Correction for Tohya et al., “Whole-Genome Sequencing-Based Re-Identification of Pseudomonas putida/fluorescens Clinical Isolates Identified by Biochemical Bacterial Identification Systems”

AUTHOR CORRECTION

Volume 10, no. 2, e02491-21, 2022, https://doi.org/10.1128/spectrum.02491-21. The following taxonomy section should appear in the main article and not in the supplemental material. (A revised supplemental material file is included with this Author Correction.)

DESCRIPTION OF NINE NOVEL SPECIES

Description of Pseudomonas sputi sp. nov.

Pseudomonas sputi (spu'ti. L. gen. n. sputi of sputum).

The cells of this species are aerobic, Gram-negative, non-spore-forming, motile, rod-shaped cells, measuring 1.0 to 2.0 μm in length and 0.5 to 0.7 μm in width. Colonies on Luria broth agar were circular, convex in shape with a creamy color, and usually 1 to 3 mm in diameter after growth for 2 days at 30°C. These bacteria grew at temperatures between 4 and 36°C, at pH 6.0 to 9.0, and in the presence of 0 to 6.0% (wt/vol) NaCl. They produced catalase and cytochrome oxidase, as well as fluorescent pigments, on King’s B agar at 30°C. In API 20NE tests, BML-PP014^T was positive for l-arginine, gelatin, glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-d-glucosamine, potassium glucose, n-capric acid, dl-malic acid, and sodium citrate. In API ZYM tests, this strain was positive for alkaline phosphatase, esterase (C₄), esterase lipase (C₈), leucine arylamidase, valine arylamidase, acid phosphatase, and naphthol-AS-BI-phosphohydrolase activities. In Biolog GN3 tests, this strain was positive for N-acetyl-d-glucosamine, α-d-glucose, d-mannose, d-fructose, d-galactose, d-fucose, l-fucose, inosine, d-mannitol, d-arabitol, glycerol, d-fructose-6-PO₄, l-alanine, l-arginine, l-aspartic acid, l-glutamic acid, l-pyroglutamic acid, l-serine, d-galacturonic acid, l-galactonic acid lactone, d-gluconic acid, d-glucuronic acid, glucuronamide, mucic acid, quinic acid, d-saccharic acid, methyl pyruvate, l-lactic acid, citric acid, α-keto-glutaric acid, l-malic acid, γ-amino-butyric acid, β-hydroxy-d,l-butyric acid, propionic acid, and acetic acid. The major fatty acids were summed feature 3 (C_16:1ω7c/C_16:1ω6c; 37.5%), C_16:0 (28.8%), and summed feature 8 (C_18:1ω7c/C_18:1ω6c; 9.9%). The type strain is BML-PP014^T (= JCM 34577^T, = LMG 32246^T), isolated from a sputum sample of a patient in Japan. The G+C content of the type strain is 60.30 mol%.

Description of Pseudomonas pseudonitroreducens sp. nov.

Pseudomonas pseudonitroreducens [pseudês, Gr. masc./fem. adj., false; nitro.re.du'cens. L. n. nitrum nitrate; L. part. adj. reducens converting to a different state; N. L. adj. nitroreducens reducing nitrate; pseudonitroreducens, N.L. masc. adj., a false (Pseudomonas) nitroreducens].

