Metabolic pathways for the whole community
© Hanson et al.; licensee BioMed Central Ltd. 2014
Received: 14 January 2014
Accepted: 8 July 2014
Published: 22 July 2014
A convergence of high-throughput sequencing and computational power is transforming biology into information science. Despite these technological advances, converting bits and bytes of sequence information into meaningful insights remains a challenging enterprise. Biological systems operate on multiple hierarchical levels from genomes to biomes. Holistic understanding of biological systems requires agile software tools that permit comparative analyses across multiple information levels (DNA, RNA, protein, and metabolites) to identify emergent properties, diagnose system states, or predict responses to environmental change.
Here we adopt the MetaPathways annotation and analysis pipeline and Pathway Tools to construct environmental pathway/genome databases (ePGDBs) that describe microbial community metabolism using MetaCyc, a highly curated database of metabolic pathways and components covering all domains of life. We evaluate Pathway Tools’ performance on three datasets with different complexity and coding potential, including simulated metagenomes, a symbiotic system, and the Hawaii Ocean Time-series. We define accuracy and sensitivity relationships between read length, coverage and pathway recovery and evaluate the impact of taxonomic pruning on ePGDB construction and interpretation. Resulting ePGDBs provide interactive metabolic maps, predict emergent metabolic pathways associated with biosynthesis and energy production and differentiate between genomic potential and phenotypic expression across defined environmental gradients.
This multi-tiered analysis provides the user community with specific operating guidelines, performance metrics and prediction hazards for more reliable ePGDB construction and interpretation. Moreover, it demonstrates the power of Pathway Tools in predicting metabolic interactions in natural and engineered ecosystems.
Community interactions between uncultivated microorganisms give rise to dynamic metabolic networks integral to ecosystem function and global scale biogeochemical cycles . Metagenomics bridges the “cultivation gap” through plurality or single-cell sequencing by providing direct and quantitative insight into microbial community structure and function [2, 3]. Although, new technologies are rapidly expanding our capacity to chart microbial sequence space, persistent computational and analytical bottlenecks impede comparative analyses across multiple information levels (DNA, RNA, protein and metabolites) [4, 5]. This in turn limits our ability to convert the genetic potential and phenotypic expression of microbial communities into predictive insights and technological or therapeutic innovations.
Functional genes operate within the structure of metabolic pathways and reactions that define metabolic networks. Despite this fact, few metagenomic studies use pathway-centric approaches to predict microbial community interaction networks based on known biochemical rules. Recently, algorithms for pathway prediction and metabolic flux have been developed for environmental sequence information including the Human Microbiome Project Unified Metabolic Analysis Network (HUMAnN) and Predicted Relative Metabolic Turnover (PRMT). HUMAnN uses an integer optimization algorithm that conservatively computes a parsimonious minimum set of reactions along KEGG pathways based on pathway presence, absence or completion [6, 7]. PRMT infers metabolic flux based on normalized enzyme activity counts mapped to KEGG pathways across multiple metagenomes . Because KEGG pathways are coarse and do not discriminate between pathway variants, both modes of analysis have limited metabolic resolution . Moreover, neither HUMAnN nor PRMT provides a coherent structure for exploring and interpreting predicted KEGG pathways.
One alternative to HUMAnN and PRMT is Pathway Tools, a production-quality software environment supporting metabolic inference and flux balance analysis based on the MetaCyc database of metabolic pathways and enzymes representing all domains of life [10–13]. Unlike KEGG or SEED subsystems, MetaCyc emphasizes smaller, evolutionarily conserved or co-regulated units of metabolism and contains the largest collection (over 2000) of experimentally validated metabolic pathways. Extensively commented pathway descriptions, literature citations, and enzyme properties combined within a pathway/genome database (PGDB) provide a coherent structure for exploring and interpreting predicted pathways. Although initially conceived for cellular organisms, recent development of the MetaPathways pipeline extends the PGDB concept to environmental sequence information enabling pathway-centric insights into microbial community structure and function [14, 15].
