TY - JOUR
T1 - Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates
AU - Fehlner-Peach, Hannah
AU - Magnabosco, Cara
AU - Raghavan, Varsha
AU - Scher, Jose U.
AU - Tett, Adrian
AU - Cox, Laura M.
AU - Gottsegen, Claire
AU - Watters, Aaron
AU - Wiltshire-Gordon, John D.
AU - Segata, Nicola
AU - Bonneau, Richard
AU - Littman, Dan R.
N1 - Funding Information:
We thank Paul Zappile and Adriana Heguy at the NYU Genome Technology Center for sequencing support. We thank Rhina Medina and Lucy Alvarado for sample collection, Michael Fischbach for Bacteroides strains, Gretchen Diehl for critical reading of the manuscript, and Dawn Hershey for helpful discussions about dietary fiber. We thank Curtis Huttenhower for helpful discussions and for connecting us with N.S. and A.T. The graphical abstract was created with biorender.com . The NYU Genome Technology Center was partially supported by the Cancer Center Support Grant ( P30CA016087 ). H.F.-P. was supported by the NIH ( TL1TR001447 and T32CA009161 ). J.U.S. is funded through NIH/ NIAMS R01AR074500 . J.U.S. is further supported by The Riley Family Foundation , The Beatrice Snyder Foundation , the Rheumatology Research Foundation , and the Judith and Stewart Colton Center for Autoimmunity . L.M.C. was supported by the NIH ( UL1RR029893 ). N.S. was supported by European Research Council (ERC-STG project MetaPG-716575 ). R.B. was supported by the Simons Foundation . D.R.L. was supported by the Howard Hughes Medical Institute , the Judith and Stewart Colton Center for Autoimmunity , and the Kenneth Rainin Foundation .
Funding Information:
We thank Paul Zappile and Adriana Heguy at the NYU Genome Technology Center for sequencing support. We thank Rhina Medina and Lucy Alvarado for sample collection, Michael Fischbach for Bacteroides strains, Gretchen Diehl for critical reading of the manuscript, and Dawn Hershey for helpful discussions about dietary fiber. We thank Curtis Huttenhower for helpful discussions and for connecting us with N.S. and A.T. The graphical abstract was created with biorender.com. The NYU Genome Technology Center was partially supported by the Cancer Center Support Grant (P30CA016087). H.F.-P. was supported by the NIH (TL1TR001447 and T32CA009161). J.U.S. is funded through NIH/NIAMS R01AR074500. J.U.S. is further supported by The Riley Family Foundation, The Beatrice Snyder Foundation, the Rheumatology Research Foundation, and the Judith and Stewart Colton Center for Autoimmunity. L.M.C. was supported by the NIH (UL1RR029893). N.S. was supported by European Research Council (ERC-STG project MetaPG-716575). R.B. was supported by the Simons Foundation. D.R.L. was supported by the Howard Hughes Medical Institute, the Judith and Stewart Colton Center for Autoimmunity, and the Kenneth Rainin Foundation. H.F.-P. V.R. and C.M. designed the study with input from D.R.L. and R.B. H.F.-P. isolated Prevotella and designed and performed all experiments; isolation strategy was by L.M.C. J.U.S. provided stool samples from NORA patients. C.M. analyzed 16S and genome sequencing data. V.R. predicted PULs from the isolate genomes and helped design growth experiments. A.T. and N.S. identified susC clusters in metagenomic data. C.G. provided technical assistance for growth experiments and analysis of PULs. A.W. and J.D.W.-G. helped analyze genome and growth data. H.F.-P. wrote the manuscript with contributions from V.R. C.M. and D.R.L. and input from all other authors. The authors declare no competing interests.
Publisher Copyright:
© 2019 Elsevier Inc.
PY - 2019/11/13
Y1 - 2019/11/13
N2 - Gut-dwelling Prevotella copri (P. copri), the most prevalent Prevotella species in the human gut, have been associated with diet and disease. However, our understanding of their diversity and function remains rudimentary because studies have been limited to 16S and metagenomic surveys and experiments using a single type strain. Here, we describe the genomic diversity of 83 P. copri isolates from 11 human donors. We demonstrate that genomically distinct isolates, which can be categorized into different P. copri complex clades, utilize defined sets of polysaccharides. These differences are exemplified by variations in susC genes involved in polysaccharide transport as well as polysaccharide utilization loci (PULs) that were predicted in part from genomic and metagenomic data. Functional validation of these PULs showed that P. copri isolates utilize distinct sets of polysaccharides from dietary plant, but not animal, sources. These findings reveal both genomic and functional differences in polysaccharide utilization across human intestinal P. copri strains.
AB - Gut-dwelling Prevotella copri (P. copri), the most prevalent Prevotella species in the human gut, have been associated with diet and disease. However, our understanding of their diversity and function remains rudimentary because studies have been limited to 16S and metagenomic surveys and experiments using a single type strain. Here, we describe the genomic diversity of 83 P. copri isolates from 11 human donors. We demonstrate that genomically distinct isolates, which can be categorized into different P. copri complex clades, utilize defined sets of polysaccharides. These differences are exemplified by variations in susC genes involved in polysaccharide transport as well as polysaccharide utilization loci (PULs) that were predicted in part from genomic and metagenomic data. Functional validation of these PULs showed that P. copri isolates utilize distinct sets of polysaccharides from dietary plant, but not animal, sources. These findings reveal both genomic and functional differences in polysaccharide utilization across human intestinal P. copri strains.
KW - diet
KW - human microbiome
KW - intestinal commensals
KW - whole genome sequencing
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U2 - 10.1016/j.chom.2019.10.013
DO - 10.1016/j.chom.2019.10.013
M3 - Article
C2 - 31726030
AN - SCOPUS:85074435391
VL - 26
SP - 680-690.e5
JO - Cell Host and Microbe
JF - Cell Host and Microbe
SN - 1931-3128
IS - 5
ER -