Pérez, J., Moraleda-Muñoz, A., Marcos-Torres, F. J. & Muñoz-Dorado, J. Bacterial predation: 75 years and counting!. Environ. Microbiol. 18, 766–779 (2016).
Google Scholar
Linares-Otoya, L. et al. Diversity and antimicrobial potential of predatory bacteria from the Peruvian coastline. Mar. Drugs. 15, E308. https://doi.org/10.3390/md15100308 (2017).
Google Scholar
Pasternak, Z. et al. By their genes ye shall know them: Genomic signatures of predatory bacteria. ISME J. 7, 756–769 (2013).
Google Scholar
Sockett, R. E. Predatory lifestyle of Bdellovibrio bacteriovorus. Ann. Rev. Microbiol. 63, 523–539 (2009).
Google Scholar
Korp, J., Vela Gurovic, M. S. & Nett, M. Antibiotics from predatory bacteria. Beilstein J. Org. Chem. 12, 594–607 (2016).
Google Scholar
Johnke, J., Fraune, S., Bosch, T. C. G., Hentschel, U. & Schulenburg, H. Bdellovibrio and like organisms are predictors of microbiome diversity in distinct host groups. Microb. Ecol. 79, 252–257 (2020).
Google Scholar
Vila, J., Moreno-Morales, J. & Ballesté-Delpierre, C. Current landscape in the discovery of novel antibacterial agents. Clin. Microbiol. Infect. https://doi.org/10.1016/j.cmi.2019.09.015 (2019).
Google Scholar
Hobley, L. et al. Dual predation by bacteriophage and Bdellovibrio bacteriovorus can eradicate Escherichia coli prey in situations where single predation cannot. J. Bacteriol. 202, e00629-19. https://doi.org/10.1128/JB.00629-19 (2020).
Google Scholar
El-Shibiny, A., Connerton, P. L. & Connerton, I. F. Enumeration and diversity of campylobacters and bacteriophages isolated during the rearing cycles of free-range and organic chickens. Appl. Environ. Microbiol. 71, 1259–1266 (2005).
Google Scholar
Wilkinson, D. A. et al. Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis. Sci. Rep. 8, 2393. https://doi.org/10.1038/s41598-018-20889-x (2018).
Google Scholar
Lee, M. D. GToTree: A user-friendly workflow for phylogenomics. Bioinformatics 35, 4162–4164 (2019).
Google Scholar
Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 10, e1002195 (2011).
Google Scholar
Edgar, R. C. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinform. 5, 113 (2004).
Google Scholar
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
Google Scholar
Hyatt, D., LoCascio, P. F., Hauser, L. J. & Uberbacher, E. C. Gene and translation initiation site prediction in metagenomic sequences. Bioinformatics 28, 2223–2230 (2012).
Google Scholar
Shen, W. & Xiong, J. TaxonKit: A cross-platform and efficient NCBI taxonomy toolkit. bioRxiv. (Accessed 1 June 2021); https://www.biorxiv.org/content/10.1101/513523v1 (2019).
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—Approximately maximum-likelihood trees for large alignments. PLoS One 5, e9490 (2010).
Google Scholar
Tange, O. GNU Parallel. (Accessed 1 June 2021); https://zenodo.org/record/1146014#.YOHaiJhKiUk (2018).
Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).
Google Scholar
Czech, L. et al. Role of the extremolytes ectoine and hydroxyectoine as stress protectants and nutrients: Genetics, phylogenomics, biochemistry, and structural Analysis. Genes (Basel). 9, E177. https://doi.org/10.3390/genes9040177 (2018).
Google Scholar
Gregson, B. H., Metodieva, G., Metodiev, M. V., Golyshin, P. N. & McKew, B. A. Differential protein expression during growth on medium versus long-chain alkanes in the obligate marine hydrocarbon-degrading bacterium Thalassolituus oleivorans MIL-1. Front. Microbiol. 9, 3130 (2018).
Google Scholar
Pasternak, Z., Ben Sasson, T., Cohen, Y., Segev, E. & Jurkevitch, E. A new comparative-genomics approach for defining phenotype-specific indicators reveals specific genetic markers in predatory bacteria. PLoS One. 10, e0142933. https://doi.org/10.1371/journal.pone.0142933 (2015).
Google Scholar
Yakimov, M. M. et al. Thalassolituus oleivorans gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons. Int. J. Syst. Evol. Microbiol. 54, 141–148 (2004).
Google Scholar
Wang, Y., Yu, M., Liu, Y., Yang, X. & Zhang, X. H. Bacterioplanoides pacificum gen. nov., sp. nov., isolated from seawater of South Pacific Gyre. Int. J. Syst. Evol. Microbiol. 66, 5010–5015 (2016).
Google Scholar
Bowditch, R. D., Baumann, L. & Baumann, P. Description of Oceanospirillum kriegii sp. nov. and O. jannaschii sp. nov. and assignment of two species of Alteromonas to this genus as O. commune comb. nov. and O. vagum comb. nov. Curr. Microbiol. 10, 221–229 (1984).
Google Scholar
Dong, C., Chen, X., Xie, Y., Lai, Q. & Shao, Z. Complete genome sequence of Thalassolituus oleivorans R6-15, an obligate hydrocarbonoclastic marine bacterium from the Arctic Ocean. Stand Genom. Sci. 9, 893–901 (2014).
Google Scholar
Choi, A. & Cho, J.-C. Thalassolituus marinus sp. nov., a hydrocarbon utilizing marine bacterium. Int. J. Syst. Evol. Microbiol. 63, 2234–2238 (2013).
Google Scholar
Alain, K., Harder, J., Widdel, F. & Zengler, K. Anaerobic utilization of toluene by marine alpha- and gammaproteobacteria reducing nitrate. Microbiology 158, 2946–2957 (2012).
