Antrihabitans stalactiti gen. nov., sp. nov., a new member of the family Nocardiaceae isolated from a cave

Lee, Soon Dong; Kim, In Seop; Verbarg, Susanne; Joung, Yochan

doi:10.1099/ijsem.0.004444

Cited by 13 publications

(4 citation statements)

References 36 publications

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“…Proteobacteria, Fusobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Clostridia (Villasante et al, 2019;Wong et al, 2013). In this study, and cellulose (Lee et al, 2020). Meanwhile, Actinobacteriota belongs to conditional pathogenic bacteria, which can infect the body and cause disease when the body's immunity is weak (Byrd et al, 2021).…”

Section: Discussionmentioning

confidence: 88%

Effects of fish meal replacement with low‐gossypol cottonseed meal on the intestinal barrier of juvenile golden pompano ( Trachinotus ovatus )

Qian

Liu

et al. 2021

Aquaculture Research

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The effects of replacing fish meal (FM) with low-gossypol cottonseed meal (LCSM) on the intestinal barrier in different segments (PI, proximal intestine; MI, middle intestine; DI, distal intestine) were studied in juvenile golden pompano (Trachinotus ovatus) using 6-week feeding trials. FM of 0% (diet_1), 20% (diet_2), 40% (diet_3) and 60% (diet_4) was replaced by LCSM. The FM-based diet (diet_1) containing 25% FM was used as control group. The intestinal morphology, mRNA expression of tight junctionrelated genes (ZO-1, Occludin, Claudin-12), antioxidant enzyme-related genes (CAT, GPx, GR, CuZnSOD) and non-specific immune response-related genes (IL-8, TNFα, C4) and microbiota of different intestine segments were detected. The results showed that the number and length of microvilli and intestinal wall thickness decreased significantly in PI of diet_3 and diet_4 groups. Meanwhile, mRNA expression of Occludin, Clauding-12 and C4 was up-regulated in PI and DI of diet_3 group; the expression of GR and CuZnSOD was up-regulated in PI and MI with increasing LCSM replacement; the expression of TNFα was up-regulated in the three segments of diet_3 group. Further, 16S rRNA amplicon sequencing revealed a significant reduction in the richness and diversity of intestinal microbial in diet_3 and diet_4 groups. At the family level and genera level, the abundance of Nocardiaceae and Rhodococcus was up-regulated in the three segments of diet_3 and diet_4 groups respectively. These results suggested that the replacement of LCSM by more than 20% causes the intestinal barrier function of juvenile golden pompano to be affected. These provide a reference for sustainable aquaculture.

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Section: Discussionmentioning

confidence: 88%

Effects of fish meal replacement with low‐gossypol cottonseed meal on the intestinal barrier of juvenile golden pompano ( Trachinotus ovatus )

Qian

Liu

et al. 2021

Aquaculture Research

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“…For sequencing of 16S rRNA genes, the 10 study strains were grown on marine agar at 30 • C for 3 days, and Microbacterium arthrosphaerae KACC 16680 T , M. luteolum KACC 14465 T , and Microbacterium terrae KACC 14470 T were cultivated on trypticase soy agar (Difco) at 30 • C for 3 days. Genomic DNA isolation was performed as described previously (Lee et al, 2020). The PCR amplification and sequencing of the 16S rRNA genes were performed using an ABI Prism 3730XL DNA analyzer with a BigDye Terminator kit v.3.1 (Invitrogen, USA) at the SolGent Company Limited (Deajon, Korea).…”

Section: S Rrna Gene Sequencing and Analysismentioning

confidence: 99%

Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium

Lee,

Yang,

Kim

2023

Front. Microbiol.

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The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA genes and whole genomes. For the construction of a more reliable and robust 16S rRNA gene phylogeny, the authentic and nearly complete 16S rRNA gene sequences of all the Microbacterium type strains were selected through pairwise comparison of the sequences contained in several public databases including the List of Prokaryotic names with Standing in Nomenclature (LPSN). The clustering of the ten study strains into five distinct groups was apparent in this single gene-based phylogenetic tree. In addition, the 16S rRNA gene sequences of a few type strains were shown to be incorrectly listed in LPSN. An overall phylogenomic clustering of the genus Microbacterium was performed with a total of 113 genomes by core genome analysis. As a result, nine major (≥ three type strains) and eight minor (two type strains) clusters were defined mostly at gene support index of 92 and mean intra-cluster OrthoANIu of >80.00%. All of the study strains were assigned to a Microbacterium liquefaciens clade and distributed further into four subclusters in the core genome-based phylogenetic tree. In vitro phenotypic assays for physiological, biochemical, and chemotaxonomic characteristics were also carried out with the ten study strains and seven closely related type strains. Comparison of the overall genomic relatedness indices (OGRI) including OrthoANIu and digital DNA–DNA hybridization supported that the study strains constituted four new species of the genus Microbacterium. In addition, some Microbacterium type strains were reclassified as members of preexisting species. Moreover, some of them were embedded in a new genus of the family Microbacteriaceae based on their distinct separation in the core genome-based phylogenetic tree and amino acid identity matrices. Based on the results here, four new species, namely, Microbacterium aurugineum sp. nov., Microbacterium croceum sp. nov., Microbacterium galbinum sp. nov., and Microbacterium sufflavum sp. nov., are described, along with the proposal of Paramicrobacterium gen. nov. containing five reclassified Microbacterium species from the “Microbacterium agarici clade”, with Paramicrobacterium agarici gen. nov., comb. nov. as the type species.

