Jeotgalibacillus Auranticolor sp. nov., Isolated from Freshwater Collected from Baiyangdian Lake Lake, China

A novel Gram-positive, strictly aerobic, rod-shaped, orange-pigmented bacterial strain, designated R-1-5s-1T, was isolated from Baiyangdian Lake, China. Strain R-1-5s-1T grew at 15-37℃ (optimum 37℃) and pH 7-11 (optimum pH 8) in Luria-Bertani medium. Based on 16S rRNA gene sequence analysis, strain R-1-5s-1T was assigned to the genus Jeotgalibacillus and showed the closest relationships with Jeotgalibacillus salarius ASL-1T (97.69%), Jeotgalibacillus alkaliphilus JC303T (97.29%), Jeotgalibacillus marinus DSM 1297T (97.15%), Jeotgalibacillus campisalis SF-57T (97.01%), and Jeotgalibacillus spp. (≤ 97%). The predominant polar lipids were phosphatidylglycerol and diphosphatidylglycerol; the major cellular fatty acids were iso-C15:0, anteiso-C15:0, iso-C17:0, and anteiso-C17:0; and the major respiratory quinones were MK-7 and MK-8. The peptidoglycan type of the cell wall was A1a linked via L-lysine as the diamino acid. The G+C content was 43.6%, and the draft genome size of strain R-1-5s-1T was 3.4 Mbp. Between strain R-1-5s-1T and the related strain J. salarius ASL-1T, the ANI and dDDH relatedness values were 78.9% and 20.8%, respectively. Phylogenetic, chemotaxonomic, and genotypic analyses revealed that strain R-1-5s-1T is a novel species in the genus Jeotgalibacillus, for which the name Jeotgalibacillus auranticolor sp. nov. is proposed. The type strain is R-1-5s-1T (=CGMCC 1.13567T=KCTC 43038T).

Leucobacter soli sp. nov., from soil amended with humic acid

A Gram-positive, non-spore-forming actinobacterium (IMT-300T) was isolated from soil amended with humic acid in Malvern, AL, USA. This soil has been used for 50+years for the cultivation of earthworms for use as fish bait. Based on 16S rRNA gene sequence similarity studies, strain IMT-300T was shown to belong to the genus Leucobacter and was closely related to the type strain of ‘Leucobacter margaritiformis’ L1T (97.8%). Similarity to all other type strains of Leucobacter species was lower than 97.2 %. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the IMT-300T genome assembly and those of the closest relative Leucobacter type strain were 81.4 and 23.3 % ( Leucobacter chironomi ), respectively. The peptidoglycan of strain IMT-300T contained l-2,4-diaminobutyric acid as the diagnostic diamino acid. In addition, glycine, d- and l-alanine and d-glutamic acid were found. The peptidoglycan type represents a variant of B2δ (B11). The major quinones were menaquinones MK-10 and MK-11. The polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylglycerol and moderate to minor amounts of two unidentified phospholipids, two unidentified glycolipids and an unidentified aminophospholipid. The polyamine pattern contained major amounts of spermidine and spermine. Strain IMT-300T contained the major fatty acids C15 : 0 anteiso, C16 : 0 iso and C17 : 0 anteiso, like other members of the genus Leucobacter . The results of ANI and dDDH analyses and physiological and biochemical tests allowed a genotypic and phenotypic differentiation of strain IMT-300T from the most closely related Leucobacter species. Strain IMT-300T represents a novel Leucobacter species, for which we propose the name Leucobacter soli sp. nov., with the type strain IMT-300T (CIP 111803T=DSM 110505T=CCM 9020T=LMG 31600T).

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 ).

