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2. The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia

Author

Schluter, Jonas, Djukovic, Ana, Taylor, Bradford P., Yan, Jinyuan, Duan, Caichen, Hussey, Grant A., Liao, Chen, Sharma, Sneh, Fontana, Emily, Amoretti, Luigi A., Wright, Roberta J., Dai, Anqi, Peled, Jonathan U., Taur, Ying, Perales, Miguel-Angel, Siranosian, Benjamin A., Bhatt, Ami S., van den Brink, Marcel R.M., Pamer, Eric G., and Xavier, Joao B.

Published
2023
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3. High-resolution analyses of associations between medications, microbiome, and mortality in cancer patients

Author

Nguyen, Chi L., Markey, Kate A., Miltiadous, Oriana, Dai, Anqi, Waters, Nicholas, Sadeghi, Keimya, Fei, Teng, Shouval, Roni, Taylor, Bradford P., Liao, Chen, Slingerland, John B., Slingerland, Ann E., Clurman, Annelie G., Maloy, Molly A., Bohannon, Lauren, Giardina, Paul A., Brereton, Daniel G., Armijo, Gabriel K., Fontana, Emily, Gradissimo, Ana, Gyurkocza, Boglarka, Sung, Anthony D., Chao, Nelson J., Devlin, Sean M., Taur, Ying, Giralt, Sergio A., Perales, Miguel-Angel, Xavier, Joao B., Pamer, Eric G., Peled, Jonathan U., Gomes, Antonio L.C., and van den Brink, Marcel R.M.

Published
2023
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5. Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota

Author

Petrone, Mary E., Rothman, Jessica E., Breban, Mallery I., Ott, Isabel M., Russell, Alexis, Lasek-Nesselquist, Erica, Badr, Hamada, Kelly, Kevin, Omerza, Greg, Renzette, Nicholas, Watkins, Anne E., Kalinich, Chaney C., Alpert, Tara, Brito, Anderson F., Earnest, Rebecca, Tikhonova, Irina R., Castaldi, Christopher, Kelly, John P., Shudt, Matthew, Plitnick, Jonathan, Schneider, Erasmus, Murphy, Steven, Neal, Caleb, Laszlo, Eva, Altajar, Ahmad, Pearson, Claire, Muyombwe, Anthony, Downing, Randy, Razeq, Jafar, Niccolai, Linda, Wilson, Madeline S., Anderson, Margaret L., Wang, Jianhui, Liu, Chen, Hui, Pei, Mane, Shrikant, Taylor, Bradford P., Hanage, William P., Landry, Marie L., Peaper, David R., Bilguvar, Kaya, Fauver, Joseph R., Vogels, Chantal B. F., Gardner, Lauren M., Pitzer, Virginia E., St. George, Kirsten, Adams, Mark D., and Grubaugh, Nathan D.

Published
2022
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7. Stochasticity and the limits to confidence when estimating R_0 of Ebola and other emerging infectious diseases

Author

Taylor, Bradford P, Dushoff, Jonathan, and Weitz, Joshua S

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Dynamic models - often deterministic in nature - were used to estimate the basic reproductive number, R_0, of the 2014-5 Ebola virus disease (EVD) epidemic outbreak in West Africa. Estimates of R_0 were then used to project the likelihood for large outbreak sizes, e.g., exceeding hundreds of thousands of cases. Yet fitting deterministic models can lead to over-confidence in the confidence intervals of the fitted R_0, and, in turn, the type and scope of necessary interventions. In this manuscript we propose a hybrid stochastic-deterministic method to estimate R_0 and associated confidence intervals (CIs). The core idea is that stochastic realizations of an underlying deterministic model can be used to evaluate the compatibility of candidate values of R_0 with observed epidemic curves. The compatibility is based on comparing the distribution of expected epidemic growth rates with the observed epidemic growth rate given "process noise", i.e., arising due to stochastic transmission, recovery and death events. By applying our method to reported EVD case counts from Guinea, Liberia and Sierra Leone, we show that prior estimates of R_0 based on deterministic fits appear to be more confident than analysis of stochastic trajectories suggests should be possible. Moving forward, we recommend including a hybrid stochastic-deterministic fitting procedure when quantifying the full R_0 CI at the onset of an epidemic due to multiple sources of noise.

