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Polysaccharides are recognized for their extensive biological functions, holding significant promise for applications in both medicine and food industries. However, their utilization is frequently constrained by challenges such as high molecular weights and indistinct sugar chain structures. Recently, two novel bacterial strains, N6 T and J3 T , were isolated from the Nakdong River in Korea. These strains, which belong to the phylum Bacteroidota , are Gram-stain-negative, non-motile, aerobic, rod-shaped bacteria and have shown polysaccharide-degrading capabilities. Through comprehensive analyses, including 16S rRNA gene sequencing, whole-genome sequencing, and detailed morphological, physiological, and chemotaxonomic characterizations, these strains have been identified as new species within the genus Flavobacterium . KEGG pathway analysis further confirmed their robust capabilities for carbohydrate utilization. Additional investigations using the dbCAN and dbCAN-PUL databases identified the presence of carbohydrate-hydrolyzing enzymes (CAZymes) and polysaccharide utilization loci (PULs) within these strains, suggesting their potential to degrade various polysaccharides. Subsequent in vitro growth experiments demonstrated that strains N6 T and J3 T can degrade chitin, β-glucan, κ-carrageenan, and cellulose. Given their diverse polysaccharide degradation abilities, these strains are formally proposed to be named Flavobacterium polysaccharolyticum sp. nov. and Flavobacterium aureirubrum sp. nov. The type strains are designated as N6 T (= KCTC 102173 T  = GDMCC 1.4609 T ) and J3 T (= KCTC 102172 T  = GDMCC 1.4608 T ), respectively.

The type 9 secretion system (T9SS) is the protein export pathway of bacteria of the Gram-negative Fibrobacteres–Chlorobi–Bacteroidetes superphylum and is an essential determinant of pathogenicity in severe periodontal disease. The central element of the T9SS is a so-far uncharacterized protein-conducting translocon located in the bacterial outer membrane. Here, using cryo-electron microscopy, we provide structural evidence that the translocon is the T9SS protein SprA. SprA forms an extremely large (36-strand) single polypeptide transmembrane β-barrel. The barrel pore is capped on the extracellular end, but has a lateral opening to the external membrane surface. Structures of SprA bound to different components of the T9SS show that partner proteins control access to the lateral opening and to the periplasmic end of the pore. Our results identify a protein transporter with a distinctive architecture that uses an alternating access mechanism in which the two ends of the protein-conducting channel are open at different times. Cryo-electron microscopy structures of the protein-conducting translocon of the type 9 secretion system reveal its architecture and mechanism of translocation.

Cells of Flavobacterium johnsoniae and of many other members of the phylum Bacteroidetes exhibit rapid gliding motility over surfaces by a unique mechanism. These cells do not have flagella or pili; instead, they rely on a novel motility apparatus composed of Gld and Spr proteins. SprB, a 669-kDa cell-surface adhesin, is required for efficient gliding. SprB was visualized by electron microscopy as thin 150-nm-long filaments extending from the cell surface. Fluorescence microscopy revealed movement of SprB proteins toward the poles of the cell at ∼2 μm/s. The fluorescent signals appeared to migrate around the pole and continue at the same speed toward the opposite pole along an apparent left-handed helical closed loop. Movement of SprB, and of cells, was rapidly and reversibly blocked by the addition of carbonyl cyanide m -chlorophenylhydrazone, which dissipates the proton gradient across the cytoplasmic membrane. In a gliding cell, some of the SprB protein appeared to attach to the substratum. The cell body moved forward and rotated with respect to this point of attachment. Upon reaching the rear of the cell, the attached SprB often was released from the substratum, and apparently recirculated to the front of the cell along a helical path. The results suggest a model for Flavobacterium gliding, supported by mathematical analysis, in which adhesins such as SprB are propelled along a closed helical loop track, generating rotation and translation of the cell body.

Background During the screening of pigment-producing microbes from domestic sources, 102 yellow- or orange-pigmented bacteria were isolated. Among these, two novel Flavobacterium strains, F. sedimentum SUN046 T and F. fluvius SUN052 T , were identified as zeaxanthin producers. A polyphasic taxonomic characterization, combined with comparative genomic analysis of 45 Flavobacterium species, was conducted to determine their taxonomic positions and explore potential evolutionary relationships in zeaxanthin biosynthesis. Results Both strains utilized the mevalonic acid (MVA) pathway and possessed the crt gene cluster ( crtB , crtI , crtY / crtY cd , and crtZ ). Strain SUN046 T exhibited unique features in the carotenoid biosynthesis pathway, notably the absence of HMG-CoA synthase (HMGCS) in the upper MVA pathway and the presence of the rare lycopene β -cyclase crtY cd , which is uncommon among bacteria. The CrtY cd in SUN046 T possessed a single active site and direct lycopene-binding modes. Conversely, CrtY in SUN052 T exhibited multiple active sites, which is flavin adenine dinucleotide (FAD) dependent. These structural differences has impacted catalytic efficiencies, as evidenced by zeaxanthin yields of 6.49 µg/mL in SUN046 T and 13.23 µg/mL in SUN052 T . Variations in carotenoid biosynthetic pathway among other Flavobacterium species were also observed. Conclusion These findings suggest that both strains represent valuable new resources for zeaxanthin production and provide foundational insights for biotechnological applications involving the genus Flavobacterium , highlighting the genetic and evolutionary complexity of microbial carotenoid biosynthesis.

