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Zhao F, Wang J. Another piece of puzzle for the human microbiome: the gut virome under dietary modulation. J Genet Genomics 2024:S1673-8527(24)00098-5. [PMID: 38710286 DOI: 10.1016/j.jgg.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024]
Abstract
The virome is the most abundant and highly variable microbial consortium in the gut. Because of difficulties in isolating and culturing gut viruses and the lack of reference genomes, the virome has remained a relatively elusive aspect of the human microbiome. In recent years, studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health. Here, we review the responses of the gut virome to dietary intake and the potential health implications, presenting changes in the gut viral community and preferences of viral members to particular diets. We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota. We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer, as well as the import of new viral members along with the diet. Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary interventions and health maintenance strategies targeting the gut microbiota.
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Affiliation(s)
- Fengxiang Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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2
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Marques Dos Santos M, Caixia L, Snyder SA. Evaluation of wastewater-based epidemiology of COVID-19 approaches in Singapore's 'closed-system' scenario: A long-term country-wide assessment. WATER RESEARCH 2023; 244:120406. [PMID: 37542765 DOI: 10.1016/j.watres.2023.120406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/07/2023]
Abstract
With the COVID-19 pandemic the use of WBE to track diseases spread has rapidly evolved into a widely applied strategy worldwide. However, many of the current studies lack the necessary systematic approach and supporting quality of epidemiological data to fully evaluate the effectiveness and usefulness of such methods. Use of WBE in a very low disease prevalence setting and for long-term monitoring has yet to be validated and it is critical for its intended use as an early warning system. In this study we seek to evaluate the sensitivity of WBE approaches under low prevalence of disease and ability to provide early warning. Two monitoring scenarios were used: (i) city wide monitoring (population 5,700,000) and (ii) community/localized monitoring (population 24,000 to 240,000). Prediction of active cases by WBE using multiple linear regression shows that a multiplexed qPCR approach with three gene targets has a significant advantage over single-gene monitoring approaches, with R2 = 0.832 (RMSE 0.053) for an analysis using N, ORF1ab and S genes (R2 = 0.677 to 0.793 for single gene strategies). A predicted disease prevalence of 0.001% (1 in 100,000) for a city-wide monitoring was estimated by the multiplexed RT-qPCR approach and was corroborated by epidemiological data evidence in three 'waves'. Localized monitoring setting shows an estimated detectable disease prevalence of ∼0.002% (1 in 56,000) and is supported by the geospatial distribution of active cases and local population dynamics data. Data analysis also shows that this approach has a limitation in sensitivity, or hit rate, of 62.5 % and an associated high miss rate (false negative rate) of 37.5 % when compared to available epidemiological data. Nevertheless, our study shows that, with enough sampling resolution, WBE at a community level can achieve high precision and accuracies for case detection (96 % and 95 %, respectively) with low false omission rate (4.5 %) even at low disease prevalence levels.
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Affiliation(s)
- Mauricius Marques Dos Santos
- Nanyang Technological University, Nanyang Environment & Water Research Institute (NEWRI), 1 Cleantech Loop, CleanTech One, #06-08, Singapore 637141
| | - Li Caixia
- Nanyang Technological University, Nanyang Environment & Water Research Institute (NEWRI), 1 Cleantech Loop, CleanTech One, #06-08, Singapore 637141
| | - Shane Allen Snyder
- Nanyang Technological University, Nanyang Environment & Water Research Institute (NEWRI), 1 Cleantech Loop, CleanTech One, #06-08, Singapore 637141; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore.
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3
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Cao X, Wang Z, Pang J, Sun L, Kondo H, Andika IB. Identification of a novel dicistro-like virus associated with the roots of tomato plants. Arch Virol 2023; 168:214. [PMID: 37523067 DOI: 10.1007/s00705-023-05843-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023]
Abstract
Viruses belonging to the family Dicistroviridae have a monopartite positive-sense single-stranded RNA genome and infect a variety of arthropods. Using high-throughput sequencing, we detected a novel dicistro-like virus, tentatively named "tomato root-associated dicistro-like virus" (TRaDLV), in the roots of tomato plants showing yellow mosaic symptoms on the leaves. The diseased tomato plants were coinfected with multiple plant viruses, and TRaDLV was present in the roots but not in the leaves. The genome of TRaDLV is 8726 nucleotides in length, excluding the poly(A) tail, and contains two open reading frames (ORFs) separated by an intergenic region (IGR). The TRaDLV genome showed characteristics similar to those of dicistroviruses, including the presence of a 3C-like protease domain, repeated amino acid sequences representing multiple copies of viral genome-linked protein (VPg)-like sequences in the ORF1 polyprotein, and a series of stem-loop structures resembling an internal ribosome entry site in the IGR. Phylogenetic analysis revealed that TRaDLV clustered with unclassified dicistro-like viruses from invertebrates or identified in samples of plant-derived material. These findings indicate the existence of a novel dicistro-like virus that may associate with plant roots or a root-inhabiting organism.
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Affiliation(s)
- Xinran Cao
- College of Plant Health and Medicine, Qingdao Agricultural University, 266109, Qingdao, China
- Shandong Agricultural University, 271018, Tai'an, China
- Shouguang International vegetable Sci-tech Fair Management Service Center, 262700, Shouguang, China
| | - Ziqi Wang
- College of Plant Health and Medicine, Qingdao Agricultural University, 266109, Qingdao, China
| | - Jianguo Pang
- University Library, Northwest A&F University, 712100, Xianyang, China
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, 712100, Xianyang, China
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, 710-0046, Kurashiki, Japan
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, 266109, Qingdao, China.
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Diversity and potential function of pig gut DNA viruses. Heliyon 2023; 9:e14020. [PMID: 36915549 PMCID: PMC10006684 DOI: 10.1016/j.heliyon.2023.e14020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Viruses are ubiquitous in the gut of animals and play an important role in the ecology of the gut microbiome. The potential effects of these substances on the growth and development of the body are not fully known. Little is known about the effects of breeding environment on pig gut virome. Here, there are 3584 viral operational taxonomic units (vOTUs) longer than 5 kb identified by virus-enriched metagenome sequencing from 25 pig fecal samples. Only a small minority of vOTUs (11.16%) can be classified at the family level, and ∼50% of the genes could be annotated, supporting the concept of pig gut as reservoirs of substantial undescribed viral genetic diversity. The composition of pig gut virome in the six regions may be related to geography. There are only 20 viral clusters (VCs) shared among pig gut virome in six regions of Shanxi Province. These viruses rarely carry antibiotic resistance genes (ARGs). At the same time, they possess abundant auxiliary metabolic genes (AMGs) potentially involved in carbon, sulfur metabolism and cofactor biosynthesis, etc. This study has revealed the unique characteristics and potential function of pig gut DNA virome and established a foundation for the recognition of the viral roles in gut environment.
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Crosstalk between the Intestinal Virome and Other Components of the Microbiota, and Its Effect on Intestinal Mucosal Response and Diseases. J Immunol Res 2022; 2022:7883945. [PMID: 36203793 PMCID: PMC9532165 DOI: 10.1155/2022/7883945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
In recent years, there has been ample evidence illustrating the effect of microbiota on gut immunity, homeostasis, and disease. Most of these studies have engaged more efforts in understanding the role of the bacteriome in gut mucosal immunity and disease. However, studies on the virome and its influence on gut mucosal immunity and pathology are still at infancy owing to limited metagenomic tools. Nonetheless, the existing studies on the virome have largely been focused on the bacteriophages as these represent the main component of the virome with little information on endogenous retroviruses (ERVs) and eukaryotic viruses. In this review, we describe the gut virome, and its role in gut mucosal response and disease progression. We also explore the crosstalk between the virome and other microorganisms in the gut mucosa and elaborate on how these interactions shape the gut mucosal immunity going from bacteriophages through ERVs to eukaryotic viruses. Finally, we elucidate the potential contribution of this crosstalk in the pathogenesis of inflammatory bowel diseases and colon cancer.
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Kennedy EA, Holtz LR. Gut virome in early life: origins and implications. Curr Opin Virol 2022; 55:101233. [PMID: 35690009 PMCID: PMC9575407 DOI: 10.1016/j.coviro.2022.101233] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 12/15/2022]
Abstract
The human body is colonized by a multitude of bacteria, fungi, and viruses, which play important roles in health and disease. Microbial colonization during early life is thought to be a particularly important period with lasting consequences for health. Viral populations in the gut are particularly dynamic in early life before they stabilize in adulthood. The composition of the early-life virome is increasingly recognized as a determinant of disease later in life. Here, we review the development of the virome in healthy infants, as well as the role of the early-life virome in the development of disease states including diarrhea, malnutrition, and autoimmune diseases.
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Affiliation(s)
- Elizabeth A Kennedy
- Washington University School of Medicine, Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, St. Louis, MO 63110, USA
| | - Lori R Holtz
- Washington University School of Medicine, Department of Pediatrics, St. Louis, MO 63110, USA.
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Chitcharoen S, Sivapornnukul P, Payungporn S. Revolutionized virome research using systems microbiology approaches. Exp Biol Med (Maywood) 2022; 247:1135-1147. [PMID: 35723062 PMCID: PMC9335507 DOI: 10.1177/15353702221102895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Currently, both pathogenic and commensal viruses are continuously being discovered and acknowledged as ubiquitous components of microbial communities. The advancements of systems microbiological approaches have changed the face of virome research. Here, we focus on viral metagenomic approach to study virus community and their interactions with other microbial members as well as their hosts. This review also summarizes challenges, limitations, and benefits of the current virome approaches. Potentially, the studies of virome can be further applied in various biological and clinical fields.
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Affiliation(s)
- Suwalak Chitcharoen
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand,Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavaret Sivapornnukul
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Sunchai Payungporn.
