A Support Vector Machine based method to distinguish proteobacterial proteins from eukaryotic plant proteins

Bacterial plant pathogens are a major threat to global food security [1]. Half of the bacterial species causing major food losses in the world belong to the major phylum Proteobacteria (Figure 1). They are found predominantly in the class Gammaproteobacteria (Xanthomonas, Pseudomonas and Erwinia) and also in the class Betaproteobacteria (Ralstonia). Gammaproteobacteria include in addition a wide variety of several medically, ecologically and scientifically important groups such as Enterobacteriaceae (Escherichia coli), Vibrionaceae and Pseudomonadaceae. Also, beneficial bacteria, such as nitrogen fixing, ammonia oxidizing and iron fixing bacteria are members of this phylum. Betaproteobacteria also include ammonia oxidizing and arsenic resistant bacteria with Burkholderiales as one of the major classes. Alphaproteobacteria is dominated mostly by nitrogen-fixing bacteria and agrobacteria. Deltaproteobacteria and Epsilonproteobacteria have aerobic genera and curved to spirilloid Wolinella spp., respectively. Zetaproteobacteria is composed of a sole member: Mariprofundus ferrooxydans which oxidizes ferrous to ferric iron [2].

Several methods are being developed to detect phytopathogens involving macromolecular sequencing, especially nucleotide sequencing [3, 4]. With the advent of next generation sequencing, testing of diseased or quarantined plants for the presence of proteobacteria will rely increasingly on massive DNA sequencing. Peptide mass spectroscopy also shows promise in such screening. The analysis of nucleotide sequences typically involves assembly of sequence reads into contigs followed by analysis using Blast [5] search to identify pathogen-derived contigs. This approach is limited in that it only identifies potential pathogens whose nucleotide sequences are included in the searched database. Thus, there is a strong need for methods to find the organismal origin of unknown DNA or peptide fragments to identify potential pathogen sequences. Machine learning techniques, such as support vector machines (SVMs) and neural networks have been used successfully to develop classifiers for a number of different biolgocial problems including predicting different categories of proteins [6–14]. As a first step towards detecting pathogenic bacteria spp., we evaluated whether a machine learning algorithm, SVM, could distinguish between proteobacterial (potential pathogen) and plant (host) proteins. Thus, we assembled datasets of proteobacterial and plant host proteins for this study. We focused on amino acid, rather than nucleotide residues, because of the greater variety of residues that can be present at any one position, allowing subtle evolutionary forces to play a role in shaping the protein sequence and its properties.

To test whether the AAC of proteobacterial and plant proteins differ significantly, we calculated AAC for both the proteobacterial (Table 1) and plant (Table 2) proteins datasets (Figure 4). We observe differences of AAC between proteobacteria and plants with respect to alanine, cysteine, glycine, lysine, arginine and serine. We also calculated the DC for these two datasets (figure not shown). We input the following vector sets for the SVM: AAC, DC and a hybrid of AAC and DC [20] models. We trained all three kernels (linear (Table 3), polynomial (Table 4) and RBF (Table 5) to identify the best-trained kernel. Comparison of the accuracies and MCCs obtained by all three kernels revealed that the RBF kernel performed best with all three redundancy percentages (Table 5). At 90% redundancy the SVM achieved a maximum accuracy of 92.44% and a 0.85 MCC for the AAC model [RBF parameters: g = 0.04, c = 4, j = 1], a maximum accuracy of 94.67% and 0.89 MCC for the DC model [g = 0.02, c = 6, j = 2] and for the hybrid model a maximum accuracy of 94.86% and a 0.90 MCC [g = 0.01, c = 8, j = 1]. At 50% redundancy, maximum accuracies for the AAC, DC and hybrid models were 91.62% (MCC 0.83) [g = 0.04, c = 2, j = 1], 94.12% (MCC 0.88) [g = 0.02, c = 4, j = 1] and 94.49% (MCC 0.89) [g = 0.01, c = 8, j = 2] respectively. At 30% redundancy, the maximum accuracies of the AAC, DC and hybrid models were 92.30% (MCC 0.84) [g = 0.05, c = 1, j = 1], 93.72% (MCC 0.87) [g = 0.03, c = 2, j = 2] and 93.84% (MCC 0.88) [g = 0.01, c = 4, j = 2]. As shown in Table 5 we achieved maximum accuracy with the hybrid model at 90% redundancy.

