The Draft Whole-Genome Sequence of the Antibiotic Producer Empedobacter haloabium ATCC 31962 Provides Indications for Its Taxonomic Reclassification

Miess, Henrike; Arlt, Patricia; Apel, Alexander Kristian; Weber, Tilmann; Nieselt, Kay; Hanssen, Friederike; Czemmel, Stefan; Nahnsen, Sven; Gross, Harald

doi:10.1128/mra.01120-19

Cited by 4 publications

(5 citation statements)

References 8 publications

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“…ATCC 31962 T was connected to an expired patent (US patent 4,409,210) involving production of the depsipeptide antibiotic empedopeptin while strain YMA4 forms a novel polyyne antifungal compound [34]. Results here confirm Miess et al [33] and the species name should be given as 'Pseudoduganella haloabia' based on the genome data. The taxonomy of this species could be partly resolved using the SeqCode system [35] or fully updated if strain YMA4 or another strain can become a replacement type strain with suitable availability from culture collections.…”

Section: Additional Taxonomic Commentary and Reclassificationssupporting

confidence: 79%

“…Results here confirm Miess et al . [33] and the species name should be given as ‘ Pseudoduganella haloabia ’ based on the genome data. The taxonomy of this species could be partly resolved using the SeqCode system [35] or fully updated if strain YMA4 or another strain can become a replacement type strain with suitable availability from culture collections.…”

Section: Resultsmentioning

confidence: 99%

“…Nomenclatural descriptions are indicated below while phenotypic details are provided in the original description papers. Also located in the Pseudoduganella armeniaca subgroup is the atypically salt-tolerant species '[Empedobacter] haloabium' [32,33], represented by ATCC 31962 T and by another strain YMA4 [34] (Table S1). This species exists in a taxonomic limbo since the original species description lacks a complete etymology and strain ATCC 31962 T is no longer available.…”

Section: Additional Taxonomic Commentary and Reclassificationsmentioning

confidence: 99%

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Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov.

Bowman

2023

International Journal of Systematic and Evolutionary Microbiology

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Based on genome-wide data, Massilia species belonging to the clade including Telluria mixta LMG 11547T should be entirely transferred to the genus Telluria owing to the nomenclatural priority of the type species Telluria mixta . This results in the transfer of 35 Massilia species to the genus Telluria . The presented data also supports the creation of two new genera since peripherally branching Massilia species are distinct from Telluria and other related genera. It is proposed that 13 Massilia species are transferred to Mokoshia gen. nov. with the type species designated Mokoshia eurypsychrophila comb. nov. The species Massilia arenosa is proposed to belong to the genus Zemynaea gen. nov. as the type species Zemynaea arenosa comb. nov. The genome-wide analysis was well supported by canonical ordination analysis of Enzyme Commission (EC) codes annotated from genomes via pannzer2. This new approach was performed to assess the conclusions of the genome-based data and reduce possible ambiguity in the taxonomic decision making. Cross-validation of EC code data compared within canonical plots validated the reclassifications and correctly visualized the expected genus-level taxonomic relationships. The approach is complementary to genome-wide methodology and could be used for testing sequence alignment based data across genetically related genera. In addition to the proposed broader reclassifications, invalidly described species ‘Massilia antibiotica’, ‘Massilia aromaticivorans’, ‘Massilia cellulosiltytica’ and ‘ Massilia humi ’ are described as Telluria antibiotica sp. nov., Telluria aromaticivorans sp. nov., Telluria cellulosilytica sp. nov. and Pseudoduganella humi sp. nov., respectively. In addition, Telluria chitinolytica is reclassified as Pseudoduganella chitinolytica comb. nov. The use of combined genome-wide and annotation descriptors compared using canonical ordination clarifies the taxonomy of Telluria and its sibling genera and provides another way to evaluate complex taxonomic data.

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Section: Additional Taxonomic Commentary and Reclassificationssupporting

confidence: 79%

Section: Resultsmentioning

confidence: 99%

Section: Additional Taxonomic Commentary and Reclassificationsmentioning

confidence: 99%

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Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov.

Bowman

2023

International Journal of Systematic and Evolutionary Microbiology

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“…Interestingly, Massilia sp. YMA4 and M. armeniaca ZMN-3 were close to Empedobacter halobium ATCC 31962 according to BLAST analysis using partial 16S rRNA gene [ 13 ]. E. halobium ATCC 31962 has also been reported to have antimicrobial potential against Gram-positive bacteria [ 14 ].…”

Section: Resultsmentioning

confidence: 99%

“…YMA4 and D. sacchari encode proline and serine, respectively. Surprisingly, we did not find the empedopeptin-related BGC from empedopeptin-producing bacteria E. haloabium ATCC 31962 through MultiGeneBlast analysis [ 13 , 30 ]. Therefore, we speculate that the whole genome of E. haloabium ATCC 31962 might not be well sequenced.…”

Section: Resultsmentioning

confidence: 99%

Integrated Omics Strategy Reveals Cyclic Lipopeptides Empedopeptins from Massilia sp. YMA4 and Their Biosynthetic Pathway

Lin

et al. 2021

Marine Drugs

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Empedopeptins—eight amino acid cyclic lipopeptides—are calcium-dependent antibiotics that act against Gram-positive bacteria such as Staphylococcus aureus by inhibiting cell wall biosynthesis. However, to date, the biosynthetic mechanism of the empedopeptins has not been well identified. Through comparative genomics and metabolomics analysis, we identified empedopeptin and its new analogs from a marine bacterium, Massilia sp. YMA4. We then unveiled the empedopeptin biosynthetic gene cluster. The core nonribosomal peptide gene null-mutant strains (ΔempC, ΔempD, and ΔempE) could not produce empedopeptin, while dioxygenase gene null-mutant strains (ΔempA and ΔempB) produced several unique empedopeptin analogs. However, the antibiotic activity of ΔempA and ΔempB was significantly reduced compared with the wild-type, demonstrating that the hydroxylated amino acid residues of empedopeptin and its analogs are important to their antibiotic activity. Furthermore, we found seven bacterial strains that could produce empedopeptin-like cyclic lipopeptides using a genome mining approach. In summary, this study demonstrated that an integrated omics strategy can facilitate the discovery of potential bioactive metabolites from microbial sources without further isolation and purification.

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Draft Genome Sequences of Six Type Strains of the Genus Massilia

Miess

Frediansyah

Göker

et al. 2020

Microbiol Resour Announc

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The Draft Whole-Genome Sequence of the Antibiotic Producer Empedobacter haloabium ATCC 31962 Provides Indications for Its Taxonomic Reclassification

Cited by 4 publications

References 8 publications

Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov.

Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov.

Integrated Omics Strategy Reveals Cyclic Lipopeptides Empedopeptins from Massilia sp. YMA4 and Their Biosynthetic Pathway

Draft Genome Sequences of Six Type Strains of the Genus Massilia

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