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Developmental Biology - Human MicroBiome

Parasitic Bacteria In Groundwater, Moose & You!

Inside your mouth lives a group of bacteria also found in the belly of a moose, dogs, cats, and dolphins...


Inside your mouth right now, there is a group of bacteria whose closest relatives can also be found in the belly of a moose, in dogs, cats, and dolphins, even in groundwater deep under the Earth's surface. In a stunning discovery, scientists have found that these organisms have adapted to these incredibly diverse environments - without radically changing the genes in their genomes.

These organisms are members of the phylum Sacchraribacteria, formerly known as TM7. These are ultra-small, parasitic bacteria with small genomes that belong to a larger group called the Candidate Phyla Radiation or CPR a mysterious "dark matter" bacteria that represent more than 25 percent of all bacterial diversity. Yet we know very little about them.

In research first published as a pre-print in 2018, and now formally in the journal Cell Reports , scientists describe that Saccharibacteria within a mammal host are more diverse than anticipated.

They also discovered certain members of the bacteria are found in the oral cavity of humans, the guts of other mammals, and in groundwater. While each environment is very different, the bacteria's tiny genomes remain almost unchanged between humans and groundwater. This indicates humans acquired the bacteria recently on the evolutionary timescale.
"It's the only bacteria we know that has hardly changed when they adapted to humans."

Jeffrey Scott McLean PhD, Microbiologist, Associate Professor of Periodontics, University of Washington School of Dentistry, and lead author of the paper.

The TM7 bacteria were a complete mystery to scientists until Dr. Xuesong He, Associate Member of Staff at the Forsyth Institute and co-author of the paper, first isolated the bacterium TM7x, a member of CPR, in 2014. Since then, researchers have learned that CPR includes a huge number of different bacteria, all with tiny genomes.
These bacteria need a host to survive and are unique as they can't make their own amino acids and nucleotides essential building blocks for life.

Previous research by Dr. Batbileg Bor, Assistant Member of Staff at the Forsyth Institute and co-author of the paper, showed that TM7 can easily jump from one bacterial host to another. This could explain how they ended up in mammals, as mammals drink groundwater.
"The most likely reason we see a large diversity of these bacteria in humans is that some groups were acquired in ancient mammal relatives and expanded over time across mammals whereas this one highly similar group more recently jumped directly into humans."

Jeffrey Scott McLean PhD.

TM7 and other ultra-small, parasitic bacteria within CPR may help play a role in health and disease we have yet to discover. Since they act as parasites - living with and killing other bacteria - TM7 could change our overall microbiome by modifying our abundance of bacteria, McLean suggests. Scientists are just scratching the surface of how much our microbiome impacts our overall health.

The fact that humans acquired TM7 recently is a discovery that has broader implications for understanding our co-evolutionary pathways with microbes living on and within us.
"I see this as a huge discovery. This creature survives in both humans and groundwater, which indicates there are similarities allowing these bacteria to adapt to humans."

Wenyuan Shi, CEO and Chief Scientific Officer, Forsyth Institute, and co-author on the paper.

Abstract Highlights

Saccharibacteria are ultra-small parasitic bacteria recently discovered in humans

Novel lineages have high genomic diversity within mammalian hosts

Novel lineages are ultra-small, with reduced genomes (<1,000 genes) and a single 16S copy

One group displays minimal genomic changes since transition from environment to humans

Summary
The first cultivated representative of the enigmatic phylum Saccharibacteria (formerly TM7) was isolated from humans and revealed an ultra-small cell size (200300 nm), a reduced genome with limited biosynthetic capabilities, and a unique parasitic lifestyle. TM7x was the only cultivated member of the candidate phyla radiation (CPR), estimated to encompass 26% of the domain Bacteria. Here we report on divergent genomes from major lineages across the Saccharibacteria phylum in humans and mammals, as well as from ancient dental calculus. These lineages are present at high prevalence within hosts. Direct imaging reveals that all groups are ultra-small in size, likely feeding off commensal bacteria. Analyses suggest that multiple acquisition events in the past led to the current wide diversity, with convergent evolution of key functions allowing Saccharibacteria from the environment to adapt to mammals. Ultra-small, parasitic CPR bacteria represent a relatively unexplored paradigm of prokaryotic interactions within mammalian microbiomes.

Authors
Jeffrey S. McLean, Batbileg Bor, Kristopher A. Kerns, Quanhui Liu, Thao T. To, Lindsey Solden, Erik L. Hendrickson, Kelly Wrighton, Wenyuan Shi and Xuesong He.

Acknowledgements
The authors would like to thank Phil Hugenholtz for helpful discussions regarding taxonomic classification for the members of the Saccharibacteria phylum. K.C.W. and L.M.S. were supported by an Early Career Award from the National Science Foundation under Award Number 1750189 . A portion of this research was performed under the Facilities Integrating Collaborations for User Science (FICUS) exploratory effort and used resources at the US Department of Energy (DOE) Joint Genome Institute (proposal ID 503154) and the Environmental Molecular Sciences Laboratory (proposal ID 49495), which are DOE Office of Science User Facilities. Facilities are operated under contract numbers DE-AC02-05CH11231 (Joint Genome Institute) and DE-AC05-76RL01830 (EMSL). This research was funded in part by NIH National Institute of Dental and Craniofacial Research (NIDCR) awards DE023810 (W.S., X.H., and J.S.M.), DE020102 (W.S., X.H., and J.S.M.), F32DE025548-01 (B.B.), T90DE021984 (T.T.T. and K.A.K.), and DE026186 (W.S., X.H., and J.S.M.).

The authors declare no competing interests.

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Jul 31 2020   Fetal Timeline   Maternal Timeline   News



The new groups of bacteria (CPR) greatly expand the known and characterized groups.
These and previously reported new groups of Archaea (DSPANN) show that the
Tree of Life is more complex than thought. CREDIT UC Berleley News..


Phospholid by Wikipedia