Results and discussion
To better constrain pathway recovery and performance in relation to ePGDB construction we compared results of MetaSim experiments using the Esherichia coli K12 substr. MG1655 genome (basis of the EcoCyc database), Sim1 and Sim2, and a subsampled 25 m metagenome from HOT  (Additional file 1: Materials and Methods, Tables S1-S4 and Figure S1). Simulations were performed at progressively larger Gm coverage. Consistent with previous observations for Sim1 and Sim2, all experiments showed that pathway recovery percentage and performance sensitivity increased with sequence coverage and sample diversity nearing an asymptote at higher coverage (Figure 2a-b). The absolute values of these patterns were sensitive to read length and likely reflected limits imposed by open reading frame prediction and BLAST/LAST-based annotation. In contrast, performance specificity was high (>85%) regardless of read length, coverage, or taxonomic diversity (Figure 2b). The rate of pathway recovery increased proportionally with increasing sample diversity at lower coverage values, as seen in the reduction of pathway recovery percentage between Sim1, Sim2 and E. coli for long read (~700 bp) and between HOT, Sim1/2 and E. coli for short read (~160 bp) datasets. Additional performance metrics can be found in Additional file 1: Tables S5–S8. Because PathoLogic performance improves with increasing read length, coverage and sample diversity, sequencing platform selection and use of assembled versus unassembled sequence information should be considered when generating ePGDBs.
When constructing PGDBs for individual genomes PathoLogic uses a process called taxonomic pruning to constrain pathway predictions within a specified taxonomic lineage by taking advantage of the curated ‘taxonomic-range’ associated with a given pathway. For example, if a pathway is found only in plants, it will be difficult to predict this pathway in the genome of a bacterial isolate when using taxonomic pruning. Such a process is intended to reduce false positive predictions in individual genomes ; However, microbial communities are composed of diverse and largely uncultivated lineages whose combined metabolic potential and phenotypic expression must be considered both within and between individuals. Thus the taxonomic origin of environmental sequence information is more difficult to ascertain with the same degree of certainty as individual microbial genomes sourced from isolates or single-cells. Indeed, the true taxonomic range of many pathways remains to be constrained given the limited number of isolate genomes and the proclivity for horizontal gene transfer within microbial communities.
In order to evaluate the impact of taxonomic pruning on pathway recovery from environmental sequence information we constructed ePGDBs enabling or disabling taxon-specific pathway distributions (Additional file 1: Table S9). We ran PathoLogic on Sim1/2 and 25 m HOT datasets with the ‘Unclassified sequences’ pruning threshold and without pruning. With taxonomic pruning enabled, long read and short read Sim1 ePGDBs exhibited a reduction of 56% (206 compared to 604) and 61% (194 compared to 499) predicted pathways, respectively. Interestingly, the subsampled 25 m HOT dataset exhibited a 28% reduction (425 compared to 593) in pathway recovery with and without pruning suggesting that increased sample complexity can partially offset taxon specific sensitivity losses. In all cases, the pathways predicted with taxonomic pruning were a subset of pathways predicted without taxonomic pruning. Given these observations we posit that strict taxonomic pruning is inappropriate for ePGDB construction while recognizing potential prediction hazards associated with pathways predicted outside of their expected taxonomic range.
To evaluate concordance between pathways predicted using environmental sequence information and reference pathways in the MetaCyc database we developed a weighted taxonomic distance (WTD) algorithm. The WTD algorithm measures the taxonomic distance between predicted coding DNA sequences (CDS), e.g., BLAST hits from the RefSeq database, and expected taxonomic range for each predicted pathway using the NCBI Taxonomy Database. The NCBI Taxonomy Database is hierarchically structured, and a path between the lowest common ancestor (LCA) of observed CDS annotations and each member of the expected taxonomic range in a pathway can be charted , where each path length represents some measure of taxonomic distance e.g. root, cellular organism, domain, phylum/division, class, order, family, genus, species. Steps on the path near the root of the hierarchy define greater evolutionary distances than those near the tips. Thus the WTD algorithm weights steps on the connecting path by a factor of , where d is the depth position of a particular taxon in the hierarchy (Additional file 1: Supplementary Note 2). To distinguish between paths descending from the expected taxonomic range and those falling outside the expected taxonomic range, paths descending from an expected taxonomic range have a non-negative distance and paths outside this range have a negative distance. The WTD algorithm gives preference to non-negative distances within expected taxonomic range(s), returning the minimum distance if found. Otherwise the maximum negative distance (i.e., closest to zero) is returned.
When the WTD algorithm was applied to HOT datasets, the taxonomic distribution of predicted pathways generally aligned with the expected taxonomic ranges of MetaCyc Pathways (Additional file 1: Figure S2). Predicted pathways were classified into four categories of taxonomic disagreement based on their WTD: “None” if the WTD was positive, and “Low”, “Medium”, and “High” if less than or equal to zero, based on distance quartiles. A pathway had “Low” taxonomic disagreement if in the upper two quartiles of negative distances (i.e., those closest to zero), “Medium” if in the second quartile, and “High” if in the bottom (i.e., most negative) quartile. Pathways with expected taxonomic ranges affiliated with bacteria and archaea dominated the “None”, “Low”, and “Medium” disagreement classes, while pathways with expected taxonomic ranges affiliated with eukaryotes including “animals”, “fungi”, and “plants” comprised the majority of the “High” disagreement class (Additional file 1: Figure S3). While not excluded from downstream analysis, pathways with distances in the “High” disagreement class are more likely to represent false positives and should be interpreted with care.
