Shewanella algicola sp. nov., a marine bacterium isolated from brown algae

Kim, Jiyoung; Yoo, Hyera; Lee, Dong-Heon; Park, So‐Hyun; Kim, Young‐Ju; Oh, Dae Jong

doi:10.1099/ijsem.0.001014

Cited by 24 publications

(13 citation statements)

References 47 publications

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“…High interspecies similarities of these HKGs were generated, making it difficult to discern closely related species. The gyrB gene has always been used as a basic detection for novel Shewanella species identification (7,(20)(21)(22). However, the criterion for gyrB analysis was not well established, and the boundary between interspecies and intraspecies similarities was inconspicuous.…”

Section: Discussionmentioning

confidence: 99%

“…The disadvantage of the application of the 16S rRNA gene was the low resolving power to discriminate closely related species due to their high sequence similarities (19). Recently, a more rapidly evolving housekeeping gene (HKG) of gyrB was selected as an alternative phylogenetic indicator for Shewanella species classification (7,(20)(21)(22). Nevertheless, the quality of sequences submitted in public databases is poor (22)(23)(24).…”

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confidence: 99%

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Multilocus Sequence Analysis, a Rapid and Accurate Tool for Taxonomic Classification, Evolutionary Relationship Determination, and Population Biology Studies of the Genus Shewanella

Fang

Wang²,

Liu³

et al. 2019

Appl Environ Microbiol

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The genus Shewanella comprises a group of marine-dwelling species with worldwide distribution. Several species are regarded as causative agents of food spoilage and opportunistic pathogens of human diseases. In this study, a standard multilocus sequence analysis (MLSA) based on six protein-coding genes (gyrA, gyrB, infB, recN, rpoA, and topA) was established as a rapid and accurate identification tool in 59 Shewanella type strains. This method yielded sufficient resolving power in regard to enough informative sites, adequate sequence divergences, and distinct interspecies branches. The stability of phylogenetic topology was supported by high bootstrap values and concordance with different methods. The reliability of the MLSA scheme was further validated by identical phylogenies and high correlations of genomes. The MLSA approach provided a robust system to exhibit evolutionary relationships in the Shewanella genus. The split network tree proposed twelve distinct monophyletic clades with identical GϩC contents and high genetic similarities. A total of 86 tested strains were investigated to explore the population biology of the Shewanella genus in China. The most prevalent Shewanella species was Shewanella algae, followed by Shewanella xiamenensis, Shewanella chilikensis, Shewanella indica, Shewanella seohaensis, and Shewanella carassii. The strains frequently isolated from clinical and food samples highlighted the importance of increasing the surveillance of Shewanella species. Based on the combined genetic, genomic, and phenotypic analyses, Shewanella upenei should be considered a synonym of S. algae, and Shewanella pacifica should be reclassified as a synonym of Shewanella japonica. IMPORTANCE The MLSA scheme based on six housekeeping genes (HKGs) (gyrA, gyrB, infB, recN, rpoA, and topA) is well established as a reliable tool for taxonomic, evolutionary, and population diversity analyses of the genus Shewanella in this study. The standard MLSA method allows researchers to make rapid, economical, and precise identification of Shewanella strains. The robust phylogenetic network of MLSA provides profound insight into the evolutionary structure of the genus Shewanella. The population genetics of Shewanella species determined by the MLSA approach plays a pivotal role in clinical diagnosis and routine monitoring. Further stud-2019. Multilocus sequence analysis, a rapid and accurate tool for taxonomic classification, evolutionary relationship determination, and population biology studies of the genus Shewanella. Appl Environ Microbiol 85:e03126-18. https://doi. Downloaded fromies on remaining species and genomic analysis will enhance a more comprehensive understanding of the microbial systematics, phylogenetic relationships, and ecological status of the genus Shewanella.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Multilocus Sequence Analysis, a Rapid and Accurate Tool for Taxonomic Classification, Evolutionary Relationship Determination, and Population Biology Studies of the Genus Shewanella

Fang

Wang²,

Liu³

et al. 2019

Appl Environ Microbiol

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“…The cecum sample has a comparably high fraction of unassigned genera and phyla compared to meat samples and is distinguished by a higher fraction of Shewanella than in all other samples (Figs 3 and 4). Shewanella are known from a variety of marine environments [39] also including marine animal intestines [40] and marine vegetation [41]. It is tempting to speculate that the caribou might have foraged on marine vegetation, but no marine chloroplasts were detected in the rumen or cecum of the caribou to give any support of such speculation.…”

Section: The Caribou Rumen Is a Potential Source Of Microbial Byprodumentioning

confidence: 99%

Microbiota in foods from Inuit traditional hunting

et al. 2020

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The foods we eat contain microorganisms that we ingest alongside the food. Industrialized food systems offer great advantages from a safety point of view, but have also been accused of depleting the diversity of the human microbiota with negative implications for human health. In contrast, artisanal traditional foods are potential sources of a diverse food microbiota. Traditional foods of the Greenlandic Inuit are comprised of animal-sourced foods prepared in the natural environment and are often consumed raw. These foods, some of which are on the verge of extinction, have not previously been microbiologically characterized. We mapped the microbiota of foods stemming from traditional Inuit land-based hunting activities. The foods included in the current study are dried muskox and caribou meat, caribou rumen and intestinal content as well as larval parasites from caribou hides, all traditional Inuit foods. This study shows that traditional drying methods are efficient for limiting microbial growth through desiccation. The results also show the rumen content of the caribou to be a highly diverse source of microbes with potential for degradation of plants. Finally, a number of parasites were shown to be included in the biodiversity of the assessed traditional foods. Taken together, the results map out a diverse source of ingested microbes and parasites that originate from the natural environment. These results have implications for understanding the nature-sourced traditional Inuit diet, which is in contrast to current day diet recommendations as well as modern industrialized food systems.

