The Microbiome and Human Biology

Abstract

Over the past few years, microbiome research has dramatically reshaped our understanding of human biology. New insights range from an enhanced understanding of how microbes mediate digestion and disease processes (e.g., in inflammatory bowel disease) to surprising associations with Parkinson's disease, autism, and depression. In this review, we describe how new generations of sequencing technology, analytical advances coupled to new software capabilities, and the integration of animal model data have led to these new discoveries. We also discuss the prospects for integrating studies of the microbiome, metabolome, and immune system, with the goal of elucidating mechanisms that govern their interactions. This systems-level understanding will change how we think about ourselves as organisms.

The Microbiome and Bone and Joint Disease

“…Lastly, as the field of the microbiome is still in its early stages, most studies examining the role of the microbiome report correlations with disease or disease processes but little attention has been paid to causative mechanisms [3]. Only through strong collaborations among microbiologists, ecologists, and musculoskeletal researchers will it be possible to understand the role of the microbiome in bones and joints.…”

“…In humans, the vast majority of the microbiome is present in the gastrointestinal tract, which consists of over 1000 distinct species of microbes in most humans [2]. Recent investigations have associated alterations in the microbiome with a number of chronic clinical conditions including obesity and diabetes, heart disease, and Alzheimer’s disease [3]. Here I review recent findings linking the microbiome to chronic diseases of bones and joints.…”

“…Second, because species within a mature microbiome are interdependent, the gut microbial community is resistant to change. Following an acute interruption such as a short-term change in diet or a short course of oral antibiotics, the composition of the gut flora mostly returns to its initial condition in composition (although some long-term changes can occur) [8, 9, 3]. The robust nature of the gut microbiota makes it difficult to colonize a microbial community with a new species, since a newly introduced species must compete with species that are already well integrated into the community.…”

How can the cystic fibrosis respiratory microbiome influence our clinical decision-making?

“…The increasing complexity of data that can now be generated with a range of different ‘omics technologies has led to interest in using systems biology approaches to integrate microbiome-derived and immunological data [69]. For example, such an approach has been employed recently to determine the relationship between nasopharyngeal microbiota characteristics and host immune response in children experiencing infection by respiratory syncytial virus [70].…”

Epigenetic treatment of dermatologic disorders

“…A maladaptation of skin microbiota (dysbiosis), for example, has been linked to exacerbated forms of diabetic foot ulcers, atopic dermatitis, psoriasis, vitiligo, and acne (Balato et al, ; Byrd et al, ; Dietert & Dietert, ; Karkman et al, ; Kundu, Mhlaba, Rangel, & Poole, ; O'Neill & Gallo, ). Thus, reshaping the microbiome (Gilbert et al, ) by modifying the genetic diversity of the various commensal bacterial compositions towards a healthier state, especially on skin (Blume‐Peytavi et al, ; Knight et al, ; McCoy et al, ; Rocha & Bagatin, ; Vollmer, West, & Lephart, ), and/or harnessing them to produce bioactive therapeutic products, including those influencing gene expression, present opportunities for therapeutic intervention (Bueso, Lehouritis, & Tangney, ; Dietert & Dietert, ; Eisenstein, ; O'Neill & Gallo, ). Indeed, therapeutic epigenetic regulation—nongenetic influences on gene expression (changes in phenotype that do not involve alterations in the genomic DNA sequence)—loosely defined as environmentally induced biological processes that silence, activate, and/or modulate gene expression pathways is increasingly garnering clinical recognition (Berson, Nativio, Berger, & Bonini, ; Cock, ; Feinberg, ; Jadotte, ; Kang, Chovatiya, & Tumbar, ; Mervis & McGee, ; Yamatsugu, Kawashima, & Kanai, ).…”