Phage-based microbiome manipulation elucidates interactions within community context Article Swipe
Tomas Hessler
,
Dawn Chiniquy
,
Benjamin A. Adler
,
Jordan Hoff
,
Ethan Tucker
,
Robert J. Huddy
,
Rohan Sachdeva
,
Shufei Lei
,
Susan T.L. Harrison
,
Rodolphe Barrangou
,
Spencer Diamond
,
Adam M. Deutschbauer
,
Jillian F. Banfield
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.06.20.660599
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.06.20.660599
Testing microbial interaction hypotheses remains a major challenge in microbiome research. Bacteriophages have the potential to probe organism-organism interactions within complex microbiomes, yet are rarely used for this purpose. Here, we isolated nine narrow host range phages that replicate in several ecologically important Variovorax species. As Variovorax CL14 degrades the plant root-stunting hormone auxin, we used phages to eliminate V. CL14 from a rhizosphere consortium and reestablished the stunted root phenotype. We used three of the phages to deplete another Variovorax , SCN45, from complex communities to test correlation network-based hypotheses of thiamine interdependencies. Genome-resolved metagenomics revealed that specific taxa decreased in relative abundance following Variovorax depletion and could be rescued by thiamine supplementation. Thus, we confirmed thiamine production as the mechanistic basis for interdependence. These experiments lay the foundation for research that employs wildtype and engineered phages to test interaction hypotheses and for targeted microbiome manipulation.
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- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2025.06.20.660599
- OA Status
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- References
- 80
- Related Works
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- OpenAlex ID
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All OpenAlex metadata
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https://doi.org/10.1101/2025.06.20.660599Digital Object Identifier
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Phage-based microbiome manipulation elucidates interactions within community contextWork title
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preprintOpenAlex work type
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enPrimary language
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2025Year of publication
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2025-06-21Full publication date if available
- Authors
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Tomas Hessler, Dawn Chiniquy, Benjamin A. Adler, Jordan Hoff, Ethan Tucker, Robert J. Huddy, Rohan Sachdeva, Shufei Lei, Susan T.L. Harrison, Rodolphe Barrangou, Spencer Diamond, Adam M. Deutschbauer, Jillian F. BanfieldList of authors in order
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https://doi.org/10.1101/2025.06.20.660599Publisher landing page
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greenOpen access status per OpenAlex
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https://doi.org/10.1101/2025.06.20.660599Direct OA link when available
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Microbiome, Context (archaeology), Computational biology, Biology, Computer science, Communication, Genetics, Psychology, PaleontologyTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.SCN45, | 83 |
| abstract_inverted_index.auxin, | 54 |
| abstract_inverted_index.narrow | 34 |
| abstract_inverted_index.phages | 37, 57, 77, 138 |
| abstract_inverted_index.rarely | 25 |
| abstract_inverted_index.within | 20 |
| abstract_inverted_index.Testing | 1 |
| abstract_inverted_index.another | 80 |
| abstract_inverted_index.complex | 21, 85 |
| abstract_inverted_index.deplete | 79 |
| abstract_inverted_index.employs | 134 |
| abstract_inverted_index.hormone | 53 |
| abstract_inverted_index.remains | 5 |
| abstract_inverted_index.rescued | 111 |
| abstract_inverted_index.several | 41 |
| abstract_inverted_index.stunted | 69 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.degrades | 49 |
| abstract_inverted_index.isolated | 32 |
| abstract_inverted_index.purpose. | 29 |
| abstract_inverted_index.relative | 103 |
| abstract_inverted_index.research | 132 |
| abstract_inverted_index.revealed | 97 |
| abstract_inverted_index.species. | 45 |
| abstract_inverted_index.specific | 99 |
| abstract_inverted_index.targeted | 145 |
| abstract_inverted_index.thiamine | 93, 113, 118 |
| abstract_inverted_index.wildtype | 135 |
| abstract_inverted_index.abundance | 104 |
| abstract_inverted_index.challenge | 8 |
| abstract_inverted_index.confirmed | 117 |
| abstract_inverted_index.decreased | 101 |
| abstract_inverted_index.depletion | 107 |
| abstract_inverted_index.eliminate | 59 |
| abstract_inverted_index.following | 105 |
| abstract_inverted_index.important | 43 |
| abstract_inverted_index.microbial | 2 |
| abstract_inverted_index.potential | 15 |
| abstract_inverted_index.replicate | 39 |
| abstract_inverted_index.research. | 11 |
| abstract_inverted_index.Variovorax | 44, 47, 81, 106 |
| abstract_inverted_index.consortium | 65 |
| abstract_inverted_index.engineered | 137 |
| abstract_inverted_index.foundation | 130 |
| abstract_inverted_index.hypotheses | 4, 91, 142 |
| abstract_inverted_index.microbiome | 10, 146 |
| abstract_inverted_index.phenotype. | 71 |
| abstract_inverted_index.production | 119 |
| abstract_inverted_index.communities | 86 |
| abstract_inverted_index.correlation | 89 |
| abstract_inverted_index.experiments | 127 |
| abstract_inverted_index.interaction | 3, 141 |
| abstract_inverted_index.mechanistic | 122 |
| abstract_inverted_index.rhizosphere | 64 |
| abstract_inverted_index.ecologically | 42 |
| abstract_inverted_index.interactions | 19 |
| abstract_inverted_index.metagenomics | 96 |
| abstract_inverted_index.microbiomes, | 22 |
| abstract_inverted_index.manipulation. | 147 |
| abstract_inverted_index.network-based | 90 |
| abstract_inverted_index.reestablished | 67 |
| abstract_inverted_index.root-stunting | 52 |
| abstract_inverted_index.Bacteriophages | 12 |
| abstract_inverted_index.Genome-resolved | 95 |
| abstract_inverted_index.interdependence. | 125 |
| abstract_inverted_index.supplementation. | 114 |
| abstract_inverted_index.organism-organism | 18 |
| abstract_inverted_index.interdependencies. | 94 |
| cited_by_percentile_year | |
| countries_distinct_count | 0 |
| institutions_distinct_count | 13 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/2 |
| sustainable_development_goals[0].score | 0.5899999737739563 |
| sustainable_development_goals[0].display_name | Zero hunger |
| citation_normalized_percentile.value | 0.23726686 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |