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Zeng C, Wan SR, Guo M, Tan XZ, Zeng Y, Wu Q, Xie JJ, Yan P, Long Y, Zheng L, Jiang ZZ, Teng FY, Xu Y. Fecal virome transplantation: A promising strategy for the treatment of metabolic diseases. Biomed Pharmacother 2024; 177:117065. [PMID: 38971010 DOI: 10.1016/j.biopha.2024.117065] [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: 04/06/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/08/2024] Open
Abstract
Metabolic diseases are a group of disorders caused by metabolic abnormalities, including obesity, diabetes, non-alcoholic fatty liver disease, and more. Increasing research indicates that, beyond inherent metabolic irregularities, the onset and progression of metabolic diseases are closely linked to alterations in the gut microbiota, particularly gut bacteria. Additionally, fecal microbiota transplantation (FMT) has demonstrated effectiveness in clinically treating metabolic diseases, notably diabetes. Recent attention has also focused on the role of gut viruses in disease onset. This review first introduces the characteristics and influencing factors of gut viruses, then summarizes their potential mechanisms in disease development, highlighting their impact on gut bacteria and regulation of host immunity. We also compare FMT, fecal filtrate transplantation (FFT), washed microbiota transplantation (WMT), and fecal virome transplantation (FVT). Finally, we review the current understanding of gut viruses in metabolic diseases and the application of FVT in treating these conditions. In conclusion, FVT may provide a novel and promising treatment approach for metabolic diseases, warranting further validation through basic and clinical research.
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Affiliation(s)
- Chen Zeng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Sheng-Rong Wan
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Man Guo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Xiao-Zhen Tan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Yan Zeng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Qi Wu
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China; Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Jia-Jie Xie
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Pijun Yan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Institute of Cardiovascular Research, Peking University, Beijing 100871, China
| | - Yang Long
- Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Lemin Zheng
- Institute of Cardiovascular Research, Peking University, Beijing 100871, China
| | - Zong-Zhe Jiang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Fang-Yuan Teng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China.
| | - Yong Xu
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Nephropathy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Sichuan Clinical Research Center for Diabetes and Metabolic Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China.
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Mogotsi MT, Ogunbayo AE, Bester PA, O'Neill HG, Nyaga MM. Longitudinal analysis of the enteric virome in paediatric subjects from the Free State Province, South Africa, reveals early gut colonisation and temporal dynamics. Virus Res 2024; 346:199403. [PMID: 38776984 PMCID: PMC11169482 DOI: 10.1016/j.virusres.2024.199403] [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: 01/31/2024] [Revised: 04/23/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
The gut of healthy neonates is devoid of viruses at birth, but rapidly becomes colonised by normal viral commensals that aid in important physiological functions like metabolism but can, in some instances, result in gastrointestinal illnesses. However, little is known about how this colonisation begins, its variability and factors shaping the gut virome composition. Thus, understanding the development, assembly, and progression of enteric viral communities over time is key. To explore early-life virome development, metagenomic sequencing was employed in faecal samples collected longitudinally from a cohort of 17 infants during their first six months of life. The gut virome analysis revealed a diverse and dynamic viral community, formed by a richness of different viruses infecting humans, non-human mammals, bacteria, and plants. Eukaryotic viruses were detected as early as one week of life, increasing in abundance and diversity over time. Most of the viruses detected are commonly associated with gastroenteritis and include members of the Caliciviridae, Picornaviridae, Astroviridae, Adenoviridae, and Sedoreoviridae families. The most common co-occurrences involved asymptomatic norovirus-parechovirus, norovirus-sapovirus, sapovirus-parechovirus, observed in at least 40 % of the samples. Majority of the plant-derived viruses detected in the infants' gut were from the Virgaviridae family. This study demonstrates the first longitudinal characterisation of the gastrointestinal virome in infants, from birth up to 6 months of age, in sub-Saharan Africa. Overall, the findings from this study delineate the composition and variability of the healthy infants' gut virome over time, which is a significant step towards understanding the dynamics and biogeography of viral communities in the infant gut.
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Affiliation(s)
- Milton Tshidiso Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Ayodeji Emmanuel Ogunbayo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Phillip Armand Bester
- Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Hester Gertruida O'Neill
- Department of Microbiology and Biochemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Martin Munene Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa.
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Farajipour H, Matin HR, Asemi Z, Sadr S, Tajabadi-Ebrahimi M, Sharifi N, Banikazemi Z, Taghizadeh M, Mirzaei H. The effects of probiotics supplements on metabolic indices and clinical signs in patients with diabetic retinopathy, a randomized double blind clinical trial. J Diabetes Metab Disord 2024; 23:1133-1140. [PMID: 38932908 PMCID: PMC11196520 DOI: 10.1007/s40200-024-01399-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 02/07/2024] [Indexed: 06/28/2024]
Abstract
Purpose This study was carried out to evaluate the effects of probiotics administration on clinical status and metabolic profiles in diabetic retinopathy (DR) patients. Methods This randomized, double-blind, placebo-controlled trial was conducted among 72 DR patients. Subjects received probiotics including Lactobacillus acidophilus, Bifidobacterium bifidum, Bifidobacterium langum, Bifidobacterium lactis daily (2 × 109 CFU/each strain) (n = 36) or placebo (starch) (n = 36) and were instructed to take one capsule daily for 12 weeks. Finally, 55 participants [probiotic group (n = 30) and placebo group (n = 25)] completed the study. Fasting blood samples were obtained at baseline and after the 12-week intervention to determine metabolic profiles. To determine the effects of probiotic supplementation on clinical symptoms and biochemical variables, we used one-way repeated measures analysis of variance. Results After the 12-week intervention, compared with the placebo, probiotic supplementation significantly decreased means serum insulin concentrations (Probiotic group: -4.9 ± 6.5vs. Placebo group: 3.0 ± 7.7 µIU/mL, Ptime×group<0.001), homeostatic model assessment for insulin resistance (Probiotic group: -2.5 ± 3.8 vs. Placebo group: 1.1 ± 2.7, Ptime×group<0.001) and hemoglobin A1c (HbA1C) (Probiotic group: -0.4 ± 0.7 vs. Placebo group: -0.02 ± 0.2%, Ptime×group=0.01), and significantly increased the quantitative insulin sensitivity check index (QUICKI) (Probiotic group: 0.02 ± 0.03 vs. Placebo group: -0.03 ± 0.04, Ptime×group<0.001). There was no significant effect of probiotic administration on other metabolic profiles and clinical symptoms. Conclusions Overall, probiotic supplementation after 12 weeks in DR patients had beneficial effects on few metabolic profiles. This study was registered under the Iranian website for clinical trials as http://www.irct.ir: IRCT20130211012438N29.
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Affiliation(s)
- Hasan Farajipour
- Department of Ophthalmology, School of Medicine, Matini Hospital, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamid Reza Matin
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Zatollah Asemi
- Faculty member of Science Department, Science Faculty, Islamic Azad University, Tehran Central branch, Tehran, Iran
| | - Saeed Sadr
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Maryam Tajabadi-Ebrahimi
- Faculty member of Science Department, Science Faculty, Islamic Azad University, Tehran Central branch, Tehran, Iran
| | - Nasrin Sharifi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Zarrin Banikazemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohsen Taghizadeh
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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Remesh AT, Viswanathan R. CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:121-135. [PMID: 38413544 DOI: 10.1007/s12560-024-09584-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications.
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Koonin EV, Kuhn JH, Dolja VV, Krupovic M. Megataxonomy and global ecology of the virosphere. THE ISME JOURNAL 2024; 18:wrad042. [PMID: 38365236 PMCID: PMC10848233 DOI: 10.1093/ismejo/wrad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 02/18/2024]
Abstract
Nearly all organisms are hosts to multiple viruses that collectively appear to be the most abundant biological entities in the biosphere. With recent advances in metagenomics and metatranscriptomics, the known diversity of viruses substantially expanded. Comparative analysis of these viruses using advanced computational methods culminated in the reconstruction of the evolution of major groups of viruses and enabled the construction of a virus megataxonomy, which has been formally adopted by the International Committee on Taxonomy of Viruses. This comprehensive taxonomy consists of six virus realms, which are aspired to be monophyletic and assembled based on the conservation of hallmark proteins involved in capsid structure formation or genome replication. The viruses in different major taxa substantially differ in host range and accordingly in ecological niches. In this review article, we outline the latest developments in virus megataxonomy and the recent discoveries that will likely lead to reassessment of some major taxa, in particular, split of three of the current six realms into two or more independent realms. We then discuss the correspondence between virus taxonomy and the distribution of viruses among hosts and ecological niches, as well as the abundance of viruses versus cells in different habitats. The distribution of viruses across environments appears to be primarily determined by the host ranges, i.e. the virome is shaped by the composition of the biome in a given habitat, which itself is affected by abiotic factors.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, United States
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, 75015 Paris, France
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Yin H, Wu S, Tan J, Guo Q, Li M, Guo J, Wang Y, Jiang X, Zhu H. IPEV: identification of prokaryotic and eukaryotic virus-derived sequences in virome using deep learning. Gigascience 2024; 13:giae018. [PMID: 38649300 PMCID: PMC11034026 DOI: 10.1093/gigascience/giae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/14/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The virome obtained through virus-like particle enrichment contains a mixture of prokaryotic and eukaryotic virus-derived fragments. Accurate identification and classification of these elements are crucial to understanding their roles and functions in microbial communities. However, the rapid mutation rates of viral genomes pose challenges in developing high-performance tools for classification, potentially limiting downstream analyses. FINDINGS We present IPEV, a novel method to distinguish prokaryotic and eukaryotic viruses in viromes, with a 2-dimensional convolutional neural network combining trinucleotide pair relative distance and frequency. Cross-validation assessments of IPEV demonstrate its state-of-the-art precision, significantly improving the F1-score by approximately 22% on an independent test set compared to existing methods when query viruses share less than 30% sequence similarity with known viruses. Furthermore, IPEV outperforms other methods in accuracy on marine and gut virome samples based on annotations by sequence alignments. IPEV reduces runtime by at most 1,225 times compared to existing methods under the same computing configuration. We also utilized IPEV to analyze longitudinal samples and found that the gut virome exhibits a higher degree of temporal stability than previously observed in persistent personal viromes, providing novel insights into the resilience of the gut virome in individuals. CONCLUSIONS IPEV is a high-performance, user-friendly tool that assists biologists in identifying and classifying prokaryotic and eukaryotic viruses within viromes. The tool is available at https://github.com/basehc/IPEV.
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Affiliation(s)
- Hengchuang Yin
- Department of Biomedical Engineering, College of Future Technology, and Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Shufang Wu
- Department of Biomedical Engineering, College of Future Technology, and Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Jie Tan
- Department of Biomedical Engineering, College of Future Technology, and Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Qian Guo
- Department of Biomedical Engineering, College of Future Technology, and Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Mo Li
- Department of Biomedical Engineering, College of Future Technology, and Center for Quantitative Biology, Peking University, Beijing 100871, China
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Jinyuan Guo
- Department of Biomedical Engineering, College of Future Technology, and Center for Quantitative Biology, Peking University, Beijing 100871, China
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Yaqi Wang
- Department of Biomedical Engineering, College of Future Technology, and Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Xiaoqing Jiang
- Department of Biomedical Engineering, College of Future Technology, and Center for Quantitative Biology, Peking University, Beijing 100871, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
| | - Huaiqiu Zhu
- Department of Biomedical Engineering, College of Future Technology, and Center for Quantitative Biology, Peking University, Beijing 100871, China
- School of Life Sciences, Peking University, Beijing 100871, China
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
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Álvarez-Espejo DM, Rivera D, Moreno-Switt AI. Bacteriophage-Host Interactions and Coevolution. Methods Mol Biol 2024; 2738:231-243. [PMID: 37966603 DOI: 10.1007/978-1-0716-3549-0_15] [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] [Indexed: 11/16/2023]
Abstract
Bacteriophages are the most abundant entity on the planet and play very relevant roles in the diversity and abundance of their bacterial hosts. These interactions are subject to several factors, such as the first encounter of the phage with its host bacterium, in which molecular interactions are fundamental. Along with this, these interactions depend on the environment and other communities present. This chapter focuses on these phage-bacteria interactions, reviewing the knowledge of the early stage (receptor-binding proteins), host responses (resistance and counter-resistance), and ecological and evolutionary models described to date. In general, knowledge has focused on a few phage-bacteria models and has been deepened by sequencing and metagenomics. The study of phage-bacteria interactions is an essential step for the development of therapies and other applications of phages in the clinical and productive environment.
