1
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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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2
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COVID-19: The Ethno-Geographic Perspective of Differential Immunity. Vaccines (Basel) 2023; 11:vaccines11020319. [PMID: 36851197 PMCID: PMC9966855 DOI: 10.3390/vaccines11020319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), the agent behind the worst global pandemic of the 21st century (COVID-19), is primarily a respiratory-disease-causing virus called SARS-CoV-2 that is responsible for millions of new cases (incidence) and deaths (mortalities) worldwide. Many factors have played a role in the differential morbidity and mortality experienced by nations and ethnicities against SARS-CoV-2, such as the quality of primary medical health facilities or enabling economies. At the same time, the most important variable, i.e., the subsequent ability of individuals to be immunologically sensitive or resistant to the infection, has not been properly discussed before. Despite having excellent medical facilities, an astounding issue arose when some developed countries experienced higher morbidity and mortality compared with their relatively underdeveloped counterparts. Hence, this investigative review attempts to analyze the issue from an angle of previously undiscussed genetic, epigenetic, and molecular immune resistance mechanisms in correlation with the pathophysiology of SARS-CoV-2 and varied ethnicity-based immunological responses against it. The biological factors discussed here include the overall landscape of human microbiota, endogenous retroviral genes spliced into the human genome, and copy number variation, and how they could modulate the innate and adaptive immune systems that put a certain ethnic genetic architecture at a higher risk of SARS-CoV-2 infection than others. Considering an array of these factors in their entirety may help explain the geographic disparity of disease incidence, severity, and subsequent mortality associated with the disease while at the same time encouraging scientists to design new experimental approaches to investigation.
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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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4
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Nishimura L, Fujito N, Sugimoto R, Inoue I. Detection of Ancient Viruses and Long-Term Viral Evolution. Viruses 2022; 14:v14061336. [PMID: 35746807 PMCID: PMC9230872 DOI: 10.3390/v14061336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.
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Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Naoko Fujito
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Correspondence: ; Tel.: +81-55-981-6795
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5
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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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Stockdale SR, Hill C. Progress and prospects of the healthy human gut virome. Curr Opin Virol 2021; 51:164-171. [PMID: 34742036 DOI: 10.1016/j.coviro.2021.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/30/2021] [Accepted: 10/08/2021] [Indexed: 12/26/2022]
Abstract
Not all viruses associated with humans cause disease. Non-pathogenic human-infecting viruses are predicted as important for immune system induction and preparation. Phages that infect bacteria are the most abundant predators of the human microbial ecosystem, promoting and maintaining bacterial diversity. Metagenomic analyses of the human gut virome and microbiome are unravelling the intricate predator-prey dynamics of phage-bacteria co-existence, co-evolution, and their interplay with the human host. While most adults harbour a distinctly individualistic and persistent community of virulent phages, new-borns are dominated by temperate phages heavily influenced by environmental exposures. The future development of microbiome-based interventions, therapeutics, and manipulation, will require a greater understanding of the human microbiome and the virome.
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Affiliation(s)
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, T12 YT20, Ireland; School of Microbiology, University College Cork, T12 YT20, Ireland.
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Abstract
Gut viruses are important, yet often neglected, players in the complex human gut microbial ecosystem. Recently, the number of human gut virome studies has been increasing; however, we are still only scratching the surface of the immense viral diversity. In this study, 254 virus-enriched fecal metagenomes from 204 Danish subjects were used to generate the Danish Enteric Virome Catalog (DEVoC) containing 12,986 nonredundant viral scaffolds, of which the majority was previously undescribed, encoding 190,029 viral genes. The DEVoC was used to compare 91 healthy DEVoC gut viromes from children, adolescents, and adults that were used to create the DEVoC. Gut viromes of healthy Danish subjects were dominated by phages. While most phage genomes (PGs) only occurred in a single subject, indicating large virome individuality, 39 PGs were present in more than 10 healthy subjects. Among these 39 PGs, the prevalences of three PGs were associated with age. To further study the prevalence of these 39 prevalent PGs, 1,880 gut virome data sets of 27 studies from across the world were screened, revealing several age-, geography-, and disease-related prevalence patterns. Two PGs also showed a remarkably high prevalence worldwide-a crAss-like phage (20.6% prevalence), belonging to the tentative AlphacrAssvirinae subfamily, and a previously undescribed circular temperate phage infecting Bacteroides dorei (14.4% prevalence), called LoVEphage because it encodes lots of viral elements. Due to the LoVEphage's high prevalence and novelty, public data sets in which the LoVEphage was detected were de novo assembled, resulting in an additional 18 circular LoVEphage-like genomes (67.9 to 72.4 kb). IMPORTANCE Through generation of the DEVoC, we added numerous previously uncharacterized viral genomes and genes to the ever-increasing worldwide pool of human gut viromes. The DEVoC, the largest human gut virome catalog generated from consistently processed fecal samples, facilitated the analysis of the 91 healthy Danish gut viromes. Characterizing the biggest cohort of healthy gut viromes from children, adolescents, and adults to date confirmed the previously established high interindividual variation in human gut viromes and demonstrated that the effect of age on the gut virome composition was limited to the prevalence of specific phage (groups). The identification of a previously undescribed prevalent phage illustrates the usefulness of developing virome catalogs, and we foresee that the DEVoC will benefit future analysis of the roles of gut viruses in human health and disease.
