IMG/M: the integrated metagenome data
management and comparative analysis system
Victor M. Markowitz1,*, I-Min A. Chen1, Ken Chu1, Ernest Szeto1, Krishna Palaniappan1,
Yuri Grechkin1, Anna Ratner1, Biju Jacob1, Amrita Pati2, Marcel Huntemann2,
Konstantinos Liolios2, Ioanna Pagani2, Iain Anderson2, Konstantinos Mavromatis2,
Natalia N. Ivanova2and Nikos C. Kyrpides2,*
1Biological Data Management and Technology Center, Computational Research Division, Lawrence Berkeley
National Laboratory, 1 Cyclotron Road, Berkeley, California, CA 94702 and2Microbial Genomics and
Metagenomics Program, Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek,
California, CA 94598, USA
Received September 19, 2011; Revised October 12, 2011; Accepted October 16, 2011
genomes (IMG/M) system provides support for com-
parative analysis of microbial community aggregate
integrated context. IMG/M integrates metagenome
data sets with isolate microbial genomes from the
IMG system. IMG/M’s data content and analytical
capabilities have been extended through regular
updates since its first release in 2007. IMG/M is
available at http://img.jgi.doe.gov/m. A companion
IMG/M systems provide support for annotation and
expert review of unpublished metagenomic data
sets (IMG/M ER: http://img.jgi.doe.gov/mer).
The number of metagenome sequence data sets generated
by various sequencing centers is rapidly increasing with
thousands of data sets already generated. Meteganome
sequencing has evolved over the past several years from
platforms to second generation 454 Life Sciences Roche
(e.g. GS FLX) and Illumina (e.g. GA II and HiSeq)
platforms. While cheaper and faster, the new platforms
produce shorter sequence fragments (reads). Short read
size, higher complexity and inherent incompleteness,
make metagenome sequences difficult to assemble and
Assembled or unassembled metagenome data sets
generated using 454 or Illumina platforms are processed
by the IMG/M annotation pipeline (3) before inclusion
into IMG/M. Unassembled reads undergo an additional
quality control step that includes quality trimming,
low-complexity region detection and masking as well as
removal of technical replicates. Subsequently, both
assembled and unassembled sequences are annotated by
the same pipeline that detects CRISPR repeats (4),
non-coding RNAs and protein-coding genes (CDSs
tRNAscan-SE (5) for tRNAs, and in-house developed
HMM models for rRNAs (6,7,8), while the CDSs are
identified using a combination of ab initio gene prediction
tools: Prodigal (9), Metagene (10), MetaGenemark (11)
and FragGeneScan (12). In addition, sequences in the
non-redundant protein database using BlastX in order to
detect the CDSs missed by ab initio tools. Conflicting gene
predictions are consolidated using a weighted schema
based on the performance of each method on simulated
data sets, with one final gene model generated for each
Analysis of the aggregate genomes (metagenomes) of
questions of phylogenetic composition and functional or
metabolic potential within individual microbiomes, as well
as comparisons across microbiomes. IMG/M provides
support for such analysis by integrating metagenome
data sets with isolate microbial genomes from the
integrated microbial genome (IMG) system (13). Using
NCBI’s RefSeq (14) as its main source of sequence data,
IMG integrates draft and complete microbial genomes
from all three domains of life with a large number of
plasmids and viruses. Similar to IMG, IMG/M records
the primary sequence information for isolate genomes
and metagenomes, their organization in scaffolds and/or
contigs as well as computationally predicted protein-
coding sequences and RNA-coding genes. Protein-coding
compared to theIMG
*To whom correspondence should be addressed. Tel: +1 925 296 5718; Fax: +1 510 486-5812; Email: firstname.lastname@example.org
Correspondence may also be addressed to Nikos C. Kyrpides. Tel: +1 925 296 5718; Fax: +1 925 296 5666; Email: email@example.com
Published online 15 November 2011Nucleic Acids Research, 2012, Vol. 40, Database issueD123–D129
Published by Oxford University Press 2011.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
genes are characterized in terms of additional annotations,
such as conserved motifs and domains (15), signal
peptides, transmembrane helices (16), pathways and
orthology relationships, which may serve as an indication
of their functions. These annotations are based on diverse
data sources, such as Clusters of Orthologous Genes
(COG) clusters and functional categories (17), Pfam
(18), TIGRfam and TIGR role categories (19), InterPro
domains (20) and KEGG (Kyoto Encyclopedia of Genes
and Genomes) Ortholog terms and pathways (21).
