Mining Indonesian Microbial Biodiversity for Novel Natural Compounds by a Combined Genome Mining and Molecular Networking Approach.

Indonesia is one of the most biodiverse countries in the world and a promising resource for novel natural compound producers. Actinomycetes produce about two thirds of all clinically used antibiotics. Thus, exploiting Indonesia's microbial diversity for actinomycetes may lead to the discovery of novel antibiotics. A total of 422 actinomycete strains were isolated from three different unique areas in Indonesia and tested for their antimicrobial activity. Nine potent bioactive strains were prioritized for further drug screening approaches. The nine strains were cultivated in different solid and liquid media, and a combination of genome mining analysis and mass spectrometry (MS)-based molecular networking was employed to identify potential novel compounds. By correlating secondary metabolite gene cluster data with MS-based molecular networking results, we identified several gene cluster-encoded biosynthetic products from the nine strains, including naphthyridinomycin, amicetin, echinomycin, tirandamycin, antimycin, and desferrioxamine B. Moreover, 16 putative ion clusters and numerous gene clusters were detected that could not be associated with any known compound, indicating that the strains can produce novel secondary metabolites. Our results demonstrate that sampling of actinomycetes from unique and biodiversity-rich habitats, such as Indonesia, along with a combination of gene cluster networking and molecular networking approaches, accelerates natural product identification.

Xylanase and feruloyl esterase from actinomycetes cultures could enhance sugarcane bagasse hydrolysis in the production of fermentable sugars.

The addition of enzymes that are capable of degrading hemicellulose has a potential to reduce the need for commercial enzymes during biomass hydrolysis in the production of fermentable sugars. In this study, a high xylanase producing actinomycete strain (Kitasatospora sp. ID06-480) and the first ethyl ferulate producing actinomycete strain (Nonomuraea sp. ID06-094) were selected from 797 rare actinomycetes, respectively, which were isolated in Indonesia. The addition (30%, v/v) of a crude enzyme supernatant from the selected strains in sugarcane bagasse hydrolysis with low-level loading (1 FPU/g-biomass) of Cellic® CTec2 enhanced both the released amount of glucose and reducing sugars. When the reaction with Ctec2 was combined with crude enzymes containing either xylanase or feruloyl esterase, high conversion yield of glucose from cellulose at 60.5% could be achieved after 72 h-saccharification.

Cellulosimicrobium marinum sp. nov., an actinobacterium isolated from sea sediment.

A novel Gram stain positive actinobacterium, designated RS-7-4(T), was isolated from a sea sediment sample collected in Indonesia, and its taxonomic position was investigated using a polyphasic approach. Strain RS-7-4(T) was observed to form vegetative hyphae in the early phase of growth, but the hyphae eventually fragmented into short rods to coccoid cells. Growth occurred at 15-37 °C, pH 6.0-11.0 and in the presence of 0-7 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain RS-7-4(T) was closely related to the members of the genus Cellulosimicrobium, with a similarity range of 98.08-99.10 %. The peptidoglycan type of strain RS-7-4(T) was found to be A4α L-Lys-L-Thr-D-Asp. The predominant menaquinone was MK-9(H4), and the major fatty acids were anteiso-C15:0, iso-C15:0 and anteiso-C17:0. The DNA G+C content was 75.6 mol%. These chemotaxonomic features corresponded to those of the genus Cellulosimicrobium. Meanwhile, the results of DNA-DNA hybridization, and physiological and biochemical tests revealed that strain RS-7-4(T) was different from the recognized species of the genus Cellulosimicrobium. Therefore, strain RS-7-4(T) represents a novel species of the genus Cellulosimicrobium, for which the name Cellulosimicrobium marinum sp. nov. is proposed. The type strain is RS-7-4(T) (=NBRC 110994(T) =InaCC A726(T)).

Halobium palmae gen. nov., sp. nov., an extremely halophilic archaeon isolated from a solar saltern.