Distributed metabolic pathways
Public good dynamics play an integral role in shaping microbial interactions through distributed networks of metabolite exchange . Such networks promote increased fitness and resilience and may explain the underlying difficulty in cultivating most environmental microorganisms [25–27]. Because ePGDBs are constructed from environmental sequence information, predicted pathways are represented by multiple donor genotypes providing different levels of sequence coverage for each reaction. By comparing pathway recovery for individual reference genomes to pathway recovery for combinations of reference genomes, it becomes formally possible to use Pathway Tools to identify distributed metabolic pathways that emerge between multiple interacting partners. To test this hypothesis, we selected four Tier-2 reference genomes used in simulation experiments and constructed ePGDBs using all possible pair-wise genome combinations (Additional file 1: Table S10). Thirty distributed pathways were identified in pair-wise genome combinations that were not predicted in PGDBs for individual cellular organisms using set-difference analysis (Additional file 1: Table S11). Common and unique reactions associated with distributed pathways could be identified as composite glyphs in the Pathway Tools genome browser (Additional file 1: Figure S4).
Comparative community metabolism
A total of 30 pathways were identified exclusively in RNA datasets including 11 pathway variants (Figure 4c and Additional file 1: Figure S6). Expressed cholesterol degradation and tetrahydrobiopterin biosynthesis I were common to all depth intervals. Unique expressed photorespiration and glycolate degradation III pathways were recovered at 25 and 75 m, while ammonia oxidation III, methane oxidation to methanol II, and arginine biosynthesis III were unique to 500 m (Additional file 1: Figure S6). More than 590 pathways were identified exclusively in DNA datasets, while 495 were shared in common between DNA and RNA datasets (Figure 4d). With respect to functional classes, unique Degradation, Biosynthesis and Energy-Metabolism pathways increased as a function of depth in DNA datasets (Additional file 1: Figure S7a). Within unique degradation classes a progression from amino acids to aromatic-compounds and secondary metabolites was observed between 25, 75, 110 and 500 m depth intervals. A similar progression was observed for a subset of Biosynthetic classes including polyamines, lipids, and cofactors and for Energy-Metabolism including C1-compounds and fermentation (Additional file 1: Figure S7b).
Consistent with previous reports, sunlit waters expressed many photosynthesis-related pathways including aerobic electron transfer, hydrogen production, and cofactors including ubiquinol, heme, vitamin B-complex (nicotinate, thiamine, cobalamin, tetrahydrofolate), chlorophyll a, and retinol biosynthesis [19, 20] (Additional file 1: Figures S9 and S10). In addition to photosynthesis, 25 and 75 m depth intervals (upper euphotic) sets included pathways associated with degradation of plant metabolites including phytate, glucuronate, mannitol, chitin, xylose, arabinose, gallate, and quinolate. Other pathways of interest identified in sunlit waters included organophosphate, urea, and aminobutyrate degradation, as well as pathways for conversion of the plant hormone indole-3 acetic acid and mercury detoxification. Below the euphotic zone, the 500 m depth interval expressed unique pathways for intra-aerobic nitrite reduction, dissimilatory nitrate reduction, the reductive monocarboxylic acid cycle, ammonia oxidation, and methane oxidation to methanol I (Additional file 1: Figure S11). Thus, comparative ePGDB analysis using the combined DNA and RNA datasets differentiated between genomic potential and phenotypic expression across defined environmental gradients in the ocean and revealed known and novel patterns of functional specialization with potential implications for nutrient and energy flow within sunlit and dark ocean waters.