We review below IMG/M’s data content growth and
analysis tool extensions since the last published report
on IMG/M (22).
Reference genome data
IMG is the source of IMG/M’s reference isolate genomes.
The current version of IMG/M is based on the content of
IMG 3.4 (V.M. Markowitz et al., submitted publication)
consisting of 6891 bacterial, archaeal, eukaryotic and viral
genomes, as well as 1186 plasmids that did not come from
a specific microbial genome sequencing project, with over
11.6 million protein coding genes.
Genomes generated as part of the Human Microbiome
Project (HMP) and the Genome Encyclopedia of Bacterial
and Archaea Genomes (GEBA) are of particular import-
ance to metagenome analysis. HMP has generated over
800 reference genomes from both cultured and uncultured
bacteria with the goal of supporting the characterization
of microbial communities found at multiple human body
sites (23). The GEBA project aims at systematically filling
the sequencing gaps along the bacterial and archaeal
branches of the tree of life (24), with the number of
sequenced GEBA genomes standing at 205 as of August
2011. While HMP reference genomes are included into
IMG/M from RefSeq via IMG, GEBA genomes are
included directly into IMG/M as soon as their annotation
is completed at Joint Genome Institute (JGI), before their
release through GenBank and RefSeq.
Unlike isolate genomes which are included into IMG and
then IMG/M from a public sequence data resource
(RefSeq), metagenome data sets are first included into
IMG/M ‘Expert Review’ version, IMG/M ER, which
allows scientists to employ IMG/M’s annotation pipeline
as well as review and curate the functional annotation of
metagenomes prior to their public release in the context of
IMG/M’s reference genomes and public metagenomes.
Genome and metagenome submissions are handled by
the IMG/ER and IMG/M ER submission site, as
illustrated in Figure 1(i).
First, the names and classification of metagenome data
sets submitted for inclusion into IMG/M ER are curated
in GOLD (25) following the five-tiered system as previ-
ously proposed (26). This classification scheme underlies
the organization of metagenome data sets in IMG/M, as
illustrated in Figure 1(ii). Similar to the phylogenetic
classification of isolate genomes, the classification of
metagenome comparative analysis in a rapidly growing
universe of metagenome data sets. Thus, all metagenome
datasets are organized
classes: environmental, host associated and engineered
classes, then further divided in subclasses characterized
by ecosystem categories (e.g. aquatic, terrestrial, air for
environmental metagenomes), ecosystem type (e.g. fresh-
water, marine), ecosystem subtype (e.g. groundwater,
drinking water), and specific ecosystem (e.g. cave water,
filtered water). Second, metagenome data sets submitted
for inclusion into IMG/M ER are associated with com-
prehensive metadata attributes following the Genome
Standards Consortium guidelines (27), as illustrated in
Figure 1(iii) and 1(iv). Note that enforcing metadata
processed is the most effective way to capture such
As of 3 October 2011, IMG/M ER contains about 870
metagenome data sets (samples) with over 163 million
protein coding genes that are part of 27 engineered,
110 environmental and 90 host-associated metagenome
studies. IMG/M contains the publicly available subset
of IMG/M ER metagenome data sets consisting of
289 metagenome data sets with over 60 million protein
coding genes, a 10-fold increase compared to August
2007 (22). These data sets are part of 14 engineered,
37 environmental and 32 host-associated studies.