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A World of Viruses Nested within Parasites: Unraveling Viral Diversity within Parasitic Flatworms (Platyhelminthes). Microbiol Spectr 2022; 10:e0013822. [PMID: 35536058 PMCID: PMC9241645 DOI: 10.1128/spectrum.00138-22] [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] [Indexed: 11/25/2022] Open
Abstract
Because parasites have an inextricable relationship with their host, they have the potential to serve as viral reservoirs or facilitate virus host shifts. And yet, little is known about viruses infecting parasitic hosts except for blood-feeding arthropods that are well-known vectors of zoonotic viruses. Herein, we uncovered viruses of flatworms (phylum Platyhelminthes, group Neodermata) that specialize in parasitizing vertebrates and their ancestral free-living relatives. We discovered 115 novel viral sequences, including 1 in Macrostomorpha, 5 in Polycladida, 44 in Tricladida, 1 in Monogenea, 15 in Cestoda, and 49 in Trematoda, through data mining. The majority of newly identified viruses constitute novel families or genera. Phylogenetic analyses show that the virome of flatworms changed dramatically during the transition of neodermatans to a parasitic lifestyle. Most Neodermata viruses seem to codiversify with their host, with the exception of rhabdoviruses, which may switch hosts more often, based on phylogenetic relationships. Neodermata rhabdoviruses also have a position ancestral to vertebrate-associated rhabdo viruses, including lyssaviruses, suggesting that vertebrate-associated rhabdoviruses emerged from a flatworm rhabdovirus in a parasitized host. This study reveals an extensive diversity of viruses in Platyhelminthes and highlights the need to evaluate the role of viral infection in flatworm-associated diseases. IMPORTANCE Little is known about the diversity of parasite-associated viruses and how these viruses may impact parasite fitness, parasite-host interactions, and virus evolution. The discovery of over a hundred viruses associated with a range of free-living and parasitic flatworms, including parasites of economic and clinical relevance, allowed us to compare the viromes of flatworms with contrasting lifestyles. The results suggest that flatworms acquired novel viruses after their transition to a parasitic lifestyle and highlight the possibility that they acquired viruses from their hosts and vice versa. An interesting example is the discovery of flatworm rhabdoviruses that have a position ancestral to rabies viruses and other vertebrate-associated rhabdoviruses, demonstrating that flatworm-associated viruses have emerged in a vertebrate host at least once in history. Therefore, parasitic flatworms may play a role in virus diversity and emergence. The roles that parasite-infecting viruses play in parasite-associated diseases remain to be investigated.
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Gelaw A, Liebert UG. Molecular Detection of Enteric Viruses in Under-Five Children with Diarrhea in Debre Tabor, Northwest Ethiopia. Infect Drug Resist 2022; 15:1981-1994. [PMID: 35480057 PMCID: PMC9035461 DOI: 10.2147/idr.s364142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
Background Viral gastroenteritis belongs to the major public health problems of infant and children worldwide. The largest proportion of morbidity and mortality occurs in Sub-Saharan Africa. Purpose Aimed to assess the burden and genetic diversity of enteric viruses among children with diarrhea. Patients and Methods A cross-sectional study was undertaken from December 2015 to April 2016 in Debre Tabor. A total of thirty-eight children, who presented with diarrhea at Debre Tabor health centers, were included. Fecal samples were collected and screened for enteric viruses by RT-PCR. Data were analyzed using SPSS software. Descriptive summary techniques were used to display the findings. Results Out of thirty-eight children screened, 52.6% were positive for at least one enteric virus. Six (30.0%) of the children had mixed enteric virus infections. Human adenovirus (HAdV) 7 (18.4%) was predominant followed by noroviruses (NoVs) 5 (13.2%), enterovirus (EV) 5 (13.2%), rotavirus A (RVA) 4 (10.5%), human astrovirus (HAstV) 2 (5.3%), and human parechovirus (HPeV) 1 (2.6%). Overall, nineteen different types of enteric virus genotypes were identified. Diverse adenovirus within species A (HAdV-12,-31), B (HAdV-3), C (HAdV-2), and F (HAdV-4) were detected. Norovirus II (GII.4 and GII.6) and norovirus I (GI.2, GI.3, and GI.5) genotypes were found. Sapovirus genotypes within genogroup II (GII.1, GII.5, and GII.6) were identified. Wild-type rotavirus G9 and P[8] genotypes were detected in one of the rotavirus positive samples. Non-polio enteroviruses within species A (coxsackie A virus (CAV) 5, CAV6, and CAV14) and C (enterovirus (EV-C) 99) were also identified. In two of the fecal samples classic HAstV-2 was detected. Conclusion Diverse enteric viruses were detected in fecal samples from under-five children with diarrhea. The detection of heterogeneous enteric viruses in this small data set highlights the need for extended multicenter studies to describe the burden and genetic diversity of enteric virus.
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Affiliation(s)
- Aschalew Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences University of Gondar, Gondar, Ethiopia
- Institute of Virology, Leipzig University, Leipzig, Germany
- Correspondence: Aschalew Gelaw, Email
| | - Uwe G Liebert
- Institute of Virology, Leipzig University, Leipzig, Germany
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Spencer L, Olawuni B, Singh P. Gut Virome: Role and Distribution in Health and Gastrointestinal Diseases. Front Cell Infect Microbiol 2022; 12:836706. [PMID: 35360104 PMCID: PMC8960297 DOI: 10.3389/fcimb.2022.836706] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/10/2022] [Indexed: 12/11/2022] Open
Abstract
The study of the intestinal microbiome is an evolving field of research that includes comprehensive analysis of the vast array of microbes – bacterial, archaeal, fungal, and viral. Various gastrointestinal (GI) diseases, such as Crohn’s disease and ulcerative colitis, have been associated with instability of the gut microbiota. Many studies have focused on importance of bacterial communities with relation to health and disease in humans. The role of viruses, specifically bacteriophages, have recently begin to emerge and have profound impact on the host. Here, we comprehensively review the importance of viruses in GI diseases and summarize their influence in the complex intestinal environment, including their biochemical and genetic activities. We also discuss the distribution of the gut virome as it relates with treatment and immunological advantages. In conclusion, we suggest the need for further studies on this critical component of the intestinal microbiome to decipher the role of the gut virome in human health and disease.
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Kim AH, Armah G, Dennis F, Wang L, Rodgers R, Droit L, Baldridge MT, Handley SA, Harris VC. Enteric virome negatively affects seroconversion following oral rotavirus vaccination in a longitudinally sampled cohort of Ghanaian infants. Cell Host Microbe 2021; 30:110-123.e5. [PMID: 34932985 PMCID: PMC8763403 DOI: 10.1016/j.chom.2021.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/22/2021] [Accepted: 11/29/2021] [Indexed: 01/04/2023]
Abstract
Rotavirus vaccines (RVVs) have substantially diminished mortality from severe rotavirus (RV) gastroenteritis but are significantly less effective in low- and middle-income countries (LMICs), limiting their life-saving potential. The etiology of RVV’s diminished effectiveness remains incompletely understood, but the enteric microbiota has been implicated in modulating immunity to RVVs. Here, we analyze the enteric microbiota in a longitudinal cohort of 122 Ghanaian infants, evaluated over the course of 3 Rotarix vaccinations between 6 and 15 weeks of age, to assess whether bacterial and viral populations are distinct between non-seroconverted and seroconverted infants. We identify bacterial taxa including Streptococcus and a poorly classified taxon in Enterobacteriaceae as positively correlating with seroconversion. In contrast, both bacteriophage diversity and detection of Enterovirus B and multiple novel cosaviruses are negatively associated with RVV seroconversion. These findings suggest that virome-RVV interference is an underappreciated cause of poor vaccine performance in LMICs. Longitudinal analysis of microbiota of Ghanaian infants receiving rotavirus vaccine Streptococcus and Enterobacteriaceae taxa positively associate with RVV seroconversion Enterovirus B, Cosavirus A, and phage richness negatively associate with RVV serostatus
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Isaacs SR, Foskett DB, Maxwell AJ, Ward EJ, Faulkner CL, Luo JYX, Rawlinson WD, Craig ME, Kim KW. Viruses and Type 1 Diabetes: From Enteroviruses to the Virome. Microorganisms 2021; 9:microorganisms9071519. [PMID: 34361954 PMCID: PMC8306446 DOI: 10.3390/microorganisms9071519] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
For over a century, viruses have left a long trail of evidence implicating them as frequent suspects in the development of type 1 diabetes. Through vigorous interrogation of viral infections in individuals with islet autoimmunity and type 1 diabetes using serological and molecular virus detection methods, as well as mechanistic studies of virus-infected human pancreatic β-cells, the prime suspects have been narrowed down to predominantly human enteroviruses. Here, we provide a comprehensive overview of evidence supporting the hypothesised role of enteroviruses in the development of islet autoimmunity and type 1 diabetes. We also discuss concerns over the historical focus and investigation bias toward enteroviruses and summarise current unbiased efforts aimed at characterising the complete population of viruses (the “virome”) contributing early in life to the development of islet autoimmunity and type 1 diabetes. Finally, we review the range of vaccine and antiviral drug candidates currently being evaluated in clinical trials for the prevention and potential treatment of type 1 diabetes.
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Affiliation(s)
- Sonia R. Isaacs
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Dylan B. Foskett
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Anna J. Maxwell
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Emily J. Ward
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Faculty of Medicine and Health, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Clare L. Faulkner
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Jessica Y. X. Luo
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - William D. Rawlinson
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Faculty of Medicine and Health, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Maria E. Craig
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Institute of Endocrinology and Diabetes, Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Faculty of Medicine and Health, Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Ki Wook Kim
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Correspondence: ; Tel.: +61-2-9382-9096
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Dastjerdi A, Everest DJ, Davies H, Denk D, Zell R. A novel dicistrovirus in a captive red squirrel ( Sciurus vulgaris). J Gen Virol 2021; 102. [PMID: 33565956 DOI: 10.1099/jgv.0.001555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Dicistroviruses are single-stranded RNA viruses in the family Dicistroviridae. The viruses have mainly been detected in arthropods and are the cause of several devastating diseases in many of these species such as honeybees. Increasingly, dicistroviruses have also been detected in both mammalian and avian species in faeces, blood and liver, but with unconfirmed pathology. Here, we report a novel dicistrovirus detected in the intestinal content of a captive red squirrel with enteritis along with the disease history, pathology and genomic characterisation of the virus. Virus particle morphology resembled those of picornaviruses with a diameter of 28-32 nm but failed to be detected using a mammalian/avian pan viral microarray. Next-generation sequencing confirmed a dicistrovirus having a typical dicistrovirus genome organization, but with the polyprotein 1 being shorter by about 100 amino acids, compared to that of other dicistroviruses. Phylogenetic analysis of ORF1 and ORF2 sequences clustered the virus with two yet unassigned dicistroviruses detected in Gorilla gorilla and a freshwater arthropod and likely to be designated to a new genus. Our data further highlights the ever-growing diversity of dicistroviruses, but the clinical significance of the virus in mammalian species and particularly red squirrels has yet to be established.