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“…Caves represent an interesting environment that is unique and distinct from other terrestrial habitats. During a screening for novel actinobacteria from a natural cave in Jeju Island, Republic of Korea, many novel bacterial strains that were affiliated to the class Actinobacteria were described [9,[11][12][13][14][15]. Among them, it was found that two actinobacterial strains, designated as D2-41 T and D3-21, showed an uncertain taxonomic rank within the order Mycobacteriales through preliminary 16S rRNA gene sequence analysis.…”

Section: Introductionmentioning

confidence: 99%

“…Members of the eight families, except for the families Hoyosellaceae and Lawsonellaceae, are known to contain mycolic acids [1,8], unique long-chain fatty acids (with 22-90 carbon atoms) found in the lipid-rich cell walls. Recently, three mycolic acid-containing genera, namely Antrihabitans [9], Presttcolla [10] and Sphaelaeibacter [11], were proposed as new members of the family Nocardiaceae.…”

Section: Introductionmentioning

confidence: 99%

Speluncibacter jeojiensis gen. nov. sp. nov., a novel bacterium of the order Mycobacteriales isolated from a cave and a proposal of Speluncibacteraceae fam. nov.

Lee,

Yang,

Han

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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Two Gram-stain-positive, aerobic, non-spore-forming, non-motile, irregular rod-shaped actinobacteria, designated as D2-41T and D3-21, were isolated from soil samples collected in a natural cave in Jeju, Republic of Korea. Both of the isolates were shown to share 100 % 16S rRNA sequence identity. The cell wall contained meso-diaminopimelic acid, arabinose and galactose. The predominant menaquinone was MK-8(H2). The polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid, an unidentified aminoglycolipid, an unidentified phospholipid and two unidentified lipids. The predominant fatty acids were C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). Mycolic acids of C30–C38 were present. The 16S rRNA gene trees showed that the organisms occupied a distinct position remotely located from recognized genera within the order Mycobacteriales, albeit with the 16S rRNA gene similarities of 97.0–97.1 % with Rhodococcus olei, Rhodococcus rhodnii and Rhodococcus triatomae. The genome sizes and DNA G+C contents of strains D2-41T and D3-21 were 4.77–4.88 Mbp and 69.8 mol%, respectively. Both of the isolates shared an average nucleotide identity of 99.4 % and digital DNA–DNA hybridization of 95.2 % to each other, revealing that strains D2-41T and D3-21 belonged to the same species. In the core genome-based phylogenomic tree, both of the isolates were found to be closely associated with members of the genus Tomitella. However, strains D2-41T and D3-21 revealed the highest amino acid identity values (mean 66.5 %, range 66.2–67.0 % with the genus Prescottella of the family Nocardiaceae, followed by the genus Tomitella (mean 64.1 %, range 63.6–64.7 %) of the family Tomitellaceae. Based on the combined data obtained here, the novel isolates belong to a new genus of the new family for which the name Speluncibacter jeojiensis gen. nov. sp. nov. is proposed, with Speluncibacteraceae fam. nov. The type strain is strain D2-41T (=KACC 17930T=DSM 101875T).

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Antrihabitans stalactiti gen. nov., sp. nov., a new member of the family Nocardiaceae isolated from a cave

Cited by 13 publications

References 36 publications

Effects of fish meal replacement with low‐gossypol cottonseed meal on the intestinal barrier of juvenile golden pompano ( Trachinotus ovatus )

Effects of fish meal replacement with low‐gossypol cottonseed meal on the intestinal barrier of juvenile golden pompano ( Trachinotus ovatus )

Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium

Speluncibacter jeojiensis gen. nov. sp. nov., a novel bacterium of the order Mycobacteriales isolated from a cave and a proposal of Speluncibacteraceae fam. nov.

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