Diversity stability and resilience of the human gut microbiota. 1. Micronutrient deficiencies during the critical first 1000-day window in children may lead to an impaired mature gut microbiota with an abnormal community structure and expressed functions. Jul 28, 2018 · The gut microbiota refers to the community of microorganisms inhabiting a defined environment along the gastrointestinal tract, and includes bacteria, fungi, protozoa, archaea, and yeasts. Multifunctional redundancy is an intrinsic property in the gut ecosystem. To characterize stability in related and unrelated individuals and its responsiveness to physiologic change (weight loss), we developed a method for bacterial 16 S This goal is formidable. Bacterial community variation in human body habitats across space Nov 4, 2014 · Human gut microbes use multiple transporters to distinguish vitamin B12 analogs and compete in the gut. Nature 489:220–230. 2012;489:220–30. Consequently, the oral microbiome might be a key factor for understanding human health over a human life-time. 1038/NATURE11550) Trillions of microbes inhabit the human intestine, forming a complex ecological community that influences normal physiology and susceptibility to disease through its collective metabolic activities and host interactions. Diversity, stability, and resilience of the human gut microbiota. What constitutes a “normal” or “healthy” intestinal microbiome is an area of active research, but key characteristics may include diversity, richness and a microbial community’s resilience Oct 13, 2020 · The ability to improve resilience of the gut microbial ecosystem prior to perturbations, or to restore its equilibrium afterwards, would offer significant benefits. 2012 Sep 13;489(7415):220-230. The disruption of the gut ecosystem by May 6, 2023 · Figure 1. Specifically, the gut microbiota harbors a diverse array of ARGs conferring The human gut microbiome is a diverse and complex ecosystem, inhabited by thousands of microbial species which coevolved within the host and are known to play an important role in health and disease. Nov 23, 2022 · Regarding the latter, four main factors have been recognized to play an essential role in the resilience and recovery of the human gut microbiota: initial composition, capability to maintain its . Here we develop a body of ecological theory to help us understand microbiome stability. Science 341 , 1237439 (2013). Aug 30, 2021 · Abstract. as "a characteristic microbial community occupying a reasonably well-defined habitat which has Aug 1, 2019 · Diet and stress modulate the gut microbiota, but the investigation of their combined effect among humans is just beginning. This stability is considered critical for good health but is poorly understood. Diet is a key modifiable factor influencing Nov 16, 2017 · A healthy microbiota is thought to be characterized by high microbial and gene diversity, presumed to reflect ecosystem stability and resilience. Aug 11, 2017 · The dawn of modern microbiota research. Nature 405, 228–233 The neuroactive potential of the human gut microbiota in quality of life and depression. Jansson 3,4 & Rob Knight 1,5,6 Jun 17, 2019 · The long-term stability of the human gut microbiota. g. Use of antimicrobial drugs are known to have pronounced effects on the human gut microbiota 3 Oct 2, 2019 · The human gut microbiota is a complex and dynamic microbial community that is integral to the maintenance of health 1, 2 and the regulation of the host immune system 3, 4. , 2009). These applications require an understanding of the dynamics and stability of the microbiota over the lifespan of an individual. However, in healthy hosts, richness would primarily reflect the stage of ecosystem development through the gut Jul 5, 2013 · Understanding the dynamics and stability of the human gut microbiota is important if its characterization is to play a role in the diagnosis, treatment, and prevention of disease. , 1998; Human Microbiome Project Consortium, 2012b; Zoetendal et al. stability dichotomy of the human microbiome is evident over a period of days, as was illustrated in the first dense time series analysis of the human microbiome 31 and confirmed in later ones 34. 2012. Bottom-up approaches characterizing Nov 15, 2012 · Longitudinal studies of the human gut microbiota based on 16S rRNA analysis have suggested that bacterial community structure is relatively stable over time in the absence of perturbations (Costello et al. Microbiol 4, 623–632 (2019). Richness of the gut microbial ecosystem appears to be a critical characteristic for a healthy gut microbiota. 