An HMP-specific version of IMG/M, contains 748
metagenome data sets generated as part of the HMP
initiative by sequencing samples collected from various
body sites (airways, gastrointestinal, oral, skin and uro-
genital), with a total of 80 million protein-coding genes
isa criticalelement forconducting
in three main ecosystem
data sets are
We briefly review below the IMG/M data analysis tools
with emphasis on the support for new metagenome
analysis tools developed since the last published report
on IMG/M (22).
Data selection and exploration
Metagenomes, genomes, genes and functions can be
selected in IMG/M using IMG specific browsers and
search tools (15), with the organization of metagenomes
using the hierarchical classification discussed above
and illustrated in Figure 1 being specific to IMG/M.
Metagenomes and genomes that result from search oper-
ations are displayed as lists from which they can be
selected for inclusion into the ‘Genome Cart’. Genes and
functions can be handled in a similar manner using the
‘Gene Cart’ and ‘Function Cart’, respectively.
Individual metagenomes can be explored using the
‘Metagenome Details’ page that provides a variety of
tools for browsing, searching for the presence of specific
genes or downloading metagenome data sets, as illustrated
in Figure 2(i). This page also provides information
(metadata) on the metagenome together with various
statistics of interest, such as the number of genes that
D124Nucleic AcidsResearch, 2012, Vol.40,Database issue
are associated with KEGG, COG, Pfam, InterPro or
One of the ‘Browse’ tools provided for metagenomes
allows examining scaffolds and contigs, whereas a new
‘Scaffold Cart’ allows selecting individual scaffolds
(rather than all the scaffolds/contigs of a meteganome)
or groups of scaffolds based on their properties such as
gene or GC content, scaffold length, read depth, as
illustrated in Figure 2(ii), and thus focus the analysis on
provides tools for including the genes of one or several
scaffolds into the ‘Gene Cart’, associating a name with
selected scaffoldsfor further
a function profile across selected scaffolds, and for
examining the phylogenetic distribution of genes for one
or several scaffolds in the cart.
The ‘Phylogenetic Distribution of Genes’, illustrated in
Figure 2(iii), provides an estimate of the phylogenetic
composition of a metagenome sample based on the distri-
bution of the best BLAST hits of the protein-coding genes
in the sample. The result of ‘Phylogenetic Distribution of
Genes’ can be displayed using the ‘Radial Phylogenetic
Tree’ viewer as illustrated in Figure 2(iv), or in a tabular
format consisting of a histogram, as illustrated in
Figure 2(v) with counts protein-coding genes in the
sample, which have best BLASTp hits to proteins of isolate
genomes in each phylum or class with >90% identity
(right column), 60–90% identity (middle column) and
30–60% identity (left column). This tabular display can
be adjusted by filtering out the phyla/classes with few or
no hits, whereby the higher the number of hits and percent
identity cutoff, the more likely it is that the sample
contains close relatives of the sequenced isolate genomes
from this phylum/class. The CDSs with best BLAST hits
to a certain taxonomic lineage can be organized by their
assignment to COGs, which in turn can be classified ac-
cording to COG Functional Categories (COG Functional
Category) or COG Pathways (COG Pathways). The latter
can be displayed in a tabular or pie chart format, as
illustrated in Figure 2(vi), thereby linking the functional
Figure 1. Metagenome data set classification and metadata characterization. (i) Metagenome data sets are submitted for annotation and inclusion
into IMG/M ER via the IMG/ER and IMG/M ER submission site. (ii) Metagenome data sets in IMG/M are organized using a hierarchical
classification similar to the phylogenetic classification of isolate genomes. (iii) Metagenome data sets submitted for inclusion into IMG/M ER are
associated with metadata characterizing the metagenome study, the associated metagenome sequencing project, environmental information, as well as
(iv) sample and sequencing information.
Nucleic Acids Research, 2012,Vol.40, Database issue D125
complement of metagenomic proteins with their likely
affiliations to different phyla/classes and indicating
possible functional specialization within the community
(functional guilds). Gene counts in the various display
formats of the results are linked to the corresponding
lists of genes, which can then be selected and added to
‘Gene Cart’ or analyzed through their ‘Gene Pages’.
