Intestinal microbiota is a plastic factor responding to environmental changes

Intestinal microbiota is a plastic factorresponding to environmental changesMarco Candela, Elena Biagi, Simone Maccaferri, Silvia Turroni and Patrizia Brigidi

Department of Pharmaceutical Sciences, University of Bologna, Bologna, Italy

Review

Traditionally regarded as stable through the entire life-span, the intestinal microbiota has now emerged as anextremely plastic entity, capable of being reconfigured inresponse to different environmental factors. In a mutu-alistic context, these microbiome fluctuations allow thehost to rapidly adjust its metabolic and immunologicperformances in response to environmental changes.Several circumstances can disturb this homeostaticequilibrium, inducing the intestinal microbiota to shiftfrom a mutualistic configuration to a disease-associatedprofile. A mechanistic comprehension of the dynamicsinvolved in this process is needed to deal more rationallywith the role of the human intestinal microbiota inhealth and disease.

Intestinal microbiota, a plastic factor of the humansuper-organismHumans are super-organisms, with 90% of their cellsconsisting of microbial cells [1,2]. A majority of thesemicrobial cells live in the gastrointestinal tract (GIT)and constitute the human intestinal microbiota [1,3]. Witha concentration of 1012 CFU/g of intestinal content, thehuman intestinal microbiota probably represents one ofthe most dense, biodiverse, and rapidly evolving bacterialecosystems on Earth [4]. Its collective genome – the intes-tinal microbiome (Box 1) – provides functional traits thathumans have not evolved by their own, and several of ourmetabolic, physiological, and immunological features de-pend on the mutualistic association with our intestinalmicrobial community [5–8]. For example, the intestinalmicrobiota enhances our digestive efficiency by degradingotherwise indigestible polysaccharides and, at the sametime, represents a fundamental barrier against GIT colo-nization by enteropathogens. Moreover, crosstalk betweenthe immune system and the GIT microbial community isessential for the development, education, and functionalityof our immune system [9,10]. Studies carried out withgerm-free (GF) mouse models revealed that ultrastructuraldevelopment of the GIT depends on its dynamic interactionwith the intestinal microbiota [11]. In a landmark studybased on three mouse models – GF, pathogen-free withnormal gut microbiota and adult conventionalized GFoffspring – Heijtz et al. demonstrated that the intestinalmicrobiota can also affect synaptogenesis during the peri-natal 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.

0966-842X/$ – see front matter � 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.101

indicated that the intestinal microbiota tunes the hostresponse to noxious stimuli [13], interfering with the be-havioral response to nociceptive and stressful insults.These recent findings reinforced hypotheses concerningthe role of intestinal microbiota in the gut–brain axis,extending the array of physiological features affected byour intestinal microbial counterpart to the field of neuro-gastroenterology.

The GIT microbiota shows an immense biodiversity atthe species level. 16S rRNA gene sequence surveys ofthe intestinal microbiota across the human populationdetected up to 1000 different bacterial species [1,9]. How-ever, at a higher phylogenetic level, microbial biocomplex-ity in the human GIT decreases, resulting in a particularphylogenetic tree characterized by only a few brancheswith a large degree of radiance at the ends. Of the 100different bacterial divisions that populate our planet, onlysix colonize the human GIT [14]: Bacteroidetes, Firmi-cutes, Actinobacteria, Proteobacteria, Fusobacteria andVerrucomicrobia. These microbial phyla generally showa well-conserved profile in terms of relative abundancein a healthy human GIT: �65% Firmicutes, �25% Bacter-oidetes, �5% Actinobacteria, up to �8% Proteobacteria,and �1% Fusobacteria and Verrucomicrobia [2,15].

Each healthy human subject possesses a specific subsetof hundreds of species out of the thousands that constitutethe human intestinal microbiota [16]. According to Turn-baugh et al., 70% of the phylotypes of individual microbiotaare subject-specific and no phylotype is present at morethan 0.5% abundance in all subjects [17]. As a result of bothnature and nurture, an adult-type intestinal microbiota isstabilized after weaning following an extremely dynamicprocess of colonization that begins at birth (Box 2) [18].

