Metagenomic systems biology of the human gut
microbiome reveals topological shifts associated with
obesity and inflammatory bowel disease
Sharon Greenbluma, Peter J. Turnbaughb, and Elhanan Borensteina,c,d,1
Departments ofaGenome Sciences andcComputer Science and Engineering, University of Washington, Seattle, WA 98195;bFAS Center for Systems Biology,
Harvard University, Cambridge, MA 02138; anddSanta Fe Institute, Santa Fe, NM 87501
Edited* by Jeffrey I. Gordon, Washington University School of Medicine in St. Louis, St. Louis, MO, and approved November 15, 2011 (received for review
October 3, 2011)
The human microbiome plays a key role in a wide range of host-
related processes and has a profound effect on human health.
Comparative analyses of the human microbiome have revealed
substantial variation in species and gene composition associated
with a variety of disease states but may fall short of providing
a comprehensive understanding of the impact of this variation on
the community and on the host. Here, we introduce a metage-
nomic systems biology computational framework, integrating
metagenomic data with an in silico systems-level analysis of met-
abolic networks. Focusing on the gut microbiome, we analyze fe-
cal metagenomic data from 124 unrelated individuals, as well as
six monozygotic twin pairs and their mothers, and generate com-
munity-level metabolic networks of the microbiome. Placing var-
iations in gene abundance in the context of these networks, we
identify both gene-level and network-level topological differences
associated with obesity and inflammatory bowel disease (IBD). We
show that genes associated with either of these host states tend
to be located at the periphery of the metabolic network and are
enriched for topologically derived metabolic “inputs.” These find-
ings may indicate that lean and obese microbiomes differ primarily
in their interface with the host and in the way they interact with
host metabolism. We further demonstrate that obese microbiomes
are less modular, a hallmark of adaptation to low-diversity envi-
ronments. We additionally link these topological variations to
community species composition. The system-level approach pre-
sented here lays the foundation for a unique framework for study-
ing the human microbiome, its organization, and its impact on
populate numerous sites in the human anatomy and harbor
over 100 trillion microbial cells (1). This complex ensemble of
microorganisms, collectively known as the human microbiome,
plays an essential role in our development, immunity, and nutri-
tion, and has a tremendous impact on our health (2). Among the
various body habitats, the most densely colonized is the distal gut.
The normal gut flora alone consists of hundreds of bacterial spe-
cies, collectively encoding an enormous gene set that is 150-fold
larger than the set of human genes (3). The gut microbiome plays
a key role in many essential processes, including vitamin and
amino acid biosynthesis, dietary energy harvest, and immune de-
velopment (4). Transferring a donor microbiota into a recipient
can induce various donor phenotypes [including increased adi-
sick recipient (7), suggesting a promising avenue for clinical ap-
plication via directed manipulation of the microbiome. Charac-
the potential to provide deep insight into both normal human
physiology and human disease, and calls for a predictive systems-
level understanding of community function and structure.
Addressing this challenge, worldwide research initiatives (3, 4)
have recently started to map the human microbiome, providing
insight into previously uncharted species and genes. Specifically,
e humans are mostly microbes. Microbial communities
sequencing 16S ribosomal RNA allows researchers to determine
the relative abundance of different taxonomic groups in a micro-
biome (8, 9). Such surveys have revealed, for example, marked
associations between the species composition of the gut micro-
biome and a variety of host phenotypes (10–12). Species profiles,
however, cannot be easily translated into function, because it is
not clear how variation in the composition of species in the
microbiome affects the metabolic activity of the community and,
consequently, the host. In contrast, metagenomic shotgun se-
quencing of community DNA and a gene-centric comparative
approach (8, 13, 14) may capture functional differences in the
metabolic potential of the community. Yet, comparative meta-
genomic analysis of the gut microbiome frequently reveals high
functional uniformity across samples and often identifies only a
small set of genes or pathways that appear to be associated with
certain host states (10, 15). Furthermore, such enriched sets offer
preliminary insights into relevant functional differences but may
not provide a comprehensive systems-level understanding of the
variation and its potential effect on the host–microbiome supra-
organism (16, 17).
microbiome, integrating metagenomic data with a systems-level
network analysis. This metagenomic systems biology approach
goes beyond traditional comparative analysis, placing shotgun
metagenomic data in the context of community-level metabolic
these networks with their abundances in different metagenomic
samples and examining systems-level topological features of
microbiomes associated with different host states allow us to
obtain insight into variation in metabolic capacity. This approach
not only the set of genes present in a microbiome but also the
complex web of interactions among these genes and by treating
the microbiome as a single “independent” biological system (18).
Computational systems biology methods and complex network
analyses have been applied widely to study microorganisms, and
a variety of approaches have been developed to create genome-
scale metabolic networks of various microbial species (19–21). In
thisstudy,wefocusonsimpleconnectivity-centered networks that
are computationally derived from homology-based large-scale
metabolic databases (22) coupled with a topological analysis.
These networks form a simplification of the actual underlying
metabolic pathways and may be relatively inaccurate and noisy.
However, topology-based analysis of such networks has proved
powerful for studyingthecharacteristics ofsingle-species metabolic
networks and their impact on various functional and evolutionary
properties, including scaling (23), metabolic functionality and
Author contributions: S.G. and E.B. designed research; S.G. performed research; S.G., P.J.T.,
and E.B. analyzed data; and S.G., P.J.T., and E.B. wrote the paper.
