softwarevitcomic: visualization tool for taxonomic ... · bacteria and archaea, mosaic structures...
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Mori et al. BMC Bioinformatics 2010, 11:332http://www.biomedcentral.com/1471-2105/11/332
Open AccessS O F T W A R E
SoftwareVITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequencesHiroshi Mori, Fumito Maruyama and Ken Kurokawa*
AbstractBackground: Understanding the community structure of microbes is typically accomplished by sequencing 16S ribosomal RNA (16S rRNA) genes. These community data can be represented by constructing a phylogenetic tree and comparing it with other samples using statistical methods. However, owing to high computational complexity, these methods are insufficient to effectively analyze the millions of sequences produced by new sequencing technologies such as pyrosequencing.
Results: We introduce a web tool named VITCOMIC (VIsualization tool for Taxonomic COmpositions of MIcrobial Community) that can analyze millions of bacterial 16S rRNA gene sequences and calculate the overall taxonomic composition for a microbial community. The 16S rRNA gene sequences of genome-sequenced strains are used as references to identify the nearest relative of each sample sequence. With this information, VITCOMIC plots all sequences in a single figure and indicates relative evolutionary distances.
Conclusions: VITCOMIC yields a clear representation of the overall taxonomic composition of each sample and facilitates an intuitive understanding of differences in community structure between samples. VITCOMIC is freely available at http://mg.bio.titech.ac.jp/vitcomic/.
BackgroundThe number of sequenced bacterial genomes hasincreased rapidly and now exceeds 1,000 [1]; however, wehave little information regarding environmentalmicrobes, largely because the majority of them are uncul-turable [2]. The taxonomic composition of a microbialcommunity can provide important clues to better under-stand its structure and ecology [3]. Analysis using 16SrRNA genes is a frequently used method to obtain thetaxonomic composition of a microbial community [4,5].Features of 16S rRNA genes include essentiality for allBacteria and Archaea, mosaic structures of highly con-served regions and variable regions [6,7], and little possi-bility for horizontal gene transfer [8]. Moreover, theavailability of numerous tools and databases specific for
the 16S rRNA genes has potentiated taxonomic analyses[9-12].
Ultra-deep sequencing of microbial communities usinga massively parallel pyrosequencer has recently uncov-ered relatively rare species in communities [5,13-15].However, the enormous amounts of sequencing data pro-duced by recent pyrosequencing studies are difficult toeffectively analyze using existing computational tools(Additional file 1) [16]. For example, the overall taxo-nomic composition of each sample is traditionally pre-sented graphically in phylogenetic trees [9,17]. However,graphical representation and comparison of overall taxo-nomic compositions for pyrosequencing data is difficultdue to the high computational complexity involved inconstructing multiple alignments and phylogenetic treesfrom millions of sequences [16,18]. Therefore, research-ers tend to use a compressed representation of taxonomiccomposition such as a bar graph or pie chart of the phy-lum-level composition. Unfortunately, these compressedrepresentations of overall taxonomic composition can bedifficult to represent differences among microbial com-
* Correspondence: [email protected] Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 B-36, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, JapanFull list of author information is available at the end of the article
© 2010 Mori et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons At-tribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in anymedium, provided the original work is properly cited.
Mori et al. BMC Bioinformatics 2010, 11:332http://www.biomedcentral.com/1471-2105/11/332
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munities, especially differences attributable to minoritytaxa [19].
To address deficiencies in the analysis of taxonomiccompositions of microbial communities, we developed arapid visualization tool, named VITCOMIC, that pres-ents overall taxonomic compositions based on large data-sets of 16S rRNA genes from microbial communities.VITCOMIC can facilitate intuitive understanding ofmicrobial communities and compare taxonomic compo-sitions between communities.
ImplementationCreation of a reference 16S rRNA gene database and their distance matrixThe reference 16S rRNA gene sequence database wasconstructed using 16S rRNA gene sequences fromgenome-sequenced strains. These data are suitable as ref-erence data because they are accurate and have well-defined taxonomic information. Genomic sequences ofBacteria and Archaea were obtained from the NCBIGenome Database [20] in September 2009. The 16SrRNA genes of each strain were detected using RNAm-mer [21]. One 16S rRNA gene was randomly sampled perspecies because there are only small sequence differencesamong 16S rRNA genes within the same genome and thesame species [22,23]. A total of 601 16S rRNA genesequences from 601 species of Bacteria and Archaea wereobtained. To calculate phylogenetic distances amongthem, all sequences were aligned using MAFFT 6.713with default parameters [24]. After constructing multiplealignments, genetic distances between sequences withKimura's two-parameter model of base substitution [25]were calculated using the dnadist program in PHYLIP3.69 [26]. The phylogenetic tree was constructed usingthe neighbor-joining method in the neighbor program inPHYLIP 3.69. The phylum-level taxonomy of the specieswas obtained from the NCBI Taxonomy Database [27].
Sample data for testing VITCOMICWe used human gut microbiome data from Turnbaugh etal. [15] to test VITCOMIC. In their study, each individualwas categorized as obese, lean, or overweight using bodymass index. DNA was extracted from the feces of eachindividual, and the V2 variable regions of 16S rRNAgenes were PCR amplified prior to pyrosequencing usinga 454 GS FLX system [28]. We used the sequences fromobese and lean individuals. The obese sample consisted of704,369 sequences from 196 individuals; the lean sampleconsisted of 291,993 sequences from 61 individuals.
Inference of a nearest relative for each sequenceUsing the human gut microbiome data, we conductedBLASTN searches against the reference 16S rRNA genedatabase to determine a nearest relative for each sample
sequence. The nearest relative is the evolutionally nearestdatabase sequence of each sample sequence. In general,the reference sequence with the highest BLAST score ischosen as the nearest relative in sequence analyses [29].However, because the 16S rRNA gene has mosaic struc-tures of highly conserved regions and variable regions[6,7], the alignments created by BLAST are often dividedby variable regions [30]. In this case, the BLAST score iscalculated for each divided alignment, because overallBLAST scores between the sample and databasesequences cannot be calculated using only the highestscore alignment. To overcome this problem, we calcu-lated a total BLAST score for alignments derived fromthe same pair of sample and database sequences. As illus-trated in Figure 1A, the total BLAST score is calculatedby summing BLAST scores of three divided alignmentsfrom the same pair of sample and database sequences(250 + 220 + 300 = 770). To identify the nearest relative ofthe sample sequence, the total BLAST score is calculatedagainst each database sequence. Upon comparison withthe total BLAST scores between database sequences, thedatabase sequence with the highest total BLAST score isadopted as the nearest relative of the sample sequence.
Alignments less than 50 bp were excluded to avoidinaccurate alignments. Because variable regions arenearly neutral, false alignments between a variable regionand a conserved region or other variable regions aresometimes constructed and included in calculations oftotal BLAST scores (Figure 1B). To calculate total BLASTscores, it is necessary to develop the function "alignmentsconsistency check". The alignments consistency checkdetects false alignment using information on positions ofaligned regions of the sample sequence and matcheddatabase sequence. Normally, the order of aligned regionsof the sample sequence is consistent with that of thematched database sequence (Figure 1A). On the otherhand, most pairs of sequences that contain false align-ments are not consistent with respect to the order ofaligned regions (Figure 1B). The alignments consistencycheck detects collapses of these consistencies andexcludes these pairs of sample and database sequences inthe target calculation of total BLAST scores.
