Genome-based Classification of Streptomyces Pinistramenti sp. nov., a Novel Actinomycete Isolated From a Pine Forest Soil in Poland With a Focus on Its Biotechnological and Ecological Properties

A genomic-based polyphasic study was undertaken to establish the taxonomic status and biotechnological and ecological potential of a Streptomyces strain, isolate SF28T, that was recovered from the litter layer in a polish Pinus sylvestris forest. The isolate had morphological characteristics and chemotaxonomic properties consistent with its classification in the genus Streptomyces. It formed long straight chains of spores with smooth surfaces, contained LL-diaminopimelic acid and glucose and ribose in whole-organism hydrolysates, produced major proportions of straight, iso- and anteiso- fatty acids, hexa- and octa-hydrogenated menaquinones with nine isoprenoid units and had a polar lipid pattern composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, glycophospholipids and three uncharacterized components. Phylogenetic trees prepared using 16S rRNA gene and multilocus gene sequences of conserved housekeeping genes showed that the isolate formed a branch that was loosely associated with the type strains of several validly published Streptomyces species. A draft genome generated for the isolate was rich in natural product-biosynthetic gene clusters with the potential to produce new specialised metabolites, notably antibiotics, and stress related genes which provide an insight into how they may have adapted to the harsh conditions that prevail in acidic forest soils. A phylogenomic tree based on the genomes of the isolate and its phylogenetic neighbours confirmed that it formed a distinct lineage well separated from its closest evolutionary relatives. The isolate shared low average nucleotide index and digital DNA:DNA hybridization values with its phylogenomic neighbours and was also distinguished from them using a combination of cultural and micromorphological properties. Given this wealth of taxonomic data it is proposed that isolate SF28T (=DSM 113360T=PCM 3163T) be classified in the genus Streptomyces as Streptomyces pinistramenti sp. nov. The isolate showed pronounced antimicrobial activity, especially against fungal plant pathogens.

Gottfriedia Endophyticus sp. nov., a Novel Indole-Acetic Acid Producing Bacterium Isolated From The Roots of Rice Plant

A Gram-stain-positive, aerobic, motile and rod-shaped bacterium, designated RG28T, was isolated from the roots of rice plant collected from paddy fields in Goyang, South Korea. Cells of the strain were oxidase-negative but catalase-positive. Strain RG28T was found to grow at 10–50°C (optimum, 25–30°C), pH 5.0–10.0 (optimum, pH 7.0) and in 1.0–5.0 % (w/v) NaCl (optimum, 0%). The cell-wall peptidoglycan contained meso-diaminopimelic acid and the predominant menaquinones were MK-7 and MK-6.The predominant cellular fatty acids were C16:0, iso-C15:0 and anteiso-C15:0. The major polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, four unidentified aminophosphoglycolipids, four unidentified aminophospholipids, two unidentified glycolipids, one unidentified aminoglycolipid and four unidentified lipids. The genomic DNA G+C content was 33.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was closely related to Gottfriedia acidiceleris CBD 119T (98.6%), Gottfriedia solisilvae LMG 18422T (98.5 %) and Gottfriedia luciferensis LMG 18422T (98.4 %). The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values between strain RG28T and type strains of Gottfriedia species were lower than the cut-offs (≥95–96 % for ANI and ≥70 % for isDDH) required to define a bacterial species. Meanwhile, the strain has the ability to produce indole-acetic acid (40.5 µg/mL). Phylogenetic, physiological and chemotaxonomic data suggested that strain RG28T represented a novel species of the genus Gottfriedia, for which the name Gottfriedia endophyticus sp. nov. is proposed, with the type strain RG28T (=KCTC 43327T=TBRC 15151T).Repositories: The draft genome and 16S rRNA gene sequences of strain RG28T have been deposited in GenBank/EMBL/DDBJ under accession numbers JAGIYQ000000000 and MW386408 respectively.