A novel and extremely halophilic archaeon, designated strain 2a_47_2T, was isolated from a solar saltern sample collected in Indonesia. Cells of the strain were Gram-stain-negative, non-motile and pleomorphic and formed orange-red pigmented colonies. Strain 2a_47_2T grew at 20-48 °C (optimum 38-41 °C), pH 6.0-8.5 (optimum pH 7.5), >1.7 M NaCl (optimum 2.6 M) and <0.5 M MgCl2 (optimum 0.3 M). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two phospholipids and sulfated diglycosyl diether. The cells mainly contained menaquinone-8. The G+C content in the genomic DNA of the strain was 67.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 2a_47_2T represents a member of the family Halorubraceae and is different from any other known halophilic archaea. This finding was also demonstrated by phylogenetic analyses based on deduced RpoB' amino acid sequences. Collectively, these results show that strain 2a_47_2T represents a novel genus and species in the family Halorubraceae, and the name Halobium palmae gen. nov., sp. nov. is proposed. The type strain is 2a_47_2T (=NBRC 111368T=InaCC Ar34T).

Haloarchaeobius baliensis sp. nov., isolated from a solar saltern.

A novel halophilic archaeon, designated strain 2b_61_3T, was isolated from a solar saltern in Indonesia. Cells of the strain were Gram-stain-negative, motile, pleomorphic rods that formed orange-red-pigmented colonies on solid medium. The isolate grew optimally at 42-44 °C, pH 6.5-7.0, and with 2.6 M NaCl, and MgCl2 was required for growth. Strain 2b_61_3T had two differential 16S rRNA genes (rrnA and rrnB), and phylogenetic analysis revealed that the strain belonged to the genus Haloarchaeobius. The rrnA and rrnB sequence similarities between strain 2b_61_3T and species of the genus Haloarchaeobius were 98.4-99.2 % and 98.5-98.8 %, respectively. The findings from the 16S rRNA gene analysis were supported by sequence analysis of rpoB', the B' subunit of RNA polymerase. On the basis of the phenotypic characteristics and phylogenetic analyses, as well as DNA-DNA hybridization experiments with Haloarchaeobius iranensis NBRC 110930T, strain 2b_61_3T represents a novel species of the genus Haloarchaeobius, for which the name Haloarchaeobius baliensis sp. nov. is proposed. The type strain is 2b_61_3T ( = NBRC 110517T = InaCC Ar2T).

Kocuria pelophila sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove.

A novel spherical actinobacterium, designated RS-2-3T, was isolated from the rhizosphere of a mangrove growing on Rambut Island, Indonesia, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain RS-2-3T was related to the members of the genus Kocuria. The highest 16S rRNA gene sequence similarity value was observed with Kocuria marina KMM 3905T (97.0 %). The peptidoglycan type of strain RS-2-3T was found to be A3α with an interpeptide bridge comprising l-Ala4-5. The predominant menaquinone was MK-7(H2) and the major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content was 71.8 mol%. These characteristics were consistent with those of members of the genus Kocuria. Meanwhile, physiological and biochemical characteristics revealed that strain RS-2-3T differed from the species of the genus Kocuria with validly published names. Therefore, strain RS-2-3T represents a novel species of the genus Kocuria, for which the name Kocuria pelophila sp. nov. is proposed. The type strain is RS-2-3T (=NBRC 110990T=InaCC A704T).

Actinoplanes tropicalis sp. nov. and Actinoplanes cibodasensis sp. nov., isolated from leaf litter.