The authors declare no conflict of interest.
*This Direct Submission article had a prearranged editor.
1To whom correspondence should be addressed. E-mail: email@example.com.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.
| January 10, 2012
| vol. 109
| no. 2 www.pnas.org/cgi/doi/10.1073/pnas.1116053109
regulation (24, 25), modularity (26, 27), essentiality and mutant
viability (28), genetic and environmental robustness (29), adapta-
tion (30, 31), and species interaction (32). To date, however, to-
pological analysis has not been used to examine community-level
metabolic networks and to study metagenome-scale metabolism.
Datasets. Illumina-derived shotgun metagenomic data from 124
unrelated Danish and Spanish individuals were analyzed (3). Of
the 124 individuals, 82 were labeled as lean/overweight [body
mass index (BMI) < 30] and 42 were labeled as obese (BMI ≥
30). Additionally, 25 were diagnosed with inflammatory bowel
disease (IBD) relative to 99 healthy individuals (SI Appendix,
Table S1). Patients who had IBD were all of Spanish descent,
and Spanish individuals were mostly labeled as lean. An addi-
tional dataset, comprising 454 FLX-derived data from six obese
and lean monozygotic twin pairs and their mothers (10), was
analyzed as well. When applicable, we applied our analysis to this
second independent dataset to confirm the validity of our results
(SI Appendix). A detailed description of each dataset is provided
in Materials and Methods.
Obtaining Community-Level Metabolic Networks. To construct a
community-level metabolic network of the gut microbiome,
metagenomic sequence reads were annotated using the Kyoto
Encyclopedia of Genes and Genomes (KEGG) database to
identify enzymatic genes (Materials and Methods). In total, 1,610
enzymes were identified and annotated with a metabolic reaction.
Overall, relative enzyme abundance across the 124 samples was
highly concordant (average pair-wise correlation coefficient: R =
0.94, Spearman correlation test), in accordance with previous
studies revealing intersample similarity in gene content (10). The
annotation data from all samples were pooled, and a network was
created in which nodes represented enzymes and enzymes cata-
lyzing successive reactions were connected by directed edges. We
excluded enzymes that were not part of the largest connected
component of the network, resulting in a total of 1,570 enzymes
(Materials and Methods).
Identifying Enzymes Associated with a Given Host State. We com-
identify enzymes associated with a given host state (e.g., obesity,
fold change in the abundance of an enzyme in samples taken from
hosts with the given state compared with its abundance in other
healthy samples (Materials and Methods; further details on the
metric choice are provided in SI Appendix). The differential
abundance score of each enzyme, defined as abs[log2(OR)],
provides a measure of the extent to which an enzyme’s abundance
differs in samples from a given host state, relative to healthy
samples.Enzymeswithadifferential abundancescorehigher than
1 (i.e., enzymes that are either 2-fold enriched or 2-fold depleted)
are defined as being associated with the given host state.
To verify that the results reported below are not dependent on
the specific choice of enrichment metric used, we further ex-
amined several alternative methods for identifying host state-
associated enzymes (including significance analysis, presence/
absence overrepresentation test, rank-based difference test, and
distribution divergence analysis; more details are provided in SI
Appendix). These enrichment metrics yielded qualitatively simi-
lar results (SI Appendix and SI Appendix, Table S3). Similarly, to
confirm that our findings do not stem from potential noise in the
read count data, we used a shuffling analysis to identify enzymes
that are “consistently” enriched or depleted across samples (SI
Appendix). Using this more stringent criterion for enzymes as-
sociated with a given host state did not qualitatively change the
results below (SI Appendix and SI Appendix, Table S3).
An overrepresentation analysis (SI Appendix) showed that
enzymes enriched in obese or IBD microbiomes are more fre-
quently involved in membrane transport [P < 0.035 (obese), P <
0.006 (IBD); SI Appendix, Table S4]. These results are consistent
with previous analysis of enriched functions in the smaller
dataset of lean and obese twins (10). In contrast, enzymes that
are depleted in obese microbiomes are more frequently involved
in cofactors and vitamin metabolism (P < 0.03), nucleotide
metabolism (P < 0.002), and transcription (P < 2.52 × 10−12),
among other processes (SI Appendix, Table S4).
Linking Host State-Associated Enzymes to Centrality. Using the
community-level network outlined above, we examined whether
enzymes that are associated with a specific host state exhibit
unique topological features. We first focused on a topologically
derived centrality measure termed betweenness centrality (25).
This measure calculates the proportion of shortest paths in
a complex network that pass through a given node, as a proxy for
the node’s location in relation to all other nodes (SI Appendix,
Fig. S2B). High centrality values are typically associated with
nodes located in the core of the network, whereas low centrality
values indicate a more peripheral location.
We found that an enzyme’s differential abundance score in
obese samples is negatively correlated with its centrality in the
network (R = −0.17, P < 1.3 × 10−12, Spearman correlation test).
