51
|
Sutcliffe SG, Reyes A, Maurice CF. Bacteriophages playing nice: Lysogenic bacteriophage replication stable in the human gut microbiota. iScience 2023; 26:106007. [PMID: 36798434 PMCID: PMC9926308 DOI: 10.1016/j.isci.2023.106007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 10/28/2022] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Bacteriophages, viruses specific to bacteria, coexist with their bacterial hosts with limited diversity fluctuations in the guts of healthy individuals where they replicate mostly via lysogenic replication. This favors 'piggy-back-the-winner' over 'kill-the-winner' dynamics which are driven by lytic bacteriophage replication. Revisiting the deep-viral sequencing data of a healthy individual sampled over 2.4 years, we explore how these dynamics occur. Prophages found in assembled bacterial metagenomes were also found extra-cellularly, as induced phage particles (iPPs), likely derived from prophage activation. These iPPs were diverse and continually present in low abundance, relative to the highly abundant but less diverse lytic phage population. The continuous detection of low levels of iPPs suggests that spontaneous induction regularly occurs in this healthy individual, possibly allowing prophages to maintain their ability to replicate and avoiding degradation and loss from the gut microbiota.
Collapse
Affiliation(s)
- Steven G. Sutcliffe
- McGill Centre for Microbiome Research, McGill University, Montreal, QC, Canada,Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA,Corresponding author
| | - Corinne F. Maurice
- McGill Centre for Microbiome Research, McGill University, Montreal, QC, Canada,Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada,Corresponding author
| |
Collapse
|
52
|
Chen C, Yan Q, Yao X, Li S, Lv Q, Wang G, Zhong Q, Tang F, Liu Z, Huang Y, An Y, Zhou J, Zhang Q, Zhang A, Ullah H, Zhang Y, Liu C, Zhu D, Li H, Sun W, Ma W. Alterations of the gut virome in patients with systemic lupus erythematosus. Front Immunol 2023; 13:1050895. [PMID: 36713446 PMCID: PMC9874095 DOI: 10.3389/fimmu.2022.1050895] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Background Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that has been linked to the dysbiosis of the gut microbiome and virome. However, the potential characterization of the gut virome in SLE patients needs to be explored more extensively. Methods Herein, we analyzed the gut viral community of 16 SLE patients and 31 healthy controls using both bulk and virus-like particle (VLP)-based metagenomic sequencing of their fecal samples. A total of 15,999 non-redundant viral operational taxonomic units (vOTUs) were identified from the metagenomic assembled contigs and used for gut virome profiling. Results SLE patients exhibited a significant decrease in gut viral diversity in the bulk metagenome dataset, but this change was not significant in the VLP metagenome dataset. Also, considerable alterations of the overall gut virome composition and remarkable changes in the viral family compositions were observed in SLE patients compared with healthy controls, as observed in both two technologies. We identified 408 vOTUs (177 SLE-enriched and 231 control-enriched) with significantly different relative abundances between patients and controls in the bulk virome, and 18 vOTUs (17 SLE-enriched in 1 control-enriched) in the VLP virome. The SLE-enriched vOTUs included numerous Siphoviridae, Microviridae, and crAss-like viruses and were frequently predicted to infect Bacteroides, Parabacteroides, and Ruminococcus_E, while the control-enriched contained numerous members of Siphoviridae and Myoviridae and were predicted to infect Prevotella and Lachnospirales_CAG-274. We explored the correlations between gut viruses and bacteria and found that some Lachnospirales_CAG-274 and Hungatella_A phages may play key roles in the virus-bacterium network. Furthermore, we explored the gut viral signatures for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of above 0.95, suggesting the potential of the gut virome in the prediction of SLE. Conclusion Our findings demonstrated the alterations in viral diversity and taxonomic composition of the gut virome of SLE patients. Further research into the etiology of SLE and the gut viral community will open up new avenues for treating and preventing SLE and other autoimmune diseases.
Collapse
Affiliation(s)
- Changming Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Xueming Yao
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | | | - Qingbo Lv
- Puensum Genetech Institute, Wuhan, China,College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Qin Zhong
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Fang Tang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Zhengqi Liu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Ying Huang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yang An
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jing Zhou
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiongyu Zhang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | | | - Hayan Ullah
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, China
| | - Can Liu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Dan Zhu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hufan Li
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Wen Sun
- Key Laboratory of Health Cultivation of the Ministry of Education, Beijing University of Chinese Medicine, Beijing, China,*Correspondence: Wen Sun, ; Wukai Ma,
| | - Wukai Ma
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China,*Correspondence: Wen Sun, ; Wukai Ma,
| |
Collapse
|
53
|
Rothschild-Rodriguez D, Hedges M, Kaplan M, Karav S, Nobrega FL. Phage-encoded carbohydrate-interacting proteins in the human gut. Front Microbiol 2023; 13:1083208. [PMID: 36687636 PMCID: PMC9853417 DOI: 10.3389/fmicb.2022.1083208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/14/2022] [Indexed: 01/09/2023] Open
Abstract
In the human gastrointestinal tract, the gut mucosa and the bacterial component of the microbiota interact and modulate each other to accomplish a variety of critical functions. These include digestion aid, maintenance of the mucosal barrier, immune regulation, and production of vitamins, hormones, and other metabolites that are important for our health. The mucus lining of the gut is primarily composed of mucins, large glycosylated proteins with glycosylation patterns that vary depending on factors including location in the digestive tract and the local microbial population. Many gut bacteria have evolved to reside within the mucus layer and thus encode mucus-adhering and -degrading proteins. By doing so, they can influence the integrity of the mucus barrier and therefore promote either health maintenance or the onset and progression of some diseases. The viral members of the gut - mostly composed of bacteriophages - have also been shown to have mucus-interacting capabilities, but their mechanisms and effects remain largely unexplored. In this review, we discuss the role of bacteriophages in influencing mucosal integrity, indirectly via interactions with other members of the gut microbiota, or directly with the gut mucus via phage-encoded carbohydrate-interacting proteins. We additionally discuss how these phage-mucus interactions may influence health and disease states.
Collapse
Affiliation(s)
| | - Morgen Hedges
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Merve Kaplan
- Department of Molecular Biology and Genetics, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Sercan Karav
- Department of Molecular Biology and Genetics, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Franklin L. Nobrega
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom,*Correspondence: Franklin L. Nobrega, ✉
| |
Collapse
|
54
|
Cervantes-Echeverría M, Gallardo-Becerra L, Cornejo-Granados F, Ochoa-Leyva A. The Two-Faced Role of crAssphage Subfamilies in Obesity and Metabolic Syndrome: Between Good and Evil. Genes (Basel) 2023; 14:139. [PMID: 36672880 PMCID: PMC9858991 DOI: 10.3390/genes14010139] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/27/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Viral metagenomic studies of the human gut microbiota have unraveled the differences in phage populations between health and disease, stimulating interest in phages' role on bacterial ecosystem regulation. CrAssphage is a common and abundant family in the gut virome across human populations. Therefore, we explored its role in obesity (O) and obesity with metabolic syndrome (OMS) in a children's cohort. We found a significantly decreased prevalence, diversity, and richness of the crAssphage Alpha subfamily in OMS mainly driven by a decrease in the Alpha_1 and Alpha_4 genera. On the contrary, there was a significant increase in the Beta subfamily in OMS, mainly driven by an increase in Beta_6. Additionally, an overabundance of the Delta_8 genus was observed in OMS. Notably, a decreased abundance of crAssphages was significantly correlated with the overabundance of Bacilli in the same group. The Bacilli class is a robust taxonomical biomarker of O and was also significantly abundant in our OMS cohort. Our results suggest that a loss of stability in the Alpha subfamily of crAssphages is associated with O and OMS. Contrary, an overabundance of the Delta subfamily was found in OMS. Our study advises the importance of considering the dual role (good and evil) of crAssphage subfamilies and their participation in conditions such as O, where we suggest that Alpha loss and Delta gain are associated with obese individuals.
Collapse
Affiliation(s)
| | | | | | - Adrian Ochoa-Leyva
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico
| |
Collapse
|
55
|
Yan A, Butcher J, Schramm L, Mack DR, Stintzi A. Multiomic spatial analysis reveals a distinct mucosa-associated virome. Gut Microbes 2023; 15:2177488. [PMID: 36823020 PMCID: PMC9980608 DOI: 10.1080/19490976.2023.2177488] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The human gut virome has been increasingly explored in recent years. However, nearly all virome-sequencing efforts rely solely on fecal samples and few studies leverage multiomic approaches to investigate phage-host relationships. Here, we combine metagenomics, metaviromics, and metatranscriptomics to study virome-bacteriome interactions at the colonic mucosal-luminal interface in a cohort of three individuals with inflammatory bowel disease; non-IBD controls were not included in this study. We show that the mucosal viral population is distinct from the stool virome and houses abundant crAss-like phages that are undetectable by fecal sampling. Through viral protein prediction and metatranscriptomic analysis, we explore viral gene transcription, prophage activation, and the relationship between the presence of integrase and temperate phages in IBD subjects. We also show the impact of deep sequencing on virus recovery and offer guidelines for selecting optimal sequencing depths in future metaviromic studies. Systems biology approaches such as those presented in this report will enhance our understanding of the human virome and its interactions with our microbiome and our health.
Collapse
Affiliation(s)
- Austin Yan
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - James Butcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Laetitia Schramm
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - David R. Mack
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada,Inflammatory Bowel Disease Centre and CHEO Research Institute, Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada,CONTACT Alain Stintzi Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| |
Collapse
|
56
|
S A, K G, A AM. Intermodulation of gut-lung axis microbiome and the implications of biotics to combat COVID-19. J Biomol Struct Dyn 2022; 40:14262-14278. [PMID: 34699326 DOI: 10.1080/07391102.2021.1994875] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The novel coronavirus disease pandemic caused by the COVID-19 virus has infected millions of people around the world with a surge in transmission and mortality rates. Although it is a respiratory viral infection that affects airway epithelial cells, a diverse set of complications, including cytokine storm, gastrointestinal disorders, neurological distress, and hyperactive immune responses have been reported. However, growing evidence indicates that the bidirectional crosstalk of the gut-lung axis can decipher the complexity of the disease. Though not much research has been focused on the gut-lung axis microbiome, there is a translocation of COVID-19 infection from the lung to the gut through the lymphatic system resulting in disruption of gut permeability and its integrity. It is believed that detailed elucidation of the gut-lung axis crosstalk and the role of microbiota can unravel the most significant insights on the discovery of diagnosis using microbiome-based-therapeutics for COVID-19. This review calls attention to relate the influence of dysbiosis caused by COVID-19 and the involvement of the gut-lung axis. It presents first of its kind details that concentrate on the momentousness of biotics in disease progression and restoration. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Aishwarya S
- Department of Bioinformatics, Stella Maris College, Chennai, India.,Centre for Advanced Studies in Crystallography and Biophysics, University of Madras, Chennai, India
| | - Gunasekaran K
- Centre for Advanced Studies in Crystallography and Biophysics, University of Madras, Chennai, India
| | - Anita Margret A
- Department of Biotechnology and Bioinformatics, Bishop Heber College, Tiruchirappalli, Tamil Nadu, India
| |
Collapse
|
57
|
Mochochoko BM, Pohl CH, O’Neill HG. Candida albicans-enteric viral interactions-The prostaglandin E 2 connection and host immune responses. iScience 2022; 26:105870. [PMID: 36647379 PMCID: PMC9839968 DOI: 10.1016/j.isci.2022.105870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The human microbiome comprises trillions of microorganisms residing within different mucosal cavities and across the body surface. The gut microbiota modulates host susceptibility to viral infections in several ways, and microbial interkingdom interactions increase viral infectivity within the gut. Candida albicans, a frequently encountered fungal species in the gut, produces highly structured biofilms and eicosanoids such as prostaglandin E2 (PGE2), which aid in viral protection and replication. These biofilms encompass viruses and provide a shield from antiviral drugs or the immune system. PGE2 is a key modulator of active inflammation with the potential to regulate interferon signaling upon microbial invasion or viral infections. In this review, we raise the perspective of gut interkingdom interactions involving C. albicans and enteric viruses, with a special focus on biofilms, PGE2, and viral replication. Ultimately, we discuss the possible implications of C. albicans-enteric virus associations on host immune responses, particularly the interferon signaling pathway.