The ‘Radial Phylogenetic Tree’ tool allows the compari-
son of up to five user-selected metagenomes in terms of
their BLAST hits to isolate genomes in a color-coded
hierarchical circular tree. The resulting tree image can
show the hits at different taxonomic levels. More statistics
of hits for each genome can be accessed by hovering the
mouse over the nodes of the tree. Finally, the genes in
a metagenome sample can be viewed in the context of
individual reference isolate genome using the ‘Protein
Recruitment Plot’ that displays the BLASTp hits of the
metagenome genes against the genes of the reference
genome, with the coordinates of the scaffold reference
genome and the BLAST percent identities shown on
the X- and Y-axis, respectively.
Comparative analysis tools are an extension of the
analogous tools in IMG (15), and allow examining the
gene content and functional capabilities of microbial
communities. We discuss below in more detail the main
metagenome-specific comparative analysis tools available
under the ‘Compare Genomes’ main menu tab of IMG/M,
as shown in Figure 3(i).
Metagenome samples can be compared in terms of
their phylogenetic composition using a variant of the
‘Phylogenetic Distribution of Genes’ tool discussed
above, which is extended to allow displaying side by side
Figure 2. Metagenome data exploration. (i) Microbiome samples, such as the Sediment microbial communities from Lake Washington for Methane
and Nitrogen Cycle sample, can be examined using the ‘Microbiome Details’ page, which provide tools for browsing, searching or downloading
the metagenome data. (ii) ‘Scaffold Cart’ allows selecting individual scaffolds or groups of scaffolds based on properties such as gene content.
(iii) The ‘Phylogenetic Distribution of Genes’ provides an estimate of the phylogenetic composition of a metagenome sample based on the distri-
bution of the best BLAST hits of the protein-coding genes in the sample. The result of ‘Phylogenetic Distribution of Genes’ can be displayed using
(iv) the ‘Radial Phylogenetic Tree’ viewer or (v) in a tabular format consisting of a histogram with counts protein-coding genes in the sample, which
have best BLASTp hits to proteins of isolate genomes in each phylum or class with >90% identity (right column), 60–90% identity (middle column)
and 30–60% identity (left column). (vi) The organization of genes by their assignment to COGs is displayed in a pie chart format.
D126 Nucleic AcidsResearch, 2012, Vol.40,Database issue
the phylogenetic distribution of best BLAST hits of
protein-coding genes in multiple metagenomes. Two
‘Abundance Profile’ tools allow comparing the func-
tional capabilitiesof metagenomes
The ‘Abundance Profile Overview’ tool provides a quick
estimate of the functional capabilities of metagenomes in
terms of the relative abundance of protein families (COGs
and Pfams) and functional families (Enzymes) across
selected metagenomes and isolate genomes. The result of
this comparison is displayed either as a heat map or in
a matrix format, with each column on the map/matrix
corresponding to a genome or metagenome, and each
row corresponding to a family. Users can ‘drill down’ by
following links to lists of genes assigned to a particular
family in a specific genome or metagenome.
A new ‘Abundance Profile Search’ tool allows finding
protein families (COGs and Pfams) in metagenomes and
isolate genomes based on their relative abundance. The
tool allows selecting the way the results will be displayed
(using raw or normalized gene counts) and setting
abundance cutoffs, as illustrated in Figure 3(ii). The
‘Abundance Profile Search Results’ consist of a list of
protein families that satisfy the search criteria together
with the metagenomes or genomes involved in the
comparison and their associated raw or normalized gene
counts, as illustrated in Figure 3(iii). Protein families can
be selected and added to the ‘Function Cart’, while gene
counts are linked to the corresponding lists of genes,
which can be subsequently selected and added to the
‘Gene Cart’ for further analysis.
