Lechevalieria
               
            
            nigeriaca sp. nov., isolated from arid soil

Camas, Mustafa; Veyisoglu, Aysel; Tatar, Demet; Saygin, Hayrettin; Çetin, Demet; Sazak, Anil; Güven, Kıymet; Şahi̇n, Nevzat

doi:10.1099/ijs.0.052266-0

Cited by 8 publications

(5 citation statements)

References 32 publications

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“…CC55, isolated from sediments of an oligotrophic environment, has the highest degree of biosynthetic novelty (BiNI=1 008.6) among all the Lentzea strains in our database. Another Lentzea strain with potential of encoding novel BGCs is Lentzea flava (BiNI=777.8), isolated from soil, Acharya Nagarjuna, India [ 55 ], and Lentzea nigeriaca (BiNI=742.5) isolated from desert soil in Nigeria [ 56 ] (Table S1). Regarding the strains of Actinokineospora , based on the BiNI, we found that the strains A. fastidiosa isolated from desert soil samples in Egypt [ 57 ], ' Actinokineospora xionganensis' isolated from lakeside soil samples in China [ 58 ], and Actinokineospora sp.…”

Section: Resultsmentioning

confidence: 99%

Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments

et al. 2023

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Calculations predict that testing of 5 000–10 000 molecules and >1 billion US dollars (£0.8 billion, £1=$1.2) are required for one single drug to come to the market. A solution to this problem is to establish more efficient protocols that reduce the high rate of re-isolation and continuous rediscovery of natural products during early stages of the drug development process. The study of ‘rare actinobacteria’ has emerged as a possible approach for increasing the discovery rate of drug leads from natural sources. Here, we define a simple genomic metric, defined as biosynthetic novelty index (BiNI), that can be used to rapidly rank strains according to the novelty of the subset of encoding biosynthetic clusters. By comparing a subset of high-quality genomes from strains of different taxonomic and ecological backgrounds, we used the BiNI score to support the notion that rare actinobacteria encode more biosynthetic gene cluster (BGC) novelty. In addition, we present the isolation and genomic characterization, focused on specialized metabolites and phenotypic screening, of two isolates belonging to genera Lentzea and Actinokineospora from a highly oligotrophic environment. Our results show that both strains harbour a unique subset of BGCs compared to other members of the genera Lentzea and Actinokineospora . These BGCs are responsible for potent antimicrobial and cytotoxic bioactivity. The experimental data and analysis presented in this study contribute to the knowledge of genome mining analysis in rare actinobacteria and, most importantly, can serve to direct sampling efforts to accelerate early stages of the drug discovery pipeline.

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Section: Resultsmentioning

confidence: 99%

Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments

et al. 2023

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“…The description is as given for Lechevalieria nigeriaca (Camas et al, 2013 ). The type strain is NJ2035 = DSM 45680 = KCTC 29057 = NRRL B-24881 = JCM 31207.…”

Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

et al. 2018

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The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

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“…The strain JB150 was isolated from the Bikaner region of the Thar desert which is known as the tropical desert of Asia that extends to India through Rajasthan and Gujarat. For comparison, seven other complete genomes of desert-actinomycetes: Actinoalloteichus spitiensis RMV-1378 (cold desert, Indian Himalaya) [10], Geodermatophilus africanus DSM 45422 (Sahara desert, Ourba) [11], Jiangella gansuensis DSM 44835 (Gansu desert, China) [12], Lechevalieria deserti DSM 45480 (Atacama desert, Chile) [13], Modestobacter excelsi 1G6 DSM 107535 (Atacama desert, Chile) [14], Streptomyces sp. DH-12 (Thar desert, India) [15], and Streptomyces sp.…”

Section: Streptomyces Have Linear Chromosomes and Their Genome Size Rmentioning

confidence: 99%

“…JB150 is linear with 72.72% of GC content and has a size of 7.32 Mbp (Table 1). For comparison, 7 other complete genomes of the desert actinomycetes namely Actinoalloteichus spitiensis RMV-1378 [10], Geodermatophilus africanus DSM 45422 [11], Jiangella gansuensis DSM 44835 [12], Lechevalieria deserti DSM 45480 [13], Modestobacter excelsi 1G6 DSM 107535 [14], Streptomyces sp. DH-12 [15] and Streptomyces sp.…”

Section: Genome Assembly and Gene Predictionsmentioning

confidence: 99%

“…Supporting Information).An examination of the integral membrane constituents of ABC transporters in JB150 and other 7 analyzed genomes revealed that J. gansuensis contains a very high number of ABC oligopeptides(13) and ABC dipeptide transporter (11) genes (Table S3, Supporting Information). A high number of ABC peptide transporters in the strain could play crucial roles in the nutrient uptake and signaling processes[95][96].…”

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confidence: 99%

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Comparative whole-genome analysis of a Thar desert strainStreptomycessp. JB150 provides deep insights into the encoded parvome and adaptations to desert edaphic system

Harwani

Begani

Lakhani

2021

Preprint

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We sequenced the genome of Streptomyces sp. JB150, isolated from a unique site of the Thar desert in India. Genome mining of the JB150 genome revealed the presence of many interesting secondary metabolic biosynthetic gene clusters (BGCs). The encoded parvome of JB150 includes non-ribosomal peptides, polyketides including β-lactone, butyrolactone, ectoine, lantipeptides, lasso peptides, melanin, resorcinol, siderophores, terpenoids, thiopeptides, and other types of hybrid compounds. Among them, ~30% BGCs displayed a high degree of novelty. The genome of JB150 was enriched for a large assortment of specialized genes coding for the production of many interesting biomolecules comprising compatible solutes, multiple stress-response regulators, transport proteins, protein secretion systems, signaling molecules, chaperones and storage reserves, etc. The presence of diverse members of CAZymes enzyme families, high numbers of riboflavin, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), trehalose and aromatic compounds synthesis genes, putative orthologues to several of the classical fatty acid synthesis components, prototrophy for many essential amino acids exhibit metabolic versatility of JB150 to inhabit in the extreme desert environment. Besides, the genome of JB150 was observed to specifically encode thiazole-oxazole-modified thiazolemicrocin (TOMM) and ectoine. The comparison of the complete genomes of Streptomyces sp. JB150 and seven other actinomycete strains belonging to different desert ecosystems unveiled the presence of many previously undetected, distinctive, biological, and genomic signatures. We propose that these genetic traits endowed by these strains are essential for their adaptation in the highly underprivileged, extreme ecosystem of the Thar desert to cope with multiple abiotic stressors, oligotrophic nutrient conditions and to produce a huge repertoire of diverse secondary metabolites.

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Lechevalieria nigeriaca sp. nov., isolated from arid soil

Cited by 8 publications

References 32 publications

Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments

Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Comparative whole-genome analysis of a Thar desert strainStreptomycessp. JB150 provides deep insights into the encoded parvome and adaptations to desert edaphic system

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