Review
Intestinal microbiota is a plastic factor responding to environmental changes Marco Candela, Elena Biagi, Simone Maccaferri, Silvia Turroni and Patrizia Brigidi Department of Pharmaceutical Sciences, University of Bologna, Bologna, Italy
Traditionally regarded as stable through the entire lifespan, the intestinal microbiota has now emerged as an extremely plastic entity, capable of being reconfigured in response to different environmental factors. In a mutualistic context, these microbiome fluctuations allow the host to rapidly adjust its metabolic and immunologic performances in response to environmental changes. Several circumstances can disturb this homeostatic equilibrium, inducing the intestinal microbiota to shift from a mutualistic configuration to a disease-associated profile. A mechanistic comprehension of the dynamics involved in this process is needed to deal more rationally with the role of the human intestinal microbiota in health and disease. Intestinal microbiota, a plastic factor of the human super-organism Humans are super-organisms, with 90% of their cells consisting of microbial cells [1,2]. A majority of these microbial cells live in the gastrointestinal tract (GIT) and constitute the human intestinal microbiota [1,3]. With a concentration of 1012 CFU/g of intestinal content, the human intestinal microbiota probably represents one of the most dense, biodiverse, and rapidly evolving bacterial ecosystems on Earth [4]. Its collective genome – the intestinal microbiome (Box 1) – provides functional traits that humans have not evolved by their own, and several of our metabolic, physiological, and immunological features depend on the mutualistic association with our intestinal microbial community [5–8]. For example, the intestinal microbiota enhances our digestive efficiency by degrading otherwise indigestible polysaccharides and, at the same time, represents a fundamental barrier against GIT colonization by enteropathogens. Moreover, crosstalk between the immune system and the GIT microbial community is essential for the development, education, and functionality of our immune system [9,10]. Studies carried out with germ-free (GF) mouse models revealed that ultrastructural development of the GIT depends on its dynamic interaction with the intestinal microbiota [11]. In a landmark study based on three mouse models – GF, pathogen-free with normal gut microbiota and adult conventionalized GF offspring – Heijtz et al. demonstrated that the intestinal microbiota can also affect synaptogenesis during the perinatal period, modulating brain development and function [12]. Furthermore, other studies carried out in GF mice Corresponding author: Candela, M. (
[email protected]) Keywords: human intestinal microbiota; plasticity; dietary habits; immune system; environment.
indicated that the intestinal microbiota tunes the host response to noxious stimuli [13], interfering with the behavioral response to nociceptive and stressful insults. These recent findings reinforced hypotheses concerning the role of intestinal microbiota in the gut–brain axis, extending the array of physiological features affected by our intestinal microbial counterpart to the field of neurogastroenterology. The GIT microbiota shows an immense biodiversity at the species level. 16S rRNA gene sequence surveys of the intestinal microbiota across the human population detected up to 1000 different bacterial species [1,9]. However, at a higher phylogenetic level, microbial biocomplexity in the human GIT decreases, resulting in a particular phylogenetic tree characterized by only a few branches with a large degree of radiance at the ends. Of the 100 different bacterial divisions that populate our planet, only six colonize the human GIT [14]: Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria and Verrucomicrobia. These microbial phyla generally show a well-conserved profile in terms of relative abundance in a healthy human GIT: 65% Firmicutes, 25% Bacteroidetes, 5% Actinobacteria, up to 8% Proteobacteria, and 1% Fusobacteria and Verrucomicrobia [2,15]. Each healthy human subject possesses a specific subset of hundreds of species out of the thousands that constitute the human intestinal microbiota [16]. According to Turnbaugh et al., 70% of the phylotypes of individual microbiota are subject-specific and no phylotype is present at more than 0.5% abundance in all subjects [17]. As a result of both nature and nurture, an adult-type intestinal microbiota is stabilized after weaning following an extremely dynamic process of colonization that begins at birth (Box 2) [18]. The phylogenetic and functional composition of the individual microbiota has been traditionally thought of as relatively stable throughout adulthood [19,20]. However, the recent adoption of longitudinal approaches in studying microbiota in the human intestinal ecosystem has suggested a new and more dynamic view of the human intestinal microbiota [21,22]. Molecular studies have been specifically designed to investigate the intestinal microbiota dynamics in response to different environmental variables, and have demonstrated an unexpected degree of plasticity in response to diet [15,21,23,24], exposure to environmental bacteria [25], geographic origins [26,27], and climate change [28]. Recently, McNulty et al. evaluated the extent of the dynamics of the microbiota in 14 people [29]. Their fecal microbiota was characterized every 2 weeks for 120 days. Some 74.6% of phylotypes and 36% of the genes identified in the individual
