MyMedR

Displaying publications 41 - 60 of 634 in total

Abstract:

Sort:

Detection of Babesia spp. in Dogs and Their Ticks From Peninsular Malaysia: Emphasis on Babesia gibsoni and Babesia vogeli Infections in Rhipicephalus sanguineus sensu lato (Acari: Ixodidae)

Prakash BK, Low VL, Vinnie-Siow WY, Tan TK, Lim YA, Morvarid AR, et al.

J Med Entomol, 2018 Aug 29;55(5):1337-1340.
PMID: 29762747 DOI: 10.1093/jme/tjy072

Canine babesiosis is an emerging tick-borne disease with a worldwide distribution, including Malaysia. While the prevalence of Babesia has been documented from dogs in Malaysia, occurrence of Babesia has been relatively little studied in their tick vectors. Accordingly, a total of 240 dogs and 140 Rhipicephalus sanguineus sensu lato (s.l.) (Acari: Ixodidae) ticks from Malaysia were molecularly screened for the presence of Babesia protozoa in the present study. Babesia gibsoni was only detected in ticks (1.4%), whereas Babesia vogeli was detected in both ticks (1.4%) and dogs (2.1%). This study highlights the detection of B. gibsoni and B. vogeli for the first time, in both adult and nymphal stages of R. sanguineus s.l. in Malaysia, suggesting the potential role of this tick species in transmitting canine babesiosis.

Matched MeSH terms: RNA, Ribosomal, 18S/genetics
Fulltext Microbiota of Palm Oil Mill Wastewater in Malaysia

Bala JD, Lalung J, Al-Gheethi AAS, Hossain K, Ismail N

Trop Life Sci Res, 2018 Jul;29(2):131-163.
PMID: 30112146 MyJurnal DOI: 10.21315/tlsr2018.29.2.10

This study was aimed at identifying indigenous microorganisms from palm oil mill effluent (POME) and to ascertain the microbial load. Isolation and identification of indigenous microorganisms was subjected to standard microbiological methods and sequencing of the 16S rRNA and 18S rRNA genes. Sequencing of the 16S rRNA and 18S rRNA genes for the microbial strains signifies that they were known as Micrococcus luteus 101PB, Stenotrophomonas maltophilia 102PB, