Displaying publications 21 - 40 of 446 in total

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  1. Kawachi M, Nakayama T, Kayama M, Nomura M, Miyashita H, Bojo O, et al.
    Curr Biol, 2021 06 07;31(11):2395-2403.e4.
    PMID: 33773100 DOI: 10.1016/j.cub.2021.03.012
    Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton,1-11 which is responsible for around 50% of global net primary production.12,13 However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads represent a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences.14-17 The phenotypic identity of this group, which does not confidently cluster in any known algal clades in 16S rRNA phylogenetic reconstructions,15 has remained unknown since the first report of environmental sequences over two decades ago. We show that rappemonads are closely related to a haptophyte microalga, Pavlomulina ranunculiformis gen. nov. et sp. nov., and belong to a new haptophyte class, the Rappephyceae. Organellar phylogenomic analyses provide strong evidence for the inclusion of this lineage within the Haptophyta as a sister group to the Prymnesiophyceae. Members of this new class have a cosmopolitan distribution in coastal and oceanic regions. The relative read abundance of Rappephyceae in a large environmental barcoding dataset was comparable to, or greater than, those of major haptophyte species, such as the bloom-forming Gephyrocapsa huxleyi and Prymnesium parvum, and this result indicates that they likely have a significant impact as primary producers. Detailed characterization of Pavlomulina allowed for reconstruction of the ancient evolutionary history of the Haptophyta, a group that is one of the most important components of extant marine phytoplankton communities.
    Matched MeSH terms: RNA, Ribosomal, 16S
  2. Gopinath D, Menon RK
    Methods Mol Biol, 2021;2327:1-15.
    PMID: 34410636 DOI: 10.1007/978-1-0716-1518-8_1
    Evidence on the role of the oral microbiome in health and disease is changing the way we understand, diagnose, and treat ailments. Numerous studies on diseases affecting the oral cavity have revealed a large amount of data that is invaluable for the advancements in diagnosing and treating these diseases. However, the clinical translation of most of these exploratory data is stalled by variable methodology between studies and non-uniform reporting of the data.Understanding the key areas that are gateways to bias in microbiome studies is imperative to overcome this challenge faced by oral microbiome research. Bias can be multifactorial and may be introduced in a microbiome research study during the formulation of the study design, sample collection and storage, or the sample processing protocols before sequencing. This chapter summarizes the recommendations from literature to eliminate bias in the microbiome research studies and to ensure the reproducibility of the microbiome research data.
    Matched MeSH terms: RNA, Ribosomal, 16S
  3. Li Y, Wen H, Chen L, Yin T
    PLoS One, 2014;9(12):e115024.
    PMID: 25502754 DOI: 10.1371/journal.pone.0115024
    The growing concern about the effectiveness of reclamation strategies has motivated the evaluation of soil properties following reclamation. Recovery of belowground microbial community is important for reclamation success, however, the response of soil bacterial communities to reclamation has not been well understood. In this study, PCR-based 454 pyrosequencing was applied to compare bacterial communities in undisturbed soils with those in reclaimed soils using chronosequences ranging in time following reclamation from 1 to 20 year. Bacteria from the Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Planctomycetes and Bacteroidetes were abundant in all soils, while the composition of predominant phyla differed greatly across all sites. Long-term reclamation strongly affected microbial community structure and diversity. Initial effects of reclamation resulted in significant declines in bacterial diversity indices in younger reclaimed sites (1, 8-year-old) compared to the undisturbed site. However, bacterial diversity indices tended to be higher in older reclaimed sites (15, 20-year-old) as recovery time increased, and were more similar to predisturbance levels nearly 20 years after reclamation. Bacterial communities are highly responsive to soil physicochemical properties (pH, soil organic matter, Total N and P), in terms of both their diversity and community composition. Our results suggest that the response of soil microorganisms to reclamation is likely governed by soil characteristics and, indirectly, by the effects of vegetation restoration. Mixture sowing of gramineae and leguminosae herbage largely promoted soil geochemical conditions and bacterial diversity that recovered to those of undisturbed soil, representing an adequate solution for soil remediation and sustainable utilization for agriculture. These results confirm the positive impacts of reclamation and vegetation restoration on soil microbial diversity and suggest that the most important phase of microbial community recovery occurs between 15 and 20 years after reclamation.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics*
  4. Abu-Bakar SB, Razali NM, Naggs F, Wade C, Mohd-Nor SA, Aileen-Tan SH
    Mol Biol Rep, 2014 Mar;41(3):1799-805.