Background Six novel cold-adapted bacteria, LB3P122 T , LT1R49 T , ZT3R17 T , ZT3R25 T , XS2P12 T , and GB2R13 T , were isolated from glaciers on the Tibetan Plateau. This study aimed to characterize their taxonomic status and elucidate their molecular adaptations to cold environments using a polyphasic approach. Results All strains were Gram-stain-negative, rod-shaped, and psychrophilic, growing at 0 °C with an optimum at 14–20 °C and at pH values of 6.0–8.0 (optimum pH 7.0). Analysis of the 16S rRNA gene sequences placed their taxonomic positions within the genus Flavobacterium , with similarities ranging from 97.2 to 98.4% to species with validly published names. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the six strains formed distinct clades with Flavobacterium gawalongense GSP16 T . Phylogenomic analysis showed that these strains clustered with Flavobacterium gawalongense GSP16 T and exhibited a close relationship with Flavobacterium urumqiense CGMCC 1.9230 T and Flavobacterium xinjiangense CGMCC 1.2749 T . Average nucleotide identity (ANI) values ranging from 82.5 to 93.6% and digital DNA-DNA hybridization (dDDH) values ranging from 26.1 to 51.5% between these strains and their closest relatives were well below the bacterial species delineation thresholds (95–96% ANI, 70% dDDH). The predominant fatty acids were iso-C 15:0 and summed feature 3 (C 16:1 ω 7 c and/or C 16:1 ω 6 c ). Genomic analysis identified genes associated with cryoprotection, oxidative stress response, cold-shock response, and osmoprotection in these strains, underscoring their adaptations to glacial environments. Conclusions Based on polyphasic taxonomic evidence, the strains represent six novel species within the genus Flavobacterium , with the proposed names Flavobacterium algoriphilum sp. nov. (LB3P122 T  = CGMCC 1.11443  T  = NBRC 114820 T ), Flavobacterium arabinosi sp. nov. (LT1R49 T  = CGMCC 1.11617 T  = NBRC 114822 T ), Flavobacterium cryoconiti sp. nov. (ZT3R17 T  = CGMCC 1.11707 T  = NBRC 114824 T ), Flavobacterium galactosi sp. nov. (ZT3R25 T  = CGMCC 1.11711 T  = NBRC 114825 T ), Flavobacterium melibiosi sp. nov. (XS2P12 T  = CGMCC 1.23198 T  = NBRC 114826 T ), and Flavobacterium algoris sp. nov. (GB2R13 T  = CGMCC 1.24741 T  = NBRC 114830 T ). These findings enhance our understanding of Flavobacterium diversity and cold adaptation in cryospheric ecosystems.

Colony spreading of Flavobacterium johnsoniae is shown to include gliding motility using the cell surface adhesin SprB, and is drastically affected by agar and glucose concentrations. Wild-type (WT) and Δ sprB mutant cells formed nonspreading colonies on soft agar, but spreading dendritic colonies on soft agar containing glucose. In the presence of glucose, an initial cell growth-dependent phase was followed by a secondary SprB-independent, gliding motility-dependent phase. The branching pattern of a Δ sprB colony was less complex than the pattern formed by the WT. Mesoscopic and microstructural information was obtained by atmospheric scanning electron microscopy (ASEM) and transmission EM, respectively. In the growth-dependent phase of WT colonies, dendritic tips spread rapidly by the movement of individual cells. In the following SprB-independent phase, leading tips were extended outwards by the movement of dynamic windmill-like rolling centers, and the lipoproteins were expressed more abundantly. Dark spots in WT cells during the growth-dependent spreading phase were not observed in the SprB-independent phase. Various mutations showed that the lipoproteins and the motility machinery were necessary for SprB-independent spreading. Overall, SprB-independent colony spreading is influenced by the lipoproteins, some of which are involved in the gliding machinery, and medium conditions, which together determine the nutrient-seeking behavior.

