Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses
Establishing a diverse gut microbiota after birth is essential for preventing illnesses later in life. However, little knowledge exists about the total viral population (virome) present in the gut of infants during the early developmental stage, with RNA viruses being generally overlooked. Therefore...
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MDPI AG
2020-11-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/12/11/1260 |
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| author | Milton T. Mogotsi Peter N. Mwangi Phillip A. Bester M. Jeffrey Mphahlele Mapaseka L. Seheri Hester G. O’Neill Martin M. Nyaga |
| author_facet | Milton T. Mogotsi Peter N. Mwangi Phillip A. Bester M. Jeffrey Mphahlele Mapaseka L. Seheri Hester G. O’Neill Martin M. Nyaga |
| author_sort | Milton T. Mogotsi |
| collection | DOAJ |
| description | Establishing a diverse gut microbiota after birth is essential for preventing illnesses later in life. However, little knowledge exists about the total viral population (virome) present in the gut of infants during the early developmental stage, with RNA viruses being generally overlooked. Therefore, this small pilot longitudinal study investigated the diversity and changes in the enteric RNA virome in healthy infants from South Africa. Faecal samples (<i>n</i> = 12) were collected from four infants at three time points (on average at 8, 13, and 25 weeks), and then sequenced on an Illumina MiSeq platform. The genomic analysis revealed a diverse population of human enteric viruses from the infants’ stools, and changes in the enteric virome composition were observed over time. The <i>Reoviridae</i> family, more specifically the Rotavirus genus, was the most common and could be linked to viral shedding due to the administration of live-attenuated oral vaccines in South Africa, followed by the <i>Picornaviridae</i> family including parechoviruses, echoviruses, coxsackieviruses, enteroviruses, and polioviruses. Polioviruses were also linked to vaccine-related shedding. <i>Astroviridae</i> (astroviruses) and <i>Caliciviridae</i> (noroviruses) were present at low abundance. It is evident that an infant’s gut is colonized by distinct viral populations irrespective of their health state. Further characterization of the human virome (with a larger participant pool) is imperative to provide more conclusive insights into the viral community structure and diversity that has been shown in the current study, despite the smaller sample size. |
| first_indexed | 2024-03-10T15:04:03Z |
| format | Article |
| id | doaj.art-6b2a5a50d3f44b0a89db2b6308caa932 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T15:04:03Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-6b2a5a50d3f44b0a89db2b6308caa9322023-11-20T19:54:50ZengMDPI AGViruses1999-49152020-11-011211126010.3390/v12111260Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic VirusesMilton T. Mogotsi0Peter N. Mwangi1Phillip A. Bester2M. Jeffrey Mphahlele3Mapaseka L. Seheri4Hester G. O’Neill5Martin M. Nyaga6Next Generation Sequencing Unit, University of the Free State, Bloemfontein 9300, South AfricaNext Generation Sequencing Unit, University of the Free State, Bloemfontein 9300, South AfricaDivision of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South AfricaDiarrhoeal Pathogens Research Unit, Department of Virology, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South AfricaDiarrhoeal Pathogens Research Unit, Department of Virology, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South AfricaDepartment of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein 9300, South AfricaNext Generation Sequencing Unit, University of the Free State, Bloemfontein 9300, South AfricaEstablishing a diverse gut microbiota after birth is essential for preventing illnesses later in life. However, little knowledge exists about the total viral population (virome) present in the gut of infants during the early developmental stage, with RNA viruses being generally overlooked. Therefore, this small pilot longitudinal study investigated the diversity and changes in the enteric RNA virome in healthy infants from South Africa. Faecal samples (<i>n</i> = 12) were collected from four infants at three time points (on average at 8, 13, and 25 weeks), and then sequenced on an Illumina MiSeq platform. The genomic analysis revealed a diverse population of human enteric viruses from the infants’ stools, and changes in the enteric virome composition were observed over time. The <i>Reoviridae</i> family, more specifically the Rotavirus genus, was the most common and could be linked to viral shedding due to the administration of live-attenuated oral vaccines in South Africa, followed by the <i>Picornaviridae</i> family including parechoviruses, echoviruses, coxsackieviruses, enteroviruses, and polioviruses. Polioviruses were also linked to vaccine-related shedding. <i>Astroviridae</i> (astroviruses) and <i>Caliciviridae</i> (noroviruses) were present at low abundance. It is evident that an infant’s gut is colonized by distinct viral populations irrespective of their health state. Further characterization of the human virome (with a larger participant pool) is imperative to provide more conclusive insights into the viral community structure and diversity that has been shown in the current study, despite the smaller sample size.https://www.mdpi.com/1999-4915/12/11/1260RNA viromerotavirusviral metagenomicsenteric viruses |
| spellingShingle | Milton T. Mogotsi Peter N. Mwangi Phillip A. Bester M. Jeffrey Mphahlele Mapaseka L. Seheri Hester G. O’Neill Martin M. Nyaga Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses Viruses RNA virome rotavirus viral metagenomics enteric viruses |
| title | Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses |
| title_full | Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses |
| title_fullStr | Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses |
| title_full_unstemmed | Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses |
| title_short | Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses |
| title_sort | metagenomic analysis of the enteric rna virome of infants from the oukasie clinic north west province south africa reveals diverse eukaryotic viruses |
| topic | RNA virome rotavirus viral metagenomics enteric viruses |
| url | https://www.mdpi.com/1999-4915/12/11/1260 |
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