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  1. Wei J, Xiao Y, Liu J, Herrera-Ulloa A, Loh KH, Xu K
    Sci Data, 2024 Feb 23;11(1):234.
    PMID: 38395996 DOI: 10.1038/s41597-024-03070-0
    Pampus argenteus (Euphrasen, 1788) is one of the major fishery species in coastal China. Pampus argenteus has a highly specialized morphology, and its declining fishery resources have encouraged massive research efforts on its aquacultural biology. In this study, we reported the first high-quality chromosome-level genome of P. argenteus obtained by integrating Illumina, PacBio HiFi, and Hi-C sequencing techniques. The final size of the genome was 518.06 Mb, with contig and scaffold N50 values of 20.47 and 22.86 Mb, respectively. The sequences were anchored and oriented onto 24 pseudochromosomes based on Hi-C data corresponding to the 24-chromatid karyotype of P. argenteus. A colinear relationship was observed between the P. argenteus genome and that of a closely related species (Scomber japonicus). A total of 24,696 protein-coding genes were identified from the genome, 98.9% of which were complete BUSCOs. This report represents the first case of high-quality chromosome-level genome assembly for P. argenteus and can provide valuable information for future evolutionary, conservation, and aquacultural research.
    Matched MeSH terms: Sequence Analysis, DNA
  2. Wang H, Zheng K, Wang M, Ma K, Ren L, Guo R, et al.
    Microbiol Spectr, 2024 Feb 06;12(2):e0336723.
    PMID: 38214523 DOI: 10.1128/spectrum.03367-23
    Shewanella is a prevalent bacterial genus in deep-sea environments including marine sediments, exhibiting diverse metabolic capabilities that indicate its significant contributions to the marine biogeochemical cycles. However, only a few Shewanella phages were isolated and deposited in the NCBI database. In this study, we report the isolation and characterization of a novel Shewanella phage, vB_SbaS_Y11, that infects Shewanella KR11 and was isolated from the sewage in Qingdao, China. Transmission electron microscopy revealed that vB_SbaS_Y11 has an icosahedral head and a long tail. The genome of vB_SbaS_Y11 is a linear, double-stranded DNA with a length of 62,799 bp and a G+C content of 46.9%, encoding 71 putative open reading frames. No tRNA genes or integrase-related feature genes were identified. An uncharacterized anti-CRISPR AcrVA2 gene was detected in its genome. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analyses indicate that vB_SbaS_Y11 has a novel genomic architecture and shares low similarity to Pseudomonas virus H66 and Pseudomonas phage F116. vB_SbaS_Y11 represents a potential new family-level virus cluster with eight metagenomic assembled viral genomes named Ranviridae.IMPORTANCEThe Gram-negative Shewanella bacterial genus currently includes about 80 species of mostly aquatic Gammaproteobacteria, which were isolated around the globe in a multitude of environments, such as freshwater, seawater, coastal sediments, and the deepest trenches. Here, we present a Shewanella phage vB_SbaS_Y11 that contains an uncharacterized anti-CRISPR AcrVA2 gene and belongs to a potential virus family, Ranviridae. This study will enhance the knowledge about the genome, diversity, taxonomic classification, and global distribution of Shewanella phage populations.
    Matched MeSH terms: Sequence Analysis, DNA
  3. Li W, Ren Q, Feng J, Lee SY, Liu Y
    PLoS One, 2024;19(1):e0297164.
    PMID: 38241246 DOI: 10.1371/journal.pone.0297164
    Deer products from sika deer (Cervus nippon) and red deer (C. elaphus) are considered genuine and used for Traditional Chinese Medicine (TCM) materials in China. Deer has a very high economic and ornamental value, resulting in the formation of a characteristic deer industry in the prescription preparation of traditional Chinese medicine, health food, cosmetics, and other areas of development and utilization. Due to the high demand for deer products, the products are expensive and have limited production, but the legal use of deer is limited to only two species of sika deer and red deer; other wild deer are prohibited from hunting, so there are numerous cases of mixing and adulteration of counterfeit products and so on. There have been many reports that other animal (pig, cow, sheep, etc.) tissues or organs are often used for adulteration and confusion, resulting in poor efficacy of deer traditional medicine and trade fraud in deer products. To authenticate the deer products in a rapid and effective manner, the analysis used 22 deer products (antler, meat, bone, fetus, penis, tail, skin, and wool) that were in the form of blind samples. Total DNA extraction using a modified protocol successfully yielded DNA from the blind samples that was useful for PCR. Three candidate DNA barcoding loci, cox1, Cyt b, and rrn12, were evaluated for their discrimination strength through BLAST and phylogenetic clustering analyses. For the BLAST analysis, the 22 blind samples obtained 100% match identity across the three gene loci tested. It was revealed that 12 blind samples were correctly labeled for their species of origin, while three blind samples that were thought to originate from red deer were identified as C. nippon, and seven blind samples that were thought to originate from sika deer were identified as C. elaphus, Dama dama, and Rangifer tarandus. DNA barcoding analysis showed that all three gene loci were able to distinguish the two Cervus species and to identify the presence of adulterant species. The DNA barcoding technique was able to provide a useful and sensitive approach in identifying the species of origin in deer products.
    Matched MeSH terms: Sequence Analysis, DNA
  4. Tian X, Teo WFA, Wee WY, Yang Y, Ahmed H, Jakubovics NS, et al.
    BMC Genomics, 2023 Dec 04;24(1):734.
    PMID: 38049764 DOI: 10.1186/s12864-023-09831-2
    BACKGROUND: Actinomyces strains are commonly found as part of the normal microflora on human tissue surfaces, including the oropharynx, gastrointestinal tract, and female genital tract. Understanding the diversity and characterization of Actinomyces species is crucial for human health, as they play an important role in dental plaque formation and biofilm-related infections. Two Actinomyces strains ATCC 49340 T and ATCC 51655 T have been utilized in various studies, but their accurate species classification and description remain unresolved.

    RESULTS: To investigate the genomic properties and taxonomic status of these strains, we employed both 16S rRNA Sanger sequencing and whole-genome sequencing using the Illumina HiSeq X Ten platform with PE151 (paired-end) sequencing. Our analyses revealed that the draft genome of Actinomyces acetigenes ATCC 49340 T was 3.27 Mbp with a 68.0% GC content, and Actinomyces stomatis ATCC 51655 T has a genome size of 3.08 Mbp with a 68.1% GC content. Multi-locus (atpA, rpoB, pgi, metG, gltA, gyrA, and core genome SNPs) sequence analysis supported the phylogenetic placement of strains ATCC 51655 T and ATCC 49340 T as independent lineages. Digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) analyses indicated that both strains represented novel Actinomyces species, with values below the threshold for species demarcation (70% dDDH, 95% ANI and AAI). Pangenome analysis identified 5,731 gene clusters with strains ATCC 49340 T and ATCC 51655 T possessing 1,515 and 1,518 unique gene clusters, respectively. Additionally, genomic islands (GIs) prediction uncovered 24 putative GIs in strain ATCC 49340 T and 16 in strain ATCC 51655 T, contributing to their genetic diversity and potential adaptive capabilities. Pathogenicity analysis highlighted the potential human pathogenicity risk associated with both strains, with several virulence-associated factors identified. CRISPR-Cas analysis exposed the presence of CRISPR and Cas genes in both strains, indicating these strains might evolve a robust defense mechanism against them.

    CONCLUSION: This study supports the classification of strains ATCC 49340 T and ATCC 51655 T as novel species within the Actinomyces, in which the name Actinomyces acetigenes sp. nov. (type strain ATCC 49340 T = VPI D163E-3 T = CCUG 34286 T = CCUG 35339 T) and Actinomyces stomatis sp. nov. (type strain ATCC 51655 T = PK606T = CCUG 33930 T) are proposed.

