Ancy Thomas
- Proteins and Metabolites Team, AgResearch, Lincoln, Christchurch, New Zealand
| | - Cameron J Mitchell
- School of Kinesiology, University of British Columbia, Vancouver, BC, Canada.,Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Nina Zeng
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Randall F D'Souza
- Liggins Institute, University of Auckland, Auckland, New Zealand.,Discipline of Nutrition, University of Auckland, Auckland, New Zealand
| | - Farha Ramzan
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Pankaja Sharma
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Scott O Knowles
- Food, Nutrition, and Health Team, AgResearch, Auckland University, Auckland, New Zealand
| | - Nicole C Roy
- Liggins Institute, University of Auckland, Auckland, New Zealand.,Food, Nutrition, and Health Team, AgResearch, Auckland University, Auckland, New Zealand.,Department of Nutrition, University of Otago, Dunedin, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Anders Sjödin
- Department of Nutrition, Exercise, and Sports, Copenhagen University, Copenhagen, Denmark
| | - Karl-Heinz Wagner
- Department of Nutritional Sciences and Research Platform Active Ageing, University of Vienna, Vienna, Austria
| | - Amber M Milan
- Liggins Institute, University of Auckland, Auckland, New Zealand.,Food, Nutrition, and Health Team, AgResearch, Auckland University, Auckland, New Zealand
| | - Sarah M Mitchell
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - David Cameron-Smith
- Liggins Institute, University of Auckland, Auckland, New Zealand.,Agency for Science, Technology, and Research, Singapore Institute for Clinical Sciences, Singapore, Singapore
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49
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Calabrese CM, Valentini A, Calabrese G. Gut Microbiota and Type 1 Diabetes Mellitus: The Effect of Mediterranean Diet. Front Nutr 2021; 7:612773. [PMID: 33521039 PMCID: PMC7838384 DOI: 10.3389/fnut.2020.612773] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
Type 1 diabetes mellitus (T1DM) is a chronic autoimmune disease resulting from a complex interplay between genetic susceptibility and environmental factors. Regarding the latter, gut microbiota has a pivotal role in the pathogenesis of T1DM, by affecting intestinal permeability, molecular mimicry, and modulating innate and adaptive immune system, as described in several previous studies. The composition of the gut microbiota is largely influenced by diet. Some observational studies have shown that a low fiber intake is associated with the development of many inflammatory and immune-mediated diseases. In this context, the Mediterranean diet (MD), which is based on high consumption of cereals (preferably as whole grains), legumes, nuts, vegetables, fruits, olive oil, and fish, could play a protective role. Many of the characteristic components of MD have functional characteristics with positive effects on health and well-being. Eating habits are the main significant determinants of the microbial multiplicity of the intestine and the food components influence both microbial populations and their metabolic activities from the early stages of life. Moreover, food metabolites influence the immune response. The intestine is considered the primary site where food metabolites mediate their effects, through epithelial integrity or mucosal immunity. The compromised epithelial integrity allows the translocation of bacteria and/or the diffusion of their products, such as food antigens and lipopolysaccharides, from the intestinal lumen to the tissues, which could enhance the stimulation of immune cells, contributing to the pathogenesis of autoimmune diseases, such as T1DM. The intake of a high amount of fiber and therefore of prebiotics with MD allows the microbiota to have a good microbial balance. Moreover, as more dietary fibers are ingested, a higher amount of short-chain fatty acids (SCFAs) is produced by anaerobic gut microbiota, promoting gut homeostasis, to which also contribute tryptophan metabolites and omega-3-fatty acids. Furthermore, the higher intake of polyunsaturated fatty acids and omega-3-fatty-acids contribute to a better metabolic control. In this review we report the relationship between gut microbiota and T1DM and we explore the effects of Mediterranean diet on microbiota as a potential therapeutic strategy, aimed at preventing or delaying progression of T1DM and its complications.
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Affiliation(s)
| | - Alessia Valentini
- Dipartimento di Medicina Interna, Ospedale Madre Giuseppina Vannini, Rome, Italy
| | - Giorgio Calabrese
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Alessandria, Italy
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50
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Elhag DA, Kumar M, Al Khodor S. Exploring the Triple Interaction between the Host Genome, the Epigenome, and the Gut Microbiome in Type 1 Diabetes. Int J Mol Sci 2020; 22:ijms22010125. [PMID: 33374418 PMCID: PMC7795494 DOI: 10.3390/ijms22010125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
Type 1 diabetes (T1D) is an auto-immune disorder characterized by a complex interaction between the host immune system and various environmental factors in genetically susceptible individuals. Genome-wide association studies (GWAS) identified different T1D risk and protection alleles, however, little is known about the environmental factors that can be linked to these alleles. Recent evidence indicated that, among those environmental factors, dysbiosis (imbalance) in the gut microbiota may play a role in the pathogenesis of T1D, affecting the integrity of the gut and leading to systemic inflammation and auto-destruction of the pancreatic β cells. Several studies have identified changes in the gut microbiome composition in humans and animal models comparing T1D subjects with controls. Those changes were characterized by a higher abundance of Bacteroides and a lower abundance of the butyrate-producing bacteria such as Clostridium clusters IV and XIVa. The mechanisms by which the dysbiotic bacteria and/or their metabolites interact with the genome and/or the epigenome of the host leading to destructive autoimmunity is still not clear. As T1D is a multifactorial disease, understanding the interaction between different environmental factors such as the gut microbiome, the genetic and the epigenetic determinants that are linked with the early appearance of autoantibodies can expand our knowledge about the disease pathogenesis. This review aims to provide insights into the interaction between the gut microbiome, susceptibility genes, epigenetic factors, and the immune system in the pathogenesis of T1D.
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