Graphical representation of the taxonomic composition of the sampleAfter determining the nearest relative of each samplesequence, an average similarity between the samplesequence and the nearest relative was calculated fromeach set of alignments (Figure 1A). Information on thenearest relative and the average similarity is representedas a circle plot (Figures 2 and 3). In the figures, each spe-cies name in the reference 16S rRNA gene database isplaced outside of the most lateral circle with ordered phy-logenetic relatedness. Physical distances between nearest
Mori et al. BMC Bioinformatics 2010, 11:332http://www.biomedcentral.com/1471-2105/11/332
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species in the plot indicate genetic distances of 16S rRNAgenes between them. The font color for each speciesname corresponds to its phylum name. Large circles indi-cate boundaries of BLAST average similarities (innermost circle starting at 80%, followed by 85, 90, 95 and100% similarity of the database sequence). Small coloreddots represent average similarities of each sequenceagainst the nearest relative species. The size of these dotsindicates relative abundance of sequences in the sample.The figure produced by VITCOMIC contains four cate-gories of dot size that indicate the relative abundance ofthe sample sequence: smallest dot < 1%; second smallestdot < 5%; third smallest dot < 10% (largest dot in Figures 2and 3); and the largest dot > 10%. The results are output-ted as a Postscript file that can be viewed at high resolu-tion. The overall workflow of VITCOMIC is described inFigure 4. The input file of VITCOMIC is basically a resultfile of BLAST against our reference 16S rRNA genesequence database. Our reference database can be down-
loaded from the VITCOMIC web site http://mg.bio.titech.ac.jp/vitcomic/. When analyzing smallamounts of data (less than 100,000 sequences), the multi-FASTA file before BLAST is accepted as the input file.The VITCOMIC web site contains detailed instructionsfor users.
Comparison of taxonomic compositions between samplesTo compare taxonomic compositions between samples,VITCOMIC clusters sample sequences using single-link-age clustering with 99% similarity as follows. When asample sequence is assigned to a reference speciesaccording to a certain average similarity as describedabove, VITCOMIC rounds down the average similarity tothe integer. If the rounded average similarity and thematched reference species are identical between samplesequences, VITCOMIC clusters these sequencestogether. For example, one sequence was assigned toBacillus subtilis with 98.8% average similarity, whereasanother sequence was assigned to B. subtilis with 98.1%
Figure 1 Calculation of total BLAST scores and average similarities. (A) A diagram of calculated total BLAST scores and average similarities be-tween the sample and database sequences. (B) An example of a collapse of the alignment consistency caused by a false alignment.
similarity 95.3 %score 250
similarity 98.2 %score 220
similarity 97.5 %score 300
Average similarity 97 %Total score 770
Reference 16S rRNA sequence of Species A
sequence a_1
sequence a_2
Alignments consistency is broken
A. Normal case
B. Strange case
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average similarity; VITCOMIC clusters these sequencesin the B. subtilis 98% cluster. After applying this single-linkage clustering based on reference sequences with 99%similarity to each sample, VITCOMIC compares the clus-tering results to identify common clusters between sam-ples. When the cluster that is assigned to the samereference species and sequence similarity exists both ofthe samples, the cluster is designated as a common clus-ter between samples. Using information on commonclusters between samples, VITCOMIC creates a mergedplot the one shown in Figure 5. Gray dots indicate com-mon clusters between the obese and lean samples, greendots indicate specific clusters of the obese samples, andorange dots indicate specific clusters of the lean samples.
For statistical comparison of taxonomic compositionsbetween samples, VITCOMIC calculates three types ofsimilarity indices for taxonomic compositions betweensamples using the clustering result (Jaccard index, Len-non index, and Yue and Clayton theta index) [31]. Theseindices are shown in the lower-right portion of themerged plot (Figure 5).
ResultsUsing VITCOMIC, the overall taxonomic compositionsof both the obese and lean samples could be clearly visu-alized (Figure 2 = obese; Figure 3 = lean). Large coloreddots indicate relatively abundant taxa in each sample (rel-ative abundance > 1%). These large colored dots are dis-
Figure 2 Mapping result for the human gut sample from obese individuals.
10095908580 Escherichia_coliEscherichia_fergusoniiShigella_flexneriShigella_boydiiShigella_sonneiShigella_dysenteriaeCitrobacter_koseriSalmonella_entericaErwinia_tasmaniensisCronobacter_sakazakiiPectobacterium_carotovorumDickeya_zeaePectobacterium_atrosepticumEnterobacter_sp.Klebsiella_pneumoniaeDickeya_dadantiiEdwardsiella_ictaluriSodalis_glossinidiusSerratia_proteamaculansYersinia_enterocoliticaYersinia_pseudotuberculosisYersinia_pestisPhotorhabdus_asymbioticaPhotorhabdus_luminescensProteus_mirabilisCandidatus_HamiltonellaBuchnera_aphidicolaBaumannia_cicadellinicola
Candidatus_BlochmanniaWigglesworthia_glossinidiaAliivibrio_salmonicidaVibrio_fischeriVibrio_splendidusVibrio_harveyiVibrio_parahaemolyticus
Vibrio_vulnificusPhotobacterium_profundum
Vibrio_choleraeHaemophilus_somnus
Actinobacillus_succinogenes
Actinobacillus_pleuropneumoniae
Haemophilus_ducreyi
Mannheimia_succiniciproducens
Aggregatibacter_aphrophilus
Haemophilus_influenzae
Haemophilus_parasuis
Pasteurella_multocida
Tolumonas_auensis
Aeromonas_salmonicida
Aeromonas_hydrophila
Shewanella_woodyi
Shewanella_sediminis
Shewanella_loihica
Shewanella_halifaxensis
Shewanella_pealeana
Shewanella_piezotolerans
Shewanella_amazonensis
Shewanella_frigidimarina
Shewanella_denitrificans
Shewanella_baltica
Shewanella_sp.
Shewanella_putrefaciens
Shewanella_oneidensis
Alteromonas_macleodii
Pseudoalteromonas_atlantica
Pseudoalteromonas_haloplanktis
Psychromonas_ingrahamii
Colwellia_psychrerythraea
Idiomarina_loihiensis
Alcanivorax_borkumensis
Marinomonas_sp.
Chromohalobacter_salexigens
Cellvibrio_japonicus
Teredinibacter_turnerae
Saccharophagus_degradans
Marinobacter_aquaeolei
Hahella_chejuensis
Azotobacter_vinelandii
Pseudomonas_fluorescens
Pseudomonas_syringae
Pseudomonas_mendocina
Pseudomonas_stutzeri
Pseudomonas_entomophila
Pseudomonas_putida
Pseudomonas_aeruginosa
Legionella_pneumophila
Acinetobacter_sp.
Acinetobacter_baumannii
Psychrobacter_sp.
Psychrobacter_cryohalolentis
Psychrobacter_arcticus
Dichelobacter_nodosus
Thiomicrospira_crunogena
Candidatus_Ruthia
Candidatus_Vesicomyosocius
Candidatus_Carsonella
Francisella_philomiragia
Francisella_novicida
Francisella_tularensis
Acidithiobacillus_ferrooxidans
Nitrosococcus_oceani
Methylococcus_capsulatus
Thioalkalivibrio_sp.
Halorhodospira_halophila
Alkalilimnicola_ehrlichii
Coxiella_burnetii
Stenotrophomonas_m
altophilia
Xanthomonas_oryzae
Xanthomonas_axonopodis
Xanthomonas_cam
pestris
Xylella_fastidiosa
Leptothrix_cholodnii
Methylibium
_petroleiphilum
Verminephrobacter_eiseniae
Delftia_acidovorans
Diaphorobacter_sp.