The result of the validation datatsets on six species (on all three models) are shown in Table 6. The hybrid model trained at 90% redundancy had the best accuracy only with exception of Rhizobium fredii for which the 50% redundant model was better. As can be seen from Table 5, the hybrid model at 90% redundancy performed best overall for most species. It is possible that the decrease in performance obtained by removing more proteins based on their similarities is not due to the identity value, but due to a resulting imbalance in the training datasets since the redundancy criteria affected proteobacterial protein numbers more strongly than they did the plant protein numbers. Because these estimates are sensitive to the threshold for distinguishing positives from negatives, we constructed a ROC curve to examine the model's accuracy. ROC has been used to show the accuracy of constructed models [21–29]. The ROC curve is a graphical representation of sensitivity (true positive rate) vs. one minus specificity (false positive rate or true negative rate) for any binary classifier system [30]. It is a threshold independent evaluation parameter and gives a value known as Area Under Curve (AUC) (Figure 5) which shows the performance of a classifier in a two class problem [31]. The higher the AUC, the more accurate the model. In the present study the AUC for hybrid model was 0.985 and therefore demonstrated the accuracy of the model.

AAC	Serratia marcescens (127)	Acidovorax citrulli (314)	Rhizobium fredii (16)	Solanum lycopersicum (413)	Phaseolus vulgaris (159)	Cucurbita pepo (15)
30	78.74	98.09	75	93.46	94.97	100
50	70.87	96.18	75	94.19	96.23	100
90	70.87	97.77	75	93.46	96.86	100
DC
30	73.23	96.82	75	94.19	97.48	100
50	75.59	97.45	68.75	94.92	96.84	100
90	74.8	97.77	62.5	95.16	98.72	100
Hybrid (AAC+DC)
30	74.8	96.5	75	95.4	98.74	100
50	79.53	99.04	81.25	93.46	97.48	100
90	81.1	99.04	79.53	93.95	98.11	100

The accuracy is calculated by dividing the number of correct predictions by total number of protein inputs. The numbers of reviewed proteins are shown in parentheses.

This SVM model can be used to assign a query sequence as to whether it originated from a plant or proteobacterium, thus enabling timely detection of the infection. It may also be used to identify food contamination with bacteria by screening samples by sequencing. SVM models can be used to work in the area of animal proteins. As we have developed a model for plant and proteobacteria, another model can be designed for animal protein and pathogenic proteobacterial proteins. Thus, SVMs can be used in a variety of fields of study.

The SVM models based on the hybrid approach using both amino acid and dipeptide features exhibited the maximum accuracy on both threshold dependent and threshold independent parameters. Best results were obtained with an RBF kernel and considering protein sets that did not contain any proteins that are more than 90% identical to another protein in the dataset. SVMs have great potential to handle large datasets and thus can be used for sorting proteobacterial sequences from a mixed background, like those found in metagenomic sequence data. As such, an SVM classifier would be a step forward in surveillance techniques for bacteria that lack previously characterized relatives. It may be useful for determining protein sequences obtained from non-sequenced genomes not yet present in Genbank. Other features like domains specific to nitrogen oxidising or fixing bacteria can also be used even to distinguish a pathogenic proteobacterium from a non-pathogenic proteobacterium. This may be used to determine the kinds of bacterial pathogens present in food samples thus improving food security. Human pathogens that are proteobacterial in nature also exist. Specific SVM models can be trained or designed to distinguish them. Thus SVMs hold greater potential for solving a variety of problems in biology.