The phylogenetic and functional composition of the indi-vidual microbiota has been traditionally thought of as rela-tively stable throughout adulthood [19,20]. However, therecent adoption of longitudinal approaches in studyingmicrobiota in the human intestinal ecosystem has suggesteda new and more dynamic view of the human intestinalmicrobiota [21,22]. Molecular studies have been specificallydesigned to investigate the intestinal microbiota dynamicsin response to different environmental variables, and havedemonstrated an unexpected degree of plasticity in responseto 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 dynam-ics of the microbiota in 14 people [29]. Their fecal microbiotawas characterized every 2 weeks for 120 days. Some 74.6% ofphylotypes and 36% of the genes identified in the individual

6/j.tim.2012.05.003 Trends in Microbiology, August 2012, Vol. 20, No. 8 385

mailto:[email protected]

http://dx.doi.org/10.1016/j.tim.2012.05.003

Box 1. The human microbiome

The collective genome of the human intestinal microbiota (micro-

biome) 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 re-

vealed 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.

Review Trends in Microbiology August 2012, Vol. 20, No. 8

microbiota complement were variable in a period of 4months, demonstrating the relevant degree of phylogeneticand functional plasticity of the human intestinal microbiota.

On the basis of static comparisons of the intestinalmicrobiota among groups of subjects having a differenthealth status, traditional studies have allowed microbiol-ogists to detect a core microbiome, defined as a constantand shared fraction of the human microbiome, fundamen-tal in supporting the mutualistic symbiotic relationshipwith the host [30]. However, longitudinal studieshighlighted that the intestinal microbiota of each individ-ual is an extremely dynamic entity [21,22,29], raisingquestions about how significant this degree of plasticityis for human health and homeostasis. This review sum-marizes the most recent and significant studies on theintestinal microbiota, highlighting its dynamic nature inrelation to different environmental stressors. In addition,the importance of this plasticity for human health ishighlighted by describing situations in which this dynamichomeostasis is compromised, resulting in disease. Thesereported findings and hypotheses could strengthen thedirection in which research in intestinal microbial ecologyis moving, shifting from a static view to a dynamic, andperhaps pliable, vision of the intestinal ecosystem.

386

Dynamics of the intestinal microbiota in response todiet, environmental microorganisms and geographyThe most remarkable example of plasticity of the gutmicrobiota is provided by its capacity to rapidly respondto dietary changes (Table 1). In fact, an individual’s micro-biota is able to both compositionally and functionallyadapt itself to changes in diet in a 1–3-day period[21,23]. A molecular study of diet-dependent microbiotadynamics in 14 overweight men revealed that the individ-ual microbiota adapts its phylogenetic profile in responseto the main types of ingested fermentable carbohydrates.Interestingly, these fluctuations were influenced by theindividual’s complement of microbial species, showingsubject-specific diet-dependent changes in the microbiotaphylotypes [23]. In a second dynamic study, the intestinalmicrobiota of lean subjects under caloric restriction wasinvestigated for a 4-day period [15]. Subjects enrolled inthe study recorded all components of their diets daily,allowing correlation to the adaptation of their intestinalmicrobiota to macro- and micronutrient consumption. Asignificant association was observed between the phylo-genetic and functional structure of the intestinal micro-biota and fiber and protein intake. In a recent publication,Wu et al. differentiated long- and short-term dietaryresponses of the human intestinal microbiota [24]. Theimpact of a long-term dietary habit on the intestinalmicrobiota was studied in a cohort of 98 healthy volun-teers. Focusing on 78 taxa showing �0.2% abundance in atleast one sample and appearing in more than 10% of thesamples, the authors evaluated the association betweenbacterial taxon abundance and the intake of specific nu-trient classes. This taxon–nutrient correlation analysisrevealed that the human intestinal microbiota is character-ized by bacterial groups showing a reciprocal inverse asso-ciation with nutrients from fat and plant products.Analogous taxon–nutrient inverse correlations were ob-served for proteins versus carbohydrates, and fat versuscarbohydrates. Within the same study, 10 subjects weresequestered in a hospital environment and enrolled in ashort-term controlled feeding study by randomization tohigh-fat and low-fiber or low-fat and high-fiber diets.Changes in their intestinal microbiota were significantwithin the first 24 h of the controlled dietary regime, con-firming the data reported by Walker et al. [23]. Identicalshort-term diets did not overcome the inter-individualvariations, preserving the high degree of inter-individualvariability of the human intestinal microbiota. Interesting-ly, the comparison between long- and short-term dietarychanges revealed that the intestinal microbiota consists ofbacterial groups affected by short-term dietary changes andothers that are exclusively modulated by long-term dietaryhabits, such as those referred to as human enterotypes [31].In the context of these recent findings, a hypothesis regard-ing how the dietary habits of the USA within the past 30years have shaped the human intestinal microbiota hasbeen advanced [21]. According to the authors, the increasein total caloric intake has prompted a general reduction inthe phylogenetic and functional complexity of the humanintestinal microbiota.