Published
2016

9. The gut microbiota is associated with immune cell dynamics in humans

Author

Schluter, Jonas, Peled, Jonathan U., Taylor, Bradford P., Markey, Kate A., Smith, Melody, Taur, Ying, and Niehus, Rene

Subjects
Microbiota (Symbiotic organisms) -- Physiological aspects, Immune system -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The gut microbiota influences development.sup.1-3 and homeostasis.sup.4-7 of the mammalian immune system, and is associated with human inflammatory.sup.8 and immune diseases.sup.9,10 as well as responses to immunotherapy.sup.11-14. Nevertheless, our understanding of how gut bacteria modulate the immune system remains limited, particularly in humans, where the difficulty of direct experimentation makes inference challenging. Here we study hundreds of hospitalized--and closely monitored--patients with cancer receiving haematopoietic cell transplantation as they recover from chemotherapy and stem-cell engraftment. This aggressive treatment causes large shifts in both circulatory immune cell and microbiota populations, enabling the relationships between the two to be studied simultaneously. Analysis of observed daily changes in circulating neutrophil, lymphocyte and monocyte counts and more than 10,000 longitudinal microbiota samples revealed consistent associations between gut bacteria and immune cell dynamics. High-resolution clinical metadata and Bayesian inference allowed us to compare the effects of bacterial genera in relation to those of immunomodulatory medications, revealing a considerable influence of the gut microbiota--together and over time--on systemic immune cell dynamics. Our analysis establishes and quantifies the link between the gut microbiota and the human immune system, with implications for microbiota-driven modulation of immunity. Influence of the gut microbiome on the human immune system is revealed by systems analysis of vast clinical data from decades of electronic health records paired with massive longitudinal microbiome sequencing., Author(s): Jonas Schluter [sup.1] [sup.2] , Jonathan U. Peled [sup.3] [sup.4] , Bradford P. Taylor [sup.2] , Kate A. Markey [sup.3] [sup.4] , Melody Smith [sup.3] [sup.4] , Ying Taur [...]

Published
2020
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10. Sink-traps are a major source for carbapenemase-producing Enterobacteriaceae transmission

Author

Regev-Yochay, Gili, primary, Margalit, Ili, additional, Smollan, Gillian, additional, Rapaport, Rotem, additional, Tal, Ilana, additional, Hanage, William P., additional, Pinas Zade, Nani, additional, Jaber, Hanaa, additional, Taylor, Bradford P., additional, Che, You, additional, Rahav, Galia, additional, Zimlichman, Eyal, additional, and Keller, Nati, additional

Published
2023
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11. The virus of my virus is my friend: ecological effects of virophage with alternative modes of coinfection

Author

Taylor, Bradford P., Cortez, Michael H., and Weitz, Joshua S.

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Virophages are viruses that rely on the replication machinery of other viruses to reproduce within eukaryotic hosts. Two different modes of coinfection have been posited based on experimental observation. In one mode, the virophage and virus enter the host independently. In the other mode, the virophage adheres to the virus so both virophage and virus enter the host together. Here we ask: what are the ecological effects of these different modes of coinfection? In particular, what ecological effects are common to both infection modes, and what are the differences particular to each mode? We develop a pair of biophysically motivated ODE models of viral-host population dynamics, corresponding to dynamics arising from each mode of infection. We find both modes of coinfection allow for the coexistence of the virophage, virus, and host either at a stable fixed point or through cyclical dynamics. In both models, virophage tend to be the most abundant population and their presence always reduces the viral abundance and increases the host abundance. However, we do find qualitative differences between models. For example, via extensive sampling of biologically relevant parameter space, we only observe bistability when the virophage and virus enter the host together. We discuss how such differences may be leveraged to help identify modes of infection in natural environments from population level data.

Published
2013

14. Classifying closed 2-orbifolds with Euler characteristics

Author

DuVal, Whitney, Schulte, John, Seaton, Christopher, and Taylor, Bradford

Subjects
Mathematics - Differential Geometry, Mathematics - Algebraic Topology, 57R20 (Primary), 57S17, 22A22 (Secondary), 57P99
Abstract

We determine the extent to which the collection of $\Gamma$-Euler-Satake characteristics classify closed 2-orbifolds. In particular, we show that the closed, connected, effective, orientable 2-orbifolds are classified by the collection of $\Gamma$-Euler-Satake characteristics corresponding to free or free abelian $\Gamma$ and are not classified by those corresponding to any finite collection of finitely generated discrete groups. Similarly, we show that such a classification is not possible for non-orientable 2-orbifolds and any collection of $\Gamma$, nor for noneffective 2-orbifolds. As a corollary, we generate families of orbifolds with the same $\Gamma$-Euler-Satake characteristics in arbitrary dimensions for any finite collection of $\Gamma$; this is used to demonstrate that the $\Gamma$-Euler-Satake characteristics each constitute new invariants of orbifolds., Comment: 17 pages

Published
2009
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15. On the Stability of Electrostatic Orbits

