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Chryseobacterium spp. are Gram-negative, opportunistic pathogens antibiotic-resistant commonly found in the environment. The aim of this study was to investigate potential sources of Chryseobacterium infections in healthcare settings by comparing clinical and environmental isolates using phenotypic and genotypic analyses. Between June and July 2023, six cases of infection with Chryseobacterium spp. were identified in a hospital in Apulia, southern Italy. Environmental sampling (air, surfaces and water) was performed in parallel with routine clinical investigations. Isolates were subjected to antibiotic susceptibility testing and genotypic analysis using Sanger and Next-Generation Sequencing. Five cases of Chryseobacterium spp. infection were recorded in the Gastroenterology Department (Pavilion A) and one in the Vertebral Surgery Department (Pavilion B). C. indologenes was identified in blood and tracheal aspirate samples using MALDI-TOF MS. Environmental analysis carried out in the pavilions A and B isolated C. indologenes from sink tap in Pavilion B. Subsequently, genome sequencing revealed that Chryseobacterium strains misidentified as C. indologenes were more closely related to C. arthrosphaerae . Genetic analysis confirmed the cluster hypothesis involving four patients from the pavilion A, while no genetic link was found between the environmental and clinical strains. Innovative molecular methods in clinical and environmental investigations have allowed more accurate identification of the etiologic agent and possibly tracing the source of infection in the nosocomial setting. Control measures, such as patient isolation and room disinfection, have prevented the spread of infection.

Springtails are important members of the soil fauna and play a key role in plant litter decomposition, for example through stimulation of the microbial activity. However, their interaction with soil microorganisms remains poorly understood and it is unclear which microorganisms are associated to the springtail (endo) microbiota. Therefore, we assessed the structure of the microbiota of the springtail Orchesella cincta (L.) using 16S rRNA gene amplicon sequencing. Individuals were sampled across sites in the field and the microbiota and in particular the endomicrobiota were investigated. The microbiota was dominated by the families of Rickettsiaceae , Enterobacteriaceae and Comamonadaceae and at the genus level the most abundant genera included Rickettsia , Chryseobacterium , Pseudomonas , and Stenotrophomonas . Microbial communities were distinct for the interior of the springtails for measures of community diversity and exhibited structure according to collection sites. Functional analysis of the springtail bacterial community suggests that abundant members of the microbiota may be associated with metabolism including decomposition processes. Together these results add to the understanding of the microbiota of springtails and interaction with soil microorganisms including their putative functional roles.

Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

Strain wdc7T, a rod-shaped bacterium, was isolated from soil in the Gotjawal Forest on Jeju Island, South Korea. Strain wdc7T was Gram stain-negative, facultatively anaerobic, catalase- and oxidase positive, yellow pigmented, and non-flagellated. It grew at 4–37 °C and pH 5.0–8.0 in 0–3% (w/v) NaCl. 16S rRNA gene sequencing analysis revealed that strain wdc7T belonged to the genus Chryseobacterium and was most closely related to Chryseobacterium salivictor NBC 122T, with a sequence similarity of 98.51%. Menaquinone 6 was the sole respiratory quinone, and C15:0 anteiso, C15:0 iso, and summed feature 9 were the major fatty acids. The genome length was 3.30 Mbp, with a 37% G + C content. Average amino acid identity, average nucleotide identity, and digital DNA–DNA relatedness between strain wdc7T and C. salivictor NBC 122T were 93.52%, 92.80%, and 49.7%, respectively. Digital genomic and polyphasic analyses showed that strain wdc7T likely represented a new species of the genus Chryseobacterium. We proposed the name Chryseobacterium gotjawalense sp. nov., with wdc7T (= KCTC 92440T = JCM 35602T) as the type strain.

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, designated NBC 122T, was isolated from freshwater of the Nakdong River Republic of Korea. Growth occurred at pH 5.0–8.0 (optimum, pH 7.0), at 4–37 °C (optimum, 25 °C), and with 0–3.5% (w/v) NaCl (optimum, 1%). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain NBC 122T belongs to the genus Chryseobacterium and is most closely related to Chryseobacterium antarcticum AT1013T (97.85%). The average nucleotide identity and in silico DNA–DNA hybridization (DDH) values between strain NBC 122T and related Chryseobacterium species were 77.77–80.28 and 20.9–23.2%, respectively. The strain NBC 122T contained MK-6 as the major respiratory quinone. The major fatty acids included anteiso C15:0, iso C15:0, summed feature 9 (C17:1 iso ω9c, C16:0 10-methyl) and iso C17:0 3-OH, and the polar lipids were phosphatidylethanolamine, five unidentified aminolipids and six unidentified lipids. The DNA G + C content was 37.5 mol%. On the basis of a 16S rRNA gene phylogeny and comparative phenotypic analyses, strain NBC 122T represents a novel species in the genus Chryseobacterium, for which the name Chryseobacterium salivictor sp. nov. is proposed. The type strain is NBC122T (= KCTC 72248T = JCM 33980T).

