Diversity and Ecology of <i>Caudoviricetes</i> Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts
The human gut harbors numerous viruses infecting the human host, microbes, and other inhabitants of the gastrointestinal tract. Most of these viruses remain undiscovered, and their influence on human health is unknown. Here, we characterize viral genomes in gut metagenomic data from 1950 individuals...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-10-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/14/10/2305 |
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| author | Anastasia Gulyaeva Sanzhima Garmaeva Alexander Kurilshikov Arnau Vich Vila Niels P. Riksen Mihai G. Netea Rinse K. Weersma Jingyuan Fu Alexandra Zhernakova |
| author_facet | Anastasia Gulyaeva Sanzhima Garmaeva Alexander Kurilshikov Arnau Vich Vila Niels P. Riksen Mihai G. Netea Rinse K. Weersma Jingyuan Fu Alexandra Zhernakova |
| author_sort | Anastasia Gulyaeva |
| collection | DOAJ |
| description | The human gut harbors numerous viruses infecting the human host, microbes, and other inhabitants of the gastrointestinal tract. Most of these viruses remain undiscovered, and their influence on human health is unknown. Here, we characterize viral genomes in gut metagenomic data from 1950 individuals from four population and patient cohorts. We focus on a subset of viruses that is highly abundant in the gut, remains largely uncharacterized, and allows confident complete genome identification—phages that belong to the class <i>Caudoviricetes</i> and possess genome terminal repeats. We detect 1899 species-level units belonging to this subset, 19% of which do not have complete representative genomes in major public gut virome databases. These units display diverse genomic features, are predicted to infect a wide range of microbial hosts, and on average account for <1% of metagenomic reads. Analysis of longitudinal data from 338 individuals shows that the composition of this fraction of the virome remained relatively stable over a period of 4 years. We also demonstrate that 54 species-level units are highly prevalent (detected in >5% of individuals in a cohort). Finally, we find 34 associations between highly prevalent phages and human phenotypes, 24 of which can be explained by the relative abundance of potential hosts. |
| first_indexed | 2024-03-09T19:22:44Z |
| format | Article |
| id | doaj.art-371e61bccdf54e19baa29a652b6e8f07 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T19:22:44Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-371e61bccdf54e19baa29a652b6e8f072023-11-24T03:11:09ZengMDPI AGViruses1999-49152022-10-011410230510.3390/v14102305Diversity and Ecology of <i>Caudoviricetes</i> Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch CohortsAnastasia Gulyaeva0Sanzhima Garmaeva1Alexander Kurilshikov2Arnau Vich Vila3Niels P. Riksen4Mihai G. Netea5Rinse K. Weersma6Jingyuan Fu7Alexandra Zhernakova8Department of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The NetherlandsDepartment of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The NetherlandsDepartment of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The NetherlandsDepartment of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The NetherlandsDepartment of Internal Medicine, Radboud University Medical Center, 6525GA Nijmegen, The NetherlandsDepartment of Internal Medicine, Radboud University Medical Center, 6525GA Nijmegen, The NetherlandsDepartment of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The NetherlandsDepartment of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The NetherlandsDepartment of Genetics, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The NetherlandsThe human gut harbors numerous viruses infecting the human host, microbes, and other inhabitants of the gastrointestinal tract. Most of these viruses remain undiscovered, and their influence on human health is unknown. Here, we characterize viral genomes in gut metagenomic data from 1950 individuals from four population and patient cohorts. We focus on a subset of viruses that is highly abundant in the gut, remains largely uncharacterized, and allows confident complete genome identification—phages that belong to the class <i>Caudoviricetes</i> and possess genome terminal repeats. We detect 1899 species-level units belonging to this subset, 19% of which do not have complete representative genomes in major public gut virome databases. These units display diverse genomic features, are predicted to infect a wide range of microbial hosts, and on average account for <1% of metagenomic reads. Analysis of longitudinal data from 338 individuals shows that the composition of this fraction of the virome remained relatively stable over a period of 4 years. We also demonstrate that 54 species-level units are highly prevalent (detected in >5% of individuals in a cohort). Finally, we find 34 associations between highly prevalent phages and human phenotypes, 24 of which can be explained by the relative abundance of potential hosts.https://www.mdpi.com/1999-4915/14/10/2305human gut metagenome<i>Caudoviricetes</i>human phenotypes |
| spellingShingle | Anastasia Gulyaeva Sanzhima Garmaeva Alexander Kurilshikov Arnau Vich Vila Niels P. Riksen Mihai G. Netea Rinse K. Weersma Jingyuan Fu Alexandra Zhernakova Diversity and Ecology of <i>Caudoviricetes</i> Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts Viruses human gut metagenome <i>Caudoviricetes</i> human phenotypes |
| title | Diversity and Ecology of <i>Caudoviricetes</i> Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts |
| title_full | Diversity and Ecology of <i>Caudoviricetes</i> Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts |
| title_fullStr | Diversity and Ecology of <i>Caudoviricetes</i> Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts |
| title_full_unstemmed | Diversity and Ecology of <i>Caudoviricetes</i> Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts |
| title_short | Diversity and Ecology of <i>Caudoviricetes</i> Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts |
| title_sort | diversity and ecology of i caudoviricetes i phages with genome terminal repeats in fecal metagenomes from four dutch cohorts |
| topic | human gut metagenome <i>Caudoviricetes</i> human phenotypes |
| url | https://www.mdpi.com/1999-4915/14/10/2305 |
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