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Affiliation(s)
- Akbar Dastjerdi
- Animal and Plant Health Agency (APHA)-Weybridge, Addlestone, Surrey, KT15 3NB, UK
| | - David J Everest
- Animal and Plant Health Agency (APHA)-Weybridge, Addlestone, Surrey, KT15 3NB, UK
| | - Hannah Davies
- School of Veterinary Medicine, University of Surrey, Guildford, GU2 7XH, UK.,Animal and Plant Health Agency (APHA)-Weybridge, Addlestone, Surrey, KT15 3NB, UK
| | - Daniela Denk
- International Zoo Veterinary Group (IZVG), Station House, Parkwood Street, Keighley, West Yorkshire, BD21 4NQ, UK
| | - Roland Zell
- Section for Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich-Schiller-Universität Jena, Hans-Knöll-Str. 2, Germany
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Umeoguaju FU, Ephraim-Emmanuel BC, Patrick-Iwuanyanwu KC, Zelikoff JT, Orisakwe OE. Plant-Derived Food Grade Substances (PDFGS) Active Against Respiratory Viruses: A Systematic Review of Non-clinical Studies. Front Nutr 2021; 8:606782. [PMID: 33634160 PMCID: PMC7900554 DOI: 10.3389/fnut.2021.606782] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/15/2021] [Indexed: 12/11/2022] Open
Abstract
Human diet comprises several classes of phytochemicals some of which are potentially active against human pathogenic viruses. This study examined available evidence that identifies existing food plants or constituents of edible foods that have been reported to inhibit viral pathogenesis of the human respiratory tract. SCOPUS and PUBMED databases were searched with keywords designed to retrieve articles that investigated the effect of plant-derived food grade substances (PDFGS) on the activities of human pathogenic viruses. Eligible studies for this review were those done on viruses that infect the human respiratory tract. Forty six (46) studies met the specified inclusion criteria from the initial 5,734 hits. The selected studies investigated the effects of different PDFGS on the infectivity, proliferation and cytotoxicity of different respiratory viruses including influenza A virus (IAV), influenza B virus (IBV), Respiratory syncytial virus (RSV), human parainfluenza virus (hPIV), Human coronavirus NL63 (HCoV-NL63), and rhinovirus (RV) in cell lines and mouse models. This review reveals that PDFGS inhibits different stages of the pathological pathways of respiratory viruses including cell entry, replication, viral release and viral-induced dysregulation of cellular homeostasis and functions. These alterations eventually lead to the reduction of virus titer, viral-induced cellular damages and improved survival of host cells. Major food constituents active against respiratory viruses include flavonoids, phenolic acids, tannins, lectins, vitamin D, curcumin, and plant glycosides such as glycyrrhizin, acteoside, geniposide, and iridoid glycosides. Herbal teas such as guava tea, green and black tea, adlay tea, cistanche tea, kuding tea, licorice extracts, and edible bird nest extracts were also effective against respiratory viruses in vitro. The authors of this review recommend an increased consumption of foods rich in these PDFGS including legumes, fruits (e.g berries, citrus), tea, fatty fish and curcumin amongst human populations with high prevalence of respiratory viral infections in order to prevent, manage and/or reduce the severity of respiratory virus infections.
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Affiliation(s)
- Francis U. Umeoguaju
- World Bank Africa Centre of Excellence in Public Health and Toxicological Research (ACE-PUTOR), University of Port Harcourt, Port Harcourt, Nigeria
| | - Benson C. Ephraim-Emmanuel
- World Bank Africa Centre of Excellence in Public Health and Toxicological Research (ACE-PUTOR), University of Port Harcourt, Port Harcourt, Nigeria
- Department of Dental Health Sciences, Ogbia, Bayelsa State College of Health Technology, Otakeme, Nigeria
| | - Kingsley C. Patrick-Iwuanyanwu
- World Bank Africa Centre of Excellence in Public Health and Toxicological Research (ACE-PUTOR), University of Port Harcourt, Port Harcourt, Nigeria
| | - Judith T. Zelikoff
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, NY, United States
| | - Orish Ebere Orisakwe
- World Bank Africa Centre of Excellence in Public Health and Toxicological Research (ACE-PUTOR), University of Port Harcourt, Port Harcourt, Nigeria
- Department of Experimental Pharmacology and Toxicology, Faculty of Pharmacy, University of Port Harcourt, Port Harcourt, Nigeria
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15
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Abstract
The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the 'virome'. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 1031 particles on Earth. The human virome is similarly vast and complex, consisting of approximately 1013 particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral 'dark matter'. Nevertheless, it is now clear that viral community states can be associated with adverse outcomes for the human host, whereas other states are characteristic of health. In this Review, we provide an overview of research on the human virome and highlight outstanding recent studies that explore the assembly, composition and dynamics of the human virome as well as host-virome interactions in health and disease.
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16
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Holtz LR. Putting the Virome on the Map: The Influence of Host Geography and Ethnicity on the Gut Virome. Cell Host Microbe 2020; 28:636-637. [PMID: 33181076 DOI: 10.1016/j.chom.2020.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We know little about factors that ordain the composition of the diverse community of viruses (virome) in the human gut. In this issue of Cell Host & Microbe, Zuo et al. highlight the importance of geography, urbanization, ethnicity, and diet on the shape of the adult gut DNA virome.
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Affiliation(s)
- Lori R Holtz
- Washington University Department of Pediatrics, St. Louis, MO, USA.
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17
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Tan SK, Granados AC, Bouquet J, Hoy-Schulz YE, Green L, Federman S, Stryke D, Haggerty TD, Ley C, Yeh MT, Jannat K, Maldonado YA, Andino R, Parsonnet J, Chiu CY. Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination. Sci Rep 2020; 10:15392. [PMID: 32958861 PMCID: PMC7506025 DOI: 10.1038/s41598-020-71791-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 07/09/2020] [Indexed: 12/22/2022] Open
Abstract
The potential role of enteric viral infections and the developing infant virome in affecting immune responses to the oral poliovirus vaccine (OPV) is unknown. Here we performed viral metagenomic sequencing on 3 serially collected stool samples from 30 Bangladeshi infants following OPV vaccination and compared findings to stool samples from 16 age-matched infants in the United States (US). In 14 Bangladeshi infants, available post-vaccination serum samples were tested for polio-neutralizing antibodies. The abundance (p = 0.006) and richness (p = 0.013) of the eukaryotic virome increased with age and were higher than seen in age-matched US infants (p < 0.001). In contrast, phage diversity metrics remained stable and were similar to those in US infants. Non-poliovirus eukaryotic virus abundance (3.68 log10 vs. 2.25 log10, p = 0.002), particularly from potential viral pathogens (2.78log10 vs. 0.83log10, p = 0.002), and richness (p = 0.016) were inversely associated with poliovirus shedding. Following vaccination, 28.6% of 14 infants tested developed neutralizing antibodies to all three Sabin types and also exhibited higher rates of poliovirus shedding (p = 0.020). No vaccine-derived poliovirus variants were detected. These results reveal an inverse association between eukaryotic virome abundance and poliovirus shedding. Overall gut virome ecology and concurrent viral infections may impact oral vaccine responsiveness in Bangladeshi infants.
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Affiliation(s)
- Susanna K Tan
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jerome Bouquet
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yana Emmy Hoy-Schulz
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Lauri Green
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Doug Stryke
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Thomas D Haggerty
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine Ley
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ming-Te Yeh
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Kaniz Jannat
- Environmental Intervention Unit, Infectious Disease Division, International Centre for Diarrheal Disease Research, Dhaka, Bangladesh
| | - Yvonne A Maldonado
- Division of Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Julie Parsonnet
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
- Division of Infectious Diseases, Department of Medicine, University of California, 185 Berry Street, Box #0134, San Francisco, CA, 94107, USA.
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18
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Zuo T, Sun Y, Wan Y, Yeoh YK, Zhang F, Cheung CP, Chen N, Luo J, Wang W, Sung JJY, Chan PKS, Wang K, Chan FKL, Miao Y, Ng SC. Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization. Cell Host Microbe 2020; 28:741-751.e4. [PMID: 32910902 DOI: 10.1016/j.chom.2020.08.005] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/06/2020] [Accepted: 08/11/2020] [Indexed: 12/21/2022]
Abstract
The human-gut-DNA virome is highly diverse and individual specific, but little is known of its variation at a population level. Here, we report the fecal DNA virome of 930 healthy adult subjects from two regions in China (Hong Kong and Yunnan) spanning six ethnicities (Han, Zang, Miao, Bai, Dai, and Hani), and including urban and rural residents for each ethnicity. Twenty host factors were found to significantly correlate with the human-gut virome variation, with geography carrying the strongest impact and ethnicity-distinct diets associating with certain viral species. Urbanization enhances interindividual dissimilarities between gut viromes, with the duration of urban residence associating with multiple bacteriophages, including Lactobacillus phage and Lactococcus phage. Overall, the gut virome presents more heterogeneity relative to the bacterial microbiome across the examined Chinese populations. This study highlights population-based variations and the importance of host and environmental factors in shaping the DNA virome in the human gut.
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Affiliation(s)
- Tao Zuo
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Yang Sun
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China
| | - Yating Wan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun Kit Yeoh
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Fen Zhang
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun Pan Cheung
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Nan Chen
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Juan Luo
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China
| | - Wen Wang
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China
| | - Joseph J Y Sung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kunhua Wang
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China
| | - Francis K L Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Yinglei Miao
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China.
| | - Siew C Ng
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China.
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19
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Kim MW, Sharp CR, Boyd CJ, Twomey LN. Faecal PCR panel results and clinical findings in Western Australian dogs with diarrhoea. Aust Vet J 2020; 98:563-569. [PMID: 32839975 DOI: 10.1111/avj.13008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 12/01/2022]
Abstract
AIM To describe faecal PCR (fPCR) results and clinical findings of dogs seen at a university teaching hospital for diarrhoea. DESIGN Retrospective case series (April 2015 to July 2018). PROCEDURE Data were collected from the hospital electronic medical records. Data extracted included signalment, history, clinical signs, treatment, fPCR panel results, other faecal diagnostic test results and antimicrobial use. RESULTS One hundred and sixty-eight dogs with diarrhoea had a fPCR panel submitted. Most dogs (115, 68.5%) had diarrhoea of 3 days or less duration. Clostridium perfringens alpha toxin gene was most frequently detected (156, 92.9%) by fPCR, followed by Campylobacter spp. (55, 32.7%), canine parvovirus (CPV) (29, 17.3%), Salmonella spp. (14, 8.3%) and Giardia spp. (9, 5.4%). For the 45 dogs that had a negative point-of-care CPV test, 13 were CPV fPCR positive; some of which were adult dogs with current vaccination status. A total of 94/168 (56%) dogs received antimicrobials at some time during the treatment of diarrhoea. CONCLUSION Faecal PCR panels can identify dogs with enteric organisms in their faeces that traditional faecal diagnostics may miss, thus contributing additional information to the diagnostic process. Nonetheless, fPCR results should be interpreted in light of the clinical findings, and particular consideration given to avoiding inappropriate use of antimicrobials. This study highlights that testing for C. perfringens alpha toxin gene is not likely to be diagnostically helpful, and that adult dogs with diarrhoea might be identified as CPV positive with PCR testing, despite a negative point-of-care CPV test result and a current vaccination status.
