Overproduction of Xanthophyll Pigment in Flavobacterium sp. JSWR-1 under Optimized Culture Conditions

Flavobacterium can synthesize xanthophyll, particularly the pigment zeaxanthin, which has significant economic value in nutrition and pharmaceuticals. Recently, the use of carotenoid biosynthesis by bacteria and yeast fermentation technology has shown to be very efficient and offers significant advantages in large-scale production, cost-effectiveness, and safety. In the present study, JSWR-1 strain capable of producing xanthophyll pigment was isolated from a freshwater reservoir in Wanju-gun, Republic of Korea. Based on the morphological, physiological, and molecular characteristics, JSWR-1 classified as belonging to the Flavobacterium species. The bacterium is strictly aerobic, Gram-negative, rod-shaped, and psychrophilic. The completed genome sequence of the strain Flavobacterium sp. JSWR-1 is predicted to be a single circular 3,425,829-bp chromosome with a G+C content of 35.2% and 2,941 protein-coding genes. The optimization of carotenoid production was achieved by small-scale cultivation, resulting in zeaxanthin being identified as the predominant carotenoid pigment. The enhancement of zeaxanthin biosynthesis by applying different light-irradiation, variations in pH and temperature, and adding carbon and nitrogen supplies to the growth medium. A significant increase in intracellular zeaxanthin concentrations was also recorded during fed-batch fermentation achieving a maximum of 16.69 ± 0.71 mg/l, corresponding to a product yield of 4.05 ± 0.15 mg zeaxanthin per gram cell dry weight. Batch and fed-batch culture extracts exhibit significant antioxidant activity. The results demonstrated that the JSWR-1 strain can potentially serve as a source for zeaxanthin biosynthesis.

Flavobacterium okayamense sp. nov. isolated from surface seawater

Strain KK2020170T, a Gram-stain negative, yellow colony-forming bacterium, was isolated from surface seawater sampled in Kojima Bay, Okayama, Japan. Phylogenetic analysis based on the 16S rRNA gene revealed that strain KK2020170T belongs to the genus Flavobacterium, with Flavobacterium haoranii LQY-7T (98.1% similarity) being its closest relative, followed by Flavobacterium sediminis MEBiC07310T (96.9%) and Flavobacterium urocaniciphilum YIT 12746T (96.0%). Whole-genome shotgun sequencing showed that strain KK2020170T, when paralleled with F. haoranii LQY-7 T, had 81.3% average nucleotide identity, and 24.6% in silico DNA-DNA hybridization values, respectively. The DNA G + C content of strain KK2020170T was 31.1 mol%. The most abundant fatty acids (> 10%) of strain KK2020170T were iso-C15: 0, iso-C17: 0 3-OH and iso-C15: 1 G. The dominant respiratory quinone of the strain was menaquinone MK-6. Based on the phylogenetic and phenotypic analysis results, we propose that strain KK2020170T represents a novel species, for which the name Flavobacterium okayamense sp. nov. has been proposed. The type strain is KK2020170T (= ATCC TSD-280 T = NBRC 115344 T).

Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum sp. nov., F. limnophilum sp. nov., F. lacustre sp. nov., and F. eburneipallidum sp. nov

Eleven bacterial strains were isolated from freshwater environments and identified as Flavobacterium based on 16S rRNA gene sequence analyses. Complete genome sequences of the 11 strains ranged from 3.45 to 5.83 Mb with G + C contents of 33.41-37.31%. The average nucleotide identity (ANI) values showed that strains IMCC34515^T and IMCC34518 belonged to the same species, while the other nine strains represented each separate species. The ANI values between the strains and their closest Flavobacterium species exhibited ≤ 91.76%, indicating they represent each novel species. All strains had similar characteristics such as being Gram-stain-negative, rod-shaped, and contained iso-C_15:0 as the predominant fatty acid, menaquinone-6 as the respiratory quinone, and phosphatidylethanolamine and aminolipids as major polar lipids. Genomic, phylogenetic, and phenotypic characterization confirmed that the 11 strains were distinct from previously recognized Flavobacterium species. Therefore, Flavobacterium praedii sp. nov. (IMCC34515^T = KACC 22282 ^T = NBRC 114937 ^T), Flavobacterium marginilacus sp. nov. (IMCC34673^T = KACC 22284 ^T = NBRC 114940 ^T), Flavobacterium aestivum sp. nov. (IMCC34774^T = KACC 22285 ^T = NBRC 114941 ^T), Flavobacterium flavigenum sp. nov. (IMCC34775^T = KACC 22286 ^T = NBRC 114942 ^T), Flavobacterium luteolum sp. nov. (IMCC34776^T = KACC 22287 ^T = NBRC 114943 ^T), Flavobacterium gelatinilyticum sp. nov. (IMCC34777^T = KACC 22288 ^T = NBRC 114944 ^T), Flavobacterium aquiphilum sp. nov. (IMCC34779^T = KACC 22289 ^T = NBRC 114945 ^T), Flavobacterium limnophilum sp. nov. (IMCC36791^T = KACC 22290 ^T = NBRC 114947 ^T), Flavobacterium lacustre sp. nov. (IMCC36792^T = KACC 22291 ^T = NBRC 114948 ^T), and Flavobacterium eburneipallidum sp. nov. (IMCC36793^T = KACC 22292 ^T = NBRC 114949 ^T) are proposed as novel species.