    Matched MeSH terms: Sequence Analysis, DNA
  5. Chantavorakit T, Muangham S, Aaron TWF, Duangmal K, Hong K
    Int J Syst Evol Microbiol, 2023 Nov;73(11).
    PMID: 37994910 DOI: 10.1099/ijsem.0.006177
    The taxonomic position of two novel Actinoallomurus strains isolated from rhizosphere soil of wild rice (Oryza rufipogon Griff.) was established using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WRP6H-15T and WRP9H-5T were closely related to Actinoallomurus spadix JCM 3146T and Actinoallomurus purpureus TTN02-30T. Chemotaxonomic and morphological characteristics of both strains were consistent with members of the genus Actinoallomurus, while phenotypic properties, genome-based comparisons and phylogenomic analyses distinguished strains WRP6H-15T and WRP9H-5T from their closest phylogenetic relatives. The two strains showed nearly identical 16S rRNA gene sequences (99.9 %). Strain WRP6H-15T showed 68.7 % digital DNA-DNA hybridization, 95.9 % average nucleotide identity (ANI) based on blast and 96.4 % ANI based on MUMmer to strain WRP9H-5T. A phylogenomic tree based on draft genome sequences of the strains and representative of the genus Actinoallomurus confirmed the phylogenetic relationships. The genomes sizes of strains WRP6H-15T and WRP9H-5T were 9.42 Mb and 9.68 Mb, with DNA G+C contents of 71.5 and 71.3 mol%, respectively. In silico analysis predicted that the strains contain biosynthetic gene clusters encoding for specialized metabolites. Characterization based on chemotaxonomic, phylogenetic, phenotypic and genomic evidence demonstrated that strains WRP6H-15T and WRP9H-5T represent two novel species of the genus Actinoallomurus, for which the names Actinoallomurus soli sp. nov. (type strain WRP6H-15T=TBRC 15726T=NBRC 115556T) and Actinoallomurus rhizosphaericola sp. nov. (type strain WRP9H-5T=TBRC 15727T=NBRC 115557T) are proposed.
    Matched MeSH terms: Sequence Analysis, DNA
  6. Ge F, Guo R, Liang Y, Chen Y, Shao H, Sung YY, et al.
    Virus Res, 2023 Oct 15;336:199226.
    PMID: 37739268 DOI: 10.1016/j.virusres.2023.199226
    Stutzerimonas stutzeri is an opportunistic pathogenic bacterium belonging to the Gammaproteobacteria, exhibiting wide distribution in the environment and playing significant ecological roles such as nitrogen fixation or pollutant degradation. Despite its ecological importance, only two S. stutzeri phages have been isolated to date. Here, a novel S. stutzeri phage, vB_PstS_ZQG1, was isolated from the surface seawater of Qingdao, China. Transmission electron microscopy analysis indicates that vB_PstS_ZQG1 has a morphology characterized by a long non-contractile tail. The genomic sequence of vB_PstS_ZQG1 contains a linear, double-strand 61,790-bp with the G+C content of 53.24% and encodes 90 putative open reading frames. Two auxiliary metabolic genes encoding TolA protein and nucleotide pyrophosphohydrolase were identified, which are likely involved in host adaptation and phage reproduction. Phylogenetic and comparative genomic analyses demonstrated that vB_PstS_ZQG1 exhibits low similarity with previously isolated phages or uncultured viruses (average nucleotide identity values range from 21.7 to 29.4), suggesting that it represents a novel viral genus by itself, here named as Fuevirus. Biogeographic analysis showed that vB_PstS_ZQG1 was only detected in epipelagic and mesopelagic zone with low abundance. In summary, our findings of the phage vB_PstS_ZQG1 will provide helpful insights for further research on the interactions between S. stutzeri phages and their hosts, and contribute to discovering unknown viral sequences in the metagenomic database.
    Matched MeSH terms: Sequence Analysis, DNA
  7. Zhu HY, Wei YH, Guo LC, Wei XY, Li JN, Zhang RP, et al.
    Int J Syst Evol Microbiol, 2023 Oct;73(10).
    PMID: 37847534 DOI: 10.1099/ijsem.0.006076