Partitioning the set of enzymes in the network into those that are
associated with obesity (as defined above) and all other enzymes,
we similarly found that centrality scores of obesity-associated
enzymes are significantly lower (P < 8.9 × 10−6, Wilcoxon rank-
sum test; Fig. 1A). As further validation, we note that decreased
centrality is not associated with equivalent sets of randomly se-
lected enzymes (P < 8 × 10−4). Significantly lower centrality
scores can also be observed when examining obesity-enriched
and obesity-depleted enzymes separately (P < 0.03 and P < 7.4 ×
10−6, respectively, Wilcoxon rank-sum test; Fig. 1A), suggesting
that obesity is characterized by both gain and loss of peripheral
enzymes. Similarly, partitioning the enzymes in the network into
three centrality-based tiers (Materials and Methods), we find
a significant overrepresentation of obesity-associated enzymes in
the peripheral tier of the network: 29.1% of the enzymes in this
tier are associated with obesity compared with only 19.4% and
18.6% of the enzymes in the intermediate and central tiers, re-
spectively (Fig. 1B). Using the more stringent criterion defined
above for identifying enzymes that are consistently associated
with obesity yields a similar trend: 13.6%, 10.4%, and 9.8% of
the enzymes in the periphery, intermediate, and central tiers,
respectively, are consistently associated with obesity (SI Appen-
dix). This negative association between obesity-associated dif-
ferential abundance and centrality was confirmed in the analysis
of the smaller twin-mother trios dataset (R = −0.15, P < 9.7 ×
10−8; additional results are presented in SI Appendix).
Interestingly, a similar pattern is observed in enzymes associ-
Spearman correlation test), and the centrality scores of IBD-as-
sociated enzymes are significantly lower than the centrality scores
of enzymes not associated with IBD (P < 9.5 × 10−6, Wilcoxon
rank-sum test; P < 0.003 and P < 0.0002 for IBD-enriched and
IBD-depleted enzymes, respectively). Similarly, IBD-associated
enzymes are significantly overrepresented in the peripheral tier of
the network: 30.1% of the enzymes in this tier are associated with
IBD compared with only 22.8% and 19.0% of the enzymes in the
intermediate and central tiers, respectively (Fig. 1B, Inset). A
similar trend is observed when considering only consistently as-
sociated enzymes (8.8%, 5.4%, and 6.1%, respectively).
We confirmed that the above patterns, linking host state-as-
sociated enzymes to centrality, are robust to several alternative
network construction methods [e.g., using the SEED annotation
framework (33) rather than KEGG] and are not affected by using
different threshold values to filter out low count reads and po-
tential noise (SI Appendix and SI Appendix, Table S3). To vali-
date that the above results are not the outcome of population
substructure, we repeated the analysis for obesity-associated
differential abundance using only the Danish individuals and the
analysis for IBD-associated differential abundance using only the
Greenblum et al.PNAS
| January 10, 2012
| vol. 109
| no. 2
Spanish individuals. Using these subpopulation samples, we still
observed a significant correlation between centrality and differ-
ential abundance (SI Appendix, Table S3). We further confirmed
that this correlation between differential abundance and cen-
trality is not solely a product of the overrepresentation of
transport enzymes (which are likely to be found at the periphery
of the network) in obese microbiomes (SI Appendix and SI Ap-
pendix, Table S3).
Large-scale metabolic data (e.g., KEGG) are often based on
automated, comparison-based, genome annotation (22), and are
therefore bound to be incomplete and imprecise (34). Such in-
accurate metabolic annotations may markedly affect various
complex network properties and can potentially have a dramatic
impact on our results. However, using a sensitivity analysis to
examine the effect of missing or erroneous annotation data (SI
Appendix and SI Appendix, Figs. S4 and S5), we verified that the
calculated centrality scores and the pertaining results reported
above are fairly robust to such inaccuracies in the raw metabolic
Linking Host State-Associated Enzymes to Additional Topological
Features. We next examined a number of additional topological
measures for each enzyme in the network, including in-degree,
out-degree, neighborhood connectivity, and clustering coefficient
(Materials and Methods). In contrast to centrality, these measures
are more local in nature, taking into account only the immediate
neighborhood of each enzyme, and hence capture a different
aspect of network topology. The seed set of the network was also
identified using a previously published seed detection method
(31), and it consisted of 126 enzymes. The seed detection
method applies a graph theory-based algorithm to analyze the
topology of a given network and identify the minimal set of to-
pological “input” nodes sufficient to activate all other nodes in
the network (more details are provided in SI Appendix). The seed
sets of metabolite-based networks of a large array of microbial
species were shown to be a successful proxy for the biochemical
environments of these species and to provide insights into their
ecology (31, 32, 35).
Although both enriched and depleted enzymes exhibit low
centrality as described above, we found that enriched enzymes
differ dramatically from depleted enzymes in respect to such
local topological features. Specifically, enzymes enriched in
obese microbiomes have a significantly lower clustering co-
efficient (P < 7.8 × 10−4, Wilcoxon rank-sum test) and lower in-
degree (P < 0.004) compared with enzymes that are not associ-
ated with obesity (Fig. 2 A and B). In contrast, enzymes depleted
in obese microbiomes have a significantly higher clustering co-
efficient (P < 0.006, Wilcoxon rank-sum test) and higher in-de-
gree (P < 0.02) compared with nonassociated enzymes. IBD-
associated enzymes follow similar trends but are not statistically
significant because of smaller sample size (SI Appendix, Fig. S6).
We additionally found that enzymes identified as network seeds
have significantly higher differential abundance scores (P < 4.8 ×
10−6, Wilcoxon rank-sum test) compared with non-seeds and
that such network seeds are overrepresented among obesity- and
IBD-associated enzymes [P < 2.7 × 10−4(obesity) and P < 2.6 ×
10−3(IBD); more details are provided in SI Appendix].
