S
Shijie Zhao
Researcher at Massachusetts Institute of Technology
Publications - 18
Citations - 1210
Shijie Zhao is an academic researcher from Massachusetts Institute of Technology. The author has contributed to research in topics: Microbiome & Genome. The author has an hindex of 7, co-authored 13 publications receiving 524 citations. Previous affiliations of Shijie Zhao include Peking University.
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Journal ArticleDOI
Adaptive Evolution within Gut Microbiomes of Healthy People
Shijie Zhao,Tami D. Lieberman,Mathilde Poyet,Mathilde Poyet,Kathryn M. Kauffman,Sean M. Gibbons,Mathieu Groussin,Mathieu Groussin,Ramnik J. Xavier,Eric J. Alm +9 more
TL;DR: It is found that intra-individual B. fragilis populations contain substantial de novo nucleotide and mobile element diversity, preserving years of within-person history, and adapts within individual microbiomes, pointing to factors that promote long-term gut colonization.
Journal ArticleDOI
A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research
Mathilde Poyet,Mathilde Poyet,Mathieu Groussin,Mathieu Groussin,Sean M. Gibbons,Julian Avila-Pacheco,Xiaofang Jiang,Xiaofang Jiang,Sean M. Kearney,Sean M. Kearney,Alison Perrotta,B. Berdy,B. Berdy,Shijie Zhao,Tami D. Lieberman,Tami D. Lieberman,Paige Swanson,Mark Smith,S. Roesemann,J. E. Alexander,S. A. Rich,Jonathan Livny,Hera Vlamakis,Clary B. Clish,Kevin Bullock,Amy Deik,Justin M. Scott,Kerry A. Pierce,Ramnik J. Xavier,Ramnik J. Xavier,Ramnik J. Xavier,Eric J. Alm +31 more
TL;DR: It is shown that microbial species maintain stable population sizes within and across humans and that commonly used ‘omics’ survey methods are more reliable when using averages over multiple days of sampling.
Journal ArticleDOI
An omics-based framework for assessing the health risk of antimicrobial resistance genes
An-Ni Zhang,An-Ni Zhang,Jeffry M. Gaston,Chengzhen L. Dai,Shijie Zhao,Mathilde Poyet,Mathilde Poyet,Mathieu Groussin,Mathieu Groussin,Xiaole Yin,Li-Guan Li,Mark C.M. van Loosdrecht,Edward Topp,Michael R. Gillings,William P. Hanage,James M. Tiedje,Katya Moniz,Eric J. Alm,Eric J. Alm,Tong Zhang +19 more
TL;DR: In this article, an omics-based framework was developed to evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity, and the authors classified humanassociated, mobile ARGs (3.6% of all ARGs) as the highest risk.
Journal ArticleDOI
Transmission of human-associated microbiota along family and social networks
Ilana L. Brito,Thomas Gurry,Shijie Zhao,Katherine H. Huang,Sarah Young,Terrence P. Shea,Waisea Naisilisili,Aaron Jenkins,Stacy D. Jupiter,Dirk Gevers,Eric J. Alm,Eric J. Alm +11 more
TL;DR: It is found that women harbour strains more closely related to those harboured by their familial and social contacts than men, and that transmission patterns of oral-associated and gut-associated microbiota need not be the same.
Posted ContentDOI
SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases
Fuqing Wu,Amy Xiao,Jianbo Zhang,Katya Moniz,Noriko Endo,Federica Armas,Richard Bonneau,Megan A. Brown,Mary Bushman,Peter R. Chai,Peter R. Chai,Claire Duvallet,Timothy B. Erickson,Timothy B. Erickson,Katelyn Foppe,Newsha Ghaeli,Xiaoqiong Gu,William P. Hanage,Katherine H. Huang,Wei Lin Lee,Mariana Matus,Kyle A. McElroy,Jonathan Nagler,Steven F Rhode,Mauricio Santillana,Mauricio Santillana,Joshua A. Tucker,Stefan Wuertz,Shijie Zhao,Janelle R. Thompson,Eric J. Alm +30 more
TL;DR: In this article, the authors used longitudinal wastewater analysis to track SARS-CoV-2 dynamics in wastewater at a major urban wastewater treatment facility in Massachusetts, between early January and May 2020.