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.
Highlights
The microbiome is enormously complex and its composition varies between individuals, but within the same individual spatially and temporally (Lozupone et al, 2012; Faith et al, 2013)
Germ-free and gnotobiotic mice often do not develop normal immune systems or gastrointestinal function (Brestoff and Artis, 2013). This problem was addressed in part by work in which a cocktail of eight microbial species known as the altered Schaedler flora (ASF) was identified (Schaedler et al, 1965; Dewhirst et al, 1999)
We present a novel approach to characterizing microbial communities in vitro, and the results of applying this approach to gain insights into a model microbial community known as the ASF
Summary
Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota. Matthew B Biggs, Gregory L Medlock, Thomas J Moutinho, Hannah J Lees, Jonathan R Swann, Glynis L Kolling and Jason A Papin. The altered Schaedler flora (ASF) is a model microbial community with both in vivo and in vitro relevance. We provide the first characterization of the ASF community in vitro, independent of a murine host. 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 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. The ISME Journal (2017) 11, 426–438; doi:10.1038/ismej.2016.130; published online 8 November 2016
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