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Prezioso C, Van Ghelue M, Pietropaolo V, Moens U. Detection of Quebec Polyomavirus DNA in Samples from Different Patient Groups. Microorganisms 2021; 9:microorganisms9051082. [PMID: 34070030 PMCID: PMC8158138 DOI: 10.3390/microorganisms9051082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
Polyomaviruses infect many species, including humans. So far, 15 polyomaviruses have been described in humans, but it remains to be established whether all of these are genuine human polyomaviruses. The most recent polyomavirus to be detected in a person is Quebec polyomavirus (QPyV), which was identified in a metagenomic analysis of a stool sample from an 85-year-old hospitalized man. We used PCR to investigate the presence of QPyV DNA in urine samples from systemic lupus erythematosus (SLE) patients (67 patients; 135 samples), multiple sclerosis patients (n = 35), HIV-positive patients (n = 66) and pregnant women (n = 65). Moreover, cerebrospinal fluid from patients with suspected neurological diseases (n = 63), nasopharyngeal aspirates from patients (n = 80) with respiratory symptoms and plasma samples from HIV-positive patients (n = 65) were examined. QPyV DNA was found in urine from 11 (16.4%), 10 (15.4%) and 5 (14.3%) SLE patients, pregnant women, and multiple sclerosis patients, respectively. No QPyV DNA could be detected in the other samples. Alignment with the only available QPyV sequence in the GenBank revealed amino acid substitutions in the HI-loop of capsid protein VP1 in 6/28 of the isolates. Our results show that QPyV viruria can occur, but whether it may cause clinical symptoms in the patients remains to be determined.
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Affiliation(s)
- Carla Prezioso
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy;
- IRCSS San Raffaele Pisana, Microbiology of Chronic Neuro-degenerative Pathologies, 00163 Rome, Italy
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, 9038 Tromsø, Norway;
- Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy;
- Correspondence: (V.P.); (U.M.)
| | - Ugo Moens
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway
- Correspondence: (V.P.); (U.M.)
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Tan X, Chai T, Duan J, Wu J, Zhang H, Li Y, Huang Y, Hu X, Zheng P, Song J, Ji P, Jin X, Zhang H, Xie P. Dynamic changes occur in the DNA gut virome of female cynomolgus macaques during aging. Microbiologyopen 2021; 10:e1186. [PMID: 33970533 PMCID: PMC8087919 DOI: 10.1002/mbo3.1186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/17/2022] Open
Abstract
Aging is a critical factor affecting physical health and disease in mammals. Emerging evidence indicates that aging may affect the gut bacteriome in cynomolgus macaques, but little is known about whether or how the gut virome changes with age. Here, we compared the DNA gut viral composition of 16 female cynomolgus monkeys (Macaca fascicularis) at three life stages (young, adult, and old) using the shotgun metagenome sequencing method. We found that the DNA gut virome from these monkeys differed substantially among the three groups. The gut viruses were dominated by bacteriophages, the most abundant of which was the Caudovirales order (i.e., Siphoviridae, Myoviridae, and Podoviridae families). Additionally, the co‐occurrence analysis revealed that the age‐related bacteriophages were correlated in an extensive and complex manner with the main intestinal bacteria (i.e., Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria phyla). Furthermore, the age‐related DNA gut viral functions were enriched for genetic information processing, nucleotide, and folate metabolism. Our gut virome analysis provides new insight into how aging influences the gut virome of non‐human primates.