Collapse
Affiliation(s)
- Bonang M. Mochochoko
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, 9301, South Africa
| | - Carolina H. Pohl
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, 9301, South Africa,Corresponding author
| | - Hester G. O’Neill
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, 9301, South Africa,Corresponding author
| |
Collapse
|
58
|
Wang Z, Guo K, Liu Y, Huang C, Wu M. Dynamic impact of virome on colitis and colorectal cancer: Immunity, inflammation, prevention and treatment. Semin Cancer Biol 2022; 86:943-954. [PMID: 34656791 PMCID: PMC9008076 DOI: 10.1016/j.semcancer.2021.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/20/2021] [Accepted: 10/08/2021] [Indexed: 02/05/2023]
Abstract
The gut microbiome includes a series of microorganism genomes, such as bacteriome, virome, mycobiome, etc. The gut microbiota is critically involved in intestine immunity and diseases, including inflammatory bowel disease (IBD) and colorectal cancer (CRC); however, the underlying mechanism remains incompletely understood. Clarifying the relationship between microbiota and inflammation may profoundly improve our understanding of etiology, disease progression, patient management, and the development of prevention and treatment. In this review, we discuss the latest studies of the influence of enteric viruses (i.e., commensal viruses, pathogenic viruses, and bacteriophages) in the initiation, progression, and complication of colitis and colorectal cancer, and their potential for novel preventative approaches and therapeutic application. We explore the interplay between gut viruses and host immune systems for its effects on the severity of inflammatory diseases and cancer, including both direct and indirect interactions between enteric viruses with other microbes and microbial products. Furthermore, the underlying mechanisms of the virome's roles in gut inflammatory response have been explained to infer potential therapeutic targets with examples in specific clinical trials. Given that very limited literature has thus far discussed these various topics with the gut virome, we believe these extensive analyses may provide insight into the understanding of the molecular pathogenesis of IBD and CRC, which could help add the design of improved therapies for these important human diseases.
Collapse
Affiliation(s)
- Zhihan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA
| | - Kai Guo
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yingying Liu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA.
| |
Collapse
|
59
|
Gulyaeva A, Garmaeva S, Kurilshikov A, Vich Vila A, Riksen NP, Netea MG, Weersma RK, Fu J, Zhernakova A. Diversity and Ecology of Caudoviricetes Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts. Viruses 2022; 14:2305. [PMID: 36298860 PMCID: PMC9610469 DOI: 10.3390/v14102305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022] Open
Abstract
The human gut harbors numerous viruses infecting the human host, microbes, and other inhabitants of the gastrointestinal tract. Most of these viruses remain undiscovered, and their influence on human health is unknown. Here, we characterize viral genomes in gut metagenomic data from 1950 individuals from four population and patient cohorts. We focus on a subset of viruses that is highly abundant in the gut, remains largely uncharacterized, and allows confident complete genome identification—phages that belong to the class Caudoviricetes and possess genome terminal repeats. We detect 1899 species-level units belonging to this subset, 19% of which do not have complete representative genomes in major public gut virome databases. These units display diverse genomic features, are predicted to infect a wide range of microbial hosts, and on average account for <1% of metagenomic reads. Analysis of longitudinal data from 338 individuals shows that the composition of this fraction of the virome remained relatively stable over a period of 4 years. We also demonstrate that 54 species-level units are highly prevalent (detected in >5% of individuals in a cohort). Finally, we find 34 associations between highly prevalent phages and human phenotypes, 24 of which can be explained by the relative abundance of potential hosts.
Collapse
Affiliation(s)
- Anastasia Gulyaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The Netherlands
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, 9713GZ Groningen, The Netherlands
| | - Niels P. Riksen
- Department of Internal Medicine, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands
| | - Mihai G. Netea
- Department of Internal Medicine, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands
| | - Rinse K. Weersma
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, 9713GZ Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The Netherlands
| |
Collapse
|
60
|
Lau HCH, Yu J. Uncovering novel human gut virome using ultra-deep metagenomic sequencing. Chin Med J (Engl) 2022; 135:2395-2397. [PMID: 36583859 PMCID: PMC9945418 DOI: 10.1097/cm9.0000000000002382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Indexed: 12/31/2022] Open
Affiliation(s)
- Harry Cheuk Hay Lau
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, the Chinese University of Hong Kong, Hong Kong SAR, China
| | | |
Collapse
|
61
|
Microbiome-phage interactions in inflammatory bowel disease. Clin Microbiol Infect 2022:S1198-743X(22)00506-7. [PMID: 36191844 DOI: 10.1016/j.cmi.2022.08.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Inflammatory bowel diseases (IBD) constitute a group of auto-inflammatory disorders impacting the gastrointestinal tract and other systemic organs. The gut microbiome contributes to IBD pathology through multiple mechanisms. Bacteriophages (hence termed phages) are viruses that are able to specifically infect bacteria. Considered as part of the gut microbiome, phages may impact bacterial community structure in various clinical contexts. Additionally, exogenous phage administration may represent a means of suppressing IBD-associated pathobionts, yet utilization of phage therapy remains at an early developmental phase. OBJECTIVES Herein, we summarize the latest advances in understanding endogenous phage impacts on the gut microbiome in health and in IBD. We highlight the prospect of phage utilization as a targeted mode of pathobiont eradication, in preventing and treating IBD manifestations and complications. SOURCES Selected peer-reviewed publications regarding the role of phages in health and in IBD, published between 2013 and 2022. CONTENT The human gut microbiome is increasingly suggested to play a significant role in the onset and progression of multiple non-communicable diseases such as IBD. Several studies suggest that this effect may be mediated by discrete disease-contributing commensals. However, eradication of such pathogenic bacteria remains a daunting unmet task. Altered community structure in IBD may be influenced by blooms of phages within the gut bacterial ecosystem. Moreover, combinations of phages specifically targeting disease-contributing pathobiont strain clades may be harnessed as potential eradication treatment preventing and treating IBD, while bearing minimal adverse impacts on the surrounding bacterial microbiome. IMPLICATIONS Understanding endogenous phage-gut commensal interactions in health and in IBD may enable phage utilization in precision gut microbiome editing, towards treating IBD and other non-communicable microbiome-associated diseases. Nevertheless, developing phage combination-mediated IBD pathobiont eradication treatment modalities will likely necessitate better strain-level bacterial target identification and resolution of treatment-related challenges, such as phage delivery, off-target effects, and bacterial resistance.
Collapse
|
62
|
Santiago-Rodriguez TM, Hollister EB. Unraveling the viral dark matter through viral metagenomics. Front Immunol 2022; 13:1005107. [PMID: 36189246 PMCID: PMC9523745 DOI: 10.3389/fimmu.2022.1005107] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses are part of the microbiome and have essential roles in immunology, evolution, biogeochemical cycles, health, and disease progression. Viruses influence a wide variety of systems and processes, and the continued discovery of novel viruses is anticipated to reveal new mechanisms influencing the biology of diverse environments. While the identity and roles of viruses continue to be discovered and understood through viral metagenomics, most of the sequences in virome datasets cannot be attributed to known viruses or may be only distantly related to species already described in public sequence databases, at best. Such viruses are known as the viral dark matter. Ongoing discoveries from the viral dark matter have provided insights into novel viruses from a variety of environments, as well as their potential in immunological processes, virus evolution, health, disease, therapeutics, and surveillance. Increased understanding of the viral dark matter will continue with a combination of cultivation, microscopy, sequencing, and bioinformatic efforts, which are discussed in the present review.
Collapse
|
63
|
Nishijima S, Nagata N, Kiguchi Y, Kojima Y, Miyoshi-Akiyama T, Kimura M, Ohsugi M, Ueki K, Oka S, Mizokami M, Itoi T, Kawai T, Uemura N, Hattori M. Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort. Nat Commun 2022; 13:5252. [PMID: 36068216 PMCID: PMC9448778 DOI: 10.1038/s41467-022-32832-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/17/2022] [Indexed: 11/19/2022] Open
Abstract
Indigenous bacteriophage communities (virome) in the human gut have a huge impact on the structure and function of gut bacterial communities (bacteriome), but virome variation at a population scale is not fully investigated yet. Here, we analyse the gut dsDNA virome in the Japanese 4D cohort of 4198 deeply phenotyped individuals. By assembling metagenomic reads, we discover thousands of high-quality phage genomes including previously uncharacterised phage clades with different bacterial hosts than known major ones. The distribution of host bacteria is a strong determinant for the distribution of phages in the gut, and virome diversity is highly correlated with anti-viral defence mechanisms of the bacteriome, such as CRISPR-Cas and restriction-modification systems. We identify 97 various intrinsic/extrinsic factors that significantly affect the virome structure, including age, sex, lifestyle, and diet, most of which showed consistent associations with both phages and their predicted bacterial hosts. Among the metadata categories, disease and medication have the strongest effects on the virome structure. Overall, these results present a basis to understand the symbiotic communities of bacteria and their viruses in the human gut, which will facilitate the medical and industrial applications of indigenous viruses.
Collapse
Affiliation(s)
- Suguru Nishijima
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Computational Bio Big Data Open Innovation Lab., National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Naoyoshi Nagata
- Department of Gastroenterological Endoscopy, Tokyo Medical University, Tokyo, Japan.
- Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Tokyo, Japan.
| | - Yuya Kiguchi
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yasushi Kojima
- Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Moto Kimura
- Department of Clinical Research Strategic Planning Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Mitsuru Ohsugi
- Department of Diabetes, Endocrinology, and Metabolism, Center Hospital, National Center for Global Health and Medicine, Tokyo, Japan
- Diabetes and Metabolism Information Center, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kohjiro Ueki
- Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- AIDS Clinical Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Masashi Mizokami
- Genome Medical Sciences Project, Research Institute, National Center for Global Health and Medicine, Chiba, Japan
| | - Takao Itoi
- Department of Gastroenterology and Hepatology, Tokyo Medical University, Tokyo, Japan
| | - Takashi Kawai
- Department of Gastroenterological Endoscopy, Tokyo Medical University, Tokyo, Japan
| | - Naomi Uemura
- Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Kohnodai Hospital, Tokyo, Japan
| | - Masahira Hattori
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| |
Collapse
|
64
|
Zhao L, Shi Y, Lau HCH, Liu W, Luo G, Wang G, Liu C, Pan Y, Zhou Q, Ding Y, Sung JJY, Yu J. Uncovering 1058 Novel Human Enteric DNA Viruses Through Deep Long-Read Third-Generation Sequencing and Their Clinical Impact. Gastroenterology 2022; 163:699-711. [PMID: 35679948 DOI: 10.1053/j.gastro.2022.05.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 05/17/2022] [Accepted: 05/31/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND & AIMS Lack of viral reference genomes poses a challenge to virome study. We investigated human gut virome and its clinical implication by ultra-deep metagenomic sequencing. METHODS We extracted sufficient viral DNA from human feces for ultra-deep PacBio sequencing (>10 μg) and Illumina sequencing (>1 μg). Upon de novo assembly and 6 stages of strict filtering, viral genomes were generated and validated in 3 cohorts of 2819 published fecal metagenomes. Diagnostic performance of assembled viruses for colorectal cancer were tested in a training cohort and 2 independent validation cohorts. Virus mapping ratio, evolutionary history, and virus status (lytic or temperate) were also examined. RESULTS The mean amount of extracted viral DNA increased by 14-fold compared with previous protocols. We obtained PacBio long reads and Illumina short reads with 290-fold higher depth than previous studies. We assembled and validated 1178 contigs as complete viral genomes, of which 1058 were newly identified. Thirteen viral genomes (398-839 kb) that are longer than the largest bacteriophage found in humans (393 kb) were discovered. Phylogenetic tree was constructed based on Hidden Markov Models alignment scores of 4 conserved viral proteins. Incorporating our assembled genomes into the National Center for Biotechnology Information database improved the mapping ratio of published metagenomes ≤18 times. Lytic viruses (75.9% ± 12.2% of total) were predominantly present in our sample. A biomarker panel of 14 novel viruses could discriminate patients with colorectal cancer from controls with an area under the receiver operating characteristics curve of 0.87 in the training cohort, which was validated with areas under the receiver operating characteristics curve of 0.85 and 0.73 in 2 independent cohorts. CONCLUSIONS We uncovered 1058 novel human gut viruses. These findings can contribute to clinical diagnosis, current viral reference genome, and future virome investigation.
Collapse
Affiliation(s)
- Liuyang Zhao
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Yu Shi
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Harry Cheuk-Hay Lau
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Weixin Liu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Guangwen Luo
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Guoping Wang
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Changan Liu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Yasi Pan
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Qiming Zhou
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Yanqiang Ding
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong
| | - Joseph Jao-Yiu Sung
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Jun Yu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Shenzhen Research Institute, Sha Tin, New Territories, Hong Kong.
| |
Collapse
|
65
|
Yutin N, Rayko M, Antipov D, Mutz P, Wolf YI, Krupovic M, Koonin EV. Varidnaviruses in the Human Gut: A Major Expansion of the Order Vinavirales. Viruses 2022; 14:1842. [PMID: 36146653 PMCID: PMC9502842 DOI: 10.3390/v14091842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 11/29/2022] Open
Abstract
Bacteriophages play key roles in the dynamics of the human microbiome. By far the most abundant components of the human gut virome are tailed bacteriophages of the realm Duplodnaviria, in particular, crAss-like phages. However, apart from duplodnaviruses, the gut virome has not been dissected in detail. Here we report a comprehensive census of a minor component of the gut virome, the tailless bacteriophages of the realm Varidnaviria. Tailless phages are primarily represented in the gut by prophages, that are mostly integrated in genomes of Alphaproteobacteria and Verrucomicrobia and belong to the order Vinavirales, which currently consists of the families Corticoviridae and Autolykiviridae. Phylogenetic analysis of the major capsid proteins (MCP) suggests that at least three new families should be established within Vinavirales to accommodate the diversity of prophages from the human gut virome. Previously, only the MCP and packaging ATPase genes were reported as conserved core genes of Vinavirales. Here we report an extended core set of 12 proteins, including MCP, packaging ATPase, and previously undetected lysis enzymes, that are shared by most of these viruses. We further demonstrate that replication system components are frequently replaced in the genomes of Vinavirales, suggestive of selective pressure for escape from yet unknown host defenses or avoidance of incompatibility with coinfecting related viruses. The results of this analysis show that, in a sharp contrast to marine viromes, varidnaviruses are a minor component of the human gut virome. Moreover, they are primarily represented by prophages, as indicated by the analysis of the flanking genes, suggesting that there are few, if any, lytic varidnavirus infections in the gut at any given time. These findings complement the existing knowledge of the human gut virome by exploring a group of viruses that has been virtually overlooked in previous work.
Collapse
Affiliation(s)
- Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Mike Rayko
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, 199004 St. Petersburg, Russia
| | - Dmitry Antipov
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, 199004 St. Petersburg, Russia
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, F-75015 Paris, France
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| |
Collapse
|
66
|
Gang J, Wang H, Xue X, Zhang S. Microbiota and COVID-19: Long-term and complex influencing factors. Front Microbiol 2022; 13:963488. [PMID: 36033885 PMCID: PMC9417543 DOI: 10.3389/fmicb.2022.963488] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/25/2022] [Indexed: 01/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). According to the World Health Organization statistics, more than 500 million individuals have been infected and more than 6 million deaths have resulted worldwide. Although COVID-19 mainly affects the respiratory system, considerable evidence shows that the digestive, cardiovascular, nervous, and reproductive systems can all be involved. Angiotensin-converting enzyme 2 (AEC2), the target of SARS-CoV-2 invasion of the host is mainly distributed in the respiratory and gastrointestinal tract. Studies found that microbiota contributes to the onset and progression of many diseases, including COVID-19. Here, we firstly conclude the characterization of respiratory, gut, and oral microbial dysbiosis, including bacteria, fungi, and viruses. Then we explore the potential mechanisms of microbial involvement in COVID-19. Microbial dysbiosis could influence COVID-19 by complex interactions with SARS-CoV-2 and host immunity. Moreover, microbiota may have an impact on COVID-19 through their metabolites or modulation of ACE2 expression. Subsequently, we generalize the potential of microbiota as diagnostic markers for COVID-19 patients and its possible association with post-acute COVID-19 syndrome (PACS) and relapse after recovery. Finally, we proposed directed microbiota-targeted treatments from the perspective of gut microecology such as probiotics and prebiotics, fecal transplantation and antibiotics, and other interventions such as traditional Chinese medicine, COVID-19 vaccines, and ACE2-based treatments.
Collapse
Affiliation(s)
- Jiaqi Gang
- Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Oncology, Xiuwu County People’s Hospital, Jiaozuo, China
| | - Haiyu Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangsheng Xue
- Department of Oncology, Xiuwu County People’s Hospital, Jiaozuo, China
| | - Shu Zhang
- Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
67
|
Bhardwaj K, Garg A, Pandey AD, Sharma H, Kumar M, Vrati S. Insights into the human gut virome by sampling a population from the Indian subcontinent. J Gen Virol 2022; 103. [PMID: 35951476 DOI: 10.1099/jgv.0.001774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gut virome plays an important role in human physiology but remains poorly understood. This study reports an investigation of the human gut DNA-virome of a previously unexplored ethnic population through metagenomics of faecal samples collected from individuals residing in Northern India. Analysis shows that, similar to the populations investigated earlier, majority of the identified virome belongs to bacteriophages and a smaller fraction (<20 %) consists of viruses that infect animals, archaea, protists, multiple domains or plants. However, crAss-like phages, in this population, are dominated by the genera VI, VII and VIII. Interestingly, it also reveals the presence of a virus family, Sphaerolipoviridae, which has not been detected in the human gut earlier. Viral families, Siphoviridae, Myoviridae, Podoviridae, Microviridae, Herelleviridae and Phycodnaviridae are detected in all of the analysed individuals, which supports the existence of a core virome. Lysogeny-associated genes were found in less than 10 % of the assembled genomes and a negative correlation was observed in the richness of bacterial and free-viral species, suggesting that the dominant lifestyle of gut phage is not lysogenic. This is in contrast to some of the earlier studies. Further, several hundred high-quality viral genomes were recovered. Detailed characterization of these genomes would be useful for understanding the biology of these viruses and their significance in human physiology.
Collapse
Affiliation(s)
- Kanchan Bhardwaj
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India.,Manav Rachna International Institute of Research and Studies, Sector-43, Aravali hills, Faridabad-121 004, Haryana, India
| | - Anjali Garg
- Department of Biophysics, University of Delhi, South Campus, New Delhi-110021, India
| | - Abhay Deep Pandey
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India
| | - Himani Sharma
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi, South Campus, New Delhi-110021, India
| | - Sudhanshu Vrati
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-Gurugram Expressway, Faridabad-121 001, Haryana, India
| |
Collapse
|
68
|
Viral biogeography of the mammalian gut and parenchymal organs. Nat Microbiol 2022; 7:1301-1311. [PMID: 35918425 PMCID: PMC7614033 DOI: 10.1038/s41564-022-01178-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 06/21/2022] [Indexed: 01/13/2023]
Abstract
The mammalian virome has been linked to health and disease but our understanding of how it is structured along the longitudinal axis of the mammalian gastrointestinal tract (GIT) and other organs is limited. Here, we report a metagenomic analysis of the prokaryotic and eukaryotic virome occupying luminal and mucosa-associated habitats along the GIT, as well as parenchymal organs (liver, lung and spleen), in two representative mammalian species, the domestic pig and rhesus macaque (six animals per species). Luminal samples from the large intestine of both mammals harboured the highest loads and diversity of bacteriophages (class Caudoviricetes, family Microviridae and others). Mucosal samples contained much lower viral loads but a higher proportion of eukaryotic viruses (families Astroviridae, Caliciviridae, Parvoviridae). Parenchymal organs contained bacteriophages of gut origin, in addition to some eukaryotic viruses. Overall, GIT virome composition was specific to anatomical region and host species. Upper GIT and mucosa-specific viruses were greatly under-represented in distal colon samples (a proxy for faeces). Nonetheless, certain viral and phage species were ubiquitous in all samples from the oral cavity to the distal colon. The dataset and its accompanying methodology may provide an important resource for future work investigating the biogeography of the mammalian gut virome.
Collapse
|
69
|
Sabar MA, Honda R, Haramoto E. CrAssphage as an indicator of human-fecal contamination in water environment and virus reduction in wastewater treatment. WATER RESEARCH 2022; 221:118827. [PMID: 35820313 DOI: 10.1016/j.watres.2022.118827] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/03/2022] [Accepted: 07/04/2022] [Indexed: 05/14/2023]
Abstract
Viral indicators of human-fecal contamination in wastewaters and environmental waters have been getting much attention in the past decade. Cross-assembly phage (crAssphage) is the most abundant DNA virus in human feces. Recently, the usefulness of crAssphage as a microbial source tracking and water quality monitoring tool for human-fecal contamination has been highlighted. Here, we conducted a comprehensive review on crAssphage in water, focusing on detection methodology, concentration range in various waters and wastewaters, specificity to human-fecal contamination, and reduction in wastewater treatment systems. This review highlights that crAssphage is globally distributed in wastewaters and various fecal-contaminated water bodies at high concentrations without seasonal fluctuations. CrAssphage is highly specific to human-fecal contamination and is rarely found in animal feces. It also has a good potential as a performance indicator to ensure virus reduction in wastewater treatment systems. Accordingly, crAssphage could be an effective tool for monitoring of human-fecal contamination and potential presence of fecal pathogenic microbes in environmental waters. Bridging the research gaps highlighted in this review would make crAssphage a powerful tool to support the control of water-related health risks.