Two actinomycete strains, designated LIPI11-2-Ac034T and LIPI11-2-Ac042T, were isolated from leaf litter collected from Cibodas Botanical Garden, West Java, Indonesia. Phylogenetic analysis based on 16S rRNA gene sequences suggested that both isolates belong to the genus Actinoplanes. These isolates were closely related to Actinoplanes ferrugineus and Actinoplanes durhamensis with similarity values of 98.2 % and 97.7 % respectively, for strain LIPI11-2-Ac034T, and 99.0 % and 97.4-97.7 % respectively for strain LIPI11-2-Ac042T. Both isolates grew well on ISP 7 medium with brown soluble pigment production. Spores were motile and sporangia were irregular. The isolates contained meso-diaminopimelic acid in cell-wall hydrolysates, and mannose, glucose and galactose in whole-cell hydrolysates. The predominant menaquinone of strain LIPI11-2-Ac034T was MK-9(H4) while that of strain LIPI11-2-Ac042T was MK-9(H6). The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C15 : 0 for strain LIPI11-2-Ac034T, and iso-C16 : 0, anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 for strain LIPI11-2-Ac042T. Phosphatidylethanolamine was detected as the diagnostic polar lipid. The DNA G+C contents of strains LIPI11-2-Ac034T and LIPI11-2-Ac042T were 71.5 and 70.7 mol%, respectively. Based on the differential phenotypic characteristics and the results of DNA-DNA hybridization and phylogenetic analysis, it is proposed that strains LIPI11-2-Ac034T and LIPI11-2-Ac042T represent two novel species of the genus Actinoplanes, for which the names Actinoplanes tropicalis sp. nov. (type strain LIPI11-2-Ac034T = InaCC A459T = NBRC 110973T) and Actinoplanes cibodasensis sp. nov. (type strain LIPI11-2-Ac042T = InaCC A458T = NBRC 110974T) are proposed.

Cryptosporangium cibodasense sp. nov., isolated from leaf litter in Indonesia.

A novel actinomycete strain, designated LIPI11-2-Ac046T, was isolated from a leaf litter sample obtained from Cibodas Botanical Garden, West Java, Indonesia, using the rehydration and centrifugation method. The taxonomic status of this organism was established using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain LIPI11-2-Ac046T had the closest sequence similarities with members of the genus Cryptosporangium (97.99-98.90 %). The strain grew well on ISP 4 and ISP 5 media and formed sporangia. Spores of this strain were motile. The strain grew in the presence of 0-2 % (w/v) NaCl and the temperature range of 15-28 8C. The cell-wall hydrolysate contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell hydrolysate contained mannose, glucose, galactose, ribose and xylose, together with one unidentified O-methyl-pentose. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8), and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were C18 : 1ω9c, iso-C16 : 0, C16 : 0 andC17 : 1ω9c. These phenotypic characteristics corresponded to those of the genus Cryptosporangium. Meanwhile, the results of DNA-DNA hybridization as well as physiological and biochemical analyses distinguished strain LIPI11-2-Ac046T from known members of the genus Cryptosporangium. On the basis of these data, it is proposed that strain LIPI11-2-Ac046T represents a novel species of the genus Cryptosporangium, with the name Cryptosporangium cibodasense sp. nov. The type strain is LIPI11-2-Ac046T (=InaCC A457T=NBRC 110976T).

Serinibacter tropicus sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove, and emended description of the genus Serinibacter.

A novel Gram-stain-positive actinobacterium, designated PS-14-7(T), was isolated from the rhizosphere of a mangrove on Pramuka Island, Indonesia, and its taxonomic position was investigated using a polyphasic approach. The peptidoglycan type of strain PS-14-7(T) was A4α and lysine was the diagnostic diamino acid of the peptidoglycan. The predominant menaquinone was MK-8(H4) and the major fatty acids were anteiso-C(15 : 0), C(16 : 0) and iso-C(16 : 0). The DNA G+C content was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain PS-14-7(T) was closely related to Serinibacter salmoneus Kis4-28(T) (99.6%). However, DNA-DNA hybridization and phenotypic characteristics revealed that strain PS-14-7(T) differed from Serinibacter salmoneus . Therefore, strain PS-14-7(T) represents a novel species of the genus Serinibacter , for which the name Serinibacter tropicus sp. nov. is proposed. The type strain is PS-14-7(T) ( = NBRC 110108(T) = InaCC A 515(T)). An emended description of the genus Serinibacter is also proposed.

