The gut microbiome in cardio-metabolic health

16 Pages·2015·1.38 MB·English

by  Tue H Hansen

Hansenetal.GenomeMedicine (2015) 7:33
DOI10.1186/s13073-015-0157-z
REVIEW Open Access
The gut microbiome in cardio-metabolic health
Tue H Hansen1, Rikke J Gøbel1, Torben Hansen1,2 and Oluf Pedersen1*
structure and function. The gut microbiota maintains
Abstract
several essential functions, including colonic fermenta-
With the prevalence of cardio-metabolic disorders tion of dietary fibers; extraction of nutrients; synthesis
reaching pandemic proportions, the search for of certain vitamins; prevention against colonization by
modifiable causative factors has intensified. One pathogens; maturation of the intestinal epithelium and
suchpotentialfactoristhevastmicrobialcommunity immune system; release of metabolites to the systemic
inhabiting the human gastrointestinal tract, the tissues; and modulation of gastrointestinal hormone re-
gut microbiota. For the past decade evidence has lease and nerve function [5-8]. It is thus increasingly
accumulated showing the association of distinct recognized that the configuration and activity of the gut
changesingutmicrobiotacompositionandfunction microbiota, influenced by host genotype and additional
with obesity, type 2 diabetes and cardiovascular environmental factors, affect host biology in numerous
disease. Although causality in humans and the ways.
pathophysiological mechanisms involved have yet Recent studies in animal models and humans have
to be decisively established, several studies have found correlations between specific alterations in the
demonstrated that the gut microbiota, as an gut microbiota community structure and the onset of
environmental factor influencing the metabolic diabetes, obesity and CVD. There is evidence for the
state of the host, is readily modifiable through a influence of diet on the gut microbiota in various
variety of interventions. In this review we provide diseases, and several microbial metabolites have been
anoverviewofthedevelopmentofthegutmicrobiome shown to have a significant effect on the metabolic
and its compositional and functional changes in health of the host through pathways that influence
relation to cardio-metabolic disorders, and give an intestinal health, such as mucosal permeability, in-
update on recent progress in how this could be flammation and immune function [9-11]. Lifestyle-
exploited in microbiota-based therapeutics. related shifts in the bacterial composition and func-
tion can break the delicate balance of the microbial
composition and lead to a state of chronic disequilib-
Introduction
rium referred to as dysbiosis, a condition that has
The dramatic increase in the prevalence of obesity
been associated with several pathologies, including
worldwide [1,2] is associated with serious health risks,
obesity and T2D [12-17].
including increased susceptibility to co-morbidities such
In this review, we examine what current technologies
as type 2 diabetes (T2D) and cardiovascular disease
have taught us about the origins and composition of the
(CVD). Both genetic susceptibility and environmental
gut microbiome, and how this is associated with cardio-
factors (such as intrauterine conditions, physical inactiv-
metabolic disease. We consider recent studies that pro-
ity, smoking and unhealthy dietary habits) are involved
vide insights into the role of the human gut microbiota
in the pathogenesis of cardio-metabolic disorders [3,4].
in the metabolic health spectrum, and discuss how this
Recent findings suggest that the environmental compo-
relationship can be exploited and modulated to improve
nent in the developmentof metabolicdysfunction is me-
health.
diated, at least in part, through an altered gut microbial
Gut microbiota composition
*Correspondence:[email protected] Culture-independent methods are now being used to
1TheNovoNordiskFoundationCenterforBasicMetabolicResearch,Section analyze microbial ecosystems, combining high-throughput
ofMetabolicGenetics,FacultyofHealthandMedicalSciences,Universityof
sequencing of nucleic acids (DNA, RNA) with advanced
Copenhagen,Universitetsparken1,KøbenhavnØ2100,Denmark
Fulllistofauthorinformationisavailableattheendofthearticle bioinformatics for taxonomic mapping. Before these
©2015Hansenetal.;licenseeBioMedCentral.ThisisanOpenAccessarticledistributedunderthetermsoftheCreative
CommonsAttributionLicense(http://creativecommons.org/licenses/by/4.0),whichpermitsunrestricteduse,distribution,and
reproductioninanymedium,providedtheoriginalworkisproperlycredited.TheCreativeCommonsPublicDomain
Dedicationwaiver(http://creativecommons.org/publicdomain/zero/1.0/)appliestothedatamadeavailableinthisarticle,
unlessotherwisestated.
Hansenetal.GenomeMedicine (2015) 7:33 Page2of16
approaches, only those microbes that could be cul- As a result of the application of these technologies,
tured were characterized, comprising about 20% of much has been learned about the origins and compos-
the total [18]. Because the majority of intestinal bac- ition of the human microbiome in the past 10 years.
terial species are anaerobic and difficult to cultivate, Although the human gut is not entirely sterile in utero
gene-based studies have now been developed to study [27,28], the extensive colonization of the gastrointestinal
the broad spectrum of both anaerobic and aerobic gut tract begins at birth through the transfer of bacteria
bacteria. These technologies include targeted rRNA gene from the vagina, anus and skin of the mother. In this
markerssuchas16SrRNAgenesequencing,whichfocus way the newborn gut is colonized by facultative anaer-
on microbial composition and diversity, and untargeted obic bacteria, such as Enterobacteriaceae, streptococci
shotgun sequencing, which in addition enables assess- and staphylococci, and these bacterial communities are
ment of the functional capability of the gut microbiota highly variable in the early stage [29]. The specific bac-
(Box1andFigure1)[19]. terial pattern differs in children delivered vaginally or by
Box1:Gutmicrobiotaresearchmethodologies
16SrRNA-basedprofiling
16SrRNAgeneprofilinginvolvestargetedamplificationandsubsequentnext-generationsequencingofphylogeneticallyinformative
markersequencesofmicrobialDNA[20].Thetaxonomiclevelofinformationvariesaccordingtothesubsequentappliedtechnology:
denaturinggradientgelelectrophoresis(DGGE),temperaturegradientgelelectrophoresis(TGGE)andterminalrestrictionfragment
lengthpolymorphism(T-RFLP)givepoortaxonomicinformation,whereasphylogenicmicroarrays(suchasHitChip),454pyrosequencing
andIlluminaMiSeq/HiSeqplatformsprovidequantitativeinformationandextendedtaxonomicidentification[21,22].
From16SrRNAdatathenumberofdifferenttaxapresentinasampleandtheirrelativeabundancecanbeestimatedbycomparisons
withreference-sequencedatabasesorbyusingsoftwarepackagestoclusterhighlysimilarsequencesintoOTUs[21].Thus,targeted16S
rRNAsequencingcandescribethebacterialcommunityintermsofwhichtaxaorOTUsarepresent,theirrelativeabundance,andtheir
phylogeneticrelationships[22].Intheliteratureon16SrRNA-derivedtaxathetermphylotypeisoftenusedinsteadofspecies,asthis
method of taxonomic classification is not based on phenotypic characteristics of the microbe but on phylogenetic analysis of 16S
rRNA sequences. About 3 million aligned and annotated 16S rRNA sequences are currently available as part of the Ribosomal
Database Project [23].
Shotgunsequencing(quantitativemetagenomics)
Incontrasttothetargeted16SrRNAapproach,theuntargetedmetagenomicsapproachinvolvesdirectnext-generationsequencingof
community DNA without amplification of specific regions. By in-depth sequencing the whole genomic content of the gut
microbiota rather than marker genes alone, a less biased and higher-resolution view of the bacterial composition can be
acquired through comparison with bacterial reference genomes and microbial gene catalogs [24] or through de novo assembly
[25]. In addition, information can be gained about additional elements of the microbial community, including fungi and viruses.
The 2014 metagenomic catalog of the human gut microbiome (consisting of 1,267 individual metagenomes compiled from the
Metagenomics of the Human Intestinal Tract (MetaHIT) consortium, Chinese and Human Microbiome Project studies) includes
up to 9.9 million non-redundant genes [26]. In addition to benefits in terms of improved taxonomic description, shotgun
metagenomic sequencing enables a more detailed assessment of the functional potential of the microbial community through
comparison with databases of metabolic pathways (such as the Kyoto Encyclopedia of Genes and Genomes) [21]. The
overwhelming amount of shotgun sequencing-based metagenomics data requires a continued development and improvement
of bioinformatics tools to enhance the analysis and understanding of the complexity of the human gut microbiome. This need
isclearlyillustratedbythefactthatcurrentlyonlyaminorityofthegutmicrobialgenescanbeannotatedtoknowngenomesof
culturedmicrobes.Therefore,advancedbioinformaticsmethodsbasedonco-abundancehavebeendevelopedtoenablegrouping
ofmicrobialgenesinto741largeMetaGenomicUnits(MGUs)representingas-yetunculturedbacterialspecies.Characteristically,
each MGU contains more than 700 microbial genes [25]. An example of a quantitative metagenomics pipeline is given in
Figure 1.
Hansenetal.GenomeMedicine (2015) 7:33 Page3of16
Figure1Exampleofaquantitativemetagenomicspipeline.Ametagenomicspipelineinvolvesaseriesofsequentialandcrucialsteps.Firstly,
samplingoftherelevantbiologicalmaterialandsubsequentextractionofDNAareconductedinastandardizedmannertoensuregood-quality
DNAinhighnanogramormicrogramquantity.Secondly,alibraryispreparedbyfusingDNAfragmentswithadaptermoleculesfollowedbyPCR
amplificationandnext-generationsequencing,whichproducesmillionsofshortreads(about150to800bpdependingonthesequencing
platform)thatarethenassembledintolongercontigs.Finally,microbialgenesareidentifiedandannotatedtoknownfunctionsortaxonomic
unitsbasedonhomologysearchesagainstavailablereferencecatalogs.Forfurtherdetailssee[166].
