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The long-known resistance to pathogens provided by host-associated microbiota fostered the notion that adding protective bacteria could prevent or attenuate infection. However, the identification of endogenous or exogenous bacteria conferring such protection is often hindered by the complexity of host microbial communities. Here, we used zebrafish and the fish pathogen Flavobacterium columnare as a model system to study the determinants of microbiota-associated colonization resistance. We compared infection susceptibility in germ-free, conventional and reconventionalized larvae and showed that a consortium of 10 culturable bacterial species are sufficient to protect zebrafish. Whereas survival to F. columnare infection does not rely on host innate immunity, we used antibiotic dysbiosis to alter zebrafish microbiota composition, leading to the identification of two different protection strategies. We first identified that the bacterium Chryseobacterium massiliae individually protects both larvae and adult zebrafish. We also showed that an assembly of 9 endogenous zebrafish species that do not otherwise protect individually confer a community-level resistance to infection. Our study therefore provides a rational approach to identify key endogenous protecting bacteria and promising candidates to engineer resilient microbial communities. It also shows how direct experimental analysis of colonization resistance in low-complexity in vivo models can reveal unsuspected ecological strategies at play in microbiota-based protection against pathogens.

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.

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.

Many plants associate with endophytic microbes that improve root phosphorus (P) uptake. Understanding the interactions between roots and endophytes can enable efforts to improve P utilization. Here, we characterize the interactions between lateral roots of endophytes in a core collection of 50 rapeseed ( Brassica napus L.) genotypes with differing sensitivities to low P conditions. With the correlation analysis result between bacterial abundance and plant physiological indices of rapeseeds, and inoculation experiments on plates and soil, we identify one Flavobacterium strain (C2) that significantly alleviates the P deficiency phenotype of rapeseeds. The underlying mechanisms are explored by performing the weighted gene coexpression network analysis (WGCNA), and conducting genome-wide association studies (GWAS) using Flavobacterium abundance as a quantitative trait. Under P-limited conditions, C2 regulates fatty acid and lipid metabolic pathways. For example, C2 improves metabolism of linoleic acid, which mediates root suberin biosynthesis, and enhances P uptake efficiency. In addition, C2 suppresses root jasmonic acid biosynthesis, which depends on α -linolenic acid metabolism, improving C2 colonization and activating P uptake. This study demonstrates that adjusting the endophyte composition can modulate P uptake in B. napus plants, providing a basis for developing agricultural microbial agents. Based on the correlation analysis of various omics data from Brassica napus L., authors identify one Flavobacterium strain C2 which mitigates P deficiency by regulating fatty acid metabolism and enhancing P uptake, indicating potential strategies to improve P utilization in rapeseeds.

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.

Interactions between parasite, host and host-associated microbiota are increasingly understood as important determinants of disease progression and morbidity. Salmon lice, including the parasitic copepod Lepeophtheirus salmonis and related species, are perhaps the most important problem facing Atlantic Salmon aquaculture after feed sustainability. Salmon lice parasitize the surface of the fish, feeding off mucus, scales and underlying tissue. Secondary bacterial infections are a major source of associated morbidity. In this study we tracked the diversity and composition of Salmo salar skin surface microbiota throughout a complete L. salmonis infection cycle among 800 post-smolts as compared to healthy controls. Among infected fish we observed a significant reduction in microbial richness (Chao1, P = 0.0136), raised diversity (Shannon, P < 7.86e-06) as well as highly significant destabilisation of microbial community composition (Pairwise Unifrac, beta-diversity, P < 1.86e-05; P = 0.0132) by comparison to controls. While undetectable on an individual level, network analysis of microbial taxa on infected fish revealed the association of multiple pathogenic genera ( Vibrio, Flavobacterium, Tenacibaculum, Pseudomonas ) with high louse burdens. We discuss our findings in the context of ecological theory and colonisation resistance, in addition to the role microbiota in driving primary and secondary pathology in the host.

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.

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.

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.

   β-1,6-Glucan plays a crucial role in fungal cell walls by linking the outer layer of mannoproteins and the inner layer of β-1,3-glucan, contributing significantly to the maintenance of cell wall rigidity. Therefore, the hydrolysis of β-1,6-glucan by β-1,6-glucanase directly leads to the disintegration of the fungal cell wall. Here, a novel β-1,6-glucanase Fl Glu30 was identified from the endophytic Flavobacterium sp. NAU1659 and heterologously expressed in Escherichia coli BL21 (DE3). The optimal reaction conditions of purified Fl Glu30 were 50℃ and pH 6.0, resulting in a specific activity of 173.1 U/mg using pustulan as the substrate. The hydrolyzed products of Fl Glu30 to pustulan were mainly gentianose within 1 h of reaction. With the extension of reaction time, gentianose was gradually hydrolyzed to glucose, indicating that Fl Glu30 is an endo-β-1,6-glucanase. The germination of Magnaporthe oryzae Guy11 spores could not be inhibited by Fl Glu30, but the appressorium formation of spores was completely inhibited under the concentration of 250.0 U/mL Fl Glu30. The disruptions of cell wall and accumulation of intracellular reactive oxide species (ROS) were observed in Fl Glu30-treated M. oryzae Guy11 cells, suggesting the significant importance of β-1,6-glucan as a potential antifungal target and the potential application of Fl Glu30. Key points • β-1,6-Glucan is a key component maintaining the rigid structure of fungal cell wall. • β-1,6-Glucanase is an antifungal protein with significant potential applications. • FlGlu30 is the first reported β-1, 6-glucanase derived from Flavobacterium.