Tropicihabitans flavus gen. nov., sp. nov., a new member of the family Cellulomonadaceae.

Two novel Gram-stain positive actinobacteria, designated PS-14-16(T) and RS-7-1, were isolated from the rhizosphere of a mangrove and sea sediment, respectively, and their taxonomic positions were investigated by a polyphasic approach. Both strains were observed to form vegetative hyphae in the early phase of growth but the hyphae eventually fragment into short rods to coccoid cells. The peptidoglycan type of both strains was found to be A4α. Their predominant menaquinone was identified as MK-9(H4) and the major fatty acid as anteiso-C(15:0). The DNA G+C content was determined to be 68.4-68.5 mol%. 16S rRNA gene sequencing revealed that strains PS-14-16(T) and RS-7-1 were related to members of the family Cellulomonadaceae. Their nearest phylogenetic neighbour was found to be Sediminihabitans luteus, which is currently the only species of the genus Sediminihabitans, with a similarity of 97.94%. However, strains PS-14-16(T) and RS-7-1 were distinguishable from the members of the genus Sediminihabitans and the other genera within the family Cellulomonadaceae in terms of chemotaxonomic characteristics and phylogenetic relationship. The results of DNA-DNA hybridization experiments indicated that strains PS-14-16(T) and RS-7-1 belong to the same species. Strains PS-14-16(T) and RS-7-1 are concluded to represent a novel genus and species of the family Cellulomonadaceae, for which the name Tropicihabitans flavus gen. nov., sp. nov. is proposed. The type strain of T. flavus is PS-14-16(T) (=NBRC 110109(T) = IanCC A 516(T)). [corrected].

Xylanopectinolytic enzymes by marine actinomycetes from sediments of Sarena Kecil, North Sulawesi: high potential to produce galacturonic acid and xylooligosaccharides from raw biomass.

BACKGROUND: Actinomycetes isolated from marine habitats are known to have the potential for novel enzymes that are beneficial in the industry. In-depth knowledge is necessary given the variety of this bacterial group in Indonesia and the lack of published research. Actinomycetes isolates (BLH 5-14) obtained from marine sediments of Sarena Kecil, Bitung, North Sulawesi, Indonesia, showed an ability to produce pectinase and xylanase that have equal or even higher potential for pectic-oligosaccharides (POS) and xylooligosaccharides (XOS) production from raw biomass than from commercial substrates. This study's objective was to characterize both enzymes to learn more for future research and development. RESULTS: Pectinase had the highest activity on the 6th day (1.44±0.08 U/mL) at the optimum pH of 8.0 and optimum temperature of 50 °C. Xylanase had the maximum activity on the 6th day (4.33±0.03 U/mL) at optimum pH 6.0 and optimum temperature 60 °C. Hydrolysis and thin layer chromatography also showed that pectinase was able to produce monosaccharides such as galacturonic acid (P1), and xylanase was able to yield oligosaccharides such as xylotriose (X3), xylotetraose (X4), and xylopentaose (X5). BLH 5-14 identified as the genus Streptomyces based on the 16S rDNA sequences and the closely related species Streptomyces tendae (99,78%). CONCLUSIONS: In the eco-friendly paper bleaching industry, Streptomyces tendae has demonstrated the potential to create enzymes with properties that can be active in a wide range of pH levels. The oligosaccharides have the potential as prebiotics or dietary supplements with anti-cancer properties. Further research is needed to optimize the production, purification, and development of the application of pectinase and xylanase enzymes produced by Actinomycetes isolates.

Chemical Composition and Sensory Profiles of Fermented Cocoa Beans Obtained from Various Regions of Indonesia.