Metabolic Processing of Selenium-based Bioisostere of meso-diaminopimelic Acid in Live Bacteria

The bacterial cell wall supports cell shape and prevents lysis due to internal turgor pressure. A primary component of all known bacterial cell walls is the peptidoglycan (PG) layer, which is comprised of repeating units of sugars connected to short and unusual peptides. The various steps within PG biosynthesis are often the target of antibiotics as they are essential for cellular growth and survival. Synthetic mimics of PG have proven to be indispensable tools to study bacterial cell growth and remodeling. Yet, a common component of PG, meso-diaminopimelic acid (m-DAP) at the third position of the stem peptide, remains challenging to build synthetically and is not commercially available. Here, we describe the synthesis and metabolic processing of a selenium-based bioisostere of a m-DAP analogue, selenolanthionine. We show that selenolanthionine is installed within the PG of live bacteria by the native cell wall crosslinking machinery in several mycobacteria species. We envision that this probe will supplement the current methods available for investigating PG crosslinking in m-DAP containing organisms.

Micromonospora humida sp. nov., exhibiting antimicrobial potential, isolated from riverside soil

An actinobacterial strain designated MMS20-R1-14T was isolated from a riverside soil sample. Colonies on agar plates were orange to strong orange brown in colour, which later became black. The cells grew at 10–40 °C (optimum, 37 °C), pH 5.0–11.0 (pH 8.0) and in the presence of 0–4 % NaCl (1 %). The 16S rRNA gene sequence of strain MMS20-R1-14T showed highest similarities to Micromonospora wenchangensis CCTCC AA 2012002T (99.51 %) and Micromonospora rifamycinica AM105T (99.37 %). The orthoANI values between strain MMS20-R1-14T and the two type strains were 95.72 and 90.99 %, and the digital DNA–DNA hybridization values were 63.6 and 40.8 %, respectively, thus confirming the distinction of strain MMS20-R1-14T from its mostly related species. The DNA G+C content of strain MMS20-R1-14T was 72.9 mol%. The strain contained meso-diaminopimelic acid as the major cell-wall amino acid, and the characteristic whole-cell sugars were arabinose, xylose, glucose, ribose and rhamnose. The main cellular fatty acids were C18 : 1 ω9c, iso-C15 : 0 and iso-C16 : 0, the diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the predominant menaquinones were MK-10(H4) and MK-10(H6), all of which were consistent with those of Micromonospora . Strain MMS20-R1-14T showed antimicrobial activity against a range of bacterial and yeast species. The genome of the strain was found to contain 33 potential biosynthetic gene clusters for secondary metabolites, thus showing a high potential as a producer of bioactive compounds. On the basis of these phenotypic, genotypic and chemotaxonomic data, strain MMS20-R1-14T merits recognition as representing a novel species of the genus Micromonospora , for which the name Micromonospora humida sp. nov. (type strain=MMS20 R1-14T=KCTC 49541T=JCM 34494T) is proposed.

Paenibacillus tianjinensis sp. nov., isolated from corridor air

A Gram-stain-positive, facultatively anaerobic, non-motile, endospore-forming and rod-shaped bacterium, occurring singly or in pairs, designated TB2019T, was isolated from environmental monitoring samples of corridor air collected at the Tianjin Institute for Drug Control, Tianjin Province (PR China). The isolate was able to grow at 15–40 °C (optimum growth at 37 °C), pH 6.0–8.0 (pH 7.0) and in the presence of 0–2% (w/v) NaCl (0% NaCl). Comparison of 16S rRNA gene sequences indicated that TB2019T was most closely related to Paenibacillus typhae CGMCC 1.11012T (98.63%), Paenibacillus albidus Q4-3T (98.19%), Paenibacillus borealis DSM 13188T (97.55%), Paenibacillus helianthi P26ET (97.33%) and Paenibacillus odorifer DSM 15391T (97.19%). The digital DNA–DNA hybridization and the average nucleotide identity values between TB2019T and the five type strains mentioned above ranged from 20.7 to 25.0% and 75.2 to 81.3%, respectively, and the genomic DNA G+C content was 49.52 mol%. The diagnostic cell-wall sugar was ribose, and the diagnostic amino acid was meso-diaminopimelic acid. The polar lipids of TB2019T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. MK-7 was the predominant menaquinone, and anteiso-C15:0 (30.6%) was the major fatty acid. Based on the polyphasic taxonomic data, strain TB2019T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus tianjinensis sp. nov. is proposed. The type strain is TB2019T (=CICC 25065T=JCM 34610T).

