Digitalizing the Microbiome for Human Health

Chemical interplay between gut microbiota and epigenetics: Implications in circadian biology

Circadian rhythms are intrinsic molecular mechanisms that synchronize biological functions with the day/night cycle. The mammalian gut is colonized by a myriad of microbes, collectively named the gut microbiota. The microbiota impacts host physiology via metabolites and structural components. A key mechanism is the modulation of host epigenetic pathways, especially histone modifications. An increasing number of studies indicate the role of the microbiota in regulating host circadian rhythms. However, the mechanisms remain largely unknown. Here, we summarize studies on microbial regulation of host circadian rhythms and epigenetic pathways, highlight recent findings on how the microbiota employs host epigenetic machinery to regulate circadian rhythms, and discuss its impacts on host physiology, particularly immune and metabolic functions. We further describe current challenges and resources that could facilitate research on microbiota-epigenetic-circadian rhythm interactions to advance our knowledge of circadian disorders and possible therapeutic avenues.

Metabolic control by the microbiome

The interaction between the metabolic activities of the intestinal microbiome and its host forms an important part of health. The basis of this interaction is in part mediated by the release of microbially-derived metabolites that enter the circulation. These products of microbial metabolism thereby interface with the immune, metabolic, or nervous systems of the host to influence physiology. Here, we review the interactions between the metabolic activities of the microbiome and the systemic metabolism of the host. The concept that the endocrine system includes more than just the eukaryotic host component enables the rational design of exogenous interventions that shape human metabolism. An improved mechanistic understanding of the metabolic microbiome-host interaction may therefore pioneer actionable microbiota-based diagnostics or therapeutics that allow the control of host systemic metabolism via the microbiome.

Machine learning on microbiome research in gastrointestinal cancer

Gastrointestinal cancer maintains the highest incidence and mortality rate among all cancers globally. In addition to genetic causes, it has been reported that individuals' diet and composition of the gastrointestinal microbiome have profound impacts on gastrointestinal cancer development. Microbiome research has risen in popularity to provide alternative insights into cancer development and potential therapeutic effect. However, there is a lack of an effective analytical tool to comprehend the massive amount of data generated from high-throughput sequencing methods. Artificial intelligence is another rapidly developing field that has strong application potential in microbiome research. Deep learning and machine learning are two subfields under the umbrella of artificial intelligence. Here we discuss the current approaches to study the gut microbiome, as well as the applications and challenges of implementing artificial intelligence in microbiome research.

Guardian genes ensuring subsistence of oral Streptococcus mutans

Despite the substantial research advancements on oral diseases, dental caries remains a major healthcare burden. A disease of microbial dysbiosis, dental caries is characterised by the formation of biofilms that assist demineralisation and destruction of the dental hard tissues. While it is well understood that this is a multi-kingdom biofilm-mediated disease, it has been elucidated that acid producing and acid tolerant bacteria play pioneering roles in the process. Specifically, Streptococcus mutans houses major virulence pathways that enable it to thrive in the oral cavity and cause caries. This pathogen adheres to the tooth substrate, forms biofilms, resists external stress, produces acids, kills closely related species, and survives the acid as well as the host clearance mechanisms. For an organism to be able to confer such virulence, it requires a large and complex gene network which synergise to establish disease. In this review, we have charted how these multi-faceted genes control several caries-related functions of Streptococcus mutans. In a futuristic thinking approach, we also briefly discuss the potential roles of omics and machine learning, to ease the study of non-functional genes that may play a major role and enable the integration of experimental data.

The Microbiome as a Circadian Coordinator of Metabolism

The microbiome is critically involved in the regulation of systemic metabolism. An important but poorly understood facet of this regulation is the diurnal activity of the microbiome. Herein, we summarize recent developments in our understanding of the diurnal properties of the microbiome and their integration into the circadian regulation of organismal metabolism. The microbiome may be involved in the detrimental consequences of circadian disruption for host metabolism and the development of metabolic disease. At the same time, the mechanisms by which microbiome diurnal activity is integrated into host physiology reveal several translational opportunities by which the time of day can be harnessed to optimize microbiome-based therapies. The study of circadian microbiome properties may thus provide a new avenue for treating disorders associated with circadian disruption from the gut.