The chemical composition and sensory profile of cocoa beans are essential factors determining the quality of cocoa-based products. In this study, cocoa bean samples were collected from various regions of Indonesia, including Aceh, Banten, Bali, East Java, West Sumatra, West Sulawesi, East Kalimantan, and Yogyakarta. The cocoa beans were fermented and sun-dried according to the producers' protocols and local practices. The sensory profile, fat content, total phenolic content, and the composition of sugars, organic acids, and amino acids of the cocoa bean samples were analyzed. The results revealed that the chemical composition and sensory profiles of the samples were diverse. The sensory profiles of cocoa liquor samples were described by low intensities of cocoa notes with the occurrence of fruity, floral, spicy, and sweet notes. The concentration of acetic acid, lactic acid, and some amino acids (glutamic acid, proline, and methionine) was associated with fresh fruit, browned fruit, and roasted note of the cocoa liquor, respectively. The variation in the environmental conditions and postharvest practices contributed to the diversity of cocoa beans' chemical and sensory characteristics.

Expression of Codon-Optimized Gene Encoding Murine Moloney Leukemia Virus Reverse Transcriptase in Escherichia coli.

Moloney murine leukemia virus reverse transcriptase (MMLV-RT) is the most frequently used enzyme in molecular biology for cDNA synthesis. To date, reverse transcription coupled with Polymerase Chain Reaction, known as RT-PCR, has been popular as an excellent approach for the detection of SARS-CoV-2 during the COVID-19 pandemic. In this study, we aimed to improve the enzymatic production and performance of MMLV-RT by optimizing both codon and culture conditions in E. coli expression system. By applying the optimized codon and culture conditions, the enzyme was successfully overexpressed and increased at high level based on the result of SDS-PAGE and Western blotting. The total amount of MMLV-RT has improved 85-fold from 0.002 g L-1 to 0.175 g L-1 of culture. One-step purification by nickel affinity chromatography has been performed to generate the purified enzyme for further analysis of qualitative and quantitative RT activity. Overall, our investigation provides useful strategies to enhance the recombinant enzyme of MMLV-RT in both production and performance. More importantly, the enzyme has shown promising activity to be used for RT-PCR assay.

Harnessing originally robust yeast for rapid lactic acid bioproduction without detoxification and neutralization.

Acidic and chemical inhibitor stresses undermine efficient lactic acid bioproduction from lignocellulosic feedstock. Requisite coping treatments, such as detoxification and neutralizing agent supplementation, can be eliminated if a strong microbial host is employed in the process. Here, we exploited an originally robust yeast, Saccharomyces cerevisiae BTCC3, as a production platform for lactic acid. This wild-type strain exhibited a rapid cell growth in the presence of various chemical inhibitors compared to laboratory and industrial strains, namely BY4741 and Ethanol-red. Pathway engineering was performed on the strain by introducing an exogenous LDH gene after disrupting the PDC1 and PDC5 genes. Facilitated by this engineered strain, high cell density cultivation could generate lactic acid with productivity at 4.80 and 3.68 g L-1 h-1 under semi-neutralized and non-neutralized conditions, respectively. Those values were relatively higher compared to other studies. Cultivation using real lignocellulosic hydrolysate was conducted to assess the performance of this engineered strain. Non-neutralized fermentation using non-detoxified hydrolysate from sugarcane bagasse as a medium could produce lactic acid at 1.69 g L-1 h-1, which was competitive to the results from other reports that still included detoxification and neutralization steps in their experiments. This strategy could make the overall lactic acid bioproduction process simpler, greener, and more cost-efficient.

The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia.