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Review Box 1. The human microbiome The collective genome of the human intestinal microbiota (microbiome) has been estimated to contain 100 times more genes than the 2.85 billion base pairs in the human genome [1,64]. Its functional assignment revealed that it is generally enriched for clusters of orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) categories involved in metabolism [5,17]. In particular, pathways involved in carbohydrate metabolism, energy metabolism, generation of short-chain fatty acids, amino acid metabolism, biosynthesis of secondary metabolites, and metabolism of cofactors and vitamins are highly represented in the human intestinal microbiome. Interestingly, the percentage of sequences assigned to carbohydrate-active enzymes (CAZymes) is greater than for all the other KEGG pathways. A total of 156 CAZy families have been found within at least one human gut microbiome [17]. This high glycobiome complexity confers to the human intestinal microbiota the capacity to degrade several glycans that cannot be metabolized by the human host, ranging from the host glycans enclosed in mucus to the array of glycans contained in plant polysaccharides, and supports the limited saccharolytic diversity encoded by the human genome. Characterization of the human microbiome is still in its infancy. According to the most recent reports, its functional assignment rate is approximately 60% [18,31], showing that a significant fraction of the microbiome is not represented in any of the 1511 published reference genomes. Moreover, the open pan-genome curves for 151 intestinal isolates, together with the outstanding degree of novelty shown by their genomes with respect to non-intestinal bacteria, highlight the remarkable functional diversity of this microbial ecosystem and indicate that the unassigned fraction of the human microbiome is probably greater than estimated [60]. Even if it is commonly accepted that all individuals share a core microbiome [18,30] encoding genes involved in key metabolic functions, a comparative analysis of intestinal microbiomes revealed that each subject also possesses considerable microbiome variability, comprising a unique set of subject-specific functional genes that corresponds to 25% of the total genes in the microbiome [61]. Although much of this genetic diversity is still unassigned and its impact on the human physiological phenotype is unknown, the variable microbiome undoubtedly provides an expanded view of the genetic variability of the human super-organism. Its complete functional attribution will allow the final limits of genetic variation in humans to be computed.
microbiota complement were variable in a period of 4 months, demonstrating the relevant degree of phylogenetic and functional plasticity of the human intestinal microbiota. On the basis of static comparisons of the intestinal microbiota among groups of subjects having a different health status, traditional studies have allowed microbiologists to detect a core microbiome, defined as a constant and shared fraction of the human microbiome, fundamental in supporting the mutualistic symbiotic relationship with the host [30]. However, longitudinal studies highlighted that the intestinal microbiota of each individual is an extremely dynamic entity [21,22,29], raising questions about how significant this degree of plasticity is for human health and homeostasis. This review summarizes the most recent and significant studies on the intestinal microbiota, highlighting its dynamic nature in relation to different environmental stressors. In addition, the importance of this plasticity for human health is highlighted by describing situations in which this dynamic homeostasis is compromised, resulting in disease. These reported findings and hypotheses could strengthen the direction in which research in intestinal microbial ecology is moving, shifting from a static view to a dynamic, and perhaps pliable, vision of the intestinal ecosystem. 386
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Dynamics of the intestinal microbiota in response to diet, environmental microorganisms and geography The most remarkable example of plasticity of the gut microbiota is provided by its capacity to rapidly respond to dietary changes (Table 1). In fact, an individual’s microbiota is able to both compositionally and functionally adapt itself to changes in diet in a 1–3-day period [21,23]. A molecular study of diet-dependent microbiota dynamics in 14 overweight men revealed that the individual microbiota adapts its phylogenetic profile in response to the main types of ingested fermentable carbohydrates. Interestingly, these fluctuations were influenced by the individual’s complement of microbial species, showing subject-specific diet-dependent changes in the microbiota phylotypes [23]. In a second dynamic study, the intestinal microbiota of lean subjects under caloric restriction was investigated for a 4-day period [15]. Subjects enrolled in the study recorded all components of their diets daily, allowing correlation to the adaptation of their intestinal microbiota to macro- and micronutrient consumption. A significant association was observed between the phylogenetic and functional structure of the intestinal microbiota and fiber and protein intake. In a recent publication, Wu et al. differentiated long- and short-term dietary