Such distinct topological properties may additionally beused as
potentially informative attributes and to highlight biomarkers for
involvement in obesity and IBD. Specifically, we examined
enzymes enriched in obese or IBD microbiomes, and within these
sets, we focused on enzymes that also exhibit the topological
features identified above (low centrality, low in-degree, and low
clustering coefficient; SI Appendix, Table S2). We find that a large
fraction of these enzymes within both the obesity-enriched and
the IBD-enriched enzymes are involved in either the phospho-
transferase system (PTS; 28.6% and 20.6% among obesity- and
IBD-enriched enzymes, respectively) or the nitrate reductase
pathway (17.1% and 17.6% among obesity- and IBD-enriched
enzymes, respectively). Notably, the PTS is a Eubacteria-specific
strategy for transporting sugar into the cell, and it has been spe-
cifically associated with members of the Firmicutes phylum (36).
Use of this transport system has been implicated in regulation of
carbohydrate uptake (37) and was found to be up-regulated fol-
lowing a switch to a high-fat/high-sugar “Western” diet in mice
(38). Recently a PTS enzyme (FrvX) was found to be a biomarker
for IBD (39). Similarly, nitrate reductase is a critical component
in the conversion of nitrate into nitrite and nitric oxide, and it is
not synthesized by human DNA. Elevated levels of nitric oxide
have been associated with both IBD (40) and obesity-induced
insulin resistance (41), as well as other serious carcinogenic and
for xenobiotic metabolism, most notably those for the metabolism
of choline and p-cresol, which have been linked to various host
diseases and metabolic phenotypes (SI Appendix).
Linking Topological Variation to Community Species Composition.
Shotgun metagenomic data and community-level models provide
a functional view of community metabolism. Ultimately, how-
ever, differences in community gene content reflect differences
in species composition. Understanding the link between varia-
tion in community-level topological properties and community
composition can provide valuable insight into the mechanism by
which community activity changes as a result of compositional
shifts. Because a full decomposition of shotgun metagenomic
data into species-specific data is not yet feasible, we studied the
distribution of genes of interest across a large array of reference
genomes. Specifically, examining the genomes of 326 fully se-
quenced, prevalent, gut-dwelling microbial species (Materials and
Methods), we found that enzymes associated with either obese or
IBD microbiomes tend to be present in fewer genomes than
nonassociated enzymes [P < 10−54(obesity), P < 10−56(IBD),
Wilcoxon rank-sum test; SI Appendix, Fig. S7]. Obesity-associ-
ated enzymes were also present in fewer genomes than randomly
selected sets of enzymes (P < 10−4; SI Appendix). Moreover, the
centrality of enzymes in the community-level metabolic network
is correlated with the number of reference genomes in which
these enzymes occur (R = 0.23, P < 10−17, Spearman correlation
test; SI Appendix, Fig. S8). A universal association between
centrality and prevalence has also been demonstrated recently
for a smaller set of species that were not associated with the
enzymes vs. all other enzymes in the network. Obesity-associated enzymes
are further divided into enzymes that are enriched or depleted in obese
microbiomes. (B) Proportion of enzymes that are associated with obesity
(main plot) and IBD (Inset) within three equally populated centrality-based
network tiers. Each concentrical pie chart depicts the percent of enzymes
within a specific centrality tier that are classified as enriched or depleted.
Enzymes associated with obesity or IBD are found in significantly higher
proportions in the peripheral tier (P < 5.6 × 10−6[obesity], P < 4.8 × 10−5[IBD];
Hypergeometric enrichment test). This result still holds considering alterna-
tive or stricter criteria for association with the host state (SI Appendix).
(A) Mean and SE of the centrality scores of obesity-associated
| www.pnas.org/cgi/doi/10.1073/pnas.1116053109Greenblum et al.
human microbiome (43). These findings suggest that the varia-
tion in community-level metabolism associated with obesity and
IBD may be induced by an increase or decrease in the abundance
of a relatively small subset of species.
Linking Host State to Network-Level Topological Properties. Finally,
we examined whether host state-associated differences also
translate into differences in network-level topological features.
Sequence reads derived from lean-healthy, obese-healthy, and
lean-IBD samples were pooled separately and used to construct
state-specific metabolic networks. Calculating various network-
level topological features for each of these networks, we found
that the variation associated with host state goes beyond a limited
set of enriched or depleted enzymes and also induces global dif-
ferences in network topology. Specifically, obese microbiomes
were found to induce a less modular metabolic network than lean
microbiomes. Interestingly, reduced modularity in the metabolic
networks of single species has recently been associated with lower
variation in the environment (Discussion). A rarefaction analysis
was performed to confirm that all networks derived from each of
the three sample groups reached a stable topology within the
available coverage (Fig. 3A). An extensive shuffling-based anal-
ysis (Fig. 3B, SI Appendix, and SI Appendix, Figs. S9–S11) dem-
onstrated that the difference in the level of modularity between
obese and lean microbiomes is statistically significant (P < 0.027)
and is not expected at random from multiple individual realiza-
tions of networks with similar topological properties.
Taken together, the topological features that were found to vary
with obesity and IBD suggest a characteristic mode of deviation
from a normal microbiome organization that may be associated
with a disease state. This suggests that in addition to, or poten-
tially as a consequence of, alterations in the abundance of in-
dividual genes or functional classes, disease may be associated
with higher order modes of deviation in the microbiome. Clearly,
such associations alone cannot directly implicate a mechanism
for disease; both obesity and IBD are poorly understood diseases
and embody extremely complex phenotypes. Accordingly, the
system-level observations reported in this study can have multi-
ple alternative interpretations and stem from mechanisms that
are yet unknown. These observations, however, allow us to posit
intriguing hypotheses for further study.