Pathway prediction hazards
While the construction of ePGDBs promotes pathway-centric analysis of environmental sequence information, prediction hazards need to be considered for optimal interpretive power. One common hazard is the ‘multiple mapping problem,’ arising when an enzyme catalyzes conserved or promiscuous reaction steps across multiple pathways or enzyme commission (EC) numbers representing classes with non-specific substrate activity. For example EC 126.96.36.199 represents a non-specific enzyme class for beta-D-glucosides, allowing for spurious prediction of specific carbohydrate degradation pathways. Moreover, PathoLogic has a preference for EC numbers over product descriptions that can further exacerbate false discovery associated with non-specific enzyme classes. Hazards manifesting themselves within pathway variants sharing a number of common or reversible reaction steps have previously been described by Caspi and colleagues in the context of PGDB construction for cellular organisms . For example, the tricarboxylic acid cycle (TCA) cycle has at least eight pathway variants associated with different taxonomic groups and several incomplete or reversible forms that share multiple reactions steps. Pathologic has difficulty differentiating between TCA cycle variants when reversible pathway components are present even when a diagnostic step such as ATP-citrate lyase for the reductive TCA cycle is missing from the input data. A similar problem occurs when a regulatory protein is used to provide evidence that a pathway exists even when catalytic pathway components are missing from the input. Given that we constructed ePGDBs without taxonomic pruning and that PathoLogic uses automated annotations from multiple taxonomic groups when predicting pathways from environmental sequence information, taxon specific pathways such as plant hormone biosynthesis or innate immunity can be predicted even when organisms known to encode such pathways are absent from the dataset. As described in the performance considerations section, WTD can be used to discern differences between the predicted and expected taxonomic range of pathways pointing to potential hazards prior to interpretation. Indeed, the extent to which these predicted pathways reflect previously unrecognized variants or prediction artifacts remains to be determined. Moreover, this hazard has the potential to confound distributed metabolic pathway identification when sequence coverage is low or microbial community composition is extremely uneven. Some examples of these hazards from the HOT analysis are provided in Additional file 1: Table S13.
While advances in high throughput sequencing technologies are rapidly giving rise to tens of thousands of environmental datasets, the computational and analytic powers needed to organize, interpret and mobilize these datasets have lagged behind. Conventional BLAST-based annotation methods combined with gene-centric analyses tend to overlook the network properties of microbial communities driving ecological and biogeochemical interactions. We argue that pathway-centric analyses via the MetaPathways pipeline and Pathway Tools provides the scientific user community with an end-to-end solution for comparing ePGDBs constructed from environmental sequence information revealing known and novel network properties. As with any automated analysis, this method is no replacement for manual curation. Indeed, we have highlighted specific instances where taxonomic range, idiosyncratic annotation, multifunctional enzymes, regulatory functions, and reversible enzymatic forms predicted by Pathway Tools result in interpretive hazards that require expert knowledge to resolve.
Continued development efforts are needed to improve on existing features and add new functionality to both the MetaPathways pipeline and Pathway Tools. Specifically, improved import features amenable to categorical metadata e.g., taxonomic origin, location, depth, etc., need to be integrated with Pathway Tools 'groups', a feature that enables users to integrate external data and group pathways and objects within Pathway Tools. The ‘groups’ feature in turn needs to be better integrated into the ‘omics’ viewer allowing for improved pathway navigation and page summaries within the Pathway Tools browser. Tooltip enhancements that summarize the categorical data mentioned above could further enhance the browsing experience. Current ePGDBs are constructed using concatenated CDS sequences and improved viewing features are needed that map coverage and noncoding sequence information onto complete contigs. Finally, the PathoLogic algorithm should be improved to incorporate the described prediction hazards and WTD into its calculations. Specifically, one can imagine tree-based algorithmic improvements to PathoLogic akin to the WTD described here that integrate taxonomic information with enzyme or pathway directionality.
Despite current limitations, ePGDBs provide an interactive and holistic data structure in which to investigate distributed metabolism and differentiate between microbial community metabolic potential and phenotypic expression. Thus, ePGBDs provide a functional blueprint of microbial community metabolism that can be harnessed to engineer microbial consortia with defined emergent properties. These properties can in turn be transferred to industrial strains or modeled using MetaFlux to improve process performance . Although the set-difference and visual inspection methods used to identify distributed metabolic pathways described here do not scale for big datasets, future algorithmic improvements will enable comparisons of reference genomes and metagenomes in large numbers. Indeed, splitting the proverbial “reaction arrows” for each step in a given metabolic pathway into taxonomic bins provides a basis for integer optimization methods that compute “distribution” scores and a baseline for monitoring changes in the reaction network associated with environmental change or even human health status. Looking forward, we envision an open source collection of ePGDBs, called EngCyc analogous to BioCyc , which can be queried and compared online revealing the network properties of microbial communities in natural and engineered ecosystems on a truly global scale.