Author

Banerjee, Shubho, Taylor, Bradford, and Banerjee, Anand

Subjects
Physics - Classical Physics, Physics - General Physics
Abstract

We analyze the stability of two charged conducting spheres orbiting each other. Due to charge polarization, the electrostatic force between the two spheres deviates significantly from $1/r^2$ as they come close to each other. As a consequence, there exists a critical angular momentum, $L_c$, with a corresponding critical radius $r_c$. For $L > L_c$ two circular orbits are possible: one at $r > r_c$ that is stable and the other at $r < r_c$ that is unstable. This critical behavior is analyzed as a function of the charge and the size ratios of the two spheres., Comment: Added references, corrected typos, clarified language

Published
2008
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16. Sink-traps are a major source for carbapenemase-producing Enterobacteriaceaetransmission

Author

Regev-Yochay, Gili, Margalit, Ili, Smollan, Gillian, Rapaport, Rotem, Tal, Ilana, Hanage, William P., Pinas Zade, Nani, Jaber, Hanaa, Taylor, Bradford P., Che, You, Rahav, Galia, Zimlichman, Eyal, and Keller, Nati

Abstract

AbstractObjective:We studied the extent of carbapenemase-producing Enterobacteriaceae (CPE) sink contamination and transmission to patients in a nonoutbreak setting.Methods:During 2017–2019, 592 patient-room sinks were sampled in 34 departments. Patient weekly rectal swab CPE surveillance was universally performed. Repeated sink sampling was conducted in 9 departments. Isolates from patients and sinks were characterized using pulsed-field gel electrophoresis (PFGE), and pairs of high resemblance were sequenced by Oxford Nanopore and Illumina. Hybrid assembly was used to fully assemble plasmids, which are shared between paired isolates.Results:In total, 144 (24%) of 592 CPE-contaminated sinks were detected in 25 of 34 departments. Repeated sampling (n = 7,123) revealed that 52%–100% were contaminated at least once during the sampling period. Persistent contamination for >1 year by a dominant strain was common. During the study period, 318 patients acquired CPE. The most common species were Klebsiella pneumoniae, Escherichia coli, and Enterobacterspp. In 127 (40%) patients, a contaminated sink was the suspected source of CPE acquisition. For 20 cases with an identical sink-patient strain, temporal relation suggested sink-to-patient transmission. Hybrid assembly of specific sink-patient isolates revealed that shared plasmids were structurally identical, and SNP differences between shared pairs, along with signatures for potential recombination events, suggests recent sharing of the plasmids.Conclusions:CPE-contaminated sinks are an important source of transmission to patients. Although traditionally person-to-person transmission has been considered the main route of CPE transmission, these data suggest a change in paradigm that may influence strategies of preventing CPE dissemination.

Published
2024
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21. Enterobacteriaceae isolated from patients share antibiotic resistance conferring plasmids recently acquired from those isolated from sinks in the same treatment room

Author

Taylor, Bradford P, primary, Che, You, additional, Passarelli, Hemanoel, additional, Smollan, Gill, additional, Cohen, Carmit, additional, Rapaport, Rotem, additional, Tal, Ilana, additional, Zade, Nani Pinas, additional, Jaber, Hanaa, additional, Keller, Nati, additional, Hanage, William P, additional, and Regev-Yochay, Gili, additional

Published
2022
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22. Beyond consensus sequence: a quantitative scheme for inferring transmission using deep sequencing in a bacterial transmission model

Author

Senghore, Madikay, primary, Read, Hannah, additional, Oza, Priyali, additional, Johnson, Sarah, additional, Passarelli-Araujo, Hemanoel, additional, Taylor, Bradford P, additional, Ashley, Stephen, additional, Grey, Alex, additional, Callendrello, Alanna, additional, Lee, Robyn, additional, Goddard, Matthew R, additional, Lumley, Thomas, additional, Hanage, William P, additional, and Wiles, Siouxsie, additional

Published
2022
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23. The TaxUMAP atlas: efficient display of large clinical microbiome data reveals ecological competition involved in protection against bacteremia

Author

Schluter, Jonas, primary, Djukovic, Ana, additional, Taylor, Bradford P., additional, Yan, Jinyuan, additional, Duan, Caichen, additional, Hussey, Grant A., additional, Liao, Chen, additional, Sharma, Sneh, additional, Fontana, Emily, additional, Amoretti, Luigi A., additional, Wright, Roberta J., additional, Dai, Anqi, additional, Peled, Jonathan U., additional, Taur, Ying, additional, Perales, Miguel-Angel, additional, Siranosian, Benjamin A., additional, Bhatt, Ami S., additional, van den Brink, Marcel R.M., additional, Pamer, Eric G., additional, and Xavier, Joao B., additional

Published
2022
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24. Understanding Early Pandemic Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in a Medical Center by Incorporating Public Sequencing Databases to Mitigate Bias

