Unveiling the etiology of peritonsillar abscess using next generation sequencing

BACKGROUND

Peritonsillar abscess (PTA) is a severe deep neck space infection with an insufficiently characterized bacterial etiology. We aimed to reveal the bacteria associated with PTA applying next generation sequencing (NGS). Tonsil biopsies and pus samples of 91 PTA patients were analysed applying NGS method.

RESULTS

Over 400 genera and 800 species belonging to 34 phyla were revealed. The most abundant species in both sample types were Streptococcus pyogenes, Fusobacterium necrophorum and Fusobacterium nucleatum. When present, S. pyogenes was normally a predominant species, although it was recovered as a minor population in some samples dominated by F. nucleatum and occasionally F. necrophorum. S. pyogenes and F. necrophorum were the predominant species (> 10% in a community) in 28 (31%) pus samples, while F. nucleatum in 21 (23%) and S. anginosus in 8 (9%) pus samples. We observed no substantial differences between the microbial findings in pus and tonsil biopsies.

CONCLUSIONS

The most probable causative agents of PTA according to our NGS-study include Streptococcus pyogenes, Fusobacterium necrophorum and Fusobacterium nucleatum. Some other streptococci (S. anginosus) and anaerobes (Prevotella, Porphyromonas) may contribute to the infection as well. Pus of the peritonsillar abscess is more representative specimen for microbiological examination than the tonsillar tissue. Our results are important in the context of optimizing the handling of the PTA patients.

Marnyiella aurantia, gen. nov., sp. nov., a novel bacterial species of the family Weeksellaceae that could produce flexirubin type pigments

Two Gram-stain-negative, non-spore-forming, rod-shaped, and obligately aerobic bacteria, designated strains CX-624T and cx-311, were isolated from soil samples in Qinghai Province, China. The two strains grew best at 28 °C on the plate with Tryptone soya agar (TSA). Cells formed circular, convex, translucent, smooth, and orange colonies with approximately 1.0 mm diameter after 2 days of incubation on TSA at 28 °C. The strains were oxidase-negative and catalase-positive. The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0, and major polar lipids included phosphatidylethanolamine, an unidentified aminophospholipid, four unidentified lipids and an aminolipid. MK-6 was the sole menaquinone in strain CX-624T. Comparative analysis of the nearly full-length 16S rRNA gene sequences showed strains CX-624T and cx-311 were member of the family Weeksellaceae, with the highest similarity to Kaistella haifensis H38T (96.66 %), Epilithonimonas pallida DSM 18015T (96.59 %), and Chryseobacterium gambrini DSM 18014T (96.53 %). Both phylogenetic analysis of the 16S rRNA gene and 177 core genes revealed that strains CX-624T and cx-311 formed an independent clade. Average nucleotide identity values (< 72.64 %), average amino-acid identity values (<72.61 %) and digital DNA-DNA hybridization (< 21.10 %) indicated that the strains CX-624T and cx-311 should constitute a novel genus. The DNA G+C contents of strains CX-624T and cx-311 were 43.0 mol% and 42.7 mol%. According to the data obtained in this study, strain CX-624T represents a novel species belonging to a novel genus of the Weeksellaceae, for which the name Marnyiella aurantia gen. nov., sp. nov. is proposed. The type strain is CX-624T (=GDMCC 1.1714T = JCM 33925T).

Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021

A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.

Atypical flavobacteria recovered from diseased fish in the Western United States

Flavobacterial diseases, caused by bacteria in the order Flavobacteriales, are responsible for devastating losses in farmed and wild fish populations worldwide. The genera Flavobacterium (Family Flavobacteriaceae) and Chryseobacterium (Weeksellaceae) encompass the most well-known agents of fish disease in the order, but the full extent of piscine-pathogenic species within these diverse groups is unresolved, and likely underappreciated. To identify emerging agents of flavobacterial disease in US aquaculture, 183 presumptive Flavobacterium and Chryseobacterium isolates were collected from clinically affected fish representing 19 host types, from across six western states. Isolates were characterized by 16S rRNA gene sequencing and phylogenetic analysis using the gyrB gene. Antimicrobial susceptibility profiles were compared between representatives from each major phylogenetic clade. Of the isolates, 52 were identified as Chryseobacterium species and 131 as Flavobacterium. The majority of Chryseobacterium isolates fell into six clades (A-F) consisting of ≥ 5 fish isolates with ≥ 70% bootstrap support, and Flavobacterium into nine (A-I). Phylogenetic clades showed distinct patterns in antimicrobial susceptibility. Two Chryseobacterium clades (F & G), and four Flavobacterium clades (B, G-I) had comparably high minimal inhibitory concentrations (MICs) for 11/18 antimicrobials tested. Multiple clades in both genera exhibited MICs surpassing the established F. psychrophilum breakpoints for oxytetracycline and florfenicol, indicating potential resistance to two of the three antimicrobials approved for use in finfish aquaculture. Further work to investigate the virulence and antigenic diversity of these genetic groups will improve our understanding of flavobacterial disease, with applications for treatment and vaccination strategies.