Taken together, current research on microbiota plasticityin response to diet leads to a dynamic view in which the

Table 1. Response of the human intestinal microbiota to different dietary interventions

Study design Type of diet or nutrients Microbiota response Refs

Randomized crossover study:

14 overweight subjects,

3-week intervention

Diet high in resistant

starch (type III RS)

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

[23]

Reduced carbohydrate

weight-loss diet (high

protein diet)

No changes at phylum level

#Firmicutes spp. belonging to Roseburia genus, Eubacterium

rectale group and relatives

At phylotype level: #Collinsella aerofaciens,

"Oscillibacter valericigenes

Cross-sectional study (COMBO)

to assess long-term dietary habits:

food frequency questionnaire,

98 healthy subjects

Fats "Bacteroidetes, Actinobacteria

#Firmicutes, Proteobacteria

[24]

Fiber #Bacteroidetes, Actinobacteria

"Firmicutes, Proteobacteria

Animal proteins Positively associated with the Bacteroidetes enterotype

Carbohydrates and

simple sugars

Positively associated with the Prevotella enterotype

Controlled feeding study (CASE)

to assess short-term dietary habits:

randomization to specific diets,

10 healthy subjects, 10 day intervention

High-fat low-fiber versus

low-fat high-fiber

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

Caloric restriction: 18 lean subjects,

4 day dietary record

Proteins Protein intake is significantly associated with KEGG orthology

groups

[15]

Insoluble dietary fibers Insoluble dietary fiber intake is significantly associated with

bacterial operational taxonomic unit (OTU) content


intestinal microbiota continuously changes in response tolong- and short-term dietary habits [32]. Through selectionof microbial populations that optimally degrade the avail-able substrates, these continuous microbiota fluctuationsprovide the host with the capability to readily adapt todietary changes. Supporting this hypothesis, in a milestonepublication, Hehemann et al. reported the first experimentalevidence that the consumption of foods containing environ-mental bacteria is the most likely mechanism that promotescarbohydrate-active enzyme (CAZyme) update in the GITmicrobiome [33]. According to the authors, the microbiomein Japanese people recently acquired the porphyrinase genefrom the seaweed-associated marine bacterium Zobelliagalactanivorans from a lateral gene transfer event favoredby consumption of non-roasted dietary seaweed in Japanesesushi. The presence of CAZyme porphyrinase in their micro-biome complement allows Japanese people to extract energyfrom the red marine algal porphyrin by means of the bacte-rial fermentation of this indigestible polysaccharide toshort-chain fatty acids in the gut. These findings highlightthe key role of the intestinal microbiome as a plastic andadaptable factor that improves the metabolic capacity of thehuman super-organism for more efficient extraction of en-ergy from the diet.

The human intestinal microbiota shows a second degreeof plasticity with regard to its response to constant exposureto environmental bacteria. The continuous interaction be-tween intestinal microbiota and environmental microorgan-isms during the entire course of human life is emerging as astrategic factor for the modulation of our immune functions

[8,11,22,34]. In particular, microbiota fluctuations in re-sponse to key environmental microbes during infancy arefundamental for proper development and education of theimmune system. According to the ‘old friend hypothesis’,exposure to environmental microbes from contaminatedfoods, feces, or livestock, which have been present through-out mammalian evolution, is necessary to prime the physi-ology of our immune system [25,34–36]. Recently, studiescarried out in mice demonstrated a role in programmingmany aspects of effector CD4+T cell and B cell differentiationfor specific intestinal microbial groups, such as segmentedfilamentous bacteria – Clostridium-related symbionts in theintestinal microbiota [37] – and Clostridium leptum andClostridium coccoides [8,37,38]. By orchestrating T cell dif-ferentiation into various pro- and anti-inflammatory sub-sets, such as T helper 2 (TH2), TH17, and regulatory T cells,these microorganisms can fine-tune our immune systemfrom the earliest stages of life [10,11,38].