The cells of this species are aerobic, Gram-negative, non-spore-forming, motile, rod-shaped cells, being 1.0 to 2.0 μm in length and 0.5 to 0.7 μm in width. Colonies on Luria broth agar were circular, convex in shape with a creamy color, and usually 1 to 1.5 mm in diameter after growth for 2 days at 30°C. These bacteria grew at temperatures between 8 and 36°C, at pH 5.5 to 9.0, and in the presence of 0 to 6.0% (wt/vol) NaCl. They produced catalase and cytochrome oxidase, as well as fluorescent pigments, on King’s B agar at 30°C. In API 20NE tests, BML-PP015^T was positive for potassium nitrate, l-arginine, glucose, potassium glucose, n-capric acid, adipic acid, dl-malic acid, sodium citrate, and phenylmercuric acetate. In API ZYM tests, this strain was positive for alkaline phosphatase, esterase (C₄), esterase lipase (C₈), leucine arylamidase, valine arylamidase, acid phosphatase, and naphthol-AS-BI-phosphohydrolase activities. In Biolog GN3 tests, this strain was positive for α-d-glucose, d-fucose, l-fucose, glycerol, d-fructose-6-PO₄, l-alanine, l-arginine, l-aspartic acid, l-glutamic acid, l-serine, l-galactonic acid lactone, d-gluconic acid, glucuronamide, quinic acid, p-hydroxy-phenylacetic acid, methyl pyruvate, l-lactic acid, citric acid, α-keto-glutaric acid, l-malic acid, γ-amino-butyric acid, β-hydroxy-d,l-butyric acid, propionic acid, and acetic acid. The major fatty acids are summed feature 3 (C_16:1ω7c/C_16:1ω6c; 27.4%), summed feature 8 (C_18:1ω7c/C_18:1ω6c; 26.0%), and C_16:0 (22.5%). The type strain is BML-PP015^T (= JCM 34578^T, = LMG 32247^T), isolated from a sputum sample of a patient in Japan. The G+C content of the type strain is 64.50 mol%.

Description of Pseudomonas parasichuanensis sp. nov.

Pseudomonas parasichuanensis [pa.ra. Gr. prep. beside, alongside, near, like; si.chuan.en'sis. N.L. fem. adj. referring to Sichuan Province, People’s Republic of China and the specific epithet of a Pseudomonas species; parasichuanensis. N.L. masc. adj. next to (Pseudomonas) sichuanensis].

The cells of this species are aerobic, Gram-negative, non-spore-forming, motile, rod-shaped cells, being 1.0 to 1.5 μm in length and 0.6 to 0.9 μm in width. Colonies on Luria broth agar were circular, convex in shape with a creamy color, and usually 1 to 2 mm in diameter after growth for 2 days at 30°C. These bacteria grew at temperatures between 8 and 36°C, at pH 6.0 to 9.0, and in the presence of 0 to 6.0% (wt/vol) NaCl. They produced catalase and cytochrome oxidase, as well as fluorescent pigments, on King’s B agar at 30°C. In API 20NE tests, BML-PP020^T was positive for l-arginine, gelatin, glucose, potassium gluconate, n-capric acid, dl-malic acid, sodium citrate, and phenylmercuric acetate. In API ZYM tests, the strain was positive for alkaline phosphatase, esterase (C₄), esterase lipase (C₈), leucine arylamidase, valine arylamidase, trypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, and β-galactosidase activities. In Biolog GN3 tests, this strain was positive for gentiobiose, α-d-glucose, d-mannose, d-fructose, d-galactose, 3-methyl glucose, d-fucose, l-fucose, l-rhamnose, glycerol, d-fructose-6-PO₄, d-aspartic acid, d-serine, l-alanine, l-arginine, l-aspartic acid, l-glutamic acid, l-histidine, l-pyroglutamic acid, l-serine, d-galacturonic acid, l-galactonic acid lactone, d-gluconic acid, d-glucuronic acid, glucuronamide, mucic acid, quinic acid, d-saccharic acid, p-hydroxy-phenylacetic acid, methyl pyruvate, l-lactic acid, citric acid, α-keto-glutaric acid, d-malic acid, l-malic acid, Tween 40, γ-amino-butyric acid, α-hydroxy-butyric acid, β-hydroxy-d,l-butyric acid, α-keto-butyric acid, acetoacetic acid, propionic acid, acetic acid, and formic acid. The major fatty acids are summed feature 3 (C_16:1ω7c/C_16:1ω6c; 32.6%), C_16:0 (27.7%), and summed feature 8 (C_18:1ω7c/C_18:1ω6c; 15.0%). The type strain is BML-PP020^T (= JCM 34580^T, = LMG 32249^T), isolated from a vaginal discharge sample of a patient in Japan. The G+C content of the type strain is 64.19 mol%.