responses of the human intestinal microbiota [24]. The impact of a long-term dietary habit on the intestinal microbiota was studied in a cohort of 98 healthy volunteers. Focusing on 78 taxa showing 0.2% abundance in at least one sample and appearing in more than 10% of the samples, the authors evaluated the association between bacterial taxon abundance and the intake of specific nutrient classes. This taxon–nutrient correlation analysis revealed that the human intestinal microbiota is characterized by bacterial groups showing a reciprocal inverse association with nutrients from fat and plant products. Analogous taxon–nutrient inverse correlations were observed for proteins versus carbohydrates, and fat versus carbohydrates. Within the same study, 10 subjects were sequestered in a hospital environment and enrolled in a short-term controlled feeding study by randomization to high-fat and low-fiber or low-fat and high-fiber diets. Changes in their intestinal microbiota were significant within the first 24 h of the controlled dietary regime, confirming the data reported by Walker et al. [23]. Identical short-term diets did not overcome the inter-individual variations, preserving the high degree of inter-individual variability of the human intestinal microbiota. Interestingly, the comparison between long- and short-term dietary changes revealed that the intestinal microbiota consists of bacterial groups affected by short-term dietary changes and others that are exclusively modulated by long-term dietary habits, such as those referred to as human enterotypes [31]. In the context of these recent findings, a hypothesis regarding how the dietary habits of the USA within the past 30 years have shaped the human intestinal microbiota has been advanced [21]. According to the authors, the increase in total caloric intake has prompted a general reduction in the phylogenetic and functional complexity of the human intestinal microbiota. Taken together, current research on microbiota plasticity in response to diet leads to a dynamic view in which the
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Table 1. Response of the human intestinal microbiota to different dietary interventions Study design Randomized crossover study: 14 overweight subjects, 3-week intervention
Type of diet or nutrients Diet high in resistant starch (type III RS)
Reduced carbohydrate weight-loss diet (high protein diet)
Cross-sectional study (COMBO) to assess long-term dietary habits: food frequency questionnaire, 98 healthy subjects
Controlled feeding study (CASE) to assess short-term dietary habits: randomization to specific diets, 10 healthy subjects, 10 day intervention
Caloric restriction: 18 lean subjects, 4 day dietary record
Fats Fiber Animal proteins Carbohydrates and simple sugars High-fat low-fiber versus low-fat high-fiber
Proteins Insoluble dietary fibers
intestinal microbiota continuously changes in response to long- and short-term dietary habits [32]. Through selection of microbial populations that optimally degrade the available substrates, these continuous microbiota fluctuations provide the host with the capability to readily adapt to dietary changes. Supporting this hypothesis, in a milestone publication, Hehemann et al. reported the first experimental evidence that the consumption of foods containing environmental bacteria is the most likely mechanism that promotes carbohydrate-active enzyme (CAZyme) update in the GIT microbiome [33]. According to the authors, the microbiome in Japanese people recently acquired the porphyrinase gene from the seaweed-associated marine bacterium Zobellia galactanivorans from a lateral gene transfer event favored by consumption of non-roasted dietary seaweed in Japanese sushi. The presence of CAZyme porphyrinase in their microbiome complement allows Japanese people to extract energy from the red marine algal porphyrin by means of the bacterial fermentation of this indigestible polysaccharide to short-chain fatty acids in the gut. These findings highlight the key role of the intestinal microbiome as a plastic and adaptable factor that improves the metabolic capacity of the human super-organism for more efficient extraction of energy from the diet. The human intestinal microbiota shows a second degree of plasticity with regard to its response to constant exposure to environmental bacteria. The continuous interaction between intestinal microbiota and environmental microorganisms during the entire course of human life is emerging as a strategic factor for the modulation of our immune functions
Microbiota response No changes at phylum level "Ruminococcaceae "Firmicutes spp. belonging to Roseburia genus, Eubacterium rectale group and relatives At phylotype level: "Ruminococcus bromii, "E. rectale, "Oscillibacter valericigenes No changes at phylum level #Firmicutes spp. belonging to Roseburia genus, Eubacterium rectale group and relatives At phylotype level: #Collinsella aerofaciens, "Oscillibacter valericigenes "Bacteroidetes, Actinobacteria #Firmicutes, Proteobacteria #Bacteroidetes, Actinobacteria "Firmicutes, Proteobacteria Positively associated with the Bacteroidetes enterotype Positively associated with the Prevotella enterotype
Refs [23]
