Optimizing methods and dodging pitfalls in microbiome research

Autor: Dorothy Kim, Casey E. Hofstaedter, Chunyu Zhao, Lisa Mattei, Ceylan Tanes, Erik Clarke, Abigail Lauder, Scott Sherrill-Mix, Christel Chehoud, Judith Kelsen, Máire Conrad, Ronald G. Collman, Robert Baldassano, Frederic D. Bushman, Kyle Bittinger

Publikováno v: Microbiome, Vol 5, Iss 1, Pp 1-14 (2017)

Abstract Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls,

Externí odkaz: https://doaj.org/article/b4734cebc798435bbb26b8cc6d6c1d5a

Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates

Autor: Joshua M. Taylor, Erik L. Clarke, Kate Baker, Abigail Lauder, Dorothy Kim, Aubrey Bailey, Gary D. Wu, Ronald G. Collman, Lara Doyle-Meyers, Kasi Russell-Lodrigue, James Blanchard, Frederic D. Bushman, Rudolf Bohm

Publikováno v: PeerJ, Vol 6, p e4612 (2018)

Idiopathic chronic enterocolitis (ICE) is one of the most commonly encountered and difficult to manage diseases of captive rhesus macaques (Macaca mulatta). The etiology is not well understood, but perturbations in gut microbial communities have been

Externí odkaz: https://doaj.org/article/7cfe6e3d6b9f4c3e84c2de0fb8b778ac

Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low–Microbial Content Samples

Autor: Leslie A. Litzky, Casey E. Hofstaedter, Ayannah S. Fitzgerald, Anna Dubaniewicz, Ronald G. Collman, Michael Feldman, Wojciech Biernat, Milton D. Rossman, Erik L. Clarke, Young Hwang, Bartlomiej Rekawiecki, Karen C. Patterson, Ize Imai, Abigail Lauder, Hanna Majewska, Frederic D. Bushman, Kyle Bittinger

Publikováno v: American Journal of Respiratory and Critical Care Medicine. 197:225-234

The etiology of sarcoidosis is unknown, but microbial agents are suspected as triggers.We sought to identify bacterial, fungal, or viral lineages in specimens from patients with sarcoidosis enriched relative to control subjects using metagenomic DNA

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8cc7e02922bfc39c59308fa76f966850
https://doi.org/10.1164/rccm.201705-0891oc

Wild bonobos host geographically restricted malaria parasites including a putative new Laverania species

Autor: Lindsey J. Plenderleith, Steve Ahuka-Mundeke, Martine Peeters, Abigail Lauder, Paul M. Sharp, Weimin Liu, Scott Sherrill-Mix, Terese B. Hart, Beatrice H. Hahn, Gerald H. Learn, George M. Shaw, Jef Dupain, Cintia Garai, Paco Bertolani, Alexander V. Georgiev, Jean Bosco N. Ndjango, Yingying Li, Sesh A. Sundararaman, Dorothy E. Loy, Erik J. Scully, John Hart, Alexa N. Avitto

Publikováno v: Nature Communications, Vol 8, Iss 1, Pp 1-14 (2017)
Nature Communications
Liu, W, Sherrill-Mix, S, Learn, G H, Scully, E J, Li, Y, Avitto, A N, Loy, D E, Lauder, A P, Sundararaman, S A, Plenderleith, L J, Ndjango, J B N, Georgiev, A V, Ahuka-Mundeke, S, Peeters, M, Bertolani, P, Dupain, J, Garai, C, Hart, J A, Hart, T B, Shaw, G M, Sharp, P M & Hahn, B H 2017, ' Wild bonobos host geographically restricted malaria parasites including a putative new Laverania species ', Nature Communications, vol. 8, no. 1, 1635 . https://doi.org/10.1038/s41467-017-01798-5

Malaria parasites, though widespread among wild chimpanzees and gorillas, have not been detected in bonobos. Here, we show that wild-living bonobos are endemically Plasmodium infected in the eastern-most part of their range. Testing 1556 faecal sampl

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d31a7287c0c31625d3c4fa405822843d
https://doi.org/10.1038/s41467-017-01798-5

Optimizing methods and dodging pitfalls in microbiome research

Autor: Lisa M. Mattei, Judith R. Kelsen, Dorothy Kim, Casey E. Hofstaedter, Frederic D. Bushman, Ceylan Tanes, Ronald G. Collman, Scott Sherrill-Mix, Erik L. Clarke, Maire A. Conrad, Chunyu Zhao, Christel Chehoud, Kyle Bittinger, Robert N. Baldassano, Abigail Lauder

Publikováno v: Microbiome, Vol 5, Iss 1, Pp 1-14 (2017)
Microbiome

Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls, organize

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e767f33a8a31557d64bf2c1340c610be
https://doi.org/10.1186/s40168-017-0267-5