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      Personalized Diets based on the Gut Microbiome as a Target for Health Maintenance: from Current Evidence to Future Possibilities

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          Abstract

          Recently, the concept of personalized nutrition has been developed, which states that food components do not always lead to the same metabolic responses, but vary from person to person. Although this concept has been studied based on individual genetic backgrounds, researchers have recently explored its potential role in the gut microbiome. The gut microbiota physiologically communicates with humans by forming a bidirectional relationship with the micronutrients, macronutrients, and phytochemicals consumed by the host. Furthermore, the gut microbiota can vary from person to person and can be easily shifted by diet. Therefore, several recent studies have reported the application of personalized nutrition to intestinal microflora. This review provides an overview of the interaction of diet with the gut microbiome and the latest evidence in understanding the inter-individual differences in dietary responsiveness according to individual baseline gut microbiota and microbiome-associated dietary intervention in diseases. The diversity of the gut microbiota and the presence of specific microorganisms can be attributed to physiological differences following dietary intervention. The difference in individual responsiveness based on the gut microbiota has the potential to become an important research approach for personalized nutrition and health management, although further well-designed large-scale studies are warranted.

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          Structure, Function and Diversity of the Healthy Human Microbiome

          Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin, and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics, and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analyzed the largest cohort and set of distinct, clinically relevant body habitats to date. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families, and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology, and translational applications of the human microbiome.
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            Diet rapidly and reproducibly alters the human gut microbiome

            Long-term diet influences the structure and activity of the trillions of microorganisms residing in the human gut 1–5 , but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here, we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila, and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale, and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals 2 , reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi, and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids, and the outgrowth of microorganisms capable of triggering inflammatory bowel disease 6 . In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.
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              Human gut microbiome viewed across age and geography

              Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ between human populations when viewed from the perspective of component microbial lineages, encoded metabolic functions, stage of postnatal development, and environmental exposures, we characterized bacterial species present in fecal samples obtained from 531 individuals representing healthy Amerindians from the Amazonas of Venezuela, residents of rural Malawian communities, and inhabitants of USA metropolitan areas, as well as the gene content of 110 of their microbiomes. This cohort encompassed infants, children, teenagers and adults, parents and offspring, and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the representation of genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial species assemblages and functional gene repertoires were noted between individuals residing in the USA compared to the other two countries. These distinctive features are evident in early infancy as well as adulthood. In addition, the similarity of fecal microbiomes among family members extends across cultures. These findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations, and the impact of Westernization.
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                Author and article information

                Journal
                J Microbiol Biotechnol
                J Microbiol Biotechnol
                Journal of Microbiology and Biotechnology
                The Korean Society for Microbiology and Biotechnology
                1017-7825
                1738-8872
                28 December 2022
                25 October 2022
                25 October 2022
                : 32
                : 12
                : 1497-1505
                Affiliations
                [1]Research Group of Personalized Diet, Korea Food Research Institute, Jeollabuk-do 55365, Republic of Korea
                Author notes
                [* ] Corresponding author Phone: +82-63-219-9446 Fax: +82-63-219-9876 E-mail: shinjh@ 123456kfri.re.kr
                [†]

                These authors contributed equally to this work.

                Article
                jmb-32-12-1497
                10.4014/jmb.2209.09050
                9843811
                36398438
                593ad637-77b2-437d-b8d6-418de54e5820
                Copyright © 2022 by the authors. Licensee KMB.

                This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.

                History
                : 30 September 2022
                : 16 October 2022
                : 18 October 2022
                Categories
                Special Topic – Gut Microbiome
                Environmental Microbiology and Biotechnology (EMB)
                Microbiome

                diet,personalized nutrition,gut microbiota,enterotype,human health

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