Modulation of antibiotic effects on microbial communities by resource competition

Autor: Daniel P. Newton, Po-Yi Ho, Kerwyn Casey Huang

Publikováno v: Nature Communications, Vol 14, Iss 1, Pp 1-12 (2023)

Abstract Antibiotic treatment significantly impacts the human gut microbiota, but quantitative understanding of how antibiotics affect community diversity is lacking. Here, we build on classical ecological models of resource competition to investigat

Externí odkaz: https://doaj.org/article/4039c7418f3a4f7a9bba6daa8128765a

Assembly of gut-derived bacterial communities follows 'early-bird' resource utilization dynamics

Autor: Andrés Aranda-Díaz, Lisa Willis, Taylor H. Nguyen, Po-Yi Ho, Jean Vila, Tani Thomsen, Taylor Chavez, Rose Yan, Feiqiao Brian Yu, Norma Neff, Alvaro Sanchez, Sylvie Estrela, Kerwyn Casey Huang

Publikováno v: bioRxiv

Diet can impact host health through changes to the gut microbiota, yet we lack mechanistic understanding linking nutrient availability and microbiota composition. Here, we use thousands of microbial communities culturedin vitrofrom human feces to unc

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1b1ba2cbce0f703b7a18cf5c707e1fb8
https://europepmc.org/articles/PMC9882107/

Details Matter: Noise and Model Structure Set the Relationship between Cell Size and Cell Cycle Timing

Autor: Felix Barber, Po-Yi Ho, Andrew W. Murray, Ariel Amir

Publikováno v: Frontiers in Cell and Developmental Biology, Vol 5 (2017)

Organisms across all domains of life regulate the size of their cells. However, the means by which this is done is poorly understood. We study two abstracted “molecular” models for size regulation: inhibitor dilution and initiator accumulation. W

Externí odkaz: https://doaj.org/article/1ab109a4c11c4016a084dbe09c94da18

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Autor: Robert C, Jones, Jim, Karkanias, Mark A, Krasnow, Angela Oliveira, Pisco, Stephen R, Quake, Julia, Salzman, Nir, Yosef, Bryan, Bulthaup, Phillip, Brown, William, Harper, Marisa, Hemenez, Ravikumar, Ponnusamy, Ahmad, Salehi, Bhavani A, Sanagavarapu, Eileen, Spallino, Ksenia A, Aaron, Waldo, Concepcion, James M, Gardner, Burnett, Kelly, Nikole, Neidlinger, Zifa, Wang, Sheela, Crasta, Saroja, Kolluru, Maurizio, Morri, Serena Y, Tan, Kyle J, Travaglini, Chenling, Xu, Marcela, Alcántara-Hernández, Nicole, Almanzar, Jane, Antony, Benjamin, Beyersdorf, Deviana, Burhan, Kruti, Calcuttawala, Matthew M, Carter, Charles K F, Chan, Charles A, Chang, Stephen, Chang, Alex, Colville, Rebecca N, Culver, Ivana, Cvijović, Gaetano, D'Amato, Camille, Ezran, Francisco X, Galdos, Astrid, Gillich, William R, Goodyer, Yan, Hang, Alyssa, Hayashi, Sahar, Houshdaran, Xianxi, Huang, Juan C, Irwin, SoRi, Jang, Julia Vallve, Juanico, Aaron M, Kershner, Soochi, Kim, Bernhard, Kiss, William, Kong, Maya E, Kumar, Angera H, Kuo, Rebecca, Leylek, Baoxiang, Li, Gabriel B, Loeb, Wan-Jin, Lu, Sruthi, Mantri, Maxim, Markovic, Patrick L, McAlpine, Antoine, de Morree, Karim, Mrouj, Shravani, Mukherjee, Tyler, Muser, Patrick, Neuhöfer, Thi D, Nguyen, Kimberly, Perez, Ragini, Phansalkar, Nazan, Puluca, Zhen, Qi, Poorvi, Rao, Hayley, Raquer-McKay, Nicholas, Schaum, Bronwyn, Scott, Bobak, Seddighzadeh, Joe, Segal, Sushmita, Sen, Shaheen, Sikandar, Sean P, Spencer, Lea C, Steffes, Varun R, Subramaniam, Aditi, Swarup, Michael, Swift, Will, Van Treuren, Emily, Trimm, Stefan, Veizades, Sivakamasundari, Vijayakumar, Kim Chi, Vo, Sevahn K, Vorperian, Wanxin, Wang, Hannah N W, Weinstein, Juliane, Winkler, Timothy T H, Wu, Jamie, Xie, Andrea R, Yung, Yue, Zhang, Angela M, Detweiler, Honey, Mekonen, Norma F, Neff, Rene V, Sit, Michelle, Tan, Jia, Yan, Gregory R, Bean, Vivek, Charu, Erna, Forgó, Brock A, Martin, Michael G, Ozawa, Oscar, Silva, Angus, Toland, Venkata N P, Vemuri, Shaked, Afik, Kyle, Awayan, Olga Borisovna, Botvinnik, Ashley, Byrne, Michelle, Chen, Roozbeh, Dehghannasiri, Adam, Gayoso, Alejandro A, Granados, Qiqing, Li, Gita, Mahmoudabadi, Aaron, McGeever, Julia Eve, Olivieri, Madeline, Park, Neha, Ravikumar, Geoff, Stanley, Weilun, Tan, Alexander J, Tarashansky, Rohan, Vanheusden, Peter, Wang, Sheng, Wang, Galen, Xing, Rebecca, Culver, Les, Dethlefsen, Po-Yi, Ho, Shixuan, Liu, Jonathan S, Maltzman, Ross J, Metzger, Koki, Sasagawa, Rahul, Sinha, Hanbing, Song, Bruce, Wang, Steven E, Artandi, Philip A, Beachy, Michael F, Clarke, Linda C, Giudice, Franklin W, Huang, Kerwyn Casey, Huang, Juliana, Idoyaga, Seung K, Kim, Mark, Krasnow, Christin S, Kuo, Patricia, Nguyen, Thomas A, Rando, Kristy, Red-Horse, Jeremy, Reiter, David A, Relman, Justin L, Sonnenburg, Albert, Wu, Sean M, Wu, Tony, Wyss-Coray

Publikováno v: Science
Tabula Sapiens Consortium* 2022, ' The Tabula Sapiens : A multiple-organ, single-cell transcriptomic atlas of humans ', Science (New York, N.Y.), vol. 376, no. 6594, pp. eabl4896 . https://doi.org/10.1126/science.abl4896

INTRODUCTION: Although the genome is often called the blueprint of an organism, it is perhaps more accurate to describe it as a parts list composed of the various genes that may or may not be used in the different cell types of a multicellular organi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f726fc016f86cd4ce8c15a69dce9f6be
https://pubmed.ncbi.nlm.nih.gov/36198687

Author response: Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas

Autor: Po-Yi Ho, Benjamin H Good, Kerwyn Casey Huang

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::bc63394a4dd91dbdac06d68e0c8061ec
https://doi.org/10.7554/elife.75168.sa2