    PMID: 24443224 DOI: 10.1007/s11033-014-3029-5
    A total of 30 specimens belonging to five species, namely; Cryptozona siamensis, Sarika resplendens and Sarika sp. from the family Ariophantidae as well as Quantula striata and Quantula sp. from the family Dyakiidae were collected from the Langkawi Island in Northern Peninsular Malaysia. All specimens were identified through comparisons of shell morphology and amplification of a 500 bp segment of the 16S rRNA mtDNA gene. To assess phylogenetic insights, the sequences were aligned using ClustalW and phylogenetic trees were constructed. The analyses showed two major lineages in both Maximum Parsimony and Neighbour Joining phylogenetic trees. Each putative taxonomic group formed a monophyletic cluster. Our study revealed low species and intraspecies genetic diversities based on the 16S rRNA gene sequences. Thus, this study has provided an insight of land snail diversity in populations of an island highly influenced by anthropogenic activities through complementary use of shell morphological and molecular data.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics*
  5. Chong CW, Goh YS, Convey P, Pearce D, Tan IK
    Extremophiles, 2013 Sep;17(5):733-45.
    PMID: 23812890 DOI: 10.1007/s00792-013-0555-3
    A range of small- to moderate-scale studies of patterns in bacterial biodiversity have been conducted in Antarctica over the last two decades, most suggesting strong correlations between the described bacterial communities and elements of local environmental heterogeneity. However, very few of these studies have advanced interpretations in terms of spatially associated patterns, despite increasing evidence of patterns in bacterial biogeography globally. This is likely to be a consequence of restricted sampling coverage, with most studies to date focusing only on a few localities within a specific Antarctic region. Clearly, there is now a need for synthesis over a much larger spatial to consolidate the available data. In this study, we collated Antarctic bacterial culture identities based on the 16S rRNA gene information available in the literature and the GenBank database (n > 2,000 sequences). In contrast to some recent evidence for a distinct Antarctic microbiome, our phylogenetic comparisons show that a majority (~75 %) of Antarctic bacterial isolates were highly similar (≥99 % sequence similarity) to those retrieved from tropical and temperate regions, suggesting widespread distribution of eurythermal mesophiles in Antarctic environments. However, across different Antarctic regions, the dominant bacterial genera exhibit some spatially distinct diversity patterns analogous to those recently proposed for Antarctic terrestrial macroorganisms. Taken together, our results highlight the threat of cross-regional homogenisation in Antarctic biodiversity, and the imperative to include microbiota within the framework of biosecurity measures for Antarctica.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  6. Amin NM, Bunawan H, Redzuan RA, Jaganath IB
    Int J Mol Sci, 2010;12(1):39-45.
    PMID: 21339975 DOI: 10.3390/ijms12010039
    Erwinia mallotivora was isolated from papaya infected with dieback disease showing the typical symptoms of greasy, water-soaked lesions and spots on leaves. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain belonged to the genus Erwinia and was united in a monophyletic group with E. mallotivora DSM 4565 (AJ233414). Earlier studies had indicated that the causal agent for this disease was E. papayae. However, our current studies, through Koch's postulate, have confirmed that papaya dieback disease is caused by E. mallotivora. To our knowledge, this is the first new discovery of E. mallotivora as a causal agent of papaya dieback disease in Peninsular Malaysia. Previous reports have suggested that E. mallotivora causes leaf spot in Mallotus japonicus. However, this research confirms it also to be pathogenic to Carica papaya.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  7. Ransangan J, Mustafa S
    J Aquat Anim Health, 2009 Sep;21(3):150-5.