Collapse
Affiliation(s)
| | - Ryo Honda
- Faculty of Geoscience and Civil Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Eiji Haramoto
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Japan
| |
Collapse
|
70
|
Imai T, Inoue R, Nishida A, Yokota Y, Morishima S, Kawahara M, Kusada H, Tamaki H, Andoh A. Features of the gut prokaryotic virome of Japanese patients with Crohn's disease. J Gastroenterol 2022; 57:559-570. [PMID: 35689701 DOI: 10.1007/s00535-022-01882-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/16/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND/AIMS The gut virome is mainly composed of bacteriophages and influences gut homeostasis and pathogenic conditions. In this study, we analyzed the gut prokaryotic virome in Japanese patients with Crohn's disease (CD). MATERIALS/METHODS We collected 19 fecal samples from CD patients and 16 samples from healthy controls. The gut bacteriome was analyzed by 16S rRNA gene sequencing and the virome was profiled by shotgun metagenomic sequencing. RESULTS Despite no differences in richness and evenness, there was a significant difference in the overall structure of the gut virome between CD patients and controls (P = 0.013). CrAssphage and Staphylococcus virus, belonging to the order Caudovirales, were dominant in the gut virome of controls and CD patients. The abundance of crAssphage was significantly greater in CD patients than controls (P = 0.021). Lactococcus, Enterococcus and Lactobacillus phages were present only in CD patients, while Xanthomonas and Escherichia phages were unique to the controls. In the gut bacteriome of CD patients, richness and evenness were significantly lower, and a significant difference in the overall structure was observed between groups (P = 0.014). The gut bacteriome of CD patients was characterized by a decrease of the genera Faecalibacterium, Roseburia, and Ruminococcus and an increase of the family Enterobacteriaceae. There were more significant correlations between viruses and bacteria in CD patients than controls. CONCLUSIONS The gut virome of CD patients was distinct from that of healthy controls in a Japanese population. An altered gut virome may be one of the factors associated with the bacterial dysbiosis of CD.
Collapse
Affiliation(s)
- Takayuki Imai
- Department of Medicine, Shiga University of Medical Science, Seta-Tsukinowa, Otsu, Shiga, 520-2192, Japan
| | - Ryo Inoue
- Department of Applied Biological Science, Faculty of Agriculture, Setsunan University, Hirakata, Osaka, 573-0101, Japan
| | - Atsushi Nishida
- Department of Medicine, Shiga University of Medical Science, Seta-Tsukinowa, Otsu, Shiga, 520-2192, Japan
| | - Yoshihiro Yokota
- Department of Medicine, Shiga University of Medical Science, Seta-Tsukinowa, Otsu, Shiga, 520-2192, Japan
| | - So Morishima
- Department of Applied Biological Science, Faculty of Agriculture, Setsunan University, Hirakata, Osaka, 573-0101, Japan
| | - Masahiro Kawahara
- Department of Medicine, Shiga University of Medical Science, Seta-Tsukinowa, Otsu, Shiga, 520-2192, Japan
| | - Hiroyuki Kusada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8566, Japan
| | - Akira Andoh
- Department of Medicine, Shiga University of Medical Science, Seta-Tsukinowa, Otsu, Shiga, 520-2192, Japan.
| |
Collapse
|
71
|
Buttimer C, Sutton T, Colom J, Murray E, Bettio PH, Smith L, Bolocan AS, Shkoporov A, Oka A, Liu B, Herzog JW, Sartor RB, Draper LA, Ross RP, Hill C. Impact of a phage cocktail targeting Escherichia coli and Enterococcus faecalis as members of a gut bacterial consortium in vitro and in vivo. Front Microbiol 2022; 13:936083. [PMID: 35935217 PMCID: PMC9355613 DOI: 10.3389/fmicb.2022.936083] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/01/2022] [Indexed: 01/14/2023] Open
Abstract
Escherichia coli and Enterococcus faecalis have been implicated as important players in human gut health that have been associated with the onset of inflammatory bowel disease (IBD). Bacteriophage (phage) therapy has been used for decades to target pathogens as an alternative to antibiotics, but the ability of phage to shape complex bacterial consortia in the lower gastrointestinal tract is not clearly understood. We administered a cocktail of six phages (either viable or heat-inactivated) targeting pro-inflammatory Escherichia coli LF82 and Enterococcus faecalis OG1RF as members of a defined community in both a continuous fermenter and a murine colitis model. The two target strains were members of a six species simplified human microbiome consortium (SIHUMI-6). In a 72-h continuous fermentation, the phage cocktail caused a 1.1 and 1.5 log (log10 genome copies/mL) reduction in E. faecalis and E. coli numbers, respectively. This interaction was accompanied by changes in the numbers of other SIHUMI-6 members, with an increase of Lactiplantibacillus plantarum (1.7 log) and Faecalibacterium prausnitzii (1.8 log). However, in germ-free mice colonized by the same bacterial consortium, the same phage cocktail administered twice a week over nine weeks did not cause a significant reduction of the target strains. Mice treated with active or inactive phage had similar levels of pro-inflammatory cytokines (IFN-y/IL12p40) in unstimulated colorectal colonic strip cultures. However, histology scores of the murine lower GIT (cecum and distal colon) were lower in the viable phage-treated mice, suggesting that the phage cocktail did influence the functionality of the SIHUMI-6 consortium. For this study, we conclude that the observed potential of phages to reduce host populations in in vitro models did not translate to a similar outcome in an in vivo setting, with this effect likely brought about by the reduction of phage numbers during transit of the mouse GIT.
Collapse
Affiliation(s)
- Colin Buttimer
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Tom Sutton
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Joan Colom
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ellen Murray
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Pedro H. Bettio
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Linda Smith
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | | | - Akihiko Oka
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Internal Medicine II, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Bo Liu
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeremy W. Herzog
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - R. Balfour Sartor
- Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| |
Collapse
|
72
|
Sinha A, Li Y, Mirzaei MK, Shamash M, Samadfam R, King IL, Maurice CF. Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis. MICROBIOME 2022; 10:105. [PMID: 35799219 PMCID: PMC9264660 DOI: 10.1186/s40168-022-01275-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/13/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Inflammatory bowel diseases (IBDs) including Crohn's disease (CD) and ulcerative colitis (UC) are characterized by chronic and debilitating gut inflammation. Altered bacterial communities of the intestine are strongly associated with IBD initiation and progression. The gut virome, which is primarily composed of bacterial viruses (bacteriophages, phages), is thought to be an important factor regulating and shaping microbial communities in the gut. While alterations in the gut virome have been observed in IBD patients, the contribution of these viruses to alterations in the bacterial community and heightened inflammatory responses associated with IBD patients remains largely unknown. RESULTS Here, we performed in vivo microbial cross-infection experiments to follow the effects of fecal virus-like particles (VLPs) isolated from UC patients and healthy controls on bacterial diversity and severity of experimental colitis in human microbiota-associated (HMA) mice. Shotgun metagenomics confirmed that several phages were transferred to HMA mice, resulting in treatment-specific alterations in the gut virome. VLPs from healthy and UC patients also shifted gut bacterial diversity of these mice, an effect that was amplified during experimental colitis. VLPs isolated from UC patients specifically altered the relative abundance of several bacterial taxa previously implicated in IBD progression. Additionally, UC VLP administration heightened colitis severity in HMA mice, as indicated by shortened colon length and increased pro-inflammatory cytokine production. Importantly, this effect was dependent on intact VLPs. CONCLUSIONS Our findings build on recent literature indicating that phages are dynamic regulators of bacterial communities in the gut and implicate the intestinal virome in modulating intestinal inflammation and disease. Video Abstract.
Collapse
Affiliation(s)
- Anshul Sinha
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Yue Li
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, Guangdong, China
| | - Mohammadali Khan Mirzaei
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
- Institute of Virology, Helmholtz Center Munich and Technical University of Munich, 85764, Neuherberg, Bavaria, Germany
| | - Michael Shamash
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Rana Samadfam
- Charles River Laboratories, 22022 Transcanadienne, Senneville, QC, H9X 3R3, Canada
| | - Irah L King
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada.
- McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, QC, Canada.
| | - Corinne F Maurice
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada.
- McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, QC, Canada.
| |
Collapse
|
73
|
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: 52] [Impact Index Per Article: 26.0] [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.
Collapse
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.
| |
Collapse
|
74
|
Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome. Nat Commun 2022; 13:3594. [PMID: 35739117 PMCID: PMC9226167 DOI: 10.1038/s41467-022-31390-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022] Open
Abstract
There is significant interest in altering the course of cardiometabolic disease development via gut microbiomes. Nevertheless, the highly abundant phage members of the complex gut ecosystem -which impact gut bacteria- remain understudied. Here, we show gut virome changes associated with metabolic syndrome (MetS), a highly prevalent clinical condition preceding cardiometabolic disease, in 196 participants by combined sequencing of bulk whole genome and virus like particle communities. MetS gut viromes exhibit decreased richness and diversity. They are enriched in phages infecting Streptococcaceae and Bacteroidaceae and depleted in those infecting Bifidobacteriaceae. Differential abundance analysis identifies eighteen viral clusters (VCs) as significantly associated with either MetS or healthy viromes. Among these are a MetS-associated Roseburia VC that is related to healthy control-associated Faecalibacterium and Oscillibacter VCs. Further analysis of these VCs revealed the Candidatus Heliusviridae, a highly widespread gut phage lineage found in 90+% of participants. The identification of the temperate Ca. Heliusviridae provides a starting point to studies of phage effects on gut bacteria and the role that this plays in MetS.
Collapse
|
75
|
Li S, Guo R, Zhang Y, Li P, Chen F, Wang X, Li J, Jie Z, Lv Q, Jin H, Wang G, Yan Q. A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome. iScience 2022; 25:104418. [PMID: 35663034 PMCID: PMC9160773 DOI: 10.1016/j.isci.2022.104418] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/26/2022] [Accepted: 05/12/2022] [Indexed: 12/18/2022] Open
Abstract
The human oral cavity is a hotspot of numerous, mostly unexplored, viruses that are important for maintaining oral health and microbiome homeostasis. Here, we analyzed 2,792 publicly available oral metagenomes and proposed the Oral Virus Database (OVD) comprising 48,425 nonredundant viral genomes (≥5 kbp). The OVD catalog substantially expanded the known phylogenetic diversity and host specificity of oral viruses, allowing for enhanced delineation of some underrepresented groups such as the predicted Saccharibacteria phages and jumbo viruses. Comparisons of the viral diversity and abundance of different oral cavity habitats suggested strong niche specialization of viromes within individuals. The virome variations in relation to host geography and properties were further uncovered, especially the age-dependent viral compositional signatures in saliva. Overall, the viral genome catalog describes the architecture and variability of the human oral virome, while offering new resources and insights for current and future studies.
