Francisella salimarina sp. nov., isolated from coastal seawater

Li, Lianghui; Luo, Hai-Min; Feng, Jun-Hui; Ming, Yu-Zhen; Zheng, Min-Ling; Deng, Guang-Yuan; Cha, Chen; Li, Wenjun; Xiao, Min; Qu, Pinghua

doi:10.1099/ijsem.0.004164

Cited by 14 publications

(4 citation statements)

References 54 publications

(49 reference statements)

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“…The scheme provided in Table 4 can be used for the identification of Francisellaceae. According to our data and the literature [13][14][15][16][17][18][19], the 5182-5185 mass of the 50S ribosomal protein L34 was specific for the Francisella genus. Within the Francisella genus, the species F. tularensis could be differentiated from the other Francisella species by the histone-like protein form Beta (Hu-beta) mass (selected biomarker 9449).…”

Section: Francisella Identification By Biomarkersupporting

confidence: 71%

“…Manual adjustments were made when necessary. F. salinarina [19], F. oppertunistica [31], A. frigiaqua, A. inopinata [32], and Pseudofrancisella aestuarii [33] are genetically related to F. tularensis. Except for F. oppertunistica, the species were found in cold (sea)water without any relation to human pathogenicity.…”

Section: Calculation Of Biomarker Masses From Dna Sequencesmentioning

confidence: 99%

“…To overcome this, an in-house library was created to distinguish F. tularensis subspecies [13]. Francisella-specific biomarkers were studied for F. tularensis, with and without subspecies differentiation, and for F. philomiragia, F. halioticida and F.salimarina [13][14][15][16][17][18][19]. An in-house database was also described limited to F. tularensis ssp.…”

Section: Introductionmentioning

confidence: 99%

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Identification of Francisella tularensis Subspecies in a Clinical Setting Using MALDI-TOF MS: An In-House Francisella Library and Biomarkers

et al. 2023

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Francisella tularensis is a zoonotic bacterium that is endemic in large parts of the world. It is absent in the standard library of the most applied matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems: the Vitek MS and the Bruker Biotyper system. The additional Bruker MALDI Biotyper Security library contains F. tularensis without subspecies differentiation. The virulence of F. tularensis differs between the subspecies. The F. tularensis subspecies (ssp.) tularensis is highly pathogenic, whereas the subspecies holarctica displays lower virulence and subspecies novicida and F. tularensis ssp. mediasiatica are hardly virulent. To differentiate the Francisellaceae and the F. tularensis-subspecies, an in-house Francisella library was built with the Bruker Biotyper system and validated together with the existing Bruker databases. In addition, specific biomarkers were defined based on the main spectra of the Francisella strains supplemented with in silico genome data. Our in-house Francisella library accurately differentiates the F. tularensis subspecies and the other Francisellaceae. The biomarkers correctly differentiate the various species within the genus Francisella and the F. tularensis subspecies. These MALDI-TOF MS strategies can successfully be applied in a clinical laboratory setting as a fast and specific method to identify F. tularensis to subspecies level.

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Section: Francisella Identification By Biomarkersupporting

confidence: 71%

Section: Calculation Of Biomarker Masses From Dna Sequencesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification of Francisella tularensis Subspecies in a Clinical Setting Using MALDI-TOF MS: An In-House Francisella Library and Biomarkers

et al. 2023

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“…A substantial proportion of these "other" bacteria (5.0% and 12.0% in the ONT 16S and ONT Custom, respectively) belonged to Francisella species, which could not be classified to species level with SILVA taxonomy. Further classification of sequences matching to this taxon was performed with EMBL-EBI/ ENA taxonomy, which revealed that over 99.9% of these sequences matched best to F. salina (synonym F. marina, now F. salimarina; Li et al 2020), indicating this was due to the absence of this species in the SILVA taxonomy. Taking this into account, the average relative abundance of bacteria that should not be present in the mock community was reduced to 5.8% for both ONT protocols.…”

Section: Mock Community Analysismentioning

confidence: 99%

Comparison of high‐throughput sequencing methods for bacterial microbiota profiling in catfish aquaculture

Older,

Yamamoto,

Griffin

et al. 2023

N American J Aquac

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ObjectiveBacterial community profiling in aquaculture can be useful for monitoring environmental conditions that may lead to disease outbreaks, understanding the impact of dietary treatments on fish health, and identifying microbes that have potential as probiotics. Microbiota characterization is commonly performed with high‐throughput sequencing using short‐read platforms (i.e., Illumina) targeting variable regions of the bacterial 16S ribosomal RNA (rRNA) gene. Long‐read platforms (i.e., Oxford Nanopore Technologies [ONT]) enable sequencing of full‐length 16S rRNA genes. While short‐read platforms are highly accurate, long‐read platforms sacrifice sequence quality in exchange for longer read lengths.MethodsHerein, a typical short‐read approach (Illumina MiSeq; V4 region of 16S rRNA gene) was compared with two near‐full‐length 16S rRNA gene ONT protocols (ONT Custom and ONT 16S). Sequencing was performed on a mock community composed of fish‐relevant bacteria, in addition to samples (digesta, gill, skin) obtained from 10 hybrid catfish (female Channel Catfish Ictalurus punctatus × male Blue Catfish I. furcatus) and their environment (pond and holding tank). Fish were euthanized with either an overdose of MS‐222 or cranial concussion and subsequent pithing to enable comparisons of these sequencing protocols in the context of a realistic experimental design.ResultThe ONT Custom protocol best recapitulated the theoretical composition of the mock community, followed by the ONT 16S and Illumina MiSeq protocols. Phylum‐level composition was consistent within sample type across sequencing methods. However, at lower levels there were biases for several taxa, particularly in pond samples. Euthanasia method also appeared to introduce differences, primarily on the cutaneous communities. The three sequencing methods consistently identified significant differences between euthanasia methods, with Illumina MiSeq revealing the greatest differences. While all strategies performed comparably for digesta, skin, and water samples, the ONT strategies underperformed for gill samples.ConclusionDepending on application, results indicate that near‐full‐length 16S rRNA gene nanopore sequencing is a viable option for aquaculture microbiota studies.

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