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Affiliation(s)
- Diana M Álvarez-Espejo
- Escuela de Medicina Veterinaria, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Dácil Rivera
- Escuela de Medicina Veterinaria, Universidad Andres Bello, Santiago, Chile
| | - Andrea I Moreno-Switt
- Escuela de Medicina Veterinaria, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Hsieh SY, Savva GM, Telatin A, Tiwari SK, Tariq MA, Newberry F, Seton KA, Booth C, Bansal AS, Wileman T, Adriaenssens EM, Carding SR. Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus-Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Int J Mol Sci 2023; 24:17267. [PMID: 38139096 PMCID: PMC10744171 DOI: 10.3390/ijms242417267] [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: 11/15/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Understanding how the human virome, and which of its constituents, contributes to health or disease states is reliant on obtaining comprehensive virome profiles. By combining DNA viromes from isolated virus-like particles (VLPs) and whole metagenomes from the same faecal sample of a small cohort of healthy individuals and patients with severe myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), we have obtained a more inclusive profile of the human intestinal DNA virome. Key features are the identification of a core virome comprising tailed phages of the class Caudoviricetes, and a greater diversity of DNA viruses including extracellular phages and integrated prophages. Using an in silico approach, we predicted interactions between members of the Anaerotruncus genus and unique viruses present in ME/CFS microbiomes. This study therefore provides a framework and rationale for studies of larger cohorts of patients to further investigate disease-associated interactions between the intestinal virome and the bacteriome.
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Affiliation(s)
- Shen-Yuan Hsieh
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - George M. Savva
- Core Science Resources, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (G.M.S.); (C.B.)
| | - Andrea Telatin
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - Sumeet K. Tiwari
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - Mohammad A. Tariq
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - Fiona Newberry
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - Katharine A. Seton
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - Catherine Booth
- Core Science Resources, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (G.M.S.); (C.B.)
| | | | - Thomas Wileman
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Evelien M. Adriaenssens
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - Simon R. Carding
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
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9
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Zhang Y, Yao W, Zhang W, Wen Y, Hua Y, Ji P, Wei Y. Yujin powder improves large intestine dampness-heat syndrome by regulating gut microbiota and serum metabolism. Biomed Chromatogr 2023; 37:e5719. [PMID: 37605605 DOI: 10.1002/bmc.5719] [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: 05/17/2023] [Revised: 07/22/2023] [Accepted: 07/27/2023] [Indexed: 08/23/2023]
Abstract
Large intestine dampness-heat syndrome (LIDHS) is a common syndrome type in animal diarrheal diseases. Yujin powder (YJP) is one of the classic prescriptions for treating damp-heat diarrhea. The aim of this study was to investigate the regulatory effects of YJP on gut microbiota and serum metabolism in LIDHS rats using 16S rRNA sequencing and nontargeted metabolomics. The LIDHS rat model was induced through a high-sugar and high-fat diet, exposure to a high-temperature and high-humidity environment, and infection with Escherichia coli. The results demonstrated that the administration of YJP resulted in a decrease in the abundance of Desulfovibrio, Parabacteroides, Bacteroides, Allobaculum, Escherichia, Butyricimonas, Parasutterella, and Blautia and an increase in Ruminococcus, Akkermansia, Roseburia, and Lachnoclostridium. A total of 25 potential biomarkers were identified in three groups of rats. These metabolites were primarily involved in glycerophospholipid metabolism, taurine and hypotaurine metabolism, glycerol ester metabolism, arachidonic acid metabolism, primary bile acid synthesis, and tryptophan metabolism. Our study demonstrated that YJP has the potential to alleviate LIDHS by modulating gut microbial and serum metabolic homeostasis. These results establish a foundation and offer valuable guidance for the utilization of YJP in the treatment of LIDHS.
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Affiliation(s)
- Yahui Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Wanling Yao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Wangdong Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Yanqiao Wen
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Yongli Hua
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Peng Ji
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Yanming Wei
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
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10
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Hashimi M, Sebrell TA, Hedges JF, Snyder D, Lyon KN, Byrum SD, Mackintosh SG, Crowley D, Cherne MD, Skwarchuk D, Robison A, Sidar B, Kunze A, Loveday EK, Taylor MP, Chang CB, Wilking JN, Walk ST, Schountz T, Jutila MA, Bimczok D. Antiviral responses in a Jamaican fruit bat intestinal organoid model of SARS-CoV-2 infection. Nat Commun 2023; 14:6882. [PMID: 37898615 PMCID: PMC10613288 DOI: 10.1038/s41467-023-42610-x] [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: 12/03/2022] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
Bats are natural reservoirs for several zoonotic viruses, potentially due to an enhanced capacity to control viral infection. However, the mechanisms of antiviral responses in bats are poorly defined. Here we established a Jamaican fruit bat (JFB, Artibeus jamaicensis) intestinal organoid model of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Upon infection with SARS-CoV-2, increased viral RNA and subgenomic RNA was detected, but no infectious virus was released, indicating that JFB organoids support only limited viral replication but not viral reproduction. SARS-CoV-2 replication was associated with significantly increased gene expression of type I interferons and inflammatory cytokines. Interestingly, SARS-CoV-2 also caused enhanced formation and growth of JFB organoids. Proteomics revealed an increase in inflammatory signaling, cell turnover, cell repair, and SARS-CoV-2 infection pathways. Collectively, our findings suggest that primary JFB intestinal epithelial cells mount successful antiviral interferon responses and that SARS-CoV-2 infection in JFB cells induces protective regenerative pathways.
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Affiliation(s)
- Marziah Hashimi
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - T Andrew Sebrell
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Jodi F Hedges
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Deann Snyder
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Katrina N Lyon
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Stephanie D Byrum
- University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology, Little Rock, AR, USA
- Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Samuel G Mackintosh
- University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology, Little Rock, AR, USA
| | - Dan Crowley
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
- Department of Public & Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Michelle D Cherne
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - David Skwarchuk
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Amanda Robison
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Barkan Sidar
- Montana State University, Chemical and Biological Engineering Department, Bozeman, MT, USA
- Center for Biofilm Engineering, Bozeman, MT, USA
| | - Anja Kunze
- Montana State University, Electrical and Computer Engineering Department, Bozeman, MT, USA
| | - Emma K Loveday
- Montana State University, Chemical and Biological Engineering Department, Bozeman, MT, USA
- Center for Biofilm Engineering, Bozeman, MT, USA
| | - Matthew P Taylor
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Connie B Chang
- Montana State University, Chemical and Biological Engineering Department, Bozeman, MT, USA
- Center for Biofilm Engineering, Bozeman, MT, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - James N Wilking
- Montana State University, Chemical and Biological Engineering Department, Bozeman, MT, USA
- Center for Biofilm Engineering, Bozeman, MT, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Seth T Walk
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology and Center of Vector-Borne Infectious Diseases, Colorado State University, Fort, Collins, CO, USA
| | - Mark A Jutila
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA
| | - Diane Bimczok
- Montana State University, Department of Microbiology and Cell Biology, Bozeman, MT, USA.
- Center for Biofilm Engineering, Bozeman, MT, USA.
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11
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Emencheta SC, Olovo CV, Eze OC, Kalu CF, Berebon DP, Onuigbo EB, Vila MMDC, Balcão VM, Attama AA. The Role of Bacteriophages in the Gut Microbiota: Implications for Human Health. Pharmaceutics 2023; 15:2416. [PMID: 37896176 PMCID: PMC10609668 DOI: 10.3390/pharmaceutics15102416] [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: 08/22/2023] [Revised: 09/18/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Bacteriophages (phages) are nano-sized viruses characterized by their inherent ability to live off bacteria. They utilize diverse mechanisms to absorb and gain entry into the bacterial cell wall via the release of viral genetic material, which uses the replication mechanisms of the host bacteria to produce and release daughter progeny virions that attack the surrounding host cells. They possess specific characteristics, including specificity for particular or closely related bacterial species. They have many applications, including as potential alternatives to antibiotics against multi-resistant bacterial pathogens and as control agents in bacteria-contaminated environments. They are ubiquitously abundant in nature and have diverse biota, including in the gut. Gut microbiota describes the community and interactions of microorganisms within the intestine. As with bacteria, parasitic bacteriophages constantly interact with the host bacterial cells within the gut system and have obvious implications for human health. However, it is imperative to understand these interactions as they open up possible applicable techniques to control gut-implicated bacterial diseases. Thus, this review aims to explore the interactions of bacteriophages with bacterial communities in the gut and their current and potential impacts on human health.
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Affiliation(s)
- Stephen C. Emencheta
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, Brazil; (M.M.D.C.V.); (V.M.B.)
| | - Chinasa V. Olovo
- Department of Microbiology, University of Nigeria, Nsukka 410001, Nigeria;
| | - Osita C. Eze
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Chisom F. Kalu
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Dinebari P. Berebon
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Ebele B. Onuigbo
- Department of Pharmaceutical Microbiology and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria; (S.C.E.); (O.C.E.); (C.F.K.); (E.B.O.)
| | - Marta M. D. C. Vila
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, Brazil; (M.M.D.C.V.); (V.M.B.)
| | - Victor M. Balcão
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, Brazil; (M.M.D.C.V.); (V.M.B.)
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
| | - Anthony A. Attama
- Department of Pharmaceutics, University of Nigeria, Nsukka 410001, Nigeria
- Institute for Drug-Herbal Medicine-Excipient Research and Development, University of Nigeria, Nsukka 410001, Nigeria
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12
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Champagne-Jorgensen K, Luong T, Darby T, Roach DR. Immunogenicity of bacteriophages. Trends Microbiol 2023; 31:1058-1071. [PMID: 37198061 DOI: 10.1016/j.tim.2023.04.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023]
Abstract
Hundreds of trillions of diverse bacteriophages (phages) peacefully thrive within and on the human body. However, whether and how phages influence their mammalian hosts is poorly understood. In this review, we explore current knowledge and present growing evidence that direct interactions between phages and mammalian cells often induce host inflammatory and antiviral immune responses. We show evidence that, like viruses of the eukaryotic host, phages are actively internalized by host cells and activate conserved viral detection receptors. This interaction often generates proinflammatory cytokine secretion and recruitment of adaptive immune programs. However, significant variability exists in phage-immune interactions, suggesting an important role for structural phage characteristics. The factors leading to the differential immunogenicity of phages remain largely unknown but are highly influenced by their human and bacterial hosts.
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Affiliation(s)
- Kevin Champagne-Jorgensen
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Tiffany Luong
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Taylor Darby
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Dwayne R Roach
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Viral Information Institute, San Diego State University, San Diego, CA 92182, USA.