    Three strains belonging to the basidiomycetous yeast genus Vishniacozyma were isolated from marine water samples collected from intertidal zones in Liaoning province, northeast China. Phylogenetic analyses based on the sequences of the small subunit (SSU) ribosomal DNA (rDNA), the D1/D2 domain of the large subunit (LSU) ribosomal DNA (rDNA), the internal transcribed spacer region (ITS), the two subunits of DNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1), and the mitochondrial gene cytochrome b (CYTB) showed that these strains together with 20 strains from various geographic and ecological origins from other regions of the world represent a novel species in the genus Vishniacozyma. We propose the name Vishniacozyma pseudocarnescens sp. nov. (holotype CGMCC 2.6457) for the new species, which differs phenotypically from its close relatives V. carnescens, V. tephrensis, and V. victoriae by its ability to grow at 30 °C and on 50 % (w/v) glucose-yeast extract agar.
    Matched MeSH terms: Sequence Analysis, DNA
  8. Chen Y, Guo R, Liang Y, Luo L, Han Y, Wang H, et al.
    Virus Res, 2023 Sep;334:199183.
    PMID: 37499764 DOI: 10.1016/j.virusres.2023.199183
    Stutzerimonas stutzeri is an opportunistic pathogen widely distributed in the environment and displays diverse metabolic capabilities. In this study, a novel lytic S. stutzeri phage, named vB_PstM_ZRG1, was isolated from the seawater in the East China Sea (29°09'N, 123°39'E). vB_PstM_ZRG1 was stable at temperatures ranging from -20°C to 65°C and across a wide range of pH values from 3 to 10. The genome of vB_PstM_ZRG1 was determined to be a double-stranded DNA with a genome size of 52,767 bp, containing 78 putative open reading frames (ORFs). Three auxiliary metabolic genes encoded by phage vB_PstM_ZRG1 were predicted, including Toll/interleukin-1 receptor (TIR) domain, proline-alanine-alanine-arginine (PAAR) protein and SGNH (Ser-Gly-Asn-His) family hydrolase, especially TIR domain is not common in isolated phages. Phylogenic and network analysis showed that vB_PstM_ZRG1 has low similarity to other phage genomes in the GenBank and IMG/VR database, and might represent a novel viral genus, named Elithevirus. Additionally, the distribution map results indicated that vB_PstM_ZRG1 could infect both extreme colds- and warm-type hosts in the marine environment. In summary, our finding provided basic information for further research on the relationship between S. stutzeri and their phages, and expanded our understanding of genomic characteristics, phylogenetic diversity and distribution of Elithevirus.
    Matched MeSH terms: Sequence Analysis, DNA
  9. Zhu HY, Wei XY, Liu XZ, Bai FY
    Int J Syst Evol Microbiol, 2023 May;73(5).
    PMID: 37191980 DOI: 10.1099/ijsem.0.005865
    A yeast strain belonging to the basidiomycetous yeast genus Cystofilobasidium was isolated from a marine sediment sample collected in an intertidal zone in Shandong province, PR China. The results of phylogenetic analyses based on sequences of the D1/D2 domain of the 26S ribosomal RNA gene and the internal transcribed spacer (ITS) region indicate that this strain, together with three other strains isolated from basal ice collected in Norway, the gut of an insect and an alga collected in Russia, represent a novel species of the genus, for which the name Cystofilobasidium josepaulonis sp. nov. (holotype strain CGMCC 2.6672T) is proposed. The novel species differs from the known species of the genus Cystofilobasidium by 1.7 %-4.1 and 11.3 %-17.1 % mismatches in the D1/D2 domain and the ITS region, respectively. This species forms teliospores on potato dextrose agar (PDA) and 10 % V8 juice agar, but teliospore germination with basidia was not observed.
    Matched MeSH terms: Sequence Analysis, DNA
  10. Haigh AL, Gibernau M, Maurin O, Bailey P, Carlsen MM, Hay A, et al.
    Am J Bot, 2023 Feb;110(2):e16117.
    PMID: 36480380 DOI: 10.1002/ajb2.16117
    PREMISE: Recent phylogenetic studies of the Araceae have confirmed the position of the duckweeds nested within the aroids, and the monophyly of a clade containing all the unisexual flowered aroids plus the bisexual-flowered Calla palustris. The main objective of the present study was to better resolve the deep phylogenetic relationships among the main lineages within the family, particularly the relationships between the eight currently recognized subfamilies. We also aimed to confirm the phylogenetic position of the enigmatic genus Calla in relation to the long-debated evolutionary transition between bisexual and unisexual flowers in the family.