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Affiliation(s)
- Xunmin Tan
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, China
| | - Tingjia Chai
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, China.,State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
| | - Jiajia Duan
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, China.,The M.O.E. Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Jing Wu
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, China.,The M.O.E. Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Hanping Zhang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, China
| | - Yifan Li
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, China
| | - Yu Huang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, China
| | - Xi Hu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Zheng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, China
| | - Jinlin Song
- College of Stomatology, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, Chongqing, China.,Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Ping Ji
- College of Stomatology, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, Chongqing, China
| | - Xin Jin
- Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, Chongqing, China.,Key Laboratory of Psychoseomadsy, Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Hongmei Zhang
- College of Stomatology, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, Chongqing, China
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, Chongqing Medical University, Chongqing, China
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10
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Hedžet S, Rupnik M, Accetto T. Novel Siphoviridae Bacteriophages Infecting Bacteroides uniformis Contain Diversity Generating Retroelement. Microorganisms 2021; 9:microorganisms9050892. [PMID: 33919474 PMCID: PMC8143477 DOI: 10.3390/microorganisms9050892] [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: 03/26/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
Intestinal phages are abundant and important components of gut microbiota, yet the isolated and characterized representatives that infect abundant gut bacteria are sparse. Here we describe the isolation of human intestinal phages infecting Bacteroidesuniformis. Bacteroides is one of the most common bacterial groups in the global human gut microbiota; however, to date not many Bacteroides specific phages are known. Phages isolated in this study belong to a novel viral genus, Bacuni, within the Siphoviridae family. Their genomes encode diversity-generating retroelements (DGR), which were shown in other bacteriophages to promote phage adaptation to rapidly changing environmental conditions and to broaden their host range. Three isolated phages showed 99.83% genome identity but one of them infected a distinct B. uniformis strain. The tropism of Bacuni phages appeared to be dependent on the interplay of DGR mediated sequence variations of gene encoding putative phage fimbrial tip proteins and mutations in host genes coding for outer-membrane proteins. We found prophages with up to 85% amino acid similarity over two-thirds of the Bacuni phage genome in the B. acidifaciens and Prevotella sp. genomes. Despite the abundance of Bacteroides within the human microbiome, we found Bacuni phages only in a limited subset of published gut metagenomes.
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Affiliation(s)
- Stina Hedžet
- Centre for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food (NLZOH), 2000 Maribor, Slovenia; (S.H.); (M.R.)
| | - Maja Rupnik
- Centre for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food (NLZOH), 2000 Maribor, Slovenia; (S.H.); (M.R.)
- Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Tomaž Accetto
- Animal Science Department, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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Yan Q, Wang Y, Chen X, Jin H, Wang G, Guan K, Zhang Y, Zhang P, Ayaz T, Liang Y, Wang J, Cui G, Sun Y, Xiao M, Kang J, Zhang W, Zhang A, Li P, Liu X, Ulllah H, Ma Y, Li S, Ma T. Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis. Virus Evol 2021; 7:veab022. [PMID: 33959381 PMCID: PMC8087960 DOI: 10.1093/ve/veab022] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Trillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remains unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, for example ethnic origin, on the gut virome is rarely investigated. Here, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing twenty-four healthy adults and six children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individuals' gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were not only inherited from that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between viruses and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (P < 0.001), and they both correlated the holistic bacterial composition and vice versa. This study provides an overview of the gut viral community in Chinese and visiting Pakistanis and proposes a considerable role of ethnic origin in shaping the virome.