Specifically, we find that enzymes typifying various host states
tend to have low centrality and are found mostly in the periphery
of the network. As the topology of the network reflects metabolic
interdependencies between enzymes (rather than physical loca-
steps that are relatively remote (as measured by their distance
along various metabolic pathways) from the core of the network
and that are closer functionally to the microbiome environment
(44). The most peripheral enzymes, for example, represent either
the microbiome’s first metabolic steps (i.e., enzymes that rely on
substrates that are not produced by any other enzyme in the
microbiome) or end points (enzymes that produce metabolites
that are not utilized by other microbiome enzymes). Such
enzymes are likely to directly use or produce metabolites that
characterize the gut environment, forming an interface between
microbial and human metabolism. Our results therefore suggest
that much of the enzyme-level variation associated with obesity or
IBD relates to changes in the way the microbiome interacts with
the gut environment rather than variation in core metabolic
processes. This variation corresponds to both gain and loss of
certain peripheral metabolic enzymes, as suggested by the re-
duced centrality of both enriched and depleted enzymes. This is
also supported by the reported link between differentially abun-
dant enzymes and seed enzymes. Obesity-enriched enzymes,
however, specifically possess further topological properties
characteristic of network input points (low in-degree and low
clustering coefficient). While several mechanisms that link the
microbiotatoobesity havebeenreported,thisfinding maysuggest
that obesemicrobiomes arecapableofusingadiverserepertoireof
energy sources, accounting for their increased capacity for energy
extraction from the diet (5). Interestingly, it has also been shown
that functionally peripheral enzymes (those involved in nutrient
uptake and first metabolic steps) are more likely to be horizon-
tally transferred (44) and are gained and lost more frequently
during the evolution of individual microbial organisms (31). This
similarity between the adaptive variation that occurs in single
species across an evolutionary time scale and community-level
variation across samples further supports our treatment of the
community as a comprehensive biological system.
Our topology-based system approach has also suggested can-
didate biomarkers involved in obesity and IBD. In addition to
PTSs used for the import of dietary carbohydrates, both obesity
and IBD were significantly associated with genes for the pro-
duction of NO2and the metabolism of choline and p-cresol. The
unexpectedly high overlap between these disease-associated gene
sets (SI Appendix, Table S2) may be indicative of some common
underlying triggers of disease or, alternatively, a conserved re-
sponse of the gut microbiome to disease. Follow-up studies using
gnotobiotic mouse models colonized by microbial isolates with
the ability to perform these key functions, “humanized” mouse
models colonized with samples taken from paired healthy and
diseased human donors, and human intervention studies will be
critical to determine which aspects of the gut microbiome may
contribute to disease and the precise mechanisms that link this
complex microbial metabolic network to host physiology.
Our results further demonstrate that the variation associated
with obesity and IBD induces a reduced network-wide modular-
ity. Recent studies of metabolic network topologies across the
bacterial tree of life revealed marked variation in network mod-
ularity and identified several genetic and environmental deter-
minants affecting metabolic modularity (27, 45). Specifically,
these studies demonstrated that reduced metabolic modularity
in single-species networks is associated with organisms inhabiting
less variable environments. Our analysis, however, presents a
unique characterization of community-level modularity and dem-
onstrates consistent differences that are associated with the host
state. It is intriguing to extrapolate findings from single-species
analyses and to hypothesize that reduced community-level modu-
larity in obese microbiomes may be associated with decreased
variability in the gut environment or with the lack of temporal
regularities (46). Furthermore, this reduced modularity may be
construed as a functional manifestation of the reported decrease in
species diversity that has been observed in obese individuals (10).
In silico models of microbial communities are currently still
scarce (19) and mostly focus on simulated communities com-
prising a handful of species and on pair-wise interactions among
enriched (red; n = 170), depleted (green; n = 180), and other (gray; n = 1213)
enzymes in obese microbiomes. Clustering coefficient is defined as the ratio
between the total number of edges connecting a node’s neighbors and the
potential number of edges that could exist between them. In-degree
denotes the number of edges terminating at a node. (C) Mean and SE of the
differential abundance scores of seeds vs. non-seed enzymes.
Mean and SE of the clustering coefficient (A) and in-degree (B) of
Greenblum et al.PNAS
| January 10, 2012
| vol. 109
| no. 2
community members (21, 47–49). Here, in contrast, we take an
integrative approach, treating the microbiome as a single supra-
organismal system (17) and examining the metabolic network of
the community as a whole (50). Moreover, this study focuses on
the topology of this metagenome-based network and on the re-
lationship between its topology and the host state. As with any
attempt to represent a dynamic and stochastic set of biological
processes via a simple model, our analysis is subject to various
assumptions and simplifications. Our framework ignores bound-
aries between species and compartmentalization of various meta-
bolic processes (information on analyzing communities as
supraorganisms is provided in SI Appendix). Additionally, topo-
logical analysis of connectivity-based and static networks explicitly
ignores several features of metabolic reactions, such as metabolic
rates and dynamic regulation. Furthermore, our analysis considers
metabolism alone and does not account for other processes that
may be involved (e.g., immune response). Such simple models,
however, are extremely useful for studying systems for which data
are stilllimited and our ability to construct more involved models is
hindered. Here, for example, they facilitate the integration of
multiple modes of microbiome characterization and support anal-
ysis using the rich set of tools developed for systems biology and
complex network analysis. As our understanding of the human
microbiome improves, better models can be constructed, poten-
tially using the collective effort of the research community (51, 52).
