Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

Morteza Roodgar; Benjamin H. Good; Nandita R. Garud; Stephen Martis; Mohan Avula; Wenyu Zhou; Samuel Lancaster; Hayan Lee; Afshin Babveyh; Sophia Nesamoney; Katherine S. Pollard; Michael P. Snyder

doi:10.1101/2019.12.21.886093

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Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

View ORCID ProfileMorteza Roodgar, View ORCID ProfileBenjamin H. Good, View ORCID ProfileNandita R. Garud, Stephen Martis, Mohan Avula, Wenyu Zhou, Samuel Lancaster, Hayan Lee, Afshin Babveyh, Sophia Nesamoney, Katherine S. Pollard, View ORCID ProfileMichael P. Snyder

doi: https://doi.org/10.1101/2019.12.21.886093

Morteza Roodgar

1Department of Genetics, Stanford University, Stanford, California, 94305

2Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305

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Benjamin H. Good

3Department of Applied Physics, Stanford University, Stanford, California 94305

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For correspondence: bhgood@stanford.edu katherine.pollard@gladstone.ucsf.edu mpsnyder@stanford.edu

Nandita R. Garud

4Department of Ecology and Evolutionary Biology, University of California Los Angeles

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Stephen Martis

5Department of Physics, University of California, Berkeley, CA 94720

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Mohan Avula

1Department of Genetics, Stanford University, Stanford, California, 94305

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Wenyu Zhou

1Department of Genetics, Stanford University, Stanford, California, 94305

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Samuel Lancaster

1Department of Genetics, Stanford University, Stanford, California, 94305

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Hayan Lee

1Department of Genetics, Stanford University, Stanford, California, 94305

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Afshin Babveyh

1Department of Genetics, Stanford University, Stanford, California, 94305

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Sophia Nesamoney

1Department of Genetics, Stanford University, Stanford, California, 94305

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Katherine S. Pollard

6Gladstone Institutes, San Francisco, CA 94158

7Department of Epidemiology & Biostatistics, University of California, San Francisco, Ca 94158

8Chan Zuckerberg Biohub, San Francisco, CA 94158

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For correspondence: bhgood@stanford.edu katherine.pollard@gladstone.ucsf.edu mpsnyder@stanford.edu

Michael P. Snyder

1Department of Genetics, Stanford University, Stanford, California, 94305

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For correspondence: bhgood@stanford.edu katherine.pollard@gladstone.ucsf.edu mpsnyder@stanford.edu

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Posted December 23, 2019.

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Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

Morteza Roodgar, Benjamin H. Good, Nandita R. Garud, Stephen Martis, Mohan Avula, Wenyu Zhou, Samuel Lancaster, Hayan Lee, Afshin Babveyh, Sophia Nesamoney, Katherine S. Pollard, Michael P. Snyder

bioRxiv 2019.12.21.886093; doi: https://doi.org/10.1101/2019.12.21.886093

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Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

Morteza Roodgar, Benjamin H. Good, Nandita R. Garud, Stephen Martis, Mohan Avula, Wenyu Zhou, Samuel Lancaster, Hayan Lee, Afshin Babveyh, Sophia Nesamoney, Katherine S. Pollard, Michael P. Snyder

bioRxiv 2019.12.21.886093; doi: https://doi.org/10.1101/2019.12.21.886093

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