Changes in microbiome composition are detectable within the first 24 h of controlled feeding Bacterial functional categories change significantly in response to diet No reduction in UniFrac distance between individuals fed the same diet No significant changes in Archaea, Bacteria and Eukarya concentrations No stable switching between Bacteroidetes enterotype and Prevotella enterotype after 10 days of controlled feeding Protein intake is significantly associated with KEGG orthology groups Insoluble dietary fiber intake is significantly associated with bacterial operational taxonomic unit (OTU) content
[24]
[15]
[8,11,22,34]. In particular, microbiota fluctuations in response to key environmental microbes during infancy are fundamental for proper development and education of the immune system. According to the ‘old friend hypothesis’, exposure to environmental microbes from contaminated foods, feces, or livestock, which have been present throughout mammalian evolution, is necessary to prime the physiology of our immune system [25,34–36]. Recently, studies carried out in mice demonstrated a role in programming many aspects of effector CD4+ T cell and B cell differentiation for specific intestinal microbial groups, such as segmented filamentous bacteria – Clostridium-related symbionts in the intestinal microbiota [37] – and Clostridium leptum and Clostridium coccoides [8,37,38]. By orchestrating T cell differentiation into various pro- and anti-inflammatory subsets, such as T helper 2 (TH2), TH17, and regulatory T cells, these microorganisms can fine-tune our immune system from the earliest stages of life [10,11,38]. Interestingly, it has been reported that the human intestinal microbiota shows a surprising degree of plasticity in response to climate change and geography. In a longitudinal study of 15 healthy Finnish subjects for 7 weeks, overseas travel was associated with a high decrease in similarity between samples from the same subject [28]. Changes in diet and exposure to new environmental microbes, as well as a different climate and stress, can account for this travel-related plasticity of the intestinal microbiota. The impact of geographic origin on intestinal microbiota composition was demonstrated in an extensive comparative analysis of intestinal microbiota 387
Review Box 2. Acquisition and aging of the intestinal microbiota We are born sterile in a microbial world. During the neonatal period we are involved in a complex and dynamic interplay with environmental microbes that, after weaning, culminates in the acquisition of an adult-type intestinal microbial community [65,66]. Perinatal events and early environmental exposure play a pivotal role in determining the acquisition of the infant microbiota and have lasting effects on the phylogenetic structure of the later adult intestinal ecosystem. The mother’s vagina is regarded as the first microbial source for the microbiota of the newborn [67]. However, the biodiversity of the vaginal ecosystem is relatively low, dominated by Lactobacillus species, so the environment encountered by the infant at and immediately after birth, such as the mother’s skin and fecal microbiota, living conditions and child-rearing practices, is of great importance [21,68]. Moreover, by modulating the early Bifidobacterium-dominated architecture of the infant gut microbiota, the mother’s milk has a relevant role in the process of microbiota assembly [69]. In this key period of our life, the intestinal microbiota dramatically fluctuates in response to stochastic microbial exposure. At weaning, with the introduction of a solid diet, developmental changes in the gut mucosa and maturation of the intestinal immune system stabilize the ecosystem, which converges to a more constant, adult-like phylogenetic architecture, with progressively increasing functional and taxonomic complexity [65,70]. In this scenario, if and how human genetics plays a role in the process of assembly of the individual intestinal microbiota is still controversial. According to Turnbaugh et al., monozygotic and dizygotic twins showed a comparable degree of similarity between their intestinal microbial communities, demonstrating that host genotype is secondary to environmental exposure in shaping gut microbial ecology [17]. However, another study showed a slightly reduced microbiota similarity profile in dizygotic compared to monozygotic twins [71]. Moreover, in a recent study in murine models, Benson et al. identified 18 host quantitative trait loci showing a significant linkage to intestinal microbial taxa [72]. In conclusion, the intestinal microbiota can be viewed as a factor that is in part vertically inherited from the mother, in part horizontally transferred from the environment, and in part controlled by host genetic factors. The crosstalk with its microbial counterpart accompanies the human host throughout adulthood, until aging and its related pathophysiological conditions start to affect this mutualistic relationship. Changes in lifestyle and diet, as well as immunosenescence, lead to increased intestinal permeability and decreased motility, and strongly impact on the intestinal microbiota, favoring proinflammatory pathobionts (Enterobacteriaceae) to the detriment of immunomodulatory bacterial groups (Clostridium cluster IV and XIVa, Bifidobacterium). This aged-type microbiota could play a role in consolidating the ‘inflamm-aging’ process by establishing a selfsustained inflammatory loop detrimental for host health [40,73]. However, from an ecological perspective, the ability of the host to re-establish a mutualistic relationship with this compromised microbial community may represent a necessary step for the human host to maintain health and reach longevity.