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13
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Rajput M, Thakur N. Editorial: Advances in host-pathogen interactions for diseases in animals and birds. Front Vet Sci 2023; 10:1282110. [PMID: 37766859 PMCID: PMC10520279 DOI: 10.3389/fvets.2023.1282110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Affiliation(s)
- Mrigendra Rajput
- Department of Biology, University of Dayton, Dayton, OH, United States
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14
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Guo Y, Li Z, Dong S, Si X, Ta N, Liang H, Xu L. Multiple infections of zoonotic pathogens in wild Brandt's voles (Lasiopodomys brandtii). Vet Med Sci 2023; 9:2201-2211. [PMID: 37491010 PMCID: PMC10508490 DOI: 10.1002/vms3.1214] [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: 06/16/2022] [Revised: 06/03/2023] [Accepted: 07/08/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND The frequent interactions of rodents with humans make them a common source of zoonotic infections. Brandt's vole is the dominant rodent species of the typical steppe in Inner Mongolia, and it is also an important pest in grassland. OBJECTIVES To obtain an initial unbiased measure of the microbial diversity and abundance in the blood and intestinal tracts and to detect the pathogens carried by wild Brandt's voles in Hulun Buir, Inner Mongolia. METHODS Twenty wild adult Brandt's voles were trapped using live cages, and 12 intestinal samples were collected for metagenomic analysis and 8 blood samples were collected for meta-transcriptomic analysis. We compared the sequencing data with pathogenic microbiota databases to analyse the phylogenetic characteristics of zoonotic pathogens carried by wild voles. RESULTS A total of 122 phyla, 79 classes, 168 orders, 382 families and 1693 genera of bacteria and a total of 32 families of DNA and RNA viruses in Brandt's voles were characterized. We found that each sample carried more than 10 pathogens, whereas some pathogens that were low in abundance were still at risk of transmission to humans. CONCLUSION This study improves our understanding of the viral and bacterial diversity in wild Brandt's voles and highlights the multiple viral and bacterial pathogens carried by this rodent. These findings may serve as a basis for developing strategies targeting rodent population control in Hulun Buir and provide a better approach to the surveillance of pathogenic microorganisms in wildlife.
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Affiliation(s)
- Yongman Guo
- Vanke School of Public HealthTsinghua UniversityBeijingChina
- Institute for Healthy ChinaTsinghua UniversityBeijingChina
| | - Zhengrun Li
- Vanke School of Public HealthTsinghua UniversityBeijingChina
- Institute for Healthy ChinaTsinghua UniversityBeijingChina
| | - Shike Dong
- Vanke School of Public HealthTsinghua UniversityBeijingChina
- Institute for Healthy ChinaTsinghua UniversityBeijingChina
| | - Xiaoyan Si
- Inner Mongolia Autonomous Region Center for Disease Control and PreventionHohhotChina
| | - Na Ta
- Inner Mongolia Autonomous Region Center for Disease Control and PreventionHohhotChina
| | - Hanwei Liang
- Vanke School of Public HealthTsinghua UniversityBeijingChina
- Institute for Healthy ChinaTsinghua UniversityBeijingChina
| | - Lei Xu
- Vanke School of Public HealthTsinghua UniversityBeijingChina
- Institute for Healthy ChinaTsinghua UniversityBeijingChina
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15
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Jędrusiak A, Fortuna W, Majewska J, Górski A, Jończyk-Matysiak E. Phage Interactions with the Nervous System in Health and Disease. Cells 2023; 12:1720. [PMID: 37443756 PMCID: PMC10341288 DOI: 10.3390/cells12131720] [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: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
The central nervous system manages all of our activities (e.g., direct thinking and decision-making processes). It receives information from the environment and responds to environmental stimuli. Bacterial viruses (bacteriophages, phages) are the most numerous structures occurring in the biosphere and are also found in the human organism. Therefore, understanding how phages may influence this system is of great importance and is the purpose of this review. We have focused on the effect of natural bacteriophages in the central nervous system, linking them to those present in the gut microbiota, creating the gut-brain axis network, as well as their interdependence. Importantly, based on the current knowledge in the field of phage application (e.g., intranasal) in the treatment of bacterial diseases associated with the brain and nervous system, bacteriophages may have significant therapeutic potential. Moreover, it was indicated that bacteriophages may influence cognitive processing. In addition, phages (via phage display technology) appear promising as a targeted therapeutic tool in the treatment of, among other things, brain cancers. The information collected and reviewed in this work indicates that phages and their impact on the nervous system is a fascinating and, so far, underexplored field. Therefore, the aim of this review is not only to summarize currently available information on the association of phages with the nervous system, but also to stimulate future studies that could pave the way for novel therapeutic approaches potentially useful in treating bacterial and non-bacterial neural diseases.
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Affiliation(s)
- Adam Jędrusiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.J.); (J.M.); (A.G.)
| | - Wojciech Fortuna
- Department of Neurosurgery, Wroclaw Medical University, Borowska 213, 54-427 Wroclaw, Poland;
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland
| | - Joanna Majewska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.J.); (J.M.); (A.G.)
| | - Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.J.); (J.M.); (A.G.)
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland
- Infant Jesus Hospital, The Medical University of Warsaw, 02-006 Warsaw, Poland
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.J.); (J.M.); (A.G.)
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16
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Narat V, Salmona M, Kampo M, Heyer T, Rachik AS, Mercier-Delarue S, Ranger N, Rupp S, Ambata P, Njouom R, Simon F, Le Goff J, Giles-Vernick T. Higher convergence of human-great ape enteric eukaryotic viromes in central African forest than in a European zoo: a One Health analysis. Nat Commun 2023; 14:3674. [PMID: 37339968 DOI: 10.1038/s41467-023-39455-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
Human-animal pathogenic transmissions threaten both human and animal health, and the processes catalyzing zoonotic spillover and spillback are complex. Prior field studies offer partial insight into these processes but overlook animal ecologies and human perceptions and practices facilitating human-animal contact. Conducted in Cameroon and a European zoo, this integrative study elucidates these processes, incorporating metagenomic, historical, anthropological and great ape ecological analyses, and real-time evaluation of human-great ape contact types and frequencies. We find more enteric eukaryotic virome sharing between Cameroonian humans and great apes than in the zoo, virome convergence between Cameroonian humans and gorillas, and adenovirus and enterovirus taxa as most frequently shared between Cameroonian humans and great apes. Together with physical contact from hunting, meat handling and fecal exposure, overlapping human cultivation and gorilla pillaging in forest gardens help explain these findings. Our multidisciplinary study identifies environmental co-use as a complementary mechanism for viral sharing.
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Affiliation(s)
- Victor Narat
- Eco-anthropologie, MNHN/CNRS/Univ. Paris Cité, Paris, France
| | - Maud Salmona
- Virology, AP-HP, Hôpital Saint Louis, Paris, France
- INSIGHT U976, INSERM, Université Paris Cité, Paris, France
| | - Mamadou Kampo
- Anthropology and Ecology of Disease Emergence Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | | | | | | | - Noémie Ranger
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Stephanie Rupp
- Department of Anthropology, City University of NewYork - Lehman College, NewYork, NY, USA
| | - Philippe Ambata
- Ministry of Agriculture and Rural Development, Yaounde, Cameroon
| | | | - François Simon
- Virology, AP-HP, Hôpital Saint Louis, Paris, France
- INSIGHT U976, INSERM, Université Paris Cité, Paris, France
| | - Jérôme Le Goff
- Virology, AP-HP, Hôpital Saint Louis, Paris, France.
- INSIGHT U976, INSERM, Université Paris Cité, Paris, France.
| | - Tamara Giles-Vernick
- Anthropology and Ecology of Disease Emergence Unit, Institut Pasteur, Université Paris Cité, Paris, France.
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17
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Kannampuzha S, Gopalakrishnan AV, Padinharayil H, Alappat RR, Anilkumar KV, George A, Dey A, Vellingiri B, Madhyastha H, Ganesan R, Ramesh T, Jayaraj R, Prabakaran DS. Onco-Pathogen Mediated Cancer Progression and Associated Signaling Pathways in Cancer Development. Pathogens 2023; 12:770. [PMID: 37375460 DOI: 10.3390/pathogens12060770] [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: 03/11/2023] [Revised: 05/20/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Infection with viruses, bacteria, and parasites are thought to be the underlying cause of about 8-17% of the world's cancer burden, i.e., approximately one in every five malignancies globally is caused by an infectious pathogen. Oncogenesis is thought to be aided by eleven major pathogens. It is crucial to identify microorganisms that potentially act as human carcinogens and to understand how exposure to such pathogens occur as well as the following carcinogenic pathways they induce. Gaining knowledge in this field will give important suggestions for effective pathogen-driven cancer care, control, and, ultimately, prevention. This review will mainly focus on the major onco-pathogens and the types of cancer caused by them. It will also discuss the major pathways which, when altered, lead to the progression of these cancers.
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Affiliation(s)
- Sandra Kannampuzha
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Hafiza Padinharayil
- Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur 680596, India
| | - Reema Rose Alappat
- Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur 680596, India
- Post Graduate and Research Department of Zoology, Maharajas College, Ernakulam 682011, India
| | - Kavya V Anilkumar
- Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur 680596, India
- Post Graduate and Research Department of Zoology, Maharajas College, Ernakulam 682011, India
| | - Alex George
- Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur 680596, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata 700073, India
| | - Balachandar Vellingiri
- Stem Cell and Regenerative Medicine/Translational Research, Department of Zoology, School of Basic Sciences, Central University of Punjab (CUPB), Bathinda 151401, India
| | - Harishkumar Madhyastha
- Department of Cardiovascular Physiology, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Raja Ganesan
- Institute for Liver and Digestive Diseases, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Thiyagarajan Ramesh
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Rama Jayaraj
- Jindal Institute of Behavioral Sciences (JIBS), Jindal Global Institution of Eminence Deemed to Be University, Sonipat 131001, India
- Director of Clinical Sciences, Northern Territory Institute of Research and Training, Darwin, NT 0909, Australia
| | - D S Prabakaran
- Department of Radiation Oncology, College of Medicine, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju 28644, Republic of Korea
- Department of Biotechnology, Ayya Nadar Janaki Ammal College, Srivilliputhur Main Road, Sivakasi 626124, India
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18
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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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Blachier F. Amino Acid-Derived Bacterial Metabolites in the Colorectal Luminal Fluid: Effects on Microbial Communication, Metabolism, Physiology, and Growth. Microorganisms 2023; 11:1317. [PMID: 37317289 DOI: 10.3390/microorganisms11051317] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Undigested dietary and endogenous proteins, as well as unabsorbed amino acids, can move from the terminal part of the ileum into the large intestine, where they meet a dense microbial population. Exfoliated cells and mucus released from the large intestine epithelium also supply nitrogenous material to this microbial population. The bacteria in the large intestine luminal fluid release amino acids from the available proteins, and amino acids are then used for bacterial protein synthesis, energy production, and in other various catabolic pathways. The resulting metabolic intermediaries and end products can then accumulate in the colorectal fluid, and their concentrations appear to depend on different parameters, including microbiota composition and metabolic activity, substrate availability, and the capacity of absorptive colonocytes to absorb these metabolites. The aim of the present review is to present how amino acid-derived bacterial metabolites can affect microbial communication between both commensal and pathogenic microorganisms, as well as their metabolism, physiology, and growth.