Marseille-P9602 T is a Chryseobacterium -like strain that we isolated from planarian Schmidtea mediterranea and characterized by taxono-genomic approach. We found that Marseille-P9602 T strain exhibits a 16S rRNA gene sequence similarity of 98.76% with Chryseobacterium scophthalmum LMG 13028 T strain, the closest phylogenetic neighbor. Marseille-P9602 T strain was observed to be a yellowish-pigmented, Gram-negative, rod-shaped bacterium, growing in aerobic conditions and belonging to the Flavobacteriaceae family. The major fatty acids detected are 13-methyl-tetradecanoic acid (57%), 15-methylhexadecenoic acid (18%) and 12-methyl-tetradecanoic acid (8%). Marseille-P9602 strain size was found from genome assembly to be of 4,271,905 bp, with a 35.5% G + C content. The highest values obtained for Ortho-ANI and dDDH were 91.67% and 44.60%, respectively. Thus, hereby we unravel that Marseille-P9602 strain is sufficiently different from other closed related species and can be classified as a novel bacterial species, for which we propose the name of Chryseobacterium schmidteae sp. nov. Type strain is Marseille-P9602 T (= CSUR P9602 T  = CECT 30295 T ).

Four yellow pigmented strains (91A-561ᵀ, 91A-576, 91A-593ᵀ, and JM-1085ᵀ) isolated from plant materials, showed 97.2–98.7 % 16S rRNA gene sequence similarities among each other and were studied in a polyphasic approach for their taxonomic allocation. Cells of all four isolates were rod-shaped and stained Gram-negative. Comparative 16S rRNA gene sequence analysis showed that the four bacteria had highest sequence similarities to Chryseobacterium formosense (97.2–98.7 %), Chryseobacterium gwangjuense (97.1–97.8 %), and Chryseobacterium defluvii (94.6–98.0 %). Sequence similarities to all other Chryseobacterium species were below 97.5 %. Fatty acid analysis of the four strains showed Chryseobacterium typical profiles consisting of major fatty acids C₁₅:₀ iso, C₁₅:₀ iso 2-OH/C₁₆:₁ ω7c, C₁₇:₁ iso ω9c, and C₁₇:₀ iso 3-OH, but showed also slight differences. DNA–DNA hybridizations with type strains of C. gwangjuense, C. formosense, and C. defluvii resulted in values below 70 %. Isolates 91A-561ᵀ and 91A-576 showed DNA–DNA hybridization values >80 % indicating that they belonged to the same species; but nucleic acid fingerprinting showed that the two isolates represent two different strains. DNA–DNA hybridization results and the differentiating biochemical and chemotaxonomic properties showed, that both strains 91A-561ᵀ and 91A-576 represent a novel species, for which the name Chryseobacterium geocarposphaerae sp. nov. (type strain 91A-561ᵀ=LMG 27811ᵀ=CCM 8488ᵀ) is proposed. Strains 91A-593ᵀ and JM-1085ᵀ represent two additional new species for which we propose the names Chyrseobacterium zeae sp. nov. (type strain JM-1085ᵀ=LMG 27809ᵀ, =CCM 8491ᵀ) and Chryseobacterium arachidis sp. nov. (type strain 91A-593ᵀ=LMG 27813ᵀ, =CCM 8489ᵀ), respectively.