    PMID: 20043399 DOI: 10.1577/H09-002.1
    The grow out of Asian seabass Lates calcarifer in marine net-cages is a popular aquaculture activity in Malaysia. Production of this species is greatly affected by the occurrence of vibriosis, which causes heavy mortality. Generally, young fish are more susceptible; they exhibit anorexia and skin darkening, followed by heavy mortality. The acutely affected older fish may also exhibit bloody lesions around the anus and the base of the fins. Twenty-one bacterial isolates obtained from internal organs (kidney, heart, spleen and liver) of the affected specimens were subjected to phenotypic characterization, testing for antibiotic susceptibility, and 16S ribosomal DNA sequencing. The sequencing result showed that all of the bacterial isolates belonged to Vibrio harveyi. The phenotypic characterization, however, identified 4 of the bacterial isolates as V. harveyi, 16 as V. parahaemolyticus, and 1 as V. alginolyticus. These findings suggest that biochemical features alone cannot be reliably used to identify bacterial pathogens, including V. harveyi, in aquaculture. Antibiotic susceptibility assays showed that some antibiotics, including oxytetracycline, nitrofurantoin, furazolidone, streptomycin, sulfamethoxazole, chloramphenicol, nalidixic acid, and oxolinic acid were effective against V. harveyi. Considering the side effects of these antibiotics, however, their use is not recommended in the aquaculture of Asian seabass.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics*
  8. Nkem BM, Halimoon N, Yusoff FM, Johari WLW, Zakaria MP, Medipally SR, et al.
    Mar Pollut Bull, 2016 Jun 15;107(1):261-268.
    PMID: 27085593 DOI: 10.1016/j.marpolbul.2016.03.060
    In this study, we isolated two indigenous hydrocarbon-degrading bacteria from tarball found in Rhu Sepuluh beach, Terengganu, Malaysia. These bacteria were identified based on their physiological characteristic and 16S rRNA gene sequence analysis, and they showed 99% similarity with Cellulosimicrobium cellulans DSM 43879 and Acinetobacter baumannii ATCC 19606 respectively. Their hydrocarbon-degrading capabilities were tested using diesel-oil as sole carbon source. Results analysed using GC-MS, showed diesel-oil alkanes were degraded an average 64.4% by C. cellulans and 58.1% by A. baumannii with medium optical density reaching 0.967 (C. cellulans) and 1.515 (A. baumannii) in minimal salt media at 32°C for 10days. Individual diesel-oil alkanes were degraded between 10%-95.4% by C. cellulans and 0.2%-95.9% by A. baumannii. Both strains utilized diesel-oil for growth. The study suggests both strains are part of indigenous hydrocarbon-degrading bacteria in tarball with potential for bioremediation of oil-polluted marine environment.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  9. Azrizal-Wahid N, Sofian-Azirun M, Low VL
    PMID: 33609991 DOI: 10.1016/j.cimid.2021.101621
    Flea-borne pathogens were screened from 100 individual cat fleas using a PCR approach, of which 38 % were infected with at least one bacterium. Overall, 28 % of the flea samples were positive for Bartonella as inferred from ITS DNA region. Of these, 25 % (7/28) were identified as Bartonella clarridgeiae, 42.9 % (12/28) as Bartonella henselae consisted of two different strains, and 32.1 % (9/28) as Bartonella koehlerae, which was detected for the first time in Malaysia. Sequencing of gltA amplicons detected Rickettsia DNA in 14 % of cat flea samples, all of them identified as Rickettsia asembonensis (100 %). None of the flea samples were positive for Mycoplasma DNA in 16S rRNA gene detection. Four fleas were co-infected with Bartonella and Rickettsia DNAs. Statistical analyses reveal no significant association between bacterial infection and mtDNA diversity of the cat flea. Nevertheless, in all types of pathogen infections, infected populations demonstrated lower nucleotide and haplotype diversities compared to uninfected populations. Moreover, lower haplotype numbers were observed in infected populations.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  10. Ernieenor FCL, Apanaskevich DA, Ernna G, Mariana A
    Exp Appl Acarol, 2020 Jan;80(1):137-149.
    PMID: 31832837 DOI: 10.1007/s10493-019-00439-4
    Identifying certain species of Dermacentor ticks in Malaysia is challenging as there is no comprehensive work on their systematics and lack of specific taxonomic keys. In this study, we described and characterized D. steini ticks collected from a forest reserve in the vicinity of the Forest Research Institute of Malaysia using integrated phenotypic and genotypic traits. In total two males and three females of questing D. steini ticks were morphologically identified using specific illustrated taxonomic keys based on their special characters. Further confirmation and characterization of the tick species were then examined using PCR, followed by sequencing partial mitochondrial 16S rDNA gene (mt-rrs). Clustering analysis based on mt-rrs was carried out by constructing neighbor-joining tree topology to clarify the genetic variation of local D. steini. Based on external morphological characterizations, all ticks were successfully identified down to the species as adult D. steini. The molecular traits based on phylogenetic tree provide very strong support for the monophyletic clade of D. steini including high percentages of similarity (97-100%) with available sequences in GenBank. Furthermore, a low intraspecific variation (4%) among the species of D. steini was observed but it was genetically different from other Dermacentor species with high interspecific value (8-15%). These findings produced the first genotypic data of D. steini using 16S rDNA gene which confirmed the presence of this species in Malaysia. Moreover, this study supports the taxonomic status of local D. steini and adds to the knowledge of accurate identification of ticks.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  11. Ahmed A, Ijaz M, Ghauri HN, Aziz MU, Ghaffar A, Naveed M, et al.