26, 27 Faecal microbiome analyses have revealed a seemingly consistent association between disease and a reduction in the observed or estimated number of species in a sample Jul 5, 2023 · Moreover, the stability of the gut microbiota was reported earlier in the humans (15, 36), and the human gut microbiota remains stable across longer durations . Apr 23, 2022 · Introduction. e. Functional redundancy allows the host to maintain a healthy gut microbiota to preserve stability and resilience in response to perturbations . Lozupone 1 , Jesse I. Studying mouse gut microbiota, one group reported that 57% of the variations in the Jul 7, 2022 · Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R (2012) Diversity, stability and resilience of the human gut microbiota. Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments. Therefore, identifying which microbial Dec 26, 2023 · Undoubtedly, perturbations in the stability of the gut micro-biota, such as the loss of specific taxonomic groups or a de-crease in microbial diversity, can adversely impact host health16. In this review, we focus on stability and resilience as essential ecological charact Sep 13, 2012 · The stability of the ecosystem in which gut microbiota is embedded is thought to increase with its diversity, which is usually assessed using two ecological indices-alpha diversity and beta Dec 11, 2014 · Keywords: Microbiome, Diet, Gut. In that study, two subjects provided daily samples of their oral, skin and faecal microbiota, one for six months and the other for Sep 1, 2020 · Indeed, diversity within the gut microbiota has been reported to play a positive role in promoting microbial resilience and enhancing its stability [45]. Coverage evaluation of universal bacterial primers using the metagenomic datasets. The microbiota in the gut consists of several strains of bacteria and yeasts. A microbiome (from Ancient Greek μικρός (mikrós) 'small', and βίος (bíos) 'life') is the community of microorganisms that can usually be found living together in any given habitat. The maturation of the human microbiota is thus an example of ecological succession 4 , 26 , 27 , in which communities undergo consecutive compositional and functional changes following initial Sep 1, 2012 · The human gut contains a dense, complex, and diverse microbial community, comprising the gut microbiome. 1038/nature11550 Powered by Pure , Scopus & Elsevier Fingerprint Engine™ Sep 1, 2012 · Dramatic changes in the gut microbiota occur during early life, with an increase in diversity and stability over the first three years 4,26,27 (Fig. Oct 27, 2023 · The metabolic processes performed by the human gut microbiota have a crucial impact on human metabolism and health [1,2,3]. 1 2 Gut microbiota composition varies among individuals and throughout development, and is dependent on host genotype and environ- Feb 15, 2024 · Overall, the gut microbiota is a critical element in stress-related psychiatric disorders, as microbial genes in the human body outnumber human genes by 150-fold (111). Gut microbiota diversity is believed to be associated with microbiota stability and resilience . Gordon 2 , Janet K. For instance, various human gut bacteria produce the short-chain fatty Oct 8, 2022 · The diversity-stability debate. Science. 2 Dysbiosis and its impact on host physiology Dysbiosis defines compositional and/or functional imbalance in the microbial ecology to an extent that exceeds its resistance and resilience Nov 22, 2019 · Abstract. The human gut harbors a large and complex community of beneficial microbes that remain stable over long periods. BMC Microbiol 12: 66. The gut microbiota changes substantially during infancy and toddlerhood in terms of both taxonomic composition and diversity. Gut microbiota recovery after chemotherapy treatment. Jan 1, 2017 · In addition to the resilience of the gut microbiota, the gut microbiome exhibits functional redundancy, which guarantees that the key functions are maintained for normal gut functioning [28,30]. Oct 16, 2016 · There is a complicated bi-directional relationship between the intestinal microbiota and host which is vital to health and likely promotes disease. The study of the healthy microbiome has been greatly enriched for bacteria [ 7, 9 ], with less attention given to other microbial domains. [PMC free article] [Google Scholar] Dethlefsen L, Huse S, Sogin ML, Relman DA. 1 In addition, the human microbiota, also known as “the hidden organ,” contribute over 150 times more genetic information than that of the entire This goal is formidable. 2014; 15:47–57. 