Flavobacterium potami sp. nov., a multi-metal resistance genes harbouring bacterium isolated from shallow river silt

Environmental pollution by heavy metals is becoming an increasing problem and has become a matter of great concern due to the adverse effects worldwide. In this study, we report a novel strain of multi-metal resistant bacteria. A Gram-stain-negative, strictly aerobic, non-motile, yellow, rod-shaped strain 17A^T, was isolated from the shallow silt of Fuyang River located in Longdian town, Hengshui city, Hebei province, China. Strain 17A^T grew at 20-35 °C (optimum, 30 °C), pH 5-10 (optimum, pH 7) and 0-2% (w/v) NaCl (optimum, 1%). Phylogenetic analyses of 16S rRNA gene sequences showed that strain 17A^T was closely related to members of the genus Flavobacterium, and had the highest 16S rRNA gene sequence similarity with 'Flavobacterium panacis' DCY106^T (97.5%), followed by Flavobacterium johnsoniae subsp. johnsoniae UW101^T (97.3%), Flavobacterium cutihirudinis E89^T (97.2%), Flavobacterium limi THG-AG6.4^T (97.2%), Flavobacterium hibisci THG-HG1.4^T (97.2%) and Flavobacterium johnsoniae subsp. aurantiacum DSM 6792^T (97.1%). The genome size of strain 17A^T was 5.4 Mb and the DNA G + C content was 34.0%. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values among strain 17A^T and reference strains were in the ranges of 79.8-86.1%, 24.1-31.4% and 80.5-88.6%, respectively, lower than the threshold values for species delineation. Strain 17A^T contained iso-C_15:0 and C_16:0 3-OH as the predominant fatty acids (≥ 10%). The main isoprenoid quinone of strain 17A^T was identified as MK-6. The polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids, two unidentified aminophospholipids and six unidentified lipids. Comparative genomics analysis between strain 17A^T and its reference type strains revealed that there are a number of metal-resistant genes in strain 17A^T, which are located in 15 gene clusters responsible for the copper homeostasis, cobalt-zinc-cadmium resistance, copper resistance, and arsenic/antimony resistance, with the copper resistance protein NlpE being unique to 17A^T. Combined data from phenotypic, phylogenetic and chemotaxonomic studies demonstrated that strain 17A^T is a representative of a novel species within the genus Flavobacterium, for which the name Flavobacterium potami sp. nov. is proposed. The type strain is 17A^T (= GDMCC 1.2723^T = JCM 34833^T).

Flavobacterium litorale sp. nov., isolated from red alga

A Gram-stain-negative and rod-shaped bacterial strain (WSW3-B6T) was isolated from red alga collected from the West Sea, Republic of Korea. Cells of strain WSW3-B6T were non-motile, aerobic and produced slightly yellow and mucoid colonies on marine agar. The strain grew optimally at 23–30 °C, with 0.5–4 % NaCl (w/v) and at pH 6.5–8.5. A phylogenetic analysis of the 16S rRNA gene revealed that strain WSW3-B6T belongs to the genus Flavobacterium within the family Flavobacteriaceae , having the highest sequence similarity to Flavobacterium arcticum SM1502T (96.7%), followed by Flavobacterium salilacus subsp. altitudinum LaA7.5T (96.2%) and Flavobacterium salilacus subsp. salilacus SaA2.12T (96.2%). The complete sequence of a circular chromosome of strain WSW3-B6T determined by combination of Oxford Nanopore and Illumina platforms comprised a total 2 725 095 bp with G+C content of 37.1 mol%. A comparative analysis based on the whole genome also showed the distinctiveness of strain WSW3-B6T. The average nucleotide identity (ANI) values between strain WSW3-B6T and the closest strains F. arcticum SM1502T, F. salilacus subsp. altitudinum LaA7.5T and F. salilacus subsp. salilacus SaA2.12T were 78.3, 77.8 and 77.7 %, respectively, while the digital DNA–DNA hybridization (dDDH) values between strain WSW3-B6T and the above closely related strains were 21.0, 20.4 and 20.3 %, respectively. Both the ANI and dDDH values supported the creation of a new species in the genus Flavobacterium . The major fatty acids (>10 %) were iso-C15 : 0 (19.3 %), C16 : 0 (14.0 %), iso-C17 : 0 3-OH (13.1 %) and C18 : 0 (10.7 %). The polar lipids of strain WSW3-B6T included phosphatidylethanolamine, three unidentified aminolipids and three unidentified lipids. Moreover, MK-6 was the only respiratory quinone. A comparison of the phylogenetic distinctiveness and the unique phenotypic and chemotaxonomic characteristics among strain WSW3-B6T and closely related type strains supported that strain WSW3-B6T (=KCTC 82708T=GDMCC 1.2627T) represents a novel species of the genus Flavobacterium , for which the name Flavobacterium litorale sp. nov. is proposed.