Background: Indonesia is one of the Southeast Asian countries with high case numbers of COVID-19 with up to 4.2 million confirmed cases by 29 October 2021. Understanding the genome of SARS-CoV-2 is crucial for delivering public health intervention as certain variants may have different attributes that can potentially affect their transmissibility, as well as the performance of diagnostics, vaccines, and therapeutics. Objectives: We aimed to investigate the dynamics of circulating SARS-CoV-2 variants over a 15-month period in Bogor and its surrounding areas in correlation with the first and second wave of COVID-19 in Indonesia. Methods: Nasopharyngeal and oropharyngeal swab samples collected from suspected patients from Bogor, Jakarta and Tangerang were confirmed for SARS-CoV-2 infection with RT-PCR. RNA samples of those confirmed patients were subjected to whole genome sequencing using the ARTIC Network protocol and sequencer platform from Oxford Nanopore Technologies (ONT). Results: We successfully identified 16 lineages and six clades out of 202 samples (male n = 116, female n = 86). Genome analysis revealed that Indonesian lineage B.1.466.2 dominated during the first wave (n = 48, 23.8%) while Delta variants (AY.23, AY.24, AY.39, AY.42, AY.43 dan AY.79) were dominant during the second wave (n = 53, 26.2%) following the highest number of confirmed cases in Indonesia. In the spike protein gene, S_D614G and S_P681R changes were dominant in both B.1.466.2 and Delta variants, while N439K was only observed in B.1.466.2 (n = 44) and B.1.470 (n = 1). Additionally, the S_T19R, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, S_D950N and S_V1264L changes were only detected in Delta variants, consistent with those changes being characteristic of Delta variants in general. Conclusions: We demonstrated a shift in SARS-CoV-2 variants from the first wave of COVID-19 to Delta variants in the second wave, during which the number of confirmed cases surpassed those in the first wave of COVID-19 pandemic. Higher proportion of unique mutations detected in Delta variants compared to the first wave variants indicated potential mutational effects on viral transmissibility that correlated with a higher incidence of confirmed cases. Genomic surveillance of circulating variants, especially those with higher transmissibility, should be continuously conducted to rapidly inform decision making and support outbreak preparedness, prevention, and public health response.

Actinophytocola timorensis sp. nov. and Actinophytocola corallina sp. nov., isolated from soil.

Two actinomycete strains, ID05-A0653(T) and ID06-A0464(T), were isolated from soils of West Timor and Lombok island, respectively, in Indonesia. 16S rRNA gene sequence analysis clearly demonstrated that the isolates belonged to the family Pseudonocardiaceae and were closely related to the genus Actinophytocola. Strains ID05-A0653(T) and ID06-A0464(T) exhibited 98.1 and 98.2 % 16S rRNA gene sequence similarity, respectively, with Actinophytocola oryzae GMKU 367(T). The isolates grew well on ISP media and produced white aerial mycelium. Short spore chains were formed directly on the substrate mycelium. The isolates contained meso-diaminopimelic acid, arabinose and galactose as cell-wall components, MK-9(H(4)) as the sole isoprenoid quinone, iso-C(16 : 0) as the major cellular fatty acid and phosphatidylethanolamine as the diagnostic polar lipid. The DNA G+C contents of strains ID05-A0653(T) and ID06-A0464(T) were 69.7 and 71.2 mol%, respectively. On the basis of phenotypic characteristics, DNA-DNA relatedness and 16S rRNA gene sequence comparisons, strains ID05-A0653(T) and ID06-A0464(T) each represent a novel species of the genus Actinophytocola, for which the names Actinophytocola timorensis sp. nov. (type strain ID05-A0653(T)  = BTCC B-673(T)  = NBRC 105524(T)) and Actinophytocola corallina sp. nov. (type strain ID06-A0464(T)  = BTCC B-674(T)  = NBRC 105525(T)) are proposed.

Potential secondary metabolite from Indonesian Actinobacteria (InaCC A758) against Mycobacterium tuberculosis.