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Affiliation(s)
- M W Kim
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - C R Sharp
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - C J Boyd
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - L N Twomey
- VetPath Laboratory Services, Belmont, Western Australia, Australia
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20
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Enteric Viral Co-Infections: Pathogenesis and Perspective. Viruses 2020; 12:v12080904. [PMID: 32824880 PMCID: PMC7472086 DOI: 10.3390/v12080904] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 02/06/2023] Open
Abstract
Enteric viral co-infections, infections involving more than one virus, have been reported for a diverse group of etiological agents, including rotavirus, norovirus, astrovirus, adenovirus, and enteroviruses. These pathogens are causative agents for acute gastroenteritis and diarrheal disease in immunocompetent and immunocompromised individuals of all ages globally. Despite virus–virus co-infection events in the intestine being increasingly detected, little is known about their impact on disease outcomes or human health. Here, we review what is currently known about the clinical prevalence of virus–virus co-infections and how co-infections may influence vaccine responses. While experimental investigations into enteric virus co-infections have been limited, we highlight in vivo and in vitro models with exciting potential to investigate viral co-infections. Many features of virus–virus co-infection mechanisms in the intestine remain unclear, and further research will be critical.
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21
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Gut Microbiota and Liver Interaction through Immune System Cross-Talk: A Comprehensive Review at the Time of the SARS-CoV-2 Pandemic. J Clin Med 2020; 9:jcm9082488. [PMID: 32756323 PMCID: PMC7464500 DOI: 10.3390/jcm9082488] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023] Open
Abstract
Background and aims: The gut microbiota is a complex ecosystem containing bacteria, viruses, fungi, yeasts and other single-celled organisms. It is involved in the development and maintenance of both innate and systemic immunity of the body. Emerging evidence has shown its role in liver diseases through the immune system cross-talk. We review herein literature data regarding the triangular interaction between gut microbiota, immune system and liver in health and disease. Methods: We conducted a search on the main medical databases for original articles, reviews, meta-analyses, randomized clinical trials and case series using the following keywords and acronyms and their associations: gut microbiota, microbiome, gut virome, immunity, gastrointestinal-associated lymphoid tissue (GALT), non-alcoholic fatty liver disease (NAFLD), non-alcoholic steato-hepatitis (NASH), alcoholic liver disease, liver cirrhosis, hepatocellular carcinoma. Results: The gut microbiota consists of microorganisms that educate our systemic immunity through GALT and non-GALT interactions. The latter maintain health but are also involved in the pathophysiology and in the outcome of several liver diseases, particularly those with metabolic, toxic or immune-mediated etiology. In this context, gut virome has an emerging role in liver diseases and needs to be further investigated, especially due to the link reported between severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection and hepatic dysfunctions. Conclusions: Changes in gut microbiota composition and alterations in the immune system response are involved in the pathogenesis of metabolic and immune-mediated liver diseases.
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22
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Desai C, Handley SA, Rodgers R, Rodriguez C, Ordiz MI, Manary MJ, Holtz LR. Growth velocity in children with Environmental Enteric Dysfunction is associated with specific bacterial and viral taxa of the gastrointestinal tract in Malawian children. PLoS Negl Trop Dis 2020; 14:e0008387. [PMID: 32574158 PMCID: PMC7310680 DOI: 10.1371/journal.pntd.0008387] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 05/13/2020] [Indexed: 12/22/2022] Open
Abstract
Environmental enteric dysfunction (EED) is characterized by diffuse villous atrophy of the small bowel. EED is strongly associated with stunting, a major public health problem linked to increased childhood morbidity and mortality. EED and subsequent stunting of linear growth are surmised to have microbial origins. To interrogate this relationship, we defined the comprehensive virome (eukaryotic virus and bacteriophage) and bacterial microbiome of a longitudinal cohort of rural Malawian children with extensive metadata and intestinal permeability testing at each time point. We found thirty bacterial taxa differentially associated with linear growth. We detected many eukaryotic viruses. Neither the total number of eukaryotic families nor a specific viral family was statistically associated with improved linear growth. We identified 3 differentially abundant bacteriophage among growth velocities. Interestingly, there was a positive correlation between bacteria and bacteriophage richness in children with subsequent adequate/moderate growth which children with subsequent poor growth lacked. This suggests that a disruption in the equilibrium between bacteria and bacteriophage communities might be associated with subsequent poor growth. Future studies of EED and stunting should include the evaluation of viral communities in addition to bacterial microbiota to understand the complete microbial ecology of these poorly understood entities.
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Affiliation(s)
- Chandni Desai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Scott A. Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rachel Rodgers
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Cynthia Rodriguez
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Maria I. Ordiz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Mark J. Manary
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pediatrics, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Lori R. Holtz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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23
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Tsatsakis A, Petrakis D, Nikolouzakis TK, Docea AO, Calina D, Vinceti M, Goumenou M, Kostoff RN, Mamoulakis C, Aschner M, Hernández AF. COVID-19, an opportunity to reevaluate the correlation between long-term effects of anthropogenic pollutants on viral epidemic/pandemic events and prevalence. Food Chem Toxicol 2020; 141:111418. [PMID: 32437891 PMCID: PMC7211730 DOI: 10.1016/j.fct.2020.111418] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 02/07/2023]
Abstract
Occupational, residential, dietary and environmental exposures to mixtures of synthetic anthropogenic chemicals after World War II have a strong relationship with the increase of chronic diseases, health cost and environmental pollution. The link between environment and immunity is particularly intriguing as it is known that chemicals and drugs can cause immunotoxicity (e.g., allergies and autoimmune diseases). In this review, we emphasize the relationship between long-term exposure to xenobiotic mixtures and immune deficiency inherent to chronic diseases and epidemics/pandemics. We also address the immunotoxicologic risk of vulnerable groups, taking into account biochemical and biophysical properties of SARS-CoV-2 and its immunopathological implications. We particularly underline the common mechanisms by which xenobiotics and SARS-CoV-2 act at the cellular and molecular level. We discuss how long-term exposure to thousand chemicals in mixtures, mostly fossil fuel derivatives, exposure toparticle matters, metals, ultraviolet (UV)–B radiation, ionizing radiation and lifestyle contribute to immunodeficiency observed in the contemporary pandemic, such as COVID-19, and thus threaten global public health, human prosperity and achievements, and global economy. Finally, we propose metrics which are needed to address the diverse health effects of anthropogenic COVID-19 crisis at present and those required to prevent similar future pandemics. Developmental exposure to environmental factors can disrupt the immune system. Long-term low-dose exposure to chemical mixtures is linked to imunodeficiency Immunodeficiency contributes to chronic diseases and the current Covid-19 pandemics. Environmental chemicals and microorganisms share similar molecular pathomechanisms (AhR pathway). Understanding the underlying pathomechanisms helps to improve public health.
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Affiliation(s)
- Aristidis Tsatsakis
- Laboratory of Toxicology, Medical School, University of Crete, Voutes, 71409 Heraklion, Crete, Greece; Department of Analytical and Forensic Medical Toxicology, Sechenov University, 2-4 Bolshaya Pirogovskaya st., 119991 Moscow, Russia; Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York, NY 10461, USA.
| | - Demetrious Petrakis
- Laboratory of Toxicology, Medical School, University of Crete, Voutes, 71409 Heraklion, Crete, Greece.
| | | | - Anca Oana Docea
- Department of Toxicology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania.
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania.
| | - Marco Vinceti
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, I-41125 Modena, Italy.
| | - Marina Goumenou
- Laboratory of Toxicology, Medical School, University of Crete, Voutes, 71409 Heraklion, Crete, Greece
| | - Ronald N Kostoff
- School of Public Policy, Georgia Institute of Technology, Gainesville, VA, 20155, USA.
| | - Charalampos Mamoulakis
- Department of Urology, University General Hospital of Heraklion, Medical School, University of Crete, 71003 Heraklion, Crete, Greece.
| | - Michael Aschner
- Department of Analytical and Forensic Medical Toxicology, Sechenov University, 2-4 Bolshaya Pirogovskaya st., 119991 Moscow, Russia; Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York, NY 10461, USA.
| | - Antonio F Hernández
- Department of Legal Medicine and Toxicology, University of Granada School of Medicine, 180016 Granada, Spain.
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Ugboko HU, Nwinyi OC, Oranusi SU, Oyewale JO. Childhood diarrhoeal diseases in developing countries. Heliyon 2020; 6:e03690. [PMID: 32322707 PMCID: PMC7160433 DOI: 10.1016/j.heliyon.2020.e03690] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 12/27/2022] Open
Abstract
Diarrhoeal diseases collectively constitute a serious public health challenge globally, especially as the leading cause of death in children (after respiratory diseases). Childhood diarrhoea affecting children under the age of five accounts for approximately 63% of the global burden. Accurate and timely detection of the aetiology of these diseases is very crucial; but conventional methods, apart from being laborious and time-consuming, often fail to identify difficult-to-culture pathogens. The aetiological agent of an average of up to 40% of cases of diarrhoea cannot be identified. This review gives an overview of the recent trends in the epidemiology and treatment of diarrhoea and aims at highlighting the potentials of metagenomics technique as a diagnostic method for enteric infections.
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Affiliation(s)
- Harriet U Ugboko
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Canaanland, KM 10, Idiroko Road, P.M.B, 1023, Ota, Ogun State, Nigeria
| | - Obinna C Nwinyi
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Canaanland, KM 10, Idiroko Road, P.M.B, 1023, Ota, Ogun State, Nigeria
| | - Solomon U Oranusi
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Canaanland, KM 10, Idiroko Road, P.M.B, 1023, Ota, Ogun State, Nigeria
| | - John O Oyewale
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Canaanland, KM 10, Idiroko Road, P.M.B, 1023, Ota, Ogun State, Nigeria
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25
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Wang C, Li Q, Ren J. Microbiota-Immune Interaction in the Pathogenesis of Gut-Derived Infection. Front Immunol 2019; 10:1873. [PMID: 31456801 PMCID: PMC6698791 DOI: 10.3389/fimmu.2019.01873] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022] Open
Abstract
Gut-derived infection is among the most common complications in patients who underwent severe trauma, serious burn, major surgery, hemorrhagic shock or severe acute pancreatitis (SAP). It could cause sepsis and multiple organ dysfunction syndrome (MODS), which are regarded as a leading cause of mortality in these cases. Gut-derived infection is commonly caused by pathological translocation of intestinal bacteria or endotoxins, resulting from the dysfunction of the gut barrier. In the last decades, the studies regarding to the pathogenesis of gut-derived infection mainly focused on the breakdown of intestinal epithelial tight junction and increased permeability. Limited information is available on the roles of intestinal microbial barrier in the development of gut-derived infection. Recently, advances of next-generation DNA sequencing techniques and its utilization has revolutionized the gut microecology, leading to novel views into the composition of the intestinal microbiota and its connections with multiple diseases. Here, we reviewed the recent progress in the research field of intestinal barrier disruption and gut-derived infection, mainly through the perspectives of the dysbiosis of intestinal microbiota and its interaction with intestinal mucosal immune cells. This review presents novel insights into how the gut microbiota collaborates with mucosal immune cells to involve the development of pathological bacterial translocation. The data might have important implication to better understand the mechanism underlying pathological bacterial translocation, contributing us to develop new strategies for prevention and treatment of gut-derived sepsis.