A microbial transporter of the dietary antioxidant ergothioneine

Low-molecular-weight (LMW) thiols are small-molecule antioxidants required for the maintenance of intracellular redox homeostasis. However, many host-associated microbes, including the gastric pathogen Helicobacter pylori, unexpectedly lack LMW-thiol biosynthetic pathways. Using reactivity-guided metabolomics, we identified the unusual LMW thiol ergothioneine (EGT) in H. pylori. Dietary EGT accumulates to millimolar levels in human tissues and has been broadly implicated in mitigating disease risk. Although certain microorganisms synthesize EGT, we discovered that H. pylori acquires this LMW thiol from the host environment using a highly selective ATP-binding cassette transporter-EgtUV. EgtUV confers a competitive colonization advantage in vivo and is widely conserved in gastrointestinal microbes. Furthermore, we found that human fecal bacteria metabolize EGT, which may contribute to production of the disease-associated metabolite trimethylamine N-oxide. Collectively, our findings illustrate a previously unappreciated mechanism of microbial redox regulation in the gut and suggest that inter-kingdom competition for dietary EGT may broadly impact human health.

Chryseobacterium faecale sp. nov., isolated from camel feces

Strain F4T (=KACC 22401T=JCM 34836T), a novel Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterium, was isolated from camel (Camelus bactrianus) faeces. The newly identified bacterial strain F4T was grown in Reasoner's 2A medium [0–2 % (w/v) NaCl (optimum, 0 %), pH 7.0–8.0 (optimum, pH 7.0), and 18–40 °C (optimum, 30 °C)]. Phylogenetic analysis based on 16S rRNA gene sequencing confirmed that strain F4T belonged to the genus Chryseobacterium , with its closest neighbours being Chryseobacterium haifense DSM 19056T (98.0 %), Chryseobacterium anthropi CCUG 52764T (97.3 %), Chryseobacterium montana WG4T (95.7 %) and Chryseobacterium koreensis Chj70T (94.7 %). Complete genome sequence of strain F4T was obtained using a hybrid assembly pipeline integrating sequences obtained using both the Oxford Nanopore and Illumina platforms. Genomic comparisons of strain F4T with type species in the genus Chryseobacterium were conducted using digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity, resulting in values of ≤20.5, ≤77.9 and ≤80.8 %, respectively. The genomic DNA G+C content of type strain F4T was 39.7 mol%. The major fatty acids of the strain F4T were anteiso-C15 : 0 and iso-C18 : 3, and MK-6 was its major respiratory quinone. Moreover, the major polar lipid of strain F4T was phosphatidylethanolamine. The genome of strain F4T harbours only one antibiotic resistance gene (blaCME-1) encoding a β-lactamase, which attributes β-lactam antibiotic resistance. Based on the results of our chemotaxonomic, genotypic and phenotype analyses, strain F4T is identified as a novel species of the genus Chryseobacterium , for which the name Chryseobacterium faecale sp. nov. is proposed.

Pathogenic Potential and Control of Chryseobacterium Species from Clinical, Fish, Food and Environmental Sources

Chryseobacterium species are isolated and taxonomically evaluated from a wide range of sources. While C. gleum and C. indologenes have been implicated in human disease, the potential pathogenicity of numerous other species have not been investigated. The aims were therefore to evaluate 37 Chryseobacterium species and Elizabethkingia meningoseptica from environmental, food, fish, water and clinical sources for production of haemolysis, growth at 37 °C, and production of virulence enzymes. The control of these strains were investigated by determination of antimicrobial and disinfectant resistance. All the species produced α- or β-haemolysis. In terms of growth at 37 °C and production of virulence enzymes, C. soldanellicola (environmental), C. oranimense (food) and C. koreense (natural mineral water) could be potential human pathogens. Chryseobacterium piscium might be pathogenic to fish. Trimethoprim could be the most effective antimicrobial for the treatment of a Chryseobacterium species infection, while the disinfectants that contain poly-dimethyl ammonium chloride or benzalkonium chloride could be regarded as the most effective for decontamination of surfaces contaminated with Chryseobacterium species.

