Multiomic analysis reveals cellular, transcriptomic and epigenetic changes in intestinal pouches of ulcerative colitis patients

Authors: Yu Zhao, Ran Zhou, Bingqing Xie, Cambrian Y. Liu, Martin Kalski, Candace M. Cham, Zhiwei Jiang, Jason Koval, Christopher R. Weber, David T. Rubin, Mitch Sogin, Sean Crosson, Mengjie Chen, Jun Huang, Aretha Fiebig, Sushila Dalal, Eugene B. Chang, Anindita Basu, Sebastian Pott

Source: Nature Communications, Vol 16, Iss 1, Pp 1-18 (2025)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/113cd4564391427f9da4fabf290fe6d0

Protocol to characterize longitudinal gut motility in mice using transit time, tissue harvest, and whole-mount immunostaining

Authors: Mary E. Frith, Purna C. Kashyap, David R. Linden, Eugene B. Chang

Source: STAR Protocols, Vol 6, Iss 2, Pp 103761- (2025)

Subject Terms: Metabolism, Model Organisms, Systems biology, Science (General), Q1-390

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666166725001674; https://doaj.org/toc/2666-1667

Access URL: https://doaj.org/article/3ed5ca0aa633419594a9779c95882494

Microbiota-dependent early-life programming of gastrointestinal motility

Authors: Mary E. Frith, Purna C. Kashyap, David R. Linden, Betty Theriault, Eugene B. Chang

Source: iScience, Vol 27, Iss 10, Pp 110895- (2024)

Subject Terms: Neuroscience, Developmental neuroscience, Microbiome, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004224021205; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/795d8a497b2d4732adeb8f6c5e9b6afe

Sodium oligomannate alters gut microbiota, reduces cerebral amyloidosis and reactive microglia in a sex-specific manner

Authors: Megan E. Bosch, Hemraj B. Dodiya, Julia Michalkiewicz, Choonghee Lee, Shabana M. Shaik, Ian Q. Weigle, Can Zhang, Jack Osborn, Aishwarya Nambiar, Priyam Patel, Samira Parhizkar, Xiaoqiong Zhang, Marie L. Laury, Prasenjit Mondal, Ashley Gomm, Matthew John Schipma, Dania Mallah, Oleg Butovsky, Eugene B. Chang, Rudolph E. Tanzi, Jack A. Gilbert, David M. Holtzman, Sangram S. Sisodia

Source: Molecular Neurodegeneration, Vol 19, Iss 1, Pp 1-26 (2024)

Subject Terms: Alzheimer’s disease, Microbiome, Sodium oligomannate, Microglia, Neuroinflammation, Neurology. Diseases of the nervous system, RC346-429, Geriatrics, RC952-954.6

File Description: electronic resource

Relation: https://doaj.org/toc/1750-1326

Access URL: https://doaj.org/article/5d6226d85e844091868e4f867d83ad18

Correction: Sodium oligomannate alters gut microbiota, reduces cerebral amyloidosis and reactive microglia in a sex-specific manner

Authors: Megan E. Bosch, Hemraj B. Dodiya, Julia Michalkiewicz, Choonghee Lee, Shabana M. Shaik, Ian Q. Weigle, Can Zhang, Jack Osborn, Aishwarya Nambiar, Priyam Patel, Samira Parhizkar, Xiaoqiong Zhang, Marie L. Laury, Prasenjit Mondal, Ashley Gomm, Matthew John Schipma, Dania Mallah, Oleg Butovsky, Eugene B. Chang, Rudolph E. Tanzi, Jack A. Gilbert, David M. Holtzman, Sangram S. Sisodia

Source: Molecular Neurodegeneration, Vol 19, Iss 1, Pp 1-2 (2024)

Subject Terms: Neurology. Diseases of the nervous system, RC346-429, Geriatrics, RC952-954.6

File Description: electronic resource

Relation: https://doaj.org/toc/1750-1326

Access URL: https://doaj.org/article/14d8b48203894334ae62b75a08c5835b

Antibiotic‐Induced Gut Microbiota Dysbiosis Modulates Host Transcriptome and m6A Epitranscriptome via Bile Acid Metabolism

Authors: Meng Yang, Xiaoqi Zheng, Jiajun Fan, Wei Cheng, Tong‐Meng Yan, Yushan Lai, Nianping Zhang, Yi Lu, Jiali Qi, Zhengyi Huo, Zihe Xu, Jia Huang, Yuting Jiao, Biaodi Liu, Rui Pang, Xiang Zhong, Shi Huang, Guan‐Zheng Luo, Gina Lee, Christian Jobin, A. Murat Eren, Eugene B Chang, Hong Wei, Tao Pan, Xiaoyun Wang

Source: Advanced Science, Vol 11, Iss 28, Pp n/a-n/a (2024)

Subject Terms: bile acids, epitranscriptome, gut microbiota, N6‐Methyladenosine, transcriptome, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2198-3844