    PMID: 32829184 DOI: 10.1016/j.cimid.2020.101524
    Feline anaplasmosis is considered as an emerging tick-borne disease of zoonotic potential. The aim of current study was to investigate the molecular prevalence of anaplasmosis, associated risk factors, and alterations in hematological parameters of domestic cats from Lahore, Pakistan. Blood samples of 100 domestic cats from district Lahore were examined microscopically and the extracted genomic DNA from each sample was processed for the amplification of 16 S rRNA gene of Anaplasma. PCR confirmed isolates were purified for sequencing. The data regarding the risk factors was collected in a predesigned questionnaire and statistically analyzed by logistic regression analysis. The study found a molecular prevalence of 13% (13/100) among analyzed blood samples. The nucleotide analysis of Anaplasmataceae species sequences amplified by PCR showed high resemblance (99%) with isolates from Korea, Japan, Malaysia, Philippines, and India. The potential risk factors found to be significantly associated (p 
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  12. Ong SY, Kho HP, Riedel SL, Kim SW, Gan CY, Taylor TD, et al.
    J Biotechnol, 2018 Jan 10;265:31-39.
    PMID: 29101024 DOI: 10.1016/j.jbiotec.2017.10.017
    Polyhydroxyalkanoates (PHAs) are produced in microbes as a source of carbon and energy storage. They are biodegradable and have properties similar to synthetic plastics, which make them an interesting alternative to petroleum-based plastics. In this study, a refined method of recovering PHA from Cupriavidus necator biomass was proposed by incorporating the use of the yellow mealworm (the larval phase of the mealworm beetle, Tenebrio molitor) as partial purification machinery, followed by washing of the fecal pellets with distilled water and sodium hydroxide. The PHA contents of the cells used in this study were 55wt% (produced from palm olein) and 60 wt% (produced from waste animal fats). The treatment of distilled water and NaOH further increased the purity of PHA to 94%. In parallel, analysis of the 16S rRNA metagenomic sequencing of the mealworm gut microbiome has revealed remarkable changes in the bacterial diversity, especially between the mealworms fed with cells produced from palm olein and waste animal fats. This biological recovery of PHA from cells is an attempt to move towards a green and sustainable process with the aim of reducing the use of harmful solvents and strong chemicals during polymer purification. The results obtained show that - purities of >90%, without a reduction in the molecular weight, can be obtained through this integrative biological recovery approach. In addition, this study has successfully shown that the cells, regardless of their origins, were readily consumed by the mealworms, and there is a correlation between the feed type and the mealworm gut microbiome.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  13. Zhang XL, Li GX, Ge YM, Iqbal NM, Yang X, Cui ZD, et al.
    Antonie Van Leeuwenhoek, 2021 Jun;114(6):845-857.
    PMID: 33770293 DOI: 10.1007/s10482-021-01563-1
    During the study into the microbial biodiversity and bioactivity of the Microcystis phycosphere, a new yellow-pigmented, non-motile, rod-shaped bacterium containing polyhydroxybutyrate granules designated as strain Z10-6T was isolated from highly-toxic Microcystis aeruginosa Kützing M.TN-2. The new isolate produces active bioflocculating exopolysaccharides. Phylogenetic analysis based on 16S rRNA gene sequences indicated strain Z10-6T belongs to the genus Sphingopyxis with highest similarity to Sphingopyxis solisilvae R366T (98.86%), and the similarity to other Sphingopyxis members was less than 98.65%. However, both low values obtained by phylogenomic calculation of average nucleotide identity (ANI, 85.5%) and digital DNA-DNA hybridization (dDDH, 29.8%) separated the new species from its closest relative. The main polar lipids were sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid and one unidentified aminophospholipid. The predominant fatty acids were summed feature 8, C17:1ω6c, summed feature 3, C16:0, C18:1ω7c 11-methyl and C14:0 2-OH. The respiratory quinone was ubiqunone-10, with spermidine as the major polyamine. The genomic DNA G + C content was 64.8 mol%. Several biosynthesis pathways encoding for potential new bacterial bioactive metabolites were found in the genome of strain Z10-6T. The polyphasic analyses clearly distinguished strain Z10-6T from its closest phylogenetic neighbors. Thus, it represents a novel species of the genus Sphingopyxis, for which the name Sphingopyxis microcysteis sp. nov. is proposed. The type strain is Z10-6T (= CCTCC AB2017276T = KCTC 62492T).
