Global diversity of enterococci and description of 18 previously unknown species

• 成果类型: Article
• 署名作者: Schwartzman, Julia A.; Lebreton, Francois; Salamzade, Rauf; Shea, Terrance; Martin, Melissa J.; Schaufler, Katharina; Urhan, Aysun; Abeel, Thomas; Camargo, Ilana L. B. C.; Sgardioli, Bruna F.; Prichula, Janira; Frazzon, Ana Paula Guedes; Giribet, Gonzalo; Van Tyne, Daria; Treinish, Gregg; Innis, Charles J.; Wagenaar, Jaap A.; Whipple, Ryan M.; Manson, Abigail L.; Earl, Ashlee M.; Gilmore, Michael S.
• 署名单位: Harvard University; Harvard Medical School; Harvard University; Harvard Medical School; University of Southern California; Walter Reed Army Institute of Research (WRAIR); United States Department of Defense; United States Army; Harvard University; Massachusetts Institute of Technology (MIT); Broad Institute; University of Wisconsin System; University of Wisconsin Madison; Universitat Greifswald; University of Kiel; Schleswig Holstein University Hospital; University of Kiel; Delft University of Technology; Universidade de Sao Paulo; Universidade Federal do Rio Grande do Sul; Harvard University; Harvard University; Pennsylvania Commonwealth System of Higher Education (PCSHE); University of Pittsburgh; Utrecht University
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-15195
• DOI: 10.1073/pnas.2310852121
• 发表日期: 2024-02-27
• 关键词: sp-nov; lactococcus-lactis; presumptive identification; terrestrial arthropods; gene inactivation; bacterial; genome; reclassification; differentiation; annotation

摘要

Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococcal species are now known. Two species, Enterococcus faecalis and Enterococcus faecium, are common constituents of the human microbiome. They are also now leading causes of multidrug- resistant hospital- associated infection. The basis for host association of enterococcal species is unknown. To begin identifying traits that drive host association, we collected 886 enterococcal strains from widely diverse hosts, ecologies, and geographies. This identified 18 previously undescribed species expanding genus diversity by >25%. These species harbor diverse genes including toxins and systems for detoxification and resource acquisition. Enterococcus faecalis and E. faecium were isolated from diverse hosts highlighting their generalist properties. Most other species showed a more restricted distribution indicative of specialized host association. The expanded species diversity permitted the Enterococcus genus phylogeny to be viewed with unprecedented resolution, allowing features to be identified that distinguish its four deeply rooted clades, and the entry of genes associated with range expansion such as B- vitamin biosynthesis and flagellar motility to be mapped to the phylogeny. This work provides an unprecedentedly broad and deep view of the genus Enterococcus, including insights into its evolution, potential new threats to human health, and where substantial additional enterococcal diversity is likely to be found.