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Bacteriophage populations mirror those of bacterial pathogens at sites of infection
Bacteriophages, viruses that parasitize bacteria, are known to be abundant at sites of bacterial colonization, but the relationship between phages and bacteria at sites of infection is unclear. Bacteriophages are highly specific to their bacterial host species, and so we hypothesize that phage popul...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Microbiology
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10469793/ https://www.ncbi.nlm.nih.gov/pubmed/37526425 http://dx.doi.org/10.1128/msystems.00497-23 |
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author | Haddock, N. L. Barkal, L. J. Bollyky, P. L. |
author_facet | Haddock, N. L. Barkal, L. J. Bollyky, P. L. |
author_sort | Haddock, N. L. |
collection | PubMed |
description | Bacteriophages, viruses that parasitize bacteria, are known to be abundant at sites of bacterial colonization, but the relationship between phages and bacteria at sites of infection is unclear. Bacteriophages are highly specific to their bacterial host species, and so we hypothesize that phage populations would mirror those of bacterial pathogens within infected tissues. To test this, here we study publicly available cell-free DNA (cfDNA) generated using next-generation sequencing of infected bodily fluids, including urine, joint fluid, peritoneal fluid, bronchoalveolar lavage fluid, cerebrospinal fluid, and abscess fluid, as well as uninfected control samples. These were analyzed using a computational pipeline for identifying bacteriophage sequences in cfDNA. We find that bacteriophage sequences are present in both infected and uninfected bodily fluids and represent a variety of bacteriophage morphologies and bacterial hosts. Additionally, phages from Escherichia coli, Streptococcus, and Staphylococcus aureus are overrepresented both in terms of proportion and diversity in fluids infected with these same pathogens. These data indicate that phages reflect the relative abundance of their bacterial hosts at sites of infection. Bacteriophage sequences may help inform future investigative and diagnostic approaches that utilize cell-free DNA to study the microbiome within infected tissues. IMPORTANCE: Bacteriophages are an active area of investigation in microbiome research, but most studies have focused on phage populations at sites of bacterial colonization. Little is known about bacteriophage ecology at sites of active infection. To address this gap in knowledge, we utilized a publicly available data set to study bacteriophage populations in cell-free DNA collected from sites of infection. We find that phages reflect the relative abundance of their bacterial hosts at sites of infection. These studies may lead to future investigative and diagnostic approaches that incorporate phages as well as bacterial cell-free DNA. |
format | Online Article Text |
id | pubmed-10469793 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Society for Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-104697932023-09-01 Bacteriophage populations mirror those of bacterial pathogens at sites of infection Haddock, N. L. Barkal, L. J. Bollyky, P. L. mSystems Observation Bacteriophages, viruses that parasitize bacteria, are known to be abundant at sites of bacterial colonization, but the relationship between phages and bacteria at sites of infection is unclear. Bacteriophages are highly specific to their bacterial host species, and so we hypothesize that phage populations would mirror those of bacterial pathogens within infected tissues. To test this, here we study publicly available cell-free DNA (cfDNA) generated using next-generation sequencing of infected bodily fluids, including urine, joint fluid, peritoneal fluid, bronchoalveolar lavage fluid, cerebrospinal fluid, and abscess fluid, as well as uninfected control samples. These were analyzed using a computational pipeline for identifying bacteriophage sequences in cfDNA. We find that bacteriophage sequences are present in both infected and uninfected bodily fluids and represent a variety of bacteriophage morphologies and bacterial hosts. Additionally, phages from Escherichia coli, Streptococcus, and Staphylococcus aureus are overrepresented both in terms of proportion and diversity in fluids infected with these same pathogens. These data indicate that phages reflect the relative abundance of their bacterial hosts at sites of infection. Bacteriophage sequences may help inform future investigative and diagnostic approaches that utilize cell-free DNA to study the microbiome within infected tissues. IMPORTANCE: Bacteriophages are an active area of investigation in microbiome research, but most studies have focused on phage populations at sites of bacterial colonization. Little is known about bacteriophage ecology at sites of active infection. To address this gap in knowledge, we utilized a publicly available data set to study bacteriophage populations in cell-free DNA collected from sites of infection. We find that phages reflect the relative abundance of their bacterial hosts at sites of infection. These studies may lead to future investigative and diagnostic approaches that incorporate phages as well as bacterial cell-free DNA. American Society for Microbiology 2023-08-01 /pmc/articles/PMC10469793/ /pubmed/37526425 http://dx.doi.org/10.1128/msystems.00497-23 Text en Copyright © 2023 Haddock et al. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Observation Haddock, N. L. Barkal, L. J. Bollyky, P. L. Bacteriophage populations mirror those of bacterial pathogens at sites of infection |
title | Bacteriophage populations mirror those of bacterial pathogens at sites of infection |
title_full | Bacteriophage populations mirror those of bacterial pathogens at sites of infection |
title_fullStr | Bacteriophage populations mirror those of bacterial pathogens at sites of infection |
title_full_unstemmed | Bacteriophage populations mirror those of bacterial pathogens at sites of infection |
title_short | Bacteriophage populations mirror those of bacterial pathogens at sites of infection |
title_sort | bacteriophage populations mirror those of bacterial pathogens at sites of infection |
topic | Observation |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10469793/ https://www.ncbi.nlm.nih.gov/pubmed/37526425 http://dx.doi.org/10.1128/msystems.00497-23 |
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