among people from Korea, China, Japan and the USA [27]. Data analysis revealed that gut microbiota profiles clustered according to geographic origin. In particular, Americans were characterized by higher abundance of Firmicutes, Japanese had more Actinobacteria, and Koreans and Chinese showed a Bacteroidetes-rich gut microbiota. Analogously, a comparative study between children from Europe and Burkina Faso showed significant country-related differences in the fecal microbial community [26]. Children from Burkina Faso were enriched in Bacteroidetes and Actinobacteria, and depleted in Firmicutes and Proteobacteria compared to the European children. According to the authors, these country-related differences in intestinal microbiota profiles can result from host genetics, as well as several environmental variables, such 388
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as climate and particular dietary habits and lifestyle of those in each country. The recent adoption of longitudinal approaches in studying the human intestinal microbiota highlighted an unexpected degree of phylogenetic and functional plasticity of our symbiont microbial counterpart. This dynamic nature is strategic for several important features of human biology, such as adaptation to different diets and environments and modulation of the immune system. Disturbance of the microbiota–host mutualistic relationship Under some circumstances, diet and other environmental factors, as well as factors of endogenous origin, such as chronic inflammation [9,39] and aging [40,41] (Box 2), can force the intestinal microbiota to shift from a mutualistic configuration supporting health and homeostasis to a disease-associated profile, usually characterized by a lower level of phylogenetic and functional biodiversity (Figure 1). The unbalanced intestinal microbiota observed in obese people [17] and the progressive loss of key intestinal microbial groups as a result of a Westernized lifestyle [21] provide two remarkable examples of disturbance of the microbiota–host mutualism triggered by environmental stressors. The recent pandemic of obesity in Westernized countries reflects environmental and lifestyle changes, among which dietary factors play a major role [42–45]. In this scenario, diet-dependent changes in the microbiota are perceived as probably being involved in the etiology and severity of obesity [17,30,46,47]. High-fat dietary habits can have a dramatic impact on the intestinal microbial community. To explain this phenomenon, Turnbaugh et al. suggested an intriguing metaphor by comparing the obese gut microbiota to fertilized runoff, whereby, with respect to the high diversity of a rainforest, a low-diversity community blooms on application of an abnormal energy input [17]. According to the authors, compared to lean controls, the intestinal microbiota of obese people is significantly less diverse and generally characterized by higher abundance of Firmicutes and Actinobacteria and a corresponding decrease in Bacteroidetes. However, Duncan et al. reported conflicting results, failing to detect any relationship between the proportion of Bacteroidetes in fecal samples and obesity [48]. This lack of consensus suggested that the link between microbiota and obesity is probably more complex than the mere phylum-level Bacteroidetes:Firmicutes ratio. The latter hypothesis has been recently reinforced by a comparative analysis of gene-level and network-level topological differences between lean and obese microbiomes [49]. As a result of adaptation to a low-diversity environment, the obese microbiome is characterized by reduced modularity and the enrichment of peripheral enzymes with a low clustering coefficient. According to the authors, this variation in community-level metabolism may be induced by an increase or decrease in relative abundance of a small subset of species, which changes the way in which the microbiome interfaces with the environment and the host. The functional annotation of the obese microbiome revealed that the obese-type microbial community
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3
n
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Figure 1. Dynamics that force disturbance of the microbiota–host mutualism. Under certain conditions, environmental stressors (diet and/or other environmental factors, such as infection, hygiene, and sanitization) and factors of endogenous origin (such as inflammation or aging) can force the intestinal microbiota to shift from the mutualistic configuration that supports homeostasis (from 1 to n) to a disease-associated profile, generally characterized by a lower level of phylogenetic and functional biodiversity. Different healthy configurations are represented, showing the variability within and between individuals.