Cocaine esterase occurrence in global wastewater microbiomes and potential for biotransformation of novel psychoactive substances

The analysis of drugs in wastewater for forensic purposes has been constantly increasing and the investigation of the potential interaction between drugs or metabolites and sewage microbiota is important. The results demonstrated that cocaine esterase genes were widely distributed in 1142 global wastewater samples collected from 64 countries and linked to several bacterial species. In addition, in silico predictions indicated that carfentanil, 4F-MDMB-BINACA, 5F-MDMB-PICA, MDMB-4en-PINACA and mitragynine might also undergo microbial hydrolysis, in a similar fashion of cocaine degradation by cocaine esterase. In conclusion, it was demonstrated the microbial potential to hydrolyze drugs of abuse in wastewater environments, contributing to the critical evaluation of potential metabolites as biomarkers for microbial and human transformation of drugs in wastewater.

Chryseobacterium schmidteae sp. nov. a novel bacterial species isolated from planarian Schmidtea mediterranea

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).

Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens

The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species (Chryseobacterium arachidiradicis, Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae) to the genus Epilithonimonas and eleven (Chryseobacterium anthropi, Chryseobacterium antarcticum, Chryseobacterium carnis, Chryseobacterium chaponense, Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum, Chryseobacterium palustre, Chryseobacterium solincola, Chryseobacterium treverense and Chryseobacterium yonginense) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.

Isolation of Chryseobacterium siluri sp. nov., from liver of diseased catfish (Silurus asotus)

Yellow-pigmented, circular bacteria (strain SNU WT7) were isolated from the liver of moribund eastern catfish (Silurus asotus). Our study focused on the taxonomic description of SNU WT7 using phylogenetic, phenotypic, and chemotaxonomic analyses. The 16S rRNA gene sequence of the SNU WT7 strain was highly similar to that of Chryseobacterium haifense H38^T (97.29% similarity), followed by Chryseobacterium hominis P2K6^T (97.22% similarity), while other species exhibited similarity values of less than 97.0%. The genome of strain SNU WT7 displayed average nucleotide identity and genome-to-genome distance values of 72.35% and 22.0%, respectively, which clearly indicated that the novel species was distant from the other Chryseobacterium species, with its closest relative being C. haifense H38^T. Furthermore, the phenotypic characteristics, including acid production from glucose, D-fructose, lactose, and maltose, of strain SNU WT 7 differed from those of C. haifense H38^T. The major polar lipid of the strain was phosphatidylethanolamine, and several unidentified aminolipids and lipids were also present. Similar to other Chryseobacterium species, the quinone system was composed mainly of MK-6. The genome of SNU WT7 is 2,690,367 bp with a G + C content of 43.6%. Taken together, our data indicate that the isolate SNU WT7 represents a novel species of the genus Chryseobacterium. Thus, we present the name Chryseobacterium siluri sp. nov. for the novel type strain SNU WT7^T (KCTC 72626, JCM 33707).

Diverse Environmental Microbiota as a Tool to Augment Biodiversity in Urban Landscaping Materials