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  14. Yang Q, Ge YM, Iqbal NM, Yang X, Zhang XL
    Antonie Van Leeuwenhoek, 2021 Jul;114(7):1091-1106.
    PMID: 33895907 DOI: 10.1007/s10482-021-01580-0
    Marine phycosphere harbors unique cross-kingdom associations with enormous ecological significance in aquatic ecosystems as well as relevance for algal biotechnology industry. During our investigating the microbial composition and bioactivity of marine phycosphere microbiota (PM), a novel lightly yellowish and versatile bacterium designated strain AM1-D1T was isolated from cultivable PM of marine dinoflagellate Alexandrium minutum amtk4 that produces high levels of paralytic shellfish poisoning toxins (PSTs). Strain AM1-D1T demonstrates notable bioflocculanting bioactivity with bacterial exopolysaccharides (EPS), and microalgae growth-promoting (MGP) potential toward its algal host. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AM1-D1T was affiliated to the members of genus Sulfitobacter within the family Rhodobacteraceae, showing the highest sequence similarity of 97.9% with Sulfitobacter noctilucae NB-68T, and below 97.8% with other type strains. The complete genome of strain AM1-D1T consisted of a circular 3.84-Mb chromosome and five circular plasmids (185, 95, 15, 205 and 348 Kb, respectively) with the G+C content of 64.6%. Low values obtained by phylogenomic calculations on the average nucleotide identity (ANI, 77.2%), average amino acid identity (AAI, 74.7%) and digital DNA-DNA hybridization (dDDH, 18.6%) unequivocally separated strain AM1-D1T from its closest relative. The main polar lipids were identified as phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, one unidentified phospholipid and one unidentified lipid. The predominant fatty acids (> 10%) were C18:1 ω7c, C19:0 cyclo ω8c and C16:0. The respiratory quinone was Q-10. The genome of strain AM1-D1T was predicted to encode series of gene clusters responsible for sulfur oxidation (sox) and utilization of dissolved organic sulfur exometabolites from marine dinoflagellates, taurine (tau) and dimethylsulfoniopropionate (DMSP) (dmd), as well as supplementary vitamin B12 (cob), photosynthesis carotenoids (crt) which are pivotal components during algae-bacteria interactions. Based on the evidences by the polyphasic characterizations, strain AM1-D1T represents a novel species of the genus Sulfitobacter, for which the name Sulfitobacter alexandrii sp. nov. is proposed. The type strain is AM1-D1T (= CCTCC 2017277T = KCTC 62491T).
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  15. Nurul AAN, Danish-Daniel AM, Okomoda VT, Asma NA
    Appl Microbiol Biotechnol, 2020 Sep;104(17):7391-7407.
    PMID: 32676710 DOI: 10.1007/s00253-020-10781-y
    The Labroides dimidiatus is one of the most traded marine ornamental fishes worldwide, yet not much is known about the microflora associated with this fish. This study is designed to investigate the bacteria composition associated with captive L. dimidiatus and its surrounding aquarium water. The fish and carriage water were obtained from well-known ornamental fish suppliers in Terengganu Malaysia. Bacteria present on the skin and in the stomach and the aquarium water were enumerated using culture-independent approaches and next-generation sequencing (NGS) technology. A total of 3,238,564 valid reads and 828 total operational taxonomic units (OTUs) were obtained from the three metagenomic libraries using NGS analysis. Of all the 15 phyla identified in this study, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the most prevalent in all samples. Also, 170 families belonging to 36 bacteria classes were identified. Although many of the bacteria families were common in the skin, gut, and aquarium water (39%), about 26% of the families were exclusive to the aquarium water alone. Therefore, any substantial change in the structure and abundance of microbiota (especially pathogenic bacteria) reported in this study may serve as an early sign for disease infection in the species under captivity. KEY POINTS: • Proteobacteria was the most dominant. • The microbiota was either shared or exclusively in samples.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  16. Radzi R, Muangmai N, Broady P, Wan Omar WM, Lavoue S, Convey P, et al.