Cesarean section, with the latter affecting microbiota (about 15%) and Actinobacteria (about 15%), but less
composition inboth infancy [30] and childhood [31] and abundant microbial phyla, such as Verrucomicrobia
being associated with a reduced bacterial diversity [32]. (about 2%), Proteobacteria (about 1%) and Methano-
This offers a potential explanation for the increased risk bacteriales (archaea) (about 1%), are also represented
of atopic disorders [33] and obesity [34] observed in [24,39-41]. Despite the phylum-level similarities, the
children delivered by Cesarean section. In addition, the species-level composition is highly variable between
gut colonization pattern differs between full-term and individuals, caused by environmental influence and
preterm infants [35]. The immature preterm gut along geneticpredisposition[42,43].Contrarytothehighinter-
with prolonged admission at neonatal care units and the individual variation [44,45], with up to 2,187-fold vari-
possible use of broad spectrum antibiotics delay the es- ability of microbial abundance at the species level [24],
tablishment of a beneficial bacterial community and en- the structure of the gut microbiota of an individual re-
ablethegrowth ofpotentially pathogenicbacteria[35]. mainsrelativelystableovertimeintheabsenceofperturb-
Besides mode of delivery and gestational age, neonatal ation [46,47], until advanced age when the microbiota
diet is a determining factor, and Escherichia coli and becomes less diverse and more unstable, probably related
streptococci are the first bacteria to appear in newborn toalterationinimmunecompetencies[48].
breast-fed infants, followed by bifidobacteria, which
quicklybecome predominant.Themicrobiotaofformula- The association of gut microbiota with
fed infants shows even higher variability and diversity, cardio-metabolic disorders
havinglowercountsofbifidobacteriaandhighercountsof The prevalence of cardio-metabolic disorders (obesity,
clostridia and enterococci [29]. Weaning and the transi- T2D and CVD) is increasing globally and has for several
tiontosolidfoodsconfersacompositionalchangetowards years been the number one cause of death worldwide
a more adult-like microbiota dominated by Clostridium [49]. Within the past decade the role of the gut micro-
spp. and Bacteroides spp. [36], with a stable adult-like biota inmetabolic disorders hasbeen extensively investi-
microbiota, often referred to as ‘the core microbiome’ gated (Table 1), and accumulating evidence indicates
[37],beingestablishedatapproximatelythe age of 3years that a state of bacterial dysbiosis contributes to differ-
[38]. Most bacterial species in the adult human gut ences in body weight, insulin sensitivity, glucose metab-
belongtothephylaFirmicutes(about60%),Bacteroidetes olism and other cardio-metabolic risk factors among
Table1Humanmetagenomicstudiesofthegutmicrobiomeandcardio-metabolictraits H
a
n
Study Aim Numberofparticipants Design Method Mainfindings s
e
n
Leyetal.(2006)[41] Toinvestigatetheeffectofeithera 14adults;12obese,2lean Randomizedintervention 16SrRNA (cid:129)IncreasedabundanceofFirmicutesand e
t
carbohydrate-orfat-restricteddiet reducedabundanceofBacteroidetes a
ongutmicrobialecology inobese l.G
e
(cid:129)IncreasedabundanceofBacteroidetes no
m
anddecreasedabundanceofFirmicutes e
following1yearofeitherfat-or M
e
carbohydrate-restrictedlow-caloriediet d
ic
(cid:129)IncreaseinBacteroidetescorrelatedwith ine
bodyweightreductionregardlessofdiet (2
0
Zhangetal.(2009)[161] Toinvestigatemicrobiotacomposition 9adults;3lean,3morbidly Cross-sectional 16SrRNA,qPCR (cid:129)Firmicutesdominantinnormalweight 15
inmorbidobesityandfollowingRYGB obese,3postRYGB andobese,decreasedinpostRYGB ) 7:3
3
(cid:129)Gamma-Proteobacteriaincreasedwhereas
Clostridiadecreasedpost-RYGB
(cid:129)Prevotellaceaehighlyenrichedinobese
(cid:129)Methanobacterialeshighlyabundantin
obese,whilenon-detectableinnormal
weight
Turnbaughetal.(2009)[37] Toinvestigatetheinfluenceofhost 154adults;31MZtwinpairs, Cross-sectional 16SrRNA (cid:129)LowerproportionofBacteroidetesand
genotype,environmentalexposure 23DZtwinpairs,(concordant ahigherproportionofActinobacteria
andhostadiposity forobesityorleanness), inobese
46mothers
(cid:129)Obesityassociatedwithreduceddiversity
(cid:129)Obesemicrobiomeenrichedforgenes
involvedinmacronutrientmetabolism
Larsenetal.(2010)[12] Toinvestigatedifferencesingut 20adults;10T2D,10NGT Cross-sectional 16SrRNA,qPCR (cid:129)DecreaseddiversityinT2D
microbiotacompositionassociated
(cid:129)Firmicutes,includingClostridia,
withT2D
decreasedinT2D
(cid:129) The ratio of the phylogenetic groups
