Phenotype Microarrays (Biolog Inc., USA) were used to examine the metabolic potential of Pseudomonas sp. ANT_H12B. The Phenotype Microarrays (PM) assays involved panels for carbon (PM01 and PM02—190 of C sources), nitrogen (PM03—95 of N sources), as well as phosphorus and sulfur usage (PM04—59 of P and 35 of S sources). PM assays were performed according to the standard protocols recommended by the manufacturer for gram-negative bacteria and described by Gharaie et al. [30 (link)]. All assays were performed in triplicates using an OmniLog device (Biolog Inc., USA). All data were collected by OmniLog PM System software (Biolog Inc., USA).
Omnilog device
Manufactured by Biolog
Sourced in United States
The Omnilog device is a laboratory instrument used for the rapid identification and characterization of microorganisms. It measures the metabolic activity of various microbial strains under different growth conditions. The Omnilog device generates data on the utilization of different carbon sources and other biochemical activities, providing a comprehensive profile of the tested microorganisms.
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6 protocols using omnilog device
1
Metabolic Profiling of Pseudomonas sp. ANT_H12B
2
Comprehensive Phenotypic Characterization of Streptomyces
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The isolates and S. ghanaensis NRRL B-12104T were examined for standard biochemical, degradative and physiological characteristics after Williams et al. (1983 (link)) and enzyme profiles determined using API-ZYM kits (BioMerieux) employing a standardised inoculum corresponding to 5 on the McFarland scale (Murray et al. 1999 ) and the protocol provided by the manufacturer. The oxidation of carbon sources and resistance to inhibitory compounds were determined using GENIII microplates in an Omnilog device (Biolog Inc., Haywood, USA). The microplates were inoculated with cell suspensions made in a ‘gelling’ inoculating fluid at a cell density of 98% transmittance with a run time of 7 days in phenotypic microarray mode at 28 °C. The exported data were analysed using the opm package for R version 1.0.6. (Vaas et al. 2012 (link), 2013 (link)). The Biolog tests were carried out in duplicate.
3
Phenotypic Characterization of Bacterial Strains
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Strain ncl2T and N. vaccinii DSM 43285T were screened for a broad range of phenotypic properties, including their ability to metabolize diverse sole carbon and nitrogen sources, to grow in the presence of several concentrations of sodium chloride, at a range of pH values and in the presence of antibiotics using GENIII microplates and an OMNILOG device (Biolog Inc., Hayward, CA, USA), as described previously [8 ]. The resultant data were analysed using version 1.3.36 of the OPM package [62 , 63 ]. They were also tested for their ability to produce niacin, arylsulfatase after 3 days [64 ], and to reduce tellurite [65 ]. All of these tests were carried out in duplicate using a standard inoculum. Enzymatic and additional metabolic properties of the strains were determined using API-ZYM kits and the protocol provided by the manufacturer (Biomerieux, France).
4
Physiological and Biochemical Profiling of Streptomyces
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Strain H9T and the type strains of the three reference Streptomyces species were examined for a range of standard biochemical, degradative and physiological properties using media and methods described by Williams et al. (1983 (link)). Enzyme profiles of the strains were determined using API ZYM kits (bioMérieux) following the manufacturer’s instructions. A standard inoculum corresponding to 5 on the McFarland scale (Murray et al. 1999 ) was used to inoculate all of these tests. In addition, the ability of the strains to oxidise diverse carbon and nitrogen sources and to show resistance to inhibitory compounds were determined using GEN III microplates in an Omnilog device (BIOLOG Inc., Haywood, USA). The exported data were analysed using the opm package for R (Vaas et al. 2012 (link), 2013 (link)) version 1.06. All of these tests were carried out in duplicate.
5
Comparative Mycobacterial Phenotypic Analysis
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Strain L1T and its phylogenetic neighbour, M. sphagni DSM 44076T, were examined for a broad range of biochemical tests known to be of value in mycobacterial systematics: arylsulfatase after 3 and 14 days (Tomioka et al., 1990 (link)), catalase (de Waard and Robledo, 2007 ), heat stable catalase (Sequeira de Latini and Barrera, 2008 ), nitrate reduction (Vincent et al., 2003 ) and potassium tellurite tolerance (Kilburn et al., 1969 (link); Kent and Kubica, 1985 ). Moreover, the growth of these strains was also evaluated in the presence of a wide range of carbon, nitrogen substrates and inhibitory compounds using GENIII microplates. The latter were inoculated with a bacterial suspension as described by Nouioui et al. (2017) (link) and then incubated at 28°C for 5 days in an Omnilog device (Biolog Inc., Hayward, United States). The resultants data were analysed using opm package version 1.3 (Vaas et al., 2012 (link), 2013 (link)). Furthermore, the enzymatic activities of strains L1T and M. sphagni DSM 44076 T were determined using API coryne kit and following the manufacturer’s instruction (Biomérieux, France). Each test was performed in duplicate.
6
Comprehensive Mycobacterial Phenotypic Profiling
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The two strains and their close phylogenetic neighbours were examined for phenotypic tests found to be useful in mycobacterial systematics (Magee and Ward 2012, Nouioui et al. 2017 ).
The strains were tested for their ability to use sole carbon and sole nitrogen sources, to grow in the presence of several concentrations of sodium chloride, at a range of pH values and in the presence of antibiotics using GENIII microplates and an Omnilog device (BIOLOG, Hayward, CA). The tests were carried out in duplicate using freshly prepared inocula (OD600-0.3-0.6) harvested from the mid-logarithmic growth phase of PMG agar plates incubated at 28°C for 7 days. The resultant data were exported and analysed using the opm package version 1.3.36 (Vaas et al. 2012 (Vaas et al. , 2013)) . The strains were also examined for their ability to produce arylsulfatase after 3 and 14 days (Tomioka et al. 1990 ), catalase (Palomino et al. 2007 (link)) and heat stable catalase (Sequeira de Latini and Barrera 2008) and for niacin accumulation (Kent and Kubica 1985) , resistance to potassium tellurite (Kent and Kubica 1985; Kilburn et al. 1969) , degradation of Tween 80 (Ribón 2012 (link)) and urea hydrolysis (Palomino et al. 2007 (link)) using the media and incubation conditions described in these references. All of these tests were carried out in duplicate using the standard inoculum.
The strains were tested for their ability to use sole carbon and sole nitrogen sources, to grow in the presence of several concentrations of sodium chloride, at a range of pH values and in the presence of antibiotics using GENIII microplates and an Omnilog device (BIOLOG, Hayward, CA). The tests were carried out in duplicate using freshly prepared inocula (OD600-0.3-0.6) harvested from the mid-logarithmic growth phase of PMG agar plates incubated at 28°C for 7 days. The resultant data were exported and analysed using the opm package version 1.3.36 (Vaas et al. 2012 (Vaas et al. , 2013)) . The strains were also examined for their ability to produce arylsulfatase after 3 and 14 days (Tomioka et al. 1990 ), catalase (Palomino et al. 2007 (link)) and heat stable catalase (Sequeira de Latini and Barrera 2008) and for niacin accumulation (Kent and Kubica 1985) , resistance to potassium tellurite (Kent and Kubica 1985; Kilburn et al. 1969) , degradation of Tween 80 (Ribón 2012 (link)) and urea hydrolysis (Palomino et al. 2007 (link)) using the media and incubation conditions described in these references. All of these tests were carried out in duplicate using the standard inoculum.
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