Experimental validation of model components and parameters is
crucial for a successful and accurate reconstruction. Moving for-
ward, microbiome-wide models can further integrate transcrip-
tional and metabolomics-based data. Such manually curated
models may ultimately provide a predictive framework, similar to
the one available for individual species, for targeted community
manipulation and for informing clinical interventions.
In essence, this study represents an important step in the de-
velopment of a “metagenomic systems biology” approach. Such
an approach can potentially advance metagenomic research in
the same way systems biology advanced genomics, appreciating
not only the parts list of a system but the complex interactions
among parts and the impact of these interactions on function and
dynamics. Future work will also include identifying specific sets
of enzymes responsible for systems-level patterns, characterizing
the implications of various topological variations, and linking this
variation to changes in species composition. Clearly, our un-
derstanding of the complexity of the gut microbiome is still
lacking, and much work still remains to be done before exact
mechanisms are identified. Future clinical applications may focus
on specific functions rather than on system-level properties of
the microbiome. Yet, this systems biology approach provides
a complementary viewpoint to comparative and functional
metagenomics in gaining valuable intuition concerning the
function of the microbiome as a system and in identifying po-
tential biomarkers for further validation.
Materials and Methods
microbiome. The first study (3) examined 576.7 gigabases of Illumina-derived
sequences from 124 European individuals labeled with BMI (kg/m2) and IBD
data. The second study (10) examined 454 FLX-derived sequences from six
twin-mother trios from the Missouri Adolescent Female Twin Study binned
according to BMI. All sequence data were mapped to KEGG orthologous
groups (KOs) using BLASTX (additional details are provided in SI Appendix).
Enzyme Enrichment. To identify enzymes (KOs) that are associated with
obesity, the abundance of each enzyme in the set of samples obtained from
obese individuals was compared with its abundance in lean/overweight
individuals. To prevent the confounding effects of overlapping host states,
samples labeled with IBD were excluded from this analysis. For each enzyme,
k, an OR was calculated according to OR(k) = [∑s = obeseAsk/∑s = obese(∑i≠k
Asi)]/[∑s = leanAsk/∑s = lean(∑i≠kAsi)] where Askdenotes the abundance of
enzyme k in sample s, obese denotes the set of obese samples, and lean
denotes the set of lean/overweight samples (SI Appendix, Fig. S3). More
details on this choice of enrichment metric are provided in SI Appendix. The
differential abundance score was defined as the absolute value of the fold
change in OR, abs[log2(OR)]. Obesity-associated enzymes were those with
a differential abundance score >1. Obesity-associated enzymes were further
classified as obesity-enriched (OR > 2) or obesity-depleted (OR < 0.5) (SI
Appendix, Table S2 A and B). IBD-associated enzymes were identified in a
similar manner (SI Appendix, Table S2 C and D). When calculating IBD-as-
sociated ORs, samples labeled as obese were excluded from the analysis. A
more stringent OR-based analysis was used to identify enzymes that were
consistently enriched or depleted (SI Appendix). Additionally, a number of
other statistical methods were used to quantify differential abundance and
identified enzymes associated with a given host state (SI Appendix). Re-
peating the analysis with these alternative methods yielded qualitatively
similar results (SI Appendix and SI Appendix, Table S3).
Network Construction. A community-level metabolic network was constructed
from the entire set of enzymes found in any sample (SI Appendix). The KEGG
database was used to annotate enzymes with metabolic reactions. Each en-
zyme may be associated with multiple reactions, and each reaction may be
associated with multiple enzymes. Using this mapping, an enzyme-based
of a reaction catalyzed by enzyme 1 is a substrate metabolite of a reaction
catalyzed by enzyme 2 (SI Appendix, Fig. S1B). For both datasets, 98% of the
enzymes were part of a single giant, connected component. The network was
trimmed to include only the nodes and edges that were part of this giant
component, and only these enzymes were used in the subsequent analysis. To
create host state-specific networks, the same procedure was followed using
only the set of enzymes recovered from samples in a given host state.
Topology-Based Measures and Analysis. Topological features of each enzyme
in the network were calculated with the Cytoscape NetworkAnalyzer plug-in
(53). The overall correlation across all topological features supported by the
NetworkAnalyzer plug-in was calculated, and a feature set without any
pairwise correlations >0.95 was selected for further analysis. This feature set
included betweenness centrality (defined as the proportion of shortest paths
passing through a node), clustering coefficient (defined as the proportion of
existing edges between a node’s neighbors), neighborhood connectivity
(average number of neighbors of a node’s neighbors), in-degree (number of
edges terminating in a node), and out-degree (number of edges originating
in a node). SI Appendix, Fig. S2B provides additional illustrations and exam-
ples of these features. The betweenness centrality feature was used
Enzymes were further classified as peripheral, intermediate, or central by
three equally populated bins, which we termed centrality tiers.