Description of Pseudomonas paraglycinae sp. nov.

Pseudomonas paraglycinae [pa.ra. Gr. prep. beside, alongside, near, like; gly.ci'nae. N.L. gen. n. glycinae of Glycine max, soybean and the specific epithet of a Pseudomonas species; paraglycinae. N.L. masc. adj. next to (Pseudomonas) glycinae].

The cells of this species are aerobic, Gram-negative, non-spore-forming, motile, rod-shaped cells, being 1.0 to 2.0 μm in length and 0.6 to 0.8 μm in width. Colonies on Luria broth agar were circular, convex in shape with a creamy color, and usually 2 to 4 mm in diameter after growth for 2 days at 30°C. These bacteria grew at temperatures between 4 and 36°C, at pH 6.0 to 9.0, and in the presence of 0 to 6.0% (wt/vol) NaCl. They produced catalase and cytochrome oxidase, as well as fluorescent pigments, on King’s B agar at 30°C. In API 20NE tests, BML-PP023^T was positive for l-arginine, gelatin, glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-d-glucosamine, potassium gluconate, n-capric acid, dl-malic acid, and sodium citrate. In API ZYM tests, the strain was positive for alkaline phosphatase, esterase (C₄), esterase lipase (C₈), lipase (C₁₄), leucine arylamidase, valine arylamidase, trypsin, acid phosphatase, and naphthol-AS-BI-phosphohydrolase activities. In Biolog GN3 tests, this strain was positive for N-acetyl-d-glucosamine, α-d-glucose, d-mannose, d-fructose, d-galactose, d-fucose, l-fucose, inosine, d-mannitol, d-arabitol, myo-inositol, glycerol, d-fructose-6-PO₄, l-alanine, l-arginine, l-aspartic acid, l-glutamic acid, l-pyroglutamic acid, l-serine, l-galactonic acid lactone, d-gluconic acid, glucuronamide, mucic acid, quinic acid, d-saccharic acid, methyl pyruvate, l-lactic acid, citric acid, α-keto-glutaric acid, l-malic acid, Tween 40, γ-amino-butyric acid, β-hydroxy-d,l-butyric acid, propionic acid, and acetic acid. The major fatty acids are summed feature 3 (C_16:1ω7c/C_16:1ω6c; 39.3%), C_16:0 (31.4%), and summed feature 8 (C_18:1ω7c/C_18:1ω6c; 9.9%). The type strain is BML-PP023^T (= JCM 34581^T, = LMG 32250^T), isolated from a sputum sample of a patient in Japan. The G+C content of the type strain is 60.68 mol%.

Description of Pseudomonas ceruminis sp. nov.

Pseudomonas ceruminis (ceru'mi.nis L. gen. neut.n. ceruminis of cerumen).

