GeM-Pro: a tool for genome functional mining and microbial profiling
- 114 Downloads
Gem-Pro is a new tool for gene mining and functional profiling of bacteria. It initially identifies homologous genes using BLAST and then applies three filtering steps to select orthologous gene pairs. The first one uses BLAST score values to identify trivial paralogs. The second filter uses the shared identity percentages of found trivial paralogs as internal witnesses of non-orthology to set orthology cutoff values. The third filtering step uses conditional probabilities of orthology and non-orthology to define new cutoffs and generate supportive information of orthology assignations. Additionally, a subsidiary tool, called q-GeM, was also developed to mine traits of interest using logistic regression (LR) or linear discriminant analysis (LDA) classifiers. q-GeM is more efficient in the use of computing resources than Gem-Pro but needs an initial classified set of homologous genes in order to train LR and LDA classifiers. Hence, q-GeM could be used to analyze new set of strains with available genome sequences, without the need to rerun a complete Gem-Pro analysis. Finally, Gem-Pro and q-GeM perform a synteny analysis to evaluate the integrity and genomic arrangement of specific pathways of interest to infer their presence. The tools were applied to more than 2 million homologous pairs encoded by Bacillus strains generating statistical supported predictions of trait contents. The different patterns of encoded traits of interest were successfully used to perform a descriptive bacterial profiling.
KeywordsBacterial profiling Gene mining Orthology Phylogenomic analysis Plant growth–promoting rhizobacteria Bacillus
MATM and MDP are CONICET fellows; CM, LD, and ME are researchers of the same institution. MP is professor at UNR.
This study was funded by Agencia Nacional de Promoción Científica y Tecnológica (PICT 2014-1513 to CM, PICT 2015-2361 to ME, PICT-2016-0426 to LD).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
- Belbahri L, Bouket AC, Rekik I, Alenezi FN, Vallat A, Luptakova L, Petrovova E, Oszako T, Cherrad S, Vacher S, Rateb ME (2017) Comparative genomics of Bacillus amyloliquefaciens strains reveals a core genome with traits for habitat adaptation and a secondary metabolites rich accessory genome. Front Microbiol 8:1–15. https://doi.org/10.3389/fmicb.2017.01438 Google Scholar
- Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heinemeyer I, Morgenstern B, Voss B, Hess WR, Reva O, Junge H, Voigt B, Jungblut PR, Vater J, Süssmuth R, Liesegang H, Strittmatter A, Gottschalk G, Borriss R (2007) Comparative analysis of the complete genome sequence of the plant growth–promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol 25:1007–1014. https://doi.org/10.1038/nbt1325 Google Scholar
- Chowdhury SP, Dietel K, Rändler M, Schmid M, Junge H, Borriss R, Hartmann A, Grosch R (2013) Effects of Bacillus amyloliquefaciens FZB42 on lettuce growth and health under pathogen pressure and its impact on the rhizosphere bacterial community. PLoS One 8:1–10. https://doi.org/10.1371/journal.pone.0068818 Google Scholar
- Chowdhury SP, Uhl J, Grosch R, Alquéres S, Pittroff S, Dietel K, Schmitt-Kopplin P, Borriss R, Hartmann A (2015b) Cyclic lipopeptides of Bacillus amyloliquefaciens subsp. plantarum colonizing the lettuce rhizosphere enhance plant defense responses toward the bottom rot pathogen Rhizoctonia solani. Mol Plant-Microbe Interact 28:984–995. https://doi.org/10.1094/MPMI-03-15-0066-R Google Scholar
- Espariz M, Zuljan FA, Esteban L, Magni C (2016) Taxonomic identity resolution of highly phylogenetically related strains and selection of phylogenetic markers by using genome-scale methods: the Bacillus pumilus group case. PLoS One 11:e0163098. https://doi.org/10.1371/journal.pone.0163098 Google Scholar
- Forslund K (2011) The relationship between orthology, protein domain architecture and protein function. Stockholm University, StockholmGoogle Scholar
- Gu Q, Yang Y, Yuan Q, Shi G, Wu L, Lou Z, Huo R, Wu H, Borriss R, Gao X (2017) Bacillomycin D produced by Bacillus amyloliquefaciens is involved in the antagonistic interaction with the plant-pathogenic fungus Fusarium graminearum. Appl Environ Microbiol 83. doi: https://doi.org/10.1128/AEM.01075-17
- James G, Witten D, Hastie T, Tibshirani R (2013) An introduction to statistical learning. Springer New York, New YorkGoogle Scholar
- Jensen RA (2001) Orthologs and paralogs - we need to get it right. Genome Biol 2:INTERACTIONS1002. https://doi.org/10.1186/gb-2001-2-8-interactions1002 Google Scholar
- Kim B-Y, Lee S, Ahn J, Song J, Kim W, Weon H (2015) Complete genome sequence of Bacillus amyloliquefaciens subsp. plantarum CC178, a phyllosphere bacterium antagonistic to plant pathogenic fungi. Genome Announc 3:1–2. https://doi.org/10.1128/genomeA.01368-14
- Koumoutsi A, Chen X, Henne A, Hitzeroth G, Franke P, Vater J, Borriss R, Liesegang H (2004) Structural and functional characterization of gene clusters directing nonribosomal synthesis of bioactive cyclic lipopeptides in Bacillus amyloliquefaciens strain FZB42. J Bacteriol 186:1084–1096. https://doi.org/10.1128/JB.186.4.1084
- Liu Z, Budiharjo A, Wang P, Shi H, Fang J, Borriss R, Zhang K, Huang X (2013) The highly modified microcin peptide plantazolicin is associated with nematicidal activity of Bacillus amyloliquefaciens FZB42. Appl Microbiol Biotechnol 97:10081–10090. https://doi.org/10.1007/s00253-013-5247-5 Google Scholar
- Ryu CM, Farag MA, Hu CH, Reddy MS, Wei HX, Pare PW, Kloepper JW (2003) Bacterial volatiles promote growth in Arabidopsis. Proc Natl Acad Sci U S A 100:4927–4932. https://doi.org/10.1073/pnas.0730845100
- Schneider K, Chen X-H, Vater J, Franke P, Nicholson G, Borriss R, Süssmuth RD (2007) Macrolactin is the polyketide biosynthesis product of the pks2 cluster of Bacillus amyloliquefaciens FZB42. J Nat Prod 70:1417–1423. https://doi.org/10.1021/np070070k