The Spearman correlation test was used to examine the correlation be-
tween differential abundance scores and each topological feature. A Wil-
coxon rank-sum test was used to compare the topology scores of host state-
associated enzymes (and specifically enriched or depleted enzymes) with the
scores obtained for non-associated enzymes. A Hypergeometric enrichment
tion analysis of the modularity of pooled lean-healthy, obese-healthy, and
IBD-lean microbiomes. The plot depicts the mean (solid lines) and SD (dotted
lines) of five rounds of rarefaction analysis, obtained by calculating the
modularity of networks derived from progressively smaller randomly se-
lected sets of reads. (B) Difference between the modularity of the obese-
specific and lean-healthy–specific network is plotted (dashed blue line)
against a null distribution of differences obtained via random grouping of
samples (more details are provided in SI Appendix). The observed difference
in modularity is significantly greater than the expected difference according
to this null distribution.
Modularity of host state-specific metabolic networks. (A) Rarefac-
| www.pnas.org/cgi/doi/10.1073/pnas.1116053109Greenblum et al.
test was used to examine the over-representation of host state-associated
enzymes in each centrality tier.
Network-Level Topological Features of Host State-Specific Networks. Samples
were divided into three distinct groups: lean-healthy, obese-healthy, and
lean-IBD. The three obese-IBD samples were not used in this analysis. Three
separate host state-specific networks were created from the pooled set of
enzymes identified within each group. Network-level features, including
node count, density (the ratio of edges to nodes), and modularity, were
calculated for each network. Here, we define and calculate modularity
according to the formulation presented by Newman (54). For a particular
division of a network into discrete modules, modularity is defined as the
number of edges between nodes that belong to the same module minus the
expected number of such edges in an equivalent randomized network,
normalized by the total number of edges. The modularity of the network is
calculated for the division that maximizes this value. This modularity value
measures how well a network can be partitioned into densely connected
modules with relatively few edges running between modules. Rarefaction
curves were generated for each of these measures by considering an in-
creasingly larger random subset of reads from each group. The statistical
significance of these measures was assessed using null distributions calcu-
lated from randomized networks (SI Appendix).
Seed Set Identification. The metabolic seed set (more details are provided in SI
Appendix), representing enzymes operating on exogenously acquired com-
pounds, was calculated according to the method described by Borenstein
et al. (31).
ACKNOWLEDGMENTS. We thank Junjie Qin for assistance in downloading
and analyzing the data from 124 unrelated individuals. The metagenomic
sequence comparisons in this paper were run on the Odyssey cluster
supported by the FAS Sciences Division Research Computing Group. S.G. is
supported by “Interdisciplinary Training in Genomic Sciences” National Hu-
man Genome Research Institute Grant T32 HG00035. P.J.T. is supported by
National Institutes of Health Grant P50 GM068763. E.B. is an Alfred P. Sloan
1. Ley RE, Peterson DA, Gordon JI (2006) Ecological and evolutionary forces shaping
microbial diversity in the human intestine. Cell 124:837–848.
2. Dethlefsen L, McFall-Ngai M, Relman DA (2007) An ecological and evolutionary per-
spective on human-microbe mutualism and disease. Nature 449:811–818.
3. Qin J, et al.; MetaHIT Consortium (2010) A human gut microbial gene catalogue es-
tablished by metagenomic sequencing. Nature 464:59–65.
4. Turnbaugh PJ, et al. (2007) The human microbiome project. Nature 449:804–810.
5. Turnbaugh PJ, et al. (2006) An obesity-associated gut microbiome with increased
capacity for energy harvest. Nature 444:1027–1031.
6. Vijay-Kumar M, et al. (2010) Metabolic syndrome and altered gut microbiota in mice
lacking Toll-like receptor 5. Science 328:228–231.
7. Khoruts A, Dicksved J, Jansson JK, Sadowsky MJ (2010) Changes in the composition of
the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-
associated diarrhea. J Clin Gastroenterol 44:354–360.
8. Gill SR, et al. (2006) Metagenomic analysis of the human distal gut microbiome. Sci-
9. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI (2008) Worlds within worlds:
Evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6:776–788.
10. Turnbaugh PJ, et al. (2009) A core gut microbiome in obese and lean twins. Nature
11. Peterson J, et al.; NIH HMP Working Group (2009) The NIH Human Microbiome Pro-
ject. Genome Res 19:2317–2323.
12. Hartman AL, et al. (2009) Human gut microbiome adopts an alternative state
following small bowel transplantation. Proc Natl Acad Sci USA 106:17187–
13. Tringe SG, et al. (2005) Comparative metagenomics of microbial communities. Science
14. White JR, Nagarajan N, Pop M (2009) Statistical methods for detecting differentially
abundant features in clinical metagenomic samples. PLOS Comput Biol 5:e1000352.
15. Kurokawa K, et al. (2007) Comparative metagenomics revealed commonly enriched
gene sets in human gut microbiomes. DNA Res 14:169–181.
16. Lederberg J (2000) Infectious history. Science 288:287–293.
17. Gordon JI, Klaenhammer TR (2011) A rendezvous with our microbes. Proc Natl Acad
Sci USA 108(Suppl 1):4513–4515.
18. Raes J, Bork P (2008) Molecular eco-systems biology: Towards an understanding of
community function. Nat Rev Microbiol 6:693–699.
19. Oberhardt MA, Palsson BØ, Papin JA (2009) Applications of genome-scale metabolic
reconstructions. Mol Syst Biol 5:320.
20. Tepper N, Shlomi T (2010) Predicting metabolic engineering knockout strategies for
chemical production: Accounting for competing pathways. Bioinformatics 26:
21. Klitgord N, Segrè D (2010) Environments that induce synthetic microbial ecosystems.
PLOS Comput Biol 6:e1001002.
