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Gholamzad A, Khakpour N, Hashemi SMA, Goudarzi Y, Ahmadi P, Gholamzad M, Mohammadi M, Hashemi M. Exploring the virome: An integral part of human health and disease. Pathol Res Pract 2024; 260:155466. [PMID: 39053136 DOI: 10.1016/j.prp.2024.155466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/06/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024]
Abstract
The human microbiome is a complex network of microorganisms that includes viruses, bacteria, and fungi. The gut virome is an essential component of the immune system, which is responsible for regulating the growth and responses of the host's immune system. The virome maintains a crucial role in the development of numerous diseases, including inflammatory bowel disease (IBD), Crohn's disease, and neurodegenerative disorders. The human virome has emerged as a promising biomarker and therapeutic target. This comprehensive review summarizes the present understanding of the virome and its implications in matters of health and disease, with a focus on the Human Microbiome Project.
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Affiliation(s)
- Amir Gholamzad
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Niloofar Khakpour
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Ali Hashemi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Yalda Goudarzi
- Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Parisa Ahmadi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehrdad Gholamzad
- Department of Microbiology and Immunology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mahya Mohammadi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology ,Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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2
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Chibuye M, Mende DR, Spijker R, Simuyandi M, Luchen CC, Bosomprah S, Chilengi R, Schultsz C, Harris VC. Systematic review of associations between gut microbiome composition and stunting in under-five children. NPJ Biofilms Microbiomes 2024; 10:46. [PMID: 38782939 PMCID: PMC11116508 DOI: 10.1038/s41522-024-00517-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Childhood stunting is associated with impaired cognitive development and increased risk of infections, morbidity, and mortality. The composition of the enteric microbiota may contribute to the pathogenesis of stunting. We systematically reviewed and synthesized data from studies using high-throughput genomic sequencing methods to characterize the gut microbiome in stunted versus non-stunted children under 5 years in LMICs. We included 14 studies from Asia, Africa, and South America. Most studies did not report any significant differences in the alpha diversity, while a significantly higher beta diversity was observed in stunted children in four out of seven studies that reported beta diversity. At the phylum level, inconsistent associations with stunting were observed for Bacillota, Pseudomonadota, and Bacteroidota phyla. No single genus was associated with stunted children across all 14 studies, and some associations were incongruent by specific genera. Nonetheless, stunting was associated with an abundance of pathobionts that could drive inflammation, such as Escherichia/Shigella and Campylobacter, and a reduction of butyrate producers, including Faecalibacterium, Megasphera, Blautia, and increased Ruminoccoccus. An abundance of taxa thought to originate in the oropharynx was also reported in duodenal and fecal samples of stunted children, while metabolic pathways, including purine and pyrimidine biosynthesis, vitamin B biosynthesis, and carbohydrate and amino acid degradation pathways, predicted linear growth. Current studies show that stunted children can have distinct microbial patterns compared to non-stunted children, which could contribute to the pathogenesis of stunting.
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Affiliation(s)
- Mwelwa Chibuye
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Daniel R Mende
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Rene Spijker
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Michelo Simuyandi
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Chaluma C Luchen
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Samuel Bosomprah
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Department of Biostatistics, School of Public Health, University of Ghana, Legon, Accra, Ghana
| | - Roma Chilengi
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- The Zambia National Public Health Institute (ZNPHI), Lusaka, Zambia
| | - Constance Schultsz
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Vanessa C Harris
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
- Division of Infectious Diseases, Department of Internal Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
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Zhao F, Wang J. Another piece of puzzle for the human microbiome: the gut virome under dietary modulation. J Genet Genomics 2024:S1673-8527(24)00098-5. [PMID: 38710286 DOI: 10.1016/j.jgg.2024.04.013] [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: 03/02/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024]
Abstract
The virome is the most abundant and highly variable microbial consortium in the gut. Because of difficulties in isolating and culturing gut viruses and the lack of reference genomes, the virome has remained a relatively elusive aspect of the human microbiome. In recent years, studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health. Here, we review the responses of the gut virome to dietary intake and the potential health implications, presenting changes in the gut viral community and preferences of viral members to particular diets. We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota. We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer, as well as the import of new viral members along with the diet. Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary interventions and health maintenance strategies targeting the gut microbiota.
