Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2023.07.03.547516v1?rss=1
Authors: Josephs-Spaulding, J., Rajput, A., Hefner, Y., Szubin, R., Balasubramanian, A., Li, G., Zielinski, D. C., Jahn, L., Sommer, M., Phaneuf, P., Palsson, B. O.
Abstract:
Limosilactobacillus reuteri, a probiotic microbe instrumental to human health and sustainable food production, adapts to diverse environmental shifts via dynamic gene expression. We applied independent component analysis to 117 high-quality RNA-seq datasets to decode its transcriptional regulatory network (TRN), identifying 35 distinct signals that modulate specific gene sets. This study uncovers the fundamental properties of L. reuteri's TRN, deepens our understanding of its arginine metabolism, and the co-regulation of riboflavin metabolism and fatty acid biosynthesis. It also sheds light on conditions that regulate genes within a specific biosynthetic gene cluster and the role of isoprenoid biosynthesis in L. reuteri's adaptive response to environmental changes. Through the integration of transcriptomics and machine learning, we provide a systems-level understanding of L. reuteri's response mechanism to environmental fluctuations, thus setting the stage for modeling the probiotic transcriptome for applications in microbial food production.
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