Human activities typically lead to simplified urban diversity, which in turn reduces microbial exposure and increases the risk to urban dwellers from non-communicable diseases. To overcome this, we developed a microbial inoculant from forest and agricultural materials that resembles microbiota in organic soils. Three different sand materials (sieved, safety, and sandbox) commonly used in playgrounds and other public spaces were enriched with 5% of the inoculant. Skin microbiota on fingers (identified from bacterial 16S rDNA determined using Illumina MiSeq sequencing) was compared after touching non-enriched and microbial inoculant-enriched sands. Exposure to the non-enriched materials changed the skin bacterial community composition in distinct ways. When the inoculant was added to the materials, the overall shift in community composition was larger and the differences between different sand materials almost disappeared. Inoculant-enriched sand materials increased bacterial diversity and richness but did not affect evenness at the OTU level on skin. The Firmicutes/Bacteroidetes ratio was higher after touching inoculant-enriched compared to non-enriched sand materials. The relative abundance of opportunistic pathogens on skin was 40–50% before touching sand materials, but dropped to 14 and 4% after touching standard and inoculant-enriched sand materials, respectively. When individual genera were analyzed, Pseudomonas sp. and Sphingomonas sp. were more abundant after touching standard, non-enriched sand materials, while only the relative abundance of Chryseobacterium sp. increased after touching the inoculant-enriched materials. As Chryseobacterium is harmless for healthy persons, and as standard landscaping materials and normal skin contain genera that include severe pathogens, the inoculant-enriched materials can be considered safe. Microbial inoculants could be specifically created to increase the proportion of non-pathogenic bacterial taxa and minimize the transfer of pathogenic taxa. We recommend further study into the usability of inoculant-enriched materials and their effects on the bacterial community composition of human skin and on the immune response.

Long-term dynamics of the bacterial community in a Swedish full-scale wastewater treatment plant

The operational efficiency of activated sludge wastewater treatment plants depends to a large extent on the microbial community structure of the activated sludge. The aims of this paper are to describe the composition of the bacterial community in a Swedish full-scale activated sludge wastewater treatment plant, to describe the dynamics of the community and to elucidate possible causes for bacterial community composition changes. The bacterial community composition in the activated sludge was described using 16S rRNA gene libraries and monitored for 15 months by a terminal restriction fragment (T-RF) length polymorphism (T-RFLP) analysis of the 16S rRNA gene. Despite variable environmental conditions, a large fraction of the observed T-RFs were present at all times, making up at least 50% in all samples, possibly representing a relatively stable core fraction of the bacterial community. However, the proportions of the different T-RFs in this fraction as well as the T-RFs in the more variable fraction showed a significant variation over time and temperature. The difference in community composition between summer and winter coincided with observed differences in floc structure. These observations suggest a relationship between floc properties and bacterial community composition, although additional experiments are required to determine causality.

Genome-Based Taxonomic Classification of Bacteroidetes

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.

High-quality genome sequence and description of Chryseobacterium senegalense sp. nov

Strain FF12^T was isolated from the mouth of a West African lungfish (Protopterus annectens) in Senegal. MALDI-TOF-MS did not provide any identification. This strain exhibited a 97.97% 16S rRNA sequence identity with Kaistella flava. Using a polyphasic study including phenotypic and genomic analyses, strain FF12^T is Gram-negative, aero-anaerobic, oxidase-positive, non-motile, non-spore-forming, and exhibited a genome of 4,397,629 bp with a G+C content of 35.1% that coded 4,001 protein-coding and 55 RNA genes. On the basis of these data, we propose the creation of Chryseobacterium senegalense strain FF12^T.

Chryseobacterium frigidum sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of Chryseobacterium bernardetii and Chryseobacterium taklimakanense

A yellow, Gram-reaction-negative, non-motile, aerobic bacterium, designated D07^T, was isolated from a tundra soil near Ny-Ålesund, Svalbard archipelago, Norway (78° N). Growth occurred at 4-37 °C (optimum 28-30 °C) and at pH 6.0-9.0 (optimum pH 7.0-8.0). The strain produced flexirubin-type pigments. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D07^T belonged to the genus Chryseobacterium in the family Flavobacteriaceae. The 16S rRNA gene sequence of this strain showed 93.83 and 93.31 % sequence similarity, respectively, to those of Chryseobacterium contaminans C26^T and Chryseobacterium taklimakanense X-65^T. Strain D07^T contained anteiso-C_15 : 0 (25.91 %), iso-C_15 : 0 (16.05 %), iso-C_16 : 0 3-OH (9.64 %), iso-C_16 : 0 (9.42 %) and iso-C_14 : 0 (7.36 %) as the predominant cellular fatty acids, MK-6 as the major respiratory quinone and phosphatidylethanolamine, five unknown aminolipids and three unknown lipids as the main polar lipids. The DNA G+C content was 49.3 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain D07^T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium frigidum sp. nov. is proposed. The type strain is D07^T ( = CCTCC AB 2011160^T = KCTC 42897^T). Emended descriptions of Chryseobacterium bernardetii and Chryseobacterium taklimakanense are also provided.