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Affiliation(s)
- Fengxiang Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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4
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Lu D, Wu Y, Fu M, Wu Y, Wang Z, Lin J, Yang Q. CALB1: Anovel antiviral factor in chicken ileal mucus. Int J Biol Macromol 2023; 253:127007. [PMID: 37734520 DOI: 10.1016/j.ijbiomac.2023.127007] [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: 06/28/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
Intestinal mucus is the first line of defense against pathogens and has several active components. Poultry have a short intestine, the mucus of which may contain antiviral components. We hence investigated the antiviral components of mucus and explored their mechanisms of action. Initially, we isolated chicken intestinal mucus proteins that significantly inhibited the replication of avian viruses. The ileum 10-30 kDa protein fraction showed the greatest inhibition of viral replication. Moreover, liquid chromatography-mass spectrometry revealed 12 high-abundance proteins in the ileum 10-30 kDa protein fraction. Among them, we investigated the antiviral activity of calcium binding protein 1 (CALB1). Furthermore, eukaryotically and prokaryotically expressed CALB1 significantly suppressed the replication of avian viruses, possibly by binding calcium ions and/or inducing autophagy. In conclusion, we isolated and identified CALB1 from chicken intestinal mucus, which suppressed replication of avian viruses by regulating cellular calcium-ion homeostasis and autophagy.
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Affiliation(s)
- Danqing Lu
- College of Life Sciences, SanYa Institute of Nanjing Agricultural University, Nanjing Agricultural University, Weigang 1, Nanjing, Jiangsu 210095, PR China
| | - Yang Wu
- College of Life Sciences, SanYa Institute of Nanjing Agricultural University, Nanjing Agricultural University, Weigang 1, Nanjing, Jiangsu 210095, PR China
| | - Mei Fu
- College of Veterinary medicine, Nanjing Agricultural University, Wei gang 1, Nanjing, Jiangsu 210095, PR China
| | - Yaotang Wu
- College of Veterinary medicine, Nanjing Agricultural University, Wei gang 1, Nanjing, Jiangsu 210095, PR China
| | - Zhisheng Wang
- Institute of Veterinary Immunology and Engineering, National Research Center of Engineering and Technology for Veterinary Biologicals, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China
| | - Jian Lin
- College of Life Sciences, SanYa Institute of Nanjing Agricultural University, Nanjing Agricultural University, Weigang 1, Nanjing, Jiangsu 210095, PR China; College of Veterinary medicine, Nanjing Agricultural University, Wei gang 1, Nanjing, Jiangsu 210095, PR China.
| | - Qian Yang
- College of Veterinary medicine, Nanjing Agricultural University, Wei gang 1, Nanjing, Jiangsu 210095, PR China
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Jones HJ, Bourke CD, Swann JR, Robertson RC. Malnourished Microbes: Host-Microbiome Interactions in Child Undernutrition. Annu Rev Nutr 2023; 43:327-353. [PMID: 37207356 DOI: 10.1146/annurev-nutr-061121-091234] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Childhood undernutrition is a major global health burden that is only partially resolved by nutritional interventions. Both chronic and acute forms of child undernutrition are characterized by derangements in multiple biological systems including metabolism, immunity, and endocrine systems. A growing body of evidence supports a role of the gut microbiome in mediating these pathways influencing early life growth. Observational studies report alterations in the gut microbiome of undernourished children, while preclinical studies suggest that this can trigger intestinal enteropathy, alter host metabolism, and disrupt immune-mediated resistance against enteropathogens, each of which contribute to poor early life growth. Here, we compile evidence from preclinical and clinical studies and describe the emerging pathophysiological pathways by which the early life gut microbiome influences host metabolism, immunity, intestinal function, endocrine regulation, and other pathways contributing to child undernutrition. We discuss emerging microbiome-directed therapies and consider future research directions to identify and target microbiome-sensitive pathways in child undernutrition.