Metabolic pathway analysis
Environmental PGDBs were constructed from public datsets using MetaPathways (http://github.com/hallamlab/MetaPathways/)  with default parameter settings: open reading frame (ORF) detection by Prodigal (minimum length 60 amino acids), functional annotation by BLAST (e-value 1e-5, blast-score ratio 0.4) against protein databases KEGG , COG , MetaCyc  (version 16.0), and RefSeq  (Downloaded August 2012), and pathway prediction via the PathoLogic algorithm with taxonomic pruning disabled. Predicted pathways and associated annotated CDS sequences were extracted from created ePGDBs using the utility script extract_pathway_table_from_pgdb.pl included with MetaPathways.
Pathway prediction on simulated data
Simulated sequencing experiments were performed using MetaSim  with the parameter settings: Long read: clone size 36000 bp, Gaussian error, mean read length 700 bp, standard deviation 100 bp; Short read: Gaussian error, mean 160 bp, standard deviation 40 bp) against the E. coli K12 MG1655 complete nucleotide genome (GenBank: NC_000913) at a series of fractional levels (1/32, 1/16, 1/8, 1/4, 1/2, 1/1) of the total combined length of starting component genomes (Gm). Pathways were predicted using the MetaPathways pipeline, as described above, against each of the resulting sequence sets (Additional file 1: Tables S3 and S4). A classification performance analysis was performed; True positives (TP) were pathways found in both the simulated sample pathways (test set) and the complete gold standard E. coli genome. True negatives (TN) were pathways not predicted in the test set or gold standard. False positives (FP) were pathways found in the test set but not in the gold standard. Finally, false negatives (FN) were pathways found in the gold standard but not in the test set. Multiple summary statistics for the resulting confusion tables (Sensitivity (Recall), Specificity, Precision, Accuracy, F-measure, and Matthew’s Correlation Coefficient (MCC)) were calculated. A summary of these performance statistics is provided in the supplement (Additional file 1: Note S1: ‘A Note on Confusion Table Statistics’).
Simulated metagenomes: Sim1, Sim2
Simulated sequencing experiments of metagenomes Sim1 and Sim2 were generated and analyzed as described above for E. coli. To minimize name-mapping problems, we used prokaryotic genomes from the tier-2 BioCyc database collection . The Sim1 metagenome was composed of ten tier-2 BioCyc genomes (Additional file 1: Table S2) in equal copy number, while Sim2 was composed of the Caulobacter cresentus NA1000 genome in 20-fold excess relative to other genomes (Additional file 1: Figure S1). A classification performance analysis was performed as described above with the set of 646 pathways predicted from the complete tier-2 genomes used to derive Sim1 and Sim2 representing the gold standard (Additional file 1: Tables S5-S8).
Simulated metagenomes: HOT (25 m)
A 25 m metagenome from the Hawaii ocean time series was sub-sampled with replacement to different fractional levels (1/20, 1/10, 3/20, 1/5, 2/5, 3/5, 4/5, and 1/1) and pathways were predicted as described above. Similarly, a classification performance analysis was performed with the set of 864 pathways predicted from the complete 454 run representing the gold standard (Additional file 1: Tables S7 and S8).
Taxonomic pruning experiments
The full-Gm simulated sequencing samples for Sim1 and Sim2, both short and long read lengths, and the full-Gm HOT (25 m) sample, had their pathways predicted with the above method, but with taxonomic pruning enabled using the taxonomic lineage parameter set to “Unclassified sequences”. The number of predicted pathways were tabulated and compared with the pathways previously predicted with taxonomic pruning disabled. As simple set analysis showed that within a sample the pruned pathways were a strict subset of the “no-pruning” ones, and the reduction in pathways was calculated (Additional file 1: Table S9).
Weighted taxonomic distance
For each predicted pathway in the HOT dataset, a weighted taxonomic distance (WTD) distance was calculated using the WTD algorithm (Additional file 1: Supplementary Note 2). First, the lowest common ancestor algorithm (LCA) was applied to a pathway’s RefSeq CDS sequences. The WTD algorithm calculates a weighted distance D between the observed LCA taxonomy x obs and the pathway’s expected taxonomic range(s) x exp ∈ TR(MetaCyc)(p), where TR(MetaCyc)(p) is the set of taxonomic range(s) for a given pathway p on the NCBI Taxonomy Database hierarchy.
