Ruegeria halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi

Kim, Young‐Ok; Park, Sooyeon; Nam, Bo‐Hye; Kang, So-Jung; Hur, Young Baek; Lee, Sang-Jun; Oh, Tae-Kwang; Yoon, Jung‐Hoon

doi:10.1099/ijs.0.031609-0

Cited by 36 publications

(14 citation statements)

References 26 publications

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“…While the MALDI-TOF profile has been recorded for many pathogens because of the numerous clinical isolates already characterized, environmental bacteria are poorly represented in terms of MALDI-TOF m/z databases. For example, only eight Ruegeria species from the Roseobacter clade have been described and named although they are frequently found in the marine environment (Uchino et al, 1998;Gonzalez et al, 2003;Lee et al, 2007;Muramatsu et al, 2007;Yi et al, 2007;Vandecandelaere et al, 2008;Lai et al, 2010;Oh et al, 2011;Kim et al, 2012). This data set appears to be too poor for the development of a confident MALDI-TOF pattern with the objective to discriminate bacteria belonging to this genera from the numerous and highly diverse members of the Roseobacter clade.…”

Section: Introductionmentioning

confidence: 99%

Shotgun nanoLC‐MS/MS proteogenomics to document MALDI‐TOF biomarkers for screening new members of the Ruegeria genus

Christie-Oleza

Piña-Villalonga

Guérin

et al. 2012

Environmental Microbiology

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The identification of bacteria by means of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry directly using whole cells has become a standard method in clinical diagnosis due to its rapidity and simplicity. Nevertheless, the analysis of environmental samples with this approach still represents a challenge due to the enormous microbial diversity existing on earth and the lack of a comprehensive database. Most of the environmentally relevant species comprise only one unique strain, while pathogens such as Escherichia coli, with 667 described strains, are well documented. In such case, identification of the proteins responsible for the peak signals within MALDI-TOF spectra can give crucial information for species discrimination. To give higher confidence in MALDI-TOF biomarker description we exploited information from proteins identified by shotgun nanoLC-MS/MS, consisting of the identification and quantification of low-molecular-weight proteins after SDS-PAGE, in-gel trypsin proteolysis and analysis of tryptic peptides. We also proposed the standardization of the inclusion of internal calibrants in the bacterial sample to improve the accuracy of the MALDI-TOF measurements. In this way, nine candidate biomarkers were tentatively proposed for Ruegeria lacuscaerulensis ITI-1157. The conserved biomarkers were theoretically deduced for all other Ruegeria strains whose genomes have been sequenced and their corresponding m/z MALDI-TOF signals were estimated. Among these, DNA-binding protein, HU, and ribosomal proteins, L29, L30, L32 and S17, were shown experimentally to be also the most prominent and conserved signals in the other strain tested, Ruegeria pomeroyi DSS-3. Thus, we suggested that these five biomarkers, which give rise to 10 m/z peak signals derived from the mono- and doubly protonated proteins, are the best candidates for identifying bacteria belonging to the Ruegeria genus, and quickly assessed their phylogenetic proximity to described species. As an application of these biomarkers, we quickly screened 30 seawater bacterial isolates by MALDI-TOF and found one belonging to the Ruegeria genus, as further confirmed by 16S RNA sequencing. Due to its simplicity and effectiveness, this technique could be of immense value in monitoring bacteria in the environment in the near future.

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Section: Introductionmentioning

confidence: 99%

Shotgun nanoLC‐MS/MS proteogenomics to document MALDI‐TOF biomarkers for screening new members of the Ruegeria genus

Christie-Oleza

Piña-Villalonga

Guérin

et al. 2012

Environmental Microbiology

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“…n. microbium a Table 2. Differential characteristics of the genus Antarcticimicrobium and closely related genera in the family Rhodobacteraceae Genera: 1, Antarcticimicrobium gen. nov. (strain S4J41 T and Ruegeria lutea JCM 30927 T , this study); 2, Ruegeria [30,[37][38][39][40][41][42][43][44][45][46][47][48][49][50][51]; 3, Phaeobacter (this study and [30,[52][53][54][55][56]); 4, Puniceibacterium (this study and [5,57]); 5, Sulfitobacter (this study and [58][59][60][61][62][63][64][65][66][67][68][69][70][71][72][73]); 6, Pseudopuniceibacterium [36]. +, Positive; -, negative; w, weakly positive; v, variable results among different species.…”

Section: Description Of Antarcticimicrobium Gen Novmentioning

confidence: 71%

Antarcticimicrobium sediminis gen. nov., sp. nov., isolated from Antarctic intertidal sediment, transfer of Ruegeria lutea to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov.