Chryseobacterium arachidiradicis sp. nov., isolated from the geocarposphere (soil around the peanut) of very immature peanuts (Arachis hypogaea)

A yellow-pigmented bacterial strain, 91A-612(T), isolated from the geocarposphere (soil around the peanut) of very immature peanuts (Arachis hypogaea) in Alabama, USA, was studied for its taxonomic position. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence with the sequences of the type strains of the most closely related species showed that the strain belongs to the genus Chryseobacterium, showing the highest sequence similarities to the type strains of Chryseobacterium molle (98.4%), C. pallidum (98.3%) and C. hominis (97.8%). The 16S rRNA gene sequence similarities to the type strains of all other species of the genus Chryseobacterium were below 97.0%. The fatty acid profile of strain 91A-612(T) consisted of the major fatty acids iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c) and iso-C17 : 0 3-OH. Major compounds in the polar lipid profile were phosphatidylethanolamine and several unidentified lipids, including two lipids that did not contain a sugar moiety, an amino group or a phosphate group (L3, L8), and an aminolipid (AL1). The quinone system was composed mainly of MK-6. The polyamine pattern contained sym-homospermidine as the major compound and moderate amounts of spermidine and spermine. DNA-DNA hybridizations between strain 91A-612(T) and the type strains of C. molle, C. pallidum and C. hominis resulted in relatedness values well below 70%. These data and the differentiating biochemical and chemotaxonomic properties showed that isolate 91A-612(T) represents a novel species of the genus Chryseobacterium, for which we propose the name Chryseobacterium arachidiradicis sp. nov. (type strain 91A-612(T) = LMG 27814(T)= CCM 8490(T) = CIP 110647(T)).

Chryseobacterium shandongense sp. nov., isolated from soil

YF-3T is a Gram-stain-negative, non-motile, non-spore-forming, yellow-orange, rod-shaped bacterium. Optimal growth conditions were at 30 °C, pH 7.0 and 1 % (w/v) NaCl. Phylogenetic analysis, on the basis of the 16S rRNA gene sequence, showed that strain YF-3T was closely related to the strains Chryseobacterium hispalense AG13T and Chryseobacterium taiwanense Soil-3-27T with 98.71 % and 96.93 % sequence similarity, respectively. Strain YF-3T contained MK-6 as the main menaquinone and had a polyamine pattern with sym-homospermidine as the major component. Its major polar lipid was phosphatidylethanolamine. The dominant fatty acids of strain YF-3T were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content of strain YF-3T was 37 mol%. The DNA-DNA relatedness levels between strain YF-3T and the most closely related strains, C. hispalense AG13T and C. taiwanense Soil-3-27T, were 31.7 ± 2.1 % and 28.4 ± 5.4 %, respectively. Based on these results, a novel species named Chryseobacterium shandongense sp. nov. is proposed. The type strain is YF-3T ( = CCTCC AB 2014060T = JCM 30154T).

Emerging flavobacterial infections in fish: A review

Flavobacterial diseases in fish are caused by multiple bacterial species within the family Flavobacteriaceae and are responsible for devastating losses in wild and farmed fish stocks around the world. In addition to directly imposing negative economic and ecological effects, flavobacterial disease outbreaks are also notoriously difficult to prevent and control despite nearly 100 years of scientific research. The emergence of recent reports linking previously uncharacterized flavobacteria to systemic infections and mortality events in fish stocks of Europe, South America, Asia, Africa, and North America is also of major concern and has highlighted some of the difficulties surrounding the diagnosis and chemotherapeutic treatment of flavobacterial fish diseases. Herein, we provide a review of the literature that focuses on Flavobacterium and Chryseobacterium spp. and emphasizes those associated with fish.