possesses a lower level of functional diversity and is enriched in genes involved in carbohydrate, lipid and amino acid metabolism, demonstrating an overall increase in fermentative capacity with respect to the lean-type microbiome [17]. Furthermore, transplantation of the obesity-associated intestinal microbiota into GF mice resulted in a greater increase in total body fat than colonization with the lean-type intestinal microbiota [50]. In agreement with the ‘energy harvest hypothesis’ [51], these data indicate that the obesity-associated intestinal microbiota can significantly contribute to disease severity by increasing energy harvest from the diet. Moreover, it has been shown that high-fat diet-dependent microbiota alterations negatively affect intestinal permeability, reducing expression of the tight junction proteins zona occludens-1 and occludin [52]. The consequent increase in circulating levels of lipopolysaccharide can significantly contribute to the development of obesity-related inflammatory liver diseases, such as non-alcoholic fatty liver disease, non-alcoholic steatohepatitis, and insulin resistance [53]. In conclusion, the abnormal dietary habits of obese people result in a severe intestinal microbiota transition from a healthy profile to an obesogenic one, which supports obesity and associated comorbidities (Figure 2) [46,47]. According to the ‘hygiene hypothesis’, a Westernized lifestyle compromises the mutualistic relationship between humans and their intestinal microbiota. Antibiotic use, sanitization, bathing, clean water and sterile foods, which are typical of Western societies, favor a profound decrease in the microbial biodiversity humans are exposed to over their lifespan [35]. Even if this has provided numerous benefits in terms of reduced infant mortality and increased life expectancy, it has also come at a cost of a progressive loss of key bacterial groups from the intestinal microbiota, the socalled old friends, which are essential for the development and tuning of our immune system [8]. The lack of immunological crosstalk with these old friends – especially during infancy – leads to an immune system inclined to inappropriate activation, which is characteristic of emerging chronic inflammatory diseases (Figure 3) [34,54]. Confirming this
hypothesis, allergy, autoimmune disorders, inflammatory bowel diseases, and type 2 diabetes, all resulting from chronic inflammatory responses, are dramatically increasing in developing countries, where Westernized lifestyles are becoming more and more common [7,21,22,55,56]. Known as the ‘disappearing microbiota hypothesis’ [25], this theory has been recently strengthened by a comparative study of the intestinal microbiota from children from Europe and rural Africa [26]. According to the authors, European children were deprived of microbial groups that may have a role in host immune education. Furthermore, a recent extensive study carried out on a birth cohort of 411 European children at high risk of allergy who were followed for 6 years by clinical assessments at 6-month intervals demonstrated that bacterial diversity in the early intestinal microbiota is inversely associated with the risk of allergic sensitization [57]. Environmental stressors, such as high-fat dietary habits or excessive sanitization, can overcome the resilience of
High-fat dietary habits
Pathophysiology of obesity
Obesogenic microbiota • Low phylogenetic and functional diversity • Enrichment in genes involved in energy metabolism
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Figure 2. Disturbance of the microbiota–host mutualistic interaction in response to high-fat diet. The massive caloric intake from a high-fat diet forces a reconfiguration of the intestinal microbiota, reducing its phylogenetic diversity and enriching the microbiome with genes involved in energy metabolism. Characterized by high fermentative capacity, this obesogenic microbiota profile increases the host energy harvest from the diet, contributing to the pathophysiology of obesity.
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Westernized lifestyle
Decreased microbial diversity in living environments
Shrinkage of the microbiota diversity
Susceptible host Chronic inflammatory diseases
Inappropriate activation of the immune system
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Figure 3. Hygiene hypothesis and intestinal microbiota. A Westernized lifestyle compromises the microbial load and diversity in living environments. This results in a general shrinkage of the microbiota diversity, with the progressive loss of ‘old friends’, defined as components of the microbiota essential for the development and tuning of our immune system. In a susceptible host, a decrease in this key microbial component results in an immune system that is more prone to inappropriate activation, a characteristic of emerging chronic inflammatory diseases in Western countries. In a feedback loop, chronic inflammation affects the composition of the microbiota, supporting a low-diversity proinflammatory community that feeds into consolidation of the inflammatory status.