where ea,b is an edge between nodes a and b in the path and d(a) is the depth of node a. If x exp descends from the expected taxonomic range x obs , then the WTD is assigned a positive value and WTD for paths descending outside this range are assigned a negative value. After calculating the WTDs for all pairs x exp , x obs , the WTD algorithm first attempts to return the minimum non-negative distance e.g., WTD corresponding to the closest x exp where x obs is a descendant of x exp , and returns the maximum negative score e.g., closest to zero if all observed and expected taxonomies diverge. For each dataset, predicted pathways were assigned to a “Disagreement Class” based on the following criteria: (i) pathways with positive WTD were given the “None” class, (ii) pathways with distances greater than the median of negative WTDs were given the “Low” class, (iii) pathways within the 2nd quartile were given the “Medium” class, and (iv) pathways in the lower quartile were given the “High” disagreement class (Additional file 1: Figure S2). The expected taxonomic ranges of each pathway where then collapsed into the higher taxonomic levels: “root”, “cellular organisms”, “prokaryotes”, “archaea”, “bacteria”, “eukaryotes”, “animals”, “fungi”, ”plants”, and “other”, as defined on the NCBI Taxonomy Database hierarchy and pathway frequencies and disagreement classes were summarized for each sample (Additional file 1: Figure S3).
Distributed metabolic pathway prediction
Four genomes of similar size and complexity from the tier-2 dataset were combined in a pairwise manner: Aurantimonas manganoxydans SI85-9A (GenBank: NZ_AAPJ00000000.1), Bacillus subtilis subtilis 168 (GenBank: AL009126.3), Caulobacter crescentus NA1000 (GenBank: CP001340.1), and Helicobacter pylori 26695 (GenBank: AE000511.1), abbreviated by the first character of their proper names, A, B, C, and H, respectively. The six pair-wise and four original genomes were analyzed as described above for E. coli (Additional file 1: Table S10). Pathways predicted in the combined PGDBs were considered candidates for distributed metabolism if they were absent from PGDBs for individual genomes (i.e., found in A and B combined, but not in either A or B individually) (Additional file 1: Table S11 and Additional file 2). Candidate pathways were manually inspected and deemed ‘plausible’ if there was sufficient coverage, i.e., 75% of reactions in a pathway had associated CDS sequences from both taxa (Additional file 1: Figure S4).
Similarly, the Candidatus Moranella endobia and Candidatus Tremblaya princeps genomes (GenBank: NC-015735 and NC-015736) were downloaded from NCBI and analyzed as described above for E. coli. Resulting PGDBs for individual and combined genomes were manually inspected for amino acid biosynthetic pathways described in McCutcheon and Dohlen  (Additional file 1: Figure S5).
Hawaii ocean time-series
Unassembled metagenomic and transcriptomic pyrosequences from the Hawaii Ocean Time-series (10 m, 75 m, 110 m, and 500 m) were obtained from the NCBI Sequence Read Archive (SRA Accession: SRX007372, SRX007369, SRX007370, SRX007371, SRX016893, SRX016897, SRX156384, SRX156385) and run through the MetaPathways pipeline using default settings (Additional file 3). To avoid spurious predictions, only pathways with more than ten mapped CDS sequences in an individual sample were used in downstream analysis. The pathways with nine or fewer mapped CDS sequences represent the lower quartile of pathway annotations (Figure 4a, Additional file 4). Pathway CDS counts for each sample were normalized to the total number of unannotated ORFs in each dataset. Count data was then converted to percentages providing relative ORF abundance for each pathway (Additional file 5), along with their weighted taxonomic distances and sample-wise disagreement classes (Additional file 6). Relative CDS abundance of the top-40 pathways from DNA and RNA datasets were compared (Additional file 1: Figure S8). In addition, pathways predicted in the DNA and RNA datasets were compared at each depth interval to provide sample-wise fractions for each depth e.g., DNA-only, DNA-RNA, and RNA-only (Figure 4c). Given the small number of pathways in the RNA-only sets no set-difference analysis was needed (Additional file 1: Figure S6). The DNA-only sets were declined and tabulated at various levels of the MetaCyc pathway hierarchy (Additional file 1: Figure S7). A final four-way set analysis was performed on the DNA-only and DNA-RNA pathways at each depth (Figure 4d, Additional files 7 and 8). DNA-RNA set-difference subsets with more than 5 predicted pathways were compared in detail (Additional file 1: Figures S9-S14). All data transformations, set operations, and comparisons were performed in the R statistical environment (http://www.r-project.org), and visualized using the ggplot graphical package (http://ggplot2.org) and d3.js graphical library (http://d3js.org/).
Availability of supporting data
The ten full-length genomes used to create simulated metagenomes can be downloaded from GenBank under accession numbers AE008687-AE008690, NZ_AAPJ00000000.1, AL009126.3, AE005673, CP001340.1, AE000511.1, AE000516, AL123456, NC_007604.1, AE003852, and AE003853.