17, 49 In agreement with our second hypothesis, we Mar 30, 2023 · The gut microbiota is immensely diverse, varies between individuals and can fluctuate over time - especially during disease and early development. Understanding the factors that underlie changes in the composition and function of the gut microbiota will aid in the design of therapies that Jan 1, 2018 · Fig. 14e −05; Figure 5 B). The gut microbiota has recently attracted attention as a reservoir of ARGs17. Jan 10, 2019 · Considering the characteristics of gut microbiota such as the large diversity, the stability and resilience, and the symbiotic interaction with the host, we can define the host and the microorganisms inhabiting it as a “superorganism” [8,9] which performs immune and metabolic functions . [PMC free article] [Google Scholar] May 11, 2023 · During infancy, gut microbiota development is a crucial process involved in the establishment of microbe–host interactions which may persist throughout adulthood, and which are believed to The human gut microbiota: stability and diversity. The first 1000 cultured species of the human gastrointestinal microbiota. Baseline Stability! Disturbance! Recovery Dynamics! Colonic Lavage! (Weekly Sampling)! (Daily Sampling)! (Weekly Sampling)! = Fecal and Urine ! Samples Taken ! May 11, 2022 · Microbial extinctions within the human gut microbiome associated with a Westernized lifestyle also provide an example of homeostatic failure. Aug 1, 2018 · The bacterial community of the human distal intestine is one of the richest microbial environments on earth, consisting of >10 12 cells and hundreds of species [1]. It is estimated that human body contains as many as 10 14 microbial cells ( 1 ), and our appreciation of their contribution to host physiology, disease and behaviour is increasing rapidly ( 2 – 5 ). Existing evidence suggests bidirectional relationships among stress/mood, diet, and the gut microbiota, which ultimately form either a vicious or virtuous cycle. Cell Host Microbe. In defining host health, it remains unclear whether diversity is paramount, or whether greater weight is held by gut microbiota composition or mono- or multiple-functional capacity of the Jul 5, 2013 · Microbiota stability followed a power-law function, which when extrapolated suggests that most strains in an individual are residents for decades. Depending on the initial microbiota state and other Feb 1, 2018 · The gut microbiota has been a topic of immense interest over the last years, as its composition and diversity seem to be intimately linked to health and disease 1. May 1, 2016 · Recent studies demonstrate the importance of taking into account the contribution of stability, resistance, resilience, and redundancy features to the functional status of a given microbiota under disturbance in a temporal framework. Pubmed Central PMCID: 3791589. The gut microbiota is immensely diverse, varies between individuals and can fluctuate over time - especially during disease and early development, viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments. Mar 20, 2017 · In this review, we try to promote and apply ecological theory to understand the dynamics and diversity of human commensal microbiota. Early life is a critical period as our gut microbiota establishes here and may impact both current and future health. The Western diet, high in saturated fat, processed foods, and refined sugar, starkly contrasts with fiber-rich, plantbased diets of indigenous cultures. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Low diversity is associated with an imbalance between pro‐ and anti‐inflammatory species and may The human gut microbiome is a diverse and complex ecosystem, inhabited by thousands of microbial species which coevolved within the host and are known to play an important role in health and disease. ' Nov 25, 2014 · The human gut is home to trillions of microbes that form a symbiotic relationship with the human host. Aug 4, 2023 · This is because the gut microbiota has a high degree of functional redundancy, where phylogenetically unrelated taxa contain genes that perform similar functions . The human microbiome, though, spans the tree of life and thus includes archaea, viruses, and eukaryotes. As greater than 98% of isolated genetic sequences present in the gut come from bacteria, the term and the focus of most research in this area largely refer Dec 30, 2013 · The human gastro-intestinal tract hosts a complex and diverse microbial community, whose collective genetic coding capacity vastly exceeds that of the human genome. However, extrinsic factors, diet, and Aug 8, 2016 · The ecosystem follows dynamic fluctuations in microbial composition during the first three years of life, with major increase in diversity, to reach a relatively stable equilibrium. We have developed an in vitro 40-plex platform that provides an oxygen gradient to metabolites which affect human physiology and are, therefore, considered an important factor for maintain-ing health. This study characterizes the human gut microbiota over time, and it provides important new evidence that the microbiota of an individual is quite stable over years and likely decades. Stombaugh 1 , Jeffrey I. In this review Jul 24, 2013 · Terms and Methods. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. May 7, 2015 · Follow‐up studies and, particularly, intervention studies aimed at restoring the normal composition of the gut microbiota are needed. Nature . The long-term stability of the human gut microbiota. The human gut microbiome is a complex ecosystem, densely colonised by thousands of microbial species. This complex community, collectively known as the microbiota (their genes are known as the microbiome), contains Sep 1, 2012 · Dramatic changes in the gut microbiota occur during early life, with an increase in diversity and stability over the first three years 4,26,27 (Fig. Article Google Scholar Costello, E. Jan 24, 2019 · The long-term stability of the human gut microbiota. In this context, we explore the changes in the microbiota that are relevant to human health, especially in light of the rise of chronic inflammatory disorders. Nat. Specific physiologic features of this relationship include the development of innate and adaptive immunity, relative susceptibilities to Mar 2, 2020 · As a point of nomenclature, the microbial species that inhabit the gastrointestinal tract are known as gut microbiota, while the genomes of the microbiota are known as the gut microbiome. Large cohort studies can provide further Mar 30, 2022 · Quagliariello, A. (C) Host response. Gut bacteria are key regulators of digestion along Mar 4, 2013 · Diversity, stability and resilience of the human gut microbiota. Technological advances in multi-‘omic platforms such as metataxonomics and metagenomics, have helped fuel the recent expansion of microbiota research (Marchesi and Ravel, 2015), especially on humans, as exemplified by large-scale efforts such as The Human Microbiome Project, started in 2007 (Peterson et al. To further estimate the resilience of the Stability and Resilience in the Human Microbiome: Response of Gut Microbiota to Colonic Lavage. Apr 24, 2018 · Faecal microbiota richness is considered a hallmark of gut health and stability. The Western diet fosters a distinct gut microbiota signature with low gut microbiota diversity and greater gut leakiness, which may contribute to metabolic syndrome and chronic disease onset The microbiota should be considered as just another component of the human epigenetic landscape. Pathogens exploit the antibiotic-induced inflammatory conditions. Apr 4, 2023 · The complex, dynamic environment of the human lower gastrointestinal tract is colonized by hundreds of bacterial species that impact health and performance. It varies among individuals and depends on host genotype and environmental factors, such as diet and antibiotics. The origin of “microbiota” can be dated back to early 1900s. This Sep 20, 2019 · Genetic variations between human populations are limited but the genetic and metabolic diversity of gut microbiota between populations are enormous. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Thus, health is also a reflection of the diversity and composition of gut microbiota and its metabolic status. Aug 29, 2018 · The changes in the microbiota of adult visitors occurred mostly within individual variation clouds, and only the skin microbiota—and not the gut, oral, or nasal microbiota—converged among adult visitors, suggesting a lack of taxon transmission or acquisition of new diversity; therefore, the microbiota plasticity was modeled by diet, within A healthy gut microbial ecosystem is generally thought to be characterised by high bacterial richness and diversity, presumed to reflect ecosystem stability and resilience. Early microbial exposure, diet, age, breed, and antibiotics have all been implicated to the onset and maintenance of microbial diversity in the human gut . Human Microbiota—communities of microscopic living organisms found on, in humans (viruses, bacteria, archaea, eukarya) Microbiome—collective genomes of microbiota. Diversity, stability and resilience of the human gut microbiota. The healthy adult gut microbiota is typically dominated by anaerobic members of the Firmicutes and Bacteroidetes phyla and is known to provide key functions for maintaining health, including production of metabolites that promote Apr 4, 2018 · The plasticity vs. It was found that a vast number of microorganisms, including bacteria, yeasts, and viruses, coexist in various sites of the human body (gut, skin, lung, oral cavity). The prevalence of psychiatric disorders that do not respond to conventional treatments calls for a more nuanced and in-depth understanding into how peripheral physiology Dec 23, 2022 · The human microbiota is essential to the health of the host and can be affected by many features 1,2. In fact, several studies have focused on the stability of nonhuman primate gut microbiota (39, 40), which may take into