The cells of this species are aerobic, Gram-negative, non-spore-forming, motile, rod-shaped cells, being 1.0 to 2.0 μm in length and 0.7 to 0.8 μm in width. Colonies on Luria broth agar were circular, convex in shape with a creamy color, and usually 1 to 2 mm in diameter after growth for 2 days at 30°C. These bacteria grew at temperatures between 8 and 36°C, at pH 6.0 to 9.0, and in the presence of 0 to 6.0% (wt/vol) NaCl. They produced catalase and cytochrome oxidase, as well as fluorescent pigments, on King’s B agar at 30°C. In API 20NE tests, BML-PP028^T was positive for l-arginine, glucose, d-mannose, d-mannitol, potassium glucose, n-capric acid, dl-malic acid, sodium citrate, and phenylmercuric acetate. In API ZYM tests, the strain was positive for alkaline phosphatase, esterase (C₄), esterase lipase (C₈), leucine arylamidase, valine arylamidase, trypsin, acid phosphatase, and naphthol-AS-BI-phosphohydrolase activities. In Biolog GN3 tests, this strain was positive for gentiobiose, d-melibiose, α-d-glucose, d-mannose, d-fructose, d-galactose, 3-methyl glucose, d-fucose, l-fucose, l-rhamnose, inosine, d-mannitol, d-arabitol, glycerol, d-fructose-6-PO₄, d-serine, l-alanine, l-arginine, l-aspartic acid, l-glutamic acid, l-histidine, l-pyroglutamic acid, l-serine, d-galacturonic acid, l-galactonic acid lactone, d-gluconic acid, d-glucuronic acid, glucuronamide, quinic acid, methyl pyruvate, l-lactic acid, citric acid, α-keto-glutaric acid, d-malic acid, l-malic acid, bromo-succinic acid, γ-amino-butyric acid, α-hydroxy-butyric acid, β-hydroxy-d,l-butyric acid, α-keto-butyric acid, acetoacetic acid, propionic acid, acetic acid, and formic acid. The major fatty acids are C_16:0 (42.3%), summed feature 3 (C_16:1ω7c/C_16:1ω6c; 17.5%), and C_17:0cyclo (11.9%). The type strain is BML-PP028^T (= JCM 34110^T, = DSM 111127^T), isolated from an ear discharge sample of a patient in Japan. The G+C content of the type strain is 61.67 mol%.

Description of Pseudomonas parakoreensis sp. nov.

Pseudomonas parakoreensis [pa.ra. Gr. prep. beside, alongside, near, like; ko.re.en'sis N.L. fem. adj. koreensis, pertaining to Korea and the specific epithet of a Pseudomonas species; parakoreensis. N.L. masc. adj. next to (Pseudomonas) koreensis].

The cells of this species are aerobic, Gram-negative, non-spore-forming, motile, rod-shaped cells, being 1.0 to 2.0 μm in length and 0.6 to 0.7 μm in width. Colonies on Luria broth agar were circular, convex in shape with a creamy color, and usually 1 to 3 mm in diameter after growth for 2 days at 30°C. These bacteria grew at temperatures between 4 and 36°C, at pH 6.0 to 8.5, and in the presence of 0 to 5.0% (wt/vol) NaCl. They produced catalase and cytochrome oxidase, as well as fluorescent pigments, on King’s B agar at 30°C. In API 20NE tests, BML-PP030^T was positive for l-arginine, gelatin, glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-d-glucosamine, potassium glucose, n-capric acid, dl-malic acid, and sodium citrate. In API ZYM tests, the strain was positive for alkaline phosphatase, esterase (C₄), esterase lipase (C₈), lipase (C₁₄), leucine arylamidase, valine arylamidase, trypsin, acid phosphatase, and naphthol-AS-BI-phosphohydrolase activities. In Biolog GN3 tests, this strain was positive for N-acetyl-d-glucosamine, α-d-glucose, d-mannose, d-galactose, d-fucose, l-fucose, inosine, d-mannitol, d-arabitol, glycerol, d-fructose-6-PO₄, d-serine, l-alanine, l-arginine, l-aspartic acid, l-glutamic acid, l-histidine, l-pyroglutamic acid, l-serine, d-galacturonic acid, l-galactonic acid lactone, d-gluconic acid, d-glucuronic acid, glucuronamide, mucic acid, quinic acid, d-saccharic acid, methyl pyruvate, l-lactic acid, citric acid, α-keto-glutaric acid, l-malic acid, bromo-succinic acid, Tween 40, γ-amino-butyric acid, β-hydroxy-d,l-butyric acid, propionic acid, and acetic acid. The major fatty acids are summed feature 3 (C_16:1ω7c/C_16:1ω6c; 37.8%), C_16:0 (31.6%), and summed feature 8 (C_18:1ω7c/C_18:1ω6c; 10.7%). The type strain is BML-PP030^T (= JCM 34582^T, = LMG 32251^T), isolated from a throat swab sample of a patient in Japan. The G+C content of the type strain is 60.09 mol%.