    PLoS One, 2019;14(11):e0224395.
    PMID: 31682631 DOI: 10.1371/journal.pone.0224395
    Terrestrial cyanobacteria are very diverse and widely distributed in Antarctica, where they can form macroscopically visible biofilms on the surfaces of soils and rocks, and on benthic surfaces in fresh waters. We recently isolated several terrestrial cyanobacteria from soils collected on Signy Island, South Orkney Islands, Antarctica. Among them, we found a novel species of Nodosilinea, named here as Nodosilinea signiensis sp. nov. This new species is morphologically and genetically distinct from other described species. Morphological examination indicated that the new species is differentiated from others in the genus by cell size, cell shape, filament attenuation, sheath morphology and granulation. 16S rDNA phylogenetic analyses clearly confirmed that N. signiensis belongs to the genus Nodosilinea, but that it is genetically distinct from other known species of Nodosilinea. The D1-D1´ helix of the 16S-23S ITS region of the new species was also different from previously described Nodosilinea species. This is the first detailed characterization of a member of the genus Nodosilinea from Antarctica as well as being a newly described species.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  17. Madhaiyan M, Saravanan VS, See-Too WS
    Int J Syst Evol Microbiol, 2020 Jun;70(6):3924-3929.
    PMID: 32441614 DOI: 10.1099/ijsem.0.004217
    Phylogenetic analysis based on 16S rRNA gene sequences of the genus Streptomyces showed the presence of six distinguishable clusters, with 100 % sequence similarity values among strains in each cluster; thus they shared almost the same evolutionary distance. This result corroborated well with the outcome of core gene (orthologous gene clusters) based genome phylogeny analysis of 190 genomes including the Streptomyces species in those six clusters. These preeminent results led to an investigation of genome-based indices such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) for the strains in those six clusters. Certain strains recorded genomic indices well above the threshold values (70 %, 95-96 % and >95 % for dDDH, ANI and AAI, respectively) determined for species affiliation, suggesting only one type strain belongs to described species and the other(s) may need to be reduced in taxa to a later heterotypic synonym. To conclude, the results of comprehensive analyses based on phylogenetic and genomic indices suggest that the following six reclassifications are proposed: Streptomyces flavovariabilis as a later heterotypic synonym of Streptomyces variegatus; Streptomyces griseofuscus as a later heterotypic synonym of Streptomyces murinus; Streptomyces kasugaensis as a later heterotypic synonym of Streptomyces celluloflavus; Streptomyces luridiscabiei as a later heterotypic synonym of Streptomyces fulvissimus; Streptomyces pharetrae as a later heterotypic synonym of Streptomyces glaucescens; and Streptomyces stelliscabiei as a later heterotypic synonym of Streptomyces bottropensis.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  18. Loh WLC, Huang KC, Ng HS, Lan JC
    J Biosci Bioeng, 2020 Aug;130(2):187-194.
    PMID: 32334990 DOI: 10.1016/j.jbiosc.2020.03.007
    Carotenoids serve as one of the most important group of naturally-occurring lipid-soluble pigments which exhibit great biological activities such as antioxidant, anti-inflammatory and provitamin A activities. Owing to their advantageous health effects, carotenoids are widely applied in various industries. Microbial carotenoids synthesis therefore has attracted increasing attention in recent years. In the present study, a marine microorganism originally isolated from seawater in northern Taiwan was determined to be a strain of Gordonia terrae based on its 16S rRNA gene sequence. The strain G. terrae TWRH01 has the ability to synthesize and accumulate the intracellular pigments was identified by gas chromatography-mass spectrometry (GC-MS). The biochemical production characteristics of this strain were studied by employing different fermentation strategies. Findings suggested that G. terrae TWRH01 can actively grow and efficiently synthesize carotenoids in medium adjusted to pH 7 containing 16 g L-1 sucrose as the carbon source, 16 g L-1 yeast extract as the nitrogen source, 0.6 M NaCl concentration, and supplemented with 0.45% (v/v) 1 M CaCl2. Results revealed that the optimization of fermentation yielded 15.29 g L-1 dry biomass and 10.58 μmol L-1 relative β-carotene concentration. According to GC-MS analysis, the orange-red colored pigments produced were identified as carotenoid derivatives, mainly echinenone and adonixanthin 3'-β-d-glucoside. Therefore, the new bacterial strain showed a highly potential bioresource for the commercial production of natural carotenoids.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  19. Chigurupati S, Vijayabalan S, Selvarajan KK, Alhowail A, Kauser F
    J Complement Integr Med, 2020 Dec 22;18(2):319-325.