account long-term sampling and sampling difficulties. , weeks Sep 11, 2012 · Key takeaway: 'Understanding the diversity, stability, and resilience of the human gut microbiota can help design therapies that target it, promoting health and reducing disease susceptibility. PubMed PMID: 23828941. Article CAS Google Scholar Moon J, Choi SH, Yoon CH, Kim MK (2020) Gut dysbiosis is prevailing in Sjgren’s syndrome and is related to dry eye severity. Similarly Jan 23, 2020 · The gut microbiota has been shown to play diverse roles in human health and disease although the underlying mechanisms have not yet been fully elucidated. Furthermore, it is also likely that alterations to the microbiota in other body habitat, e. Thus, we investigated if the Euclidean distances between the microbiome profiles at each visit for each participant were Mar 1, 2020 · By maintaining diversity of the gut microbial community, social transmission of microorganisms may benefit host health in numerous ways [170]. Feb 11, 2023 · Microbiome response to diet, but not the host bioactive lipid response, is associated to initial microbiome diversity. Modulation of the microbiota by Apr 23, 2022 · Generally, the microbiota diversity increases in the time between childhood and adulthood and decreases at older age (over 70). During health, the intestinal microbiota provides many benefits to the host and is generally resistant to colonization by new species; however, disruption of this complex community can lead to pathogen invasion, inflammation, and disease. Among these molecules, two main classes of steroids, cholesterol and bile acids, denote two Apr 5, 2016 · Much has been described in the past decade based primarily on 16S rRNA gene amplicon sequencing regarding the diversity, structure, stability and dynamics of human microbiota in their various body habitats, most notably within the gastrointestinal tract (GIT). the skin ( Weyrich et al . In this article, we summarise recent advances in microbiome studies across both Western and non-Western populations, either in cross-sectional or longitudinal surveys, and over various age groups, revealing a considerable diversity and variability in the Mar 30, 2016 · Most of the Human diseases affecting westernized countries are associated with dysbiosis and loss of microbial diversity in the gut microbiota. K. doi: 10. Recent breakthroughs in Feb 2, 2015 · The microbiota is composed of a significant number of different bacteria, approximately 160 species per person per fecal sample, and this ecosystem plays an important role in human health. The Western way of life, with a wide use of antibiotics and other environmental triggers, may reduce the number of bacterial predators leading to a decrease in microbial diversity of the Human gut. The composition of the gut microbiota is unique to each individual and tends to remain relatively stable throughout life, yet daily transient fluctuations are observed. For example,diversity may help to promote stability and resilience of the gut microbiome [142], and is often linked to good health, though this is not always the case [140]. It was defined more precisely in 1988 by Whipps et al. et al. Aug 1, 2017 · The result is less diversity and fitness of commensal bacteria in the gut. The human gut is inhabited by trillions of microorganisms composing a dynamic ecosystem implicated in health and disease. 2013 Jul 5; 341 (6141):1237439. The maturation of the human microbiota is thus an example of ecological succession 4 , 26 , 27 , in which communities undergo consecutive compositional and functional changes following initial Mar 31, 2016 · Most of the Human diseases affecting westernized countries are associated with dysbiosis and loss of microbial diversity in the gut microbiota. As a consequence, the gut microbiota produces metabolites from a large range of molecules that host’s enzymes are not able to convert. 21 Before the formation of a relatively stable gut microbiota Diversity, stability and resilience of the human gut microbiota Catherine A. Article CAS PubMed PubMed Central Google Scholar Rajilic-Stojanovic M, de Vos WM. A common, measurable outcome used in microbiome research is the diversity of microbes within a given body habitat, which has been defined as the number Nov 6, 2015 · Abstract. , 16S rRNA gene-based surveys) Metagenomics—study of genetic material directly from environmental samples; genetic or. Phylogenetic or taxonomic composition (e. Microbiota-accessible carbohydrates (MAC) acquired from dietary fiber impact the diversity and composition of the human gut microbiome, but they are notably reduced in the low fiber, high fat Western diet. Thus, it is of importance to understand how different factors govern the complex microbial colonization patterns in this period. (A) When