Collapse
Affiliation(s)
- Shenghui Li
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
- Puensum Genetech Institute, Wuhan 430076, China
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Peng Li
- Puensum Genetech Institute, Wuhan 430076, China
| | - Fang Chen
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Jing Li
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing 100044, China
| | - Zhuye Jie
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| |
Collapse
|
76
|
Rashed R, Valcheva R, Dieleman LA. Manipulation of Gut Microbiota as a Key Target for Crohn's Disease. Front Med (Lausanne) 2022; 9:887044. [PMID: 35783604 PMCID: PMC9244564 DOI: 10.3389/fmed.2022.887044] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
Crohn's disease (CD) is an inflammatory bowel disease (IBD) sub-type characterized by transmural chronic inflammation of the gastrointestinal tract. Research indicates a complex CD etiology involving genetic predisposition and immune dysregulation in response to environmental triggers. The chronic mucosal inflammation has been associated with a dysregulated state, or dysbiosis, of the gut microbiome (bacteria), mycobiome (fungi), virome (bacteriophages and viruses), and archeaome (archaea) further affecting the interkingdom syntrophic relationships and host metabolism. Microbiota dysbiosis in CD is largely described by an increase in facultative anaerobic pathobionts at the expense of strict anaerobic Firmicutes, such as Faecalibacterium prausnitzii. In the mycobiome, reduced fungal diversity and fungal-bacteria interactions, along with a significantly increased abundance of Candida spp. and a decrease in Saccharomyces cerevisiae are well documented. Virome analysis also indicates a significant decrease in phage diversity, but an overall increase in phages infecting bacterial groups associated with intestinal inflammation. Finally, an increase in methanogenic archaea such as Methanosphaera stadtmanae exhibits high immunogenic potential and is associated with CD etiology. Common anti-inflammatory medications used in CD management (amino-salicylates, immunomodulators, and biologics) could also directly or indirectly affect the gut microbiome in CD. Other medications often used concomitantly in IBD, such as antibiotics, antidepressants, oral contraceptives, opioids, and proton pump inhibitors, have shown to alter the gut microbiota and account for increased susceptibility to disease onset or worsening of disease progression. In contrast, some environmental modifications through alternative therapies including fecal microbiota transplant (FMT), diet and dietary supplements with prebiotics, probiotics, and synbiotics have shown potential protective effects by reversing microbiota dysbiosis or by directly promoting beneficial microbes, together with minimal long-term adverse effects. In this review, we discuss the different approaches to modulating the global consortium of bacteria, fungi, viruses, and archaea in patients with CD through therapies that include antibiotics, probiotics, prebiotics, synbiotics, personalized diets, and FMT. We hope to provide evidence to encourage clinicians and researchers to incorporate these therapies into CD treatment options, along with making them aware of the limitations of these therapies, and indicate where more research is needed.
Collapse
|
77
|
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.
Collapse
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:
| |
Collapse
|
78
|
Chu Y, Guo S, Cui D, Fu X, Ma Y. DeephageTP: a convolutional neural network framework for identifying phage-specific proteins from metagenomic sequencing data. PeerJ 2022; 10:e13404. [PMID: 35698617 PMCID: PMC9188312 DOI: 10.7717/peerj.13404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/18/2022] [Indexed: 01/14/2023] Open
Abstract
Bacteriophages (phages) are the most abundant and diverse biological entity on Earth. Due to the lack of universal gene markers and database representatives, there about 50-90% of genes of phages are unable to assign functions. This makes it a challenge to identify phage genomes and annotate functions of phage genes efficiently by homology search on a large scale, especially for newly phages. Portal (portal protein), TerL (large terminase subunit protein), and TerS (small terminase subunit protein) are three specific proteins of Caudovirales phage. Here, we developed a CNN (convolutional neural network)-based framework, DeephageTP, to identify the three specific proteins from metagenomic data. The framework takes one-hot encoding data of original protein sequences as the input and automatically extracts predictive features in the process of modeling. To overcome the false positive problem, a cutoff-loss-value strategy is introduced based on the distributions of the loss values of protein sequences within the same category. The proposed model with a set of cutoff-loss-values demonstrates high performance in terms of Precision in identifying TerL and Portal sequences (94% and 90%, respectively) from the mimic metagenomic dataset. Finally, we tested the efficacy of the framework using three real metagenomic datasets, and the results shown that compared to the conventional alignment-based methods, our proposed framework had a particular advantage in identifying the novel phage-specific protein sequences of portal and TerL with remote homology to their counterparts in the training datasets. In summary, our study for the first time develops a CNN-based framework for identifying the phage-specific protein sequences with high complexity and low conservation, and this framework will help us find novel phages in metagenomic sequencing data. The DeephageTP is available at https://github.com/chuym726/DeephageTP.
Collapse
Affiliation(s)
- Yunmeng Chu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese, Shenzhen, Guangdong, P.R. China,Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, Fujian, P.R. China
| | - Shun Guo
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese, Shenzhen, Guangdong, P.R. China
| | - Dachao Cui
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese, Shenzhen, Guangdong, P.R. China
| | - Xiongfei Fu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese, Shenzhen, Guangdong, P.R. China
| | - Yingfei Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese, Shenzhen, Guangdong, P.R. China
| |
Collapse
|
79
|
Zheng W, Zhao S, Yin Y, Zhang H, Needham DM, Evans ED, Dai CL, Lu PJ, Alm EJ, Weitz DA. High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome. Science 2022; 376:eabm1483. [PMID: 35653470 DOI: 10.1126/science.abm1483] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Characterizing complex microbial communities with single-cell resolution has been a long-standing goal of microbiology. We present Microbe-seq, a high-throughput method that yields the genomes of individual microbes from complex microbial communities. We encapsulate individual microbes in droplets with microfluidics and liberate their DNA, which we then amplify, tag with droplet-specific barcodes, and sequence. We explore the human gut microbiome, sequencing more than 20,000 microbial single-amplified genomes (SAGs) from a single human donor and coassembling genomes of almost 100 bacterial species, including several with multiple subspecies strains. We use these genomes to probe microbial interactions, reconstructing the horizontal gene transfer (HGT) network and observing HGT between 92 species pairs; we also identify a significant in vivo host-phage association between crAssphage and one strain of Bacteroides vulgatus. Microbe-seq contributes high-throughput culture-free capabilities to investigate genomic blueprints of complex microbial communities with single-microbe resolution.
Collapse
Affiliation(s)
- Wenshan Zheng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shijie Zhao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yehang Yin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,College of Computer Science and Technology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Huidan Zhang
- School of Engineering and Applied Sciences (SEAS), Harvard University, Cambridge, MA, USA
| | - David M Needham
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Ocean Ecosystems Biology, GEOMAR, Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Ethan D Evans
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chengzhen L Dai
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter J Lu
- School of Engineering and Applied Sciences (SEAS), Harvard University, Cambridge, MA, USA.,Department of Physics, Harvard University, Cambridge, MA, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David A Weitz
- School of Engineering and Applied Sciences (SEAS), Harvard University, Cambridge, MA, USA.,Department of Physics, Harvard University, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| |
Collapse
|
80
|
Cheng L, Deng Z, Tao H, Song W, Xing B, Liu W, Kong L, Yuan S, Ma Y, Wu Y, Huang X, Peng Y, Wong NK, Liu Y, Wang Y, Shen Y, Li J, Xiao M. Harnessing stepping-stone hosts to engineer, select, and reboot synthetic bacteriophages in one pot. CELL REPORTS METHODS 2022; 2:100217. [PMID: 35637913 PMCID: PMC9142689 DOI: 10.1016/j.crmeth.2022.100217] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/07/2022] [Accepted: 04/25/2022] [Indexed: 11/24/2022]
Abstract
Advances in synthetic genomics have led to a great demand for genetic manipulation. Trimming any process to simplify and accelerate streamlining of genetic code into life holds great promise for synthesizing and studying organisms. Here, we develop a simple but powerful stepping-stone strategy to promote genome refactoring of viruses in one pot, validated by successful cross-genus and cross-order rebooting of 90 phages infecting 4 orders of popular pathogens. Genomic sequencing suggests that rebooting outcome is associated with gene number and DNA polymerase availability within phage genomes. We integrate recombineering, screening, and rebooting processes in one pot and demonstrate genome assembly and genome editing of phages by stepping-stone hosts in an efficient and economic manner. Under this framework, in vitro assembly, yeast-based assembly, or genetic manipulation of native hosts are not required. As additional stepping-stone hosts are being developed, this framework will open doors for synthetic phages targeting more pathogens and commensals.
Collapse
Affiliation(s)
- Li Cheng
- BGI-Shenzhen, Shenzhen 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Ziqing Deng
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
- BGI-Beijing, Beijing 100101, China
| | - Haoran Tao
- BGI-Shenzhen, Shenzhen 518083, China
- University of the Chinese Academy of Sciences, Beijing 101408, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Wenchen Song
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Bo Xing
- BGI-Shenzhen, Shenzhen 518083, China
- University of the Chinese Academy of Sciences, Beijing 101408, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Wenfeng Liu
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Lingxin Kong
- BGI-Shenzhen, Shenzhen 518083, China
- University of the Chinese Academy of Sciences, Beijing 101408, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Shengjian Yuan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yingfei Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yayun Wu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xun Huang
- Infection Control Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yun Peng
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, 518112 Shenzhen, China
| | - Nai-Kei Wong
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, 518112 Shenzhen, China
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, State Key Discipline of Infectious Disease, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen Third People's Hospital, 518112 Shenzhen, China
| | - Yun Wang
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518120, China
| | - Yue Shen
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, BGI-Shenzhen, Shenzhen 518120, China
| | - Junhua Li
- BGI-Shenzhen, Shenzhen 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| |
Collapse
|
81
|
Wang Y, Zheng G, Wang D, Zhou L. Occurrence of bacterial and viral fecal markers in municipal sewage sludge and their removal during sludge conditioning processes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 310:114802. [PMID: 35228166 DOI: 10.1016/j.jenvman.2022.114802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/08/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Fecal contamination in wastewater treatment system may pose severe threats to human health, but the detailed contamination of fecal bacterial and viral pathogens in municipal sewage sludge remains unclear. In addition, it is also unclear how sludge conditioning treatments would impact the distribution of fecal markers in conditioned sewage sludge. Before addressing these two issues, the possible polymerase chain reaction (PCR) inhibition effect when determining the abundances of fecal markers in both sludge solids and sludge supernatants should be solved, and methods of effectively concentrating fecal markers from sludge supernatant should also be developed. In the present study, we found that the serial tenfold dilution effectively reduced the PCR inhibition effect when determining the abundances of fecal markers including cross-assembly phages (CrAssphage), JC polyomavirus (JCPyV), human-specific HF183 bacteroides (HF183), human BK polyomavirus (BKPyV), human adenovirus (HAdV) and Escherichia coli (EC), while the utilization of negatively charged HA membrane was effective to recover fecal markers from sludge supernatant. The results of a six-month monitoring revealed that gene markers of CrAssphage, JCPyV, HF183, BKPyV, HAdV, and EC can be detected in municipal sewage sludge collected from a local wastewater treatment plant. Among the investigated four chemical conditioning methods, i.e., chemical conditioning with polyacrylamide (PAM), Fe[III]/CaO, or Fenton's reagent, and chemical acidification conditioning, chemical conditioning with Fenton's reagent was much more effective than the other three conditioning methods to reduce the abundances of fecal markers in the supernatant and solid of conditioned sewage sludge. Furthermore, the investigated fecal markers in the conditioned sewage sludge can be simultaneously attenuated by employing suitable conditioning methods, consequently reducing the associated environmental risks.
Collapse
Affiliation(s)
- Yuhang Wang
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; College of Materials and Chemical Engineering, Pingxiang University, Pingxiang, 337055, China
| | - Guanyu Zheng
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
| | - Dianzhan Wang
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lixiang Zhou
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
| |
Collapse
|
82
|
Gupta B, Rai R, Oertel M, Raeman R. Intestinal Barrier Dysfunction in Fatty Liver Disease: Roles of Microbiota, Mucosal Immune System, and Bile Acids. Semin Liver Dis 2022; 42:122-137. [PMID: 35738255 PMCID: PMC9307091 DOI: 10.1055/s-0042-1748037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) describes a spectrum of progressive liver diseases ranging from simple steatosis to steatohepatitis and fibrosis. Globally, NAFLD is the leading cause of morbidity and mortality associated with chronic liver disease, and NAFLD patients are at a higher risk of developing cirrhosis and hepatocellular carcinoma. While there is a consensus that inflammation plays a key role in promoting NAFLD progression, the underlying mechanisms are not well understood. Recent clinical and experimental evidence suggest that increased hepatic translocation of gut microbial antigens, secondary to diet-induced impairment of the intestinal barrier may be important in driving hepatic inflammation in NAFLD. Here, we briefly review various endogenous and exogenous factors influencing the intestinal barrier and present recent advances in our understanding of cellular and molecular mechanisms underlying intestinal barrier dysfunction in NAFLD.