Interestingly, it has been reported that the humanintestinal microbiota shows a surprising degree of plastici-ty in response to climate change and geography. In alongitudinal study of 15 healthy Finnish subjects for7 weeks, overseas travel was associated with a high de-crease in similarity between samples from the samesubject [28]. Changes in diet and exposure to new environ-mental microbes, as well as a different climate and stress,can account for this travel-related plasticity of the intesti-nal microbiota. The impact of geographic origin on intesti-nal microbiota composition was demonstrated in anextensive comparative analysis of intestinal microbiota

387

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 environ-

mental 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 rela-

tionship. Changes in lifestyle and diet, as well as immunosenes-

cence, 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 self-

sustained 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 clus-tered according to geographic origin. In particular, Amer-icans were characterized by higher abundance ofFirmicutes, Japanese had more Actinobacteria, andKoreans and Chinese showed a Bacteroidetes-rich gutmicrobiota. Analogously, a comparative study between chil-dren from Europe and Burkina Faso showed significantcountry-related differences in the fecal microbial communi-ty [26]. Children from Burkina Faso were enriched in Bac-teroidetes and Actinobacteria, and depleted in Firmicutesand Proteobacteria compared to the European children.According to the authors, these country-related differencesin intestinal microbiota profiles can result from hostgenetics, as well as several environmental variables, such

388

as climate and particular dietary habits and lifestyle of thosein each country.

The recent adoption of longitudinal approaches instudying the human intestinal microbiota highlighted anunexpected degree of phylogenetic and functional plastici-ty of our symbiont microbial counterpart. This dynamicnature is strategic for several important features of humanbiology, such as adaptation to different diets and environ-ments and modulation of the immune system.

Disturbance of the microbiota–host mutualisticrelationshipUnder some circumstances, diet and other environmentalfactors, as well as factors of endogenous origin, such aschronic inflammation [9,39] and aging [40,41] (Box 2), canforce the intestinal microbiota to shift from a mutualisticconfiguration supporting health and homeostasis to adisease-associated profile, usually characterized by alower level of phylogenetic and functional biodiversity(Figure 1). The unbalanced intestinal microbiota observedin obese people [17] and the progressive loss of key intestinalmicrobial groups as a result of a Westernized lifestyle [21]provide two remarkable examples of disturbance of themicrobiota–host mutualism triggered by environmentalstressors.

The recent pandemic of obesity in Westernizedcountries reflects environmental and lifestyle changes,among which dietary factors play a major role [42–45].In this scenario, diet-dependent changes in the microbiotaare perceived as probably being involved in the etiologyand severity of obesity [17,30,46,47]. High-fat dietaryhabits can have a dramatic impact on the intestinal micro-bial community. To explain this phenomenon, Turnbaughet al. suggested an intriguing metaphor by comparing theobese gut microbiota to fertilized runoff, whereby, withrespect to the high diversity of a rainforest, a low-diversitycommunity blooms on application of an abnormal energyinput [17]. According to the authors, compared to leancontrols, the intestinal microbiota of obese people is sig-nificantly less diverse and generally characterized byhigher abundance of Firmicutes and Actinobacteria anda corresponding decrease in Bacteroidetes. However, Dun-can et al. reported conflicting results, failing to detect anyrelationship between the proportion of Bacteroidetes infecal samples and obesity [48]. This lack of consensussuggested that the link between microbiota and obesityis probably more complex than the mere phylum-levelBacteroidetes:Firmicutes ratio. The latter hypothesishas been recently reinforced by a comparative analysisof gene-level and network-level topological differences be-tween lean and obese microbiomes [49]. As a result ofadaptation to a low-diversity environment, the obesemicrobiome is characterized by reduced modularity andthe enrichment of peripheral enzymes with a low cluster-ing coefficient. According to the authors, this variation incommunity-level metabolism may be induced by an in-crease or decrease in relative abundance of a small subsetof species, which changes the way in which the microbiomeinterfaces with the environment and the host.

The functional annotation of the obese microbiomerevealed that the obese-type microbial community

Bio

div

ersi

ty

Disease

Homeostasis

Disease

1 2 3 n

Environmental/endogenous stressors

TRENDS in Microbiology

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.