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Affiliation(s)
- François Blachier
- Université Paris-Saclay, AgroParisTech, INRAe, UMR PNCA, 91120 Palaiseau, France
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20
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Chen X, Mendes BG, Alves BS, Duan Y. Phage therapy in gut microbiome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:93-118. [PMID: 37770177 DOI: 10.1016/bs.pmbts.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Phage therapy, the use of bacteriophage viruses for bacterial infection treatment, has been around for almost a century, but with the increase in antibiotic use, its importance has declined rapidly. There has been renewed interest in revisiting this practice due to the general decline in the effectiveness of antibiotics, combined with improved understanding of human microbiota and advances in sequencing technologies. Phage therapy has been proposed as a clinical alternative to restore the gut microbiota in the absence of an effective treatment. That is due to its immunomodulatory and bactericidal effects against its target bacteria. In the gastrointestinal diseases field, phage therapy has been studied mainly as a promising tool in infectious diseases treatment, such as cholera and diarrhea. However, many studies have been conducted in non-communicable diseases, such as the targeting of adherent invasive Escherichia coli in Crohn's disease, the treatment of Clostridioides difficile in ulcerative colitis, the eradication of Fusobacterium nucleatum in colorectal cancer, the targeting of alcohol-producing Klebsiella pneumoniae in non-alcoholic fatty liver disease, or Enterococcus faecalis in alcohol-associated hepatitis. This review will summarize the changes in the gut microbiota and the phageome in association with some gastrointestinal and liver diseases and highlight the recent scientific advances in phage therapy as a therapeutic tool for their treatment.
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Affiliation(s)
- Xingyao Chen
- Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Beatriz G Mendes
- Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Campus Universitário Trindade, Florianópolis, Santa Catarina, Brazil
| | - Bruno Secchi Alves
- Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Campus Universitário Trindade, Florianópolis, Santa Catarina, Brazil
| | - Yi Duan
- Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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21
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Kazakova P, Abasolo N, de Cripan SM, Marquès E, Cereto-Massagué A, Garcia L, Canela N, Tormo R, Torrell H. Gut Microbiome and Small RNA Integrative-Omic Perspective of Meconium and Milk-FED Infant Stool Samples. Int J Mol Sci 2023; 24:ijms24098069. [PMID: 37175775 PMCID: PMC10179101 DOI: 10.3390/ijms24098069] [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: 03/30/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
The human gut microbiome plays an important role in health, and its initial development is conditioned by many factors, such as feeding. It has also been claimed that this colonization is guided by bacterial populations, the dynamic virome, and transkingdom interactions between host and microbial cells, partially mediated by epigenetic signaling. In this article, we characterized the bacteriome, virome, and smallRNome and their interaction in the meconium and stool samples from infants. Bacterial and viral DNA and RNA were extracted from the meconium and stool samples of 2- to 4-month-old milk-fed infants. The bacteriome, DNA and RNA virome, and smallRNome were assessed using 16S rRNA V4 sequencing, viral enrichment sequencing, and small RNA sequencing protocols, respectively. Data pathway analysis and integration were performed using the R package mixOmics. Our findings showed that the bacteriome differed among the three groups, while the virome and smallRNome presented significant differences, mainly between the meconium and stool of milk-fed infants. The gut environment is rapidly acquired after birth, and it is highly adaptable due to the interaction of environmental factors. Additionally, transkingdom interactions between viruses and bacteria can influence host and smallRNome profiles. However, virome characterization has several protocol limitations that must be considered.
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Affiliation(s)
- Polina Kazakova
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Nerea Abasolo
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Sara Martinez de Cripan
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | | | - Adrià Cereto-Massagué
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Lorena Garcia
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Núria Canela
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Ramón Tormo
- ESPGHAN, European Society for Paediatric Gastroenterology, Hepatology and Nutrition, 1201 Geneva, Switzerland
- Gastroenterology and Nutrition Pediatric Center, 08006 Barcelona, Spain
| | - Helena Torrell
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
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22
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Imdad A, Pandit NG, Zaman M, Minkoff NZ, Tanner-Smith EE, Gomez-Duarte OG, Acra S, Nicholson MR. Fecal transplantation for treatment of inflammatory bowel disease. Cochrane Database Syst Rev 2023; 4:CD012774. [PMID: 37094824 PMCID: PMC10133790 DOI: 10.1002/14651858.cd012774.pub3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a chronic, relapsing disease of the gastrointestinal (GI) tract that is thought to be associated with a complex interplay between the immune system, the GI tract lining, the environment, and the gut microbiome, leading to an abnormal inflammatory response in genetically susceptible individuals. An altered composition of the gut's native microbiota, known as dysbiosis, may have a major role in the pathogenesis of ulcerative colitis (UC) and Crohn disease (CD), two subtypes of IBD. There is growing interest in the correction of this underlying dysbiosis using fecal microbiota transplantation (FMT). OBJECTIVES To evaluate the benefits and safety profile of FMT for treatment of IBD in adults and children versus autologous FMT, placebo, standard medication, or no intervention. SEARCH METHODS We searched CENTRAL, MEDLINE, Embase, two clinical trial registries, and the reference sections of published trials through 22 December 2022. SELECTION CRITERIA We included randomized controlled trials that studied adults and children with UC or CD. Eligible intervention arms used FMT, defined as the delivery of healthy donor stool containing gut microbiota to a recipient's GI tract, to treat UC or CD. DATA COLLECTION AND ANALYSIS Two review authors independently screened studies for inclusion. Our primary outcomes were: 1. induction of clinical remission, 2. maintenance of clinical remission, and 3. serious adverse events. Our secondary outcomes were: 4. any adverse events, 5. endoscopic remission, 6. quality of life, 7. clinical response, 8. endoscopic response, 9. withdrawals, 10. inflammatory markers, and 11. microbiome outcomes. We used the GRADE approach to assess the certainty of evidence. MAIN RESULTS We included 12 studies with 550 participants. Three studies were conducted in Australia; two in Canada; and one in each of the following: China, the Czech Republic, France, India, the Netherlands, and the USA. One study was conducted in both Israel and Italy. FMT was administered in the form of capsules or suspensions and delivered by mouth, nasoduodenal tube, enema, or colonoscopy. One study delivered FMT by both oral capsules and colonoscopy. Six studies were at overall low risk of bias, while the others had either unclear or high risk of bias. Ten studies with 468 participants, of which nine studies focused on adults and one focused on children, reported induction of clinical remission in people with UC at longest follow-up (range 6 to 12 weeks) and showed that FMT may increase rates of induction of clinical remission in UC compared to control (risk ratio (RR) 1.79, 95% confidence interval (CI) 1.13 to 2.84; low-certainty evidence). Five studies showed that FMT may increase rates of induction of endoscopic remission in UC at longest follow-up (range 8 to 12 weeks); however, the CIs around the summary estimate were wide and included a possible null effect (RR 1.45, 95% CI 0.64 to 3.29; low-certainty evidence). Nine studies with 417 participants showed that FMT may result in little to no difference in rates of any adverse events (RR 0.99, 95% CI 0.85 to 1.16; low-certainty evidence). The evidence was very uncertain about the risk of serious adverse events (RR 1.77, 95% CI 0.88 to 3.55; very low-certainty evidence) and improvement in quality of life (mean difference (MD) 15.34, 95% CI -3.84 to 34.52; very low-certainty evidence) when FMT was used to induce remission in UC. Two studies, of which one also contributed data for induction of remission in active UC, assessed maintenance of remission in people with controlled UC at longest follow-up (range 48 to 56 weeks). The evidence was very uncertain about the use of FMT for maintenance of clinical remission (RR 2.97, 95% CI 0.26 to 34.42; very low-certainty evidence) and endoscopic remission (RR 3.28, 95% CI 0.73 to 14.74; very low-certainty evidence). The evidence was also very uncertain about the risk of serious adverse events, risk of any adverse events, and improvement in quality of life when FMT was used to maintain remission in UC. None of the included studies assessed use of FMT for induction of remission in people with CD. One study with 21 participants reported data on FMT for maintenance of remission in people with CD. The evidence was very uncertain about the use of FMT for maintenance of clinical remission in CD at 24 weeks (RR 1.21, 95% CI 0.36 to 4.14; very low-certainty evidence). The evidence was also very uncertain about the risk of serious or any adverse events when FMT was used to maintain remission in CD. None of the studies reported data on use of FMT for maintenance of endoscopic remission or improvement in quality of life in people with CD. AUTHORS' CONCLUSIONS FMT may increase the proportion of people with active UC who achieve clinical and endoscopic remission. The evidence was very uncertain about whether use of FMT in people with active UC impacted the risk of serious adverse events or improvement in quality of life. The evidence was also very uncertain about the use of FMT for maintenance of remission in people with UC, as well as induction and maintenance of remission in people with CD, and no conclusive statements could be made in this regard. Further studies are needed to address the beneficial effects and safety profile of FMT in adults and children with active UC and CD, as well as its potential to promote longer-term maintenance of remission in UC and CD.
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Affiliation(s)
- Aamer Imdad
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology and Nutrition, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Natasha G Pandit
- Norton College of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Muizz Zaman
- Norton College of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Nathan Zev Minkoff
- Pediatric Gastroenterology, Hepatology and Nutrition, Valley Children's Hospital, Madera, CA, USA
| | - Emily E Tanner-Smith
- Counseling Psychology and Human Services, University of Oregon, Eugene, Oregon, USA
| | - Oscar G Gomez-Duarte
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Sari Acra
- Department of Pediatrics, D. Brent Polk Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Maribeth R Nicholson
- Department of Pediatrics, D. Brent Polk Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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23
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Mo R, Zhang M, Wang H, Liu T, Liu P, Wu Y. Chitosan Enhances Intestinal Health in Cats by Altering the Composition of Gut Microbiota and Metabolites. Metabolites 2023; 13:metabo13040529. [PMID: 37110186 PMCID: PMC10145270 DOI: 10.3390/metabo13040529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/10/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023] Open
Abstract
The interaction between gut microbiota and the health of the host has gained increasing attention. Chitosan is a natural alkaline polysaccharide with a wide range of beneficial effects. However, rare studies have been observed on the effects of dietary chitosan supplementation on intestinal health in cats. A total of 30 cats with mild diarrhea were divided into three groups, receiving a basic diet with 0 (CON), 500 (L-CS) or 2000 (H-CS) mg/kg chitosan. Samples of blood and feces were collected and analyzed for serology and gut microbiota composition. The results demonstrated that chitosan alleviated symptoms of diarrhea, with enhanced antioxidant capability and decreased inflammatory biomarker levels in serum. Chitosan reshaped the composition of gut microbiota in cats that the beneficial bacteria Allobaculum was significantly increased in the H-CS group. Acetate and butyrate contents in feces were significantly higher in the H-CS group in comparison to the CON group (p < 0.05). In conclusion, the addition of dietary chitosan in cats enhanced intestinal health by modulating their intestinal microbes and improved microbiota-derived SCFA production. Our results provided insights into the role of chitosan in the gut microbiota of felines.
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Affiliation(s)
- Ruixia Mo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Mingrui Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Haotian Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tianyi Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Pan Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yi Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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24
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Liang L, Saunders C, Sanossian N. Food, gut barrier dysfunction, and related diseases: A new target for future individualized disease prevention and management. Food Sci Nutr 2023; 11:1671-1704. [PMID: 37051344 PMCID: PMC10084985 DOI: 10.1002/fsn3.3229] [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: 08/06/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 03/09/2023] Open
Abstract
Dysfunction of gut barrier is known as "leaky gut" or increased intestinal permeability. Numerous recent scientific evidences showed the association between gut dysfunction and multiple gastrointestinal tract (GI) and non-GI diseases. Research also demonstrated that food plays a crucial role to cause or remedy gut dysfunction related to diseases. We reviewed recent articles from electronic databases, mainly PubMed. The data were based on animal models, cell models, and human research in vivo and in vitro models. In this comprehensive review, our aim focused on the relationship between dietary factors, intestinal permeability dysfunction, and related diseases. This review synthesizes currently available literature and is discussed in three parts: (a) the mechanism of gut barrier and function, (b) food and dietary supplements that may promote gut health, and food or medication that may alter gut function, and (c) a table that organizes the synthesized information by general mechanisms for diseases related to leaky gut/intestinal permeability and associated dietary influences. With future research, dietary intervention could be a new target for individualized disease prevention and management.