Google Scholar
Liu, J., Wu, W., Chen, C., Sun, F. & Chen, Y. Prokaryotic diversity, composition structure, and phylogenetic analysis of microbial communities in leachate sediment ecosystems. Appl. Microbiol. Biotechnol. 91, 1659–1675 (2011).
Google Scholar
Yakimov, M. M., Timmis, K. N. & Golyshin, P. N. Obligate oil-degrading marine bacteria. Curr. Opin. Biotechnol. 18, 257–266 (2007).
Google Scholar
McKew, B. A. et al. Efficacy of intervention strategies for bioremediation of crude oil in marine systems and effects on indigenous hydrocarbonoclastic bacteria. Environ. Microbiol. 9, 1562–1571 (2007).
Google Scholar
Satomi, M., Kimura, B., Hamada, T., Harayama, S. & Fujii, T. Phylogenetic study of the genus Oceanospirillum based on 16S rRNA and gyrB genes: emended description of the genus Oceanospirillum, description of Pseudospirillum gen. nov., Oceanobacter gen. nov. and Terasakiella gen. nov. and transfer of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. no. Int. J. Syst. Evol. Microbiol. 52, 739–747 (2002).
Google Scholar
Qin, Q. L. et al. A proposed genus boundary for the prokaryotes based on genomic insights. J. Bacteriol. 196, 2210–2215 (2014).
Google Scholar
Nicholson, A. C. et al. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int. J. Syst. Evol. Microbiol. 70, 4432–4450 (2020).
Google Scholar
Yarza, P. et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat. Rev. Microbiol. 12, 635–645 (2014).
Google Scholar
Barco, R. A. et al. A genus definition for Bacteria and Archaea based on a standard genome relatedness index. MBio 11, e02475-192020. https://doi.org/10.1128/mBio.02475-19 (2020).
Google Scholar
Andersson, J. O. & Andersson, S. G. Insights into the evolutionary process of genome degradation. Curr. Opin. Genet. Dev. 9, 664–671 (1999).
Google Scholar
Wall, D. & Kaiser, D. Type IV pili and cell motility. Mol. Microbiol. 32, 1–10 (1999).
Google Scholar
Jenal, U. & Malone, J. Mechanisms of cyclic-di-GMP signaling in bacteria. Ann. Rev. Genet. 40, 385–407 (2006).
Google Scholar
Dow, J. M., Fouhy, Y., Lucey, J. F. & Ryan, R. P. The HD-GYP domain, cyclic di-GMP signaling, and bacterial virulence to plants. Mol. Plant Microbe Interact. 19, 1378–1384 (2006).
Google Scholar
Hobley, L. et al. Discrete cyclic di-GMP-dependent control of bacterial predation versus axenic growth in Bdellovibrio bacteriovorus. PLoS Pathog. 8, e1002493. https://doi.org/10.1371/journal.ppat.1002493 (2012).
Google Scholar
Seccareccia, I., Kovács, Á. T., Gallegos-Monterrosa, R. & Nett, M. Unraveling the predator-prey relationship of Cupriavidus necator and Bacillus subtilis. Microbiol. Res. 192, 231–238 (2016).
Google Scholar
Mu, D. S. et al. Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments. Microbiome 8, 1262020 (2020).
Google Scholar
Zepeda, V. K. et al. Terasakiispira papahanaumokuakeensis gen. nov., sp. nov., a gammaproteobacterium from Pearl and Hermes Atoll, Northwestern Hawaiian Islands. Int. J. Syst. Evol. Microbiol. 65, 3609–3617 (2015).
Google Scholar
Terasaki, Y. Transfer of five species and two subspecies of Spirillum to other genera (Aquaspirillum and Oceanospirillum), with emended descriptions of the species and subspecies. Int. J. Syst. Evol. Microbiol. 29, 130–144 (1979).
Baker, D. A. & Park, R. W. Changes in morphology and cell wall structure that occur during growth of Vibrio sp. NCTC4716 in batch culture. J. Gen. Microbiol. 86, 12–28 (1975).
Google Scholar
Ng, L. K., Sherburne, R., Taylor, D. E. & Stiles, M. E. Morphological forms and viability of Campylobacter species studied by electron microscopy. J. Bacteriol. 164, 338–343 (1985).
Google Scholar
Reshetnyak, V. I. & Reshetnyak, T. M. Significance of dormant forms of Helicobacter pylori in ulcerogenesis. World J. Gastroenterol. 23, 4867–4878 (2017).
Google Scholar
Loc Carrillo, C. et al. Bacteriophage therapy to reduce Campylobacter jejuni colonization of broiler chickens. Appl. Environ. Microbiol. 71, 6554–6563 (2005).
Google Scholar
Clinical and Laboratory Standards Institute. Methods for determining bactericidal activity of antimicrobial agents; approved guideline M26-A. Clin. Lab. Stand. Inst. 19, 7 (1999).
Legat, A., Gruber, C., Zangger, K., Wanner, G. & Stan-Lotter, H. Identification of polyhydroxyalkanoates in Halococcus and other haloarchaeal species. Appl. Microbiol. Biotechnol. 87, 1119–1127 (2010).
Google Scholar
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
Google Scholar
Tamura, K. & Nei, M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512–526 (1993).
Google Scholar
Felsenstein, J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39, 783–791 (1985).
Google Scholar
Rodriguez-R, L. M. & Konstantinidis, K. T. Bypassing cultivation to identify bacterial species. Microbe 9, 111–118 (2014).
Huerta-Cepas, J. et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol. Biol. Evol. 34, 2115–2122 (2017).
Google Scholar
Source: Ecology - nature.com
