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Pargin E, Roach MJ, Skye A, Papudeshi B, Inglis LK, Mallawaarachchi V, Grigson SR, Harker C, Edwards RA, Giles SK. The human gut virome: composition, colonization, interactions, and impacts on human health. Front Microbiol 2023; 14:963173. [PMID: 37293229 PMCID: PMC10244655 DOI: 10.3389/fmicb.2023.963173] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
The gut virome is an incredibly complex part of the gut ecosystem. Gut viruses play a role in many disease states, but it is unknown to what extent the gut virome impacts everyday human health. New experimental and bioinformatic approaches are required to address this knowledge gap. Gut virome colonization begins at birth and is considered unique and stable in adulthood. The stable virome is highly specific to each individual and is modulated by varying factors such as age, diet, disease state, and use of antibiotics. The gut virome primarily comprises bacteriophages, predominantly order Crassvirales, also referred to as crAss-like phages, in industrialized populations and other Caudoviricetes (formerly Caudovirales). The stability of the virome's regular constituents is disrupted by disease. Transferring the fecal microbiome, including its viruses, from a healthy individual can restore the functionality of the gut. It can alleviate symptoms of chronic illnesses such as colitis caused by Clostridiodes difficile. Investigation of the virome is a relatively novel field, with new genetic sequences being published at an increasing rate. A large percentage of unknown sequences, termed 'viral dark matter', is one of the significant challenges facing virologists and bioinformaticians. To address this challenge, strategies include mining publicly available viral datasets, untargeted metagenomic approaches, and utilizing cutting-edge bioinformatic tools to quantify and classify viral species. Here, we review the literature surrounding the gut virome, its establishment, its impact on human health, the methods used to investigate it, and the viral dark matter veiling our understanding of the gut virome.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Sarah K. Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
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Ezzatpour S, Mondragon Portocarrero ADC, Cardelle-Cobas A, Lamas A, López-Santamarina A, Miranda JM, Aguilar HC. The Human Gut Virome and Its Relationship with Nontransmissible Chronic Diseases. Nutrients 2023; 15:977. [PMID: 36839335 PMCID: PMC9960951 DOI: 10.3390/nu15040977] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
The human gastrointestinal tract contains large communities of microorganisms that are in constant interaction with the host, playing an essential role in the regulation of several metabolic processes. Among the gut microbial communities, the gut bacteriome has been most widely studied in recent decades. However, in recent years, there has been increasing interest in studying the influences that other microbial groups can exert on the host. Among them, the gut virome is attracting great interest because viruses can interact with the host immune system and metabolic functions; this is also the case for phages, which interact with the bacterial microbiota. The antecedents of virome-rectification-based therapies among various diseases were also investigated. In the near future, stool metagenomic investigation should include the identification of bacteria and phages, as well as their correlation networks, to better understand gut microbiota activity in metabolic disease progression.