Acidovorax_sp.
Acidovorax_citrulli
Variovorax_paradoxus
Polaromonas_naphthalenivorans
Polaromonas_sp.
Rhodoferax_ferrireducens
Nitrosospira_m
ultiformis
Nitrosom
onas_eutropha
Nitrosom
onas_europaea
Thauera_sp.
Aromatoleum
_aromaticum
Azoarcus_sp.
Dechlorom
onas_aromatica
Thiobacillus_denitrificans
Burkholderia_phym
atum
Burkholderia_xenovorans
Burkholderia_thailandensis
Burkholderia_m
allei
Burkholderia_pseudom
allei
Burkholderia_glum
ae
Burkholderia_m
ultivorans
Burkholderia_vietnam
iensis
Burkholderia_am
bifaria
Burkholderia_sp.
Burkholderia_cenocepacia
Bordetella_bronchiseptica
Bordetella_parapertussis
Bordetella_pertussis
Bordetella_petrii
Bordetella_avium
Herm
iniimonas_arsenicoxydans
Janthinobacterium_sp.
Polynucleobacter_necessarius
Cupriavidus_taiw
anensis
Ralstonia_eutropha
Ralstonia_m
etallidurans
Ralstonia_pickettii
Ralstonia_solanacearum
Methylotenera_m
obilis
Methylovorus_sp.
Methylobacillus_flagellatus
Laribacter_hongkongensis
Chrom
obacterium_violaceum
Neisseria_gonorrhoeae
Neisseria_m
eningitidis
Magnetococcus_sp.
Acidiphilium
_cryptum
Gluconobacter_oxydans
Granulibacter_bethesdensis
Gluconacetobacter_diazotrophicus
Candidatus_P
elagibacter
Neorickettsia_risticii
Neorickettsia_sennetsu
Ehrlichia_rum
inantium
Ehrlichia_chaffeensis
Ehrlichia_canis
Anaplasm
a_phagocytophilum
Anaplasm
a_marginale
Wolbachia_sp.
Wolbachia_endosym
biont
Orientia_tsutsugam
ushi
Rickettsia_prow
azekii
Rickettsia_typhi
Rickettsia_akari
Rickettsia_canadensis
Rickettsia_bellii
Rickettsia_felis
Rickettsia_m
assiliae
Rickettsia_peacockii
Rickettsia_rickettsii
Rickettsia_africae
Rickettsia_conorii
Candidatus_Liberibacter
Candidatus_H
odgkinia
Rhodospirillum
_rubrum
Rhodospirillum
_centenum
Magnetospirillum
_magneticum
Novosphingobium
_aromaticivorans
Sphingopyxis_alaskensis
Erythrobacter_litoralis
Sphingom
onas_wittichii
Zym
omonas_m
obilisM
aricaulis_maris
Hirschia_baltica
Hyphom
onas_neptuniumP
arvibaculum_lavam
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aracoccus_denitrificansR
hodobacter_sphaeroidesD
inoroseobacter_shibaeJannaschia_sp.R
oseobacter_denitrificansR
uegeria_sp.R
uegeria_pomeroyi
Methylobacterium
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ethylobacterium_nodulans
Methylobacterium
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ethylobacterium_populi
Methylobacterium
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Methylobacterium
_extorquensO
ligotropha_carboxidovoransN
itrobacter_hamburgensis
Nitrobacter_w
inogradskyiR
hodopseudomonas_palustris
Bradyrhizobium
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radyrhizobium_japonicum
Methylocella_silvestris
Beijerinckia_indica
Xanthobacter_autotrophicus
Azorhizobium
_caulinodansM
esorhizobium_sp.
Mesorhizobium
_lotiB
artonella_bacilliformis
Bartonella_quintana
Bartonella_henselae
Bartonella_graham
ii
Bartonella_tribocorum
Ochrobactrum
_anthropi
Brucella_canis
Brucella_ovis
Brucella_abortus
Brucella_suis
Brucella_m
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inorhizobium_m
edicae
Sinorhizobium
_meliloti
Rhizobium
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hizobium_etli
Rhizobium
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Agrobacterium
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Agrobacterium
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grobacterium_tum
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Phenylobacterium
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Caulobacter_sp.
Caulobacter_crescentus
Helicobacter_pylori
Helicobacter_acinonychis
Helicobacter_hepaticus
Wolinella_succinogenes
Sulfurim
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Sulfurovum
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Cam
pylobacter_hominis
Cam
pylobacter_concisus
Cam
pylobacter_curvus
Cam
pylobacter_fetus
Cam
pylobacter_lari
Cam
pylobacter_jejuni
Nautilia_profundicola
Nitratiruptor_sp.
Salinibacter_ruber
Candidatus_A
moebophilus
Cytophaga_hutchinsonii
Candidatus_S
ulcia
Gram
ella_forsetii
Flavobacterium_johnsoniae
Flavobacterium_psychrophilum
Candidatus_Azobacteroides
Parabacteroides_distasonis
Bacteroides_vulgatus
Bacteroides_fragilis
Bacteroides_thetaiotaomicron
Porphyromonas_gingivalis
Chloroherpeton_thalassium
Prosthecochloris_aestuarii
Chlorobium_chlorochromatii
Pelodictyon_phaeoclathratiforme
Chlorobium_phaeobacteroides
Chlorobium_lim
icola
Pelodictyon_luteolum
Chlorobaculum_parvum
Chlorobium_tepidum
Bdellovibrio_bacteriovorus
Leptospira_biflexa
Leptospira_borgpetersenii
Leptospira_interrogans
Brachyspira_hyodysenteriae
Borrelia_recurrentis
Borrelia_duttonii
Borrelia_turicatae
Borrelia_hermsii
Borrelia_afzelii
Borrelia_garinii
Borrelia_burgdorferi
Treponema_denticola
Treponema_pallidum
Lawsonia_intracellularis
Desulfovibrio_magneticus
Desulfovibrio_salexigens
Desulfovibrio_desulfuricans
Desulfovibrio_vulgaris
Anaeromyxobacter_sp.
Anaeromyxobacter_dehalogenans
Myxococcus_xanthus
Sorangium_cellulosum
Syntrophobacter_fumaroxidans
Desulfotalea_psychrophila
Desulfobacterium_autotrophicum
Desulfatibacillum_alkenivorans
Desulfococcus_oleovorans
Syntrophus_aciditrophicus
Pelobacter_carbinolicus
Geobacter_bemidjiensis
Geobacter_sp.
Geobacter_uraniireducens
Geobacter_lovleyi
Pelobacter_propionicus
Geobacter_metallireducens
Geobacter_sulfurreducens
Candidatus_Solibacter
Acidobacterium_capsulatum
Candidatus_Koribacter
Elusimicrobium_minutum
uncultured_Termite
Fusobacterium_nucleatum
Acholeplasma_laidlawii
Aster_yellows
Mycoplasma_capricolum
Onion_yellowsCandidatus_Phytoplasma
Mycoplasma_mycoidesMesoplasma_florum
Mycoplasma_arthritidisMycoplasma_pulmonisMycoplasma_agalactiae Mycoplasma_synoviaeMycoplasma_mobile Mycoplasma_conjunctivae Mycoplasma_hyopneumoniae
Mycoplasma_penetrans Ureaplasma_urealyticumUreaplasma_parvum Mycoplasma_pneumoniae
Mycoplasma_genitaliumMycoplasma_gallisepticum Eubacterium_rectale
Eubacterium_eligensClostridium_phytofermentans
Alkaliphilus_oremlandii
Alkaliphilus_metalliredigens
Clostridium_difficileFinegoldia_magna
Paenibacillus_sp.