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Affiliation(s)
- Qiulong Yan
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Yu Wang
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
- Institute of Translational Medicine, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing 210029, China
| | - Xiuli Chen
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Hao Jin
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
- College of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Saihan District, Hohhot 010018, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Kuiqing Guan
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Yue Zhang
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Pan Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200032, China
| | - Taj Ayaz
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Yanshan Liang
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Junyi Wang
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Guangyi Cui
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Yuanyuan Sun
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Manchun Xiao
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Jian Kang
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Wei Zhang
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Aiqin Zhang
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Peng Li
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Xueyang Liu
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Hayan Ulllah
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Yufang Ma
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Shenghui Li
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Tonghui Ma
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
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12
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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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Gregory AC, Zablocki O, Zayed AA, Howell A, Bolduc B, Sullivan MB. The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut. Cell Host Microbe 2020; 28:724-740.e8. [PMID: 32841606 PMCID: PMC7443397 DOI: 10.1016/j.chom.2020.08.003] [Citation(s) in RCA: 280] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/14/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022]
Abstract
The gut microbiome profoundly affects human health and disease, and their infecting viruses are likely as important, but often missed because of reference database limitations. Here, we (1) built a human Gut Virome Database (GVD) from 2,697 viral particle or microbial metagenomes from 1,986 individuals representing 16 countries, (2) assess its effectiveness, and (3) report a meta-analysis that reveals age-dependent patterns across healthy Westerners. The GVD contains 33,242 unique viral populations (approximately species-level taxa) and improves average viral detection rates over viral RefSeq and IMG/VR nearly 182-fold and 2.6-fold, respectively. GVD meta-analyses show highly personalized viromes, reveal that inter-study variability from technical artifacts is larger than any "disease" effect at the population level, and document how viral diversity changes from human infancy into senescence. Together, this compact foundational resource, these standardization guidelines, and these meta-analysis findings provide a systematic toolkit to help maximize our understanding of viral roles in health and disease.
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Affiliation(s)
- Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Allison Howell
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA.
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Monaghan TM, Sloan TJ, Stockdale SR, Blanchard AM, Emes RD, Wilcox M, Biswas R, Nashine R, Manke S, Gandhi J, Jain P, Bhotmange S, Ambalkar S, Satav A, Draper LA, Hill C, Kashyap RS. Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome. Gut Microbes 2020; 12:1752605. [PMID: 32459982 PMCID: PMC7781581 DOI: 10.1080/19490976.2020.1752605] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrheal diseases, particularly Clostridioides difficile, in rural-agricultural and urban populations in Central India, where there is widespread unregulated antibiotic use. We utilized shotgun metagenomics to comprehensively characterize the bacterial and viral fractions of the gut microbiome and their encoded functions in 105 participants. RESULTS We observed distinct rural-urban differences in bacterial and viral populations, with geography exhibiting a greater influence than diarrheal status. Clostridioides difficile disease was more commonly observed in urban subjects, and their microbiomes were enriched in metabolic pathways relating to the metabolism of industrial compounds and genes encoding resistance to 3rd generation cephalosporins and carbapenems. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, phage variation could be directly related to shifts in bacterial populations, with the auxiliary metabolic potential of rural-associated phages enriched for carbon and amino acid energy metabolism. CONCLUSIONS We report distinct differences in antimicrobial resistance gene profiles, enrichment of metabolic pathways and phage composition between rural and urban populations, as well as a higher burden of Clostridioides difficile disease in the urban population. Our results reveal that geography is the key driver of variation in urban and rural Indian microbiomes, with acute diarrheal disease, including C. difficile disease exerting a lesser impact. Future studies will be required to understand the potential role of dietary, cultural, and genetic factors in contributing to microbiome differences between rural and urban populations.