Chryseobacterium artocarpi sp. nov., isolated from the rhizosphere soil of Artocarpus integer

A bacterial strain, designated UTM-3T, isolated from the rhizosphere soil of Artocarpus integer (cempedak) in Malaysia was studied to determine its taxonomic position. Cells were Gram-stain-negative, non-spore-forming rods, devoid of flagella and gliding motility, that formed yellow-pigmented colonies on nutrient agar and contained MK-6 as the predominant menaquinone. Comparative analysis of the 16S rRNA gene sequence of strain UTM-3T with those of the most closely related species showed that the strain constituted a distinct phyletic line within the genus Chryseobacterium with the highest sequence similarities to Chryseobacterium lactis NCTC 11390T, Chryseobacterium viscerum 687B-08T, Chryseobacterium tructae 1084-08T, Chryseobacterium arthrosphaerae CC-VM-7T, Chryseobacterium oncorhynchi 701B-08T, Chryseobacterium vietnamense GIMN1.005T, Chryseobacterium bernardetii NCTC 13530T, Chryseobacterium nakagawai NCTC 13529T, Chryseobacterium gallinarum LMG 27808T, Chryseobacterium culicis R4-1AT, Chryseobacterium flavum CW-E2T, Chryseobacterium aquifrigidense CW9T, Chryseobacterium ureilyticum CCUG 52546T, Chryseobacterium indologenes NBRC 14944T, Chryseobacterium gleum CCUG 14555T, Chryseobacterium jejuense JS17-8T, Chryseobacterium oranimense H8T and Chryseobacterium joostei LMG 18212T. The major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c, followed by summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7t) and iso-C17 : 0 3-OH, and the polar lipid profile consisted of phosphatidylethanolamine and several unknown lipids. The DNA G+C content strain UTM-3T was 34.8 mol%. On the basis of the phenotypic and phylogenetic evidence, it is concluded that the isolate represents a novel species of the genus Chryseobacterium , for which the name Chryseobacterium artocarpi sp. nov. is proposed. The type strain is UTM-3T ( = CECT 8497T = KCTC 32509T).

Chryseobacterium viscerum sp. nov., isolated from diseased fish

A taxonomic study was carried out on five Gram-staining-negative, catalase- and oxidase-positive, rod-shaped bacteria isolated from the gills and livers of five diseased rainbow trout. The five novel isolates were designated strains 687B-08T, 445-08, 452-08, 453B-08 and 967B-08. In phylogenetic analyses based on 16S rRNA gene sequences, the five novel strains appeared almost identical (99.0–100 % sequence similarity) and to belong to the genus Chryseobacterium . Strain 687B-08T (the strain selected to represent the five novel isolates) was found to be most closely related to Chryseobacterium oncorhynchi 701B-08T (98.9 % sequence similarity), Chryseobacterium ureilyticum F-Fue-04IIIaaaaT (98.6 %), Chryseobacterium indologenes ATCC 29897T (98.3 %), Chryseobacterium jejuense JS17-8T (98.1 %) and Chryseobacterium gleum ATCC 35910T (98.1 %). In DNA–DNA hybridizations, DNA–DNA relatedness values of 99–100 % were recorded between the five novel strains. Lower DNA–DNA relatedness values (21–57 %) were recorded between strain 687B-08T and C. oncorhynchi 701B-08T, C. ureilyticum F-Fue-04IIIaaaaT and the type strains of other closely related, established species of the genus Chryseobacterium . The predominant respiratory quinone of strain 687B-08T was MK-6 and the major cellular fatty acids were iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and C16 : 1ω6c. The G+C content of the genomic DNA of strain 687B-08T was 38.6 mol%. Based on the phenotypic and genotypic evidence, the five novel strains isolated from rainbow trout represent a single, novel species of the genus Chryseobacterium , for which the name Chryseobacterium viscerum sp. nov. is proposed. The type strain is 687B-08T ( = CECT 7793T  = CCUG 60103T).

Chryseobacterium rigui sp. nov., isolated from an estuarine wetland

A bacterium, designated strain CJ16(T), was isolated from the estuarine wetland of the Han River. Cells of the isolate were yellow-pigmented, Gram-stain-negative, non-motile and rod-shaped. Growth of strain CJ16(T) was observed in TSB at 5-37 °C (optimum 30 °C), at pH 5.0-9.0 (optimum pH 6.0) and with 0-3 % (w/v) NaCl (optimum 0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CJ16(T) was most closely related to Chryseobacterium hagamense KCTC 22545(T) (97.2 % 16S rRNA gene sequence similarity). Genomic relatedness based on DNA-DNA hybridization between strain CJ16(T) and C. hagamense KCTC 22545(T) was 23 % (strain CJ16(T) as probe) and 19 % (strain KCTC 22545(T) as probe). Chemotaxonomic analysis revealed that strain CJ16(T) possessed MK-6 as the major isoprenoid quinone and sym-homospermidine as the predominant polyamine. The predominant fatty acids were iso-C15 : 0 (26.9 %), iso-C17 : 0 3-OH (16.8 %) and summed feature 9 (comprising C16 : 0 10-methyl and/or iso-C17 : 1ω9c; 10.5 %). The DNA G+C content of strain CJ16(T) was 37.9 mol%. Based on phenotypic, genotypic and phylogenetic studies, strain CJ16(T) represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium rigui sp. nov. is proposed. The type strain is CJ16(T) ( = KACC 16560(T)  = JCM 18078(T)).