The symbiotic Candidatus Moranella endobia and Candidatus Tremblaya princeps genomes can be downloaded from GenBank under accession numbers NC-015735 and NC-015736). The Hawaii Ocean Time series datasets can be downloaded from the NCBI Sequence Read Archive under accession numbers SRX007372, SRX007369, SRX007370, SRX007371, SRX016893, SRX016897, SRX156384, SRX156385.
This work was carried out under the auspices of Genome Canada, Genome British Columbia, Genome Alberta, the Natural Science and Engineering Research Council (NSERC) of Canada, the Canadian Foundation for Innovation (CFI) and the Canadian Institute for Advanced Research (CIFAR) through grants awarded to SJH. The Western Canadian Research Grid (WestGrid) provided access to high-performance computing resources. KMK was supported by the Tula Foundation funded Centre for Microbial Diversity and Evolution (CMDE). NWH was supported by a four year doctoral fellowship (4YF) administered through the UBC Graduate Program in Bioinformatics. We would like to thank Suzanne Paley, Ron Caspi, and Quang Ong of SRI International for their patience, technical support, and lucid discussions on the function of Pathway Tools and the PathoLogic algorithm, Antoine Pagé for his participation in preliminary performance evaluations and all members of the Hallam Lab for helpful comments along the way.
- Falkowski PG, Fenchel T, Delong EF: The microbial engines that drive Earth's biogeochemical cycles. Science. 2008, 320: 1034-1039.PubMedView ArticleGoogle Scholar
- Handelsman J: Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2005, 69: 195-195.PubMed CentralView ArticleGoogle Scholar
- Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken RS: Genomic sequencing of single microbial cells from environmental samples. Curr Opin Microbiol. 2008, 11: 198-204.PubMed CentralPubMedView ArticleGoogle Scholar
- Wooley JC, Ye Y: Metagenomics: facts and artifacts, and computational challenges. J Comput Sci Technol. 2009, 25: 71-81.PubMed CentralPubMedView ArticleGoogle Scholar
- Hey AJ, Tansley S, Tolle KM: Microsoft Research. The fourth paradigm: data-intensive scientific discovery. 2009Google Scholar
- Ye Y, Doak TG: A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol. 2009, 5: e1000465-PubMed CentralPubMedView ArticleGoogle Scholar
- Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BJ, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C: Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol. 2012, 8: e1002358-PubMed CentralPubMedView ArticleGoogle Scholar
- Larsen PE, Collart FR, Field D, Meyer F, Keegan KP, Henry CS, McGrath J, Quinn J, Gilbert JA: Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. Microb Inform Exp. 2011, 1: 4-PubMed CentralPubMedView ArticleGoogle Scholar
- Altman T, Travers M, Kothari A, Caspi R, Karp PD: A systematic comparison of the MetaCyc and KEGG pathway databases. BMC Bioinformatics. 2013, 14: 112-PubMed CentralPubMedView ArticleGoogle Scholar
- Karp PD, Paley S, Romero P: The pathway tools software. Bioinformatics. 2002, 18: S225-S232.PubMedView ArticleGoogle Scholar
- Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY, Tissier C, Zhang P, Karp PD: MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2006, 34: D511-D516.PubMed CentralPubMedView ArticleGoogle Scholar
- Karp PD, Latendresse M, Caspi R: The pathway tools pathway prediction algorithm. Stand Genomic Sci. 2011, 5: 424-429.PubMed CentralPubMedView ArticleGoogle Scholar
- Latendresse M, Krummenacker M, Trupp M, Karp PD: Construction and completion of flux balance models from pathway databases. Bioinformatics. 2012, 28: 388-396.PubMed CentralPubMedView ArticleGoogle Scholar
- Konwar KM, Hanson NW, Pagé AP, Hallam SJ: MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information. BMC Bioinformatics. 2013, 14: 202-PubMed CentralPubMedView ArticleGoogle Scholar
- Hanson NW, Konwar KM, Wu S-J, Hallam SJ: MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds. Conf Proc IEEE Comp Intel in Bioinf and Comp Biology. 2014, 1-7. 28
- Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahrén D, Tsoka S, Darzentas N, Kunin V, López-Bigas N: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 2005, 33: 6083-6089.PubMed CentralPubMedView ArticleGoogle Scholar
- McCutcheon JP, von Dohlen CD: An interdependent metabolic patchwork in the nested symbiosis of mealybugs. Curr Biol. 2011, 21: 1366-1372.PubMed CentralPubMedView ArticleGoogle Scholar