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Affiliation(s)
- Helen J Jones
- Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom;
| | - Claire D Bourke
- Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom;
| | - Jonathan R Swann
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ruairi C Robertson
- Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom;
- Microenvironment and Immunity Unit, INSERM U1224, Institut Pasteur, Université Paris Cité, Paris, France
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6
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Pheeha SM, Tamuzi JL, Chale-Matsau B, Manda S, Nyasulu PS. A Scoping Review Evaluating the Current State of Gut Microbiota Research in Africa. Microorganisms 2023; 11:2118. [PMID: 37630678 PMCID: PMC10458939 DOI: 10.3390/microorganisms11082118] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The gut microbiota has emerged as a key human health and disease determinant. However, there is a significant knowledge gap regarding the composition, diversity, and function of the gut microbiota, specifically in the African population. This scoping review aims to examine the existing literature on gut microbiota research conducted in Africa, providing an overview of the current knowledge and identifying research gaps. A comprehensive search strategy was employed to identify relevant studies. Databases including MEDLINE (PubMed), African Index Medicus (AIM), CINAHL (EBSCOhost), Science Citation index (Web of Science), Embase (Ovid), Scopus (Elsevier), WHO International Clinical Trials Registry Platform (ICTRP), and Google Scholar were searched for relevant articles. Studies investigating the gut microbiota in African populations of all age groups were included. The initial screening included a total of 2136 articles, of which 154 were included in this scoping review. The current scoping review revealed a limited number of studies investigating diseases of public health significance in relation to the gut microbiota. Among these studies, HIV (14.3%), colorectal cancer (5.2%), and diabetes mellitus (3.9%) received the most attention. The top five countries that contributed to gut microbiota research were South Africa (16.2%), Malawi (10.4%), Egypt (9.7%), Kenya (7.1%), and Nigeria (6.5%). The high number (n = 66) of studies that did not study any specific disease in relation to the gut microbiota remains a gap that needs to be filled. This scoping review brings attention to the prevalent utilization of observational study types (38.3%) in the studies analysed and emphasizes the importance of conducting more experimental studies. Furthermore, the findings reflect the need for more disease-focused, comprehensive, and population-specific gut microbiota studies across diverse African regions and ethnic groups to better understand the factors shaping gut microbiota composition and its implications for health and disease. Such knowledge has the potential to inform targeted interventions and personalized approaches for improving health outcomes in African populations.
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Affiliation(s)
- Sara M. Pheeha
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
- Department of Chemical Pathology, Faculty of Medicine and Health Sciences, Sefako Makgatho Health Sciences University, Pretoria 0208, South Africa
- National Health Laboratory Service, Dr George Mukhari Academic Hospital, Pretoria 0208, South Africa
| | - Jacques L. Tamuzi
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
| | - Bettina Chale-Matsau
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria, Pretoria 0028, South Africa
- National Health Laboratory Service, Steve Biko Academic Hospital, Pretoria 0002, South Africa
| | - Samuel Manda
- Department of Statistics, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0028, South Africa
| | - Peter S. Nyasulu
- Division of Epidemiology and Biostatistics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa; (S.M.P.)