Brevibacillus_brevis
Anoxybacillus_flavithermus
Geobacillus_sp.
Geobacillus_thermodenitrificans
Geobacillus_kaustophilus
Exiguobacterium_sp.
Exiguobacterium_sibiricum
Lysinibacillus_sphaericus
Oceanobacillus_iheyensis
Bacillus_halodurans
Bacillus_clausii
Bacillus_pumilus
Bacillus_amyloliquefaciens
Bacillus_subtilis
Bacillus_licheniformis
Bacillus_cytotoxicus
Bacillus_weihenstephanensis
Bacillus_thuringiensis
Bacillus_anthracis
Bacillus_cereus
Listeria_welshimeri
Listeria_innocua
Listeria_monocytogenes
Enterococcus_faecalis
Macrococcus_caseolyticus
Staphylococcus_carnosus
Staphylococcus_saprophyticus
Staphylococcus_haemolyticus
Staphylococcus_aureus
Staphylococcus_epidermidis
Leuconostoc_citreum
Leuconostoc_mesenteroides
Oenococcus_oeni
Lactobacillus_salivariu
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Lactobacillus_ferm
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Lactobacillus_reuteri
Lactobacillus_casei
Lactobacillus_sakei
Pediococcu
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Lactobacill
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Lactobacill
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Lactobacill
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Thermoplasma_volcanium
Thermoplasma_acidophilum
Picrophilus_torridus
Methanoculleus_marisnigri
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Methanosphaerula_palustris
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Methanosaeta_thermophila
Methanococcoides_burtonii
Methanosarcina_barkeri
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Haloquadratum_walsbyi
Natronomonas_pharaonis
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Relative abundance <= 1%
Relative abundance <= 5%
Relative abundance <= 10%
Relative abundance > 10%
Mori et al. BMC Bioinformatics 2010, 11:332http://www.biomedcentral.com/1471-2105/11/332
Page 5 of 9
tributed almost identically between obese and leansamples and are located at related species of Clostridium,Eubacterim, and Bacteroides. These taxa are the abun-dant in the normal human gut microbiome [32]. Smalldots that are located at the most lateral circle indicateclosely related strains of the genome-sequenced strains.These strains are Escherichia coli and Proteus mirabilis inProteobacteria, Enterococcus faecalis and the group ofLactobacillus in Firmicutes, groups of Bifidobacteriumand Propionibacterium in Actinobacteria, and Akkerman-sia muciniphila in Verrucomicrobia. It is well establishedthat some of these strains inhabit the human gut, whereasothers do not [33-39]. In Figures 2 and 3, several dots aredistributed on the 80-90% lines, indicating that several
taxa distantly related to genome-sequenced strainsinhabit the human gut. These results were consistentwith the study of Turnbaugh et al. [15].
Differences between the obese and lean samples areclearly evident in Figure 5, which was created by the com-paring function of VITCOMIC. Gray dots indicate com-mon taxa between the obese and lean samples; green dotsindicate specific taxa of the obese samples, and orangedots indicate specific taxa of the lean samples. Themajority of taxa appear to be common between obese andlean samples, although certain taxa could be specific tothe obese or lean sample (for example, the phylum Acti-nobacteria in the obese sample as described in the studyof Turnbaugh et al. [15]). Figure 6 presents a higher reso-
Figure 3 Mapping result for the human gut sample from lean individuals.
10095908580 Escherichia_coliEscherichia_fergusoniiShigella_flexneriShigella_boydiiShigella_sonneiShigella_dysenteriaeCitrobacter_koseriSalmonella_entericaErwinia_tasmaniensisCronobacter_sakazakiiPectobacterium_carotovorumDickeya_zeaePectobacterium_atrosepticumEnterobacter_sp.Klebsiella_pneumoniaeDickeya_dadantiiEdwardsiella_ictaluriSodalis_glossinidiusSerratia_proteamaculansYersinia_enterocoliticaYersinia_pseudotuberculosisYersinia_pestisPhotorhabdus_asymbioticaPhotorhabdus_luminescensProteus_mirabilisCandidatus_HamiltonellaBuchnera_aphidicolaBaumannia_cicadellinicola
Candidatus_BlochmanniaWigglesworthia_glossinidiaAliivibrio_salmonicidaVibrio_fischeriVibrio_splendidusVibrio_harveyiVibrio_parahaemolyticus
Vibrio_vulnificusPhotobacterium_profundum
Vibrio_choleraeHaemophilus_somnus
Actinobacillus_succinogenes
Actinobacillus_pleuropneumoniae
Haemophilus_ducreyi
Mannheimia_succiniciproducens
Aggregatibacter_aphrophilus
Haemophilus_influenzae
Haemophilus_parasuis
Pasteurella_multocida
Tolumonas_auensis
Aeromonas_salmonicida
Aeromonas_hydrophila
Shewanella_woodyi
Shewanella_sediminis
Shewanella_loihica
Shewanella_halifaxensis
Shewanella_pealeana
Shewanella_piezotolerans
Shewanella_amazonensis
Shewanella_frigidimarina
Shewanella_denitrificans
Shewanella_baltica
Shewanella_sp.
Shewanella_putrefaciens
Shewanella_oneidensis
Alteromonas_macleodii
Pseudoalteromonas_atlantica
Pseudoalteromonas_haloplanktis
Psychromonas_ingrahamii
Colwellia_psychrerythraea
Idiomarina_loihiensis
Alcanivorax_borkumensis
Marinomonas_sp.
Chromohalobacter_salexigens
Cellvibrio_japonicus
Teredinibacter_turnerae
Saccharophagus_degradans
Marinobacter_aquaeolei
Hahella_chejuensis
Azotobacter_vinelandii
Pseudomonas_fluorescens
Pseudomonas_syringae
Pseudomonas_mendocina
Pseudomonas_stutzeri
Pseudomonas_entomophila
Pseudomonas_putida
Pseudomonas_aeruginosa
Legionella_pneumophila
Acinetobacter_sp.
Acinetobacter_baumannii
Psychrobacter_sp.
Psychrobacter_cryohalolentis
Psychrobacter_arcticus
Dichelobacter_nodosus
Thiomicrospira_crunogena
Candidatus_Ruthia
Candidatus_Vesicomyosocius
Candidatus_Carsonella
Francisella_philomiragia
Francisella_novicida
Francisella_tularensis
Acidithiobacillus_ferrooxidans
Nitrosococcus_oceani
Methylococcus_capsulatus
Thioalkalivibrio_sp.
Halorhodospira_halophila
Alkalilimnicola_ehrlichii
Coxiella_burnetii
Stenotrophomonas_m
altophilia
Xanthomonas_oryzae
Xanthomonas_axonopodis
Xanthomonas_cam
pestris
Xylella_fastidiosa
Leptothrix_cholodnii
Methylibium
_petroleiphilum
Verminephrobacter_eiseniae
Delftia_acidovorans
Diaphorobacter_sp.
Acidovorax_sp.
Acidovorax_citrulli
Variovorax_paradoxus
Polaromonas_naphthalenivorans
Polaromonas_sp.
Rhodoferax_ferrireducens
Nitrosospira_m
ultiformis
Nitrosom
onas_eutropha
Nitrosom
onas_europaea
Thauera_sp.
Aromatoleum
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Azoarcus_sp.