the distribution of intestinal microorganisms is in a stable Dec 7, 2022 · Gut microbiota composition varies among individuals and throughout the growth state, and is dependent on host genotype and environmental factors. At a scale of millions of years, as comparative genomics reveals, microbiota composition has been marked by a long-term co-evolutionary history between microbes and their primate hosts . Nature 489: 220–230 [PMC free article] [Google Scholar] Mao DP, Zhou Q, Chen CY, Quan ZX 2012. Feb 7, 2019 · Understanding its diversity, stability, and resilience and how these influence health is a remarkably hard problem. Apr 27, 2016 · Archaea, viruses, fungi, and other eukaryotes. Sep 1, 2012 · Dramatic changes in the gut microbiota occur during early life, with an increase in diversity and stability over the first three years 4,26,27 (Fig. Nature. At a much smaller scale (i. Shared strains were recovered from family members but not from unrelated individuals. , 2015 ), may trigger systemic effects not least via immune system responses. Pathogens use sugars and inorganic compounds generated by the intestinal microbiota as carbon or energy sources and perform anaerobic respiration in the inflammatory conditions caused by antibiotics. & Knight, R. High-impact pharmacological treatments such as chemotherapy can cause profound disturbance of the intestinal environment, including inflammation, breakdown of mucosal barriers, and shifts in the gut microbiota composition. The Western diet fosters a distinct gut microbiota signature with low gut microbiota diversity and greater gut leakiness, which may contribute to metabolic syndrome and chronic disease onset Explore millions of resources from scholarly journals, books, newspapers, videos and more, on the ProQuest Platform. 5). Gut microbial composition is highly impacted by food and food habits. The microbial colonization of the infant gut is known to play a key role in immunological and metabolic pathways impacting on human health. Rajilić-Stojanović, M. With its diversity, its composition fluctuates at different stages of life and varies in healthy and sick persons [ 1 ]. These key functions are conserved among individuals and this set of genes is normally referred to as a core microbiome [1,31]. , 2009; Franks et al. The maturation of the human microbiota is thus an example of ecological succession 4 , 26 , 27 , in which communities undergo consecutive compositional and functional changes following initial Jul 5, 2013 · Our growing understanding of the human gut microbiota as an indicator of and contributor to human health suggests that it will play important roles in the diagnosis, treatment, and ultimately prevention of human disease. Sampling of individuals who consumed a monotonous liquid diet for up to 32 weeks indicated that changes in strain Dec 11, 2014 · The human gut harbours diverse and abundant microbes, forming a complex ecological system that interacts with host and environmental factors. Much has been described in the past decade based primarily on 16S rRNA gene amplicon sequencing regarding the diversity, structure, stability and dynamics of human microbiota in their various Feb 17, 2023 · This was coupled with acute disbalance of the gut microbiota β-diversity and significant changes from the original state from 18 to 24 h post-treatment when the host expelled the worms (Dunn test of mean Bray Curtis distance within time points, adj p = 3. The gut microbiota is immensely diverse, varies between individuals and can fluctuate over time — especially during disease and early development. Aug 1, 2019 · The Western diet, high in saturated fat, processed foods, and refined sugar, starkly contrasts with fiber-rich, plant-based diets of indigenous cultures. Ex vivo study of the functional interactions between microbial community members in conditions representative of those in the gut is an ongoing challenge. 1 2 Gut microbiota composition varies among individuals and throughout development, and is dependent on host genotype and environ- Apr 27, 2016 · Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. , 1998). Gut microbiota profiling and gut–brain crosstalk in children affected by pediatric acute-onset neuropsychiatric syndrome and pediatric autoimmune neuropsychiatric Mar 20, 2022 · In humans, the gut is the main site for the survival of the human microbiota. Sep 12, 2012 · (DOI: 10. 展开 Jun 13, 2016 · To adress the debate over the discrete 27,28 or continuous 29 nature of human gut microbiota diversity, J. Long-term monitoring of the human intestinal microbiota composition. The human gut microbiota is a highly complex ecosystem consisting of communities of microorganisms that interact with each other and with their host. 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