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Affiliation(s)
- Tanya M. Monaghan
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK,Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK,CONTACT Tanya M. Monaghan NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Tim J. Sloan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Adam M. Blanchard
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Richard D. Emes
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK,Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Mark Wilcox
- Leeds Teaching Hospitals NHS Trust and University of Leeds, UK
| | - Rima Biswas
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Rupam Nashine
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Sonali Manke
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Jinal Gandhi
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Pratishtha Jain
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrejal Bhotmange
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrikant Ambalkar
- Department of Clinical Microbiology and Infection, King’s Mill Hospital, Sherwood Forest Hospitals NHS Trust, Sutton in Ashfield, UK
| | | | | | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Rajpal Singh Kashyap
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India,Rajpal Singh Kashyap Biochemistry Research Centre, Central India Institute of Medical Sciences, 88/2 Bajaj Nagar, Nagpur, Maharashtra, India
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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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16
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The Role of Rhizosphere Bacteriophages in Plant Health. Trends Microbiol 2020; 28:709-718. [DOI: 10.1016/j.tim.2020.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/11/2020] [Accepted: 04/02/2020] [Indexed: 12/12/2022]
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Gut Microbiome: Profound Implications for Diet and Disease. Nutrients 2019; 11:nu11071613. [PMID: 31315227 PMCID: PMC6682904 DOI: 10.3390/nu11071613] [Citation(s) in RCA: 523] [Impact Index Per Article: 104.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/05/2019] [Accepted: 07/11/2019] [Indexed: 02/07/2023] Open
Abstract
The gut microbiome plays an important role in human health and influences the development of chronic diseases ranging from metabolic disease to gastrointestinal disorders and colorectal cancer. Of increasing prevalence in Western societies, these conditions carry a high burden of care. Dietary patterns and environmental factors have a profound effect on shaping gut microbiota in real time. Diverse populations of intestinal bacteria mediate their beneficial effects through the fermentation of dietary fiber to produce short-chain fatty acids, endogenous signals with important roles in lipid homeostasis and reducing inflammation. Recent progress shows that an individual’s starting microbial profile is a key determinant in predicting their response to intervention with live probiotics. The gut microbiota is complex and challenging to characterize. Enterotypes have been proposed using metrics such as alpha species diversity, the ratio of Firmicutes to Bacteroidetes phyla, and the relative abundance of beneficial genera (e.g., Bifidobacterium, Akkermansia) versus facultative anaerobes (E. coli), pro-inflammatory Ruminococcus, or nonbacterial microbes. Microbiota composition and relative populations of bacterial species are linked to physiologic health along different axes. We review the role of diet quality, carbohydrate intake, fermentable FODMAPs, and prebiotic fiber in maintaining healthy gut flora. The implications are discussed for various conditions including obesity, diabetes, irritable bowel syndrome, inflammatory bowel disease, depression, and cardiovascular disease.
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Ramírez-Martínez LA, Loza-Rubio E, Mosqueda J, González-Garay ML, García-Espinosa G. Fecal virome composition of migratory wild duck species. PLoS One 2018; 13:e0206970. [PMID: 30462678 PMCID: PMC6248937 DOI: 10.1371/journal.pone.0206970] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/23/2018] [Indexed: 12/17/2022] Open
Abstract
The fecal virome comprises a complex diversity of eukaryotic viruses, phages and viruses that infect the host. However, little is known about the intestinal community of viruses that is present in wild waterfowl, and the structure of this community in wild ducks has not yet been studied. The fecal virome compositions of six species of wild dabbling ducks and one species of wild diving duck were thus analyzed. Fecal samples were collected directly from the rectums of 60 ducks donated by hunters. DNA and RNA virus particles were purified and sequenced using the MiSeq Illumina platform. The reads obtained from the sequencing were analyzed and compared with sequences in the GenBank database. Viral-related sequences from the Herpesviridae, Alloherpesviridae, Adenoviridae, Retroviridae and Myoviridae viral families showed the highest overall abundances in the samples. The virome analysis identified viruses that had not been found in wild duck feces and revealed distinct virome profiles between different species and between samples of the same species. This study increases our understanding of viruses in wild ducks as possible viral reservoirs and provides a basis for further studying and monitoring the transmission of viruses from wild animals to humans and disease outbreaks in domestic animals.