    METHODS: Nuclear DNA sequence data were generated for 128 species across 111 genera (78%) of Araceae using target sequence capture and the Angiosperms 353 universal probe set.

    RESULTS: The phylogenomic data confirmed the monophyly of the eight Araceae subfamilies, but the phylogenetic position of subfamily Lasioideae remains uncertain. The genus Calla is included in subfamily Aroideae, which has also been expanded to include Zamioculcadoideae. The tribe Aglaonemateae is newly defined to include the genera Aglaonema and Boycea.

    CONCLUSIONS: Our results strongly suggest that new research on African genera (Callopsis, Nephthytis, and Anubias) and Calla will be important for understanding the early evolution of the Aroideae. Also of particular interest are the phylogenetic positions of the isolated genera Montrichardia, Zantedeschia, and Anchomanes, which remain only moderately supported here.

    Matched MeSH terms: Sequence Analysis, DNA
  11. Syamsiah Aini S, Leow BL, Faizul Fikri MY, Muhammad Redzwan S, Faizah Hanim MS
    Trop Biomed, 2022 Dec 01;39(4):579-586.
    PMID: 36602219 DOI: 10.47665/tb.39.4.015
    Newcastle disease (ND) is an extremely contagious and fatal viral disease causing huge economic losses to the poultry industry. Following recent ND outbreaks in Sabah in commercial poultry and backyard farms, it was speculated that this could be due to a new introduction of Newcastle Disease Virus (NDV) genotype/sub-genotype. Here we report the genetic characterization of NDVs isolated from Sabah during early 2021. All isolates were amplified and sequenced with primers specific to the viral fusion (F) gene using reverse transcription-polymerase chain reaction (RT-PCR). Nucleotide sequence analysis of the F gene showed that all isolates shared similar homology of 99.4% with NDV strain from Iran isolated in 2018. Amino acid sequences of the F protein cleavage site revealed the motif of 112RRQKRF117 indicating all isolates were of virulent strain. Phylogenetic analysis demonstrated that all isolates were clustered under sub-genotype VII 1.1 and clustered together with isolates from Iran (previously known as subgenotype VIIl). The present findings suggested that there is an emerging of a new sub-genotype into the poultry population in Sabah and this sub-genotype has never been reported before in Malaysia. Therefore, transboundary monitoring and continuous surveillance should be implemented for proper control and prevention of the disease. A further molecular epidemiological analysis of NDV is needed to well understand the circulatory patterns of virulent strains of NDV in the country to prevent future outbreaks.
    Matched MeSH terms: Sequence Analysis, DNA
  12. Runtuwene LR, Sathirapongsasuti N, Srisawat R, Komalamisra N, Tuda JSB, Mongan AE, et al.
    BMC Res Notes, 2022 Feb 12;15(1):44.
    PMID: 35151353 DOI: 10.1186/s13104-022-05927-2
    OBJECTIVE: To disseminate the portable sequencer MinION in developing countries for the main purpose of battling infectious diseases, we found a consortium called Global Research Alliance in Infectious Diseases (GRAID). By holding and inviting researchers both from developed and developing countries, we aim to train the participants with MinION's operations and foster a collaboration in infectious diseases researches. As a real-life example in which resources are limited, we describe here a result from a training course, a metagenomics analysis from two blood samples collected from a routine cattle surveillance in Kulan Progo District, Yogyakarta Province, Indonesia in 2019.

    RESULTS: One of the samples was successfully sequenced with enough sequencing yield for further analysis. After depleting the reads mapped to host DNA, the remaining reads were shown to map to Theileria orientalis using BLAST and OneCodex. Although the reads were also mapped to Clostridium botulinum, those were found to be artifacts derived from the cow genome. An effort to construct a consensus sequence was successful using a reference-based approach with Pomoxis. Hence, we concluded that the asymptomatic cow might be infected with T. orientalis and showed the usefulness of sequencing technology, specifically the MinION platform, in a developing country.