Author

Turcinovic, Jacquelyn, primary, Schaeffer, Beau, additional, Taylor, Bradford P, additional, Bouton, Tara C, additional, Odom-Mabey, Aubrey R, additional, Weber, Sarah E, additional, Lodi, Sara, additional, Ragan, Elizabeth J, additional, Connor, John H, additional, Jacobson, Karen R, additional, and Hanage, William P, additional

Published
2022
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25. Early Introduction and Rise of the Omicron Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variant in Highly Vaccinated University Populations

Author

Petros, Brittany A, primary, Turcinovic, Jacquelyn, additional, Welch, Nicole L, additional, White, Laura F, additional, Kolaczyk, Eric D, additional, Bauer, Matthew R, additional, Cleary, Michael, additional, Dobbins, Sabrina T, additional, Doucette-Stamm, Lynn, additional, Gore, Mitch, additional, Nair, Parvathy, additional, Nguyen, Tien G, additional, Rose, Scott, additional, Taylor, Bradford P, additional, Tsang, Daniel, additional, Wendlandt, Erik, additional, Hope, Michele, additional, Platt, Judy T, additional, Jacobson, Karen R, additional, Bouton, Tara, additional, Yune, Seyho, additional, Auclair, Jared R, additional, Landaverde, Lena, additional, Klapperich, Catherine M, additional, Hamer, Davidson H, additional, Hanage, William P, additional, MacInnis, Bronwyn L, additional, Sabeti, Pardis C, additional, Connor, John H, additional, and Springer, Michael, additional

Published
2022
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27. Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak

Author

Siddle, Katherine J., primary, Krasilnikova, Lydia A., additional, Moreno, Gage K., additional, Schaffner, Stephen F., additional, Vostok, Johanna, additional, Fitzgerald, Nicholas A., additional, Lemieux, Jacob E., additional, Barkas, Nikolaos, additional, Loreth, Christine, additional, Specht, Ivan, additional, Tomkins-Tinch, Christopher H., additional, Paull, Jillian S., additional, Schaeffer, Beau, additional, Taylor, Bradford P., additional, Loftness, Bryn, additional, Johnson, Hillary, additional, Schubert, Petra L., additional, Shephard, Hanna M., additional, Doucette, Matthew, additional, Fink, Timelia, additional, Lang, Andrew S., additional, Baez, Stephanie, additional, Beauchamp, John, additional, Hennigan, Scott, additional, Buzby, Erika, additional, Ash, Stephanie, additional, Brown, Jessica, additional, Clancy, Selina, additional, Cofsky, Seana, additional, Gagne, Luc, additional, Hall, Joshua, additional, Harrington, Rachel, additional, Gionet, Gabrielle L., additional, DeRuff, Katherine C., additional, Vodzak, Megan E., additional, Adams, Gordon C., additional, Dobbins, Sabrina T., additional, Slack, Sarah D., additional, Reilly, Steven K., additional, Anderson, Lisa M., additional, Cipicchio, Michelle C., additional, DeFelice, Matthew T., additional, Grimsby, Jonna L., additional, Anderson, Scott E., additional, Blumenstiel, Brendan S., additional, Meldrim, James C., additional, Rooke, Heather M., additional, Vicente, Gina, additional, Smith, Natasha L., additional, Messer, Katelyn S., additional, Reagan, Faye L., additional, Mandese, Zoe M., additional, Lee, Matthew D., additional, Ray, Marianne C., additional, Fisher, Marissa E., additional, Ulcena, Maesha A., additional, Nolet, Corey M., additional, English, Sean E., additional, Larkin, Katie L., additional, Vernest, Kyle, additional, Chaluvadi, Sushma, additional, Arvidson, Deirdre, additional, Melchiono, Maurice, additional, Covell, Theresa, additional, Harik, Vaira, additional, Brock-Fisher, Taylor, additional, Dunn, Molly, additional, Kearns, Amanda, additional, Hanage, William P., additional, Bernard, Clare, additional, Philippakis, Anthony, additional, Lennon, Niall J., additional, Gabriel, Stacey B., additional, Gallagher, Glen R., additional, Smole, Sandra, additional, Madoff, Lawrence C., additional, Brown, Catherine M., additional, Park, Daniel J., additional, MacInnis, Bronwyn L., additional, and Sabeti, Pardis C., additional

Published
2022
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28. Early introduction and rise of the Omicron SARS-CoV-2 variant in highly vaccinated university populations