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“…Most of the clinically relevant isolates seem to belong to the species S. alga (Nozue et al., ). Meanwhile, many additional species of the genus Shewanella were described, such as S. abyssi (Miyazaki, Nogi, Usami, & Horikoshi, ), S. affinis (Ivanova et al., ), S. algicola (Kim et al., ), S. algidipiscicola (Satomi, Vogel, Venkateswaran, & Gram, ) , S. amazonensis (Venkateswaran, Dollhopf, Aller, Stackebrandt, & Nealson, ), S. aquimarina (Yoon, Yeo, Kim, & Oh, ), S. arctica (Kim et al., ), S. atlantica (Zhao, Manno, Thiboutot, Ampleman, & Hawari, ), S. basaltis (Chang et al., ), S. benthica (Lauro et al., ), S. canadensis (Zhao et al., ), S. chilikensis (Sucharita et al., ), S. colwelliana (Labare & Weiner, ) , S. corallii (Shnit‐Orland, Sivan, & Kushmaro, ) , S. decolorationis (Xu et al., ) , S. denitrificans (Brettar, Christen, & Hofle, ) , S. dokdonensis (Sung, Yoon, & Ghim, ) , S. donghaensis (Yang, Lee, Ryu, Kato, & Kim, ), S. fidelis (Ivanova et al., ) , S. fodinae (Kumar et al., ) , S. frigidimarina (Bowman et al., ; Bozal, Montes, Tudela, Jimenez, & Guinea, ) , S. gaetbuli (Yoon, Kang, Oh, & Park, ) , S. gelidimarina (Bowman et al., ), S. gelidii (Wang et al., ) , S. glacialipiscicola (Satomi et al., ) , S. hafniensis (Satomi, Vogel, Gram, & Venkateswaran, ) , S. halifaxensis (Zhao, Manno, Leggiadro, O'Neill, & Hawari, ) , S. halitois (Kim et al., ) , S. hanedai (Jensen, Tebo, Baumann, Mandel, & Nealson, ) , S. indica (Verma et al., ) , S. inventionis (Wang & Sun, ) , S. irciniae (Lee et al., ) , S. japonica (Ivanova et al., ) , S. kaireitica (Miyazaki et al., ) , S. litorisediminis (Lee & Yoon, ) , S. livingstonensis (Bozal et al., ) , S. loihica (Gao et al., ) , S. mangrovi (Liu, Shang, Yi, Gu, & Zeng, ) , S. marina (Park, Baik, Kim, Kim, & Seong, ), S. marinintestina (Satomi, Oikawa, & Yano, ), S. marisflavi (Yoon, Yeo, et al., ), S. morhuae (Satomi et al., ), S. olleyana (Skerratt, Bowman, & Nichols, …”

Section: Introductionmentioning

confidence: 99%

Methods for identification and differentiation of different Shewanella spp. isolates for diagnostic use

Jung‐Schroers

Jung

Ryll

et al. 2017

Journal of Fish Diseases

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Shewanella spp. are Gram-negative, rod-shaped, motile bacteria that are widely distributed in marine and freshwater environments. The bacteria are present in the physiological microflora of fish from temperate waters and are known as fish spoilage species. From clinically healthy fish and from fish with skin ulcerations, Shewanella spp. is regularly isolated, indicating a possible role as fish pathogen. In this study, 74 isolates of Shewanella spp. were analysed. For species identification, biochemical techniques, 16S rRNA sequencing, MALDI-TOF MS and the Sherlock Microbial Identification System (MIS) based on the composition of fatty acid ethyl esters were compared. The phylogenetic relationship, cytotoxicity in vitro and resistance against antibiotics were tested. The most reliable method for species identification was 16S rRNA sequencing. From diseased fish, clinically healthy fish and the aquatic environment, different Shewanella species were isolated. This indicates that Shewanella spp. is widespread in the aquatic milieu and acts as a secondary pathogen. The virulence of Shewanella spp. is probably not depending on the species but on the isolate itself. Many isolates of Shewanella spp. were showing multiresistances against antibiotic substances, especially in samples derived from retailers and in routine diagnostics, all Shewanella spp. should therefore be tested for resistances against antibiotic agents.

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Shewanella algicola sp. nov., a marine bacterium isolated from brown algae

Cited by 24 publications

References 47 publications

Multilocus Sequence Analysis, a Rapid and Accurate Tool for Taxonomic Classification, Evolutionary Relationship Determination, and Population Biology Studies of the Genus Shewanella

Multilocus Sequence Analysis, a Rapid and Accurate Tool for Taxonomic Classification, Evolutionary Relationship Determination, and Population Biology Studies of the Genus Shewanella

Microbiota in foods from Inuit traditional hunting

Methods for identification and differentiation of different Shewanella spp. isolates for diagnostic use

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