Although increased disease severity driven by intensive farming practices is problematic in food production, the role of evolutionary change in disease is not well understood in these environments. Experiments on parasite evolution are traditionally conducted using laboratory models, often unrelated to economically important systems. We compared how the virulence, growth and competitive ability of a globally important fish pathogen, Flavobacterium columnare, change under intensive aquaculture. We characterized bacterial isolates from disease outbreaks at fish farms during 2003–2010, and compared F. columnare populations in inlet water and outlet water of a fish farm during the 2010 outbreak. Our data suggest that the farming environment may select for bacterial strains that have high virulence at both long and short time scales, and it seems that these strains have also evolved increased ability for interference competition. Our results are consistent with the suggestion that selection pressures at fish farms can cause rapid changes in pathogen populations, which are likely to have long-lasting evolutionary effects on pathogen virulence. A better understanding of these evolutionary effects will be vital in prevention and control of disease outbreaks to secure food production.

This study presents taxonomic description of two novel diesel-degrading, psychrophilic strains: Kopri-42 T and Kopri-43, isolated during screening of oil-degrading psychrotrophs from oil-contaminated Arctic soil. A preliminary 16S rRNA gene sequence and phylogenetic tree analysis indicated that these Arctic strains belonged to the genus Flavobacterium , with the nearest relative being Flavobacterium psychrolimnae LMG 22018 T (98.9% sequence similarity). The pairwise 16S rRNA gene sequence identity between strains Kopri-42 T and Kopri-43 was 99.7%. The DNA-DNA hybridization value between strain Kopri-42 T and Kopri-43 was 88.6 ± 2.1% indicating that Kopri-42 T and Kopri-43 represents two strains of the same genomospecies. The average nucleotide identity and in silico DNA-DNA hybridization values between strain Kopri-42 T and nearest relative F . psychrolimnae LMG 22018 T were 92.4% and 47.9%, respectively. These values support the authenticity of the novel species and confirmed the strain Kopri-42 T belonged to the genus Flavobacterium as a new member. The morphological, physiological, biochemical and chemotaxonomic data also distinguished strain Kopri-42 T from its closest phylogenetic neighbors. Based on the polyphasic data, strains Kopri-42 T and Kopri-43 represents a single novel species of the genus Flavobacterium , for which the name Flavobacterium petrolei sp. nov. is proposed. The type strain is Kopri-42 T (=KEMB 9005-710 T  = KACC 19625 T  = NBRC 113374 T ).

A Gram-strain-negative, aerobic, yellow-colored, non-motile, and rod-shaped bacterial strain, designated IMCC34852T, was isolated from a freshwater stream in the Republic of Korea. Cellular growth occurred at 10–37 °C, pH 6.0–9.0, and with 0–0.5% (w/v) NaCl. The 16S rRNA gene sequence analysis showed that strain IMCC34852T belonged to the genus Flavobacterium and that the strain was most closely related to F. cheonhonense ARSA-15 T (97.6%), F. buctense T7T (96.7%), F. silvisoli RD-2-33 T (96.1%), and F. paronense KNUS1T (96.1%). The whole-genome sequence of strain IMCC34852T was 3.2 Mbp in size, with a DNA G + C content 37.3%. The average nucleotide identities (ANI) and digital DNA–DNA hybridization (dDDH) values between strain IMCC34852T and its related species were all below 79.8% and 22.7%, respectively, which are significantly lower than the thresholds of 95% for ANI and 70% for DDH for species delineation. The major respiratory quinone of strain IMCC34852T was menaquinone-6 (MK-6) and the predominant cellular fatty acids were iso-C15:0 (32.6%), iso-C16:0 (11.7%), iso-C15:1 G (10.3%), and iso-C14:0 (6.7%). The major polar lipids of the strain were phosphatidylethanolamine, two unidentified aminolipids and six unidentified lipids. Based on these results, it was concluded that strain IMCC34852T represents a novel species in the genus Flavobacterium, for which the name Flavobacterium rivulicola sp. nov is proposed. The type strain of the proposed novel species is IMCC34852T (= KACC 23133 T = KCTC 82066 T = NBRC 114419 T).

Naturally occurring photonic structures are responsible for the bright and vivid coloration in a large variety of living organisms. Despite efforts to understand their biological functions, development, and complex optical response, little is known of the underlying genes involved in the development of these nanostructures in any domain of life. Here, we used Flavobacterium colonies as a model system to demonstrate that genes responsible for gliding motility, cell shape, the stringent response, and tRNA modification contribute to the optical appearance of the colony. By structural and optical analysis, we obtained a detailed correlation of how genetic modifications alter structural color in bacterial colonies. Understanding of genotype and phenotype relations in this system opens the way to genetic engineering of on-demand living optical materials, for use as paints and living sensors.