Dechlorom
onas_aromatica
Thiobacillus_denitrificans
Burkholderia_phym
atum
Burkholderia_xenovorans
Burkholderia_thailandensis
Burkholderia_m
allei
Burkholderia_pseudom
allei
Burkholderia_glum
ae
Burkholderia_m
ultivorans
Burkholderia_vietnam
iensis
Burkholderia_am
bifaria
Burkholderia_sp.
Burkholderia_cenocepacia
Bordetella_bronchiseptica
Bordetella_parapertussis
Bordetella_pertussis
Bordetella_petrii
Bordetella_avium
Herm
iniimonas_arsenicoxydans
Janthinobacterium_sp.
Polynucleobacter_necessarius
Cupriavidus_taiw
anensis
Ralstonia_eutropha
Ralstonia_m
etallidurans
Ralstonia_pickettii
Ralstonia_solanacearum
Methylotenera_m
obilis
Methylovorus_sp.
Methylobacillus_flagellatus
Laribacter_hongkongensis
Chrom
obacterium_violaceum
Neisseria_gonorrhoeae
Neisseria_m
eningitidis
Magnetococcus_sp.
Acidiphilium
_cryptum
Gluconobacter_oxydans
Granulibacter_bethesdensis
Gluconacetobacter_diazotrophicus
Candidatus_P
elagibacter
Neorickettsia_risticii
Neorickettsia_sennetsu
Ehrlichia_rum
inantium
Ehrlichia_chaffeensis
Ehrlichia_canis
Anaplasm
a_phagocytophilum
Anaplasm
a_marginale
Wolbachia_sp.
Wolbachia_endosym
biont
Orientia_tsutsugam
ushi
Rickettsia_prow
azekii
Rickettsia_typhi
Rickettsia_akari
Rickettsia_canadensis
Rickettsia_bellii
Rickettsia_felis
Rickettsia_m
assiliae
Rickettsia_peacockii
Rickettsia_rickettsii
Rickettsia_africae
Rickettsia_conorii
Candidatus_Liberibacter
Candidatus_H
odgkinia
Rhodospirillum
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Rhodospirillum
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Magnetospirillum
_magneticum
Novosphingobium
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Sphingopyxis_alaskensis
Erythrobacter_litoralis
Sphingom
onas_wittichii
Zym
omonas_m
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aricaulis_maris
Hirschia_baltica
Hyphom
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arvibaculum_lavam
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aracoccus_denitrificansR
hodobacter_sphaeroidesD
inoroseobacter_shibaeJannaschia_sp.R
oseobacter_denitrificansR
uegeria_sp.R
uegeria_pomeroyi
Methylobacterium
_radiotoleransM
ethylobacterium_nodulans
Methylobacterium
_sp.M
ethylobacterium_populi
Methylobacterium
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Methylobacterium
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ligotropha_carboxidovoransN
itrobacter_hamburgensis
Nitrobacter_w
inogradskyiR
hodopseudomonas_palustris
Bradyrhizobium
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radyrhizobium_japonicum
Methylocella_silvestris
Beijerinckia_indica
Xanthobacter_autotrophicus
Azorhizobium
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esorhizobium_sp.
Mesorhizobium
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artonella_bacilliformis
Bartonella_quintana
Bartonella_henselae
Bartonella_graham
ii
Bartonella_tribocorum
Ochrobactrum
_anthropi
Brucella_canis
Brucella_ovis
Brucella_abortus
Brucella_suis
Brucella_m
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inorhizobium_m
edicae
Sinorhizobium
_meliloti
Rhizobium
_sp.R
hizobium_etli
Rhizobium
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Agrobacterium
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Agrobacterium
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grobacterium_tum
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Phenylobacterium
_zucineum
Caulobacter_sp.
Caulobacter_crescentus
Helicobacter_pylori
Helicobacter_acinonychis
Helicobacter_hepaticus
Wolinella_succinogenes
Sulfurim
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Sulfurovum
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rcobacter_butzleri
Cam
pylobacter_hominis
Cam
pylobacter_concisus
Cam
pylobacter_curvus
Cam
pylobacter_fetus
Cam
pylobacter_lari
Cam
pylobacter_jejuni
Nautilia_profundicola
Nitratiruptor_sp.
Salinibacter_ruber
Candidatus_A
moebophilus
Cytophaga_hutchinsonii
Candidatus_S
ulcia
Gram
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Flavobacterium_johnsoniae
Flavobacterium_psychrophilum
Candidatus_Azobacteroides
Parabacteroides_distasonis
Bacteroides_vulgatus
Bacteroides_fragilis
Bacteroides_thetaiotaomicron
Porphyromonas_gingivalis
Chloroherpeton_thalassium
Prosthecochloris_aestuarii
Chlorobium_chlorochromatii
Pelodictyon_phaeoclathratiforme
Chlorobium_phaeobacteroides
Chlorobium_lim
icola
Pelodictyon_luteolum
Chlorobaculum_parvum
Chlorobium_tepidum
Bdellovibrio_bacteriovorus
Leptospira_biflexa
Leptospira_borgpetersenii
Leptospira_interrogans
Brachyspira_hyodysenteriae
Borrelia_recurrentis
Borrelia_duttonii
Borrelia_turicatae
Borrelia_hermsii
Borrelia_afzelii
Borrelia_garinii
Borrelia_burgdorferi
Treponema_denticola
Treponema_pallidum
Lawsonia_intracellularis
Desulfovibrio_magneticus
Desulfovibrio_salexigens
Desulfovibrio_desulfuricans
Desulfovibrio_vulgaris
Anaeromyxobacter_sp.
Anaeromyxobacter_dehalogenans
Myxococcus_xanthus
Sorangium_cellulosum
Syntrophobacter_fumaroxidans
Desulfotalea_psychrophila
Desulfobacterium_autotrophicum
Desulfatibacillum_alkenivorans
Desulfococcus_oleovorans
Syntrophus_aciditrophicus
Pelobacter_carbinolicus
Geobacter_bemidjiensis
Geobacter_sp.
Geobacter_uraniireducens
Geobacter_lovleyi
Pelobacter_propionicus
Geobacter_metallireducens
Geobacter_sulfurreducens
Candidatus_Solibacter
Acidobacterium_capsulatum
Candidatus_Koribacter
Elusimicrobium_minutum
uncultured_Termite
Fusobacterium_nucleatum
Acholeplasma_laidlawii
Aster_yellows
Mycoplasma_capricolum
Onion_yellowsCandidatus_Phytoplasma
Mycoplasma_mycoidesMesoplasma_florum
Mycoplasma_arthritidisMycoplasma_pulmonisMycoplasma_agalactiae Mycoplasma_synoviaeMycoplasma_mobile Mycoplasma_conjunctivae Mycoplasma_hyopneumoniae
Mycoplasma_penetrans Ureaplasma_urealyticumUreaplasma_parvum Mycoplasma_pneumoniae
Mycoplasma_genitaliumMycoplasma_gallisepticum Eubacterium_rectale
Eubacterium_eligensClostridium_phytofermentans
Alkaliphilus_oremlandii
Alkaliphilus_metalliredigens
Clostridium_difficileFinegoldia_magna
Paenibacillus_sp.
Brevibacillus_brevis
Anoxybacillus_flavithermus
Geobacillus_sp.
Geobacillus_thermodenitrificans
Geobacillus_kaustophilus
Exiguobacterium_sp.