Collapse
Affiliation(s)
- Biki Gupta
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ravi Rai
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michael Oertel
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania,McGowan Institute for Regenerative Medicine, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Reben Raeman
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| |
Collapse
|
83
|
Busby TJ, Miller CR, Moran NA, Van Leuven JT. Global Composition of the Bacteriophage Community in Honey Bees. mSystems 2022; 7:e0119521. [PMID: 35343797 PMCID: PMC9040601 DOI: 10.1128/msystems.01195-21] [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: 09/30/2021] [Accepted: 03/02/2022] [Indexed: 11/23/2022] Open
Abstract
The microbial communities in animal digestive systems are critical for host development and health. They stimulate the immune system during development, synthesize important chemical compounds like hormones, aid in digestion, competitively exclude pathogens, etc. Compared to the bacterial and fungal components of the microbiome, we know little about the temporal and spatial dynamics of bacteriophage communities in animal digestive systems. Recently, the bacteriophages of the honey bee gut were characterized in two European bee populations. Most of the bacteriophages described in these two reports were novel, harbored many metabolic genes in their genomes, and had a community structure that suggests coevolution with their bacterial hosts. To describe the conservation of bacteriophages in bees and begin to understand their role in the bee microbiome, we sequenced the virome of Apis mellifera from Austin, TX, and compared bacteriophage compositions among three locations around the world. We found that most bacteriophages from Austin are novel, sharing no sequence similarity with anything in public repositories. However, many bacteriophages are shared among the three bee viromes, indicating specialization of bacteriophages in the bee gut. Our study, along with the two previous bee virome studies, shows that the bee gut bacteriophage community is simple compared to that of many animals, consisting of several hundred types of bacteriophages that primarily infect four of the dominant bacterial phylotypes in the bee gut. IMPORTANCE Viruses that infect bacteria (bacteriophages) are abundant in the microbial communities that live on and in plants and animals. However, our knowledge of the structure, dynamics, and function of these viral communities lags far behind our knowledge of their bacterial hosts. We sequenced the first bacteriophage community of honey bees from the United States and compared the U.S. honey bee bacteriophage community to those of samples from Europe. Our work is an important characterization of an economically critical insect species and shows how bacteriophage communities can contain highly conserved individuals and be highly variable in composition across a wide geographic range.
Collapse
Affiliation(s)
- Taylor J. Busby
- Global Disease Biology, University of California, Davis, Davis, California, USA
| | - Craig R. Miller
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, USA
| | - Nancy A. Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - James T. Van Leuven
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, USA
| |
Collapse
|
84
|
Nam SJ, Hu WS, Koo OK. Evaluation of crAssphage as a human-specific microbial source-tracking marker in the Republic of Korea. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:367. [PMID: 35426058 DOI: 10.1007/s10661-022-09918-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
CrAssphage is a novel and by far the most abundant bacteriophage in the human gut and has been proposed as a human-specific microbial source tracking (MST) marker. However, its global use as a human-specific MST marker requires validation in more extensive regions. The purpose of this study was to evaluate the specificity and abundance of the human-specific MST marker crAssphage with PCR and RT-PCR assays in human and animal feces in Korea. The prevalence of crAssphage was confirmed in 94 human feces samples (subjects: 19 to 45 years old) and 56 animal feces samples (from birds, raccoons, squirrels, weasels, deer, wild boars, hares, cats, and dogs). CrAssphage showed sensitivity of 0.39 and specificity of 1.00 in Korea, with a sequencing analysis showing that genotype II was dominant at 71.9%. The quantitative analysis showed that crAssphage is sufficiently abundant in human feces given the high concentration range of 4.26 to 8.25 log gene copies (GC)/ng in human feces. In conclusion, this study confirmed the crAssphage as a specific and abundant MST marker with which to identify human fecal contamination in Korea.
Collapse
Affiliation(s)
- Su Jin Nam
- Department of Food and Nutrition, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Wen Si Hu
- Department of Food Science and Engineering, Liaocheng University, Liaocheng, 252059, China
| | - Ok Kyung Koo
- Department of Food Science, Chungnam National University, Daejeon, 34134, Republic of Korea.
| |
Collapse
|
85
|
Martinez-Hernandez F, Diop A, Garcia-Heredia I, Bobay LM, Martinez-Garcia M. Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth. THE ISME JOURNAL 2022; 16:1025-1035. [PMID: 34775488 PMCID: PMC8940918 DOI: 10.1038/s41396-021-01150-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 11/09/2022]
Abstract
Viral genetic microdiversity drives adaptation, pathogenicity, and speciation and has critical consequences for the viral-host arms race occurring at the strain and species levels, which ultimately impact microbial community structure and biogeochemical cycles. Despite the fact that most efforts have focused on viral macrodiversity, little is known about the microdiversity of ecologically important viruses on Earth. Recently, single-virus genomics discovered the putatively most abundant ocean virus in temperate and tropical waters: the uncultured dsDNA virus vSAG 37-F6 infecting Pelagibacter, the most abundant marine bacteria. In this study, we report the cooccurrence of up to ≈1,500 different viral strains (>95% nucleotide identity) and ≈30 related species (80-95% nucleotide identity) in a single oceanic sample. Viral microdiversity was maintained over space and time, and most alleles were the result of synonymous mutations without any apparent adaptive benefits to cope with host translation codon bias and efficiency. Gene flow analysis used to delimitate species according to the biological species concept (BSC) revealed the impact of recombination in shaping vSAG 37-F6 virus and Pelagibacter speciation. Data demonstrated that this large viral microdiversity somehow mirrors the host species diversity since ≈50% of the 926 analyzed Pelagibacter genomes were found to belong to independent BSC species that do not significantly engage in gene flow with one another. The host range of this evolutionarily successful virus revealed that a single viral species can infect multiple Pelagibacter BSC species, indicating that this virus crosses not only formal BSC barriers but also biomes since viral ancestors are found in freshwater.
Collapse
Affiliation(s)
| | - Awa Diop
- Department of Biology, University of North Carolina at Greensboro, Greensboro, USA
| | | | - Louis-Marie Bobay
- Department of Biology, University of North Carolina at Greensboro, Greensboro, USA
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain.
| |
Collapse
|
86
|
Beller L, Deboutte W, Vieira-Silva S, Falony G, Yhossef Tito R, Rymenans L, Yinda CK, Vanmechelen B, Van Espen L, Jansen D, Shi C, Zeller M, Maes P, Faust K, Van Ranst M, Raes J, Matthijnssens J. The virota and its transkingdom interactions in the healthy infant gut. Proc Natl Acad Sci U S A 2022; 119:e2114619119. [PMID: 35320047 PMCID: PMC9060457 DOI: 10.1073/pnas.2114619119] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/08/2022] [Indexed: 02/07/2023] Open
Abstract
SignificanceMicrobes colonizing the infant gut during the first year(s) of life play an important role in immune system development. We show that after birth the (nearly) sterile gut is rapidly colonized by bacteria and their viruses (phages), which often show a strong cooccurrence. Most viruses infecting the infant do not cause clinical signs and their numbers strongly increase after day-care entrance. The infant diet is clearly reflected by identification of plant-infecting viruses, whereas fungi and parasites are not part of a stable gut microbiota. These temporal high-resolution baseline data about the gut colonization process will be valuable for further investigations of pathogenic viruses, dynamics between phages and their bacterial host, as well as studies investigating infants with a disturbed microbiota.
Collapse
Affiliation(s)
- Leen Beller
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
| | - Ward Deboutte
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
- Center for Microbiology, Flemish Institute for Biotechnology (VIB), 3000 Leuven, Belgium
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
- Center for Microbiology, Flemish Institute for Biotechnology (VIB), 3000 Leuven, Belgium
| | - Raul Yhossef Tito
- Laboratory of Molecular Bacteriology, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
- Center for Microbiology, Flemish Institute for Biotechnology (VIB), 3000 Leuven, Belgium
| | - Leen Rymenans
- Laboratory of Molecular Bacteriology, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
- Center for Microbiology, Flemish Institute for Biotechnology (VIB), 3000 Leuven, Belgium
| | - Claude Kwe Yinda
- Virus Ecology Unit, Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Hamilton, MT 59840
| | - Bert Vanmechelen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
| | - Lore Van Espen
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
| | - Daan Jansen
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
| | - Chenyan Shi
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
- Center Lab of Longhua Branch, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China
- Department of Infectious Disease, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, 518020, China
| | - Mark Zeller
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
- Center for Microbiology, Flemish Institute for Biotechnology (VIB), 3000 Leuven, Belgium
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, 3000 Leuven, Belgium
| |
Collapse
|
87
|
Tamburini FB, Maghini D, Oduaran OH, Brewster R, Hulley MR, Sahibdeen V, Norris SA, Tollman S, Kahn K, Wagner RG, Wade AN, Wafawanaka F, Gómez-Olivé FX, Twine R, Lombard Z, Hazelhurst S, Bhatt AS. Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa. Nat Commun 2022; 13:926. [PMID: 35194028 PMCID: PMC8863827 DOI: 10.1038/s41467-021-27917-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/25/2021] [Indexed: 12/15/2022] Open
Abstract
Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world's population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n = 118) or urban Soweto (n = 51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple "western-nonwestern" axis and contains undescribed microbial diversity.
Collapse
Affiliation(s)
| | - Dylan Maghini
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Ryan Brewster
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Michaella R Hulley
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | - Venesa Sahibdeen
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | - Shane A Norris
- SAMRC Developmental Pathways for Health Research Unit, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa.,School of Human Development and Health, University of Southampton, Southampton, UK
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Ryan G Wagner
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Alisha N Wade
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,INDEPTH Network, East Legon, Accra, Ghana
| | - Rhian Twine
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa. .,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA. .,School of Medicine, Stanford University, Stanford, CA, USA. .,Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA.
| |
Collapse
|
88
|
Johansen J, Plichta DR, Nissen JN, Jespersen ML, Shah SA, Deng L, Stokholm J, Bisgaard H, Nielsen DS, Sørensen SJ, Rasmussen S. Genome binning of viral entities from bulk metagenomics data. Nat Commun 2022; 13:965. [PMID: 35181661 PMCID: PMC8857322 DOI: 10.1038/s41467-022-28581-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/28/2022] [Indexed: 12/26/2022] Open
Abstract
Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal tract are not well understood. This is partly due to a paucity of whole-virome datasets and limitations in current approaches for identifying viral sequences in metagenomics data. Here, combining a deep-learning based metagenomics binning algorithm with paired metagenome and metavirome datasets, we develop Phages from Metagenomics Binning (PHAMB), an approach that allows the binning of thousands of viral genomes directly from bulk metagenomics data, while simultaneously enabling clustering of viral genomes into accurate taxonomic viral populations. When applied on the Human Microbiome Project 2 (HMP2) dataset, PHAMB recovered 6,077 high-quality genomes from 1,024 viral populations, and identified viral-microbial host interactions. PHAMB can be advantageously applied to existing and future metagenomes to illuminate viral ecological dynamics with other microbiome constituents.
