Exilibacterium tricleocarpae gen. nov., sp. nov., a marine bacterium from coralline algae Tricleocarpa sp.

Wang, Guanghua; Zheng, Xianxu; Xu, Shuailiang; Dang, Ge; Su, Hongfei; Liao, Zhiheng; Chen, Biao; Huang, Wen; Liang, Jiayuan; Yu, Kefu

doi:10.1099/ijsem.0.004189

Cited by 11 publications

(5 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1–2 and Figs S2–S4) based on 16S rRNA gene sequences and the bac120 gene set showed that the genus Aestuariicella formed a cluster with the genera Exilibacterium , Maricurvus , Pseudomaricurvus and Pseudoteredinibacter , which are recognized as members of the family Cellvibrionaceae . A similar topological structure was also indicated in previous studies based on 16S rRNA genes [32–34]. These provided evidence supporting the fact that the genus Aestuariicella should be considered as a member of the family Cellvibrionaceae .…”

Section: Phylogenetic Reconstruction and Genome Analysessupporting

confidence: 88%

“…As mentioned above, phylogenetic analysis suggested that the genus Aestuariicella was closely related to several genera of the family Cellvibrionaceae: Exilibacterium [33], Maricurvus [38], Pseudomaricurvus [39,40] and Pseudoteredinibacter [41]. In terms of chemotaxonomic analyses, the predominant isoprenoid quinone of the genus Aestuariicella was ubiquinone-8 (Q-8), which is consistent with the four genera.…”

Section: Physiology and Chemotaxonomysupporting

confidence: 57%

See 1 more Smart Citation

Aestuariicella albida sp. nov., isolated from surface water of the Yellow Sea, and proposal of the genus Aestuariicella as a member of the family Cellvibrionaceae

Xue

Zhang

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

View full text Add to dashboard Cite

A Gram-stain-negative, non-motile and aerobic bacterium, designated HHU G3-2T, was isolated from surface water of the Yellow Sea, PR China. Strain HHU G3-2T was positive for oxidase activity and negative for catalase. Optimal growth occurred at 28 °C (range, 20–37 °C), pH 7.0 (range, pH 6.0–9.0) and in the presence of 2–5 % (w/v) NaCl (range, 1–7%). Phylogenetic analysis based on 16S rRNA gene sequences and 120 ubiquitous single-copy protein-coding genes indicated that strain HHU G3-2T formed a distinct phylogenetic lineage with Aestuariicella hydrocarbonica JCM 30134T, sharing a 16S rRNA gene sequence similarity of 98.05%. Average nucleotide identity and digital DNA–DNA hybridization values between strain HHU G3-2T and A. hydrocarbonica JCM 30134T were 75.74 and 17.80%, respectively, which were below the threshold values of 95–96 and 70 %, respectively. The DNA G+C content of the genomic DNA was 51.17 mol%. The major fatty acids (>10 %) were C17 : 1 ω8c (19.8 %), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c; 15.9 %), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c; 13.8 %) and C17 : 0 (10.3 %). The predominant isoprenoid quinone was ubiquinone-8. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on the polyphasic taxonomic data, strain HHU G3-2T represents a novel species of the genus Aestuariicella , for which the name Aestuariicella albida sp. nov. is proposed. The type strain is HHU G3-2T (=MCCC 1K04224T=JCM 34652T=GDMCC 1.2418T=CGMCC 1.17397T). In addition, we proposed the genus Aestuariicella as a member of the family Cellvibrionaceae .

show abstract

Section: Phylogenetic Reconstruction and Genome Analysessupporting

confidence: 88%

Section: Physiology and Chemotaxonomysupporting

confidence: 57%

Aestuariicella albida sp. nov., isolated from surface water of the Yellow Sea, and proposal of the genus Aestuariicella as a member of the family Cellvibrionaceae

Xue

Zhang

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

View full text Add to dashboard Cite

show abstract

“…For instance, the case studies for screening ZEA- and OTA-degrading enzymes only required 1 d to predict ∼1000k candidate enzymes with one NVIDIA V100 GPU. In addition, of the screened enzymes, one OTA-degrading enzyme (OH9) was derived from Exilibacterium tricleocarpae, a marine bacterium isolated from coralline algae in the Beibu Gulf . To our knowledge, this is the first reported enzyme from a marine microbe with OTA-degrading activity.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, of the screened enzymes, one OTA-degrading enzyme (OH9) was derived from Exilibacterium tricleocarpae, a marine bacterium isolated from coralline algae in the Beibu Gulf. 36 To our knowledge, this is the first reported enzyme from a marine microbe with OTA-degrading activity. Because of the comprehensive training data set, specific EC categories of candidate enzymes were not restricted; however, researchers intending to use the PU-EPP model need to consider the application domain of PU-EPP.…”

Section: ■ Discussionmentioning

confidence: 99%

Discovery of Toxin-Degrading Enzymes with Positive Unlabeled Deep Learning

Zhang,

Xing,

Liu

et al. 2024

ACS Catal.