Exiguobacterium_sibiricum
Lysinibacillus_sphaericus
Oceanobacillus_iheyensis
Bacillus_halodurans
Bacillus_clausii
Bacillus_pumilus
Bacillus_amyloliquefaciens
Bacillus_subtilis
Bacillus_licheniformis
Bacillus_cytotoxicus
Bacillus_weihenstephanensis
Bacillus_thuringiensis
Bacillus_anthracis
Bacillus_cereus
Listeria_welshimeri
Listeria_innocua
Listeria_monocytogenes
Enterococcus_faecalis
Macrococcus_caseolyticus
Staphylococcus_carnosus
Staphylococcus_saprophyticus
Staphylococcus_haemolyticus
Staphylococcus_aureus
Staphylococcus_epidermidis
Leuconostoc_citreum
Leuconostoc_mesenteroides
Oenococcus_oeni
Lactobacillus_salivariu
s
Lactobacillus_ferm
entum
Lactobacillus_reuteri
Lactobacillus_casei
Lactobacillus_sakei
Pediococcu
s_pentosa
ceus
Lactobacill
us_brevis
Lactobacillu
s_plantarum
Lactobacill
us_delbrueck
ii
Lactobacill
us_helve
ticus
Lactobacill
us_acid
ophilus
Lactobacil
lus_gass
eri
Lactobacil
lus_johnso
nii
Lactoco
ccus_
lactis
Streptoco
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mutans
Streptoco
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s
Streptoco
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gordonii
Streptoco
ccus_
sanguinis
Streptoco
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pneumoniae
Streptoco
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suis
Streptoco
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equi
Streptoco
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Streptoco
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Streptoco
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Streptoc
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Clostri
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Clostri
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Clostri
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Clostri
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Clost
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taricus
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us
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Thermococcus_gammatolerans
Thermococcus_kodakarensis
Pyrococcus_horikoshii
Pyrococcus_abyssi
Pyrococcus_furiosus
Archaeoglobus_fulgidus
Methanopyrus_kandleri
Methanocaldococcus_jannaschii
Methanococcus_aeolicus
Methanococcus_vannielii
Methanococcus_maripaludis
Thermoplasma_volcanium
Thermoplasma_acidophilum
Picrophilus_torridus
Methanoculleus_marisnigri
Methanocorpusculum_labreanum
Methanosphaerula_palustris
Candidatus_Methanoregula
Methanospirillum_hungatei
uncultured_methanogenic
Methanosaeta_thermophila
Methanococcoides_burtonii
Methanosarcina_barkeri
Methanosarcina_acetivorans
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Haloquadratum_walsbyi
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Haloarcula_marismortui
Halobacterium_salinarumHalobacterium_sp.
Methanobrevibacter_smithii
Methanosphaera_stadtmanae
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ProteobacteriaChlorobiBacteroidetesAcidobacteriaElusimicrobiacandidatus division TG1SpirochaetesFusobacteriaFirmicutesTenericutesThermotogaeDictyoglomiChlamydiaeCyanobacteriaActinobacteriaGemmatimonadetesVerrucomicrobiaChloroflexiDeinococcus-ThermusNitrospiraePlanctomycetesAquificaeEuryarchaeotaNanoarchaeotaCrenarchaeotaThaumarchaeota
Relative abundance <= 1%
Relative abundance <= 5%
Relative abundance <= 10%
Relative abundance > 10%
Mori et al. BMC Bioinformatics 2010, 11:332http://www.biomedcentral.com/1471-2105/11/332
Page 6 of 9
lution view of the region related to Actibobacteria in Fig-ure 5.
DiscussionVITCOMIC can easily visualize overall taxonomic com-positions of large amounts of 16S rRNA gene-based com-munity analysis data. Traditional visualization methodsby constructing phylogenetic trees require a lot of com-putation time when analyzing large amounts of data [16].Even if researchers are able to construct a phylogenetictree, the tree itself can be difficult to analyze because itmay contain too many branches [29]. By contrast, taxo-nomic assignments based on BLAST are fast and can behighly parallelized [40]. Although several highly accuratetaxonomic assignment tools have been developed [41,42],the accuracy of BLAST-based taxonomic assignments isalso well validated [29,43]. In addition, calculations oftotal BLAST scores and applications of the alignmentsconsistency check improve the accuracy of the assign-ment, especially when long sequences are examined. Lon-
ger sequences containing more variable regions willgenerate a greater number of alignment divisions. Thealignments consistency check may be necessary for thestudy using the pyrosequencer because recently devel-oped pyrosequencer has improved the read length byover 400 bp [44]. Although the taxonomic assignmentusing only genome-sequenced species for the referencewould not yield the best assignment compared with theassignment using larger database that contains uncul-tured bacteria [12,45], this provisional taxonomy pro-vided by VITCOMIC is accurate enough for the visualcomparisons of taxonomic composition between sam-ples.
Compared with other tools, the most unique functionof VITCOMIC is a simultaneous visualization and com-parison of taxonomic compositions between samples(Additional file 1). Comparison of taxonomic composi-tions between samples from different microbial commu-nities is an effective means to better understandsimilarities and differences between microbial communi-
Figure 4 VITCOMIC flow chart.
Rnammer
Extract single 16S rRNA sequenceper one species
Reference 16S rRNA sequence database
MAFFT
dnadist in PHYLIP
neighbor in PHYLIP
Assign Taxonomy
Reference Tree
NCBI Genome Sequence database
NCBI TaxonomyDatabase
BLASTN
Sample 16S rRNA sequence data
Alignments consistency check
Extract hits of each query with max total scores
(nearest relative)
Create a plot using BLAST average similarities and
names of the nearest relative
User uploaded data
Mori et al. BMC Bioinformatics 2010, 11:332http://www.biomedcentral.com/1471-2105/11/332
Page 7 of 9
ties [10]. However, the comparison of several microbialcommunities can be difficult given a large number ofsequences [16]. VITCOMIC can simultaneously visualizelarge amounts of data by merging sequence data fromseveral community analysis projects (Additional files 2, 3,and 4). Additional file 2 visualizes 139,356 16S rRNAgene sequences obtained from various soils [13]. Addi-tional file 3 presents seawater microbial communitiesdata derived from 452 different 16S rRNA gene surveyscontaining 11,144,358 sequences, which were obtainedfrom the NCBI Sequence Read Archive [46]. Additionalfile 4 presents data for the human microbial communities
derived from 60 different 16S rRNA gene surveys con-taining 4,363,040 sequences, which were obtained fromNCBI Sequence Read Archive. Although detailed com-parisons among samples from different microbial com-munities are difficult due to the large number ofsequences and differing primers, VITCOMIC showedthat overall taxonomic compositions and abundant taxaare distinctly different between environments.
VITCOMIC only uses the 16S rRNA gene sequencesfrom 601 genome-sequenced bacteria as references. Thereason why we selected the reference database from 601species is the quality and quantity of the biological infor-
Figure 5 Merged results for the obese and lean human gut samples.
10095908580 Escherichia_coliEscherichia_fergusoniiShigella_flexneriShigella_boydiiShigella_sonneiShigella_dysenteriaeCitrobacter_koseriSalmonella_entericaErwinia_tasmaniensisCronobacter_sakazakiiPectobacterium_carotovorumDickeya_zeaePectobacterium_atrosepticumEnterobacter_sp.Klebsiella_pneumoniaeDickeya_dadantiiEdwardsiella_ictaluriSodalis_glossinidiusSerratia_proteamaculansYersinia_enterocoliticaYersinia_pseudotuberculosisYersinia_pestisPhotorhabdus_asymbioticaPhotorhabdus_luminescensProteus_mirabilisCandidatus_HamiltonellaBuchnera_aphidicolaBaumannia_cicadellinicola
Candidatus_BlochmanniaWigglesworthia_glossinidiaAliivibrio_salmonicidaVibrio_fischeriVibrio_splendidusVibrio_harveyiVibrio_parahaemolyticus
Vibrio_vulnificusPhotobacterium_profundum
Vibrio_choleraeHaemophilus_somnus
Actinobacillus_succinogenes
Actinobacillus_pleuropneumoniae
Haemophilus_ducreyi
Mannheimia_succiniciproducens
Aggregatibacter_aphrophilus
Haemophilus_influenzae
Haemophilus_parasuis
Pasteurella_multocida
Tolumonas_auensis
Aeromonas_salmonicida
Aeromonas_hydrophila
Shewanella_woodyi
Shewanella_sediminis
Shewanella_loihica
Shewanella_halifaxensis
Shewanella_pealeana
Shewanella_piezotolerans
Shewanella_amazonensis
Shewanella_frigidimarina
Shewanella_denitrificans
Shewanella_baltica
Shewanella_sp.