Obesogenicmicrobiota

Highfermentative

capacity

High-fat dietaryhabits

Pathophysiologyof obesity

Increase in hostenergy harvest

from diet

• Low phylogenetic an d functional di versity

• Enrichment in genes involved in energy metab olism


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.


possesses a lower level of functional diversity and isenriched in genes involved in carbohydrate, lipid andamino acid metabolism, demonstrating an overall increasein fermentative capacity with respect to the lean-typemicrobiome [17]. Furthermore, transplantation of theobesity-associated intestinal microbiota into GF miceresulted in a greater increase in total body fat than coloni-zation with the lean-type intestinal microbiota [50]. Inagreement with the ‘energy harvest hypothesis’ [51], thesedata indicate that the obesity-associated intestinal micro-biota can significantly contribute to disease severity byincreasing energy harvest from the diet. Moreover, it hasbeen shown that high-fat diet-dependent microbiotaalterations negatively affect intestinal permeability, re-ducing expression of the tight junction proteins zona occlu-dens-1 and occludin [52]. The consequent increase incirculating levels of lipopolysaccharide can significantlycontribute to the development of obesity-related inflamma-tory liver diseases, such as non-alcoholic fatty liver disease,non-alcoholic steatohepatitis, and insulin resistance [53].In conclusion, the abnormal dietary habits of obese peopleresult in a severe intestinal microbiota transition from ahealthy profile to an obesogenic one, which supports obe-sity and associated comorbidities (Figure 2) [46,47].

According to the ‘hygiene hypothesis’, a Westernizedlifestyle compromises the mutualistic relationship betweenhumans and their intestinal microbiota. Antibiotic use, san-itization, bathing, clean water and sterile foods, which aretypical of Western societies, favor a profound decrease in themicrobial biodiversity humans are exposed to over theirlifespan [35]. Even if this has provided numerous benefitsin terms of reduced infant mortality and increased lifeexpectancy, it has also come at a cost of a progressive lossof key bacterial groups from the intestinal microbiota, the so-called old friends, which are essential for the developmentand tuning of our immune system [8]. The lack of immuno-logical crosstalk with these old friends – especially duringinfancy – leads to an immune system inclined to inappropri-ate activation, which is characteristic of emerging chronicinflammatory diseases (Figure 3) [34,54]. Confirming this

hypothesis, allergy, autoimmune disorders, inflammatorybowel diseases, and type 2 diabetes, all resulting from chron-ic inflammatory responses, are dramatically increasing indeveloping countries, where Westernized lifestyles are be-coming more and more common [7,21,22,55,56]. Known asthe ‘disappearing microbiota hypothesis’ [25], this theory hasbeen recently strengthened by a comparative study of theintestinal microbiota from children from Europe and ruralAfrica [26]. According to the authors, European childrenwere deprived of microbial groups that may have a role inhost immune education. Furthermore, a recent extensivestudy carried out on a birth cohort of 411 European childrenat highrisk of allergywho were followed for 6 years by clinicalassessments at 6-month intervals demonstrated that bacte-rial diversity in the early intestinal microbiota is inverselyassociated with the risk of allergic sensitization [57].

Environmental stressors, such as high-fat dietary habitsor excessive sanitization, can overcome the resilience of

389

Shrinkage of themicrobiota diversity

Westernized lifestyle

Decreased microbialdiversity in living

environments

Inappropriateactivation of theimmune system

Chronic inflammatorydiseases

Susceptible host


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 intestinalmicrobiota and the host, compromising host health andfavoring the onset and/or severity of diseases.

Concluding remarks and future directionsIn a mutualistic context, the plasticity of the human intes-tinal microbiota guarantees rapid adaptation of the meta-bolic performance of the super-organism in response to dietand, at the same time, represents an essential prerequisitefor education of the immune system to homeostasis. Inher-ited from the mother and shaped by the composition of themother’s milk, the human intestinal microbiota could thusbe regarded as an epigenetic factor that, shaped by theenvironment, confers adaptability and resilience to thehuman super-organism. Several circumstances can disturbthis mutualistic interaction and force a shift of the intestinalmicrobiota from a mutualistic configuration to a disease-associated profile. However, to reveal the dynamics involvedin these processes and to understand to what extent theplasticity of the intestinal microbiota affects human homeo-stasis in a changing environment, a better understanding ofthe microbiota–host bionetwork is needed. The entirespecies-level phylogenetic diversity of the human intestinalmicrobiota is still to be determined. Moreover, we need touncover the real extent of the unassigned fraction of thehuman intestinal microbiome and, most importantly, thefunction of this biological dark matter [58]. This informationwill be important in dealing with the impact of intra- andinter-individual microbiome diversity on particular hostphysiological phenotypes.

Even if deep-sequencing approaches allow depiction ofthe broad phylogenetic biodiversity of the human intestinalmicrobiota [14,59], we are still far from comprehending thecorresponding degree of functional complexity [17,31,60,61].