    PMID: 34187119 DOI: 10.1515/jcim-2020-0203
    OBJECTIVES: Research on endosymbionts is emerging globally and is considered as a potential source of bioactive phytochemicals. The present study examines the antioxidant and antidiabetic of the endophytic crude extract isolated from Leucaena leucocephala leaves.

    METHODS: Endophytic bacteria were isolated from the leaves of L. leucocephala and 16S rRNA gene sequencing was used to establish their identity. The in vitro antioxidant effect of endophytic crude extract (LL) was evaluated using 2-diphenyl-1-picrylhydrazyl (DPPH) and 2, 2'-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) free radical scavenging methods. The in vitro antidiabetic properties of LL were evaluated using α-amylase and α-glucosidase enzyme inhibition assay.

    RESULTS: The isolated endophytic bacteria were identified as Cronobacter sakazakii. LL displayed potent free radical scavenging effect against ABTS and DPPH radicals with an inhibitory concentration 50% (IC50) value of 17.49 ± 0.06 and 11.3 ± 0.1 μg/mL respectively. LL exhibited α-amylase and α-glucosidase inhibition with an IC50 value of 23.3 ± 0.08 and 23.4 ± 0.1 μg/mL respectively compared to the standard drug (acarbose). Both glucose loaded normoglycemic rats and STZ induced diabetic rats treated with LL (200 mg/kg) exhibited a considerable reduction in blood glucose levels p<0.01 after 8 h of treatment when compared to normal and diabetic control rats respectively.

    CONCLUSIONS: Thus, the study shows that LL has a wellspring of natural source of antioxidants, and antidiabetic agents and phytoconstituents present in endophytes could be the rich source for bioactive compounds.

    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  20. Teo WFA, Tan GYA, Li WJ
    Int J Syst Evol Microbiol, 2021 Oct;71(10).
    PMID: 34714227 DOI: 10.1099/ijsem.0.005075
    The taxonomic positions of members within the family Pseudonocardiaceae were assessed based on phylogenomic trees reconstructed using core-proteome and genome blast distance phylogeny approaches. The closely clustered genome sequences from the type strains of validly published names within the family Pseudonocardiaceae were analysed using overall genome-related indices based on average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values. The family Pseudonocardiaceae consists of the type genus Pseudonocardia, as well as the genera Actinoalloteichus, Actinocrispum, Actinokineospora, Actinomycetospora, Actinophytocola, Actinopolyspora, Actinorectispora, Actinosynnema, Allokutzneria, Allosaccharopolyspora gen. nov., Amycolatopsis, Bounagaea, Crossiella, Gandjariella, Goodfellowiella, Haloactinomyces, Haloechinothrix, Halopolyspora, Halosaccharopolyspora gen. nov., Herbihabitans, Kibdelosporangium, Kutzneria, Labedaea, Lentzea, Longimycelium, Prauserella, Saccharomonospora, Saccharopolyspora, Saccharothrix, Salinifilum, Sciscionella, Streptoalloteichus, Tamaricihabitans, Thermocrispum, Thermotunica and Umezawaea. The G+C contents of the Pseudonocardiaceae genomes ranged from 66.2 to 74.6 mol% and genome sizes ranged from 3.69 to 12.28 Mbp. Based on the results of phylogenomic analysis, the names Allosaccharopolyspora coralli comb. nov., Halosaccharopolyspora lacisalsi comb. nov. and Actinoalloteichus caeruleus comb. nov. are proposed. This study revealed that Actinokineospora mzabensis is a heterotypic synonym of Actinokineospora spheciospongiae, Lentzea deserti is a heterotypic synonym of Lentzea atacamensis, Prauserella endophytica is a heterotypic synonym of Prauserella coralliicola, and Prauserella flava and Prauserella sediminis are heterotypic synonyms of Prauserella salsuginis. This study addresses the nomenclature conundrums of Actinoalloteichus cyanogriseus and Streptomyces caeruleus as well as Micropolyspora internatus and Saccharomonospora viridis.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
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