Bacteroides-Prevotella to Clostridium
coccoides-Eubacterium rectale and the
Bacteroidetes to Firmicutes ratio
correlated positively with 2 h
p-glucose during an OGTT
(cid:129)Beta-Proteobacteriahighlyenrichedin
T2Dandcorrelatedwith2hour
p-glucoseduringanOGTT
Jumpertzetal.(2011)[5] Toinvestigatetheeffectofcaloric 21adults;12lean,9obese Randomizedcross-over 16SrRNA (cid:129)High-caloriedietchangestherelative
intakeonmicrobiotacomposition intervention abundanceofmicrobiotaonthephylum
inleanandobese (BacteroidetesversusFirmicutes),class
(BacteroidetesversusClostridia),and P
a
orderlevel(Bacteroidalesversus g
e
Clostridiales) 4
o
f
1
6
Table1Humanmetagenomicstudiesofthegutmicrobiomeandcardio-metabolictraits(Continued) H
a
n
(cid:129)Phylum-,class-,andorder-levelchanges se
n
inmicrobiotacompositionduring e
t
interventionassociatedwithfecalcaloric a
contentinleanbutnotinobese l.G
e
Korenetal.(2011)[59] Toinvestigatethebacterialdiversity 30adults;15CVD,15healthy Cross-sectional 16SrRNA,qPCR (cid:129)Nophylum-orgenuslevelcompositional no
m
ofatheroscleroticplaque,oralcavity differencebetweenCVDpatientsand e
andgutinpatientswithCVD healthycontrols M
e
(cid:129)SeveralsharedOTUsbetween dic
atheroscleroticplaqueandfecalsamples ine
Karlssonetal.(2012)[60] Toinvestigatethemicrobiota 25adults;13CVD,12healthy Cross-sectional Quantitativemetagenomics (cid:129)Colinsellaenrichedinpatients, (20
1
compositioninpatientswithCVD controls EubacteriumandRoseburiaenriched 5
incontrols ) 7
:3
(cid:129)GeneraofClostridiales,Clostridiumand 3
Peptostreptococcusnegativelycorrelated
withhsCRP
(cid:129)Atherosclerosisassociatedwiththe
Ruminococcusenterotype
Qinetal.(2012)[13] Toinvestigatedifferencesingut 368adults;183T2Dcases, Cross-sectional Quantitativemetagenomics (cid:129)T2Dassociatedwithmoderate
microbiotacompositionandfunction 185healthycontrols dysbiosiswithadeclinein
associatedwithT2D butyrate-producingbacteria
(cid:129)Gut-microbiome-basedT2Dindex
accuratelyclassifiesT2Dindividuals
LeChatelieretal.(2013)[55] Toinvestigatethebacterialabundance 292adults;123lean,169obese Cross-sectional/ Quantitativemetagenomics (cid:129)Lowbacterialrichnessassociateswith
inleanandobese retrospective and16SrRNA increasedoveralladiposity,insulin
resistance,dyslipidemia,andamore
pronouncedinflammatoryphenotype
(cid:129)Discriminationbetweenhighversus
lowgenecountandobesitystatus
possiblefromacombinationofonly
fourspecieswithROCanalysisAUC
of0.97
(cid:129)Increasedweightgaininindividuals
withlowmicrobialgenecount
Karlssonetal.(2013)[16] Toinvestigatedifferencesingut 145adults;53T2D,49IGT, Cross-sectional Quantitativemetagenomics (cid:129)IncreasedabundanceofLactobacillus
microbiotacompositionandfunction 43NGT spp.andabundanceofClostridium
associatedwithT2D spp.decreased
(cid:129)Clostridiumspp.correlatedwithfasting
glucoseandHbA1c,whereasLactobacillus
spp.correlatednegativelywithfasting
glucose,insulin,C-peptideandTAG,and
positivelywithadiponectinandHDL
P
a
g
e
5
o
f
1
6
Table1Humanmetagenomicstudiesofthegutmicrobiomeandcardio-metabolictraits(Continued) H
a
n
(cid:129)Microbiotacompositionasdetermined se
n
bymetagenomicclustersbettercorrelated e
t
withT2Dthanknownclinicalriskfactors a
(WC,WHRandBMI) l.G
e
Zhangetal.(2013)[17] Toinvestigatedifferencesingut 121adults;44NGT,64IGT, Cross-sectional 16SrRNA (cid:129)HigherabundanceofClostridiainT2D no
m
microbiotacompositionassociated 13T2D (cid:129)Negativetrendofabundanceof e
withT2D M
StreptococcusfromNGTtoIGTtoT2D e
d
(cid:129)Enterotypeclassificationnotassociated icin
e
withglucosetolerancestatus (2
(cid:129)28OTUsassociatedwithglucose 01
5
tolerancestatus ) 7
(cid:129)Fastingglucoseassociatedwith :33

microbiotacomposition
(cid:129)Fastinginsulininverselyassociated
withalpha(intraindividual)diversity
Kongetal.(2013)[160] ToinvestigatetheimpactofRYGB 30adults;7T2D,23non-T2D Non-randomized 16SrRNA (cid:129)Increasedbacterialrichnessfollowing
onmicrobiotacomposition obese intervention RYGB,mainlywithinthephylum
Proteobacteria
(cid:129)RYGBinducedgenus-levelchangesin
microbiotacompositioncorrelatedwith
changesinwhiteadiposetissuegene
expression
Graessleretal.(2013)[14] ToinvestigatetheimpactofRYGBon 6adults;5T2D,1non-T2D Non-randomized Quantitativemetagenomics (cid:129)Relativeabundanceof22speciesan
microbiotacompositionandfunction obese intervention 11generaaffected3monthsafterRYGB
(cid:129)Overall,RYGBinducedphylum-level
changescharacterizedbyreductionin
BacteroidetesandFirmicutesandan
increaseinProteobacteriaand
Verrucomicrobia
(cid:129)Species-levelchangesdominatedby
anincreaseinA.muciniphila,E.coliand
K.pneumoniaandadecreasein
F.prausnitzii,E.rectaleandD.invisus.
