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Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals


Kate L. Ormerod1, David L. A. Wood1, Nancy Lachner1, Shaan L. Gellatly2, Joshua N. Daly1, Jeremy D. Parsons3,
Cristiana G. O. Dal
Molin4, Robin W. Palfreyman4, Lars K. Nielsen4, Matthew A. Cooper5, Mark Morrison6,
Philip M. Hansbro
2 and Philip Hugenholtz1*

 

1 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.

2 Priority Research Centre for Healthy Lungs, The University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.

3 QFAB Bioinformatics, The University of Queensland, Brisbane, Australia.

4 Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.

5 Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.

6 Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia.


ABSTRACT
Background   Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeothermic animals and are increasingly being recognized as a numerically predominant member of the gut microbiota; however, little is known about the nature of their interactions with the host.
Results   Here, we provide the first whole genome exploration of this family, for which we propose the name Candidatus Homeothermaceae,using 30 population genomes extracted from fecal samples of four different animal hosts: human, mouse, koala, and guinea pig. We infer the core metabolism of Ca. Homeothermaceaeto be that of fermentative or nanaerobic bacteria, resembling that of related Bacteroidales families. In addition, we describe three trophic guilds within the family, plant glycan (hemicellulose and pectin), host glycan, andα-glucan, each broadly defined by increased abundance of enzymes involved in the degradation of particular carbohydrates.
Conclusions   Ca. Homeothermaceaerepresentatives constitute a substantial component of the murine gut microbiota, as well as being present within the human gut, and this study provides important first insights into the nature of their residency. The presence of trophic guilds within the family indicates the potential for niche partitioning and specific roles for each guild in gut health and dysbiosis.

 

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