the dynamic symbiotic relationship between the intestinal microbiota and the host, compromising host health and favoring the onset and/or severity of diseases. Concluding remarks and future directions In a mutualistic context, the plasticity of the human intestinal microbiota guarantees rapid adaptation of the metabolic performance of the super-organism in response to diet and, at the same time, represents an essential prerequisite for education of the immune system to homeostasis. Inherited from the mother and shaped by the composition of the mother’s milk, the human intestinal microbiota could thus be regarded as an epigenetic factor that, shaped by the environment, confers adaptability and resilience to the human super-organism. Several circumstances can disturb this mutualistic interaction and force a shift of the intestinal microbiota from a mutualistic configuration to a diseaseassociated profile. However, to reveal the dynamics involved in these processes and to understand to what extent the plasticity of the intestinal microbiota affects human homeostasis in a changing environment, a better understanding of the microbiota–host bionetwork is needed. The entire species-level phylogenetic diversity of the human intestinal microbiota is still to be determined. Moreover, we need to uncover the real extent of the unassigned fraction of the human intestinal microbiome and, most importantly, the function of this biological dark matter [58]. This information will be important in dealing with the impact of intra- and inter-individual microbiome diversity on particular host physiological phenotypes. Even if deep-sequencing approaches allow depiction of the broad phylogenetic biodiversity of the human intestinal microbiota [14,59], we are still far from comprehending the corresponding degree of functional complexity [17,31,60,61]. 390
Thus, reaching the target of 900 GIT reference genomes for the Human Microbiome Project is mandatory. Moreover, we need to improve our capacity to cultivate anaerobic members of the human intestinal microbiota and unknown microbial genes need to be identified by functional genomics approaches involving massive functional screening of GIT metagenome libraries [62,63]. By sampling humans across the globe with a variety of diets and lifestyles, including ancestral hunter–gatherer lifestyles, we can increase our knowledge of the biodiversity of the human intestinal microbiota. These studies will help in exploring the limits of the genetic variability of the human super-organism, allowing comprehension about the extent to which our co-evolution with intestinal microbes could be responsible for our physiological diversity and environmental adaptation. Moreover, besides traditional comparative static studies on health and disease, longitudinal studies of the human intestinal microbiota should be encouraged, in particular for subjects involved in migration fluxes. These observational studies will allow investigation of the plasticity of the intestinal microbiota in response to environmental changes, and should shed some light on the limits of adaptability and resilience of the human super-organism. A mechanistic comprehension of the impact of the intestinal microbiota on the human physiological phenotype, together with a better understanding of the dynamics that compromise mutualistic partnerships with the human host, will allow adoption of a more rational approach in dealing with the role of the human intestinal microbiota in health and disease. References 1 Turnbaugh, P.J. et al. (2007) The human microbiome project. Nature 449, 804–810 2 Costello, E.K. et al. (2009) Bacterial community variation in human body habitats across space and time. Science 326, 1694–1697 3 Eckburg, P.B. et al. (2005) Diversity of the human intestinal microbial flora. Science 308, 1635–1638 4 Ley, R.E. et al. (2008) Worlds within worlds: evolution of the vertebrate gut microbiota. Nat. Rev. Microbiol. 6, 776–788 5 Gill, S.R. et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359 6 O’Hara, A.M. and Shanahan, F. (2006) The gut flora as a forgotten organ. EMBO Rep. 7, 688–693 7 Neish, A.S. (2009) Microbes in gastrointestinal health and disease. Gastroenterology 136, 65–80 8 Lee, Y.K. and Mazmanian, S.K. (2010) Has the microbiota played a critical role in the evolution of the adaptive immune system? Science 330, 1768–1773 9 Garrett, W.S. et al. (2010) Homeostasis and inflammation in the intestine. Cell 140, 859–870 10 Hooper, L.V. and Macpherson, A.J. (2010) Immune adaptations that maintain homeostasis with the intestinal microbiota. Nat. Rev. Immunol. 10, 159–169 11 Round, J.L. and Mazmanian, S.K. (2009) The gut microbiota shapes intestinal immune responses during health and disease. Nat. Rev. Immunol. 9, 313–323 12 Heijtz, R.D. et al. (2011) Normal gut microbiota modulates brain development and behavior. Proc. Natl. Acad. Sci. U.S.A. 108, 3047–3052 13 Fagundes, C.T. et al. (2012) Adapting to environmental stresses: the role of the microbiota in controlling innate immunity and behavioral responses. Rev. Immunol. 245, 250–264 14 Peterson, D.A. et al. (2008) Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe 3, 417–427 15 Muegge, B.D. et al. (2011) Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970–974
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