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Affiliation(s)
- Chenyang Wang
- Research Institute of General Surgery, Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Qiurong Li
- Research Institute of General Surgery, Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Jianan Ren
- Research Institute of General Surgery, Jinling Hospital, Medical School, Nanjing University, Nanjing, China
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26
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Rosshart SP, Herz J, Vassallo BG, Hunter A, Wall MK, Badger JH, McCulloch JA, Anastasakis DG, Sarshad AA, Leonardi I, Collins N, Blatter JA, Han SJ, Tamoutounour S, Potapova S, Foster St Claire MB, Yuan W, Sen SK, Dreier MS, Hild B, Hafner M, Wang D, Iliev ID, Belkaid Y, Trinchieri G, Rehermann B. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science 2019; 365:365/6452/eaaw4361. [PMID: 31371577 DOI: 10.1126/science.aaw4361] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/06/2019] [Accepted: 06/27/2019] [Indexed: 12/11/2022]
Abstract
Laboratory mouse studies are paramount for understanding basic biological phenomena but also have limitations. These include conflicting results caused by divergent microbiota and limited translational research value. To address both shortcomings, we transferred C57BL/6 embryos into wild mice, creating "wildlings." These mice have a natural microbiota and pathogens at all body sites and the tractable genetics of C57BL/6 mice. The bacterial microbiome, mycobiome, and virome of wildlings affect the immune landscape of multiple organs. Their gut microbiota outcompete laboratory microbiota and demonstrate resilience to environmental challenges. Wildlings, but not conventional laboratory mice, phenocopied human immune responses in two preclinical studies. A combined natural microbiota- and pathogen-based model may enhance the reproducibility of biomedical studies and increase the bench-to-bedside safety and success of immunological studies.
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Affiliation(s)
- Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
| | - Jasmin Herz
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Brian G Vassallo
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Ashli Hunter
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Morgan K Wall
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - John A McCulloch
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Dimitrios G Anastasakis
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Irina Leonardi
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Nicholas Collins
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joshua A Blatter
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Seong-Ji Han
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samira Tamoutounour
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Svetlana Potapova
- Laboratory of Animal Sciences Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Mark B Foster St Claire
- Laboratory of Animal Sciences Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Wuxing Yuan
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.,Leidos Biomedical Research, Inc., Microbiome and Genetics Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shurjo K Sen
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.,Leidos Biomedical Research, Inc., Microbiome and Genetics Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew S Dreier
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Benedikt Hild
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Iliyan D Iliev
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Yasmine Belkaid
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
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27
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Cordey S, Laubscher F, Hartley MA, Junier T, Pérez-Rodriguez FJ, Keitel K, Vieille G, Samaka J, Mlaganile T, Kagoro F, Boillat-Blanco N, Mbarack Z, Docquier M, Brito F, Eibach D, May J, Sothmann P, Aldrich C, Lusingu J, Tapparel C, D'Acremont V, Kaiser L. Detection of dicistroviruses RNA in blood of febrile Tanzanian children. Emerg Microbes Infect 2019; 8:613-623. [PMID: 30999808 PMCID: PMC6493270 DOI: 10.1080/22221751.2019.1603791] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fever is the leading cause of paediatric outpatient consultations in Sub-Saharan Africa. Although most are suspected to be of viral origin, a putative causative pathogen is not identified in over a quarter of these febrile episodes. Using a de novo assembly sequencing approach, we report the detection (15.4%) of dicistroviruses (DicV) RNA in sera collected from 692 febrile Tanzanian children. In contrast, DicV RNA was only detected in 1/77 (1.3%) plasma samples from febrile Tanzanian adults, suggesting that children could represent the primary susceptible population. Estimated viral load by specific quantitative real-time RT–PCR assay ranged from < 1.32E3 to 1.44E7 viral RNA copies/mL serum. Three DicV full-length genomes were obtained, and a phylogenetic analyse on the capsid region showed the presence of two clusters representing tentative novel genus. Although DicV-positive cases were detected throughout the year, a significantly higher positivity rate was observed during the rainy season. This study reveals that novel DicV RNA is frequently detected in the blood of Tanzanian children, paving the way for further investigations to determine if DicV possibly represent a new agent in humans.
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Affiliation(s)
- Samuel Cordey
- a Division of Infectious Diseases and Laboratory of Virology , University of Geneva Hospitals Geneva , Switzerland.,b University of Geneva Medical School Geneva , Switzerland
| | - Florian Laubscher
- a Division of Infectious Diseases and Laboratory of Virology , University of Geneva Hospitals Geneva , Switzerland.,b University of Geneva Medical School Geneva , Switzerland
| | - Mary-Anne Hartley
- c Department of Ambulatory Care and Community Medicine , Lausanne University Hospital Lausanne , Switzerland
| | - Thomas Junier
- d Swiss Institute of Bioinformatics Geneva , Switzerland.,e Global Health Institute, School of Life Sciences , École Polytechnique Fédérale de Lausanne Lausanne , Switzerland
| | | | - Kristina Keitel
- f Swiss Tropical and Public Health Institute , University of Basel Basel , Switzerland
| | - Gael Vieille
- a Division of Infectious Diseases and Laboratory of Virology , University of Geneva Hospitals Geneva , Switzerland.,b University of Geneva Medical School Geneva , Switzerland
| | - Josephine Samaka
- g Ifakara Health Institute , Dar es Salaam , Tanzania.,h Amana Hospital , Dar es Salaam , Tanzania
| | | | - Frank Kagoro
- g Ifakara Health Institute , Dar es Salaam , Tanzania
| | - Noémie Boillat-Blanco
- f Swiss Tropical and Public Health Institute , University of Basel Basel , Switzerland.,i Infectious Diseases Service , Lausanne University Hospital Lausanne , Switzerland
| | | | - Mylène Docquier
- k iGE3 Genomics Platform , University of Geneva Geneva , Switzerland
| | - Francisco Brito
- d Swiss Institute of Bioinformatics Geneva , Switzerland.,l Department of Genetic Medicine and Development , Faculty of Medicine of Geneva Geneva , Switzerland
| | - Daniel Eibach
- m Department of Infectious Disease Epidemiology , Bernhard Nocht Institute for Tropical Medicine Hamburg , Germany.,n German Centre for Infection Research (DZIF) , Hamburg , Germany
| | - Jürgen May
- m Department of Infectious Disease Epidemiology , Bernhard Nocht Institute for Tropical Medicine Hamburg , Germany.,n German Centre for Infection Research (DZIF) , Hamburg , Germany
| | - Peter Sothmann
- m Department of Infectious Disease Epidemiology , Bernhard Nocht Institute for Tropical Medicine Hamburg , Germany.,n German Centre for Infection Research (DZIF) , Hamburg , Germany.,o Division of Tropical Medicine, 1st Department of Medicine , University Medical Center Hamburg-Eppendorf Hamburg , Germany.,p Division of Infectious Diseases and Tropical Medicine , Medical Center of the University of Munich (LMU) Munich , Germany
| | - Cassandra Aldrich
- m Department of Infectious Disease Epidemiology , Bernhard Nocht Institute for Tropical Medicine Hamburg , Germany.,p Division of Infectious Diseases and Tropical Medicine , Medical Center of the University of Munich (LMU) Munich , Germany
| | - John Lusingu
- q National Institute for Medical Research , Tanga Research Centre , Tanga , Tanzania
| | | | - Valérie D'Acremont
- c Department of Ambulatory Care and Community Medicine , Lausanne University Hospital Lausanne , Switzerland.,f Swiss Tropical and Public Health Institute , University of Basel Basel , Switzerland
| | - Laurent Kaiser
- a Division of Infectious Diseases and Laboratory of Virology , University of Geneva Hospitals Geneva , Switzerland.,b University of Geneva Medical School Geneva , Switzerland.,r Geneva Centre for Emerging Viral Diseases Geneva , Switzerland
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28
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Mukhopadhya I, Segal JP, Carding SR, Hart AL, Hold GL. The gut virome: the 'missing link' between gut bacteria and host immunity? Therap Adv Gastroenterol 2019; 12:1756284819836620. [PMID: 30936943 PMCID: PMC6435874 DOI: 10.1177/1756284819836620] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 02/14/2019] [Indexed: 02/04/2023] Open
Abstract
The human gut virome includes a diverse collection of viruses that infect our own cells as well as other commensal organisms, directly impacting on our well-being. Despite its predominance, the virome remains one of the least understood components of the gut microbiota, with appropriate analysis toolkits still in development. Based on its interconnectivity with all living cells, it is clear that the virome cannot be studied in isolation. Here we review the current understanding of the human gut virome, specifically in relation to other constituents of the microbiome, its evolution and life-long association with its host, and our current understanding in the context of inflammatory bowel disease and associated therapies. We propose that the gut virome and the gut bacterial microbiome share similar trajectories and interact in both health and disease and that future microbiota studies should in parallel characterize the gut virome to uncover its role in health and disease.
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Affiliation(s)
- Indrani Mukhopadhya
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, UK Gut Health Group, The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Jonathan P. Segal
- St. Mark’s Hospital, Watford Road, Harrow, UK Imperial College London, South Kensington Campus, Department of Surgery and Cancer, London, UK
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, The Quadram Institute, Norwich Research Park, Norwich, Norfolk, UK Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
| | - Ailsa L. Hart
- St. Mark’s Hospital, Watford Road, Harrow, UK Imperial College London, South Kensington Campus, Department of Surgery and Cancer, London, UK
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29
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Mukherjee S, Joardar N, Sengupta S, Sinha Babu SP. Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings. J Nutr Biochem 2018; 61:111-128. [PMID: 30196243 PMCID: PMC7126101 DOI: 10.1016/j.jnutbio.2018.07.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/24/2018] [Accepted: 07/28/2018] [Indexed: 02/07/2023]
Abstract
The human gut microbiota has been the interest of extensive research in recent years and our knowledge on using the potential capacity of these microbes are growing rapidly. Microorganisms colonized throughout the gastrointestinal tract of human are coevolved through symbiotic relationship and can influence physiology, metabolism, nutrition and immune functions of an individual. The gut microbes are directly involved in conferring protection against pathogen colonization by inducing direct killing, competing with nutrients and enhancing the response of the gut-associated immune repertoire. Damage in the microbiome (dysbiosis) is linked with several life-threatening outcomes viz. inflammatory bowel disease, cancer, obesity, allergy, and auto-immune disorders. Therefore, the manipulation of human gut microbiota came out as a potential choice for therapeutic intervention of the several human diseases. Herein, we review significant studies emphasizing the influence of the gut microbiota on the regulation of host responses in combating infectious and inflammatory diseases alongside describing the promises of gut microbes as future therapeutics.