Abbreviations:AUCareaunderthecurve,BMIbodymassindex,CVDcardiovasculardisease,DZdizygotic,HDLhigh-densitylipoprotein,hsCRPhigh-sensitivityC-reactiveprotein,IGTimpairedglucosetolerance,MZmonozygotic,
NGTnormalglucosetolerance,OGTToralglucosetolerancetest,OTUoperationaltaxonomicunit,qPCRquantitativePCR,ROCreceiveroperatingcharacteristic,RYGBRoux-en-Ygastricbypass,TAGtriacylglyceride,T2Dtype2
diabetes,WCwaistcircumference,WHRwaist-hipratio.
P
a
g
e
6
o
f
1
6
Hansenetal.GenomeMedicine (2015) 7:33 Page7of16
individuals [50], strengthening the gut microbiota as a T2Dpatientsandhealthycontrolswasobserved.Astudy
potential risk factor in the pathogenesis of obesity and of145Swedishwomenwithnormal,impairedordiabetic
its co-morbidities. Here, we look at the main cardio- glucose regulation found comparable, but not identical,
metabolic traits and their associations with gut micro- compositional changes associated with T2D, suggesting
biota composition. ethnic or regional influences [16]. In both the Swedish
and the Chinese study, it was possible to discriminate
Obesity with high accuracy between T2D patients and non-
Evidence from several studies in humans and rodents diabetic controls with few metagenomic markers [13,16].
points to the gut microbiota as a contributing factor in Despite minor discrepancies between individual studies,
obesity development. Studies of the gut microbiota in evidence is mounting that T2D is associated with both
mice genetically predisposed to obesity (ob/ob) have functional and compositional changes of the gut micro-
shown a decreased Bacteroidetes-to-Firmicutes ratio biota. However, it remains to be firmly established
[39], which is associated with an increased capacity for whetherthesechangesarecausalorsecondarytophysio-
energy harvest from otherwise indigestible dietary logicalchangesorperhapspharmacologicallyinduced.
polysaccharides [51]. Studies of germ-free mice have
demonstrated that they are leaner and more resistant to Atherosclerosisandcardiovasculardisease
diet-induced obesity when introduced to a high-fat Thus far, evidence directly linking specific changes in
western-style diet than their conventional counterparts the human gut microbiota with CVD has been limited
[52,53]. After colonizing germ-free mice with microbiota to a few smaller cross-sectional studies. Although failing
from normalmice,the amount of body fatincreased and to show any overall structural difference between cases
the insulin sensitivity decreased [52]. Similarly, when and controls on either the phylum or the genus level, a
colonizing germ-free mice with fecal microbiota from study of 15 patients with clinical atherosclerosis and an
human twin pairs discordant for obesity, mice receiving equal number of healthy controls matched for sex and
microbiota from the obese twin showed more weight age showed several shared operational taxonomic units
gain and adiposity than those receiving microbiota from (OTUs) between atherosclerotic plaques and fecal sam-
the lean sibling, hinting at a causal effect for the trans- ples, suggesting that plaque microbiota may at least
planted microbial community [54]. Although inconsist- partially be of intestinal origin [59]. Further analyses
ent findings at the phylum level have been reported in using whole-genome sequencing showed that the genus
human obesity, reduced bacterial diversity has been as- Collinsella was enriched in fecal samples from patients
sociated with adiposity [37]. In the Metagenomics of the with atherosclerosis, whereas Roseburia and Eubacterium
Human Intestinal Tract (MetaHIT) study including 292 were enriched in healthy controls [60]. In the same study,
non-diabetic Danish individuals, 23% of the studied Clostridiales genera Clostridium and Peptostreptococcus
population sample had lowmicrobialgene richness,with were negatively correlated with high-sensitivity C-reactive
the bacterial gene count reduced by 40% [55]. Interest- protein, an inflammatory marker strongly associated with
ingly, individuals with low richness were characterized increasedriskofCVD[61].