    Matched MeSH terms: Sequence Analysis, DNA
  13. Puah SM, Fong SP, Kee BP, Puthucheary SD, Chua KH
    Microb Pathog, 2022 Jan;162:105345.
    PMID: 34896547 DOI: 10.1016/j.micpath.2021.105345
    Recently, Elizabethkingia species have gained attention as a cause of life-threatening infections. The identification via phenotypic methods of three important species- Elizabethkingia meningoseptica, E. anophelis and E. miricola is difficult. Our objectives were to re-assess 30 archived Flavobacterium meningosepticum isolates using 16S rRNA gene sequencing, ERIC-PCR, and biofilm formation assay. Twenty-four isolates were re-identified as E. anophelis and 6 as E. miricola. All of them had the ability to form biofilm as shown in microtiter plate assay based on crystal violet staining. Overall, E. anophelis had a higher specific biofilm formation index compared to E. miricola. A total of 42% (10 out of 24) of E. anophelis were classified as strong, 29% (7 out of 24) as moderate and 29% (7 out of 24) as weak biofilm producers. E. miricola, 17% (1 out of 6) isolates were strong biofilm producers, 50% (3 out of 6) moderate and 33% (2 out of 6) were weak producers. E. anophelis from tracheal secretions were significantly associated with (p = 0.0361) strong biofilm formation. In summary, this study showed that the isolates originally identified as F. meningosepticum were re-classified using the 16S rRNA gene as one of two Elizabethkingia species. The ability of E. anophelis to form strong biofilm in endotracheal tubes indicates their probable role in the pathogenesis of Elizabethkingia infections.
    Matched MeSH terms: Sequence Analysis, DNA
  14. Amrina RA, Furusawa G, Lau NS
    Int J Syst Evol Microbiol, 2021 Nov;71(11).
    PMID: 34752210 DOI: 10.1099/ijsem.0.005087
    A novel rod-shaped, Gram-stain-negative, strictly aerobic and alginate-degrading marine bacterium, designated CCB-QB4T, was isolated from a surface of algal turf collected from a coastal area of Penang, Malaysia. The cells showed motility by a lateral flagellum. The rod-shaped cells formed long chains end-to-end. Phylogenetic analysis based on the 16S rRNA gene sequence of strain CCB-QB4T showed 94.07, 92.69, 91.52 and 90.90 % sequence similarity to Algibacillus agarilyticus RQJ05T, Catenovulum maritimum Q1T, Catenovulum agarivorans YM01T and Catenovulum sediminis D2T, respectively. Strain CCB-QB4T formed a cluster with A. agarilyticus RQJ05T. Strain CCB-QB4T was catalase-negative, oxidase-positive, and degraded agar, alginate, and starch. Cell growth was observed at 15-40 °C, at pH 7.0-10.0 and in the presence of 1-6 % (w/v) NaCl and glucose. The major fatty acids were summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH), C16 : 0 and C18 : 1 ω7c. The polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two unidentified glycolipids, an unidentified phospholipid and unidentified lipid. The major respiratory quinone was ubiquinone-8. The genomic DNA G+C content was 46.7 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain CCB-BQ4T represents a novel species in a new genus, for which the name Saccharobesus litoralis gen. nov., sp. nov. is proposed. The type strain is CCB-QB4T (=JCM 33513T=CCB-MBL 5008T).
    Matched MeSH terms: Sequence Analysis, DNA
  15. Zhang Y, Yu J, Tan L, Wang X, Li R, Kim DY
    J Microbiol, 2021 Nov;59(11):1044-1055.
    PMID: 34570337 DOI: 10.1007/s12275-021-1361-8
    Getah virus (GETV), which was first isolated in Malaysia in 1955, and Sagiyama virus (SAGV), isolated in Japan in 1956, are members of the genus Alphavirus in the family Togaviridae. It is a consensus view that SAGV is a variant of GETV. In the present study, we determined the complete sequences of the prototype GETV MM2021 and SAGV M6-Mag132 genomic RNA extracted from plaque-purified viruses. The MM2021 genome was 11,692 nucleotides (nt) in length in the absence of 3' poly(A) tail, and the length of M6-Mag132 genome was 11,698 nt. Through sequence alignment of MM2021 and M6-Mag132, we located all the amino acid differences between these two strains, which were scattered in all the encoded proteins. Subsequently, we validated the close evolutionary relationship between GETV and SAGV by constructing phylogenetic trees based on either complete genomes or structural genomes. We eventually analyzed the growth kinetics of GETV and SAGV as well as other representative alphaviruses in various mammalian and insect cell lines. It was shown that human-oriented cell lines such as HEK-293T and Hela cells were relatively resistant to GETV and SAGV infection due to absence of proviral factors or species-specific barrier. On the other hand, both GETV and SAGV replicated efficiently in non-human cell lines. Our results provide essential genetic information for future epidemiological surveillance on Alphaviruses and lay the foundation for developing effective interventions against GETV and SAGV.
    Matched MeSH terms: Sequence Analysis, DNA
  16. Chua HS, Soh YH, Loong SK, AbuBakar S
    Ann Clin Microbiol Antimicrob, 2021 Oct 03;20(1):72.
    PMID: 34602092 DOI: 10.1186/s12941-021-00475-2
    BACKGROUND: Francisella philomiragia is a very rare opportunistic pathogen of humans which causes protean diseases such as pneumonia and other systemic infections. Subsequent failure of prompt treatment may result in poor prognosis with mortality among infected patients.