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Affiliation(s)
- Suprabhat Mukherjee
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Nikhilesh Joardar
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Subhasree Sengupta
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Santi P Sinha Babu
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India.
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30
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Siqueira JD, Dominguez-Bello MG, Contreras M, Lander O, Caballero-Arias H, Xutao D, Noya-Alarcon O, Delwart E. Complex virome in feces from Amerindian children in isolated Amazonian villages. Nat Commun 2018; 9:4270. [PMID: 30323210 PMCID: PMC6189175 DOI: 10.1038/s41467-018-06502-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/06/2018] [Indexed: 01/22/2023] Open
Abstract
The number of viruses circulating in small isolated human populations may be reduced by viral extinctions and rare introductions. Here we used viral metagenomics to characterize the eukaryotic virome in feces from healthy children from a large urban center and from three Amerindian villages with minimal outside contact. Numerous human enteric viruses, mainly from the Picornaviridae and Caliciviridae families, were sequenced from each of the sites. Multiple children from the same villages shed closely related viruses reflecting frequent transmission clusters. Feces of isolated villagers also contained multiple viral genomes of unknown cellular origin from the Picornavirales order and CRESS-DNA group and higher levels of nematode and protozoan DNA. Despite cultural and geographic isolation, the diversity of enteric human viruses was therefore not reduced in these Amazonian villages. Frequent viral introductions and/or increased susceptibility to enteric infections may account for the complex fecal virome of Amerindian children in isolated villages.
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Affiliation(s)
- Juliana D Siqueira
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, 20.231-050, Brazil
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology and of Anthropology, Rutgers University, New Brunswick, NJ, 08901-8554, USA
| | - Monica Contreras
- Center for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Orlana Lander
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela
| | - Hortensia Caballero-Arias
- Department of Anthropology, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Deng Xutao
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
| | - Oscar Noya-Alarcon
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela.,Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho, 7101, Venezuela
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, 94118, USA. .,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA.
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31
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Harris VC. The Significance of the Intestinal Microbiome for Vaccinology: From Correlations to Therapeutic Applications. Drugs 2018; 78:1063-1072. [PMID: 29943376 PMCID: PMC6061423 DOI: 10.1007/s40265-018-0941-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite unprecedented advances in understanding the intestinal microbiome, its potential to improve fields such as vaccinology has yet to be realized. This review briefly outlines the immunologic potential of the intestinal microbiome for vaccinology and highlights areas where the microbiome holds specific promise in vaccinology. Oral rotavirus vaccine effectiveness in low-income countries is used as a case study to describe how the intestinal microbiome may be employed to improve a vaccine's immunogenicity. A top-down, evidence-based approach is proposed to identify effective microbiota-based applications for vaccine improvement. Applying evidence from field studies in pertinent populations that correlate microbiome composition with vaccine effectiveness to appropriate experimental platforms will lead to the identification of safe, vaccine-supporting microbiota targets that are relevant to populations in need of improvement in vaccine-induced immunity.
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Affiliation(s)
- Vanessa C Harris
- Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands.
- Department of Medicine, Division of Infectious Diseases and Center for Experimental and Molecular Medicine (CEMM), Academic Medical Center, Amsterdam, The Netherlands.
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32
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Alcalá AC, Pérez K, Blanco R, González R, Ludert JE, Liprandi F, Vizzi E. Molecular detection of human enteric viruses circulating among children with acute gastroenteritis in Valencia, Venezuela, before rotavirus vaccine implementation. Gut Pathog 2018; 10:6. [PMID: 29483944 PMCID: PMC5822563 DOI: 10.1186/s13099-018-0232-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/18/2018] [Indexed: 01/15/2023] Open
Abstract
Background The role of rotavirus as main etiologic agent of diarrhea has been well documented worldwide, including in Venezuela. However, information about the prevalence of gastrointestinal viruses such as calicivirus, adenovirus and astrovirus is limited and the contribution of other agents as Aichi virus and klassevirus is largely unknown. To explore the etiological spectrum of diarrhea associated with agents other than rotaviruses, 227 stool samples from children under 5 years old with acute gastroenteritis, collected in Valencia (Venezuela) from 2001 to 2005, and previously tested as rotavirus-negative, were analyzed for caliciviruses, adenoviruses, astroviruses, Aichi viruses, klasseviruses, picobirnaviruses and enteroviruses by specific RT-PCRs. Results At least one viral agent was detected in 134 (59%) of the samples analyzed, mainly from children under 24 months of age and most of them belonging to the lowest socioeconomic status. Overall, enterovirus was identified as the most common viral agent (37.9%), followed by calicivirus (23.3%), adenovirus (11.5%), astrovirus (3.5%), klassevirus (1.3%) and Aichi virus (0.4%), while no picobirnavirus was detected. Klasseviruses were found during 2004 and 2005 and Aichi viruses only in 2005, indicating their circulation in Venezuela; meanwhile, the rest of the viruses were detected during the whole study period. Coinfections with two or more viruses were found in 39 (29.1%) of the infected children, most under 24 months of age. Adenovirus was involved as the coinfecting agent in at least 46.9% of the cases, but no differences concerning socio-demographic variables were observed between the coinfected and the single infected children. Conclusions The results show that various enteric viruses, including enteroviruses, caliciviruses and adenoviruses, accounted for a significant proportion of infantile diarrhea cases in Venezuela before rotavirus vaccine implementation. In addition, emerging viruses as Aichi virus and klassevirus were found, indicating the need to continue monitoring their spreading into the communities. Efforts are needed to develop more accurate methods to identify the major causes of diarrhea and to provide tools for more effective preventive measures.
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Affiliation(s)
- Ana C Alcalá
- 1Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020 Venezuela.,4Present Address: Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Mexico, D.F. Mexico
| | - Kriss Pérez
- 1Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020 Venezuela
| | - Ruth Blanco
- 1Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020 Venezuela
| | - Rosabel González
- 3Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Mexico, D.F. Mexico
| | - Juan E Ludert
- Instituto Autónomo de Biomedicina Dr. Jacinto Convit-MPPS, Caracas, Venezuela
| | - Ferdinando Liprandi
- 1Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020 Venezuela
| | - Esmeralda Vizzi
- 1Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apdo. 21827, Caracas, 1020 Venezuela
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Van Borm S, Steensels M, Mathijs E, Yinda CK, Matthijnssens J, Lambrecht B. Complete coding sequence of a novel picorna-like virus in a blackbird infected with Usutu virus. Arch Virol 2018; 163:1701-1703. [PMID: 29442227 DOI: 10.1007/s00705-018-3761-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/22/2018] [Indexed: 11/25/2022]
Abstract
Using random high-throughput RNA sequencing, the complete coding sequence of a novel picorna-like virus (a 9,228-nt contig containing 212,202 reads) was determined from a blackbird (Turdus merula) infected with Usutu virus. This sequence shares only 36% amino acid sequence identity with its closest homolog, arivirus 1, (an unclassified member of the order Picornavirales), and shares its dicistronic genome arrangement. The new virus was therefore tentatively named "blackbird arilivirus" (ari-like virus). The nearly complete genome sequence consists of at least 9,228 nt and contains two open reading frames (ORFs) encoding the nonstructural polyprotein (2235 amino acids) and structural polyprotein (769 amino acids). Two TaqMan RT-qPCR assays specific for ORF1 confirmed the presence of high levels of this novel virus in the original sample. Nucleotide composition analysis suggests that blackbird arilivirus is of dietary (plant) origin.
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Affiliation(s)
- Steven Van Borm
- Directorate Viral Diseases, Veterinary and Agrochemical Research Center CODA-CERVA, Brussels, Belgium.
| | - Mieke Steensels
- Directorate Viral Diseases, Veterinary and Agrochemical Research Center CODA-CERVA, Brussels, Belgium
| | - Elisabeth Mathijs
- Directorate Viral Diseases, Veterinary and Agrochemical Research Center CODA-CERVA, Brussels, Belgium
| | - Claude Kwe Yinda
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Bénédicte Lambrecht
- Directorate Viral Diseases, Veterinary and Agrochemical Research Center CODA-CERVA, Brussels, Belgium
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Zárate S, Taboada B, Yocupicio-Monroy M, Arias CF. Human Virome. Arch Med Res 2017; 48:701-716. [DOI: 10.1016/j.arcmed.2018.01.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/22/2018] [Indexed: 12/16/2022]
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Rampelli S, Turroni S, Schnorr SL, Soverini M, Quercia S, Barone M, Castagnetti A, Biagi E, Gallinella G, Brigidi P, Candela M. Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin. Environ Microbiol 2017; 19:4728-4735. [DOI: 10.1111/1462-2920.13938] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 08/17/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Simone Rampelli
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Stephanie L. Schnorr
- Department of Anthropology, Laboratories of Molecular Anthropology and Microbiome Research; University of Oklahoma; Norman OK USA
| | - Matteo Soverini
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Sara Quercia
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Monica Barone
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Andrea Castagnetti
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Elena Biagi
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Giorgio Gallinella
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
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Case-Control Comparison of Enteric Viromes in Captive Rhesus Macaques with Acute or Idiopathic Chronic Diarrhea. J Virol 2017; 91:JVI.00952-17. [PMID: 28659484 DOI: 10.1128/jvi.00952-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/13/2017] [Indexed: 12/12/2022] Open
Abstract
Diarrhea is the major cause of non-research-associated morbidity and mortality affecting the supply of rhesus macaques and, potentially, their responses to experimental treatments. Idiopathic chronic diarrhea (ICD) in rhesus macaques also resembles ulcerative colitis, one form of human inflammatory bowel disease. To test for viral etiologies, we characterized and compared the fecal viromes from 32 healthy animals, 31 animals with acute diarrhea, and 29 animals with ICD. The overall fractions of eukaryotic viral reads were 0.063% for the healthy group, 0.131% for the acute-diarrhea group, and 0.297% for the chronic-diarrhea group. Eukaryotic viruses belonging to 6 viral families, as well as numerous circular Rep-encoding single-stranded DNA (CRESS DNA) viral genomes, were identified. The most commonly detected sequences were from picornaviruses, making up 59 to 88% of all viral reads, followed by 9 to 17% for CRESS DNA virus sequences. The remaining 5 virus families, Adenoviridae, Astroviridae, Anelloviridae, Picobirnaviridae, and Parvoviridae, collectively made up 1 to 3% of the viral reads, except for parvoviruses, which made up 23% of the viral reads in the healthy group. Detected members of the families Picornaviridae and Parvoviridae were highly diverse, consisting of multiple genera, species, and genotypes. Coinfections with members of up to six viral families were detected. Complete and partial viral genomes were assembled and used to measure the number of matching short sequence reads in feces from the 92 animals in the two clinical and the healthy control groups. Several enterovirus genotypes and CRESS DNA genomes were associated with ICD relative to healthy animals. Conversely, higher read numbers from different parvoviruses were associated with healthy animals. Our study reveals a high level of enteric coinfections with diverse viruses in a captive rhesus macaque colony and identifies several viruses positively or negatively associated with ICD.