Zhang

Liu

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence and the genome sequence of strain S4J41 T are MK120109 and SMFP00000000, respectively. The GenBank/EMBL/DDBJ accession numbers for the genome sequences of Puniceibacterium confluentis KCTC 52765 T and 'Phaeobacter marinintestinus' CCTCC AB 2016288 T are VOJI00000000 and VOGO00000000, respectively. Seven supplementary tables and two supplementary figures available with the online version of this article.

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“…The DNA base Table 1. Differential characteristics of strain TS-T30 T and phylogenetically related genera Genera: 1, Lacimonas (strain TS-T30 T , data from this study); 2, Lutimaribacter (Iwaki et al, 2013;Yoon et al, 2009a;Yuan et al, 2009); 3, Poseidonocella (Romanenko et al, 2012); 4, Ruegeria (Huo et al, 2011;Kämpfer et al, 2013;Kim et al, 2012bKim et al, , 2014Lee et al, 2012;Muramatsu et al, 2007;Oh et al, 2011;Park & Yoon, 2012;Uchino et al, 1998;Vandecandelaere et al, 2008;Yi et al, 2007); 5, Marivita (Hwang et al, 2009;Yoon et al, 2010Yoon et al, , 2012Yoon et al, , 2013a; 6, Seohaeicola (Yoon et al, 2009b); 7, Sediminimonas (Wang et al, 2009); 8, Shimia (Chen et al, 2011;Choi & Cho, 2006;Hameed et al, 2013;…”

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confidence: 75%

Lacimonas salitolerans gen. nov., sp. nov., isolated from surface water of a saline lake

Zhong

Liu

Wang

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative bacterium, strain TS-T30 T , was isolated from a saline lake (Lake Tuosu) in Qaidam basin, Qinghai province, China, and its taxonomic position was determined by using a polyphasic approach. Cells were non-spore-forming rods, non-motile, 0.8-1.4 mm wide and 1.9-4.0 mm long. Strain TS-T30T was strictly heterotrophic and aerobic. Catalase-and oxidasepositive. Growth was observed in the presence of 0.5-11.0 % (w/v) NaCl (optimum 3.0 %), and at 10-35 8C (optimum 25 8C) and pH 6.5-10.0 (optimum pH 8.5). Strain TS-T30 T contained C 18 : 1 v7c as the only predominant fatty acid. The major respiratory quinone was Q-10. The DNA G+C content was 62 mol% (T m ). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T30 T formed a distinct lineage that was independent of other most closely related genera: Lutimaribacter (95.2-95.9 % 16S rRNA gene sequence similarities), Poseidonocella (95.4 %), Ruegeria (92.8-94.9 %), Marivita (93.6-94.9 %), Seohaeicola (94.7 %), Sediminimonas (94.7 %), Shimia (93.9-94.7 %), Oceanicola (92.6-94.5 %) and Roseicyclus (94.5 %). The major polar lipids were phosphatidylglycerol, one unidentified phospholipid and an unknown aminolipid; phosphatidylcholine was not detected. These data demonstrated that strain TS-T30 T represents a novel species of a new genus in the family

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Ruegeria halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi

Cited by 36 publications

References 26 publications

Shotgun nanoLC‐MS/MS proteogenomics to document MALDI‐TOF biomarkers for screening new members of the Ruegeria genus

Shotgun nanoLC‐MS/MS proteogenomics to document MALDI‐TOF biomarkers for screening new members of the Ruegeria genus

Antarcticimicrobium sediminis gen. nov., sp. nov., isolated from Antarctic intertidal sediment, transfer of Ruegeria lutea to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov.

Lacimonas salitolerans gen. nov., sp. nov., isolated from surface water of a saline lake

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