- Delong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard N-U, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM: Community genomics among stratified microbial assemblages in the ocean's interior. Science. 2006, 311: 496-503.PubMedView ArticleGoogle Scholar
- Stewart FJ, Sharma AK, Bryant JA, Eppley JM, Delong EF: Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities. Genome Biol. 2011, 12: R26-PubMed CentralPubMedView ArticleGoogle Scholar
- Shi Y, Tyson GW, Eppley JM, Delong EF: Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J. 2011, 5: 999-1013.PubMed CentralPubMedView ArticleGoogle Scholar
- Dale JM, Popescu L, Karp PD: Machine learning methods for metabolic pathway prediction. BMC Bioinformatics. 2010, 11: 15-PubMed CentralPubMedView ArticleGoogle Scholar
- Richter DC, Ott F, Auch AF, Schmid R, Huson DH: MetaSim—a sequencing simulator for genomics and metagenomics. PLoS ONE. 2008, 3: e3373-PubMed CentralPubMedView ArticleGoogle Scholar
- Huson DH, Auch AF, Qi J, Schuster SC: MEGAN analysis of metagenomic data. Genome Res. 2007, 17: 377-386.PubMed CentralPubMedView ArticleGoogle Scholar
- Cordero OX, Ventouras L-A, Delong EF, Polz MF: Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations. Proc Natl Acad Sci U S A. 2012, 109: 20059-20064.PubMed CentralPubMedView ArticleGoogle Scholar
- Ellers J, Toby Kiers E, Currie CR, McDonald BR, Visser B: Ecological interactions drive evolutionary loss of traits. Ecol Lett. 2012, 15: 1071-1082.PubMedView ArticleGoogle Scholar
- Lawrence D, Fiegna F, Behrends V, Bundy JG, Phillimore AB, Bell T, Barraclough TG: Species interactions alter evolutionary responses to a novel environment. PLoS Biol. 2012, 10: e1001330-PubMed CentralPubMedView ArticleGoogle Scholar
- Morris JJ, Lenski RE, Zinser ER: The Black Queen hypothesis: evolution of dependencies through adaptive gene loss. MBio. 2012, 3: e00036-12.PubMed CentralPubMedView ArticleGoogle Scholar
- Caspi R, Dreher K, Karp PD: The challenge of constructing, classifying, and representing metabolic pathways. FEMS Microbiol Lett. 2013, 345: 85-93.PubMed CentralPubMedView ArticleGoogle Scholar
- Lam P, Kuypers MMM: Microbial nitrogen cycling processes in oxygen minimum zones. Ann Rev Mar Sci. 2011, 3: 317-345.PubMedView ArticleGoogle Scholar
- Wright JJ, Konwar KM, Hallam SJ: Microbial ecology of expanding oxygen minimum zones. Nat Rev Microbiol. 2012, 10: 381-394.PubMedGoogle Scholar
- Ehrich S, Behrens D, Lebedeva E, Ludwig W, Bock E: A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium. Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Arch Microbiol. 1995, 164: 16-23.PubMedView ArticleGoogle Scholar
- Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Médigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJM, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, et al: Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature. 2006, 440: 790-794.PubMedView ArticleGoogle Scholar
- Lücker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherieb B, Ratteie T, Damstéf JSS, Spieckg E, Le Paslier D, Daimsa H: A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci U S A. 2010, 107: 13479-13484.PubMed CentralPubMedView ArticleGoogle Scholar
- Kartal B, Maalcke WJ, de Almeida NM, Cirpus I, Gloerich J, Geerts W, Op den Camp HJM, Harhangi HR, Janssen-Megens EM, Francoijs K-J, Stunnenberg HG, Keltjens JT, Jetten MSM, Strous M: Molecular mechanism of anaerobic ammonium oxidation. Nature. 2011, 479: 127-130.PubMedView ArticleGoogle Scholar
- Zumft WG: Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev. 1997, 61: 533-616.PubMed CentralPubMedGoogle Scholar
- Ganesh S, Parris DJ, Delong EF, Stewart FJ: Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. ISME J. 2013, doi:10.1038/ismej.2013.144Google Scholar
- Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28: 27-30.PubMed CentralPubMedView ArticleGoogle Scholar
- Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV: The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 2001, 29: 22-28.PubMed CentralPubMedView ArticleGoogle Scholar
- Pruitt KD, Tatusova T, Maglott DR: NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007, 35: D61-D65.PubMed CentralPubMedView ArticleGoogle Scholar
This article is published under license to 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 credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.