Brevibacillus marinus sp. nov., a thermophilic bacterium isolated from deep sea sediment in the South China Sea

A novel thermophilic bacterium, designated SCSIO 07484T, was isolated from marine sediment sampled in the South China Sea. Growth occurred at 30–60 °C, pH 6.0–8.0 and in the presence of 0–3 % (w/v) NaCl. Cells of strain SCSIO 07484T were rod-shaped and flagellum-forming. No soluble pigment was observed. The phylogenetic analysis of the 16S rRNA gene sequences indicated that SCSIO 07484T belonged to the family Paenibacillaceae and clustered with members of the genus Brevibacillus in the phylogenetic trees with less than 96.2 % similarities. The cell wall contained meso-diaminopimelic acid. Whole-cell hydrolysates contained arabinose, glucose and ribose. The predominant menaquinone was MK-7. Major fatty acids were iso-C16 : 0, iso-C15 : 0, C16 : 0 and iso-C14 : 0. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine were its diagnostic polar lipids. The whole genome size of strain SCSIO 07484T was 4 079 826 bp with a DNA G+C content of 56.2 mol%, including one circular chromosome of 3 978392 bp and one plasmid of 101434 bp. Based on the polyphasic analysis of strain SCSIO 07484T, it is considered to represent a novel species of the genus Brevibacillus , for which the name Brevibacillus marinus sp. nov. is proposed with the type strain SCSIO 07484T (=DSM 106769T=CGMCC 1.15814T).

Hoyosella lacisalsi sp. nov., a halotolerant actinobacterium isolated from the Lake Gudzhirganskoe

A Gram-stain-positive, aerobic, non-motile, non-spore-forming and coccus-shaped strain, designated strain G463T, was isolated from the rhizosphere soil of Salicornia europaea L. collected from Lake Gudzhirganskoe in Siberia. Based on 16S rRNA gene phylogeny, strain G463T belonged to the genus Hoyosella , with the highest 16S rRNA gene sequence similarity to Hoyosella altamirensis DSM 45258T (96.1%). The major fatty acids were C17:1 ω8c, C16:0, C15 : 0 and C17:0. The strain contained meso-diaminopimelic acid as the cell-wall diagnostic diamino acid and arabinose, galactose and ribose as the whole-cell sugars. MK-8 and MK-7 were the predominant menaquinones. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, one unidentified phosphoglycolipid, two unidentified glycolipids and several unidentified lipids. Acetyl was the muramyl residue. Mycolic acids (C28–C34) were present. The G+C content of the genomic DNA was 68.3 mol%. Based on its phylogenetic, phenotypic and chemotaxonomic features, strain G463T was considered to represent a novel species of the genus Hoyosella , for which the name Hoyosella lacisalsi sp. nov. is proposed. The type strain is G463T (=JCM 33650T=CGMCC 1.17230T).

Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria isolated from faeces of a patient with Crohn's disease

Cultivation and isolation of gut bacteria are necessary for understanding their role in the intestinal ecosystem. We isolated a novel bacterium, designated strain BG01T, from the faeces of a patient with Crohn's disease. Strain BG01T was a strictly anaerobic, rod-shaped, Gram-variable and endospore-forming bacterium. Strain BG01T possessed C12 : 0, C18 : 0 dimethyl aldehyde (DMA) and C18 : 1 ω9c DMA as predominant cellular fatty acids and meso-diaminopimelic acid as a diagnostic diamino acid. Strain BG01T grew at 15–45 °C (optimum, 37 °C), with 0–4 % (w/v) NaCl (optimum, 0–1 %), at pH 6–10 (optimum, pH 7) and was resistant to bile salt, but not to ampicillin, metronidazole, vancomycin and cefoperazone. Butyrate, propionate, oxalacetate and fumarate were produced as fermentation end products from Gifu anaerobic medium broth. Strain BG01T showed 97.7 % 16S rRNA gene sequence similarity, and 92.0 and 48.5 % of average nucleotide identity and digital DNA–DNA hybridization values, respectively, with Anaerostipes caccae KCTC 15019T. Genomic analysis indicated that strain BG01T had a butyrate-producing pathway. The genomic G+C content of the strain was 43.5 mol%. Results of the phenotypic, phylogenetic and genotypic analyses indicated that strain BG01T represents a novel butyrate-producing species of the genus Anaerostipes , for which the name Anaerostipes hominis sp. nov. is proposed. The type strain is BG01T (=KCTC 15617T=JCM 32275T).