390

Thus, reaching the target of 900 GIT reference genomes forthe Human Microbiome Project is mandatory. Moreover, weneed to improve our capacity to cultivate anaerobic mem-bers of the human intestinal microbiota and unknown mi-crobial genes need to be identified by functional genomicsapproaches involving massive functional screening of GITmetagenome libraries [62,63]. By sampling humans acrossthe globe with a variety of diets and lifestyles, includingancestral hunter–gatherer lifestyles, we can increase ourknowledge of the biodiversity of the human intestinal micro-biota. These studies will help in exploring the limits of thegenetic variability of the human super-organism, allowingcomprehension about the extent to which our co-evolutionwith intestinal microbes could be responsible for our physi-ological diversity and environmental adaptation. Moreover,besides traditional comparative static studies on health anddisease, longitudinal studies of the human intestinal micro-biota should be encouraged, in particular for subjects in-volved in migration fluxes. These observational studies willallow investigation of the plasticity of the intestinal micro-biota in response to environmental changes, and shouldshed some light on the limits of adaptability and resilienceof the human super-organism. A mechanistic comprehen-sion of the impact of the intestinal microbiota on the humanphysiological phenotype, together with a better understand-ing of the dynamics that compromise mutualistic partner-ships with the human host, will allow adoption of a morerational approach in dealing with the role of the humanintestinal microbiota in health and disease.

References1 Turnbaugh, P.J. et al. (2007) The human microbiome project. Nature

449, 804–8102 Costello, E.K. et al. (2009) Bacterial community variation in human

body habitats across space and time. Science 326, 1694–16973 Eckburg, P.B. et al. (2005) Diversity of the human intestinal microbial

flora. Science 308, 1635–16384 Ley, R.E. et al. (2008) Worlds within worlds: evolution of the vertebrate

gut microbiota. Nat. Rev. Microbiol. 6, 776–7885 Gill, S.R. et al. (2006) Metagenomic analysis of the human distal gut

microbiome. Science 312, 1355–13596 O’Hara, A.M. and Shanahan, F. (2006) The gut flora as a forgotten

organ. EMBO Rep. 7, 688–6937 Neish, A.S. (2009) Microbes in gastrointestinal health and disease.

Gastroenterology 136, 65–808 Lee, Y.K. and Mazmanian, S.K. (2010) Has the microbiota played a

critical role in the evolution of the adaptive immune system? Science330, 1768–1773

9 Garrett, W.S. et al. (2010) Homeostasis and inflammation in theintestine. Cell 140, 859–870

10 Hooper, L.V. and Macpherson, A.J. (2010) Immune adaptations thatmaintain homeostasis with the intestinal microbiota. Nat. Rev.Immunol. 10, 159–169

11 Round, J.L. and Mazmanian, S.K. (2009) The gut microbiota shapesintestinal immune responses during health and disease. Nat. Rev.Immunol. 9, 313–323

12 Heijtz, R.D. et al. (2011) Normal gut microbiota modulates braindevelopment and behavior. Proc. Natl. Acad. Sci. U.S.A. 108, 3047–3052

13 Fagundes, C.T. et al. (2012) Adapting to environmental stresses: therole of the microbiota in controlling innate immunity and behavioralresponses. Rev. Immunol. 245, 250–264

14 Peterson, D.A. et al. (2008) Metagenomic approaches for defining thepathogenesis of inflammatory bowel diseases. Cell Host Microbe 3,417–427

15 Muegge, B.D. et al. (2011) Diet drives convergence in gut microbiomefunctions across mammalian phylogeny and within humans. Science332, 970–974


16 Qin, J. et al. (2010) A human gut microbial gene catalogue establishedby metagenomic sequencing. Nature 464, 59–65

17 Turnbaugh, P.J. et al. (2009) A core gut microbiome in obese and leantwins. Nature 457, 480–484

18 Marchesi, J.R. (2011) Human distal gut microbiome. Environ.Microbiol. 13, 3088–3102

19 Zoetendal, E.G. et al. (1998) Temperature gradient gel electrophoresisanalysis of 16S rRNA from human fecal samples reveals stable andhost-specific communities of active bacteria. Appl. Environ. Microbiol.64, 3854–3859

20 Guarner, F. and Malagelada, J.R. (2003) Gut flora in health anddisease. Lancet 361, 512–519

21 Kau, A.L. et al. (2011) Human nutrition, the gut microbiome and theimmune system. Nature 474, 327–336

22 Maslowski, K.M. and Mackay, C.R. (2011) Diet, gut microbiota andimmune responses. Nat. Immunol. 12, 5–9

23 Walker, A.W. et al. (2011) Dominant and diet-responsive groups ofbacteria within the human colonic microbiota. ISME J. 5, 220–230