Streptomyces spirodelae sp. nov., isolated from duckweed

A novel actinobacterium, designated strain DW4-2T, was isolated from duckweed (Spirodela sp.) collected from an agricultural pond in Kasetsart University, Bangkok, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Streptomyces . Strain DW4-2T showed the highest 16S rRNA gene sequence similarity values to Streptomyces qinglanensis DSM 42035T (98.5 %), S treptomyces smyrnaeus DSM 42105T (98.4 %) and Streptomyces oryzae S16-07T (98.4 %). Digital DNA–DNA hydridization and average nucleotide identity values between the genome sequences of strain DW4-2T with S. qinglanensis DSM 42035T (29.8 and 87.8 %), S. smyrnaeus DSM 42105T (33.1 and 89.0 %) and S. oryzae S16-07T (33.0 and 88.9 %) were below the thresholds of 70 and 95–96 % for prokaryotic conspecific assignation. Chemotaxonomic data revealed that strain DW4-2T possessed MK-9(H6) and MK-9(H8) as the predominant menaquinones. It contained ll -diaminopimelic acid as the diagnostic diamino acid and glucose, ribose and trace amount of madurose in whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid, an unidentified lipid and an unidentified phospholipid. The predominant cellular fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The genomic DNA size of the strain DW4-2T was 7 310 765 bp with DNA G+C content 71.0 mol%. Genomic analysis of the genome indicated that the strain DW4-2T had the potential to produce bioactive compounds. On the basis of these genotypic and phenotypic data, it is supported that strain DW4-2T represents a novel species of the genus Streptomyces , for which the name Streptomyces spirodelae sp. nov. is proposed. The type strain is strain DW4-2T (=TBRC 13095T=NBRC 114803T).

Agilicoccus flavus gen. nov., sp. nov., a novel member of the family Dermatophilaceae isolated from the Pearl River

A novel actinobacterium, designated strain SYSU M44304T, was isolated from freshwater samples in the Pearl River Estuary. The isolate was Gram-stain-positive, aerobic, coccus-shaped, oxidase-positive and motile. The cell wall contained meso-diaminopimelic acid as its diagnostic diamino acid. The predominant menaquinone was MK-8. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine and seven unidentified phospholipids. The major fatty acids were C16 : 0 and C16 : 1. The G+C content based on genomic DNA was 73.2 mol %. The nearest phylogenetic neighbours to the novel strain were Mobilicoccus pelagius NBRC 104925T and Mobilicoccus caccae YIM 101593T. On the basis of chemotaxonomic and physiological characteristics and phylogenetic analysis, strain SYSU M44304T should be considered to represent a novel species of a new genus in the family Dermatophilaceae , for which we propose the name Agilicoccus flavus gen. nov., sp. nov. The type strain of Agilicoccus flavus is SYSU M44304T (=NBRC 114808T=CGMCC 1.18608T).

Entomomonas asaccharolytica sp. nov., isolated from Acheta domesticus

Strain F2AT, isolated from the cricket Acheta domesticus, was subjected to a polyphasic taxonomic characterization. Cells of the strain were rod-shaped, Gram-stain-negative and catalase- and oxidase-positive. It did not assimilate any carbohydrates. The strain's 16S rRNA gene sequence showed highest similarity to Entomomonas moraniae QZS01T (96.4 %). The next highest similarity values were found to representatives of related genera (<93 %). The genome size of strain F2AT was 3.2 Mbp and the G+C content was 36.4 mol%. Average nucleotide identity values based on blast and MUMmer and average amino acid identity values between strain F2AT and E. moraniae QZS01T were 74.29/74.43, 83.88 and 74.70 %, respectively. The quinone system predominantly contained ubiquinone Q-8. In the polar lipid profile, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid were detected. The polyamine pattern consisted of the major compounds putrescine and spermidine. Major fatty acids were C18 : 1 ω7c and C16 : 0 and the hydroxyl acids were C12 : 0 3-OH, C14 : 0 2-OH and C14 : 0 3-OH. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. Due to its association with the only species of the genus Entomomonas but its distinctness from E. moraniae we here propose the novel species Entomomonas asaccharolytica sp. nov. F2AT (=CCM 9136T=LMG 32211T).