by low-grade inflammation, insulin resistance, dyslipid-
emia and overall adiposity,whichpotentiallyput themat Mechanisms of microbiota-host interactions
an increased risk of progression to obesity-related co- Although convincing evidence suggests that a dysbiotic
morbidities. state of the gut microbiota composition is associated
with metabolic disease, we are still far from fully under-
Type2diabetes standing the complexities of the multiple underlying
It has been reported that patients with T2D have a dif- mechanisms, as outlined below and summarized in
ferent taxonomic composition and functional potential Figure2.
of their gut microbiome from that of non-diabetic indi- Studies of mice provide early evidence that the gut
viduals [12-17]. One recent 16S rRNA-based study ob- microbiota has an essential role in energy harvest, in
served a positive correlation between fecal bifidobacteria that germ-free mice need to consume approximately
and plasma insulin and insulin resistance [56], in dis- 30% more calories to sustain a body weight similar to
agreement with the previously detected inverse rela- conventionally raised mice [52]. An essential mechanism
tionship found in mice [57] and humans [58]. A by which the gut microbiota enhances energy harvest is
metagenomics-based study including 344 Chinese in- throughthe hydrolysis and fermentation of otherwise in-
dividuals identified a moderate degree of gut bacterial digestible dietary polysaccharides. Microbial fermenta-
dysbiosis, with a decline in butyrate-producing bacteria tion generates monosaccharides and short chain fatty
andanincreaseinopportunisticbacteriaamongT2Dpa- acids (SCFAs), which can be absorbed and used as
tients [13]. However, no difference in diversity between energy by the host [62]. Of the three main SCFAs,
Hansenetal.GenomeMedicine (2015) 7:33 Page8of16
Figure2Gutmicrobiota-hostinteractions.Theshort-chainfattyacids(SCFA)propionate,acetateandbutyrateproducedbybacterialfermentation
ofindigestiblepolysaccharidestriggerthereleaseofthesatietogenicguthormonesGLP-1andPYYfromenteroendocrineL-cells;thesehormonesin
turnregulateingestivebehaviorbyactingonthehypothalamus.Releaseofgastricinhibitorypolypeptide(GIP)fromenteroendocrineK-cellstriggered
bybutyrateisapotentpromoterofglucose-dependentinsulinsecretion,actinginconcertwithGLP-1.Throughdirecttrophiceffectsontheintestinal
epitheliumandbytriggeringthereleaseofGLP-2fromL-cells,butyratemakestheepithelialbarrierlesspermeablethroughincreasedmucus
productionandtightjunctionexpression.L-carnitineandphosphatidylcholine,bothconstituentsofredmeat,aremetabolizedbyintestinal
bacteria, releasing trimethylamine (TMA). Following absorption to the portal circulation, TMA is converted by hepatic flavin-containing
monooxygenase to the atherogenic trimethylamine-N-oxide (TMAO). The gut microbiota is heavily involved in bile acid metabolism by
performingdeconjugationanddehydroxylation.CholicacidlowershepaticlipogenesisbyactingonthefarnesoidXreceptorandincreases
theenergyexpenditurethroughfatoxidationbyinducingtheenzymaticconversionofinactivethyroxinetotheactivetri-iodothyroninein
brownadiposetissue(BAT)andskeletalmuscle.Abbreviations:CNS,centralnervoussystem.
propionate, acetate and butyrate, the latter in particular ingestive behavior of the host. Similarly, by stimulating
has attracted attention as a potential mediator of the the release of gastric inhibitory polypeptide (GIP) from
metabolic effects of dysbiosis (reviewed by Brahe et al. enteroendocrine K-cells it potentially increases host in-
[63]),withseveralstudiesinhumansdemonstratingare- sulin sensitivity in concert with GLP-1 [67]. Butyrate
duced proportion of butyrate-producing Clostridiales in also strengthens the integrity of the intestinal epithelial
T2D and CVD [13,16,60]. Butyrate acts by diverse mo- barrier through effects on mucus production [68] and
lecular mechanisms to regulate energy intake, expend- tight junction expression [69], as well as conferring
iture and storage [64,65]. It stimulates the release of the trophic effects on the epithelial cells, possibly mediated
satietogenic hormones glucagon-like peptide 1 (GLP-1) byan incretinhormone, glucagon-likepeptide 2(GLP-2)
and peptide YY (PYY) from enteroendocrine L-cells, at [70]. The overall effect of this is a reduced passage of
leastinpartbyacting asanagonist forthefree fattyacid toxic and pro-inflammatory substances across the epi-
receptors 2 and 3 (FFAR2/3) [66], thus regulating the thelial barrier. Interestingly, the presence of bacteria and
Hansenetal.GenomeMedicine (2015) 7:33 Page9of16
bacterial residues such as lipopolysaccharide in host blood is scarce, at the functional level metabolism of specific
and other tissues is linked to low grade inflammation, dietary components by the gut microbiota, particularly
obesity and T2D [71-74], emphasizing the importance of trimethylamine-containing compounds such as phosphat-
a sustained intestinal barrier in relation to metabolic idylcholine(PC)andcarnitine,hasbeenlinkedtodevelop-
disorders. ment of CVD. PC- and carnitine-rich foods include red
Another way that the gut microbiota influences the meats, fish, poultry, dairy products and eggs [88,89]. Fol-
metabolic state of the host is through an extensive in- lowing ingestion both compounds are metabolized by the
volvement in bile acid homeostasis [75]. Direct evidence gutmicrobiotatotrimethylamine(inthecaseofcarnitine,
