Defining the human microbiome

Abstract

Rapidly developing sequencing methods and analytical techniques are enhancing our ability to understand the human microbiome, and, indeed, how we define the microbiome and its constituents. In this review we highlight recent research that expands our ability to understand the human microbiome on different spatial and temporal scales, including daily timeseries datasets spanning months. Furthermore, we discuss emerging concepts related to defining operational taxonomic units, diversity indices, core versus transient microbiomes and the possibility of enterotypes. Additional advances in sequencing technology and in our understanding of the microbiome will provide exciting prospects for exploiting the microbiota for personalized medicine.

Health and environmental applications of gut microbiome: a review

“…In the study related to monozygotic and dizygotic twin pairs with similarity in obesity or leanness, it was found that a subset of common microbial genes, were shared among those twins [41]. As per the research reports, it is assumed that individuals share a "core microbiome" rather than a "core microbiota" [42].…”

“…The attainment of gut microbiota keeps on changing over few years, however, within the first year of life, infants begins to resemble of microbiota that of an adult gut [44]. As the child grows, phylogenetic diversity of the microbes in infant gut considerably increases and enriched, but significant changes also happen during the onset of breast feed, introduction of cereal, development of fever and antibiotic treatment and beginning of cooked/formulated feed materials [42,44]. The dynamic interaction between the human microbiota and the environment lead to invariable transfer of microbial communities between surfaces and individuals.…”

“…Hehemann et al [50] reported that in Japanese diet, seaweed is a common food item; the gene of which is also found included in the gut microbiome of individuals who prefers seaweed. Thus, microbes help greatly to increase the ability of the metabolism, and allowing us to digest and draw energy from a diverse range of food materials [42,50]. The defensive function of the intestinal microenvironment formed by the microbes as a whole unit creates the barrier effect or resistance to pathogenic bacteria colonization.…”

“…Clustering of microbiome from different guts from human, together with carnivores, omnivores, and herbivores showed diet based differences in the microbial composition [41]. Significantly, the microbiome within the human gut permits the digestion of varied compounds via metabolic pathways that are not directly related in the mammalian genome, thus, greatly increasing the ability of humans to take out energy from diverse diets [41,42]. The increased adiposity in individual is not only dependent on the quality or quantity of the diet, but the composition of the microbiome that can extract more energy and subsequent deposition from food [47].…”

“…Promotion of community resilience is an interesting feature that helps the microbiota to overcome the stresses. Though the areas of microbiome plasticity have yet to be elucidated, some recent findings, especially fecal microbiota transplantation (FMT) has been successful in a number of studies [42,56,57].…”