Recent Advances in Understanding the Structure and Function of the Human Microbiome

Abstract

Trillions of microbes live within our bodies in a deep symbiotic relationship. Microbial populations vary across body sites, driven by differences in the environment, immunological factors, and interactions between microbial species. Major advances in genome sequencing enable a better understanding of microbiome composition. However, most of the microbial taxa and species of the human microbiome are still unknown. Without revealing the identity of these microbes as a first step, we cannot appreciate their role in human health and diseases. A shift in the microbial balance, termed dysbiosis, is linked to a broad range of diseases from simple colitis and indigestion to cancer and dementia. The last decade has witnessed an explosion in microbiome research that led to a better understanding of the microbiome structure and function. This understanding leads to potential opportunities to develop next-generation microbiome-based drugs and diagnostic biomarkers. However, our understanding is limited given the highly personalized nature of the microbiome and its complex and multidirectional interactions with the host. In this review, we discuss: (1) our current knowledge of microbiome structure and factors that shape the microbial composition, (2) recent associations between microbiome dysbiosis and diseases, and (3) opportunities of new microbiome-based therapeutics. We analyze common themes, promises, gaps, and challenges of the microbiome research.

Akkermansia muciniphila Alters Gut Microbiota and Immune System to Improve Cardiovascular Diseases in Murine Model

“…We also failed to show a cause-effect relationship, such as the reconstitution of IL-33-reversed Akk-reduced lesion. The highly personalized microbiome and its complex and multidirectional interactions with host metabolism and immunity present potential opportunities for the development of the next generation of microbiome-based drugs and diagnostic biomarkers ( Mousa et al, 2022 ). We will continue to explore this in the subsequent scientific research.…”

The Impact of Cereal Grain Composition on the Health and Disease Outcomes

“…Among the several properties of phytochemicals, the beneficial interaction with the intestinal microbiota represents an open area of research ( 89 ). Jayachandran et al ( 90 ) explained as the “fiber gap”, i.e.…”

“…a diet with low consumption of fibers, could interfere with gut microbiota equilibrium reducing its healthy metabolites. Some of its positive effects on human health are due to the gut microbiota production of short chain fatty acids (SCFAs), such as butyrate, acetate, propionate: these molecules act as anti-inflammatory and anti-oxidant agents, insulin sensitivity modulators, epigenetic modulators ( 89 ). SCFAs are the result of fibers degradations by gut microbiota, which contribute to digest soluble fibers, which otherwise would not be metabolized in the bowl.…”

“…SCFAs are the result of fibers degradations by gut microbiota, which contribute to digest soluble fibers, which otherwise would not be metabolized in the bowl. So that, gut microbiota homeostasis is linked to dietary fibers variety, which influences SCFAs production ( 89 , 91 , 92 ). Myhrstad and colleagues analyzed the results of 16 trials conducted to investigating the role of dietary fiber in modulating gut microbiota and human metabolic regulation ( 92 ).…”

Utilization of Host and Microbiome Features in Determination of Biological Aging

“…An increasing number of aging clock inputs, models, and pipelines are being explored to achieve this formidable task, including epigenetic and inflammatory clocks [ 45 , 46 ]. There are various factors that influence the microbiome and the aging process, including intrinsic factors (genetics, gender, and ethnicity) as well as extrinsic factors (demographic, geographical, diet, physical activity, drugs, smoking, and others) [ 142 , 143 , 144 , 145 , 146 ]. Recent advances in microbiome research, including the ability to define the microbiome components and functions and the realization that microbiomes may contribute to aging-related processes, have led to the inclusion of microbiome-based features in aging clocks.…”