Long-Term In Vitro Culture Systems to Study Human Microbiome

Abstract

Microbial communities are eubiotic ecosystems that interact dynamically and synergistically with the human body. Imbalances in these interactions may cause dysbiosis by enhancing the occurrence of inflammatory conditions, such as periodontal or inflammatory bowel diseases. However, the mechanisms that lie behind eubiosis−dysbiosis transitions are still unclear and constantly being redefined. While the societal impact of these diseases is steadily increasing, the lack of a clear understanding behind the onset of the inflammatory conditions prevents the proper clinical strategies from being formulated. Although preclinical and clinical models and short-term planar in vitro cultures represent superb research tools, they are still lacking human relevance and long-term use. Bioreactors and organs-on-a-chip have attracted interest because of their ability to recreate and sustain the physical, structural, and mechanical features of the native environment, as well as to support long-term coculture of mammalian cells and the microbiome through modulation of pH and oxygen gradients. Existing devices, however, are still under development to sustain the microbiome−host coculture over long periods of time. In this scenario, to understand disease triggers and develop therapeutics, research efforts should command the development of three-dimensional constructs that would allow the investigation of processes underlying the microbial community assembly and how microorganisms influence host traits in both acute and chronic conditions.

Sustaining healthy long-term host-microbiome interactions in a physiologically relevant dynamic gingival tissue model

“…For example, Veillonella parvula , which is crucial in the colonization of the niche as a bridging taxon in sustaining the growth of multispecies in the biofilm, was found to be highly correlated with the species Streptococcus mitis (Spearman’s rank correlation value of 0.66) ( Figure 4 ), suggesting not only biofilm architecture, but also the regulation of community metabolisms and thus the preservation of a health ecosystem 71–73 . Lastly, although microbial communities and functions are shared, the composition of the microbiome is largely and highly individualized based on environmental and host factors 9,55,63 . Despite an evident inter-variability ( Figure 6 ) among samples collected at h -plaque 0, our model allowed us to show robust and consistent effects, which align with physiological conditions at the microbiome-host interface.…”

“…Pre-clinical and clinical studies are limited in investigating disease trajectories, while animal models show differences in microbiome compositions, organization, and disease initiation. Current therapies for periodontal conditions remain inadequate 7 and they are extremely costly due to routine care 6,8,9 . Yet, the application of in vitro research strategies using traditional tissue engineering strategies ( i.e., cells grown in tissue culture plastic or three-dimensional planar and static models) are still lacking several of the native human tissue nuances.…”

Three‐Dimensional Humanized Model of the Periodontal Gingival Pocket to Study Oral Microbiome

“…[14] We recapitulated several in vivo oral features, including the native architecture, oxygen gradients and human-derived multicellular populations, in an effort to provide a cost effective, robust and reliable experimental tool for acute longitudinal perturbation studies. [15] Based on structural biopolymers as building blocks, we developed a humanized 3D gingival tissue model (Figure 1) that recreates the native periodontal pocket and mimics the physiological oxygen tension, thus, able to support human micro-biome persistence with a physiologically relevant level of microbial diversity. The modulation of inflammatory markers in the presence of a healthy oral microbiome supported the humanized functional response with this model.…”

Three-dimensional humanized gingival tissue model to study oral microbiome

“…Herein, we recapitulated several in vivo oral features, including native architecture, oxygen gradients, and multicellular human population, in an effort to provide a cost effective, robust and reliable experimental tool for large scale longitudinal perturbation studies [17] . Based on structural biopolymers as building blocks, we have developed a humanized three-dimensional gingival tissue model that recreates the native periodontal pocket and mimics the physiological oxygen tension, thus, able to support human microbiome persistence with a physiologically relevant level of microbial diversity and native spatial organization.…”