Nocardia huaxiensis sp. nov., an actinomycete isolated from human skin

A novel actinomycete, designated as strain WCH-YHL-001T, was isolated from skin biopsy specimens of a patient at West China Hospital, Chengdu, Sichuan Province, PR China. The cells were Gram-positive, aerobic, heterotrophic and non-motile. They formed an extensive substrate with short aerial mycelia, whose branches fragmented into rod-shaped elements. Growth occurred at 10–40 °C, pH 5.0–12.0 and with NaCl concentrations of 0–4.0 % (w/v). The major cellular fatty acids of strain WCH-YHL-001T were C16 : 0, C18 : 1 ω9c, C18 : 0 10-methyl and summed feature 3. The predominant respiratory quinone was MK-8 (H4ω-cycl). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol mannoside, unknown phospholipids and unidentified glycolipids. The diagnostic diamino acid of peptidoglycan was meso-diaminopimelic acid. The whole-cell sugar pattern consisted of arabinose and glucose. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain WCH-YHL-001T belonged to the genus Nocardia . The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values between strain WCH-YHL-001T and type strains of Nocardia species were lower than the cut-offs (≥95–96 % for ANI and ≥70 % for isDDH) required to define a bacterial species. The genomic DNA G+C content was 67.8 mol%. Phylogenetic, physiological and chemotaxonomic data suggested that strain WCH-YHL-001T represented a novel species of the genus Nocardia , for which the name Nocardia huaxiensis sp. nov. is proposed, with the type strain WCH-YHL-001T (=GDMCC 4.181T=JCM 34475 T=NBRC 114973T).

Actinocatenispora comari sp. nov., an endophytic actinomycete isolated from aerial parts of Comarum salesowianum

A novel actinomycete, designated NUM-2625T, was isolated as an endophytic bacterium in aerial parts of Comarum salesowianum, an endemic species in the Altai, Himalaya mountain chain area, collected from Khasagt Khairkhan Mountain in Mongolia. The 16S rRNA gene sequence of strain NUM-2625T showed the highest similarity to Actinocatenispora thailandica TT2-10T (99.4 %), Actinocatenispora sera KV-744T (99.3 %), and Actinocatenispora rupis CS5-AC17T (97.7 %). Chemotaxonomic properties of strain NUM-2625T were essentially consistent with those of the genus Actinocatenispora, such as the presence of meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan, MK-9(H4) and MK-9(H6) as the major menaquinones, and iso-C16 : 0, iso-C15 : 0, iso-C14 : 0 3-OH, and anteiso-C17 : 0 as the major fatty acids. Meanwhile, digital DNA–DNA hybridization and average nucleotide identity values revealed a low relatedness between strain NUM-2625T and the other type strains of the genus Actinocatenispora . In addition, strain NUM-2625T exhibited several phenotypic properties that could be used to distinguish it from its closest relatives. Based on the results of polyphasic analyses, strain NUM-2625T represents a novel species in the genus Actinocatenispora , for which the name Actinocatenispora comari sp. nov. is proposed. The type strain is NUM-2625T (=NBRC 114660T=TBRC 13496T).

Peptide Dendrimers: From Enzyme Models to Antimicrobials and Transfection Reagents

Aiming at studying cooperativity effects between amino acids in easily accessible protein models, we have explored the chemistry of peptide dendrimers, which we obtain as pure products by solid-phase peptide synthesis using a branching diamino acid such as lysine at every second or third position in a peptide sequence, followed by reverse-phase HPLC purification. This article reviews discoveries driven by combinatorial library synthesis and screening, including enantioselective esterase and aldolase enzyme models, cobalamin binding and peroxidase dendrimers, glycopeptide dendrimer biofilm inhibitors and their X-ray crystal structures as complexes with lectins, antimicrobial peptide dendrimers active against multidrug resistant Gram-negative bacteria, and transfection reagents for siRNA and CRISPR-Cas9 plasmid DNA. Latest developments include cheminformatics and artificial intelligence for exploring the peptide chemical space, and the principle of stereorandomization to understand the role of peptide chirality in activity.

Reaction Mechanism of 2-Amido-2-Aminoacetic Acid-Formation from Amides and 2-Iminoacetic Acid: A DFT-study and Wavefunction Analysis

<p> Based on a study of Wei Zeng et. al.[7], where the synthesis of <i>gem</i>-diamino acid esters from 2-iminoacetic acid esters and amides, with various N- and C-substituents, respectively, is reported, a modeled reaction, where the latter substituents were replaced by H, was simulated by means of DFT. A reasonable reaction mechanism was found for the formation of 2-amido-2-aminoacetic acid from formamide and 2-iminoacetic acid. Moreover, possible side reactions were simulated and discussed.</p>