Author

Petros, Brittany A., primary, Turcinovic, Jacquelyn, additional, Welch, Nicole L., additional, White, Laura F., additional, Kolaczyk, Eric D., additional, Bauer, Matthew R., additional, Cleary, Michael, additional, Dobbins, Sabrina T., additional, Doucette-Stamm, Lynn, additional, Gore, Mitch, additional, Nair, Parvathy, additional, Nguyen, Tien G., additional, Rose, Scott, additional, Taylor, Bradford P., additional, Tsang, Daniel, additional, Wendlandt, Erik, additional, Hope, Michele, additional, Platt, Judy T., additional, Jacobson, Karen R., additional, Bouton, Tara, additional, Yune, Seyho, additional, Auclair, Jared R., additional, Landaverde, Lena, additional, Klapperich, Catherine M., additional, Hamer, Davidson H., additional, Hanage, William P., additional, MacInnis, Bronwyn L., additional, Sabeti, Pardis C., additional, Connor, John H., additional, and Springer, Michael, additional

Published
2022
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30. Early Introduction and Rise of the Omicron Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variant in Highly Vaccinated University Populations.

Author

Petros, Brittany A, Turcinovic, Jacquelyn, Welch, Nicole L, White, Laura F, Kolaczyk, Eric D, Bauer, Matthew R, Cleary, Michael, Dobbins, Sabrina T, Doucette-Stamm, Lynn, Gore, Mitch, Nair, Parvathy, Nguyen, Tien G, Rose, Scott, Taylor, Bradford P, Tsang, Daniel, Wendlandt, Erik, Hope, Michele, Platt, Judy T, Jacobson, Karen R, and Bouton, Tara

Subjects
PUBLIC health surveillance, COVID-19, SARS-CoV-2, COVID-19 vaccines, VIRAL load, UNIVERSITIES & colleges, RESEARCH funding, DISEASE prevalence
Abstract

Background The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly transmissible in vaccinated and unvaccinated populations. The dynamics that govern its establishment and propensity toward fixation (reaching 100% frequency in the SARS-CoV-2 population) in communities remain unknown. Here, we describe the dynamics of Omicron at 3 institutions of higher education (IHEs) in the greater Boston area. Methods We use diagnostic and variant-specifying molecular assays and epidemiological analytical approaches to describe the rapid dominance of Omicron following its introduction into 3 IHEs with asymptomatic surveillance programs. Results We show that the establishment of Omicron at IHEs precedes that of the state and region and that the time to fixation is shorter at IHEs (9.5–12.5 days) than in the state (14.8 days) or region. We show that the trajectory of Omicron fixation among university employees resembles that of students, with a 2- to 3-day delay. Finally, we compare cycle threshold values in Omicron vs Delta variant cases on college campuses and identify lower viral loads among college affiliates who harbor Omicron infections. Conclusions We document the rapid takeover of the Omicron variant at IHEs, reaching near-fixation within the span of 9.5–12.5 days despite lower viral loads, on average, than the previously dominant Delta variant. These findings highlight the transmissibility of Omicron, its propensity to rapidly dominate small populations, and the ability of robust asymptomatic surveillance programs to offer early insights into the dynamics of pathogen arrival and spread. [ABSTRACT FROM AUTHOR]

Published
2023
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31. Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts

Author

Siddle, Katherine J., primary, Krasilnikova, Lydia A., additional, Moreno, Gage K., additional, Schaffner, Stephen F., additional, Vostok, Johanna, additional, Fitzgerald, Nicholas A., additional, Lemieux, Jacob E., additional, Barkas, Nikolaos, additional, Loreth, Christine, additional, Specht, Ivan, additional, Tomkins-Tinch, Christopher H., additional, Silbert, Jillian, additional, Schaeffer, Beau, additional, Taylor, Bradford P., additional, Loftness, Bryn, additional, Johnson, Hillary, additional, Schubert, Petra L., additional, Shephard, Hanna M., additional, Doucette, Matthew, additional, Fink, Timelia, additional, Lang, Andrew S., additional, Baez, Stephanie, additional, Beauchamp, John, additional, Hennigan, Scott, additional, Buzby, Erika, additional, Ash, Stephanie, additional, Brown, Jessica, additional, Clancy, Selina, additional, Cofsky, Seana, additional, Gagne, Luc, additional, Hall, Joshua, additional, Harrington, Rachel, additional, Gionet, Gabrielle L., additional, DeRuff, Katherine C., additional, Vodzak, Megan E., additional, Adams, Gordon C., additional, Dobbins, Sabrina T., additional, Slack, Sarah D., additional, Reilly, Steven K., additional, Anderson, Lisa M., additional, Cipicchio, Michelle C., additional, DeFelice, Matthew T., additional, Grimsby, Jonna L., additional, Anderson, Scott E., additional, Blumenstiel, Brendan S., additional, Meldrim, James C., additional, Rooke, Heather M., additional, Vicente, Gina, additional, Smith, Natasha L., additional, Messer, Katelyn S., additional, Reagan, Faye L., additional, Mandese, Zoe M., additional, Lee, Matthew D., additional, Ray, Marianne C., additional, Fisher, Marissa E., additional, Ulcena, Maesha A., additional, Nolet, Corey M., additional, English, Sean E., additional, Larkin, Katie L., additional, Vernest, Kyle, additional, Chaluvadi, Sushma, additional, Arvidson, Deirdre, additional, Melchiono, Maurice, additional, Covell, Theresa, additional, Harik, Vaira, additional, Brock-Fisher, Taylor, additional, Dunn, Molly, additional, Kearns, Amanda, additional, Hanage, William P., additional, Bernard, Clare, additional, Philippakis, Anthony, additional, Lennon, Niall J, additional, Gabriel, Stacey B., additional, Gallagher, Glen R., additional, Smole, Sandra, additional, Madoff, Lawrence C., additional, Brown, Catherine M., additional, Park, Daniel J., additional, MacInnis, Bronwyn L., additional, and Sabeti, Pardis C., additional