Figure 3. Abundance profile and function comparison tools. The ‘Abundance Profile Search’ allows finding protein families (COGs and Pfams) in
metagenomes and isolate genomes based on their relative abundance, such as (ii) finding all Pfams in the Sediment microbial communities from Lake
Washington (Aerobic with added nitrate, 13C SIP) sample, which are at least twice as abundant as in the Sediment microbial communities from Lake
Washington (Aerobic without added nitrate, 13C SIP) sample and are at least twice less abundant than in Sediment microbial communities from
Lake Washington (Aerobic without added nitrate, SIP additional fraction). (iii) The ‘Abundance Profile Search Results’ consists of a list of protein
families that satisfy the search criteria together with the metagenomes or genomes involved in the comparison and their associated raw or normalized
gene counts. (iv) The ‘Function Category Comparison’ tool allows comparing a metagenome data set with other metagenome data sets or reference
genome data sets in terms of the relative abundance of functional categories (COG Pathway, KEGG Pathway, KEGG Pathway Category, Pfam
Category and TIGRfam Role Categories). (v) The result of ‘Function Category Comparison’ lists for each function category, F, the number of genes
and estimated gene copies in the target (query) metagenome associated with F and for each reference genome/metagenome the number of genes
or estimated gene copies associated with F, as well as an assessment of statistical significance in terms of associated P-value and d-rank.
Nucleic Acids Research, 2012,Vol.40, Database issueD127
The ‘Abundance Profile’ tools allow comparison of the
functional capabilities of metagenomes without assigning
statistical significance to the results. However, when
metagenomes are compared to each other or to isolate
genomes, statistical tests are needed for estimating
the statistical significance of the observed differences.
The ‘Function Comparison’ and ‘Function Category
Comparison’ tools take into account the stochastic
nature of metagenome data sets and test whether the
differences in abundance can be ascribed to chance vari-
ation or not. These tools allow comparing a metagenome
data set with other metagenome data sets or reference
genome data sets in terms of the relative abundance of
(i) protein families (COGs, Pfams and TIGRfams)
and functionalfamilies (Enzymes)
‘Function Comparison’ or (ii) functional categories
(COG Pathway, KEGG Pathway, KEGG Pathway
Category, Pfam Category and TIGRfam subroles) in the
case of ‘Function Category Comparison’, as illustrated in
Figure 3(iv). The result of these comparisons lists for
each function or function category, F, the number of
genes or estimated gene copies in the target (query)
metagenome associated with F and for each reference
genome/metagenome the number of genes or estimated
gene copies associated with F. These results include an
assessment of statistical significance in terms of associated
P-value and d-scores (for Function Comparison) or
illustrated in Figure 3(v).
in the case of
The current version of IMG/M (August 2011) contains
224 metagenome data sets (samples) that are part of
15 engineered, 36 environmental, and 34 host-associated
projects (studies). These data sets can be analyzed in the
context of 6891 bacterial, archaeal, eukaryotic and virus
reference genomes. New metagenome data sets are con-
tinuously included into IMG/M from metagenome studies
conducted at JGI and other institutes, while new reference
isolate genomes are included from IMG on a regular basis.
Data sets from next generation sequencing technology
platforms often result in million sequences rendering
storing and accessing of data in the standard relational
data bases inefficient. As we expect an exponential
growth of the size of metagenome data sets by these plat-
forms, we are devising new data management techniques
for organizing metagenome data in support of effective
We thank Shane Cannon of Lawrence Berkeley National
Lab’s National Energy Research Scientific Computing
Center for his help in carrying out large-scale gene
similarity computations for IMG/M. We thank Peter
Williams, Henrik Nordberg, Roman Nikitin and Simon
Minovitsky for their contribution to the development
and maintenance of IMG/M. The work of JGI’s
production, cloning, sequencing, assembly, finishing and
annotation teams is an essential prerequisite for IMG.
Eddy Rubin and James Bristow provided support,
advice and encouragement throughout this project.
Director, Office of Science, Office of Biological and
Environmental Research, Life Sciences Division, US
Departmentof Energy (Contract
Departmentof Energy (Contract
05CH11231); US National Institutes of Health Data
HG004866). Funding for open access charge: University
Conflict of interest statement. None declared.
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