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Affiliation(s)
- Shahrzad Ezzatpour
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Alicia del Carmen Mondragon Portocarrero
- Laboratorio de Higiene, Inspección y Control de Alimentos (LHICA), Departamento de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Alejandra Cardelle-Cobas
- Laboratorio de Higiene, Inspección y Control de Alimentos (LHICA), Departamento de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Alexandre Lamas
- Laboratorio de Higiene, Inspección y Control de Alimentos (LHICA), Departamento de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Aroa López-Santamarina
- Laboratorio de Higiene, Inspección y Control de Alimentos (LHICA), Departamento de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - José Manuel Miranda
- Laboratorio de Higiene, Inspección y Control de Alimentos (LHICA), Departamento de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Hector C. Aguilar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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Type I Diabetes Pathoetiology and Pathophysiology: Roles of the Gut Microbiome, Pancreatic Cellular Interactions, and the 'Bystander' Activation of Memory CD8 + T Cells. Int J Mol Sci 2023; 24:ijms24043300. [PMID: 36834709 PMCID: PMC9964837 DOI: 10.3390/ijms24043300] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/10/2023] Open
Abstract
Type 1 diabetes mellitus (T1DM) arises from the failure of pancreatic β-cells to produce adequate insulin, usually as a consequence of extensive pancreatic β-cell destruction. T1DM is classed as an immune-mediated condition. However, the processes that drive pancreatic β-cell apoptosis remain to be determined, resulting in a failure to prevent ongoing cellular destruction. Alteration in mitochondrial function is clearly the major pathophysiological process underpinning pancreatic β-cell loss in T1DM. As with many medical conditions, there is a growing interest in T1DM as to the role of the gut microbiome, including the interactions of gut bacteria with Candida albicans fungal infection. Gut dysbiosis and gut permeability are intimately associated with raised levels of circulating lipopolysaccharide and suppressed butyrate levels, which can act to dysregulate immune responses and systemic mitochondrial function. This manuscript reviews broad bodies of data on T1DM pathophysiology, highlighting the importance of alterations in the mitochondrial melatonergic pathway of pancreatic β-cells in driving mitochondrial dysfunction. The suppression of mitochondrial melatonin makes pancreatic β-cells susceptible to oxidative stress and dysfunctional mitophagy, partly mediated by the loss of melatonin's induction of PTEN-induced kinase 1 (PINK1), thereby suppressing mitophagy and increasing autoimmune associated major histocompatibility complex (MHC)-1. The immediate precursor to melatonin, N-acetylserotonin (NAS), is a brain-derived neurotrophic factor (BDNF) mimic, via the activation of the BDNF receptor, TrkB. As both the full-length and truncated TrkB play powerful roles in pancreatic β-cell function and survival, NAS is another important aspect of the melatonergic pathway relevant to pancreatic β-cell destruction in T1DM. The incorporation of the mitochondrial melatonergic pathway in T1DM pathophysiology integrates wide bodies of previously disparate data on pancreatic intercellular processes. The suppression of Akkermansia muciniphila, Lactobacillus johnsonii, butyrate, and the shikimate pathway-including by bacteriophages-contributes to not only pancreatic β-cell apoptosis, but also to the bystander activation of CD8+ T cells, which increases their effector function and prevents their deselection in the thymus. The gut microbiome is therefore a significant determinant of the mitochondrial dysfunction driving pancreatic β-cell loss as well as 'autoimmune' effects derived from cytotoxic CD8+ T cells. This has significant future research and treatment implications.
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Roles of the gut virome and mycobiome in faecal microbiota transplantation. Lancet Gastroenterol Hepatol 2022; 7:472-484. [DOI: 10.1016/s2468-1253(21)00303-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022]
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Velmurugan G, Dinakaran V, Rajendhran J, Swaminathan K. Blood Microbiota and Circulating Microbial Metabolites in Diabetes and Cardiovascular Disease. Trends Endocrinol Metab 2020; 31:835-847. [PMID: 33086076 DOI: 10.1016/j.tem.2020.01.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/16/2019] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
Diabetes and cardiovascular disease (CVD) have evolved as the leading cause of mortality and morbidity worldwide. In addition to traditional risk factors, recent studies have established that the human microbiota, particularly gut bacteria, plays a role in the development of diabetes and CVD. Although the presence of microbes in blood has been known for centuries, mounting evidence in this metagenomic era provides new insights into the role of the blood microbiota in the pathogenesis of non-infectious diseases such as diabetes and CVD. We highlight the origin and physiology of the blood microbiota and circulating microbial metabolites in relation to the etiology and progression of diabetes and CVD. We also discuss translational perspectives targeting the blood microbiota in the diagnosis and treatment of diabetes and CVD.