Published
2021
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32. Coronavirus Disease 2019 Vaccine Impact on Rates of Severe Acute Respiratory Syndrome Coronavirus 2 Cases and Postvaccination Strain Sequences Among Health Care Workers at an Urban Academic Medical Center: A Prospective Cohort Study

Author

Bouton, Tara C, primary, Lodi, Sara, additional, Turcinovic, Jacquelyn, additional, Schaeffer, Beau, additional, Weber, Sarah E, additional, Quinn, Emily, additional, Korn, Cathy, additional, Steiner, Jacqueline, additional, Schechter-Perkins, Elissa M, additional, Duffy, Elizabeth, additional, Ragan, Elizabeth J, additional, Taylor, Bradford P, additional, Miller, Nancy, additional, Davidoff, Ravin, additional, Hanage, William P, additional, Connor, John, additional, Pierre, Cassandra, additional, and Jacobson, Karen R, additional

Published
2021
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33. A compilation of fecal microbiome shotgun metagenomics from hospitalized patients undergoing hematopoietic cell transplantation

Author

Yan, Jinyuan, primary, Liao, Chen, additional, Taylor, Bradford P., additional, Fontana, Emily, additional, Amoretti, Luigi A., additional, Wright, Roberta J., additional, Dai, Anqi, additional, Waters, Nicholas, additional, Peled, Jonathan U., additional, Taur, Ying, additional, Perales, Miguel-Angel, additional, Siranosian, Benjamin A., additional, Bhatt, Ami S., additional, van den Brink, Marcel R.M., additional, Pamer, Eric G., additional, Schluter, Jonas, additional, and Xavier, Joao B., additional

Published
2021
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34. Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages

Author

Petrone, Mary E., primary, Rothman, Jessica E., additional, Breban, Mallery I., additional, Ott, Isabel M., additional, Russell, Alexis, additional, Lasek-Nesselquist, Erica, additional, Kelly, Kevin, additional, Omerza, Greg, additional, Renzette, Nicholas, additional, Watkins, Anne E., additional, Kalinich, Chaney C., additional, Alpert, Tara, additional, Brito, Anderson F., additional, Earnest, Rebecca, additional, Tikhonova, Irina R., additional, Castaldi, Christopher, additional, Kelly, John P., additional, Shudt, Matthew, additional, Plitnick, Jonathan, additional, Schneider, Erasmus, additional, Murphy, Steven, additional, Neal, Caleb, additional, Laszlo, Eva, additional, Altajar, Ahmad, additional, Pearson, Claire, additional, Muyombwe, Anthony, additional, Downing, Randy, additional, Razeq, Jafar, additional, Niccolai, Linda, additional, Wilson, Madeline S., additional, Anderson, Margaret L., additional, Wang, Jianhui, additional, Liu, Chen, additional, Hui, Pei, additional, Mane, Shrikant, additional, Taylor, Bradford P., additional, Hanage, William P., additional, Landry, Marie L., additional, Peaper, David R., additional, Bilguvar, Kaya, additional, Fauver, Joseph R., additional, Vogels, Chantal B.F., additional, Gardner, Lauren M., additional, Pitzer, Virginia E., additional, George, Kirsten St., additional, Adams, Mark D., additional, and Grubaugh, Nathan D., additional

Published
2021
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36. COVID-19 vaccine impact on rates of SARS-CoV-2 cases and post vaccination strain sequences among healthcare workers at an urban academic medical center: a prospective cohort study

