Other Scientists discover 18 new species of gut microbes. Global diversity of enterococci and description of 18 previously unknown species (Feb 2024)

Michael Harrop

Active member
Jul 6, 2023


Enterococci are among the most widely distributed microbes in animal gut consortia. Over 60 species have been identified, including Enterococcus faecalis and Enterococcus faecium commonly found in the human gut. Importantly, both emerged in the antibiotic era as leading causes of multidrug-resistant infection. Microbial traits that determine membership in microbiomes of various hosts are largely unknown and enterococci represent a unique opportunity to determine core underlying principles of that association. This study examined 886 enterococcal specimens from a wide range of hosts in diverse geographies and ecologies. Generalist to specialist enterococcal species were found including 18 previously undescribed species. This study identified new features associated with species radiations and provides evidence that tremendous genetic diversity in Enterococcus remains to be discovered.


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.
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