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Affiliation(s)
- Ganesan Velmurugan
- Chemomicrobiomics Laboratory, KMCH Research Foundation, Kovai Medical Center and Hospital, Coimbatore 641 014, Tamil Nadu, India.
| | - Vasudevan Dinakaran
- Chemomicrobiomics Laboratory, KMCH Research Foundation, Kovai Medical Center and Hospital, Coimbatore 641 014, Tamil Nadu, India
| | - Jeyaprakash Rajendhran
- Pathogenomics Laboratory, Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, Tamil Nadu, India
| | - Krishnan Swaminathan
- Chemomicrobiomics Laboratory, KMCH Research Foundation, Kovai Medical Center and Hospital, Coimbatore 641 014, Tamil Nadu, India
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Rabbone I, Traversi D, Scaioli G, Vallini C, Carletto G, Masante I, Durazzo M, Collo A, Belci P, Ferro A, Cadario F, Savastio S, Carrera D, Cerutti F, Siliquini R. Microbiota, epidemiological and nutritional factors related to ketoacidosis at the onset of type 1 diabetes. Acta Diabetol 2020; 57:1337-1349. [PMID: 32594251 DOI: 10.1007/s00592-020-01555-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023]
Abstract
AIMS The incidence of type 1 diabetes has increased over the last decades. The pathological pathway is not yet clear, even if genetic and environmental risk factors are known. An early diagnosis can avoid ketoacidosis and its complications. This work aims to discuss the determinants of both ketoacidosis at the onset and access by hospital emergency departments without a suspected diagnosis. METHODS An observational bi-centric prospective study was conducted in Northern Italy, on a paediatric population including Italian and migrant patients at the diabetes onset. Seventy-four type 1 diabetes patients, both Italian and migrant, were included in the study. Anthropometric, socio-economic, behavioural, clinical data were collected, and microbiota analyses were performed using stool samples. RESULTS Regular physical activity is associated with lower ketoacidosis incidence at onset (OR 0.33 95% CI 0.12-0.95 p < 0.05), as is higher blood vitamin D level (OR 0.92 95% CI 0.85-0.99 p < 0.05). Moreover, a higher weaning age (OR 0.49 95% CI 0.27-0.89 p < 0.05), higher vitamin D level (OR 0.90 95% CI 0.83-0.98 p < 0.05) and a higher level of Akkermansia muciniphila (OR 0.46 95% CI 0.25-0.87 p < 0.05) are associated factors to lower frequency of type 1 diabetes onset without a suspected diagnosis. Diabetes migrant status is not a risk factor for severe type 1 diabetes onset; on the other hand, some protective factors are significantly more diffused among Italians, such as regular sport activity and non-critical vitamin D levels. CONCLUSION Behavioural and nutritional data, such as microbiota bio-indicators, seem to be useful to identify an at-risk population to prevent ketoacidosis and its severe complications.
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Affiliation(s)
- Ivana Rabbone
- S.S.V.D. Endocrinologia E Diabetologia, O.I.R.M., A.O. Città Della Salute E Della Scienza Di Torino, Turin, Italy
- Department of Health Science, UPO University A.O.U., ''Maggiore Della Carità'', Novara, Italy
| | - Deborah Traversi
- Department of Public Health and Pediatrics, University of Study of Torino, Piazza Polonia 94, 10126, Turin, Italy.
