Deciphering the Microbiome: Integrating Theory, New Technologies, and Inclusive Science.

The diversity and functional significance of microbiomes have become increasingly clear through the extensive sampling of Earth's many habitats and the rapid adoption of new sequencing technologies. However, much remains unknown about what makes a "healthy" microbiome, how to restore a disrupted microbiome, and how microbiomes assemble. In December 2019, we convened a workshop that focused on how to identify potential "rules of life" that govern microbiome structure and function. This collection of mSystems Perspective pieces reflects many of the main challenges and opportunities in the field identified by both in-person and virtual workshop participants. By borrowing conceptual and theoretical approaches from other fields, including economics and philosophy, these pieces suggest new ways to dissect microbiome patterns and processes. The application of conceptual advances, including trait-based theory and community coalescence, is providing new insights on how to predict and manage microbiome diversity and function. Technological and analytical advances, including deep transfer learning, metabolic models, and advances in analytical chemistry, are helping us sift through complex systems to pinpoint mechanisms of microbiome assembly and dynamics. Integration of all of these advancements (theory, concepts, technology) across biological and spatial scales is providing dramatically improved temporal and spatial resolution of microbiome dynamics. This integrative microbiome research is happening in a new moment in science where academic institutions, scientific societies, and funding agencies must act collaboratively to support and train a diverse and inclusive community of microbiome scientists.

Immunomodulatory effects of bone marrow-derived mesenchymal stem cells on pro-inflammatory cytokine-stimulated human corneal epithelial cells.

PURPOSE: To investigate the modulatory effect of rat bone marrow mesenchymal stem cells (MSC) on human corneal epithelial cells (HCE-T) stimulated with pro-inflammatory cytokines interferon gamma (IFN-γ) and tumor necrosis factor alpha (TNF-α) in an in vitro co-cultured model. METHODS: HCE-T alone and co-cultured with MSC were stimulated with IFN-γ/TNF for 24 and 48 hours or left untreated. The expression of intracellular adhesion molecule (ICAM)-1, human leukocyte antigen ABC, DR and G (HLA-ABC, HLA-DR, HLA-G) were investigated by flow cytometry. Subcellular localization of nuclear factor-kappa B (NF-κB) and expression of indoleamine 2,3-dioxygenase (IDO) were assessed by immunofluorescence staining and western blot. The concentration of transforming growth factor beta 1 (TGF-ß1) in the conditioned media from different cultures was evaluated by enzyme-linked immunosorbent assay. NF-κB and TGF-ß1 signaling pathway blocking experiments were performed to analyze associations between the expression of cell surface molecules and the NF-κB transcription pathway, and the expression of IDO and TGF-ß1 signaling pathway. RESULTS: IFN-γ/TNF treatment significantly up-regulated expression of ICAM-1, HLA-ABC, and induced de novo expression of HLA-DR and IDO on HCE-T cultured alone, while HLA-G expression remained unaffected. Up-regulation was significantly inhibited by co-culture with MSC. Increased TGF-ß1 secretion was detected in 48 h IFN-γ/TNF-stimulated MSC monocultures and HCE-T/MSC co-cultures. MSC attenuated the activation of cytokine-induced NF-κB and IDO induction. Blockade of NF-κB transcription pathway by BMS-345541 significantly reduced the up-regulation of ICAM-1, HLA-ABC, HLA-DR and IDO expression, while blockade of TGF-ß1 signaling pathways reversed the modulatory effect of MSC on IDO expression. CONCLUSIONS: MSC reduced the expression of adhesion and immunoregulatory molecules on pro-inflammatory cytokine-stimulated HCE-T via the NF-κB transcription pathway. MSC attenuated expression of IDO through both NF-κB transcription and TGF-ß1 signaling pathways. Co-culture of HCEC with MSC therefore provides a useful in vitro model to study the anti-inflammatory properties of MSC on corneal epithelium.