Novel <i>Siphoviridae</i> Bacteriophages Infecting <i>Bacteroides uniformis</i> Contain Diversity Generating Retroelement
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 <i>Bacteroides</i><i>uniformis</i>....
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-04-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/5/892 |
| _version_ | 1797536764733161472 |
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| author | Stina Hedžet Maja Rupnik Tomaž Accetto |
| author_facet | Stina Hedžet Maja Rupnik Tomaž Accetto |
| author_sort | Stina Hedžet |
| collection | DOAJ |
| description | 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 <i>Bacteroides</i><i>uniformis</i>. <i>Bacteroides</i> is one of the most common bacterial groups in the global human gut microbiota; however, to date not many <i>Bacteroides</i> specific phages are known. Phages isolated in this study belong to a novel viral genus, Bacuni, within the <i>Siphoviridae</i> 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 <i>B. uniformis</i> 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 <i>B. acidifaciens</i> and <i>Prevotella</i> sp. genomes. Despite the abundance of <i>Bacteroides</i> within the human microbiome, we found Bacuni phages only in a limited subset of published gut metagenomes. |
| first_indexed | 2024-03-10T12:05:26Z |
| format | Article |
| id | doaj.art-1bbe50208b0e4f98bf916da7ec47edf1 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T12:05:26Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-1bbe50208b0e4f98bf916da7ec47edf12023-11-21T16:34:49ZengMDPI AGMicroorganisms2076-26072021-04-019589210.3390/microorganisms9050892Novel <i>Siphoviridae</i> Bacteriophages Infecting <i>Bacteroides uniformis</i> Contain Diversity Generating RetroelementStina Hedžet0Maja Rupnik1Tomaž Accetto2Centre for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food (NLZOH), 2000 Maribor, SloveniaCentre for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food (NLZOH), 2000 Maribor, SloveniaAnimal Science Department, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, SloveniaIntestinal 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 <i>Bacteroides</i><i>uniformis</i>. <i>Bacteroides</i> is one of the most common bacterial groups in the global human gut microbiota; however, to date not many <i>Bacteroides</i> specific phages are known. Phages isolated in this study belong to a novel viral genus, Bacuni, within the <i>Siphoviridae</i> 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 <i>B. uniformis</i> 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 <i>B. acidifaciens</i> and <i>Prevotella</i> sp. genomes. Despite the abundance of <i>Bacteroides</i> within the human microbiome, we found Bacuni phages only in a limited subset of published gut metagenomes.https://www.mdpi.com/2076-2607/9/5/892gut<i>Bacteroides</i>viromeprophagediversity-generating retroelement |
| spellingShingle | Stina Hedžet Maja Rupnik Tomaž Accetto Novel <i>Siphoviridae</i> Bacteriophages Infecting <i>Bacteroides uniformis</i> Contain Diversity Generating Retroelement Microorganisms gut <i>Bacteroides</i> virome prophage diversity-generating retroelement |
| title | Novel <i>Siphoviridae</i> Bacteriophages Infecting <i>Bacteroides uniformis</i> Contain Diversity Generating Retroelement |
| title_full | Novel <i>Siphoviridae</i> Bacteriophages Infecting <i>Bacteroides uniformis</i> Contain Diversity Generating Retroelement |
| title_fullStr | Novel <i>Siphoviridae</i> Bacteriophages Infecting <i>Bacteroides uniformis</i> Contain Diversity Generating Retroelement |
| title_full_unstemmed | Novel <i>Siphoviridae</i> Bacteriophages Infecting <i>Bacteroides uniformis</i> Contain Diversity Generating Retroelement |
| title_short | Novel <i>Siphoviridae</i> Bacteriophages Infecting <i>Bacteroides uniformis</i> Contain Diversity Generating Retroelement |
| title_sort | novel i siphoviridae i bacteriophages infecting i bacteroides uniformis i contain diversity generating retroelement |
| topic | gut <i>Bacteroides</i> virome prophage diversity-generating retroelement |
| url | https://www.mdpi.com/2076-2607/9/5/892 |
| work_keys_str_mv | AT stinahedzet novelisiphoviridaeibacteriophagesinfectingibacteroidesuniformisicontaindiversitygeneratingretroelement AT majarupnik novelisiphoviridaeibacteriophagesinfectingibacteroidesuniformisicontaindiversitygeneratingretroelement AT tomazaccetto novelisiphoviridaeibacteriophagesinfectingibacteroidesuniformisicontaindiversitygeneratingretroelement |