Chryseobacterium taihuense sp. nov., isolated from a eutrophic lake, and emended descriptions of the genus Chryseobacterium, Chryseobacterium taiwanense, Chryseobacterium jejuense and Chryseobacterium indoltheticum

Bacterial strain THMBM1(T) was isolated from decomposing algal scum that was collected during an algal bloom in Lake Taihu, Wuxi City, Jiangsu Province, China. Cells of strain THMBM1(T) were Gram-negative, facultatively anaerobic, non-motile rods. Colonies on tryptic soy agar were translucent and shiny with entire edges; yellow flexirubin-type pigments were produced. Growth was observed at 15-45 °C (optimum 30-37 °C), at pH 5.0-9.0 (optimum pH 8.0) and in the presence of 0-4.0 % (w/v) NaCl (optimum 0-1.0 %). Strain THMBM1(T) contained MK-6 as the sole respiratory quinone and sym-homospermidine as the predominant polyamine. The predominant cellular fatty acids were iso-C15 : 0 (53.2 %), iso-C17 : 0 3-OH (15.6 %) and iso-C17 : 1ω9c (11.9 %). The polar lipid profile consisted of phosphatidylethanolamine and five unidentified lipids. The DNA G+C content was 36.8 mol% (Tm). Strain THMBM1(T) was closely related to members of the genus Chryseobacterium, with 16S rRNA gene sequence similarities ranging from 92.9 to 97.2 %, the highest sequence similarities being with Chryseobacterium taiwanense BCRC 17412(T) (97.2 %) and C. gambrini 5-1St1a(T) (97.1 %). DNA-DNA relatedness between strain THMBM1(T) and C. taiwanense JCM 21767(T) and C. gambrini DSM 18014(T) was 34.1  and 23.0 %, respectively. Based on these results, it is concluded that strain THMBM1(T) represents a novel species, for which the name Chryseobacterium taihuense sp. nov. is proposed. The type strain is THMBM1(T) ( = CGMCC 1.10941(T)  = NBRC 108747(T)). Emended descriptions of the genus Chryseobacterium and C. taiwanense, C. jejuense and C. indoltheticum are also proposed.

Chryseobacterium solincola sp. nov., isolated from soil

A Gram-staining-negative, yellow-pigmented, strictly aerobic bacterium, designated strain 1YB-R12T, was isolated from a soil sample in western Algeria. The novel isolate was heterotrophic, chemoorganotrophic, halotolerant and psychrotolerant. The temperature and pH optima for growth were 28–30 °C and pH 7.3–8. The bacterium tolerated up to 6 % (w/v) NaCl. Cells were non-motile, non-gliding and non-spore-forming, and were characterized by a variable morphological cycle. Flexirubin-type pigments were not detected. 16S rRNA gene sequence analysis showed that strain 1YB-R12Toccupied a distinct lineage within the genusChryseobacteriumand shared highest sequence similarity withChryseobacterium haifenseLMG 24029T(96.5 %). The DNA G+C content of strain 1YB-R12Twas 40.9 mol%. The predominant cellular fatty acids were anteiso-C15 : 0(41.4 %) and iso-C15 : 0(14.4 %). On the basis of phenotypic properties and phylogenetic distinctiveness, strain 1YB-R12Tis considered to represent a novel species of the genusChryseobacterium, for which the nameChryseobacterium solincolasp. nov. is proposed. The type strain is 1YB-R12T(=DSM 22468T=CCUG 55604T).