View full text Add to dashboard Cite

Identifying functional enzymes for the catalysis of specific biochemical reactions is a major bottleneck in the de novo design of biosynthesis and biodegradation pathways. Conventional methods based on microbial screening and functional metagenomics require long verification periods and incur high experimental costs; recent data-driven methods apply only to a few common substrates. To enable rapid and high-throughput identification of enzymes for complex and less-studied substrates, we propose a robust enzyme's substrate promiscuity prediction model based on positive unlabeled learning. Using this model, we identified 15 new degrading enzymes specific for the mycotoxins ochratoxin A and zearalenone, of which six could degrade >90% mycotoxin content within 3 h. We anticipate that this model will serve as a useful tool for identifying new functional enzymes and understanding the nature of biocatalysis, thereby advancing the fields of synthetic biology, metabolic engineering, and pollutant biodegradation.

show abstract

“…Strains in this family were usually isolated from soil, marine environments or invertebrates. Interestingly, approximately 12 species from this family were reported to be eukaryotic-associated, namely: Teredinibacter turnerae [2], Teredinibacter waterburyi [3], Teredinibacter haidensis , Teredinibacter purpureus , Teredinibacter franksiae [4] and Umboniibacter marinipuniceus [5], which were isolated from molluscs; Marinibactrum halimedae [6], Agarilytica rhodophyticola [7] and Exilibacterium tricleocarpae [8], recovered from macroalga; Pseudoteredinibacter isoporae , obtained from reef-building corals [9]; and Cellvibrio diazotrophicus [10] and Cellvibrio zantedeschiae [11], recovered from rhizosphere or root of plants. Cells from Cellvibrionaceae are usually versatile in complex organic compound degradation.…”

Section: Full-textmentioning

confidence: 99%

Sessilibacter corallicola gen. nov., sp. nov., a sessile bacterium isolated from coral Porites lutea

Liu¹,

Luo

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

Self Cite

View full text Add to dashboard Cite

A Gram-stain-negative, non-spore-forming, motile, aerobic bacterium (strain C21T) was isolated from coral and identified using polyphasic identification approach. Global alignment of 16S rRNA gene sequences indicated that strain C21T shares 95.7 % sequence identity to its closest neighbour, Marinibactrum halimedae NBRC 110095T, followed by other type strains with identities of lower than 95 %. The average nucleotide identity and average amino acid identity values between strain C21T and M. halimedae NBRC 110095T were 69.6 and 64.8 %, respectively, indicating that strain C21T may represent a new species in a new genus. Phylogenetic analysis based on 16S rRNA gene and phylogenomic results indicated that strain C21T forms a distinct branch in the family Cellvibrionaceae . Cellular fatty acids and polar lipids could also readily distinguish strain C21T from closely related type strains. Therefore, strain C21T is suggested to represent a new species in a new genus, for which the name Sessilibacter corallicola gen. nov., sp. nov. is proposed. The type strain is C21T (=MCCC 1K03260T=KCTC 62317T).

show abstract

Exilibacterium tricleocarpae gen. nov., sp. nov., a marine bacterium from coralline algae Tricleocarpa sp.

Cited by 11 publications

References 34 publications

Aestuariicella albida sp. nov., isolated from surface water of the Yellow Sea, and proposal of the genus Aestuariicella as a member of the family Cellvibrionaceae

Aestuariicella albida sp. nov., isolated from surface water of the Yellow Sea, and proposal of the genus Aestuariicella as a member of the family Cellvibrionaceae

Discovery of Toxin-Degrading Enzymes with Positive Unlabeled Deep Learning

Sessilibacter corallicola gen. nov., sp. nov., a sessile bacterium isolated from coral Porites lutea

Contact Info

Product

Resources

About