OBJECTIVES: This study explored Indonesian Actinobacteria which were isolated from Curcuma zedoaria endophytic microbes and mangrove ecosystem for new antimycobacterial compounds. MATERIALS AND METHODS: Antimycobacterial activity test was carried out against Mycobacterium tuberculosis H37Rv. Chemical profiling of secondary metabolite using Gas Chromatography-Mass Spectroscopy (GC-MS) and High Resolution-Mass Spectroscopy (HR-MS) was done to the ethyl acetate extract of active strain InaCC A758. Molecular taxonomy analysis based on 16S rRNA gene and biosynthetic gene clusters analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) from InaCC A758 have been carried out. Bioassay guided isolation of ethyl acetate extract was done, then structural elucidation of active compound was performed using UV-Vis, FT-IR, and NMR spectroscopy methods. RESULTS: The chemical profiling using HR-MS revealed that InaCC A758 has the potential to produce new antimycobacterial compounds. The 16S rRNA gene sequencing showed that InaCC A758 has the closest homology to Streptomyces parvus strain NBRC 14599 (99.64%). In addition, InaCC A758 has NRPS gene and related to S. parvulus (92% of similarity), and also PKS gene related to PKS-type borrelidin of S. rochei and S. parvulus (74% of similarity). Two compounds with potential antimycobacterial were predicted as 1) Compound 1, similar to dimethenamid (C12H18ClNO2S; MW 275.0723), with MIC value of 100 µg/ml, and 2) Compound 2, actinomycin D (C62H86N12O16; MW 1254.6285), with MIC value of 0.78 µg/ml. CONCLUSION: Actinomycin D has been reported to have antimycobacterial activity, however the compound has been predicted to resemble dimethenamid had not been reported to have similar activity.

Actinokineospora baliensis sp. nov., Actinokineospora cibodasensis sp. nov. and Actinokineospora cianjurensis sp. nov., isolated from soil and plant litter.

Six actinomycete strains isolated from soil and plant-litter samples in Indonesia were studied for their taxonomic position by using a polyphasic approach. Phylogenetically, all the strains were located in the broad cluster of the genus Actinokineospora. Chemotaxonomic data [cell-wall diamino acid, meso-diaminopimelic acid; cell-wall peptidoglycan, type III (A1γ); major sugars, galactose and arabinose; major menaquinone, MK-9(H4); major fatty acid, iso-C16:0; major phospholipid, phosphatidylethanolamine] supported the affiliation of all six strains to the genus Actinokineospora. The results of DNA-DNA hybridization with DNA from type strains of Actinokineospora species with validly published names revealed three DNA-DNA relatedness groups. Group I (ID03-0561(T)) showed low relatedness to the other strains studied. The three strains in group II (ID03-0784(T), ID03-0808 and ID03-0809) formed a group with high relatedness (98-100 %) and showed low relatedness to the other strains studied. The two strains in group III (ID03-0810(T) and ID03-0813) showed 58-68 % relatedness to Actinokineospora terrae NBRC 15668(T) and showed low relatedness (2-24 %) to the other strains studied. The description of three novel species is proposed: Actinokineospora baliensis sp. nov., for the single strain in group I (type strain ID03-0561(T) =BTCC B-554(T) =NBRC 104211(T)), Actinokineospora cibodasensis sp. nov., for the strains in group II (type strain ID03-0784(T) =BTCC B-555(T) =NBRC 104212(T)), and Actinokineospora cianjurensis sp. nov., for the strains in group III (type strain ID03-0810(T) =BTCC B-558(T) =NBRC 105526(T)).

MxaF gene, a gene encoding alpha subunit of methanol dehydrogenase in and false growth of acetic acid bacteria on methanol.

MxaF gene, a gene encoding alpha subunit of methanol dehydrogenase, was investigated for acetic acid bacteria, and growth on methanol was examined for the bacteria by using various media. Of 21 strains of acetic acid bacteria studied, Acidomonas methanolica strains showed the presence of mxaF gene exclusively, and grew on a defined medium containing methanol. Further, none of the strains tested of which the growth on methanol had been previously reported, except for Acidomonas methanolica, showed the presence of mxaF gene or the growth on methanol. Precautions were taken against false growth on compounds used for identification of bacteria.