A yellow-pigmented, non-motile and rod-shaped bacterium, designated RJ-7-14 T was obtained from forest soil sampled at Cheonji-dong, Seogwipo-si, Jeju-do, South Korea. Cells were Gram-stain-negative and produced flexirubin type pigments. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RJ-7-14 T formed a lineage within the family Weeksellaceae and clustered as members of the genus Chryseobacterium . The closest members were Chryseobacterium geocarposphaerae DSM 27617 T (98.2% sequence similarity), Chryseobacterium hispalense DSM 25574 T (98.0%) and Chryseobacterium nepalense KACC 18907 T (98.0%). The sequence similarity for other members was < 98.0%. The genome was 4,276,416 bp long with 9 scaffolds and 3779 protein-coding genes. The sole respiratory quinone was MK-6. The major cellular fatty acids were iso-C 15:0 , summed feature 9 (iso-C 17:1 ω 9 c and/or C 16:0 10-methyl), summed feature 3 (iso-C 15:0 2-OH and/or C 16: 1 ω 7 c ) and iso-C 17:0 3-OH. The major polar lipid was phosphatidylethanolamine (PE). The DNA G + C content of the type strain was 37.2 mol%. In addition, the average nucleotide identity (ANIu) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain RJ-7-14 T and phylogenetically closest members were ≤ 88.2% and ≤ 35.0%, respectively, which were below the threshold values of 95–96% (for ANI) and 70% (for dDDH), suggesting the allocation of novel strain to a new species. Based on genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain RJ-7-14 T represents novel species in the genus Chryseobacterium , for which the name Chryseobacterium cheonjiense sp. nov. is proposed. The type strain is RJ-7-14 T (= KACC 21625 T  = NBRC 114362 T ).

A Gram-stain negative, strictly aerobic, rod-shaped, non-motile bacterium, designated strain DY46ᵀ, was isolated from Atlantic Ocean sediment. The isolate was found to grow in medium containing 0–3.0 % (w/v) NaCl (optimally at 0–1.0 %), at 4–37 °C and pH 5.0–8.0. Chemotaxonomic analysis detected MK-6 as the sole isoprenoid quinone. The major fatty acids were identified iso-C₁₅:₀, iso-C₁₇:₀3-OH, iso-C₁₇:₁ω9c and summed feature 3 (comprising iso-C₁₅:₀2-OH and/or C₁₆:₁ω7c). The DNA G + C content was determined to be 40.7 mol %. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that strain DY46ᵀfalls within the cluster comprising Chryseobacterium species. The levels of 16S rRNA gene sequence similarity between strain DY46ᵀand the type strains of the Chryseobacterium species with validly published names ranged from 92.4 to 99.1 %, the high values (>97 %) being with Chryseobacterium takakiae A1-2ᵀ(99.1 %), C. taiwanense BCRC 17412ᵀ(98.0 %), C. taeanense PHA3-4ᵀ(97.3 %), C. hispalense DSM 25574ᵀ(97.3 %), C. camelliae THG C4-1ᵀ(97.2 %), C. gregarium DSM 19109ᵀ(97.1 %) and C. wanjuense R2A10-2ᵀ(97.0 %). The DNA–DNA relatedness values between strain DY46ᵀand the type strains of the above closely related species were 47, 57, 24, 34, 6, 40 and 21 %, respectively. On the basis of phenotypic and genotypic characteristics, strain DY46ᵀrepresents a novel member within the genus Chryseobacterium, for which the name Chryseobacterium profundimaris is proposed. The type strain is DY46ᵀ(=CGMCC 1.12663ᵀ = JCM 19801ᵀ).

Bacteria belonging to the genus Chryseobacterium are ubiquitously distributed in natural environments, plants, and animals. Except C. indologenes and C. gleum, other Chryseobacterium species rarely cause human diseases. This study reported the whole-genome features, comparative genomic analysis, and antimicrobial susceptibility patterns of C. arthrosphaerae ED882-96 isolated in Taiwan. Strain ED882-96 was collected from the blood of a patient who had alcoholic liver cirrhosis and was an intravenous drug abuser. This isolate was initially identified as C. indologenes by using matrix-assisted laser desorption ionization–time of flight mass spectrometry. The analysis of 16S ribosomal RNA gene sequence revealed that ED882-96 shared 100% sequence identity with C. arthrosphaerae type strain CC-VM-7T. The results of whole-genome sequencing of ED882-96 showed two chromosome contigs and one plasmid. The total lengths of the draft genomes of chromosome and plasmid were 4,249,864 bp and 435,667 bp, respectively. The findings of both in silico DNA–DNA hybridization and average nucleotide identity analyses clearly demonstrated that strain ED882-96 was a species of C. arthrosphaerae. A total of 83 potential virulence factor homologs were predicted in the whole-genome sequencing of strain ED882-96. This isolate was resistant to all tested antibiotics, including β-lactams, β-lactam/β-lactamase inhibitor combinations, aminoglycosides, fluoroquinolones, tetracycline, glycylcycline, and trimethoprim-sulfamethoxazole. Only one antibiotic resistance gene was recognized in the plasmid. By contrast, many antibiotic resistance genes were identified in the chromosome. The findings of this study suggest that strain ED882-96 is a highly virulent and multidrug-resistant pathogen. Knowledge regarding genomic characteristics and antimicrobial susceptibility patterns provides valuable insights into this uncommon species.