24 Wu, G.D. et al. (2011) Linking long-term dietary patterns with gutmicrobial enterotypes. Science 334, 105–108

25 Blaser, M.J. and Falkow, S. (2009) What are the consequences of thedisappearing human microbiota? Nat. Rev. Microbiol. 7, 887–894

26 De Filippo, C. et al. (2010) Impact of diet in shaping gut microbiotarevealed by a comparative study in children from Europe and ruralAfrica. Proc. Natl. Acad. Sci. U.S.A. 107, 14691–14696

27 Nam, Y.D. et al. (2011) Comparative analysis of Korean human gutmicrobiota by barcoded pyrosequencing. PLoS ONE 6, e22109

28 Jalanka-Tuovinen, J. et al. (2011) Intestinal microbiota in healthyadults: temporal analysis reveals individual and common core andrelation to intestinal symptoms. PLoS ONE 6, e23035

29 McNulty, N.P. et al. (2011) The impact of a consortium of fermentedmilk strains on the gut microbiome of gnotobiotic mice and monozygotictwins. Sci. Transl. Med. 3, 106ra106

30 Turnbaugh, P.J. and Gordon, J.I. (2009) The core gut microbiome,energy balance and obesity. J. Physiol. 587, 4153–4158

31 Arumugam, M. et al. (2011) Enterotypes of the human gut microbiome.Nature 473, 174–180

32 Thomas, F. et al. (2011) Environmental and gut Bacteroidetes: the foodconnection. Front. Microbiol. 2, 93

33 Hehemann, J.H. et al. (2010) Transfer of carbohydrate-active enzymesfrom marine bacteria to Japanese gut microbiota. Nature 464, 908–912

34 Ehlers, S. and Kaufmann, S.H. (2010) Infection, inflammation, andchronic diseases: consequences of a modern lifestyle. Trends Immunol.31, 184–190

35 Rook, G.A. and Brunet, L.R. (2005) Microbes, immunoregulation, andthe gut. Gut 54, 317–320

36 Ohnmacht, C. et al. (2011) Intestinal microbiota, evolution of theimmune system and the bad reputation of pro-inflammatoryimmunity. Cell. Microbiol. 13, 653–659

37 Sansonetti, P.J. (2011) To be or not to be a pathogen: that is themucosally relevant question. Mucosal Immunol. 4, 8–14

38 Atarashi, K. et al. (2011) Induction of colonic regulatory T cells byindigenous Clostridium species. Science 331, 337–341

39 Sansonetti, P.J. and Medzhitov, R. (2009) Learning tolerance whilefighting ignorance. Cell 138, 416–420

40 Biagi, E. et al. (2010) Through ageing, and beyond: gut microbiota andinflammatory status in seniors and centenarians. PLoS ONE 5, e10667

41 Claesson, M.J. et al. (2011) Composition, variability, and temporalstability of the intestinal microbiota of the elderly. Proc. Natl. Acad.Sci. U.S.A. 108, 4586–4591

42 Caballero, B. (2007) The global epidemic of obesity: an overview.Epidemiol. Rev. 29, 1–5

43 Bleich, S. et al. (2008) Why is the developed world obese? Annu. Rev.Public Health 29, 273–295

44 Flegal, K.M. et al. (2010) Prevalence and trends in obesity among USadults, 1999-2008. J. Am. Med. Assoc. 303, 235–241

45 Swinburn, B.A. et al. (2011) The global obesity pandemic: shaped byglobal drivers and local environments. Lancet 378, 804–814

46 Diamant, M. et al. (2011) Do nutrient–gut–microbiota interactions playa role in human obesity, insulin resistance and type 2 diabetes? Obes.Rev. 12, 272–281

47 Greiner, T. and Backhed, F. (2011) Effects of the gut microbiota onobesity and glucose homeostasis. Trends Endocrinol. Metab. 22, 117–123

48 Duncan, S.H. et al. (2008) Human colonic microbiota associated withdiet, obesity and weight loss. Int. J. Obes. (Lond.) 32, 1720–1724

49 Greenblum, S. et al. (2012) Metagenomic systems biology of thehuman gut microbiome reveals topological shifts associated withobesity and inflammatory bowel disease. Proc. Natl. Acad. Sci.U.S.A. 109, 594–599