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
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Thahir AIA, Li M, Holmes A, Gordon A. Exploring Factors Associated with Stunting in 6-Month-Old Children: A Population-Based Cohort Study in Sulawesi, Indonesia. Nutrients 2023; 15:3420. [PMID: 37571357 PMCID: PMC10421344 DOI: 10.3390/nu15153420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Stunting in children under the age of two is a significant global concern, particularly in low- and middle-income countries like Indonesia. Intervention efforts often come too late as many of the underlying causal factors have already occurred earlier. While antenatal multiple micronutrient supplements (MMS) have demonstrated positive effects on pregnancy outcomes, their impact on infant growth in the first six months remains inadequately explored in epidemiological studies. This study aims to identify factors associated with stunting at six months in infants whose mothers received MMS. A population-based cohort study was conducted in four subdistricts of Banggai, Indonesia. Pregnant women were recruited in their third trimester and followed up until their children were six months of age. Validated questionnaires were employed to gather data on social determinants of health and diet, and standardised methods were utilised for anthropometric measurements. Stunting was determined based on the WHO child growth standards. The analysis comprised data from 152 mother-child pairs. The prevalence of stunting during early infancy (first two months) was 18.4%, which decreased to 15.8% in later infancy (at six months). Factors such as small-for-gestational-age (AOR = 11.29; 2.73-46.66), preterm birth (AOR = 6.33; 1.25-31.97), short birth length (AOR = 4.31; 1.11-16.78), maternal mid-upper arm circumference (MUAC) below 23.5 cm, and female infants (AOR = 3.27; 95%CI: 1.04-10.27) were associated with stunting at six months. This study highlights that stunting in the first six months is present at birth, with small-for-gestational-age (SGA) as a strong predictor. In addition, there was a trend to improved growth (-0.30 [-0.79 to 0.18]) in infants born to mothers who received MMS supplementation pre-pregnancy rather than during pregnancy, although it was not statistically significant.
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Affiliation(s)
- Andi Imam Arundhana Thahir
- Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney 2006, Australia;
- Department of Nutrition, Faculty of Public Health, Hasanuddin University, Makassar 90245, Indonesia
| | - Mu Li
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney 2006, Australia;
| | - Andrew Holmes
- School of Life and Environmental Science, Faculty of Science, The University of Sydney, Sydney 2006, Australia;
- Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney 2006, Australia
| | - Adrienne Gordon
- Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney 2006, Australia;
- Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney 2006, Australia
- The Royal Prince Alfred Hospital (RPA), Newborn Care, Sydney Local Health District, Sydney 2050, Australia
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8
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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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9
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Abstract
The thick mucus layer covering of the intestinal epithelium has received increasing attention, owing to its protective role in intestinal infection. However, the exact mechanisms by which the mucus increases intestinal resistance against viral infection remain largely unclear. Here, we identify prominent antiviral activity of the small intestinal mucus and extracted total mucus proteins, as evidenced by their inhibitory effects against porcine epidemic diarrhea virus (PEDV) infection. Of all the extracted mucus proteins, mucin 2 and fraction III (~70 kDa) exhibited potent antiviral activity. We further evaluated the antiviral effects of three candidate factors in fraction III and found that calpain-1 contributed substantially to its antiviral activity. In vivo studies demonstrated that oral administration of calpain-1 provided effective protection against intestinal PEDV infection. As a calcium-activated cysteine protease, calpain-1 inhibited viral invasion by binding to and hydrolyzing the S1 domain of the viral spike protein. The region between amino acids 297 and 337 in the b domain of PEDV S1 protein was critical for calpain-1-mediated hydrolysis. Further investigation indicated that calpain-1 could be produced by goblet cells between intestinal epithelia. Taken together, the results of our study revealed calpain-1 to be a novel antiviral protein in porcine small intestinal mucus, suggesting that calpain-1 has potential for defending against intestinal infections.
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Kennedy EA, Holtz LR. Gut virome in early life: origins and implications. Curr Opin Virol 2022; 55:101233. [PMID: 35690009 PMCID: PMC9575407 DOI: 10.1016/j.coviro.2022.101233] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 12/15/2022]
Abstract
The human body is colonized by a multitude of bacteria, fungi, and viruses, which play important roles in health and disease. Microbial colonization during early life is thought to be a particularly important period with lasting consequences for health. Viral populations in the gut are particularly dynamic in early life before they stabilize in adulthood. The composition of the early-life virome is increasingly recognized as a determinant of disease later in life. Here, we review the development of the virome in healthy infants, as well as the role of the early-life virome in the development of disease states including diarrhea, malnutrition, and autoimmune diseases.
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Affiliation(s)
- Elizabeth A Kennedy
- Washington University School of Medicine, Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, St. Louis, MO 63110, USA
| | - Lori R Holtz
- Washington University School of Medicine, Department of Pediatrics, St. Louis, MO 63110, USA.