22. Kanehisa M, et al. (2006) From genomics to chemical genomics: New developments in
KEGG. Nucleic Acids Res 34(Database issue):D354–D357.
23. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási AL (2000) The large-scale organi-
zation of metabolic networks. Nature 407:651–654.
24. Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED (2002) Metabolic network
structure determines key aspects of functionality and regulation. Nature 420:
25. Patil KR, Nielsen J (2005) Uncovering transcriptional regulation of metabolism by
using metabolic network topology. Proc Natl Acad Sci USA 102:2685–2689.
26. Guimerà R, Nunes Amaral LA (2005) Functional cartography of complex metabolic
networks. Nature 433:895–900.
27. Kreimer A, Borenstein E, Gophna U, Ruppin E (2008) The evolution of modularity in
bacterial metabolic networks. Proc Natl Acad Sci USA 105:6976–6981.
28. Palumbo MC, Colosimo A, Giuliani A, Farina L (2005) Functional essentiality from
topology features in metabolic networks: A case study in yeast. FEBS Lett 579:
29. Freilich S, et al. (2010) Decoupling Environment-Dependent and Independent Genetic
Robustness across Bacterial Species. PLOS Comput Biol 6:e1000690.
30. Raymond J, Segrè D (2006) The effect of oxygen on biochemical networks and the
evolution of complex life. Science 311:1764–1767.
31. Borenstein E, Kupiec M, Feldman MW, Ruppin E (2008) Large-scale reconstruction and
phylogenetic analysis of metabolic environments. Proc Natl Acad Sci USA 105:
32. Borenstein E, Feldman MW (2009) Topological signatures of species interactions in
metabolic networks. J Comput Biol 16:191–200.
33. Overbeek R, et al. (2005) The subsystems approach to genome annotation and its use
in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691–5702.
34. Green ML, Karp PD (2006) The outcomes of pathway database computations depend
on pathway ontology. Nucleic Acids Res 34:3687–3697.
35. Freilich S, et al. (2009) Metabolic-network-driven analysis of bacterial ecological
strategies. Genome Biol 10:R61.
36. Mahowald MA, et al. (2009) Characterizing a model human gut microbiota composed
of members of its two dominant bacterial phyla. Proc Natl Acad Sci USA 106:
37. Francl AL, Thongaram T, Miller MJ (2010) The PTS transporters of Lactobacillus gasseri
ATCC 33323. BMC Microbiol 10:77.
38. Turnbaugh PJ, et al. (2009) The effect of diet on the human gut microbiome: A
metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1:6ra14.
39. Chen C-S, et al. (2009) Identification of novel serological biomarkers for inflammatory
bowel disease using Escherichia coli proteome chip. Mol Cell Proteomics 8:1765–1776.
40. Kolios G, Valatas V, Ward SG (2004) Nitric oxide in inflammatory bowel disease: A
universal messenger in an unsolved puzzle. Immunology 113:427–437.
41. Gil-Ortega M, et al. (2010) Adaptative nitric oxide overproduction in perivascular
adipose tissue during early diet-induced obesity. Endocrinology 151:3299–3306.
42. Yang G-Y, Taboada S, Liao J (2009) Induced nitric oxide synthase as a major player in
the oncogenic transformation of inflamed tissue. Methods Mol Biol 512:119–156.
43. Bernhardsson S, Gerlee P, Lizana L (2011) Structural correlations in bacterial metabolic
networks. BMC Evol Biol 11:20.
44. Pál C, Papp B, Lercher MJ (2005) Adaptive evolution of bacterial metabolic networks
by horizontal gene transfer. Nat Genet 37:1372–1375.
45. Parter M, Kashtan N, Alon U (2007) Environmental variability and modularity of
bacterial metabolic networks. BMC Evol Biol 7:169.
46. Costello EK, Gordon JI, Secor SM, Knight R (2010) Postprandial remodeling of the gut
microbiota in Burmese pythons. ISME J 4:1375–1385.
47. Stolyar S, et al. (2007) Metabolic modeling of a mutualistic microbial community. Mol
Syst Biol 3:92.
48. Wintermute EH, Silver PA (2010) Emergent cooperation in microbial metabolism. Mol
Syst Biol 6:407.
49. Freilich S, et al. (2010) The large-scale organization of the bacterial network of eco-
logical co-occurrence interactions. Nucleic Acids Res 38:3857–3868.
50. Gianoulis TA, et al. (2009) Quantifying environmental adaptation of metabolic
pathways in metagenomics. Proc Natl Acad Sci USA 106:1374–1379.
51. Herrgård MJ, et al. (2008) A consensus yeast metabolic network reconstruction ob-
tained from a community approach to systems biology. Nat Biotechnol 26:1155–1160.
52. Thiele I, Palsson BØ (2010) Reconstruction annotation jamborees: A community ap-
proach to systems biology. Mol Syst Biol 6:361.
53. Assenov Y, Ramírez F, Schelhorn S-E, Lengauer T, Albrecht M (2008) Computing to-
pological parameters of biological networks. Bioinformatics 24:282–284.
54. Newman MEJ (2006) Modularity and community structure in networks. Proc Natl
Acad Sci USA 103:8577–8582.
Greenblum et al.PNAS
| January 10, 2012
| vol. 109
| no. 2