Sheet1. Page 1. Supplementary table S1 Detailed information on the 67 phenotypes used in this study. Test GIDEON II. Bergey's Test description
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1 Supplementary table S1 Detailed information on the 67 phenotypes used in this study Phenotype (a) Test GIDEON I GIDEON II Bergey's Test description type (c) GIDEON I+ (e) GIDEON I- (d) GIDEON II+ (b) total (h) GIDEON II- (g) Bergey's+ (f) total (k) Bergey's- (l) (i) total (m) Acetate utilization Aerobe Alkaline phosphatase Anaerobe Arginine dihydrolase Bacillus or coccobacillu s Beta hemolysis A variety of commercial kits are satisfactory. Includes late reactions for -positive and non-fermve negative rods Organisms which grow only in the presence of air. Most kits utilize p- nitrophenyl phosphate as substrate. Insure thorough washing if phosphate buffers are employed Organisms which do not grow in the presence of oxygen For most organisms, Moeller medium interpreted with control after 18 hours (or longer for -positive and non-fermve negative rods) Bacilli predominate Sheep blood Page 1
2 Bilesusceptible Capnophilic Casein hydrolysis Catalase Cellobiose Media and bile concentrations vary according to the species ed; Presumpto Plates useful for anaerobes Exogenous carbon dioxide (5 to 7%) must be present for growth; Gas Pak or cylinder gas are preferred Standard skimmilk/nutrient agar halo ; Presumpto Plates useful for anaerobes Perform on young colonies (up to 24 hours) using 3% hydrogen peroxide (alternative technique for Mycobacteria); Presumpto Plates useful for anaerobes reactions for positive & nonfermve Page 2
3 Citrate Coagulase production Simmons citrate medium using a light inoculum (avoid stabbing the agar). Includes late reactions for positive and nonfermve negative rods Standard or commercial slide plasma s acceptable; tube s may help differentiate Staphylococcus aureus from other taxa Coccus Coccus - clusters or groups predominate Cocci predominate The predominant forms are cocci, in clusters or irregular groups Coccus - pairs or chains predominate The predominant forms are cocci in chains or pairs Colistin- Polymyxin susceptible Standard disk diffusion technique; recommended media and disk potency may vary for specific taxa Page 3
4 D-Mannitol D-Mannose DNase reactions for positive & nonfermve reactions for positive & nonfermve Standard commercial agar s; Presumpto Plates useful for anaerobes Page 4
5 D-Sorbitol D-Xylose Esculin hydrolysis Facultative reactions for positive & nonfermve reactions for positive & nonfermve For most organisms, Moeller medium interpreted with control after 18 hours (or longer for -positive and non-fermve negative rods) Organisms which grow both in the presence and absence of air Page 5
6 Gas from glucose Gelatin hydrolysis Gas produced from D- glucose; Durham tube or gas bubbles noted in commercial kits Commercial or self prepared (or X-ray film) s interpreted after hours against control at lowered temperature; Presumpto Plates useful for anaerobes Glucose fermenter techniques are generally producing more subtle ph changes; specific techniques applied for Neisseria; Presumpto Plates useful for anaerobes Glucose oxidizer Hugh and Leifson method; in most cases 'positive' indicates nonfermve organism which oxidizes glucose Page 6
7 Glycerol reactions for positive & nonfermve Gram negative Gram positive Growth at 42 degrees C Gram-negative forms predominate Gram-positive forms predominate Media vary according to the species ed Growth in 6.5% NaCl Media vary according to the species ed Growth in KCN Growth on MacConkey agar Growth on ordinary blood agar Commercial kits based on 1:13,000 KCN are suggested Visible growth within 48 hours; or within 7 days for positive and non-fermve Visible growth on sheep blood agar within 48 hours Page 7
8 Hydrogen sulfide Indole Lactose TSI for enterobacteriaceae and most other species; Presumpto Plates useful for anaerobes. Includes late appearance of hydrogen sulfide for -positive and nonfermve negative rods A spot is acceptable for most organisms; overnight ing with a paper strip is helpful in confirming negative reactions; Presumpto Plates useful for anaerobes reactions for positive & nonfermve Page 8
9 L-Arabinose reactions for positive & nonfermve Lipase L- Rhamnose Standard egg yolk agar ; Presumpto Plates useful for anaerobes reactions for positive & nonfermve Lysine decarboxyla se For most organisms, Moeller medium interpreted with control after 18 hours (or longer for -positive and non-fermve negative rods) Page 9
10 Malonate Maltose Melibiose Methyl red Standard based on maintenance of alkaline ph (bromthymol blue) in the presence of glucose and malonate; commercial kits are acceptable reactions for positive & nonfermve reactions for positive & nonfermve Commercial or selfprepared media are generally acceptable Page 10
11 Motile Mucate utilization myo-inositol Nitrate to nitrite Nitrite to gas Standard hanging drop on fresh broth isolates for most purposes; perform at 22 to 25 degrees C if Listeria suspected A variety of commercial kits are satisfactory. Includes late reactions for -positive and non-fermve negative rods reactions for positive & nonfermve Commercial and selfprepared media are acceptable; alternative techniques used for mycobacteria Standard zinc dust applied to 'nitratenegative' organisms Page 11
12 ONPG (beta galactosidas e) Ornithine decarboxyla se Oxidase Pyrrolidonylbetanaphthylami de Commercial kits are generally satisfactory; suggest a heavy inoculum in buffered medium; yellow pigmented organisms may not be suitable for ing For most organisms, Moeller medium interpreted with control after 18 hours (or longer for -positive and non-fermve negative rods) Paper strip from appropriate media L-pyrrolidonyl-betanaphthylamide - PYR (or pyrrolidonyl arylamidase - PYRA) - reagents commercially available; read color within 10 seconds (2 minutes for Carr-Scarborough reagent) Page 12
13 Raffinose Salicin Spore formation Starch hydrolysis reactions for positive & nonfermve reactions for positive & nonfermve Note that spores may only appear in vitro, and may not be seen in clinical material Standard starch hydrolysis or Mueller- Hilton agar s developed with iodine solutions; Presumpto Plates useful for anaerobes Page 13
14 Sucrose Tartrate utilization Trehalose reactions for positive & nonfermve A variety of commercial kits are satisfactory. Includes late reactions for -positive and non-fermve negative rods reactions for positive & nonfermve Page 14
15 Urea hydrolysis Voges Proskauer Yellow pigment Christensen agar ing for most taxa; other techniques for mycobacteria, ureaplasma and other organisms as recommended. Includes late reactions for positive and nonfermve negative rods Commercial or selfprepared media are generally acceptable; the is most reliable when performed on cultures no older than three days Yellow pigment noted on sheep blood or other primary isolation agar. Includes late appearance of pigment for -positive and non-fermve negative rods (a) GIDEON phenotypes (b) Type of required for the phenotype determination in the wet lab according to GIDEON (c) Remarks on wet lab for determination of the phenotype according to GIDEON (d) Number of phenotype-positive bacteria in the GIDEON I dataset (e) Number of phenotype-negative bacteria in the GIDEON I dataset (f) Total number of bacteria with phenotype labels in the GIDEON I dataset (g) Number of phenotype-positive bacteria in the GIDEON II dataset (h) Number of phenotype-negative bacteria in the GIDEON II dataset (i) Total number of bacteria with phenotype labels in the GIDEON II dataset Page 15
16 (j) Number of phenotype-positive bacteria in the Bergey dataset (k) Number of phenotype-negative bacteria in the Bergey dataset (l) Total number of bacteria with phenotype labels in the Bergey dataset Page 16
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