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.
Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
Matthew B
0000-0001-6492-8180
MB
Biggs
Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
Gregory L
0000-0002-1571-0801
GL
Medlock
Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
Thomas J
TJ
Moutinho
Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College, London, UK.
Hannah J
HJ
Lees
Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College, London, UK.
Jonathan R
JR
Swann
Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, USA.
Glynis L
GL
Kolling
Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
Jason A
JA
Papin
D000818:Animals; D001419:Bacteria / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D003470:Culture Media; D000069196:Gastrointestinal Microbiome / Q000235:genetics / Q000502:physiology*; D054884:Host-Pathogen Interactions; D006801:Humans; D054892:Metagenome; D051379:Mice; D008954:Models, Biological
D003470:Culture Media