Description of Pseudomonas pharyngis sp. nov.

Pseudomonas pharyngis (pha.ryn'gis Gr. n. phaynx throat; Gr. Gen. n. pharyngis of the throat).

The cells of this species are aerobic, Gram-negative, non-spore-forming, motile, rod-shaped cells, being 1.0 to 1.5 μm in length and 0.8 to 0.9 μm in width. Colonies on Luria broth agar were circular, convex in shape with a creamy color, and usually 1 to 5 mm in diameter after growth for 2 days at 30°C. These bacteria grew at temperatures between 4 and 36°C, at pH 6.0 to 9.0, and in the presence of 0 to 6.0% (wt/vol) NaCl. They produced catalase and cytochrome oxidase, as well as fluorescent pigments, on King’s B agar at 30°C. In API 20NE tests, BML-PP036^T was positive for l-arginine, gelatin, glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-d-glucosamine, potassium glucose, n-capric acid, dl-malic acid, and sodium citrate. In API ZYM tests, the strain was positive for alkaline phosphatase, esterase (C₄), esterase lipase (C₈), lipase (C₁₄), leucine arylamidase, valine arylamidase, trypsin, acid phosphatase, and naphthol-AS-BI-phosphohydrolase activities. In Biolog GN3 tests, this strain was positive for N-acetyl-d-glucosamine, α-d-glucose, d-mannose, d-fructose, d-galactose, d-fucose, l-fucose, inosine, d-mannitol, d-arabitol, glycerol, d-fructose-6-PO₄, d-serine, l-alanine, l-arginine, l-aspartic acid, l-glutamic acid, l-pyroglutamic acid, l-serine, l-galactonic acid lactone, d-gluconic acid, glucuronamide, mucic acid, quinic acid, d-saccharic acid, methyl pyruvate, l-lactic acid, citric acid, α-keto-glutaric acid, l-malic acid, Tween 40, γ-amino-butyric acid, β-hydroxy-d,l-butyric acid, propionic acid, and acetic acid. The major fatty acids are summed feature 3 (C_16:1ω7c/C_16:1ω6c; 40.3%), C_16:0 (31.9%), and summed feature 8 (C_18:1ω7c/C_18:1ω6c; 8.9%). The type strain is BML-PP036^T (= JCM 34583^T, = LMG 32252^T), isolated from a throat swab sample of a patient in Japan. The G+C content of the type strain is 60.42 mol%.

Description of Pseudomonas urethralis sp. nov.

Pseudomonas urethralis (L. fem. n. urethra, the excretory canal of the urine, the urethra; L. fem. suff. -alis, suffix denoting pertaining to; N.L. fem. adj. urethralis, of or pertaining to the urethra).