Shewanella_putrefaciens
Shewanella_oneidensis
Alteromonas_macleodii
Pseudoalteromonas_atlantica
Pseudoalteromonas_haloplanktis
Psychromonas_ingrahamii
Colwellia_psychrerythraea
Idiomarina_loihiensis
Alcanivorax_borkumensis
Marinomonas_sp.
Chromohalobacter_salexigens
Cellvibrio_japonicus
Teredinibacter_turnerae
Saccharophagus_degradans
Marinobacter_aquaeolei
Hahella_chejuensis
Azotobacter_vinelandii
Pseudomonas_fluorescens
Pseudomonas_syringae
Pseudomonas_mendocina
Pseudomonas_stutzeri
Pseudomonas_entomophila
Pseudomonas_putida
Pseudomonas_aeruginosa
Legionella_pneumophila
Acinetobacter_sp.
Acinetobacter_baumannii
Psychrobacter_sp.
Psychrobacter_cryohalolentis
Psychrobacter_arcticus
Dichelobacter_nodosus
Thiomicrospira_crunogena
Candidatus_Ruthia
Candidatus_Vesicomyosocius
Candidatus_Carsonella
Francisella_philomiragia
Francisella_novicida
Francisella_tularensis
Acidithiobacillus_ferrooxidans
Nitrosococcus_oceani
Methylococcus_capsulatus
Thioalkalivibrio_sp.
Halorhodospira_halophila
Alkalilimnicola_ehrlichii
Coxiella_burnetii
Stenotrophomonas_m
altophilia
Xanthomonas_oryzae
Xanthomonas_axonopodis
Xanthomonas_cam
pestris
Xylella_fastidiosa
Leptothrix_cholodnii
Methylibium
_petroleiphilum
Verminephrobacter_eiseniae
Delftia_acidovorans
Diaphorobacter_sp.
Acidovorax_sp.
Acidovorax_citrulli
Variovorax_paradoxus
Polaromonas_naphthalenivorans
Polaromonas_sp.
Rhodoferax_ferrireducens
Nitrosospira_m
ultiformis
Nitrosom
onas_eutropha
Nitrosom
onas_europaea
Thauera_sp.
Aromatoleum
_aromaticum
Azoarcus_sp.
Dechlorom
onas_aromatica
Thiobacillus_denitrificans
Burkholderia_phym
atum
Burkholderia_xenovorans
Burkholderia_thailandensis
Burkholderia_m
allei
Burkholderia_pseudom
allei
Burkholderia_glum
ae
Burkholderia_m
ultivorans
Burkholderia_vietnam
iensis
Burkholderia_am
bifaria
Burkholderia_sp.
Burkholderia_cenocepacia
Bordetella_bronchiseptica
Bordetella_parapertussis
Bordetella_pertussis
Bordetella_petrii
Bordetella_avium
Herm
iniimonas_arsenicoxydans
Janthinobacterium_sp.
Polynucleobacter_necessarius
Cupriavidus_taiw
anensis
Ralstonia_eutropha
Ralstonia_m
etallidurans
Ralstonia_pickettii
Ralstonia_solanacearum
Methylotenera_m
obilis
Methylovorus_sp.
Methylobacillus_flagellatus
Laribacter_hongkongensis
Chrom
obacterium_violaceum
Neisseria_gonorrhoeae
Neisseria_m
eningitidis
Magnetococcus_sp.
Acidiphilium
_cryptum
Gluconobacter_oxydans
Granulibacter_bethesdensis
Gluconacetobacter_diazotrophicus
Candidatus_P
elagibacter
Neorickettsia_risticii
Neorickettsia_sennetsu
Ehrlichia_rum
inantium
Ehrlichia_chaffeensis
Ehrlichia_canis
Anaplasm
a_phagocytophilum
Anaplasm
a_marginale
Wolbachia_sp.
Wolbachia_endosym
biont
Orientia_tsutsugam
ushi
Rickettsia_prow
azekii
Rickettsia_typhi
Rickettsia_akari
Rickettsia_canadensis
Rickettsia_bellii
Rickettsia_felis
Rickettsia_m
assiliae
Rickettsia_peacockii
Rickettsia_rickettsii
Rickettsia_africae
Rickettsia_conorii
Candidatus_Liberibacter
Candidatus_H
odgkinia
Rhodospirillum
_rubrum
Rhodospirillum
_centenum
Magnetospirillum
_magneticum
Novosphingobium
_aromaticivorans
Sphingopyxis_alaskensis
Erythrobacter_litoralis
Sphingom
onas_wittichii
Zym
omonas_m
obilisM
aricaulis_maris
Hirschia_baltica
Hyphom
o nas_neptuni umP
arvibaculum_lavam
entivoransP
aracoccus_denitrificansR
hodobacter_sphaeroidesD
inoroseobacter_shibaeJannaschia_sp.R
oseobacter_denitrificansR
uegeria_sp.R
uegeria_pomeroyi
Methylobacterium
_radiotoleransM
ethylobacterium_nodulans
Methylobacterium
_sp.M
ethylobacterium_populi
Methylobacterium
_chloromethanicum
Methylobacterium
_extorquensO
ligotropha_carboxidovoransN
itrobacter_hamburgensis
Nitrobacter_w
inogradskyiR
hodopseudomonas_palustris
Bradyrhizobium
_sp.B
radyrhizobium_japonicum
Methylocella_silvestris
Beijerinckia_indica
Xanthobacter_autotrophicus
Azorhizobium
_caulinodansM
esorhizobium_sp.
Mesorhizobium
_lotiB
artonella_bacilliformis
Bartonella_quintana
Bartonella_henselae
Bartonella_graham
ii
Bartonella_tribocorum
Ochrobactrum
_anthropi
Brucella_canis
Brucella_ovis
Brucella_abortus
Brucella_suis
Brucella_m
elitensisS
inorhizobium_m
edicae
Sinorhizobium
_meliloti
Rhizobium
_sp.R
hizobium_etli
Rhizobium
_leguminosarum
Agrobacterium
_radiobacter
Agrobacterium
_vitisA
grobacterium_tum
efaciens
Phenylobacterium
_zucineum
Caulobacter_sp.
Caulobacter_crescentus
Helicobacter_pylori
Helicobacter_acinonychis
Helicobacter_hepaticus
Wolinella_succinogenes
Sulfurim
onas_denitrificans
Sulfurovum
_sp.A
rcobacter_butzleri
Cam
pylobacter_hominis
Cam
pylobacter_concisus
Cam
pylobacter_curvus
Cam
pylobacter_fetus
Cam
pylobacter_lari
Cam
pylobacter_jejuni
Nautilia_profundicola
Nitratiruptor_sp.
