Author
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
11 papers
Recent·Most cited
J. C. Boktor, G. Sharon, L. A. Verhagen Metman, D. A. Hall, P. A. Engen, Z. Zreloff, D. J. Hakim, J. W. Bostick, J. Ousey, D. Lange, G. Humphrey, G. Ackermann, M. Carlin, R. Knight, A. Keshavarzian, S. K. Mazmanian
This study analyzes the gut microbiome in Parkinson's disease across multiple cohorts, identifying consistent taxonomic and functional changes associated with the disease.
bioRxiv · Jul 20, 2022Microbiology
R. Abdel-Haq, J. C. M. Schlachetzki, J. C. Boktor, T. M. Cantu-Jungles, T. Thron, M. Zhang, J. W. Bostick, T. Khazaei, S. Chilakala, L. H. Morais, G. Humphrey, A. Keshavarzian, J. E. Katz, M. Thomson, R. Knight, , S. K. Mazmanian
A prebiotic diet reduces motor deficits and microglial activation in α-synuclein overexpressing mice by altering gut microbiota and microglial states.
bioRxiv · Jun 27, 2022Physiology
J. P. Shaffer, C. S. Carpenter, C. P. Martino, R. A. Salido, M. Bryant, K. Sanders, T. Schwartz, G. Humphrey, A. D. Swafford, R. Knight
The paper compares six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing, finding the MagMAX Microbiome kit performs best across multiple criteria.
bioRxiv · Mar 7, 2022Microbiology
R. A. Salido, C. Martino, S. Karthikeyan, S. Huang, G. Rahman, A. Gonzalez, L. S. Zaramela, K. L. Beck, S. Bhute, K. Cantrell, A. P. Carrieri, S. Farmer, N. Haiminen, G. Humphrey, H.-C. Kim, , R. Knight
The paper shows that bacterial metatranscriptomes in wastewater can distinguish SARS-CoV-2 infected from uninfected human populations without directly detecting viral transcripts.
bioRxiv · Feb 23, 2022 · PreprintMicrobiology
J. P. Shaffer, L.-F. Nothias, L. R. Thompson, S. G. Jon, R. A. Salido, S. P. Couvillion, A. D. Brejnrod, S. Huang, F. Lejzerowicz, N. Haiminen, H. L. Lutz, Q. Zhu, C. Martino, J. T. Morton, S. Karthikeyan, , St
The paper performs a multi-omics meta-analysis of microbial and metabolite data from diverse environments, revealing patterns of diversity and co-occurrence across biomes.
bioRxiv · Jun 4, 2021Ecology
J. A. Griffiths, B. B. Yoo, P. Thuy-Boun, V. Cantu, K. Weldon, C. Challis, M. J. Sweredoski, K. Y. Chan, T. M. Thron, G. Sharon, A. Moradian, G. Humphrey, Q. Zhu, J. Shaffer, D. W. Wolan, , S. Mazmanian
This study activates specific gut neurons in mice to show they influence microbiome structure and gut physiology, including bile acids and fecal output, without brain signals.
bioRxiv · Apr 12, 2021Physiology
J. P. Shaffer, C. Marotz, P. Belda-Ferre, C. Martino, S. Wandro, M. Estaki, R. A. Salido, C. S. Carpenter, L. S. Zaramela, J. J. Minich, M. B. Bryant, K. Sanders, S. Fraraccio, G. Ackermann, G. Humphrey, , R. Knight
The paper compares DNA/RNA extraction protocols for microbial community sequencing, finding one protocol equivalent or better than a standard DNA-only method for RNA-based organisms.
bioRxiv · Nov 13, 2020Ecology
A. S. Adebayo, G. Ackermann, R. C. E. Bowyer, P. M. Wells, G. Humphrey, R. Knight, T. D. Spector, C. J. Steves
This study identifies host genetic and environmental factors influencing the urinary microbiome in older women using twin data and metagenomic analysis.
bioRxiv · Nov 12, 2019Microbiology
N. Garg, A. V. Melnik, Y. Vasquez-Baeza, A. Aksenov, E. R. Hyde, A. C. McAvoy, M. Wang, R. da Silva, I. Protsyuk, J. V. Wu, A. Bouslimani, Y. W. Lim, T. Luzzatto-Knaan, W. Comstock, R. A. Quinn, , R. Knight
The paper generates 3D maps of microbiomes and metabolomes in cystic fibrosis lungs, revealing personalized and regiospecific chemical environments and microbial interactions.
bioRxiv · Jun 19, 2019 · PreprintMicrobiology
R. A. Quinn, A. Vrbanac, A. V. Melnik, K. A. Patras, M. Christy, A. T. Nelson, A. A. Aksenov, A. Tripathi, G. Humphrey, R. da Silva, R. Bussell, T. Thron, M. Wang, F. Vargas, J. Gauglitz, , P. C. Dorrestein
The paper identifies novel conjugated bile acids produced by the microbiome in mice and humans using mass spectrometry and a murine 3D model.
bioRxiv · Jun 3, 2019 · PreprintMicrobiology
D. McDonald, E. R. Hyde, J. W. Debelius, J. T. Morton, A. Gonzalez, G. Ackermann, A. A. Aksenov, B. Behsaz, C. Brennan, Y. Chen, L. DeRight Goldasicha, P. C. Dorrestein, R. R. Dunn, A. K. Fahimipourg, J. Gaffney, , Rah
The paper uses citizen-science data to analyze human stool microbiomes, revealing new insights into microbial diversity, metabolome composition, and associations with diet and health.
bioRxiv · Mar 7, 2018Microbiology