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11
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Cao Z, Sugimura N, Burgermeister E, Ebert MP, Zuo T, Lan P. The gut virome: A new microbiome component in health and disease. EBioMedicine 2022; 81:104113. [PMID: 35753153 PMCID: PMC9240800 DOI: 10.1016/j.ebiom.2022.104113] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/14/2022] [Accepted: 05/30/2022] [Indexed: 12/19/2022] Open
Abstract
The human gastrointestinal tract harbours an abundance of viruses, collectively known as the gut virome. The gut virome is highly heterogeneous across populations and is linked to geography, ethnicity, diet, lifestyle, and urbanisation. The currently known function of the gut virome varies greatly across human populations, and much remains unknown. We review current literature on the human gut virome, and the intricate trans-kingdom interplay among gut viruses, bacteria, and the mammalian host underlying health and diseases. We summarise evidence on the use of the gut virome as diagnostic markers and a therapeutic target. We shed light on novel avenues of microbiome-inspired diagnosis and therapies. We also review pre-clinical and clinical studies on gut virome-rectification-based therapies, including faecal microbiota transplantation, faecal virome transplantation, and refined phage therapy. Our review suggests that future research effort should focus on unravelling the mechanisms exerted by gut viruses/phages in human pathophysiology, and on developing phage-prompted precision therapies.
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Affiliation(s)
- Zhirui Cao
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China; Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Naoki Sugimura
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Elke Burgermeister
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Matthias P Ebert
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; DKFZ-Hector Cancer Institute, Mannheim, Germany; Mannheim Cancer Centre (MCC), University Medical Centre Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tao Zuo
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China; Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Ping Lan
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, China; Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
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12
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Tiamani K, Luo S, Schulz S, Xue J, Costa R, Khan Mirzaei M, Deng L. The role of virome in the gastrointestinal tract and beyond. FEMS Microbiol Rev 2022; 46:6608358. [PMID: 35700129 PMCID: PMC9629487 DOI: 10.1093/femsre/fuac027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 01/11/2023] Open
Abstract
The human gut virome is comprised of diverse commensal and pathogenic viruses. The colonization by these viruses begins right after birth through vaginal delivery, then continues through breastfeeding, and broader environmental exposure. Their constant interaction with their bacterial hosts in the body shapes not only our microbiomes but us. In addition, these viruses interact with the immune cells, trigger a broad range of immune responses, and influence different metabolic pathways. Besides its key role in regulating the human gut homeostasis, the intestinal virome contributes to disease development in distant organs, both directly and indirectly. In this review, we will describe the changes in the gut virome through life, health, and disease, followed by discussing the interactions between the virome, the microbiome, and the human host as well as providing an overview of their contribution to gut disease and disease of distant organs.
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Affiliation(s)
| | | | - Sarah Schulz
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Rita Costa
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Li Deng
- Corresponding author: Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany; Chair of Prevention of Microbial Diseases, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany. E-mail:
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13
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Liang G, Gao H, Bushman FD. The pediatric virome in health and disease. Cell Host Microbe 2022; 30:639-649. [PMID: 35550667 DOI: 10.1016/j.chom.2022.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/22/2022] [Accepted: 04/11/2022] [Indexed: 11/03/2022]
Abstract
Associations between the global microbiome and diseases of children have been studied extensively; however, research on the viral component of the microbiome, the "virome," is less advanced. The analysis of disease associations with the virome is often technically challenging, requiring a close examination of the "virome dark matter." The gut is a particularly rich source of viral particles, and now multiple studies have reported intriguing associations of the virome with childhood diseases. For example, virome studies have elucidated new lineages of gut viruses that appear to be tightly associated with childhood diarrhea, and consistent patterns are starting to emerge from virome studies in pediatric IBD. In this review, we summarize the methods for studying the virome and recent research on the nature of the virome during childhood, focusing on specific studies of the intestinal virome in pediatric diseases.
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Affiliation(s)
- Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| | - Hongyan Gao
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA.