    CASE PRESENTATION: The present report describes a case of F. philomiragia bacteraemia first reported in Malaysia and Asian in a 60-year-old patient with underlying end-stage renal disease (ESRF) and diabetes mellitus. He presented with Acute Pulmonary Oedema with Non-ST-Elevation Myocardial Infarction (NSTEMI) in our hospital. He was intubated in view of persistent type I respiratory failure and persistent desaturation despite post haemodialysis. Blood investigation indicated the presence of ongoing infection and inflammation. The aerobic blood culture growth of F. philomiragia was identified using the matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (Score value: 2.16) and confirmed by 16S Ribosomal DNA (16S rDNA) sequencing. He was discharged well on day 26 of admission, after completing one week of piperacillin/tazobactam and two weeks of doxycycline.

    CONCLUSION: Clinical suspicion should be raised if patients with known risk factors are presenting with pneumonia or pulmonary nodules especially as these are the most common manifestations of F. philomiragia infection. Early diagnosis via accurate laboratory identification of the organism through MALDI-TOF mass spectrometry and molecular technique such as 16S rDNA sequencing are vital for prompt treatment that results in better outcomes for the afflicted patients.

    Matched MeSH terms: Sequence Analysis, DNA
  17. 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: Sequence Analysis, DNA
  18. Baba ZA, Hamid B, Sheikh TA, Alotaibi SH, El Enshasy HA, Ansari MJ, et al.
    Molecules, 2021 Sep 23;26(19).
    PMID: 34641302 DOI: 10.3390/molecules26195758
    Soil potassium (K) supplement depends intensively on the application of chemical fertilizers, which have substantial harmful environmental effects. However, some bacteria can act as inoculants by converting unavailable and insoluble K forms into plant-accessible forms. Such bacteria are an eco-friendly approach for enhancing plant K absorption and consequently reducing utilization of chemical fertilization. Therefore, the present research was undertaken to isolate, screen, and characterize the K solubilizing bacteria (KSB) from the rhizosphere soils of northern India. Overall, 110 strains were isolated, but only 13 isolates showed significant K solubilizing ability by forming a halo zone on solid media. They were further screened for K solubilizing activity at 0 °C, 1 °C, 3 °C, 5 °C, 7 °C, 15 °C, and 20 °C for 5, 10, and 20 days. All the bacterial isolates showed mineral K solubilization activity at these different temperatures. However, the content of K solubilization increased with the upsurge in temperature and period of incubation. The isolate KSB (Grz) showed the highest K solubilization index of 462.28% after 48 h of incubation at 20 °C. The maximum of 23.38 µg K/mL broth was solubilized by the isolate KSB (Grz) at 20 °C after 20 days of incubation. Based on morphological, biochemical, and molecular characterization (through the 16S rDNA approach), the isolate KSB (Grz) was identified as Mesorhizobium sp. The majority of the strains produced HCN and ammonia. The maximum indole acetic acid (IAA) (31.54 µM/mL) and cellulase (390 µM/mL) were produced by the isolate KSB (Grz). In contrast, the highest protease (525.12 µM/mL) and chitinase (5.20 µM/mL) activities were shown by standard strain Bacillus mucilaginosus and KSB (Gmr) isolate, respectively.
    Matched MeSH terms: Sequence Analysis, DNA/methods*
  19. Ngwe Tun MM, Muthugala R, Rajamanthri L, Nabeshima T, Buerano CC, Morita K