Collapse
Affiliation(s)
- Joachim Johansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Damian R Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jakob Nybo Nissen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Statens Serum Institut, Viral & Microbial Special diagnostics, Copenhagen, Denmark
| | - Marie Louise Jespersen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Ling Deng
- Section of Food Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.,Section of Food Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Dennis Sandris Nielsen
- Section of Food Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
89
|
Lynch JB, Bennett BD, Merrill BD, Ruby EG, Hryckowian AJ. Independent host- and bacterium-based determinants protect a model symbiosis from phage predation. Cell Rep 2022; 38:110376. [PMID: 35172163 PMCID: PMC8983117 DOI: 10.1016/j.celrep.2022.110376] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/08/2021] [Accepted: 01/20/2022] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages (phages) are diverse and abundant constituents of microbial communities worldwide, capable of modulating bacterial populations in diverse ways. Here, we describe the phage HNL01, which infects the marine bacterium Vibrio fischeri. We use culture-based approaches to demonstrate that mutations in the exopolysaccharide locus of V. fischeri render this bacterium resistant to infection by HNL01, highlighting the extracellular matrix as a key determinant of HNL01 infection. Additionally, using the natural symbiosis between V. fischeri and the squid Euprymna scolopes, we show that, during colonization, V. fischeri is protected from phages present in the ambient seawater. Taken together, these findings shed light on independent yet synergistic host- and bacterium-based strategies for resisting symbiosis-disrupting phage predation, and we present important implications for understanding these strategies in the context of diverse host-associated microbial ecosystems.
Collapse
Affiliation(s)
- Jonathan B Lynch
- Pacific Biosciences Research Center, University of Hawai'i at Manoa, Honolulu, HI 96822, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Brittany D Bennett
- Pacific Biosciences Research Center, University of Hawai'i at Manoa, Honolulu, HI 96822, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Edward G Ruby
- Pacific Biosciences Research Center, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
| | - Andrew J Hryckowian
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA; Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.
| |
Collapse
|
90
|
Gulyaeva A, Garmaeva S, Ruigrok RAAA, Wang D, Riksen NP, Netea MG, Wijmenga C, Weersma RK, Fu J, Vila AV, Kurilshikov A, Zhernakova A. Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts. Cell Rep 2022; 38:110204. [PMID: 35021085 DOI: 10.1016/j.celrep.2021.110204] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/03/2021] [Accepted: 12/13/2021] [Indexed: 12/16/2022] Open
Abstract
The crAss-like phages are a diverse group of related viruses that includes some of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyze gut metagenomic data collected from 1,950 individuals from the Netherlands. We identify 1,556 crAss-like phage genomes, including 125 species-level and 32 genus-level clusters absent from the reference databases used. Analysis of their genomic features shows that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. Prediction of crAss-like phage hosts points primarily to bacteria of the phylum Bacteroidetes, consistent with previous reports. Finally, we explore the temporal stability of crAss-like phages over a 4-year period and identify associations between the abundance of crAss-like phages and several human phenotypes, including depletion of crAss-like phages in inflammatory bowel disease patients.
Collapse
Affiliation(s)
- Anastasia Gulyaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands.
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Renate A A A Ruigrok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Daoming Wang
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen 6525GA, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen 6525GA, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Rinse K Weersma
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands.
| |
Collapse
|
91
|
Tomofuji Y, Kishikawa T, Maeda Y, Ogawa K, Nii T, Okuno T, Oguro-Igashira E, Kinoshita M, Yamamoto K, Sonehara K, Yagita M, Hosokawa A, Motooka D, Matsumoto Y, Matsuoka H, Yoshimura M, Ohshima S, Nakamura S, Inohara H, Mochizuki H, Takeda K, Kumanogoh A, Okada Y. Whole gut virome analysis of 476 Japanese revealed a link between phage and autoimmune disease. Ann Rheum Dis 2021; 81:278-288. [PMID: 34880054 PMCID: PMC8761997 DOI: 10.1136/annrheumdis-2021-221267] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/23/2021] [Indexed: 12/19/2022]
Abstract
Objective The relationship between autoimmune diseases and the gut microbiome has been intensively studied, and several autoimmunity-associated bacterial taxa have been identified. However, much less is known about the roles of the gut virome in autoimmune diseases. Methods Here, we performed a whole gut virome analysis based on the shotgun sequencing of 476 Japanese which included patients with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), multiple sclerosis and healthy control subjects. Results Our case–control comparison of the viral abundance revealed that crAss-like phages, which are one of the main components of a healthy gut virome, significantly decreased in the gut of the patients with autoimmune disease, specifically the patients with RA and SLE. In addition, Podoviridae significantly decreased in the gut of the patients with SLE. To understand how these viruses affected the bacteriome, we performed a quantitative virus–bacterium association analysis and clustered regularly interspaced short palindromic repeat-based virus–bacterium interaction analysis. We identified a symbiosis between Podoviridae and Faecalibacterium. In addition, multiple bacterial targets of crAss-like phages were identified (eg, Ruminococcus spp). Conclusion Our data suggest that the gut virome can affect our body either directly or via bacteria. Our analyses have elucidated a previously missing part of the autoimmunity-associated gut microbiome and presented new candidates that contribute to the development of autoimmune diseases.
Collapse
Affiliation(s)
- Yoshihiko Tomofuji
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Toshihiro Kishikawa
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yuichi Maeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan.,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Kotaro Ogawa
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan.,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Tatsusada Okuno
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Eri Oguro-Igashira
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan.,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Makoto Kinoshita
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.,Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Mayu Yagita
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan.,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Akiko Hosokawa
- Department of Neurology, Suita Municipal Hospital, Suita, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hidetoshi Matsuoka
- Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinaga, Japan
| | - Maiko Yoshimura
- Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinaga, Japan
| | - Shiro Ohshima
- Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinaga, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hidenori Inohara
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan.,WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.,Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan .,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.,Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| |
Collapse
|
92
|
Virome Characterization in Commercial Bovine Serum Batches-A Potentially Needed Testing Strategy for Biological Products. Viruses 2021; 13:v13122425. [PMID: 34960693 PMCID: PMC8705701 DOI: 10.3390/v13122425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/21/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Bovine serum has been widely used as a universal supplement in culture media and other applications, including the manufacture of biological products and the production of synthetic meat. Currently, commercial bovine serum is tested for possible viral contaminants following regional guidelines. Regulatory agencies’ established tests focused on detecting selected animal origin viruses and are based on virus isolation, immunofluorescence, and hemadsorption assays. However, these tests may fail to detect new or emerging viruses in biological products. High-throughput sequencing is a powerful option since no prior knowledge of the viral targets is required. In the present study, we evaluate the virome of seven commercial batches of bovine serum from Mexico (one batch), New Zealand (two batches), and the United States (four batches) using a specific preparation and enrichment method for pooled samples and sequencing using an Illumina platform. A variety of circular replicase-encoding single-stranded (CRESS) DNA families (Genomoviridae, Circoviridae, and Smacoviridae) was identified. Additionally, CrAssphage, a recently discovered group of bacteriophage correlated with fecal contamination, was identified in 85% of the tested batches. Furthermore, sequences representing viral families with single-stranded DNA (Parvoviridae), double-stranded DNA (Polyomaviridae and Adenoviridae), single-stranded RNA (Flaviviridae, Picornaviridae, and Retroviridae), and double-stranded RNA (Reoviridae) were identified. These results support that high-throughput sequencing associated with viral enrichment is a robust tool and should be considered an additional layer of safety when testing pooled biologicals to detect viral contaminants overlooked by the current testing protocols.
Collapse
|
93
|
Marongiu L, Landry JJM, Rausch T, Abba ML, Delecluse S, Delecluse H, Allgayer H. Metagenomic analysis of primary colorectal carcinomas and their metastases identifies potential microbial risk factors. Mol Oncol 2021; 15:3363-3384. [PMID: 34328665 PMCID: PMC8637581 DOI: 10.1002/1878-0261.13070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/09/2021] [Accepted: 07/29/2021] [Indexed: 12/18/2022] Open
Abstract
The paucity of microbiome studies at intestinal tissues has contributed to a yet limited understanding of potential viral and bacterial cofactors of colorectal cancer (CRC) carcinogenesis or progression. We analysed whole-genome sequences of CRC primary tumours, their corresponding metastases and matched normal tissue for sequences of viral, phage and bacterial species. Bacteriome analysis showed Fusobacterium nucleatum, Streptococcus sanguinis, F. Hwasookii, Anaerococcus mediterraneensis and further species enriched in primary CRCs. The primary CRC of one patient was enriched for F. alocis, S. anginosus, Parvimonas micra and Gemella sp. 948. Enrichment of Escherichia coli strains IAI1, SE11, K-12 and M8 was observed in metastases together with coliphages enterobacteria phage φ80 and Escherichia phage VT2φ_272. Virome analysis showed that phages were the most preponderant viral species (46%), the main families being Myoviridae, Siphoviridae and Podoviridae. Primary CRCs were enriched for bacteriophages, showing five phages (Enterobacteria, Bacillus, Proteus, Streptococcus phages) together with their pathogenic hosts in contrast to normal tissues. The most frequently detected, and Blast-confirmed, viruses included human endogenous retrovirus K113, human herpesviruses 7 and 6B, Megavirus chilensis, cytomegalovirus (CMV) and Epstein-Barr virus (EBV), with one patient showing EBV enrichment in primary tumour and metastases. EBV was PCR-validated in 80 pairs of CRC primary tumour and their corresponding normal tissues; in 21 of these pairs (26.3%), it was detectable in primary tumours only. The number of viral species was increased and bacterial species decreased in CRCs compared with normal tissues, and we could discriminate primary CRCs from metastases and normal tissues by applying the Hutcheson t-test on the Shannon indices based on viral and bacterial species. Taken together, our results descriptively support hypotheses on microorganisms as potential (co)risk factors of CRC and extend putative suggestions on critical microbiome species in CRC metastasis.
Collapse
Affiliation(s)
- Luigi Marongiu
- Department of Experimental Surgery – Cancer MetastasisMedical Faculty MannheimRuprecht‐Karls University of HeidelbergMannheimGermany
| | | | - Tobias Rausch
- Genomics Core FacilityEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Mohammed L. Abba
- Department of Experimental Surgery – Cancer MetastasisMedical Faculty MannheimRuprecht‐Karls University of HeidelbergMannheimGermany
| | | | | | - Heike Allgayer
- Department of Experimental Surgery – Cancer MetastasisMedical Faculty MannheimRuprecht‐Karls University of HeidelbergMannheimGermany
| |
Collapse
|
94
|
Yasui M, Iso H, Torii S, Matsui Y, Katayama H. Applicability of pepper mild mottle virus and cucumber green mottle mosaic virus as process indicators of enteric virus removal by membrane processes at a potable reuse facility. WATER RESEARCH 2021; 206:117735. [PMID: 34673461 DOI: 10.1016/j.watres.2021.117735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/25/2021] [Accepted: 09/29/2021] [Indexed: 05/09/2023]
Abstract
Treatment of wastewater for potable reuse is increasingly becoming a suitable alternative water source to meet the growing urban water needs worldwide. Potable reuse requires reduction of enteric viruses to levels at which they do not pose a risk to human health. Advanced water treatment trains (e.g., microfiltration (MF), ultrafiltration (UF), reverse osmosis (RO), and ultraviolet light and advanced oxidation process (UV/AOP)) provide significant protection and reduce virus loads in highly treated final product waters. Even though viruses are a principal concern, the performance of virus removal by membrane processes is not easily determined. The objective of this study was to evaluate the applicability of Aichi virus (AiV), pepper mild mottle virus (PMMoV), cucumber green mottle mosaic virus (CGMMV), and cross-assembly phage (crAssphage) removal as possible process indicators for MF, UF, and RO. Virus log reduction values (LRVs) based on gene copies measured using molecular methods were determined for MF and UF. The median LRVs of all viruses obtained after MF and UF were 2.9 and 3.1, respectively. The LRVs of the proposed indicators were lower than those of human enteric viruses. The morphological and physicochemical difference among indicators was not found to affect LRVs. Therefore, all proposed indicator viruses were determined to be suitable candidates as process indicators for MF and UF. Regarding RO, most of the viruses measured in this study were undetectable in permeate. Only PMMoV and CGMMV were detected showing median LRVs of 2.8 and 2.5, respectively. PMMoV and CGMMV are recommended as good process indicators of physical virus removal for the overall water treatment process.