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14
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Quamme SH, Iversen PO. Prevalence of child stunting in Sub-Saharan Africa and its risk factors. CLINICAL NUTRITION OPEN SCIENCE 2022. [DOI: 10.1016/j.nutos.2022.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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15
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Huus KE, Hoang TT, Creus-Cuadros A, Cirstea M, Vogt SL, Knuff-Janzen K, Sansonetti PJ, Vonaesch P, Finlay BB. Cross-feeding between intestinal pathobionts promotes their overgrowth during undernutrition. Nat Commun 2021; 12:6860. [PMID: 34824233 PMCID: PMC8617199 DOI: 10.1038/s41467-021-27191-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 11/08/2021] [Indexed: 12/18/2022] Open
Abstract
Child undernutrition is a global health issue associated with a high burden of infectious disease. Undernourished children display an overabundance of intestinal pathogens and pathobionts, and these bacteria induce enteric dysfunction in undernourished mice; however, the cause of their overgrowth remains poorly defined. Here, we show that disease-inducing human isolates of Enterobacteriaceae and Bacteroidales spp. are capable of multi-species symbiotic cross-feeding, resulting in synergistic growth of a mixed community in vitro. Growth synergy occurs uniquely under malnourished conditions limited in protein and iron: in this context, Bacteroidales spp. liberate diet- and mucin-derived sugars and Enterobacteriaceae spp. enhance the bioavailability of iron. Analysis of human microbiota datasets reveals that Bacteroidaceae and Enterobacteriaceae are strongly correlated in undernourished children, but not in adequately nourished children, consistent with a diet-dependent growth synergy in the human gut. Together these data suggest that dietary cross-feeding fuels the overgrowth of pathobionts in undernutrition.
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Affiliation(s)
- K. E. Huus
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - T. T. Hoang
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - A. Creus-Cuadros
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - M. Cirstea
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - S. L. Vogt
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - K. Knuff-Janzen
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - P. J. Sansonetti
- grid.428999.70000 0001 2353 6535Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France ,grid.429007.80000 0004 0627 2381Present Address: Center for Microbes, Development and Health, Institut Pasteur de Shanghai, Shanghai, China
| | - P. Vonaesch
- grid.428999.70000 0001 2353 6535Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France ,grid.416786.a0000 0004 0587 0574Present Address: Human and Animal Health Unit, Swiss Tropical and Public Health Institute & University of Basel, Basel, Switzerland
| | - B. B. Finlay
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada ,grid.440050.50000 0004 0408 2525Canadian Institute for Advanced Research, Toronto, Ontario Canada
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16
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Wallach T. Automated Enteropathy: Discovering the Potential of Machine Learning in Environmental Enteropathy. J Pediatr Gastroenterol Nutr 2021; 72:785-786. [PMID: 33661248 PMCID: PMC8119366 DOI: 10.1097/mpg.0000000000003115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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17
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Fulci V, Stronati L, Cucchiara S, Laudadio I, Carissimi C. Emerging Roles of Gut Virome in Pediatric Diseases. Int J Mol Sci 2021; 22:4127. [PMID: 33923593 PMCID: PMC8073368 DOI: 10.3390/ijms22084127] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
In the last decade, the widespread application of shotgun metagenomics provided extensive characterization of the bacterial "dark matter" of the gut microbiome, propelling the development of dedicated, standardized bioinformatic pipelines and the systematic collection of metagenomic data into comprehensive databases. The advent of next-generation sequencing also unravels a previously underestimated viral population (virome) present in the human gut. Despite extensive efforts to characterize the human gut virome, to date, little is known about the childhood gut virome. However, alterations of the gut virome in children have been linked to pathological conditions such as inflammatory bowel disease, type 1 diabetes, malnutrition, diarrhea and celiac disease.