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Affiliation(s)
- Linda Liang
- University of Southern CaliforniaLos AngelesCaliforniaUSA
| | | | - Nerses Sanossian
- Department of NeurologyMedical School of Southern CaliforniaLos AngelesCaliforniaUSA
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25
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Impact Assessment of vB_KpnP_K1-ULIP33 Bacteriophage on the Human Gut Microbiota Using a Dynamic In Vitro Model. Viruses 2023; 15:v15030719. [PMID: 36992428 PMCID: PMC10057081 DOI: 10.3390/v15030719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/02/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
New control methods are needed to counter antimicrobial resistances and the use of bacteriophages as an alternative treatment seems promising. To that end, the effect of the phage vB_KpnP_K1-ULIP33, whose host is the hypervirulent Klebsiella pneumoniae SA12 (ST23 and capsular type K1), was assessed on intestinal microbiota, using an in vitro model: the SHIME® system (Simulator of the Human Intestinal Microbial Ecosystem). After stabilization of the system, the phage was inoculated for 7 days and its persistence in the different colons was studied until its disappearance from the system. The concentration of short chain fatty acids in the colons showed good colonization of the bioreactors by the microbiota and no significant effect related to the phage treatment. Diversity (α and β), the relative abundance of bacteria, and qPCR analysis targeting different genera of interest showed no significant variation following phage administration. Even if further in vitro studies are needed to assess the efficacy of this phage against its bacterial host within the human intestinal ecosystem, the phage ULIP33 exerted no significant change on the global colonic microbiota.
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26
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Viral Metagenomic Analysis of the Fecal Samples in Domestic Dogs (Canis lupus familiaris). Viruses 2023; 15:v15030685. [PMID: 36992396 PMCID: PMC10058366 DOI: 10.3390/v15030685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Canine diarrhea is a common intestinal illness that is usually caused by viruses, bacteria, and parasites, and canine diarrhea may induce morbidity and mortality of domestic dogs if treated improperly. Recently, viral metagenomics was applied to investigate the signatures of the enteric virome in mammals. In this research, the characteristics of the gut virome in healthy dogs and dogs with diarrhea were analyzed and compared using viral metagenomics. The alpha diversity analysis indicated that the richness and diversity of the gut virome in the dogs with diarrhea were much higher than the healthy dogs, while the beta diversity analysis revealed that the gut virome of the two groups was quite different. At the family level, the predominant viruses in the canine gut virome were certified to be Microviridae, Parvoviridae, Siphoviridae, Inoviridae, Podoviridae, Myoviridae, and others. At the genus level, the predominant viruses in the canine gut virome were certified to be Protoparvovirus, Inovirus, Chlamydiamicrovirus, Lambdavirus, Dependoparvovirus, Lightbulbvirus, Kostyavirus, Punavirus, Lederbergvirus, Fibrovirus, Peduovirus, and others. However, the viral communities between the two groups differed significantly. The unique viral taxa identified in the healthy dogs group were Chlamydiamicrovirus and Lightbulbvirus, while the unique viral taxa identified in the dogs with diarrhea group were Inovirus, Protoparvovirus, Lambdavirus, Dependoparvovirus, Kostyavirus, Punavirus, and other viruses. Phylogenetic analysis based on the near-complete genome sequences showed that the CPV strains collected in this study together with other CPV Chinese isolates clustered into a separate branch, while the identified CAV-2 strain D5-8081 and AAV-5 strain AAV-D5 were both the first near-complete genome sequences in China. Moreover, the predicted bacterial hosts of phages were certified to be Campylobacter, Escherichia, Salmonella, Pseudomonas, Acinetobacter, Moraxella, Mediterraneibacter, and other commensal microbiota. In conclusion, the enteric virome of the healthy dogs group and the dogs with diarrhea group was investigated and compared using viral metagenomics, and the viral communities might influence canine health and disease by interacting with the commensal gut microbiome.
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27
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Borin JM, Liu R, Wang Y, Wu TC, Chopyk J, Huang L, Kuo P, Ghose C, Meyer JR, Tu XM, Schnabl B, Pride DT. Fecal virome transplantation is sufficient to alter fecal microbiota and drive lean and obese body phenotypes in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.527064. [PMID: 36778328 PMCID: PMC9915734 DOI: 10.1101/2023.02.03.527064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background The gastrointestinal microbiome plays a significant role in numerous host processes and has an especially large impact on modulating the host metabolism. Prior studies have shown that when mice receive fecal transplants from obese donors that were fed high-fat diets (HFD) (even when recipient mice are fed normal diets after transplantation), they develop obese phenotypes. These studies demonstrate the prominent role that the gut microbiota play in determining lean and obese phenotypes. While much of the credit has been given to gut bacteria, studies have not measured the impact of gut viruses on these phenotypes. To address this shortcoming, we gavaged mice with viromes isolated from donors fed HFD or normal chow. By characterizing the mice’s gut bacterial biota and weight-gain phenotypes over time, we demonstrate that viruses can shape the gut bacterial community and affect weight gain or loss. Results We gavaged mice longitudinally over 4 weeks while measuring their body weights and collecting fecal samples for 16S rRNA amplicon sequencing. We evaluated mice that were fed normal chow or high-fat diets, and gavaged each group with either chow-derived fecal viromes, HFD-derived fecal viromes, or phosphate buffered saline controls. We found a significant effect of gavage type, where mice fed chow but gavaged with HFD-derived viromes gained significantly more weight than their counterparts receiving chow-derived viromes. The converse was also true: mice fed HFD but gavaged with chow-derived viromes gained significantly less weight than their counterparts receiving HFD-derived viromes. These results were replicated in two separate experiments and the phenotypic changes were accompanied by significant and identifiable differences in the fecal bacterial biota. Notably, there were differences in Lachnospirales and Clostridia in mice fed chow but gavaged with HFD-derived fecal viromes, and in Peptostreptococcales, Oscillospirales, and Lachnospirales in mice fed HFD but gavaged with chow-derived fecal viromes. Due to methodological limitations, we were unable to identify specific bacterial species or strains that were responsible for respective phenotypic changes. Conclusions This study confirms that virome-mediated perturbations can alter the fecal microbiome in an in vivo model and indicates that such perturbations are sufficient to drive lean and obese phenotypes in mice.
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Affiliation(s)
- Joshua M Borin
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Roland Liu
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Yanhan Wang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tsung-Chin Wu
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Jessica Chopyk
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Lina Huang
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Peiting Kuo
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | | | - Justin R Meyer
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Xin M Tu
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - David T Pride
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
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28
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Dagar S, Singh J, Saini A, Kumar Y, Chhabra S, Minz RW, Rani L. Gut bacteriome, mycobiome and virome alterations in rheumatoid arthritis. Front Endocrinol (Lausanne) 2023; 13:1044673. [PMID: 36699026 PMCID: PMC9868751 DOI: 10.3389/fendo.2022.1044673] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Rheumatoid arthritis (RA) is a chronic destructive autoimmune disease of the joints which causes significant pain, functional disability, and mortality. Although aberrant immune cell activation induced by the imbalance between T helper Th1/Th17 and Treg cells is implicated in the RA development, its etiopathogenesis remains unclear. The presence of mucosal inflammation and systemic IgA-isotype-autoantibodies (anti-citrullinated peptide antibodies and rheumatoid factor) in pre-clinical RA supports the mucosal origin hypothesis involving altered microbiota in disease development. The gut microbiota comprises diverse bacteria, fungal and viral components, which are critical in developing host immunity. Alterations in microbial abundance are known to exacerbate or attenuate immune responses in the gut microenvironment subsequently affecting the joints. Further, these changes can provide biomarkers for disease activity and outcome in RA. Most of the research till date has been focused on describing gut bacterial components in RA. Studies on gut mycobiome and virome components in RA are relatively new and burgeoning field. Given the paucity of mycobiome or virome specific studies in RA, this review, discusses the recent findings on alterations in gut bacterial, fungal, and viral components as well as their role in regulating the spectrum of immune-pathogenic events occurring in RA which might be explored in future as a potential therapeutic target. Further, we provide an overview on inter-kingdom interactions between bacteria, fungi, and viruses in RA. The current understanding on gut microbiota modulation for managing RA is also summarised.
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Affiliation(s)
| | | | | | | | | | | | - Lekha Rani
- Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Wang X, Geng S. Diet-gut microbial interactions influence cancer immunotherapy. Front Oncol 2023; 13:1138362. [PMID: 37035188 PMCID: PMC10081683 DOI: 10.3389/fonc.2023.1138362] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/16/2023] [Indexed: 04/11/2023] Open
Abstract
The gut microbiome is involved in the absorption and metabolism of host nutrients and modulates the immune response, affecting the efficacy of immunotherapy for cancer. In patients receiving immunotherapy, appropriate modifications of gut microbiota are thought to improve therapeutic response. Of all the factors that influence the gut microbiota, diet is the most influential and modifiable. Healthy dietary patterns as well as some specific dietary components can help the growth of beneficial microbiota in the gut, thereby protecting against cancers and promoting human health. A growing number of researches have confirmed the positive effects of a diet-gut microbiota approach as an adjuvant therapy for cancer, but controversy remains. Here, we summarize the interactions between diet and gut microbes based on previous studies, and discuss the role of gut microbiota-based dietary strategies in tumor immunotherapy, with the potential mechanisms of actions also intensively discussed.
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Affiliation(s)
- Xue Wang
- Department of Oncology, First People's Hospital of Guangyuan, Guangyuan, China
| | - Shitao Geng
- Department of Emergency, First Naval Hospital of Southern Theater Command, Zhanjiang, China
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30
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Friedrich I, Neubauer H, Kuritsyn A, Bodenberger B, Tskhay F, Hartmann S, Poehlein A, Bömeke M, Hoppert M, Schneider D, Hertel R, Daniel R. Brevundimonas and Serratia as host systems for assessing associated environmental viromes and phage diversity by complementary approaches. Front Microbiol 2023; 14:1095850. [PMID: 37025643 PMCID: PMC10070969 DOI: 10.3389/fmicb.2023.1095850] [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: 11/11/2022] [Accepted: 02/23/2023] [Indexed: 04/08/2023] Open
Abstract
Focusing on visible plaques for phage isolation leaves the question if we miss the diversity of non-plaque forming phages. We addressed this question through direct plaque-based isolation by employing the new hosts Brevundimonas pondensis LVF1 and Serratia marcescens LVF3 dsDNA, ssDNA, dsRNA, and ssRNA host-associated metavirome analysis. Of the 25 distinctive dsDNA phage isolates, 14 were associated with Brevundimonas and 11 with Serratia. TEM analysis revealed that 6 were myoviruses, 18 siphoviruses and 1 podovirus, while phages infecting Brevundimonas belonged all to siphoviruses. The associated viromes suggested a higher phage diversity in summer than in winter, and dsDNA phages were the dominant group. Isolation of vB_SmaP-Kaonashi was possible after investigating the viromes associated with Serratia, demonstrating the great potential of accompanying host-associated metavirome analysis. The ssDNA virome analysis showed that the B. pondensis LVF1 host is associated with Microviridae and Inoviridae phages, although none of them were isolated. The results demonstrated that the classical isolation technique is not exhausted, leading to the isolation of new dsDNA phages. It can be further improved by combination with metavirome techniques, which revealed further diversity.