The cells of this species are aerobic, Gram negative, non-spore-forming, motile, rod-shaped cells, being 1.0 to 2.0 μm in length and 0.8 to 1.0 μm in width. Colonies on Luria broth agar were circular, convex in shape with a creamy color, and usually 1 to 3 mm in diameter after growth for 2 days at 30°C. These bacteria grew at temperatures between 8 and 40°C, at pH 6.0 to 9.0, and in the presence of 0 to 6.0% (wt/vol) NaCl. They produced catalase and cytochrome oxidase, as well as fluorescent pigments, on King’s A and B agar at 30°C. In API 20NE tests, BML-PP042^T was positive for l-arginine, glucose, l-arabinose, d-mannose, potassium glucose, n-capric acid, dl-malic acid, and sodium citrate. In API ZYM tests, the strain was positive for alkaline phosphatase, esterase (C₄), esterase lipase (C₈), leucine arylamidase, valine arylamidase, trypsin, acid phosphatase, and naphthol-AS-BI-phosphohydrolase. In Biolog GN3 tests, this strain was positive for α-d-glucose, d-mannose, d-fructose, d-galactose, d-fucose, l-fucose, inosine, glycerol, d-fructose-6-PO₄, d-serine, l-alanine, l-arginine, l-aspartic acid, l-glutamic acid, l-histidine, l-pyroglutamic acid, l-serine, d-galacturonic acid, l-galactonic acid lactone, d-gluconic acid, d-glucuronic acid, glucuronamide, mucic acid, quinic acid, d-saccharic acid, methyl pyruvate, l-lactic acid, citric acid, α-keto-glutaric acid, l-malic acid, Tween 40, γ-amino-butyric acid, α-hydroxy-butyric acid, β-hydroxy-d,l-butyric acid, α-keto-butyric acid, acetoacetic acid, propionic acid, acetic acid, and formic acid. The major fatty acids are C_16:0 (40.0%), summed feature 3 (C_16:1ω7c/C_16:1ω6c; 23.4%), and summed feature 8 (C_18:1ω7c/C_18:1ω6c; 13.0%). The type strain is BML-PP042^T (= JCM 34111^T, = DSM 111128^T), isolated from a urethral discharge sample of a patient in Japan. The G+C content of the type strain is 62.71 mol%.

Description of Pseudomonas faucium sp. nov.

Pseudomonas faucium (fau'ci.um L. gen. pl. n. faucium, of the throat).

The cells of this species are aerobic, Gram negative, non-spore-forming, motile, rod-shaped cells, being 1.0 to 2.0 μm in length and 0.6 to 0.8 μm in width, Colonies on Luria broth agar were circular, convex in shape with a creamy color, and usually 1 to 3 mm in diameter after growth for 2 days at 30°C. These bacteria grew at temperatures between 8 and 36°C, at pH 6.0 to 9.0, and in the presence of 0 to 6.0% (wt/vol) NaCl. They produced catalase and cytochrome oxidase, as well as fluorescent pigments, on King’s B agar at 30°C. In API 20NE tests, BML-PP048^T was positive for potassium nitrate, l-arginine, glucose, d-mannose, potassium glucose, n-capric acid, dl-malic acid, sodium citrate, and phenylmercuric acetate. In API ZYM tests, the strain was positive for alkaline phosphatase, esterase (C₄), esterase lipase (C₈), leucine arylamidase, valine arylamidase, acid phosphatase, and naphthol-AS-BI-phosphohydrolase. In Biolog GN3 tests, this strain was positive for α-d-glucose, d-mannose, d-fructose, d-galactose, 3-methyl glucose, d-fucose, l-fucose, l-rhamnose, inosine, glycerol, d-fructose-6-PO₄, d-serine, l-alanine, l-arginine, l-aspartic acid, l-glutamic acid, l-histidine, l-pyroglutamic acid, l-serine, d-galacturonic acid, l-galactonic acid lactone, d-gluconic acid, d-glucuronic acid, glucuronamide, quinic acid, methyl pyruvate, l-lactic acid, citric acid, α-keto-glutaric acid, d-malic acid, l-malic acid, bromo-succinic acid, γ-amino-butyric acid, α-hydroxy-butyric acid, β-hydroxy-d,l-butyric acid, α-keto-butyric acid, acetoacetic acid, propionic acid, acetic acid, and formic acid. The major fatty acids are C_16:0 (42.2%), C_17:0cyclo (19.1%), and summed feature 3 (C_16:1ω7c/C_16:1ω6c; 12.0%). The type strain is BML-PP048^T (= JCM 34112^T, = DSM 111130^T), isolated from a throat swab sample of a patient in Japan. The G+C content of the type strain is 64.19 mol%.