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Abstract
Viruses must establish an intimate relationship with their hosts and vectors in order to infect, replicate, and disseminate; hence, viruses can be considered as symbionts with their hosts. Symbiotic relationships encompass different lifestyles, including antagonistic (or pathogenic, the most well-studied lifestyle for viruses), commensal (probably the most common lifestyle), and mutualistic (important beneficial partners). Symbiotic relationships can shape the evolution of the partners in a holobiont, and placing viruses in this context provides an important framework for understanding virus-host relationships and virus ecology. Although antagonistic relationships are thought to lead to coevolution, this is not always clear in virus-host interactions, and impacts on evolution may be complex. Commensalism implies a hitchhiking role for viruses-selfish elements just along for the ride. Mutualistic relationships have been described in detail in the past decade, and they reveal how important viruses are in considering host ecology. Ultimately, symbiosis can lead to symbiogenesis, or speciation through fusion, and the presence of large amounts of viral sequence in the genomes of everything from bacteria to humans, including some important functional genes, illustrates the significance of viral symbiogenesis in the evolution of all life on Earth.
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Affiliation(s)
- Marilyn J Roossinck
- Center for Infectious Disease Dynamics, Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania 16802;
| | - Edelio R Bazán
- Center for Infectious Disease Dynamics, Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania 16802;
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Chansaenroj J, Tuanthap S, Thanusuwannasak T, Duang-in A, Klinfueng S, Thaneskongtong N, Vutithanachot V, Vongpunsawad S, Poovorawan Y. Human enteroviruses associated with and without diarrhea in Thailand between 2010 and 2016. PLoS One 2017; 12:e0182078. [PMID: 28750058 PMCID: PMC5531555 DOI: 10.1371/journal.pone.0182078] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/12/2017] [Indexed: 11/23/2022] Open
Abstract
Non-bacterial acute gastroenteritis (AGE) associated with virus infection affects individuals living in developing countries, especially children. To investigate whether shedding of certain human enterovirus (EV) is more frequently detected in the stool of individuals with AGE of unknown etiology than individuals without AGE symptoms, we tested fecal samples collected from 2,692 individuals with diarrhea between January 2010 and December 2016. Samples were tested for rotavirus, norovirus, and EV by reverse-transcription polymerase chain reaction (RT-PCR) and adenovirus by PCR. EV-positive samples were subjected to sequencing and phylogenetic analysis to identify EV species and types. Findings were compared to EV found in 1,310 fecal samples from individuals without AGE who were diagnosed with hand, foot, and mouth disease (HFMD). While the majority of viruses identified in AGE consisted of human rotavirus (22.7%), norovirus (11.4%) and adenovirus (9.3%), we identified EV (6.2%) belonging mainly to species B, C, and rhinovirus. In contrast, >92% of EV found without AGE symptoms belonged to species A. Although AGE symptoms are not often attributed to EV infection, EV was associated with diarrhea of unknown etiology at least in 3.4% of AGE cases. While CV-A6 was most likely to be found in stools of HFMD patients, rhinovirus A and C were the two most common EV species associated with AGE. Elucidating group-specific EV infection in diseases with and without AGE will be useful in assisting identification, clinical management, and the surveillance of EV infection in the community.
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Affiliation(s)
- Jira Chansaenroj
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Supansa Tuanthap
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Thanundorn Thanusuwannasak
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ausanee Duang-in
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sirapa Klinfueng
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | | | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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Moreno PS, Wagner J, Mansfield CS, Stevens M, Gilkerson JR, Kirkwood CD. Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics. PLoS One 2017; 12:e0178433. [PMID: 28570584 PMCID: PMC5453527 DOI: 10.1371/journal.pone.0178433] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/12/2017] [Indexed: 01/01/2023] Open
Abstract
The virome has been increasingly investigated in numerous animal species and in different sites of the body, facilitating the identification and discovery of a variety of viruses. In spite of this, the faecal virome of healthy dogs has not been investigated. In this study we describe the faecal virome of healthy dogs and dogs with acute diarrhoea in Australia, using a shotgun metagenomic approach. Viral sequences from a range of different virus families, including both RNA and DNA families, and known pathogens implicated in enteric disease were documented. Twelve viral families were identified, of which four were bacteriophages. Eight eukaryotic viral families were detected: Astroviridae, Coronaviridae, Reoviridae, Picornaviridae, Caliciviridae, Parvoviridae, Adenoviridae and Papillomaviridae. Families Astroviridae, Picornaviridae and Caliciviridae were found only in dogs with acute diarrhoea, with Astroviridae being the most common family identified in this group. Due to its prevalence, characterisation the complete genome of a canine astrovirus was performed. These studies indicate that metagenomic analyses are useful for the investigation of viral populations in the faeces of dogs. Further studies to elucidate the epidemiological and biological relevance of these findings are warranted.
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Affiliation(s)
- Paloma S. Moreno
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Translational Research and Animal Clinical Trial Study (TRACTS) group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- * E-mail:
| | - Josef Wagner
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Caroline S. Mansfield
- Translational Research and Animal Clinical Trial Study (TRACTS) group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Matthew Stevens
- Australian Genome Research Facility, Melbourne, Victoria, Australia
| | - James R. Gilkerson
- Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Carl D. Kirkwood
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
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40
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Abbas AA, Diamond J, Chehoud C, Chang B, Kotzin J, Young J, Imai I, Haas A, Cantu E, Lederer D, Meyer K, Milewski R, Olthoff K, Shaked A, Christie J, Bushman F, Collman R. The Perioperative Lung Transplant Virome: Torque Teno Viruses Are Elevated in Donor Lungs and Show Divergent Dynamics in Primary Graft Dysfunction. Am J Transplant 2017; 17:1313-1324. [PMID: 27731934 PMCID: PMC5389935 DOI: 10.1111/ajt.14076] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/12/2016] [Accepted: 09/26/2016] [Indexed: 01/25/2023]
Abstract
Primary graft dysfunction (PGD) is a principal cause of early morbidity and mortality after lung transplantation, but its pathogenic mechanisms are not fully clarified. To date, studies using standard clinical assays have not linked microbial factors to PGD. We previously used comprehensive metagenomic methods to characterize viruses in lung allografts >1 mo after transplant and found that levels of Anellovirus, mainly torque teno viruses (TTVs), were significantly higher than in nontransplanted healthy controls. We used quantitative polymerase chain reaction to analyze TTV and shotgun metagenomics to characterize full viral communities in acellular bronchoalveolar lavage from donor organs and postreperfusion allografts in PGD and non-PGD lung transplant recipient pairs. Unexpectedly, TTV DNA levels were elevated 100-fold in donor lungs compared with healthy adults (p = 0.0026). Although absolute TTV levels did not differ by PGD status, PGD cases showed a smaller increase in TTV levels from before to after transplant than did control recipients (p = 0.041). Metagenomic sequencing revealed mainly TTV and bacteriophages of respiratory tract bacteria, but no viral taxa distinguished PGD cases from controls. These findings suggest that conditions associated with brain death promote TTV replication and that greater immune activation or tissue injury associated with PGD may restrict TTV abundance in the lung.
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Affiliation(s)
- A. A. Abbas
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J.M. Diamond
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - C. Chehoud
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - B. Chang
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J.J. Kotzin
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J.C. Young
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - I. Imai
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - A.R. Haas
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - E. Cantu
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - D.J. Lederer
- Departments of Medicine and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY
| | - K. Meyer
- School of Medicine and Public Health, University of Wisconsin, Madison, WI
| | - R.K. Milewski
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - K.M. Olthoff
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - A. Shaked
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J.D. Christie
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - F.D. Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Corresponding authors: Frederic Bushman: , Ronald Collman:
| | - R.G. Collman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Corresponding authors: Frederic Bushman: , Ronald Collman:
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41
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VirusSeeker, a computational pipeline for virus discovery and virome composition analysis. Virology 2017; 503:21-30. [PMID: 28110145 DOI: 10.1016/j.virol.2017.01.005] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/07/2017] [Accepted: 01/10/2017] [Indexed: 01/21/2023]
Abstract
The advent of Next Generation Sequencing (NGS) has vastly increased our ability to discover novel viruses and to systematically define the spectrum of viruses present in a given specimen. Such studies have led to the discovery of novel viral pathogens as well as broader associations of the virome with diverse diseases including inflammatory bowel disease, severe acute malnutrition and HIV/AIDS. Critical to the success of these efforts are robust bioinformatic pipelines for rapid classification of microbial sequences. Existing computational tools are typically focused on either eukaryotic virus discovery or virome composition analysis but not both. Here we present VirusSeeker, a BLAST-based NGS data analysis pipeline designed for both purposes. VirusSeeker has been successfully applied in several previously published virome studies. Here we demonstrate the functionality of VirusSeeker in both novel virus discovery and virome composition analysis.
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42
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Lim ES, Wang D, Holtz LR. The Bacterial Microbiome and Virome Milestones of Infant Development. Trends Microbiol 2016; 24:801-810. [PMID: 27353648 DOI: 10.1016/j.tim.2016.06.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/24/2016] [Accepted: 06/02/2016] [Indexed: 12/14/2022]
Abstract
The human gut harbors a complex community of bacteria, viruses, fungi, protists, and other microorganisms (collectively termed the microbiome) that impact health and disease. Emerging studies indicate that the gut bacterial microbiome and virome play an important role in healthy infant development. In turn, the composition of the microbiome during development can be influenced by factors such as dietary, environmental, and maternal conditions. As such, the microbiome trajectory during early infancy could be predictors of healthy development. Conversely, adverse early events in life may have consequences later in life. This review focuses on our understanding of the bacterial microbiome and virome during early development, conditions that might influence these processes, and their long-term implications for infant health.
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Affiliation(s)
- Efrem S Lim
- Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Lori R Holtz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
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43
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Li SX, Armstrong A, Neff CP, Shaffer M, Lozupone CA, Palmer BE. Complexities of Gut Microbiome Dysbiosis in the Context of HIV Infection and Antiretroviral Therapy. Clin Pharmacol Ther 2016; 99:600-11. [PMID: 26940481 DOI: 10.1002/cpt.363] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/26/2016] [Accepted: 02/28/2016] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus (HIV) infection is associated with an altered gut microbiome that is not consistently restored with effective antiretroviral therapy (ART). Interpretation of the specific microbiome changes observed during HIV infection is complicated by factors like population, sample type, and ART-each of which may have dramatic effects on gut bacteria. Understanding how these factors shape the microbiome during HIV infection (which we refer to as the HIV-associated microbiome) is critical for defining its role in HIV disease, and for developing therapies that restore gut health during infection.