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Affiliation(s)
- Ines Friedrich
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Hannes Neubauer
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Alisa Kuritsyn
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Bernhard Bodenberger
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Faina Tskhay
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Sara Hartmann
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Mechthild Bömeke
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Michael Hoppert
- General Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Robert Hertel
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- FG Synthetic Microbiology, Institute of Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- *Correspondence: Rolf Daniel,
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Borin JM, Liu R, Wang Y, Wu TC, Chopyk J, Huang L, Kuo P, Ghose C, Meyer JR, Tu XM, Schnabl B, Pride DT. Fecal virome transplantation is sufficient to alter fecal microbiota and drive lean and obese body phenotypes in mice. Gut Microbes 2023; 15:2236750. [PMID: 37475473 PMCID: PMC10364654 DOI: 10.1080/19490976.2023.2236750] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/10/2023] [Indexed: 07/22/2023] Open
Abstract
The gastrointestinal microbiome plays a significant role in modulating numerous host processes, including metabolism. Prior studies show that when mice receive fecal transplants from obese donors on high-fat diets (HFD) (even when recipient mice are fed normal diets after transplantation), they develop obese phenotypes, demonstrating the prominent role that gut microbiota play in determining lean and obese phenotypes. While much of the credit has been given to gut bacteria, the impact of gut viruses on these phenotypes is understudied. To address this shortcoming, we gavaged mice with viromes isolated from donors fed HFD or normal chow over a 4-week study. By characterizing the gut bacterial biota via 16S rRNA amplicon sequencing and measuring mouse weights over time, we demonstrate that transplanted viruses affect the gut bacterial community, as well as weight gain/loss. Notably, mice fed chow but gavaged with HFD-derived viromes gained more weight than their counterparts receiving chow-derived viromes. The converse was also true: mice fed HFD but gavaged with chow-derived viromes gained less weight than their counterparts receiving HFD-derived viromes. Results were replicated in two independent experiments and phenotypic changes were accompanied by significant and identifiable differences in the fecal bacterial biota. Due to methodological limitations, we were unable to identify the specific bacterial strains responsible for respective phenotypic changes. This study confirms that virome-mediated perturbations can alter the fecal microbiome in vivo and indicates that such perturbations are sufficient to drive lean and obese phenotypes in mice.
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Affiliation(s)
- Joshua M. Borin
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Roland Liu
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Yanhan Wang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tsung-Chin Wu
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Jessica Chopyk
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Lina Huang
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Peiting Kuo
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | | | - Justin R. Meyer
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Xin M. Tu
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - David T. Pride
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
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Huang Z, Liu K, Ma W, Li D, Mo T, Liu Q. The gut microbiome in human health and disease-Where are we and where are we going? A bibliometric analysis. Front Microbiol 2022; 13:1018594. [PMID: 36590421 PMCID: PMC9797740 DOI: 10.3389/fmicb.2022.1018594] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022] Open
Abstract
Background There are trillions of microbiota in our intestinal tract, and they play a significant role in health and disease via interacting with the host in metabolic, immune, neural, and endocrine pathways. Over the past decades, numerous studies have been published in the field of gut microbiome and disease. Although there are narrative reviews of gut microbiome and certain diseases, the whole field is lack of systematic and quantitative analysis. Therefore, we outline research status of the gut microbiome and disease, and present insights into developments and characteristics of this field to provide a holistic grasp and future research directions. Methods An advanced search was carried out in the Web of Science Core Collection (WoSCC), basing on the term "gut microbiome" and its synonyms. The current status and developing trends of this scientific domain were evaluated by bibliometric methodology. CiteSpace was used to perform collaboration network analysis, co-citation analysis and citation burst detection. Results A total of 29,870 articles and 13,311 reviews were retrieved from the database, which involve 42,900 keywords, 176 countries/regions, 19,065 institutions, 147,225 authors and 4,251 journals. The gut microbiome and disease research is active and has received increasing attention. Co-cited reference analysis revealed the landmark articles in the field. The United States had the largest number of publications and close cooperation with other countries. The current research mainly focuses on gastrointestinal diseases, such as inflammatory bowel disease (IBD), ulcerative colitis (UC) and Crohn's disease (CD), while extra-intestinal diseases are also rising, such as obesity, diabetes, cardiovascular disease, Alzheimer's disease, Parkinson's disease. Omics technologies, fecal microbiota transplantation (FMT) and metabolites linked to mechanism would be more concerned in the future. Conclusion The gut microbiome and disease has been a booming field of research, and the trend is expected to continue. Overall, this research field shows a multitude of challenges and great opportunities.
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Hashimi M, Sebrell T, Hedges J, Snyder D, Lyon K, Byrum S, Mackintosh SG, Cherne M, Skwarchuk D, Crowley D, Robison A, Sidar B, Kunze A, Loveday E, Taylor M, Chang C, Wilking J, Walk S, Schountz T, Jutila M, Bimczok D. Antiviral response mechanisms in a Jamaican Fruit Bat intestinal organoid model of SARS-CoV-2 infection. RESEARCH SQUARE 2022:rs.3.rs-2340919. [PMID: 36561186 PMCID: PMC9774215 DOI: 10.21203/rs.3.rs-2340919/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bats are natural reservoirs for several zoonotic viruses, potentially due to an enhanced capacity to control viral infection. However, the mechanisms of antiviral responses in bats are poorly defined. Here we established a Jamaican fruit bat (JFB) intestinal organoid model of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. JFB organoids were susceptible to SARS-CoV-2 infection, with increased viral RNA and subgenomic RNA detected in cell lysates and supernatants. Gene expression of type I interferons and inflammatory cytokines was induced in response to SARS-CoV-2 but not in response to TLR agonists. Interestingly, SARS-CoV-2 did not lead to cytopathic effects in JFB organoids but caused enhanced organoid growth. Proteomic analyses revealed an increase in inflammatory signaling, cell turnover, cell repair, and SARS-CoV-2 infection pathways. Collectively, our findings suggest that primary JFB intestinal epithelial cells can mount a successful antiviral interferon response and that SARS-CoV-2 infection in JFB cells induces protective regenerative pathways.
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Ottmann M. [These viruses that inhabit and visit us: The human virome]. Med Sci (Paris) 2022; 38:1028-1038. [PMID: 36692282 DOI: 10.1051/medsci/2022161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recent advances in new sequencing technologies have opened the way to the deciphering of human virome. So far, human virome is defined as the complete list of viruses found in human body. Those viruses could be endogenous, prokaryotic, archaeal and eukaryotic. In addition, each compartment of the human body constitutes a different microenvironment with its own virome. Viral infections can be categorized according to the outcome of the acute phase and until recently, only symptomatic and pathological infections were studied. It is now well established that a healthy person has an extremely diverse virome. This review summarizes the current state of our knowledge and also proposes another classification of the human virome based on principles of ecology.
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Affiliation(s)
- Michèle Ottmann
- Centre international de recherche en infectiologie (CIRI), université Claude Bernard-Lyon 1, université de Lyon, Inserm U1111 - CNRS UMR 5308 - ENS, Laboratoire de virologie et pathologies humaines, Faculté de médecine RTH Laennec, 7 rue Guillaume Paradin, 69372 Lyon cedex 08, France
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Characterization of a New Temperate Escherichia coli Phage vB_EcoP_ZX5 and Its Regulatory Protein. Pathogens 2022; 11:pathogens11121445. [PMID: 36558779 PMCID: PMC9782041 DOI: 10.3390/pathogens11121445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
The study of the interaction between temperate phages and bacteria is vital to understand their role in the development of human diseases. In this study, a novel temperate Escherichia coli phage, vB_EcoP_ZX5, with a genome size of 39,565 bp, was isolated from human fecal samples. It has a short tail and belongs to the genus Uetakevirus and the family Podoviridae. Phage vB_EcoP_ZX5 encodes three lysogeny-related proteins (ORF12, ORF21, and ORF4) and can be integrated into the 3'-end of guaA of its host E. coli YO1 for stable transmission to offspring bacteria. Phage vB_EcoP_ZX5 in lysogenized E. coli YO1+ was induced spontaneously, with a free phage titer of 107 PFU/mL. The integration of vB_EcoP_ZX5 had no significant effect on growth, biofilm, environmental stress response, antibiotic sensitivity, adherence to HeLa cells, and virulence of E. coli YO1. The ORF4 anti-repressor, ORF12 integrase, and ORF21 repressors that affect the lytic-lysogenic cycle of vB_EcoP_ZX5 were verified by protein overexpression. We could tell from changes of the number of total phages and the transcription level of phage genes that repressor protein is the key determinant of lytic-to-lysogenic conversion, and anti-repressor protein promotes the conversion from lysogenic cycle to lytic cycle.
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Ács N, Holohan R, Dunne LJ, Fernandes AR, Clooney AG, Draper LA, Ross RP, Hill C. Comparing In Vitro Faecal Fermentation Methods as Surrogates for Phage Therapy Application. Viruses 2022; 14:v14122632. [PMID: 36560636 PMCID: PMC9786711 DOI: 10.3390/v14122632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
The human microbiome and its importance in health and disease have been the subject of numerous research articles. Most microbes reside in the digestive tract, with up to 1012 cells per gram of faecal material found in the colon. In terms of gene number, it has been estimated that the gut microbiome harbours >100 times more genes than the human genome. Several human intestinal diseases are strongly associated with disruptions in gut microbiome composition. Less studied components of the gut microbiome are the bacterial viruses called bacteriophages that may be present in numbers equal to or greater than the prokaryotes. Their potential to lyse their bacterial hosts, or to act as agents of horizontal gene transfer makes them important research targets. In this study in vitro faecal fermentation systems were developed and compared for their ability to act as surrogates for the human colon. Changes in bacterial and viral composition occurred after introducing a high-titre single phage preparation both with and without a known bacterial host during the 24 h-long fermentation. We also show that during this timeframe 50 mL plastic tubes can provide data similar to that generated in a sophisticated faecal fermenter system. This knowledge can guide us to a better understanding of the short-term impact of bacteriophage transplants on the bacteriomes and viromes of human recipients.
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Affiliation(s)
- Norbert Ács
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | - Ross Holohan
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | - Laura J. Dunne
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | | | - Adam G. Clooney
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | | | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
- Correspondence:
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Abstract
PURPOSE OF REVIEW Recent years have seen great strides made in the field of viral metagenomics. Many studies have reported alterations in the virome in different disease states. The vast majority of the human intestinal virome consists of bacteriophages, viruses that infect bacteria. The dynamic relationship between gut bacterial populations and bacteriophages is influenced by environmental factors that also impact host health and disease. In this review, we focus on studies highlighting the dynamics of the gut virome and fluctuations associated with disease states. RECENT FINDINGS Novel correlations have been identified between the human gut virome and diseases such as obesity, necrotizing enterocolitis and severe acute respiratory syndrome coronavirus 2 infection. Further associations between the virome and cognition, diet and geography highlight the complexity of factors that can influence the dynamic relationship between gut bacteria, bacteriophages and health. SUMMARY Here, we highlight some novel associations between the virome and health that will be the foundation for future studies in this field. The future development of microbiome-based interventions, identification of biomarkers, and novel therapeutics will require a thorough understanding of the gut virome and its dynamics.