Access URL: https://doaj.org/article/108ba1867411401a919ac197dce1de39

Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient

Authors: Aretha Fiebig, Matthew K. Schnizlein, Selymar Pena-Rivera, Florian Trigodet, Abhishek Anil Dubey, Miette K. Hennessy, Anindita Basu, Sebastian Pott, Sushila Dalal, David Rubin, Mitchell L. Sogin, A. Murat Eren, Eugene B. Chang, Sean Crosson

Source: mBio, Vol 15, Iss 1 (2024)

Subject Terms: bile, deoxycholate, pouchitis, Tn-seq, Bacteroides fragilis, stress response, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/04ba6da4d1ee4dad828762f99f95006d

Phenylpropionic acid produced by gut microbiota alleviates acetaminophen-induced hepatotoxicity

Authors: Sungjoon Cho, Xiaotong Yang, Kyoung-Jae Won, Vanessa A. Leone, Eugene B. Chang, Grace Guzman, Yeonju Ko, Ok-Nam Bae, Hyunwoo Lee, Hyunyoung Jeong

Source: Gut Microbes, Vol 15, Iss 1 (2023)

Subject Terms: Mouse gut microbiota, metabolomics, CYP2E1, acetaminophen, hepatotoxicity, liver injury, Diseases of the digestive system. Gastroenterology, RC799-869

File Description: electronic resource

Relation: https://doaj.org/toc/1949-0976; https://doaj.org/toc/1949-0984

Access URL: https://doaj.org/article/44a847d2845a476a9d7eee8f022f66fe

1325 Bariatric surgery-induced modulation of gut microbiota improves response to αPD-1 immunotherapy in preclinical model of breast cancer after bariatric surgery

Authors: Eugene B Chang, Margaret S Bohm, Laura M Sipe, Sydney C Joseph, Boston W Simmons, Madeline E Pye, Ashley M Sidebottom, Joseph F Pierre, Liza Makowski

Source: Journal for ImmunoTherapy of Cancer, Vol 11, Iss Suppl 1 (2023)

Subject Terms: Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/2051-1426

Access URL: https://doaj.org/article/98eba0532a6b4fbd82337bca478fb77a

Gut microbiota modulates bleomycin-induced acute lung injury response in mice

Authors: Young me Yoon, Cara L. Hrusch, Na Fei, Gabriel M. Barrón, Kathleen A. M. Mills, Maile K. Hollinger, Tania E. Velez, Vanessa A. Leone, Eugene B. Chang, Anne I. Sperling

Source: Respiratory Research, Vol 23, Iss 1, Pp 1-14 (2022)

Subject Terms: Diseases of the respiratory system, RC705-779

File Description: electronic resource

Relation: https://doaj.org/toc/1465-993X

Access URL: https://doaj.org/article/68130328ac994fabae9d0657fd22b946

Gut microbes and the liver circadian clock partition glucose and lipid metabolism

Authors: Katya Frazier, Sumeed Manzoor, Katherine Carroll, Orlando DeLeon, Sawako Miyoshi, Jun Miyoshi, Marissa St. George, Alan Tan, Evan A. Chrisler, Mariko Izumo, Joseph S. Takahashi, Mrinalini C. Rao, Vanessa A. Leone, Eugene B. Chang

Source: The Journal of Clinical Investigation, Vol 133, Iss 18 (2023)

Subject Terms: Metabolism, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/1558-8238

Access URL: https://doaj.org/article/2b3926a172264fbfb7638c31f72999c6

Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization

Authors: Megan S. Kennedy, Manjing Zhang, Orlando DeLeon, Jacie Bissell, Florian Trigodet, Karen Lolans, Sara Temelkova, Katherine T. Carroll, Aretha Fiebig, Adam Deutschbauer, Ashley M. Sidebottom, Joash Lake, Chris Henry, Phoebe A. Rice, Joy Bergelson, Eugene B. Chang

Source: Cell Reports, Vol 42, Iss 8, Pp 113009- (2023)

Subject Terms: CP: Microbiology, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124723010203; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/50674f85df064174bd593f77f0452143

Atypical behavioral and thermoregulatory circadian rhythms in mice lacking a microbiome

Authors: Vanessa A. Leone, Kenneth G. Onishi, Megan Kennedy, Jonathan P. Riggle, Joseph F. Pierre, Andrew C. Maneval, Melanie N. Spedale, Betty R. Theriault, Eugene B. Chang, Brian J. Prendergast

Source: Scientific Reports, Vol 12, Iss 1, Pp 1-15 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/76a48434c7954ca593cab7492814ca79

A Multifunctional Neutralizing Antibody‐Conjugated Nanoparticle Inhibits and Inactivates SARS‐CoV‐2