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Affiliation(s)
- Luis Alfonso Ramírez-Martínez
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Elizabeth Loza-Rubio
- Departamento de Biotecnología en Salud Animal, Centro Nacional de Investigación Disciplinaria en Microbiología Animal, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, (CENID-Microbiología-INIFAP), Ciudad de México, México
| | - Juan Mosqueda
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Querétaro, Querétaro, México
| | - Manuel Leonardo González-Garay
- Department of Medicine, Center for Biomedical Informatics & Biostatistics, The University of Arizona, Tucson, Arizona, United States of America
| | - Gary García-Espinosa
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
- * E-mail:
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Cinek O, Kramna L, Mazankova K, Odeh R, Alassaf A, Ibekwe MU, Ahmadov G, Elmahi BME, Mekki H, Lebl J, Abdullah MA. The bacteriome at the onset of type 1 diabetes: A study from four geographically distant African and Asian countries. Diabetes Res Clin Pract 2018; 144:51-62. [PMID: 30121305 DOI: 10.1016/j.diabres.2018.08.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/22/2018] [Accepted: 08/13/2018] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Gut bacteriome profiling studies in type 1 diabetes (T1D) to date are mostly limited to populations of Europe, with two studies from China and one study each from Mexico and the USA. We therefore sought to characterize the stool bacteriome in children after onset of T1D along with age- and place-matched control subjects from four geographically distant African and Asian countries. METHODS Samples were collected from 73 children and adolescents shortly after T1D onset (Azerbaijan 19, Jordan 20, Nigeria 14, Sudan 20) and 104 matched control subjects of similar age and locale. Genotyping of major T1D susceptibility genes was performed using saliva or blood samples. The bacteriome was profiled by next-generation sequencing of 16S rDNA. Negative binomial regression was used to model associations, with adjustment for the matched structure of the study. RESULTS A significant positive association with T1D was noted for the genus Escherichia (class Gammaproteobacteria, phylum Proteobacteria), whereas Eubacterium and Roseburia, two genera of class Clostridia, phylum Firmicutes, were inversely associated with T1D. We also confirmed a previously observed inverse association with Clostridium clusters IV or XIVa. No associations were noted for richness, evenness, or enterotypes. CONCLUSIONS Based on our results, some type of distortion of the gut bacteriome appears to be a global feature of T1D, and our findings for four distant populations add new candidates to the existing list of bacteria. It remains to be established whether the observed associations are markers or causative factors.
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Affiliation(s)
- Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, V Uvalu 84, Prague 5, Czech Republic.
| | - Lenka Kramna
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, V Uvalu 84, Prague 5, Czech Republic.
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, V Uvalu 84, Prague 5, Czech Republic.
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan.
| | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan.
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria.
| | - Gunduz Ahmadov
- Endocrine Centre Baku, Str. I. Hashimov 4A, AZ1114 Baku, Azerbaijan.
| | - Bashir Mukhtar Elwasila Elmahi
- Department of Paediatrics and Child Health, University of Khartoum, Faculty of Medicine, Khartoum, Sudan; Sudan Childhood Diabetes Center, Khartoum, Sudan.
| | - Hanan Mekki
- Department of Paediatrics and Child Health, University of Khartoum, Faculty of Medicine, Khartoum, Sudan.
| | - Jan Lebl
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, V Uvalu 84, Prague 5, Czech Republic.
| | - Mohammed Ahmed Abdullah
- Department of Paediatrics and Child Health, University of Khartoum, Faculty of Medicine, Khartoum, Sudan; Sudan Childhood Diabetes Center, Khartoum, Sudan.
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Gregory AC, Sullivan MB, Segal LN, Keller BC. Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome. Respir Res 2018; 19:174. [PMID: 30208886 PMCID: PMC6136173 DOI: 10.1186/s12931-018-0878-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/03/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The role of commensal viruses in humans is poorly understood, and the impact of the virome on lung health and smoking-related disease is particularly understudied. METHODS Genetic material from acellular bronchoalveolar lavage fluid was sequenced to identify and quantify viral members of the lower respiratory tract which were compared against concurrent bronchoalveolar lavage bacterial, metabolite, cytokine and cellular profiles, and clinical data. Twenty smoker and 10 nonsmoker participants with no significant comorbidities were studied. RESULTS Viruses that infect bacteria (phages) represented the vast majority of viruses in the lung. Though bacterial communities were statistically indistinguishable across smokers and nonsmokers as observed in previous studies, lung viromes and metabolic profiles were significantly different between groups. Statistical analyses revealed that changes in viral communities correlate most with changes in levels of arachidonic acid and IL-8, both potentially relevant for chronic obstructive pulmonary disease (COPD) pathogenesis based on prior studies. CONCLUSIONS Our assessment of human lung DNA viral communities reveals that commensal viruses are present in the lower respiratory tract and differ between smokers and nonsmokers. The associations between viral populations and local immune and metabolic tone suggest a significant role for virome-host interaction in smoking related lung disease.
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Affiliation(s)
- Ann C. Gregory
- Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210 USA
| | - Leopoldo N. Segal
- Division of Pulmonary, Critical Care & Sleep Medicine, New York University School of Medicine, New York, NY 10016 USA
| | - Brian C. Keller
- Division of Pulmonary, Critical Care & Sleep Medicine, The Ohio State University College of Medicine, 201 Davis Heart & Lung Research Institute, 473 West 12th Avenue, Columbus, OH 43210 USA
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