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Affiliation(s)
- Hiba Shareefdeen
- APC Microbiome Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland.,School of Microbiology, University College Cork, Cork, Ireland
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Radzikowska U, Baerenfaller K, Cornejo‐Garcia JA, Karaaslan C, Barletta E, Sarac BE, Zhakparov D, Villaseñor A, Eguiluz‐Gracia I, Mayorga C, Sokolowska M, Barbas C, Barber D, Ollert M, Chivato T, Agache I, Escribese MM. Omics technologies in allergy and asthma research: An EAACI position paper. Allergy 2022; 77:2888-2908. [PMID: 35713644 PMCID: PMC9796060 DOI: 10.1111/all.15412] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 01/27/2023]
Abstract
Allergic diseases and asthma are heterogenous chronic inflammatory conditions with several distinct complex endotypes. Both environmental and genetic factors can influence the development and progression of allergy. Complex pathogenetic pathways observed in allergic disorders present a challenge in patient management and successful targeted treatment strategies. The increasing availability of high-throughput omics technologies, such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics allows studying biochemical systems and pathophysiological processes underlying allergic responses. Additionally, omics techniques present clinical applicability by functional identification and validation of biomarkers. Therefore, finding molecules or patterns characteristic for distinct immune-inflammatory endotypes, can subsequently influence its development, progression, and treatment. There is a great potential to further increase the effectiveness of single omics approaches by integrating them with other omics, and nonomics data. Systems biology aims to simultaneously and longitudinally understand multiple layers of a complex and multifactorial disease, such as allergy, or asthma by integrating several, separated data sets and generating a complete molecular profile of the condition. With the use of sophisticated biostatistics and machine learning techniques, these approaches provide in-depth insight into individual biological systems and will allow efficient and customized healthcare approaches, called precision medicine. In this EAACI Position Paper, the Task Force "Omics technologies in allergic research" broadly reviewed current advances and applicability of omics techniques in allergic diseases and asthma research, with a focus on methodology and data analysis, aiming to provide researchers (basic and clinical) with a desk reference in the field. The potential of omics strategies in understanding disease pathophysiology and key tools to reach unmet needs in allergy precision medicine, such as successful patients' stratification, accurate disease prognosis, and prediction of treatment efficacy and successful prevention measures are highlighted.
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Affiliation(s)
- Urszula Radzikowska
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Christine‐Kühne Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Katja Baerenfaller
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - José Antonio Cornejo‐Garcia
- Research LaboratoryIBIMA, ARADyAL Instituto de Salud Carlos III, Regional University Hospital of Málaga, UMAMálagaSpain
| | - Cagatay Karaaslan
- Department of Biology, Molecular Biology SectionFaculty of ScienceHacettepe UniversityAnkaraTurkey
| | - Elena Barletta
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - Basak Ezgi Sarac
- Department of Biology, Molecular Biology SectionFaculty of ScienceHacettepe UniversityAnkaraTurkey
| | - Damir Zhakparov
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - Alma Villaseñor
- Centre for Metabolomics and Bioanalysis (CEMBIO)Department of Chemistry and BiochemistryFacultad de FarmaciaUniversidad San Pablo‐CEU, CEU UniversitiesMadridSpain,Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | - Ibon Eguiluz‐Gracia
- Allergy UnitHospital Regional Universitario de MálagaMálagaSpain,Allergy Research GroupInstituto de Investigación Biomédica de Málaga‐IBIMAMálagaSpain
| | - Cristobalina Mayorga
- Allergy UnitHospital Regional Universitario de MálagaMálagaSpain,Allergy Research GroupInstituto de Investigación Biomédica de Málaga‐IBIMAMálagaSpain,Andalusian Centre for Nanomedicine and Biotechnology – BIONANDMálagaSpain
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Christine‐Kühne Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO)Department of Chemistry and BiochemistryFacultad de FarmaciaUniversidad San Pablo‐CEU, CEU UniversitiesMadridSpain
| | - Domingo Barber
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | - Markus Ollert
- Department of Infection and ImmunityLuxembourg Institute of HealthyEsch‐sur‐AlzetteLuxembourg,Department of Dermatology and Allergy CenterOdense Research Center for AnaphylaxisOdense University Hospital, University of Southern DenmarkOdenseDenmark
| | - Tomas Chivato
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain,Department of Clinic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | | | - Maria M. Escribese
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
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Crosstalk between the Intestinal Virome and Other Components of the Microbiota, and Its Effect on Intestinal Mucosal Response and Diseases. J Immunol Res 2022; 2022:7883945. [PMID: 36203793 PMCID: PMC9532165 DOI: 10.1155/2022/7883945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
In recent years, there has been ample evidence illustrating the effect of microbiota on gut immunity, homeostasis, and disease. Most of these studies have engaged more efforts in understanding the role of the bacteriome in gut mucosal immunity and disease. However, studies on the virome and its influence on gut mucosal immunity and pathology are still at infancy owing to limited metagenomic tools. Nonetheless, the existing studies on the virome have largely been focused on the bacteriophages as these represent the main component of the virome with little information on endogenous retroviruses (ERVs) and eukaryotic viruses. In this review, we describe the gut virome, and its role in gut mucosal response and disease progression. We also explore the crosstalk between the virome and other microorganisms in the gut mucosa and elaborate on how these interactions shape the gut mucosal immunity going from bacteriophages through ERVs to eukaryotic viruses. Finally, we elucidate the potential contribution of this crosstalk in the pathogenesis of inflammatory bowel diseases and colon cancer.
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Xiao G, Zheng L, Yan X, Gong L, Yang Y, Qi Q, Zhang X, Zhang H. Effects of Dietary Essential Oils Supplementation on Egg Quality, Biochemical Parameters, and Gut Microbiota of Late-Laying Hens. Animals (Basel) 2022; 12:ani12192561. [PMID: 36230302 PMCID: PMC9558990 DOI: 10.3390/ani12192561] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
The objective of this study was to explore the effects of adding essential oils (EO) to diets on egg quality, biochemical parameters and intestinal flora of late laying hens. The number of 252 Dawu Golden Phoenix laying hens (55 weeks old) were randomly sorted into two groups: the control group (CG) fed a basal diet and the EO group fed a basal diet with 300 mg/kg of essential oils. The average egg weight, feed-to-egg ratio, and egg production rate were determined every week. The trial started at week 55 and lasted for 8 weeks. During the experiment’s last week, 36 eggs out of each group were chosen at random to test. In our study, dietary supplementation with EO considerably decreased the egg breaking rate (p = 0.01) and increased the shell-breaking strength (p = 0.04). The treatment group’s alanine aminotransferase (ALT) levels were considerably lower than those of the control group (p = 0.03). The EO group had substantially higher total antioxidant capacity (T-AOC) and total superoxide dismutase (T-SOD) (p = 0.04 and p =0.03, respectively). However, there were no differences in alpha diversity indicators between the two groups. It is worth noting that Firmicutes were increased considerably (p < 0.05), while Spirochaetota and Proteobacteria were significantly reduced in the EO group. At genus levels, the EO supplementation increased the relative abundance of Intestinimonas (p < 0.05) and Megamonas (p < 0.01). In conclusion, a dietary supplementation of 300 mg/kg EO can improve the production performance of laying hens and the egg quality. It can also regulate the abundance of cecal flora and serum biochemical indicators.
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Affiliation(s)
- Gengsheng Xiao
- School of Life Science and Engineering, Foshan University, Foshan 528000, China
| | - Liwei Zheng
- Guangdong Guangken Animal Husbandry Engineering Research Institute, Guangzhou 510000, China
| | - Xia Yan
- Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510000, China
| | - Li Gong
- School of Life Science and Engineering, Foshan University, Foshan 528000, China
| | - Yang Yang
- School of Life Science and Engineering, Foshan University, Foshan 528000, China
| | - Qien Qi
- School of Life Science and Engineering, Foshan University, Foshan 528000, China
| | - Xiangbin Zhang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (X.Z.); (H.Z.)
| | - Huihua Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528000, China
- Correspondence: (X.Z.); (H.Z.)
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Xiao G, Liu S, Yan X, Yang Y, Qi Q, Feng X, Gong L, Zhang H. Effects of fulvic acid addition on laying performance, biochemical indices, and gut microbiota of aged hens. Front Vet Sci 2022; 9:953564. [PMID: 36118354 PMCID: PMC9479332 DOI: 10.3389/fvets.2022.953564] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
The purpose of this study was to appraise the effect of fulvic acid on production, biochemical indices, and gut microbiota of laying hens. A total of 252 Dawu Golden Phoenix laying hens (55-week-old) were allotted to two treatments randomly, each with six replicates and 21 hens per replicate, including the control group (CG) and fulvic acid (500 mg/kg) group (FA). The trial period was 8 weeks. Adding FA raised egg weight (P = 0.03), shell-breaking strength (P = 0.03), and reduced egg breaking rate (P < 0.01), compared with CG. There was no difference in eggshell thickness and egg shape index between the two treatments; however, the FA group increased egg production by 1.45% and reduced the feed-to-egg ratio by 0.09. Moreover, dietary FA decreased the aspartate aminotransferase levels in serum (P = 0.04), and glutathione peroxidase and total antioxidant capacity were increased (P = 0.02 and 0.04, respectively). Despite this, the two groups had no differences in the alpha diversity indices (PD_whole trees, Shannon, Ace, Simpson, Chao1, and goods_coverage). Obviously, at the phylum level, the abundances of Firmicutes were improved (P < 0.01), Actinobacteriota (P < 0.01), and Proteobacteria (P < 0.01) were reduced by dietary FA. Supplementation with FA could improve the abundances of Megamonas (P < 0.01) and reduce Enterobacter (P < 0.01) at the genus level. To sum up, this study showed the addition of 500 mg/kg FA may boost production and egg quality and modulate the cecal microflora abundance and serum biochemical indices of laying hens.
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Affiliation(s)
- Gengsheng Xiao
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Shun Liu
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Xia Yan
- State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yang Yang
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Qien Qi
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Xin Feng
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Li Gong
- School of Life Science and Engineering, Foshan University, Foshan, China
- *Correspondence: Huihua Zhang
| | - Huihua Zhang
- School of Life Science and Engineering, Foshan University, Foshan, China
- Li Gong
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Tao S, Zou H, Li J, Wei H. Landscapes of Enteric Virome Signatures in Early-Weaned Piglets. Microbiol Spectr 2022; 10:e0169822. [PMID: 35913177 PMCID: PMC9430488 DOI: 10.1128/spectrum.01698-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022] Open
Abstract
Diarrhea caused by early-weaning-induced stress can increase mortality rates and reduce growth performance of piglets, seriously harming the livestock industry. To date, studies on the gut microbiome of early-weaned piglets have focused almost exclusively on bacteria, while studies on their gut virome are extremely lacking. Here, we used metagenomic and metatranscriptomic sequencing combined with bioinformatic analysis techniques to preliminarily characterize the intestinal virome of early-weaned piglets at different biological classification levels. The alpha diversity of enteroviruses was generally elevated in early-weaned piglets with diarrhea, compared to healthy piglets, whereas the two groups of piglets showed no significant difference in beta diversity. In addition, the species compositions of the gut virome were similar between healthy piglets and piglets with diarrhea, while their respective dominant species were somewhat different. We also identified 58 differential DNA viruses and 16 differential RNA viruses between the two groups of piglets at all biological taxonomic levels. Of these, 1 (family Dhakavirus) and 6 (phylum Artverviricota, class Revtraviricetes, order Ortervirales, family Retroviridae, genus Gammaretrovirus, and species Kirsten murine sarcoma virus) specific viruses disappeared from the intestines of healthy piglets and piglets with diarrhea, respectively. Moreover, we found that some DNA and RNA viruses formed strong correlations among themselves or between them. IMPORTANCE This study systematically reveals the biological diversity, structure, and composition of intestinal DNA and RNA virus profiles in early-weaned piglets. Furthermore, characteristics of differences in gut viromes between early-weaned healthy piglets and piglets with diarrhea were also elucidated. Importantly, some potential biomarkers for early-weaned piglets with diarrhea were identified. These findings fill a gap for the early-weaned piglet gut virome and lay the foundation for the development of strategies to target enteroviruses for the prevention and treatment of early-weaning-induced piglet diarrhea.