Authors: Xiaolei Cai, Min Chen, Aleksander Prominski, Yiliang Lin, Nicholas Ankenbruck, Jillian Rosenberg, Mindy Nguyen, Jiuyun Shi, Anastasia Tomatsidou, Glenn Randall, Dominique Missiakas, John Fung, Eugene B. Chang, Pablo Penaloza‐MacMaster, Bozhi Tian, Jun Huang

Source: Advanced Science, Vol 9, Iss 2, Pp n/a-n/a (2022)

Subject Terms: COVID‐19, multifunctional nanoparticle, photothermal therapy, SARS‐CoV‐2, virus inactivation, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2198-3844

Access URL: https://doaj.org/article/5a87e165b630476b9dfcd6664dc1a5eb

Microbe‐Derived Butyrate and Its Receptor, Free Fatty Acid Receptor 3, But Not Free Fatty Acid Receptor 2, Mitigate Neointimal Hyperplasia Susceptibility After Arterial Injury

Authors: Michael Nooromid, Edmund B. Chen, Liqun Xiong, Katherine Shapiro, Qun Jiang, Falen Demsas, Maeve Eskandari, Medha Priyadarshini, Eugene B. Chang, Brian T. Layden, Karen J. Ho

Source: Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease, Vol 9, Iss 13 (2020)

Subject Terms: butyrate, neointimal hyperplasia, restenosis, Diseases of the circulatory (Cardiovascular) system, RC666-701

File Description: electronic resource

Relation: https://doaj.org/toc/2047-9980

Access URL: https://doaj.org/article/f13162973c26435e93b3e269b3ea5655

Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes

Authors: William J Watterson, Melikhan Tanyeri, Andrea R Watson, Candace M Cham, Yue Shan, Eugene B Chang, A Murat Eren, Savaş Tay

Source: eLife, Vol 9 (2020)

Subject Terms: droplet microfluidics, high-throughput cultivation, fecal microbial transplantation, rare bacteria, antibiotic resistance screening, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/56998; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/ef8cd5832d59451aac795414adbdc03b

High-Fat Diet Alters the Retinal Pigment Epithelium and Choroidal Transcriptome in the Absence of Gut Microbiota

Authors: Jason Xiao, Bingqing Xie, David Dao, Melanie Spedale, Mark D’Souza, Betty Theriault, Seenu M. Hariprasad, Dinanath Sulakhe, Eugene B. Chang, Dimitra Skondra

Source: Cells, Vol 11, Iss 13, p 2076 (2022)

Subject Terms: age-related macular degeneration, high-fat diet, gut microbiome, gut–choroid axis, RNA sequencing, germ-free mice, Cytology, QH573-671

File Description: electronic resource

Relation: https://www.mdpi.com/2073-4409/11/13/2076; https://doaj.org/toc/2073-4409

Access URL: https://doaj.org/article/aa489a97f2124e0d883970dfb65d083e

Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis

Authors: Michael H. Schwartz, Haipeng Wang, Jessica N. Pan, Wesley C. Clark, Steven Cui, Matthew J. Eckwahl, David W. Pan, Marc Parisien, Sarah M. Owens, Brian L. Cheng, Kristina Martinez, Jinbo Xu, Eugene B. Chang, Tao Pan, A. Murat Eren

Source: Nature Communications, Vol 9, Iss 1, Pp 1-13 (2018)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/6f8a3e52a3ef443084558e669d4b079b

Peripartum Antibiotics Promote Gut Dysbiosis, Loss of Immune Tolerance, and Inflammatory Bowel Disease in Genetically Prone Offspring

Authors: Jun Miyoshi, Alexandria M. Bobe, Sawako Miyoshi, Yong Huang, Nathaniel Hubert, Tom O. Delmont, A. Murat Eren, Vanessa Leone, Eugene B. Chang

Source: Cell Reports, Vol 20, Iss 2, Pp 491-504 (2017)

Subject Terms: microbiome, host-microbe interactions, microbiome intervention, immune development, microbial assemblage, dysbiosis, inflammatory bowel diseases, complex immune disorders, vertical transmission, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124717308914; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/f695e3d6247343a181c2510cb18a6bd7

Microbial Colonization of Germ‐Free Mice Restores Neointimal Hyperplasia Development After Arterial Injury

Authors: Edmund B. Chen, Katherine E. Shapiro, Kelly Wun, Thomas Kuntz, Betty R. Theriault, Michael J. Nooromid, Vanessa A. Leone, Katharine G. Harris, Qun Jiang, Melanie Spedale, Liqun Xiong, Jack A. Gilbert, Eugene B. Chang, Karen J. Ho

Source: Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease, Vol 9, Iss 5 (2020)

Subject Terms: microbiome, neointimal hyperplasia, restenosis, Diseases of the circulatory (Cardiovascular) system, RC666-701

File Description: electronic resource

Relation: https://doaj.org/toc/2047-9980

Access URL: https://doaj.org/article/56f732a5edd944d1a32d1c0f09ac2abb