Collapse
Key Words
- AIV, aichi virus
- Abbreviation: MF, microfiltration
- AdV, adenovirus
- CGMMV, cucumber green mottle mosaic virus
- Crassphage, cross-assembly phage
- EF, effluent
- Human enteric virus
- LRV, log reduction value
- MME, molecular method efficiencies
- MNV, Murine Norovirus
- MPC, molecular process control
- Microfiltration
- NV GI, norovirus GI
- NV GII, norovirus GII
- ORSV, Odontoglossum Ringspot Virus
- PCE, primary concentration efficiency
- PMMOV, pepper mild mottle virus
- Process indicator
- RO, reverse osmosis
- Reverse osmosis
- UF, ultrafiltration
- UV/AOP, ultraviolet light and advanced oxidation process
- Ultrafiltration
- Water reuse
Collapse
Affiliation(s)
- Midori Yasui
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Hikaru Iso
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Shotaro Torii
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | | | - Hiroyuki Katayama
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
| |
Collapse
|
95
|
Li W, Liu Z, Hu B, Zhu L. Co-occurrence of crAssphage and antibiotic resistance genes in agricultural soils of the Yangtze River Delta, China. ENVIRONMENT INTERNATIONAL 2021; 156:106620. [PMID: 33989841 DOI: 10.1016/j.envint.2021.106620] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/01/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
Agricultural soil is highly susceptible to manure contamination and thus is a potential source for the spread of pathogens and antibiotic resistance genes (ARGs). Routine monitoring fecal contamination in agricultural soil can reduce the manure-derived ARG contaminations. This study investigated the distribution of crAssphage, a highly human-specific indicator of fecal pollution, in agricultural soils in the Yangtze River Delta (YRD) of China, and its potential in serving as an indicator of soil ARGs. CrAssphage was indeed strongly correlated with the abundance of soil ARGs, and particularly tetracycline resistance gene tetW (rho = 0.55, p < 0.01). Meanwhile, with the increasing of crAssphage abundance, the frequency of multiple abundant ARGs is also increased. When the relative abundance of crAssphage in soil samples exceeded 4.94 × 10-4 copies per copy of the 16S rRNA gene, there would be more than three types of co-existing ARGs. Regional differences in crAssphage and ARGs abundances were observed for samples collected from Zhejiang, Shanghai, Jiangsu, and Anhui in the YRD, indicating different levels of fecal pollution therein. High sewage treatment capacity could contribute to the reduce of fecal pollution and the control ARG transmission in agricultural soils.
Collapse
Affiliation(s)
- Wen Li
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China.
| | - Zishu Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China.
| |
Collapse
|
96
|
Stockdale SR, Hill C. Progress and prospects of the healthy human gut virome. Curr Opin Virol 2021; 51:164-171. [PMID: 34742036 DOI: 10.1016/j.coviro.2021.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/30/2021] [Accepted: 10/08/2021] [Indexed: 12/26/2022]
Abstract
Not all viruses associated with humans cause disease. Non-pathogenic human-infecting viruses are predicted as important for immune system induction and preparation. Phages that infect bacteria are the most abundant predators of the human microbial ecosystem, promoting and maintaining bacterial diversity. Metagenomic analyses of the human gut virome and microbiome are unravelling the intricate predator-prey dynamics of phage-bacteria co-existence, co-evolution, and their interplay with the human host. While most adults harbour a distinctly individualistic and persistent community of virulent phages, new-borns are dominated by temperate phages heavily influenced by environmental exposures. The future development of microbiome-based interventions, therapeutics, and manipulation, will require a greater understanding of the human microbiome and the virome.
Collapse
Affiliation(s)
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, T12 YT20, Ireland; School of Microbiology, University College Cork, T12 YT20, Ireland.
| |
Collapse
|
97
|
Van Espen L, Bak EG, Beller L, Close L, Deboutte W, Juel HB, Nielsen T, Sinar D, De Coninck L, Frithioff-Bøjsøe C, Fonvig CE, Jacobsen S, Kjærgaard M, Thiele M, Fullam A, Kuhn M, Holm JC, Bork P, Krag A, Hansen T, Arumugam M, Matthijnssens J. A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog. mSystems 2021; 6:e0038221. [PMID: 34665009 PMCID: PMC8525569 DOI: 10.1128/msystems.00382-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/02/2021] [Indexed: 01/06/2023] Open
Abstract
Gut viruses are important, yet often neglected, players in the complex human gut microbial ecosystem. Recently, the number of human gut virome studies has been increasing; however, we are still only scratching the surface of the immense viral diversity. In this study, 254 virus-enriched fecal metagenomes from 204 Danish subjects were used to generate the Danish Enteric Virome Catalog (DEVoC) containing 12,986 nonredundant viral scaffolds, of which the majority was previously undescribed, encoding 190,029 viral genes. The DEVoC was used to compare 91 healthy DEVoC gut viromes from children, adolescents, and adults that were used to create the DEVoC. Gut viromes of healthy Danish subjects were dominated by phages. While most phage genomes (PGs) only occurred in a single subject, indicating large virome individuality, 39 PGs were present in more than 10 healthy subjects. Among these 39 PGs, the prevalences of three PGs were associated with age. To further study the prevalence of these 39 prevalent PGs, 1,880 gut virome data sets of 27 studies from across the world were screened, revealing several age-, geography-, and disease-related prevalence patterns. Two PGs also showed a remarkably high prevalence worldwide-a crAss-like phage (20.6% prevalence), belonging to the tentative AlphacrAssvirinae subfamily, and a previously undescribed circular temperate phage infecting Bacteroides dorei (14.4% prevalence), called LoVEphage because it encodes lots of viral elements. Due to the LoVEphage's high prevalence and novelty, public data sets in which the LoVEphage was detected were de novo assembled, resulting in an additional 18 circular LoVEphage-like genomes (67.9 to 72.4 kb). IMPORTANCE Through generation of the DEVoC, we added numerous previously uncharacterized viral genomes and genes to the ever-increasing worldwide pool of human gut viromes. The DEVoC, the largest human gut virome catalog generated from consistently processed fecal samples, facilitated the analysis of the 91 healthy Danish gut viromes. Characterizing the biggest cohort of healthy gut viromes from children, adolescents, and adults to date confirmed the previously established high interindividual variation in human gut viromes and demonstrated that the effect of age on the gut virome composition was limited to the prevalence of specific phage (groups). The identification of a previously undescribed prevalent phage illustrates the usefulness of developing virome catalogs, and we foresee that the DEVoC will benefit future analysis of the roles of gut viruses in human health and disease.
Collapse
Affiliation(s)
- Lore Van Espen
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Emilie Glad Bak
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leen Beller
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Lila Close
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Ward Deboutte
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Helene Bæk Juel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Trine Nielsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Deniz Sinar
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Lander De Coninck
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Christine Frithioff-Bøjsøe
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
| | - Cilius Esmann Fonvig
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
| | - Suganya Jacobsen
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Maria Kjærgaard
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Maja Thiele
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens-Christian Holm
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Aleksander Krag
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manimozhiyan Arumugam
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jelle Matthijnssens
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| |
Collapse
|
98
|
Kiguchi Y, Nishijima S, Kumar N, Hattori M, Suda W. Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads. DNA Res 2021; 28:6377780. [PMID: 34586399 DOI: 10.1093/dnares/dsab019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Indexed: 01/21/2023] Open
Abstract
The human gut bacteriophage community (phageome) plays an important role in the host's health and disease; however, the entire structure is poorly understood, partly owing to the generation of many incomplete genomes in conventional short-read metagenomics. Here, we show long-read metagenomics of amplified DNA of low-biomass phageomes with multiple displacement amplification (MDA), involving the development of a novel bioinformatics tool, split amplified chimeric read algorithm (SACRA), that efficiently pre-processed numerous chimeric reads generated through MDA. Using five samples, SACRA markedly reduced the average chimera ratio from 72% to 1.5% in PacBio reads with an average length of 1.8 kb. De novo assembly of chimera-less PacBio long reads reconstructed contigs of ≥5 kb with an average proportion of 27%, which was 1% in contigs from MiSeq short reads, thereby dramatically improving contig length and genome completeness. Comparison of PacBio and MiSeq contigs found MiSeq contig fragmentations frequently near local repeats and hypervariable regions in the phage genomes, and those caused by multiple homologous phage genomes coexisting in the community. We also developed a reference-independent method to assess the completeness of the linear phage genomes. Overall, we established a SACRA-coupled long-read metagenomics robust to highly diverse gut phageomes, identifying high-quality circular and linear phage genomes with adequate sequence quantity.
Collapse
Affiliation(s)
- Yuya Kiguchi
- Cooperative Major in Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo 169-8555, Japan
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Suguru Nishijima
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo 169-8555, Japan
- Integrated Institute for Regulatory Science, Waseda University, Tokyo 169-8555, Japan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Naveen Kumar
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Masahira Hattori
- Cooperative Major in Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| |
Collapse
|
99
|
Polo D, Lois M, Fernández-Núñez MT, Romalde JL. Detection of SARS-CoV-2 RNA in bivalve mollusks and marine sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147534. [PMID: 33984699 PMCID: PMC8099584 DOI: 10.1016/j.scitotenv.2021.147534] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 05/04/2023]
Abstract
The presence of SARS-CoV-2 in wastewater pose the question of whether this new pandemic virus could be released into watercourses and potentially continue to finally reach coastal waters. In this study, we employed two bivalve molluscan species from the genus Ruditapes as sentinel organisms to investigate the presence of SARS-CoV-2 signals in the marine coastal environment. Estuarine sediments from the natural clam banks were also analyzed. Viral RNA was detected by RT-qPCR, targeting IP4, E and N1 genomic regions. Positive samples were also subjected to a PMAxx-triton viability RT-qPCR assay in order to discriminate between intact and altered capsids, obtaining indirect information about the viability of the virus. SARS-CoV-2 RNA traces were detected in 9/12 clam samples by RT-qPCR, from which 4 were positive for two different target regions. Viral quantification ranged from
Collapse
Affiliation(s)
- David Polo
- Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Marta Lois
- Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | | | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| |
Collapse
|
100
|
Abstract
Bacteriophages (phages) have been known for over a century, but only in the last 2 decades have we really come to appreciate how abundant and diverse they are. With that realization, research groups across the globe have shown the importance of phage-based processes in a myriad of environments, including the global oceans and soils, and as part of the human microbiome. Through advances in sequencing technology, genomics, and bioinformatics, we know that the morphological diversity of bacteriophages originally used for taxonomy is eclipsed by their genomic diversity. Because we currently do not have a complete taxonomic framework or naming scheme to describe this diversity, crucial information from virome and microbiome studies is being lost. In this commentary, I will discuss recent advances in taxonomy and its importance for studies of the microbiome with examples of the human gut phageome and make recommendations for future analyses.
Collapse
|