Global survey of gut microbes uncovers 18 new bacterial species and clues to antibiotic resistance

Only 18 new bacterial species? Surprising and disappointing given the enormous effort! You almost have to believe these researchers or the involved "elite adventurers" made a mistake!

If they did not make a mistake, then this could well be a fundamental result.

"... The microbe is just one of 18 new species of Enterococcus discovered by the team, led by researchers at the Broad Institute and Massachusetts Eye and Ear. The researchers analyzed hundreds of scat, soil, and other samples that were collected from an unexplored peak in Nepal, a remote trail in Uganda, and many more places across the globe by an international team of scientists and elite adventurers.
The new species they found expand the genus diversity of known enterococcal strains by more than 25 percent and add unprecedented detail to this microbial family tree. In the new microbes’ DNA, the researchers found hundreds of novel genes that may offer clues to how enterococci are able to resist antibiotic treatment and thrive in the hospital environment.  ...
Genetic analysis of the new and existing enterococcal species allowed the team to expand the microbe’s family tree and refine its branches, or clades, yielding clues to how certain species are able to colonize particular hosts. For example, members of one clade have particularly small genomes that lack genes for amino acid biosynthesis, a hallmark of adaptation to mammalian hosts. Species in another clade carry large genomes that include genes necessary for producing the essential vitamin B12, indicating that they do not need their hosts to provide it. ..."

From the abstract:

"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."

Global survey of gut microbes uncovers 18 new bacterial species and clues to antibiotic resistance | Broad Institute Researchers examined scat from hundreds of animals around the world and pinpointed genes that could fuel drug-resistant infections.

Global diversity of enterococci and description of 18 previously unknown species (open access)

Adventure Scientist Stevie Anna Plummer holds water and scat samples collected in 2016 during an expedition to an unexplored peak in the Himalayas. 

Fig. 1. Sources for 852 Enterococcus isolates.