Actinomadura violacea sp. nov., a madurastatin A1-producing strain isolated from lichen in Thailand

An actinomycete strain, LCR2-06T, isolated from a lichen sample on rock collected from Chiang Rai Province (Pong Phra Bat Waterfall), Thailand, was characterized using a polyphasic approach. The strain grew at 25–45 °C, pH 6–11 and on International Streptomyces Project 2 agar plate with 5 % (w/v) NaCl. It contained meso-diaminopimelic acid as the diamino acid in whole-cell hydrolysates. Rhamnose, ribose, xylose, madurose, glucose and galactose were detected as whole-cell sugar hydrolysates. Mycolic acids were absent. The N-acyl type of muramic acid was acetyl. The strain contained C16 : 0, TBSA 10-methyl C18 : 0 and 2-hydroxy C16 : 0 as the predominant fatty acids and MK-9(H6), MK-9(H4) and MK-9(H8) as the major menaquinones. The major polar lipids were diphosphatidylglycerol, phosphatidylinositol and unidentified phospholipid. The draft genome of strain LCR2-06T was closely related to Actinomadura barringtoniae TBRC 7225T (99.2 %), Actinomadura nitritigenes NBRC 15918T (98.8 %), Actinomadura montaniterrae TISTR 2400T (98.5 %) and Actinomadura physcomitrii JCM 33455T (97.9 %). The draft genome of LCR2-06T was 11.1 Mb with 10 588 coding sequences with an average G+C content of 72.7 mol%. Results of genomic analysis revealed that the ANIb and ANIm values between strain LCR2-06T and A. montaniterrae TISTR 2400T were 90.0 and 92.0 %, respectively. The digital DNA–DNA hybridization value was 43.9 % in comparison with the draft genome of A. montaniterrae TISTR 2400T. The strain produced an antibacterial compound active against Bacillus subtilis ATCC 6633 and Kocuria rhizophila ATCC 9341. The results of taxonomic analysis suggested that strain LCR2-06T represented a novel species of the genus Actinomadura for which the name Actinomadura violacea sp. nov. is proposed. The type strain is LCR2-06T (=JCM 33065T=KCTC 49547T=NBRC 114810T=LMG 32136T=TISTR 2935T).

Streptomyces Pimoensis sp. nov., Isolated From the Taklimakan Desert in Xinjiang, China

A novel Streptomyces strain, designated TRM 75549T, was separated from a sample of sand in Pimo, Taklimakan desert, Xinjiang, North-West China. Phylogenetic analyses of the 16S rRNA gene sequences placed strain TRM75549T within the genus Streptomyces with the highest similarities to Streptomyces flavoviridis NBRC 12772T (98.76%). The whole-genome average nucleotide identity (ANI) value between strain TRM75549T and S. flavoviridis NBRC 12772T is 88.20%. Digital DNA-DNA hybridization (dDDH) value between strain TRM75549T and S. flavoviridis NBRC 12772T is 44.10%. They are well below the recommended 95-96% and 70% cut-off points for designated species respectively. A multi-locus sequence analysis of five house-keeping genes (atpD, gyrB, recA, rpoB and trpB) and phylogenomic analysis also illustrated that strain TRM75549T should be assigned to the genus Streptomyces. Strain TRM75549T contained MK-9 (H6) and MK-9 (H8) as predominant menaquinones. The diagnostic diamino acid of cell walls was identified as LL-diaminopimelic acid and Meso-diaminopimelic. The whole-cell sugar pattern of strain TRM 75549T consisted of mannose and glucose. The major fatty acids (>5%) were iso-C14:0, iso-C15:0, anteiso-C15:0, iso-C16:1H, iso-C16:0. The polar lipids were diphosphatidylglycerol, lysophosphatidylglycerol, phosphatidylethanolamine, phospholipids, phosphatidylglycerol, phosphatidylinositol, phosphatiylinositol mannosides and unidentified phospholipids. Strain TRM75549T could be differentiated from S. flavoviridis NBRC 12772T, based on physiological and biochemical characteristics. Based on the data from this polyphasic study presented above, strain TRM75549T is represent ative of a novel species of the genus Streptomyces, for which the name Streptomyces pimoensis sp. nov. is proposed. The type strain is TRM75549T (=CCTCC AA 2020054T=LMG 32221T ).