from rodent studies shows that treatment with broad- with γ-butyrobetaine as an intermediary metabolite),
spectrum antibiotics (for example, ampicillin) increases whichthenentersthecirculationandisconvertedbyhep-
bile acid reabsorption through increased expression of atic flavin-containing monooxygenase to trimethylamine-
the transporter SLC10A2 [76], while simultaneously in- N-oxide (TMAO) [90,91]. Studies have shown that
creasing hepatic bile acid synthesis by suppressing the TMAO was undetectable in germ-free mice following a
expression of fibroblast growth factor 15 [77]. These carnitine or choline challenge, but following colonization
findings provide clues to the molecular mechanisms of the animals with microbiota from conventional mice,
underlying the decades-old findings that germ-free ani- theygainedtheabilitytoproduceTMAO[92,93].Further-
mals have substantially higher bile acid concentration in more, antibiotic treatment in conventional mice reduced
bile[78]alongwithdecreasedbileacidexcretioninfeces TMAO production after a choline or carnitine challenge
[79].Amorerecent studygivesfurtherweighttotheim- [92,93], with similar effects reported in humans [93,94].
portance of the gut microbiota in bile acid homeostasis; Micegeneticallydeficientinphosphatidylethanolamine-N-
this [80] showed that the mouse gut microbiota regu- methyltransferase, an enzyme involved in hepatic PC
lates expression of cholesterol 7-alpha hydroxylase, the synthesis, are protected from developing atherosclerosis
rate-limiting enzyme in bile acid synthesis, through [95], whereas dietary supplementation with either carni-
deconjugationoftauro-conjugatedmuricholicacid,apo- tine, γ-butyrobetaine, cholineorTMAOincreasesathero-
tentantagonistofthefarnesoidXreceptor(FXR).Acting sclerotic plaque formation in mice genetically susceptible
on the same receptor, cholic acid reduces circulating tri- to atherosclerosis [91-93]. In addition, diet-induced
glyceride levels by decreasing the hepatic expression of TMAO production and atherosclerosis susceptibility
the SREBP-1c transcription factor controlling genes in- is transmissible through microbiota transplantation
volved in lipogenesis [81]. Interestingly, FXR deficiency [96]. It is thus well established that the gut microbiota is
has been reported to improve glucose homeostasis in intrinsically involved in TMAO production and that
obese mice [82]. In another study in mice, supplementa- TMAO,ratherthanitsprecursorscholineandcarnitine,is
tion withcholic acidprotected against andeven reversed thepro-atherogeniccompound.
diet-induced obesity; the effect was mediated by in- Although the way in which TMAO promotes the for-
creased expression of the type 2 iodothyronine deiodi- mation of atherosclerotic plaques is not entirely clear,
nase (D2) enzyme and thus increased conversion of several contributing mechanisms have been identified.
inactive thyroxine (T4) to the active tri-iodothyronine TMAO has been show to inhibit reverse cholesterol
(T3) in brown adipose tissue, effectively raising energy transport by reducing the expression of the hepatic en-
expenditure through fat oxidation [83]. Similar effects, zymes Cyp7a1 and Cyp27a1, as well as multiple bile acid
regulated by the cAMP-protein kinase A pathway by ac- transporters, while simultaneously inhibiting the expres-
tivation of the G-protein-coupled receptor TGR5, were sion of intestinal bile acid transporters Npc1L1 and
demonstrated in human skeletal muscle in vitro [83]. Abcg5/8, thus reducing bile acid synthesis and excretion
Stimulation of theTGR5 signaling pathway by bile acids by the liver and bile acid uptake in the intestine [93]. In
has also been demonstrated to induce GLP-1 release macrophages TMAO increases the efflux of cholesterol
from enteroendocrine L-cells and consequently improve through increased expression of the cholesterol trans-
glycemic regulation in obese mice [84]. These discover- porters Abca1 and Abcg1 while simultaneously in-
ies have spurred an interest in bile acids as potential creasing expression of the proatherogenic scavenger
therapeutic targets in metabolic disorders. Interestingly, receptors, CD36 and scavenger receptor A [92,93]. In
colestimide, a bile acid sequestrant, decreases body recent years several human clinical studies have dem-
weight andimprovesglucosetolerance andinsulinsensi- onstrated a clear association between trimethylamine-
tivity in diet-induced obese mice [85], and it improves containing compounds and CVD risk (Table S1 in
glycemic regulation and reduces central adiposity in Additional file 1). Plasma choline level is a strong pre-
T2Dhumansandmice[86,87]. dictor of major cardiac events in patients with suspected
Although the evidence for an association between acute coronary syndrome [97], as well as in individuals
gut microbiota and CVD at the compositional level with stable coronary artery disease; interestingly, in the
Hansenetal.GenomeMedicine (2015) 7:33 Page10of16
latter disease it is a predictor only when there are capacity ofthe gutmicrobiota tobealteredbylong-term
concomitant increased TMAO levels [98]. Similarly, car- dietary patterns [91,93], indicating that the potential
nitine is an independent predictor of prevalent CVD and benefits of dietary intervention on host metabolism
incident major cardiac events, but only with concurrent might verywell besignificant.