Chryseobacterium xinjiangense sp. nov., isolated from alpine permafrost

Strain TSBY 67(T) was isolated during a study on the phylogenetic diversity of culturable bacteria from alpine permafrost in Tianshan Mountains, China. On the basis of 16S rRNA gene sequence analysis, strain TSBY 67(T) was closely related to members of the genus Chryseobacterium and exhibited 96.8 % 16S rRNA gene sequence similarity to Chryseobacterium aquaticum 10-46(T) and Chryseobacterium soldanellicola PSD 1-4(T). Strain TSBY 67(T) grew aerobically, at 4-37 °C, with 0-2 % NaCl and at pH 6-8. Cells were Gram-staining negative, non-motile and non-spore-forming rods. The dominant cellular fatty acids were iso-C(15 : 0) (26.9 %), iso-C(17 : 0) 3-OH (16.1 %) and iso-C(17 : 1)ω9c (15.4 %). The G+C content of the DNA was 33.5 mol%. Strain TSBY 67(T) was distinguishable from its closest phylogenetic neighbours by a combination of phenotypic characteristics. Therefore, strain TSBY 67(T) represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium xinjiangense sp. nov. is proposed. The type strain is TSBY 67(T) ( = NRRL B-51308(T) = CCTCC AB 207183(T)).

Chryseobacterium treverense sp. nov., isolated from a human clinical source

A yellow-pigmented, Gram-reaction-negative bacterium isolated from a human clinical source was investigated using a polyphasic approach in order to clarify its taxonomic status. Comparative 16S rRNA gene sequence analysis showed that the new isolate constituted a distinct phyletic line within the genus Chryseobacterium, displaying >2.8 % sequence divergence with recognized species of this genus. The generic assignment was confirmed by chemotaxonomic data which revealed a fatty acid profile consisting of straight-chain saturated, monounsaturated and branched-chain fatty acids of iso-/anteiso-types as well as 3-hydroxylated fatty acids; a menaquinone with six isoprene units (MK-6) as the predominant respiratory quinone and sym-homospermidine as the predominant polyamine. The novel isolate could be distinguished from other members of the genus Chryseobacterium by a set of distinct biochemical properties. On the basis of phenotypic and phylogenetic evidence, it is proposed that the new isolate represents a novel species of the genus Chryseobacterium for which the name Chryseobacterium treverense sp. nov. is proposed. The type strain is IMMIB L-1519(T) (=DSM 22251(T)=CCUG 57657(T)).

Transfer of Sejongia antarctica, Sejongia jeonii and Sejongia marina to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov., Chryseobacterium jeonii comb. nov. and Chryseobacterium marinum comb. nov

The genus Sejongia was described in 2005, with the two species Sejongia antarctica and Sejongia jeonii, mainly on the basis of 16S rRNA gene sequence analysis. At that time, these organisms formed a quite separate branch in a 16S rRNA gene sequence-based tree, but, in subsequent studies, it became obvious that the species S. antarctica and S. jeonii and a third species, Sejongia marina, were most closely related (>95.0% similarity) to some Chryseobacterium species (e.g. Chryseobacterium hominis, C. formosense and C. haifense). In addition, there is no evidence for clear phenotypic (i.e. chemotaxonomic) differences between these organisms that justifies their assignment to different genera. For these reasons, a proposal is made to transfer these species to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov. (type strain AT1013T=JCM 12381T=IMSNU 14040T=KCTC 12225T), Chryseobacterium jeonii comb. nov. (type strain AT1047T=JCM 12382T=IMSNU 14049T=KCTC 12226T) and Chryseobacterium marinum comb. nov. (type strain IMCC3228T=KCCM 42689T=NBRC 103143T) on the basis of 16S rRNA gene sequence data and published phenotypic data.

Chryseobacterium arothri Campbell et al. 2008 is a later heterotypic synonym of Chryseobacterium hominis Vaneechoutte et al. 2007

The type strains of the species Chryseobacterium arothri (DSM 19326(T)) and Chryseobacterium hominis (NF802(T)) were compared in order to clarify the taxonomic relationship of the two species. The 16S rRNA gene sequences of the two strains shared 99.9 % identity. DNA-DNA pairing studies between the two strains showed 100 % (reciprocal, 76.0 %) relatedness. Phenotypic data, including fatty acid patterns and substrate utilization profiles, showed no pronounced differences between the type strains of the two species. On the basis of these results, we propose the reclassification of Chryseobacterium arothri Campbell et al. 2008 as a later heterotypic synonym of Chryseobacterium hominis Vaneechoutte et al. 2007.