Salinibacter_ruber
Candidatus_A
moebophilus
Cytophaga_hutchinsonii
Candidatus_S
ulcia
Gram
ella_forsetii
Flavobacterium_johnsoniae
Flavobacterium_psychrophilum
Candidatus_Azobacteroides
Parabacteroides_distasonis
Bacteroides_vulgatus
Bacteroides_fragilis
Bacteroides_thetaiotaomicron
Porphyromonas_gingivalis
Chloroherpeton_thalassium
Prosthecochloris_aestuarii
Chlorobium_chlorochromatii
Pelodictyon_phaeoclathratiforme
Chlorobium_phaeobacteroides
Chlorobium_lim
icola
Pelodictyon_luteolum
Chlorobaculum_parvum
Chlorobium_tepidum
Bdellovibrio_bacteriovorus
Leptospira_biflexa
Leptospira_borgpetersenii
Leptospira_interrogans
Brachyspira_hyodysenteriae
Borrelia_recurrentis
Borrelia_duttonii
Borrelia_turicatae
Borrelia_hermsii
Borrelia_afzelii
Borrelia_garinii
Borrelia_burgdorferi
Treponema_denticola
Treponema_pallidum
Lawsonia_intracellularis
Desulfovibrio_magneticus
Desulfovibrio_salexigens
Desulfovibrio_desulfuricans
Desulfovibrio_vulgaris
Anaeromyxobacter_sp.
Anaeromyxobacter_dehalogenans
Myxococcus_xanthus
Sorangium_cellulosum
Syntrophobacter_fumaroxidans
Desulfotalea_psychrophila
Desulfobacterium_autotrophicum
Desulfatibacillum_alkenivorans
Desulfococcus_oleovorans
Syntrophus_aciditrophicus
Pelobacter_carbinolicus
Geobacter_bemidjiensis
Geobacter_sp.
Geobacter_uraniireducens
Geobacter_lovleyi
Pelobacter_propionicus
Geobacter_metallireducens
Geobacter_sulfurreducens
Candidatus_Solibacter
Acidobacterium_capsulatum
Candidatus_Koribacter
Elusimicrobium_minutum
uncultured_Termite
Fusobacterium_nucleatum
Acholeplasma_laidlawii
Aster_yellows
Mycoplasma_capricolum
Onion_yellowsCandidatus_Phytoplasma
Mycoplasma_mycoidesMesoplasma_florum
Mycoplasma_arthritidisMycoplasma_pulmonisMycoplasma_agalactiae Mycoplasma_synoviaeMycoplasma_mobile Mycoplasma_conjunctivae Mycoplasma_hyopneumoniae
Mycoplasma_penetrans Ureaplasma_urealyticumUreaplasma_parvum Mycoplasma_pneumoniae
Mycoplasma_genitaliumMycoplasma_gallisepticum Eubacterium_rectale
Eubacterium_eligensClostridium_phytofermentans
Alkaliphilus_oremlandii
Alkaliphilus_metalliredigens
Clostridium_difficileFinegoldia_magna
Paenibacillus_sp.
Brevibacillus_brevis
Anoxybacillus_flavithermus
Geobacillus_sp.
Geobacillus_thermodenitrificans
Geobacillus_kaustophilus
Exiguobacterium_sp.
Exiguobacterium_sibiricum
Lysinibacillus_sphaericus
Oceanobacillus_iheyensis
Bacillus_halodurans
Bacillus_clausii
Bacillus_pumilus
Bacillus_amyloliquefaciens
Bacillus_subtilis
Bacillus_licheniformis
Bacillus_cytotoxicus
Bacillus_weihenstephanensis
Bacillus_thuringiensis
Bacillus_anthracis
Bacillus_cereus
Listeria_welshimeri
Listeria_innocua
Listeria_monocytogenes
Enterococcus_faecalis
Macrococcus_caseolyticus
Staphylococcus_carnosus
Staphylococcus_saprophyticus
Staphylococcus_haemolyticus
Staphylococcus_aureus
Staphylococcus_epidermidis
Leuconostoc_citreum
Leuconostoc_mesenteroides
Oenococcus_oeni
Lactobacillus_salivariu
s
Lactobacillus_ferm
entum
Lactobacillus_reuteri
Lactobacillus_casei
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Methanosarcina_acetivorans
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Halorubrum_lacusprofundi
Haloquadratum_walsbyi
Natronomonas_pharaonis
Haloarcula_marismortui
Halobacterium_salinarumHalobacterium_sp.
Methanobrevibacter_smithii
Methanosphaera_stadtmanae
Methanothermobacter_thermautotrophicus
Nitrosopumilus_maritimus
ProteobacteriaChlorobiBacteroidetesAcidobacteriaElusimicrobiacandidatus division TG1SpirochaetesFusobacteriaFirmicutesTenericutesThermotogaeDictyoglomiChlamydiaeCyanobacteriaActinobacteriaGemmatimonadetesVerrucomicrobiaChloroflexiDeinococcus-ThermusNitrospiraePlanctomycetesAquificaeEuryarchaeotaNanoarchaeotaCrenarchaeotaThaumarchaeota
Relative abundance <= 1%
Relative abundance <= 5%
Relative abundance <= 10%
Relative abundance > 10%
Jaccard index = 0.5739
Lennon index = 0.8437
Yue & Clayton theta = 0.9339
Mori et al. BMC Bioinformatics 2010, 11:332http://www.biomedcentral.com/1471-2105/11/332
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mation. These sequences are derived from genome-sequenced species, from which we can generally obtainmuch information about ecophysiology (i.e., metabolicpotentials, habitats, gene repertoires). Therefore, byadopting genome-sequenced species as the referencedatabase, we can retrieve several biological informationfor each taxon inductively by analyzing the genomicinformation of the nearest genome-sequenced speciesfrom the 16S rRNA gene-targeted analysis. These fea-tures provide valuable initiative knowledge for a follow-ing metagenomic analysis. To address the increasingnumber of genome-sequenced species, the referencedatabase of VITCOMIC will be updated periodically.
ConclusionsUsing a phylogenetic relationship with genome-sequenced strains, VITCOMIC clearly presents the over-all taxonomic composition of 16S rRNA gene-basedmicrobial community analysis data. VITCOMIC facili-
tates an intuitive understanding of differences in commu-nity structure between samples.
Availability and requirements• Project name: VITCOMIC
• Project home page: http://mg.bio.titech.ac.jp/vit-comic/
• Operating system(s): Platform independent• Programming language: Perl• Other requirements: None• License: GNU GPL• Any restrictions to use by non-academics: None
Additional material
Authors' contributionsHM and KK designed the study. HM developed the method and performed theanalyses. FM and KK provided advise on method design and analyses. HMdrafted the manuscript, and FM and KK critically revised it. All authors read andapproved the final manuscript.
AcknowledgementsWe thank Hiroyuki Toh, Tetsuya Hayashi and Takehiko Itoh for helpful discus-sions. This work was supported by a Grant-in-Aid from the Institute for Bioinfor-matics Research and Development, the Japan Science and Technology Agency (BIRD-JST) and a Grant-in-Aid for Scientific Research (C: 22592032).
Author DetailsDepartment of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 B-36, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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Received: 17 February 2010 Accepted: 18 June 2010 Published: 18 June 2010This article is available from: http://www.biomedcentral.com/1471-2105/11/332© 2010 Mori et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.BMC Bioinformatics 2010, 11:332
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doi: 10.1186/1471-2105-11-332Cite this article as: Mori et al., VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences BMC Bioinformatics 2010, 11:332