Bacteriophage populations mirror those of bacterial pathogens at sites of infection
ABSTRACT 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 ph...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2023-08-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msystems.00497-23 |
| _version_ | 1797730325291335680 |
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| author | N. L. Haddock L. J. Barkal P. L. Bollyky |
| author_facet | N. L. Haddock L. J. Barkal P. L. Bollyky |
| author_sort | N. L. Haddock |
| collection | DOAJ |
| description | ABSTRACT 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. |
| first_indexed | 2024-03-12T11:42:40Z |
| format | Article |
| id | doaj.art-88c665cbbe96441fb362bd1ed72bf716 |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-03-12T11:42:40Z |
| publishDate | 2023-08-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-88c665cbbe96441fb362bd1ed72bf7162023-08-31T13:00:43ZengAmerican Society for MicrobiologymSystems2379-50772023-08-018410.1128/msystems.00497-23Bacteriophage populations mirror those of bacterial pathogens at sites of infectionN. L. Haddock0L. J. Barkal1P. L. Bollyky2Immunology Program, School of Medicine, Stanford University , Stanford, California, USADivision of Pulmonary, Allergy, and Critical Care Medicine, School of Medicine, Stanford University , Stanford, California, USADivision of Infectious Diseases and Geographic Medicine, School of Medicine, Stanford University , Stanford, California, USAABSTRACT 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.https://journals.asm.org/doi/10.1128/msystems.00497-23phagebacteriophageinfectionbacterial infection |
| spellingShingle | N. L. Haddock L. J. Barkal P. L. Bollyky Bacteriophage populations mirror those of bacterial pathogens at sites of infection mSystems phage bacteriophage infection bacterial 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 | phage bacteriophage infection bacterial infection |
| url | https://journals.asm.org/doi/10.1128/msystems.00497-23 |
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