    Jpn J Infect Dis, 2021 Sep 22;74(5):443-449.
    PMID: 33642435 DOI: 10.7883/yoken.JJID.2020.854
    During the 2017 outbreak of severe dengue in Sri Lanka, dengue virus (DENV) serotypes 2, 3, and 4 were found to be co-circulating. Our previous study of 295 patients from the National Hospital Kandy in Sri Lanka between March 2017 and January 2018 determined that the dominant infecting serotype was DENV-2. In this study, we aimed to characterize the DENV-3 strains from non-severe and severe dengue patients from our previous study population. Patients' clinical records and previous laboratory tests, including dengue-specific nonstructural protein 1 antigen rapid test and IgM-capture and IgG enzyme-linked immunosorbent assays, were analyzed together with the present results of real-time reverse transcription polymerase chain reaction and next-generation sequencing of DENV-3. Complete genome analysis determined that DENV-3 isolates belonged to 2 different clades of genotype I and were genetically close to strains from Indonesia, China, Singapore, Malaysia, and Australia. There were 16 amino acid changes among DENV-3 isolates, and a greater number of changes were found in nonstructural proteins than in structural proteins. The emergence of DENV-3 genotype I was noted for the first time in Sri Lanka. Continuous monitoring of this newly emerged genotype and other DENV serotypes and genotypes is needed to determine their effects on future outbreaks and understand the molecular epidemiology of dengue.
    Matched MeSH terms: Sequence Analysis, DNA
  20. Yong HS, Chua KO, Song SL, Liew YJ, Eamsobhana P, Chan KG
    Mol Biol Rep, 2021 Aug;48(8):6047-6056.
    PMID: 34357549 DOI: 10.1007/s11033-021-06608-2
    BACKGROUND: Tephritid fruit flies of the genus Dacus are members of the tribe Dacini, subfamily Dacinae. There are some 274 species worldwide, distributed in Africa and the Asia-Pacific. To date, only five complete mitochondrial genomes (mitogenomes) of Dacus fruit flies have been published and are available in the GenBank.

    METHODS AND RESULTS: In view of the lack of study on their mitogenome, we sequenced (by next generation sequencing) and annotated the complete mitogenome of D. vijaysegarani from Malaysia to determine its features and phylogenetic relationship. The whole mitogenome of D. vijaysegarani has identical gene order with the published mitogenomes of the genus Dacus, with 13 protein-coding genes, two rRNA genes, 22 tRNAs, a non-coding A + T rich control region, and intergenic spacer and overlap sequences. Phylogenetic analysis based on 15 mitochondrial genes (13 PCGs and two rRNA genes), reveals Dacus, Zeugodacus and Bactrocera forming a distinct clade. The genus Dacus forms a monophyletic group in the subclade containing also the Zeugodacus group; this Dacus-Zeugodacus subclade is distinct from the Bactrocera subclade. D. (Mellesis) vijaysegarani forms a lineage with D. (Mellesis) trimacula in the subcluster containing also the lineage of D. (Mellesis) conopsoides and D. (Callantra) longicornis. D. (Dacus) bivittatus and D. (Didacus) ciliatus form a distinct subcluster. Based on cox1 sequences, the Malaysia and Vietnam taxa of D. vijaysegarani may not be conspecific.

    CONCLUSIONS: Overall, the mitochondrial genome of D. vijaysegarani provided essential molecular data that could be useful for further studies for species diagnosis, evolution and phylogeny research of other tephritid fruit flies in the future.

    Matched MeSH terms: Sequence Analysis, DNA/methods
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