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Affiliation(s)
- Shiyu Tao
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huicong Zou
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jingjing Li
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hong Wei
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
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Ma F, Huo Y, Li H, Yang F, Liao J, Han Q, Li Y, Pan J, Hu L, Guo J, Tang Z. New insights into the interaction between duodenal toxicity and microbiota disorder under copper exposure in chicken: Involving in endoplasmic reticulum stress and mitochondrial toxicity. Chem Biol Interact 2022; 366:110132. [PMID: 36030842 DOI: 10.1016/j.cbi.2022.110132] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 12/17/2022]
Abstract
Copper (Cu) has been widely used in industrial agricultural production, but excess use can lead to toxic effect on host physiology, which poses a threaten to public hygiene. However, the relationship between gut microbiota and Cu-induced intestinal toxicity is unclear. Here, we identified that intestinal flora disturbance was related to duodenal toxicity under Cu exposure. We found that excess Cu disturbed gut microbiota homeostasis, resulting in Cu accumulation and intestinal damage. In addition, Cu considerably increased intestinal permeability by reducing expression of tight junction proteins (Claudlin-1, Occludin, and ZO-1). Meanwhile, Cu could induce endoplasmic reticulum stress, mitophagy, and mitochondria-mediated apoptosis in the duodenum, with the evidence by the elevated levels of GRP78, GRP94, LC3Ⅱ/LC3Ⅰ and Caspase-3 protein expression. Correlation analysis showed that Melainabacteria was closely related to tight junction proteins and endoplasmic reticulum stress of duodenum, indicating that disturbance of intestinal flora may aggravate the toxic effect of Cu. Therefore, our results suggest that the destruction of intestinal flora induced by excessive Cu may further lead to intestinal barrier damage, ultimately leading to endoplasmic reticulum stress, mitophagy and apoptosis. This research provides a new insight into interpretation of the interrelationship between microbiota disorder and duodenal toxicity under Cu exposure.
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Affiliation(s)
- Feiyang Ma
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Yihui Huo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Huayu Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Fan Yang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jianzhao Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Qingyue Han
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Ying Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Jiaqiang Pan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Lianmei Hu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Jianying Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Zhaoxin Tang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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Yamashina T, Shimatani M, Takeo M, Sasaki K, Orino M, Saito N, Matsumoto H, Kasai T, Kano M, Horitani S, Sumimoto K, Mitsuyama T, Yuba T, Seki T, Naganuma M. Viral Infection in Esophageal, Gastric, and Colorectal Cancer. Healthcare (Basel) 2022; 10:healthcare10091626. [PMID: 36141238 PMCID: PMC9498567 DOI: 10.3390/healthcare10091626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/09/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
The human gastrointestinal tract, which constitutes the digestive system, contains a large number of virus particles that maintain organizational homeostasis and health. Conversely, viral pathogens have also attracted attention for their involvement in the pathogenesis of certain cancers, including gastrointestinal cancers. To aid prevention and treatment of these cancers, the relevance of gastrointestinal viral factors as potential risk factors needs to be carefully investigated. This review summarizes and discusses the available literature on the relationship between the development of esophageal, gastric, and colorectal cancers and their corresponding viruses. This review reveals that research on the association between colorectal cancer and viruses, in particular, is still in its infancy compared to the association between HPV and esophageal cancer and between EBV and gastric cancer.
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Affiliation(s)
- Takeshi Yamashina
- Department of Gastroenterology and Hepatology, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
| | - Masaaki Shimatani
- Department of Gastroenterology and Hepatology, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
- Correspondence: ; Tel.: +81-6-6992-1001; Fax: +81-6-6993-9677
| | - Masahiro Takeo
- Department of Gastroenterology and Hepatology, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
| | - Kotaro Sasaki
- Department of Gastroenterology and Hepatology, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
| | - Masahiro Orino
- Department of Gastroenterology and Hepatology, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
| | - Natsuko Saito
- Department of Gastroenterology and Hepatology, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
| | - Hironao Matsumoto
- Department of Gastroenterology and Hepatology, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
| | - Takeshi Kasai
- Department of Gastroenterology and Hepatology, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
| | - Masataka Kano
- Department of Gastroenterology and Hepatology, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
| | - Shunsuke Horitani
- Department of Gastroenterology and Hepatology, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
| | - Kimi Sumimoto
- Department of Gastroenterology and Hepatology, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
| | - Toshiyuki Mitsuyama
- Department of Gastroenterology and Hepatology, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
| | - Takafumi Yuba
- Department of Gastroenterology and Hepatology, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
| | - Toshihito Seki
- Division of Liver Disease Center, Kansai Medical University Medical Center, Moriguchi 570-8507, Osaka, Japan
| | - Makoto Naganuma
- The Third Department of Internal Medicine, Kansai Medical University, Hirakata 573-1010, Osaka, Japan
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45
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Huang L, Wu X, Guo S, Lv Y, Zhou P, Huang G, Duan Z, Sun W. Metagenomic-based characterization of the gut virome in patients with polycystic ovary syndrome. Front Microbiol 2022; 13:951782. [PMID: 36051758 PMCID: PMC9424824 DOI: 10.3389/fmicb.2022.951782] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/27/2022] [Indexed: 11/18/2022] Open
Abstract
Background Polycystic ovary syndrome (PCOS) is a complex disease that afflicts women of reproductive age, and its pathological mechanism has not been well explained. The gut microbiota is believed to be closely related to the development of PCOS. Although an important component of the gut microbiome, the role of the gut virome in the development of PCOS is still unclear. Methods In this study, we profiled and compared the gut viral community of 50 patients with PCOS and 43 healthy women based on the analysis of their fecal whole-metagenome dataset. Results The gut virome of PCOS patients exhibited a significant decrease in within-sample viral diversity and a remarkable alteration of the overall virome composition compared with that of healthy controls. At the family level, Siphoviridae was significantly depleted in the gut virome of patients, while Quimbyviridae was enriched. We identified 1,089 viral operational taxonomic units (vOTUs) that differed in relative abundance between the two groups, of which 455 vOTUs were enriched in PCOS patients (including numerous Bacteroidaceae phages) and 634 were enriched in controls (including numerous viruses predicted to infect Oscillospiraceae, Prevotellaceae, and Ruminococcaceae). Functional comparison of the PCOS-enriched and control-enriched vOTUs uncovered the viral functional signatures associated with PCOS. Furthermore, we demonstrated gut viral signatures for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of 0.938, demonstrating the potential of the gut virome in the prediction of PCOS. Conclusion Our findings reveal specific alterations in viral diversity and taxonomic and functional compositions of the gut virome of PCOS patients. Further studies on the etiology of PCOS and the gut viral community will offer new prospects for treating and preventing PCOS and its related diseases.
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Affiliation(s)
- Liansha Huang
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Xiaoling Wu
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Shumin Guo
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Ying Lv
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Peng Zhou
- Department of Acupuncture, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Guangrong Huang
- Department of Gynecology, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Zuzhen Duan
- Department of Gynecology, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Wen Sun
- Key Laboratory of Health Cultivation of the Ministry of Education, Beijing University of Chinese Medicine, Beijing, China
- Beijing key Laboratory of Health Cultivation, Beijing University of Chinese Medicine, Beijing, China
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Wen Sun,
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Chitcharoen S, Sivapornnukul P, Payungporn S. Revolutionized virome research using systems microbiology approaches. Exp Biol Med (Maywood) 2022; 247:1135-1147. [PMID: 35723062 PMCID: PMC9335507 DOI: 10.1177/15353702221102895] [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] [Indexed: 01/03/2023] Open
Abstract
Currently, both pathogenic and commensal viruses are continuously being discovered and acknowledged as ubiquitous components of microbial communities. The advancements of systems microbiological approaches have changed the face of virome research. Here, we focus on viral metagenomic approach to study virus community and their interactions with other microbial members as well as their hosts. This review also summarizes challenges, limitations, and benefits of the current virome approaches. Potentially, the studies of virome can be further applied in various biological and clinical fields.
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Affiliation(s)
- Suwalak Chitcharoen
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand,Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavaret Sivapornnukul
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Sunchai Payungporn.
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47
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Shkoporov AN, Turkington CJ, Hill C. Mutualistic interplay between bacteriophages and bacteria in the human gut. Nat Rev Microbiol 2022; 20:737-749. [PMID: 35773472 DOI: 10.1038/s41579-022-00755-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 12/12/2022]
Abstract
Bacteriophages (phages) are often described as obligate predators of their bacterial hosts, and phage predation is one of the leading forces controlling the density and distribution of bacterial populations. Every 48 h half of all bacteria on Earth are killed by phages. Efficient killing also forms the basis of phage therapy in humans and animals and the use of phages as food preservatives. In turn, bacteria have a plethora of resistance systems against phage attack, but very few bacterial species, if any, have entirely escaped phage predation. However, in complex communities and environments such as the human gut, this antagonistic model of attack and counter-defence does not fully describe the scope of phage-bacterium interactions. In this Review, we explore some of the more mutualistic aspects of phage-bacterium interactions in the human gut, and we suggest that the relationship between phages and their bacterial hosts in the gut is best characterized not as a fight to the death between enemies but rather as a mutualistic relationship between partners.
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Affiliation(s)
- Andrey N Shkoporov
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland. .,Department of Medicine, University College Cork, Cork, Ireland.
| | | | - Colin Hill
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland.
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48
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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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49
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Smith SE, Huang W, Tiamani K, Unterer M, Khan Mirzaei M, Deng L. Emerging technologies in the study of the virome. Curr Opin Virol 2022; 54:101231. [DOI: 10.1016/j.coviro.2022.101231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 11/03/2022]
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50
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Association of Gut Microbiota with Inflammatory Bowel Disease and COVID-19 Severity: A Possible Outcome of the Altered Immune Response. Curr Microbiol 2022; 79:184. [PMID: 35508737 PMCID: PMC9068506 DOI: 10.1007/s00284-022-02877-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 04/12/2022] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease could be induced by SARS-CoV-2, involved in alteration of gut microbiota during the respiratory viral infection. Presence of viral RNA in fecal samples for longer period, even after the clearance of the virus from respiratory tract, is suggestive of dysbiosis leading to the poor prognosis of COVID-19 in hospitalized patients. Gut microbiome (GM) plays a significant role to stimulate the modulated antiviral immune response against invading pathogens regulating the physiological homeostasis. GM profile of COVID-19 patients has revealed the drastic depletion of dominant families of commensals in the gut such as, Bacteroidaceae, Lachnospiraceae and Ruminococcaceae to be replaced with Enterococcus, Staphylococcus, Streptococcus, Serratia etc. Immune dysfunction of Th1–Th17 cells along gut-lung axis impairs the mucosal lining translocating the microorganisms including commensals and metabolites to other body organs like lungs, brain, kidney through circulation. These events may cause hyper inflammations associated with excessive secretion of cytokines and chemokines to form the cytokine storm causing ARDS. Gut virome could interact with microbiome and immune cells, help establishing the antiviral immune signaling, important for health maintenance/ or in disease progression. Essentially, these immunological strategies are needed to use in future prospective therapeutics to control the severity events.
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