| | - Giacomo Scaioli
- Department of Public Health and Pediatrics, University of Study of Torino, Piazza Polonia 94, 10126, Turin, Italy
| | - Camilla Vallini
- S.S.V.D. Endocrinologia E Diabetologia, O.I.R.M., A.O. Città Della Salute E Della Scienza Di Torino, Turin, Italy
| | - Giulia Carletto
- Department of Public Health and Pediatrics, University of Study of Torino, Piazza Polonia 94, 10126, Turin, Italy
| | - Irene Masante
- Department of Public Health and Pediatrics, University of Study of Torino, Piazza Polonia 94, 10126, Turin, Italy
| | - Marilena Durazzo
- S.C.U Medicina Interna 3, Molinette Hospital, Città Della Salute E Della Scienza Di Torino, rin, Italy
| | - Alessandro Collo
- S.C.U Medicina Interna 3, Molinette Hospital, Città Della Salute E Della Scienza Di Torino, rin, Italy
| | - Paola Belci
- S.C.U Medicina Interna 3, Molinette Hospital, Città Della Salute E Della Scienza Di Torino, rin, Italy
| | - Arianna Ferro
- S.C.U Medicina Interna 3, Molinette Hospital, Città Della Salute E Della Scienza Di Torino, rin, Italy
| | - Francesco Cadario
- Department of Health Science, UPO University A.O.U., ''Maggiore Della Carità'', Novara, Italy
| | - Silvia Savastio
- Department of Health Science, UPO University A.O.U., ''Maggiore Della Carità'', Novara, Italy
| | - Deborah Carrera
- Department of Health Science, UPO University A.O.U., ''Maggiore Della Carità'', Novara, Italy
| | - Franco Cerutti
- Department of Public Health and Pediatrics, University of Study of Torino, Piazza Polonia 94, 10126, Turin, Italy
- S.S.V.D. Endocrinologia E Diabetologia, O.I.R.M., A.O. Città Della Salute E Della Scienza Di Torino, Turin, Italy
| | - Roberta Siliquini
- Department of Public Health and Pediatrics, University of Study of Torino, Piazza Polonia 94, 10126, Turin, Italy
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Veteikis D. Antipyretics might occupy a narrow temporal position in aetiology of type 1 diabetes: Immunological and intestinal studies required. Med Hypotheses 2020; 141:109708. [PMID: 32283444 DOI: 10.1016/j.mehy.2020.109708] [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: 03/06/2020] [Accepted: 04/05/2020] [Indexed: 10/24/2022]
Abstract
Geographical variance in the incidence of type 1 diabetes mellitus (T1DM) and its etiological link to viruses and gut microbiome imply causative environmental agents. Antipyretics and especially acetaminophen received some attention recently due to the associations with some autoimmune conditions and lack of studies on the mechanisms influencing the immune system. A couple of recent studies involving large cohorts have found no association between the use of acetaminophen in early childhood and seroconversion leading to T1DM (TEDDY, involving international cohort) or diagnosis of overt T1DM (Norwegian MoBa) in the follow up years. The paper gives the supplemental argumentation for the antipyretic hypothesis presented in Medical Hypotheses in 2016 that is still valid in face of the mentioned conclusions. The hypothesis assumes that critical effect of acetaminophen and possibly other antipyretics expresses itself as the immediate influence on the immune system in the unfortunate coincidence with the other environmental factors, supposedly involving feverish, new to immunity, viral infection, all creating triggering circumstances regardless of age. Young age, in this respect should be regarded as a risk factor due to immatureness of immunity. The paper discusses that antipyretics and particularly acetaminophen need more attention evaluating their possible immunity modulations during infection or through negative effects on intestinal microbiota or both.
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Affiliation(s)
- Darijus Veteikis
- Vilnius University, Faculty of Chemistry and Geosciences, 21 M. K. Čiurlionio Str., Vilnius LT-03101, Lithuania.
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Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths. Microorganisms 2020; 8:microorganisms8040483. [PMID: 32231141 PMCID: PMC7232386 DOI: 10.3390/microorganisms8040483] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 12/20/2022] Open
Abstract
Gut microbiota refers to a complex network of microbes, which exerts a marked influence on the host’s health. It is composed of bacteria, fungi, viruses, and helminths. Bacteria, or collectively, the bacteriome, comprises a significant proportion of the well-characterized microbiome. However, the other communities referred to as ‘dark matter’ of microbiomes such as viruses (virome), fungi (mycobiome), archaea (archaeome), and helminths have not been completely elucidated. Development of new and improved metagenomics methods has allowed the identification of complete genomes from the genetic material in the human gut, opening new perspectives on the understanding of the gut microbiome composition, their importance, and potential clinical applications. Here, we review the recent evidence on the viruses, fungi, archaea, and helminths found in the mammalian gut, detailing their interactions with the resident bacterial microbiota and the host, to explore the potential impact of the microbiome on host’s health. The role of fecal virome transplantations, pre-, pro-, and syn-biotic interventions in modulating the microbiome and their related concerns are also discussed.
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