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Affiliation(s)
- S X Li
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ajs Armstrong
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA.,Department of Immunology and Microbiology, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - C P Neff
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - M Shaffer
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA.,Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - C A Lozupone
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - B E Palmer
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
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44
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Rampelli S, Soverini M, Turroni S, Quercia S, Biagi E, Brigidi P, Candela M. ViromeScan: a new tool for metagenomic viral community profiling. BMC Genomics 2016. [PMID: 26932765 DOI: 10.1186/s12864-016-2446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Bioinformatics tools available for metagenomic sequencing analysis are principally devoted to the identification of microorganisms populating an ecological niche, but they usually do not consider viruses. Only some software have been designed to profile the viral sequences, however they are not efficient in the characterization of viruses in the context of complex communities, like the intestinal microbiota, containing bacteria, archeabacteria, eukaryotic microorganisms and viruses. In any case, a comprehensive description of the host-microbiota interactions can not ignore the profile of eukaryotic viruses within the virome, as viruses are definitely critical for the regulation of the host immunophenotype. RESULTS ViromeScan is an innovative metagenomic analysis tool that characterizes the taxonomy of the virome directly from raw data of next-generation sequencing. The tool uses hierarchical databases for eukaryotic viruses to unambiguously assign reads to viral species more accurately and >1000 fold faster than other existing approaches. We validated ViromeScan on synthetic microbial communities and applied it on metagenomic samples of the Human Microbiome Project, providing a sensitive eukaryotic virome profiling of different human body sites. CONCLUSIONS ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples from reads of other microorganisms. This implies that users can fully characterize the microbiome, including bacteria and viruses, by shotgun metagenomic sequencing followed by different bioinformatic pipelines.
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Affiliation(s)
- Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Matteo Soverini
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Sara Quercia
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Elena Biagi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
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45
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Rampelli S, Soverini M, Turroni S, Quercia S, Biagi E, Brigidi P, Candela M. ViromeScan: a new tool for metagenomic viral community profiling. BMC Genomics 2016; 17:165. [PMID: 26932765 PMCID: PMC4774116 DOI: 10.1186/s12864-016-2446-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bioinformatics tools available for metagenomic sequencing analysis are principally devoted to the identification of microorganisms populating an ecological niche, but they usually do not consider viruses. Only some software have been designed to profile the viral sequences, however they are not efficient in the characterization of viruses in the context of complex communities, like the intestinal microbiota, containing bacteria, archeabacteria, eukaryotic microorganisms and viruses. In any case, a comprehensive description of the host-microbiota interactions can not ignore the profile of eukaryotic viruses within the virome, as viruses are definitely critical for the regulation of the host immunophenotype. RESULTS ViromeScan is an innovative metagenomic analysis tool that characterizes the taxonomy of the virome directly from raw data of next-generation sequencing. The tool uses hierarchical databases for eukaryotic viruses to unambiguously assign reads to viral species more accurately and >1000 fold faster than other existing approaches. We validated ViromeScan on synthetic microbial communities and applied it on metagenomic samples of the Human Microbiome Project, providing a sensitive eukaryotic virome profiling of different human body sites. CONCLUSIONS ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples from reads of other microorganisms. This implies that users can fully characterize the microbiome, including bacteria and viruses, by shotgun metagenomic sequencing followed by different bioinformatic pipelines.
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Affiliation(s)
- Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Matteo Soverini
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Sara Quercia
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Elena Biagi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, 40126, Italy.
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46
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The Human Virome in Health and Disease. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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47
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Yu J, Ordiz MI, Stauber J, Shaikh N, Trehan I, Barnell E, Head RD, Maleta K, Tarr PI, Manary MJ. Environmental Enteric Dysfunction Includes a Broad Spectrum of Inflammatory Responses and Epithelial Repair Processes. Cell Mol Gastroenterol Hepatol 2015; 2:158-174.e1. [PMID: 26973864 PMCID: PMC4769221 DOI: 10.1016/j.jcmgh.2015.12.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/03/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Environmental enteric dysfunction (EED), a chronic diffuse inflammation of the small intestine, is associated with stunting in children in the developing world. The pathobiology of EED is poorly understood because of the lack of a method to elucidate the host response. This study tested a novel microarray method to overcome limitation of RNA sequencing to interrogate the host transcriptome in feces in Malawian children with EED. METHODS In 259 children, EED was measured by lactulose permeability (%L). After isolating low copy numbers of host messenger RNA, the transcriptome was reliably and reproducibly profiled, validated by polymerase chain reaction. Messenger RNA copy number then was correlated with %L and differential expression in EED. The transcripts identified were mapped to biological pathways and processes. The children studied had a range of %L values, consistent with a spectrum of EED from none to severe. RESULTS We identified 12 transcripts associated with the severity of EED, including chemokines that stimulate T-cell proliferation, Fc fragments of multiple immunoglobulin families, interferon-induced proteins, activators of neutrophils and B cells, and mediators that dampen cellular responses to hormones. EED-associated transcripts mapped to pathways related to cell adhesion, and responses to a broad spectrum of viral, bacterial, and parasitic microbes. Several mucins, regulatory factors, and protein kinases associated with the maintenance of the mucous layer were expressed less in children with EED than in normal children. CONCLUSIONS EED represents the activation of diverse elements of the immune system and is associated with widespread intestinal barrier disruption. Differentially expressed transcripts, appropriately enumerated, should be explored as potential biomarkers.
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Key Words
- %L, lactulose permeability
- EED, environmental enteric dysfunction
- Environmental Enteropathy
- FARMS, factor analyses for robust microarray summarization
- Fecal Transcriptome
- G-CSF, granulocyte colony–stimulating factor
- HAZ, height-for-age z score
- IRON, iterative rank order normalization
- Intestinal Inflammation
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- RMA, robust multi-array average
- Stunting
- dHAZ, change in height-for-age z score
- mRNA, messenger RNA
- qPCR, quantitative polymerase chain reaction
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Affiliation(s)
- Jinsheng Yu
- Genome Technology Access Center, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - M. Isabel Ordiz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Jennifer Stauber
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Nurmohammad Shaikh
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Indi Trehan
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Erica Barnell
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Richard D. Head
- Genome Technology Access Center, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Ken Maleta
- Department of Community Health, College of Medicine, Blantyre, Malawi
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Mark J. Manary
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri,Department of Community Health, College of Medicine, Blantyre, Malawi,Children’s Nutrition Research Center, Baylor College of Medicine, Houston, Texas,Correspondence Address correspondence to: Mark J. Manary, MD, Department of Pediatrics, Washington University School of Medicine, One Children's Place, St. Louis Children's Hospital St. Louis, Missouri 63110. fax: (314) 454-4345.Department of PediatricsWashington University School of MedicineSt. LouisMissouri 63110
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48
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Scarpellini E, Ianiro G, Attili F, Bassanelli C, De Santis A, Gasbarrini A. The human gut microbiota and virome: Potential therapeutic implications. Dig Liver Dis 2015; 47:1007-12. [PMID: 26257129 PMCID: PMC7185617 DOI: 10.1016/j.dld.2015.07.008] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 02/07/2023]
Abstract
Human gut microbiota is a complex ecosystem with several functions integrated in the host organism (metabolic, immune, nutrients absorption, etc.). Human microbiota is composed by bacteria, yeasts, fungi and, last but not least, viruses, whose composition has not been completely described. According to previous evidence on pathogenic viruses, the human gut harbours plant-derived viruses, giant viruses and, only recently, abundant bacteriophages. New metagenomic methods have allowed to reconstitute entire viral genomes from the genetic material spread in the human gut, opening new perspectives on the understanding of the gut virome composition, the importance of gut microbiome, and potential clinical applications. This review reports the latest evidence on human gut "virome" composition and its function, possible future therapeutic applications in human health in the context of the gut microbiota, and attempts to clarify the role of the gut "virome" in the larger microbial ecosystem.
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Affiliation(s)
- Emidio Scarpellini
- Department of Pediatrics, Umberto I University Hospital, “Sapienza” University of Rome, Italy
| | - Gianluca Ianiro
- Division of Internal Medicine and Gastroenterology, Gemelli University Hospital, Catholic University of Sacred Heart, Italy
| | - Fabia Attili
- Division of Endoscopy, Gemelli University Hospital, Catholic University of Sacred Heart, Italy
| | - Chiara Bassanelli
- Gastroenterology Division, Umberto I University Hospital, “Sapienza” University of Rome, Italy
| | - Adriano De Santis
- Gastroenterology Division, Umberto I University Hospital, “Sapienza” University of Rome, Italy
| | - Antonio Gasbarrini
- Division of Internal Medicine and Gastroenterology, Gemelli University Hospital, Catholic University of Sacred Heart, Italy,Corresponding author at: Gastroenterology and Internal Medicine Division, Catholic University of Sacred Heart, Largo Gemelli 1, 00168 Rome, Italy. Tel.: +39 06 3015 6265; fax: +39 06 3015 6265.
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49
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Wylie TN, Wylie KM, Herter BN, Storch GA. Enhanced virome sequencing using targeted sequence capture. Genome Res 2015; 25:1910-20. [PMID: 26395152 PMCID: PMC4665012 DOI: 10.1101/gr.191049.115] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 09/22/2015] [Indexed: 12/18/2022]
Abstract
Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.
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Affiliation(s)
- Todd N Wylie
- The Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Kristine M Wylie
- The Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Brandi N Herter
- The Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Gregory A Storch
- The Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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50
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Lim ES, Zhou Y, Zhao G, Bauer IK, Droit L, Ndao IM, Warner BB, Tarr PI, Wang D, Holtz LR. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat Med 2015; 21:1228-34. [PMID: 26366711 DOI: 10.1038/nm.3950] [Citation(s) in RCA: 414] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/20/2015] [Indexed: 12/13/2022]
Abstract
The early years of life are important for immune development and influence health in adulthood. Although it has been established that the gut bacterial microbiome is rapidly acquired after birth, less is known about the viral microbiome (or 'virome'), consisting of bacteriophages and eukaryotic RNA and DNA viruses, during the first years of life. Here, we characterized the gut virome and bacterial microbiome in a longitudinal cohort of healthy infant twins. The virome and bacterial microbiome were more similar between co-twins than between unrelated infants. From birth to 2 years of age, the eukaryotic virome and the bacterial microbiome expanded, but this was accompanied by a contraction of and shift in the bacteriophage virome composition. The bacteriophage-bacteria relationship begins from birth with a high predator-low prey dynamic, consistent with the Lotka-Volterra prey model. Thus, in contrast to the stable microbiome observed in adults, the infant microbiome is highly dynamic and associated with early life changes in the composition of bacteria, viruses and bacteriophages with age.
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Affiliation(s)
- Efrem S Lim
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pathology &Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Yanjiao Zhou
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Guoyan Zhao
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Irma K Bauer
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lindsay Droit
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pathology &Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - I Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Barbara B Warner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Phillip I Tarr
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pathology &Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lori R Holtz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
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