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Human Phageprints: A high-resolution exploration of oral phages reveals globally-distributed phage families with individual-specific and temporally-stable community compositions

Mahmoudabadi, Gita and Homyk, Kelsey and Catching, Adam and Foley, Helen and Tadmor, Arbel and Mahmoudabadi, Ana and Cheung, Allison and Phillips, Rob (2019) Human Phageprints: A high-resolution exploration of oral phages reveals globally-distributed phage families with individual-specific and temporally-stable community compositions. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20190110-132257326

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Abstract

Metagenomic studies have revolutionized the study of novel phages. However these studies trade the depth of coverage for breadth. In this study we show that the targeted sequencing of a phage genomic region as small as 200-300 base pairs, can provide sufficient sequence diversity to serve as an individual-specific barcode or Phageprint. The targeted approach reveals a high-resolution view of phage communities that is not available through metagenomic datasets. By creating instructional videos and collection kits, we enabled citizen scientists to gather ~700 oral samples spanning ~100 individuals residing in different parts of the world. In examining phage communities at 6 different oral sites, and by comparing phage communities of individuals living across the globe, we were able to study the effect of spatial separation, ranging from several millimeters to thousands of kilometers. We found that the spatial separation of just a few centimeters (the distance between two oral sites) can already result in highly distinct phage community compositions. For larger distances, spanning the phage communities of different individuals living in different parts of the world, we did not observe any correlation between spatial distance and phage community composition as individuals residing in the same city did not have any more similar phage communities than individuals living on different continents. Additionally, we found that neither genetics nor cohabitation seem to play a role in the relatedness of phage community compositions across individuals. Cohabitating siblings and even identical twins did not have phage community compositions that were any more similar than those of unrelated individuals. The primary factor contributing to phage community composition relatedness is direct contact between two habitats, as is demonstrated by the similarity between oral phage community compositions of partners. Furthermore, by exploring phage communities across the span of a month, and in some cases several years, we observed highly stable community compositions. These studies consistently point to the existence of remarkably diverse and personal phage families that are stable in time and apparently present in people around the world.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1101/516864DOIDiscussion Paper
ORCID:
AuthorORCID
Mahmoudabadi, Gita0000-0002-8812-7246
Phillips, Rob0000-0003-3082-2809
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. bioRxiv preprint first posted online Jan. 10, 2019. We are grateful to members of the Phillips Lab and the Boundaries of Life Initiative for helpful discussions. This study was supported by the National Science Foundation (Graduate Research Fellowship; DGE‐1144469), the John Templeton Foundation (Boundaries of Life Initiative; 51250), the National Institute of Health (Maximizing Investigator’s Research Award; RFA-GM-17-002), and the National Institute of Health (Exceptional Unconventional Research Enabling Knowledge Acceleration; R01-GM098465).
Funders:
Funding AgencyGrant Number
NSF Graduate Research FellowshipDGE‐1144469
John Templeton Foundation51250
NIHRFA-GM-17-002
NIHR01-GM098465
Record Number:CaltechAUTHORS:20190110-132257326
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190110-132257326
Official Citation:Human Phageprints: A high-resolution exploration of oral phages reveals globally-distributed phage families with individual-specific and temporally-stable community compositions. Gita Mahmoudabadi, Kelsey Homyk, Adam Catching, Helen Foley, Arbel Tadmor, Ana Mahmoudabadi, Allison Cheung, Robert Phillips. bioRxiv 516864; doi: https://doi.org/10.1101/516864
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:92201
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:11 Jan 2019 05:09
Last Modified:19 Nov 2020 20:01

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