Author

Bouton, Tara C., primary, Lodi, Sara, additional, Turcinovic, Jacquelyn, additional, Weber, Sarah E., additional, Quinn, Emily, additional, Korn, Cathy, additional, Steiner, Jacqueline, additional, Schechter-Perkins, Elissa M., additional, Duffy, Elizabeth, additional, Ragan, Elizabeth J., additional, Taylor, Bradford P., additional, Schaeffer, Beau, additional, Miller, Nancy, additional, Davidoff, Ravin, additional, Hanage, William P., additional, Connor, John, additional, Pierre, Cassandra, additional, and Jacobson, Karen R., additional

Published
2021
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37. The microbe-derived short-chain fatty acids butyrate and propionate are associated with protection from chronic GVHD

Author

Markey, Kate A., primary, Schluter, Jonas, primary, Gomes, Antonio L. C., primary, Littmann, Eric R., primary, Pickard, Amanda J., primary, Taylor, Bradford P., primary, Giardina, Paul A., primary, Weber, Daniela, primary, Dai, Anqi, primary, Docampo, Melissa D., primary, Armijo, Gabriel K., primary, Slingerland, Ann E., primary, Slingerland, John B., primary, Nichols, Katherine B., primary, Brereton, Daniel G., primary, Clurman, Annelie G., primary, Ramos, Ruben J., primary, Rao, Arka, primary, Bush, Amy, primary, Bohannon, Lauren, primary, Covington, Megan, primary, Lew, Meagan V., primary, Rizzieri, David A., primary, Chao, Nelson, primary, Maloy, Molly, primary, Cho, Christina, primary, Politikos, Ioannis, primary, Giralt, Sergio, primary, Taur, Ying, primary, Pamer, Eric G., primary, Holler, Ernst, primary, Perales, Miguel-Angel, primary, Ponce, Doris M., primary, Devlin, Sean M., primary, Xavier, Joao, primary, Sung, Anthony D., primary, Peled, Jonathan U., primary, Cross, Justin R., primary, and van den Brink, Marcel R. M., primary

Published
2020
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38. The gut microbiota influences how circulating immune cells in humans change from one day to the next

Author

Schluter, Jonas, Peled, Jonathan U., Taylor, Bradford P., Smith, Melody, Markey, Kate A., Taur, Ying, Niehus, Rene, Staffas, Anna, Dai, Anqi, Fontana, Emily, Amoretti, Luigi A., Wright, Roberta J., Morjaria, Sejal, Fenelus, Maly, Pessin, Melissa S., Chao, Nelson J., Lew, Meagan, Bohannon, Lauren, Bush, Amy, Sung, Anthony D., Hohl, Tobias M., Perales, Miguel-Angel, van den Brink, Marcel R.M., and Xavier, Joao B.

Subjects
bacteria, biochemical phenomena, metabolism, and nutrition
Abstract

The gut microbiota influences the development and homeostasis of the mammalian immune system 1–3 , can alter immune cell compositions in mice 4–7 , and is associated with responses to immunotherapy that rely on the activity of peripheral immune cells 8–12 . Still, our understanding of how the microbiota modulates circulatory immune cells remains limited, particularly in humans where a lack of manipulative experiments makes inference challenging. Here we overcome this challenge by studying hundreds of hospitalized—and closely monitored—bone marrow transplantation patients as they recover from chemotherapy-induced immune ablation. This aggressive treatment causes large shifts in both circulatory immune cell and microbiota populations, allowing the relationships between the two to be studied simultaneously over time with unprecedented resolution. We analyzed daily changes in white blood cell counts from 2,235 patients, and 10,680 longitudinal fecal microbiota samples to identify bacterial genera consistently associated with those changes. Bayesian inference and validation across different patient cohorts revealed consistent associations between intestinal bacteria and peripheral immune cell dynamics in the context of immunomodulatory medications, clinical metadata and homeostatic feedbacks between peripheral immune cells. The quantification of validated microbiota associations enabled us to contrast the potency of fermentatively active, obligate anaerobic bacteria with that of medications with known immunomodulatory mechanism, and this way estimate the microbiota potential to alter peripheral immune cell dynamics directly in patients. Our analysis establishes and quantifies the link between the intestinal microbiota and immune cell dynamics in humans, with implications for microbiota-driven modulation of immunity and immunotherapies that rely on circulatory immune cells.

Published
2019
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40. The devil in the details: Herd immunity and pandemic response.

Author

Schaeffer, Beau, Taylor, Bradford, Bushman, Mary, and Hanage, William P.

Abstract

If enough individuals in a population are immune to a pathogen, it cannot cause an outbreak. Deliberately seeking such herd immunity through infection during a potentially lethal pandemic is contrary to all principles of public health, given the potential for uncontrolled outbreaks and risks to vulnerable populations. [ABSTRACT FROM AUTHOR]

Published
2021
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43. An association between the gut microbiota and immune cell dynamics in humans

Author

Schluter, Jonas, primary, Peled, Jonathan U., additional, Taylor, Bradford P., additional, Smith, Melody, additional, Markey, Kate A., additional, Taur, Ying, additional, Niehus, Rene, additional, Staffas, Anna, additional, Dai, Anqi, additional, Fontana, Emily, additional, Amoretti, Luigi A., additional, Wright, Roberta J., additional, Morjaria, Sejal, additional, Fenelus, Maly, additional, Pessin, Melissa S., additional, Chao, Nelson J., additional, Lew, Meagan, additional, Bohannon, Lauren, additional, Bush, Amy, additional, Sung, Anthony D., additional, Hohl, Tobias M., additional, Perales, Miguel-Angel, additional, van den Brink, Marcel R.M., additional, and Xavier, Joao B., additional

Published
2019
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47. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

Author

Weitz, Joshua S., Stock, Charles A., Wilhelm, Steven W., Bourouiba, Lydia, Coleman, Maureen L., Buchan, Alison, Follows, Michael J., Fuhrman, Jed A., Jover, Luis F., Lennon, Jay T., Middelboe, Mathias, Sonderegger, Derek L., Suttle, Curtis A., Taylor, Bradford P., Frede Thingstad, T., Wilson, William H., Eric Wommack, K., Weitz, Joshua S., Stock, Charles A., Wilhelm, Steven W., Bourouiba, Lydia, Coleman, Maureen L., Buchan, Alison, Follows, Michael J., Fuhrman, Jed A., Jover, Luis F., Lennon, Jay T., Middelboe, Mathias, Sonderegger, Derek L., Suttle, Curtis A., Taylor, Bradford P., Frede Thingstad, T., Wilson, William H., and Eric Wommack, K.

Abstract

Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic ecosystem models to include a virus component, specifically parameterized for processes taking place in the ocean euphotic zone. Crucially, we are able to solve this model analytically, facilitating evaluation of model behavior under many alternative parameterizations. Analyses reveal that the addition of a virus component promotes the emergence of complex communities. In addition, biomass partitioning of the emergent multitrophic community is consistent with well-established empirical norms in the surface oceans. At steady state, ecosystem fluxes can be probed to characterize the effects that viruses have when compared with putative marine surface ecosystems without viruses. The model suggests that ecosystems with viruses will have (1) increased organic matter recycling, (2) reduced transfer to higher trophic levels and (3) increased net primary productivity. These model findings support hypotheses that viruses can have significant stimulatory effects across whole-ecosystem scales. We suggest that existing efforts to predict carbon and nutrient cycling without considering virus effects are likely to miss essential features of marine food webs that regulate global biogeochemical cycles.The ISME Journal advance online publication, 30 January 2015; doi:10.1038/ismej.2014.220.

Published
2015

48. Quantitative Infection Dynamics of Cafeteria Roenbergensis Virus.

Author

Taylor, Bradford P., Weitz, Joshua S., Brussaard, Corina P. D., and Fischer, Matthias G.

Subjects
*DNA replication, *VIRUSES, *ADSORPTION (Chemistry), *VIRUS diseases, *DYNAMICS
Abstract

The discovery of giant viruses in unicellular eukaryotic hosts has raised new questions on the nature of viral life. Although many steps in the infection cycle of giant viruses have been identified, the quantitative life history traits associated with giant virus infection remain unknown or poorly constrained. In this study, we provide the first estimates of quantitative infection traits of a giant virus by tracking the infection dynamics of the bacterivorous protist Cafeteria roenbergensis and its lytic virus CroV. Leveraging mathematical models of infection, we quantitatively estimate the adsorption rate, onset of DNA replication, latency time, and burst size from time-series data. Additionally, by modulating the initial ratio of viruses to hosts, we also provide evidence of a potential MOI-dependence on adsorption and burst size. Our work provides a baseline characterization of giant virus infection dynamics relevant to ongoing efforts to understand the ecological role of giant viruses. [ABSTRACT FROM AUTHOR]

Published
2018
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50. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

Author

Weitz, Joshua S, primary, Stock, Charles A, additional, Wilhelm, Steven W, additional, Bourouiba, Lydia, additional, Coleman, Maureen L, additional, Buchan, Alison, additional, Follows, Michael J, additional, Fuhrman, Jed A, additional, Jover, Luis F, additional, Lennon, Jay T, additional, Middelboe, Mathias, additional, Sonderegger, Derek L, additional, Suttle, Curtis A, additional, Taylor, Bradford P, additional, Frede Thingstad, T, additional, Wilson, William H, additional, and Eric Wommack, K, additional

Published
2015
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