high TMAO levels [93]. TMAO in itself is also an
independent predictor of incident death, myocardial in- Prebiotics
farction and stroke, as well as prevalent CVD even in The term prebiotics refers to dietary components
individuals at low risk of cardiovascular events [94]. (mainly non-digestible oligosaccharides) that selectively
Interestingly, elevated TMAO levels have also been re- stimulate the growth or activity of a limited number of
ported in patients withT2D [99], chronic kidney disease microbial genera or species [111]. Studies have consist-
[100]andheartfailure[99,101],disordersthatareknown ently shown that the gut microbiota can be modulated
tobeassociatedwithanincreasedriskofCVD. by administration of inulin-type fructans and galactans,
with a preferential effect on Bifidobacteria and to some
Modulation of the gut microbiota for prevention extent Lactobacillus spp. (reviewed by Meyer and
and therapy Stasse-Wolthuis [112]). In a series of studies in rodents
With the establishment of the gut microbiota as an en- and humans, prebiotics acting through changes in
vironmental factor contributing to the development of microbiota composition have been shown to reduce en-
cardio-metabolic disorders, interest in modulating the ergyintakeandbodyweight[113,114],concomitantlyre-
microbiota composition and function as a therapeutic ducing insulin resistance and hyperglycemia [115-117].
strategy is increasing. Theoretically, mechanisms through These effects appear to be mediated by increased release
whichmodulationofthegutmicrobiotamightbeachieved of the anorexigenic gut hormones GLP-1, GLP-2 and
include lifestyle changes, such as dietary intervention or PYY [70,113,114,116,118], by reduced release of the
exercise,surgeryortheuseofpharmaceuticals,orthrough orexigenic peptide ghrelin [114,118-120], and by redu-
transplantationfromhealthydonors. cing endotoxemia by way of improved mucosal barrier
function, thus reducing levels of inflammatory markers
Diet [57,117,121-123]. Directly affecting the production of
Variation in diet composition is a major contributing SCFAs (butyrate) is another potential mechanism by
factor in determining microbiota diversity. Studies com- which prebiotics might beneficially influence host physi-
paring the diversity and phylogenetic composition of gut ology [124-126].
microbiota from individuals consuming a western-type
diet (rich in fat and animal protein) and indigenous Probiotics
people from Africa and South America (living on a diet Probiotics are live microorganisms that, when ingested
dominated by plant-based polysaccharides) have demon- in sufficient amounts, exert beneficial health effects on
strated that the former is associated with an increase in the host. The majority of known bacterial probiotics be-
the abundance of Bacteroides spp., whereas the latter is long to the Gram-positive genera of Lactobacillus and
associated with increased Prevotella spp. and overall di- Bifidobacterium, with the Nissle 1917 strain of E. coli
versity[38,102].Atthephylumlevel,studiesoftheeffect being the only extensively investigated Gram-negative
of high-fat diet in murine models have shown a decrease probiotic. The therapeutic effects of probiotics in meta-
in the ratio of Bacteroidetes to Firmicutes [103-106], al- bolic disorders have been heavily investigated for the
though human studies have not been equally consistent past decade, with promising results, although mainly in
[11,41,107]. It is clear, however, that composition and murinemodels.Severalstudiesinsuchmodelsofobesity
functional capabilities of the human gut microbiota rap- and diabetes have demonstrated an improved metabolic
idly adapt to changes in macronutrient content of the profile (including but not limited to reduced levels of
diet [9-11], mirroring studies in mice that have demon- glucose, insulin, HbA1c, LDL-cholesterol, triglyceride
strated that dietary changes result in an adaptation of and leptin) following administration of different strains
the gut microbiota within a few days [104,105,108]. Still, of lactobacilli and bifidobacteria [127-137]. Although
compositional changes following dietary intervention are human trials have been less consistent (Table S2 in
subtle and readily reversible [109,110], and although Additional file 1), the majority of studies show a benefi-
there are indications that a permanent change in diet cial metabolic effect of probiotics, with only a few
could lead to persistent effects on the structure of the smaller studies failing to show an improvement in
gut microbiota [48],the long-term effect ofdietary inter- cardio-metabolic variables.
vention in humans needs to be investigated further. Increasing knowledge about microbiota-host interac-
However, recent studies in humans and rodents have tions of specific bacterial species and their metabolites
demonstrated a remarkable ability of the metabolic has sparked an interest in so-called next-generation