Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota
Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota
The altered Schaedler flora (ASF) is a model microbial community with both in vivo and in vitro relevance. Here we provide the first characterization of the ASF community in vitro, independent of a murine host. We compared the functional genetic content of the ASF to wild murine metagenomes and found that the ASF functionally represents wild microbiomes better than random consortia of similar taxonomic composition. We developed a chemically defined medium that supported growth of seven of the eight ASF members. To elucidate the metabolic capabilities of these ASF species-including potential for interactions such as cross-feeding-we performed a spent media screen and analyzed the results through dynamic growth measurements and non-targeted metabolic profiling. We found that cross-feeding is relatively rare (32 of 3570 possible cases), but is enriched between Clostridium ASF356 and Parabacteroides ASF519. We identified many cases of emergent metabolism (856 of 3570 possible cases). These data will inform efforts to understand ASF dynamics and spatial distribution in vivo, to design pre- and probiotics that modulate relative abundances of ASF members, and will be essential for validating computational models of ASF metabolism. Well-characterized, experimentally tractable microbial communities enable research that can translate into more effective microbiome-targeted therapies to improve human health.
Animals, Bacteria/genetics, Culture Media, Gastrointestinal Microbiome/genetics, Host-Pathogen Interactions, Humans, Metagenome, Mice, Models, Biological
426-438
Biggs, Matthew B.
aec8040b-b77c-494b-a454-d714dc9a1037
Medlock, Gregory L.
41c918e5-fee8-4a6e-a422-e5f09ccc8888
Moutinho, Thomas J.
1b950a16-a3e8-42a4-87c5-fdff185efe82
Lees, Hannah J.
065ec499-13b2-4a01-bd6a-7e2102905c84
Swann, Jonathan R.
7c11a66b-f4b8-4dbf-aa17-ad8b0561b85c
Kolling, Glynis L.
502c0b3d-ac97-4850-8c38-890da2124e13
Papin, Jason A.
beec0af9-791c-4f7a-9aeb-9926049bd9d0
February 2017
Biggs, Matthew B.
aec8040b-b77c-494b-a454-d714dc9a1037
Medlock, Gregory L.
41c918e5-fee8-4a6e-a422-e5f09ccc8888
Moutinho, Thomas J.
1b950a16-a3e8-42a4-87c5-fdff185efe82
Lees, Hannah J.
065ec499-13b2-4a01-bd6a-7e2102905c84
Swann, Jonathan R.
7c11a66b-f4b8-4dbf-aa17-ad8b0561b85c
Kolling, Glynis L.
502c0b3d-ac97-4850-8c38-890da2124e13
Papin, Jason A.
beec0af9-791c-4f7a-9aeb-9926049bd9d0
Biggs, Matthew B., Medlock, Gregory L., Moutinho, Thomas J., Lees, Hannah J., Swann, Jonathan R., Kolling, Glynis L. and Papin, Jason A.
(2017)
Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota.
The ISME Journal, 11 (2), .
(doi:10.1038/ismej.2016.130).
Abstract
The altered Schaedler flora (ASF) is a model microbial community with both in vivo and in vitro relevance. Here we provide the first characterization of the ASF community in vitro, independent of a murine host. We compared the functional genetic content of the ASF to wild murine metagenomes and found that the ASF functionally represents wild microbiomes better than random consortia of similar taxonomic composition. We developed a chemically defined medium that supported growth of seven of the eight ASF members. To elucidate the metabolic capabilities of these ASF species-including potential for interactions such as cross-feeding-we performed a spent media screen and analyzed the results through dynamic growth measurements and non-targeted metabolic profiling. We found that cross-feeding is relatively rare (32 of 3570 possible cases), but is enriched between Clostridium ASF356 and Parabacteroides ASF519. We identified many cases of emergent metabolism (856 of 3570 possible cases). These data will inform efforts to understand ASF dynamics and spatial distribution in vivo, to design pre- and probiotics that modulate relative abundances of ASF members, and will be essential for validating computational models of ASF metabolism. Well-characterized, experimentally tractable microbial communities enable research that can translate into more effective microbiome-targeted therapies to improve human health.
Text
ismej2016130
- Version of Record
More information
Accepted/In Press date: 17 August 2016
e-pub ahead of print date: 8 November 2016
Published date: February 2017
Keywords:
Animals, Bacteria/genetics, Culture Media, Gastrointestinal Microbiome/genetics, Host-Pathogen Interactions, Humans, Metagenome, Mice, Models, Biological
Identifiers
Local EPrints ID: 440841
URI: http://eprints.soton.ac.uk/id/eprint/440841
ISSN: 1751-7362
PURE UUID: 73008ef3-63d1-48c7-bcae-cd22d363ff42
Catalogue record
Date deposited: 20 May 2020 16:31
Last modified: 17 Mar 2024 04:00
Export record
Altmetrics
Contributors
Author:
Matthew B. Biggs
Author:
Gregory L. Medlock
Author:
Thomas J. Moutinho
Author:
Hannah J. Lees
Author:
Glynis L. Kolling
Author:
Jason A. Papin
Download statistics
Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.
View more statistics