50 Turnbaugh, P.J. et al. (2006) An obesity-associated gut microbiomewith increased capacity for energy harvest. Nature 444, 1027–1031

51 Flint, H.J. (2011) Obesity and the gut microbiota. J. Clin.Gastroenterol. 45, S128–S132

52 Cani, P.D. et al. (2008) Changes in gut microbiota control metabolicendotoxemia-induced inflammation in high-fat diet-induced obesityand diabetes in mice. Diabetes 57, 1470–1481

53 Cani, P.D. et al. (2009) Changes in gut microbiota control inflammationin obese mice through a mechanism involving GLP-2-drivenimprovement of gut permeability. Gut 58, 1091–1103

54 Noverr, M.C. and Huffnagle, G.B. (2004) Does the microbiotaregulate immune responses outside the gut? Trends Microbiol. 12,562–568

55 Rawls, J.F. (2007) Enteric infection and inflammation alter gutmicrobial ecology. Cell Host Microbe 2, 73–74

56 Jia, W. et al. (2008) Gut microbiota: a potential new territory for drugtargeting. Nat. Rev. Drug Discov. 7, 123–129

57 Bisgaard, H. et al. (2011) Reduced diversity of the intestinal microbiotaduring infancy is associated with increased risk of allergic disease atschool age. J. Allergy Clin. Immunol. 128, 646–652

58 Marcy, Y. et al. (2007) Dissecting biological ‘‘dark matter’’ withsingle-cell genetic analysis of rare and uncultivated TM7microbes from the human mouth. Proc. Natl. Acad. Sci. U.S.A.104, 11889–11894

59 Zoetendal, E.G. et al. (2008) High-throughput diversity andfunctionality analysis of the gastrointestinal tract microbiota. Gut57, 1605–1615

60 Human Microbiome Jumpstart Reference Strains Consortium et al.(2010) A catalog of reference genomes from the human microbiome.Science 328, 994–999

61 Turnbaugh, P.J. et al. (2010) Organismal, genetic, and transcriptionalvariation in the deeply sequenced gut microbiomes of identical twins.Proc. Natl. Acad. Sci. U.S.A. 107, 7503–7508

62 Tasse, L. et al. (2010) Functional metagenomics to mine the humangut microbiome for dietary fiber catabolic enzymes. Genome Res. 20,1605–1612

63 Gloux, K. et al. (2011) A metagenomic b-glucuronidase uncovers a coreadaptive function of the human intestinal microbiome. Proc. Natl.Acad. Sci. U.S.A. 108, 4539–4546

64 Gordon, J.I. and Klaenhammer, T.R. (2011) A rendezvous with ourmicrobes. Proc. Natl. Acad. Sci. U.S.A. 108, 4513–4515

65 Palmer, C. et al. (2007) Development of the human infant intestinalmicrobiota. PLoS Biol. 5, 1556–1573

66 Koenig, J.E. et al. (2011) Succession of microbial consortia in thedeveloping infant gut microbiome. Proc. Natl. Acad. Sci. U.S.A. 108,4578–4585

67 Dominguez-Bello, M.G. et al. (2010) Delivery mode shapes theacquisition and structure of the initial microbiota across multiplebody habitats in newborns. Proc. Natl. Acad. Sci. U.S.A. 107,11971–11975

68 Dominguez-Bello, M.G. and Blaser, M.J. (2011) The human microbiotaas a marker for migrations of individuals and populations. Annu. Rev.Anthropol. 40, 451–474

69 Sela, D.A. and Mills, D.A. (2010) Nursing our microbiota: molecularlinkages between bifidobacteria and milk oligosaccharides. TrendsMicrobiol. 18, 298–307

70 Dominguez-Bello, M.G. et al. (2011) Development of the humangastrointestinal microbiota and insights from high-throughputsequencing. Gastroenterology 140, 1713–1719

71 Stewart, J.A. et al. (2005) Investigations into the influence of hostgenetics on the predominant Eubacteria in the faecal microflora ofchildren. J. Med. Microbiol. 54, 1239–1242

72 Benson, A.K. et al. (2010) Individuality in gut microbiota composition isa complex polygenic trait shaped by multiple environmental and hostgenetic factors. Proc. Natl. Acad. Sci. U.S.A. 107, 18933–18938

73 Biagi, E. et al. (2012) Ageing of the human metaorganism: the microbialcounterpart. Age (Dordr.) 34, 247–267

391

Documents

Intestinal microbiota is a plastic factor responding to environmental changes