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Affiliation(s)
- Valerio Fulci
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Laura Stronati
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Salvatore Cucchiara
- Department of Women’s and Children’s Health, Sapienza University of Rome, 00161 Rome, Italy;
| | - Ilaria Laudadio
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Claudia Carissimi
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
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18
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Bassaganya-Riera J, Berry EM, Blaak EE, Burlingame B, le Coutre J, van Eden W, El-Sohemy A, German JB, Knorr D, Lacroix C, Muscaritoli M, Nieman DC, Rychlik M, Scholey A, Serafini M. Goals in Nutrition Science 2020-2025. Front Nutr 2021; 7:606378. [PMID: 33665201 PMCID: PMC7923694 DOI: 10.3389/fnut.2020.606378] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
Five years ago, with the editorial board of Frontiers in Nutrition, we took a leap of faith to outline the Goals for Nutrition Science - the way we see it (1). Now, in 2020, we can put ourselves to the test and take a look back. Without a doubt we got it right with several of the key directions. To name a few, Sustainable Development Goals (SDGs) for Food and Nutrition are part of the global public agenda, and the SDGs contribute to the structuring of international science and research. Nutritional Science has become a critical element in strengthening work on the SDGs, and the development of appropriate methodologies is built on the groundwork of acquiring and analyzing big datasets. Investigation of the Human Microbiome is providing novel insight on the interrelationship between nutrition, the immune system and disease. Finally, with an advanced definition of the gut-brain-axis we are getting a glimpse into the potential for Nutrition and Brain Health. Various milestones have been achieved, and any look into the future will have to consider the lessons learned from Covid-19 and the sobering awareness about the frailty of our food systems in ensuring global food security. With a view into the coming 5 years from 2020 to 2025, the editorial board has taken a slightly different approach as compared to the previous Goals article. A mind map has been created to outline the key topics in nutrition science. Not surprisingly, when looking ahead, the majority of scientific investigation required will be in the areas of health and sustainability. Johannes le Coutre, Field Chief Editor, Frontiers in Nutrition.
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Affiliation(s)
- Josep Bassaganya-Riera
- Nutritional Immunology and Molecular Medicine Laboratory (NIMML) Institute, Blacksburg, VA, United States
| | - Elliot M Berry
- Braun School of Public Health, Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Ellen E Blaak
- Department of Human Biology, Maastricht University, Maastricht, Netherlands
| | | | - Johannes le Coutre
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Willem van Eden
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands
| | - Ahmed El-Sohemy
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - J Bruce German
- Department of Food Science and Technology, University of California, Davis, Davis, CA, United States
| | - Dietrich Knorr
- Institute of Food Technology and Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Christophe Lacroix
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Maurizio Muscaritoli
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - David C Nieman
- Human Performance Laboratory, Department of Biology, Appalachian State University, Kannapolis, NC, United States
| | - Michael Rychlik
- Technical University of Munich, Analytical Food Chemistry, Freising, Germany
| | - Andrew Scholey
- Centre for Human Psychopharmacology, Swinburne University, Melbourne, VIC, Australia
| | - Mauro Serafini
- Functional Food and Metabolic Stress Prevention Laboratory, Faculty of Biosciences and Technologies for Agriculture, Food and Environment, University of Teramo, Teramo, Italy
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19
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Abstract
The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the 'virome'. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 1031 particles on Earth. The human virome is similarly vast and complex, consisting of approximately 1013 particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral 'dark matter'. Nevertheless, it is now clear that viral community states can be associated with adverse outcomes for the human host, whereas other states are characteristic of health. In this Review, we provide an overview of research on the human virome and highlight outstanding recent studies that explore the assembly, composition and dynamics of the human virome as well as host-virome interactions in health and disease.
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20
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Holtz LR. Putting the Virome on the Map: The Influence of Host Geography and Ethnicity on the Gut Virome. Cell Host Microbe 2020; 28:636-637. [PMID: 33181076 DOI: 10.1016/j.chom.2020.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We know little about factors that ordain the composition of the diverse community of viruses (virome) in the human gut. In this issue of Cell Host & Microbe, Zuo et al. highlight the importance of geography, urbanization, ethnicity, and diet on the shape of the adult gut DNA virome.
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Affiliation(s)
- Lori R Holtz
- Washington University Department of Pediatrics, St. Louis, MO, USA.
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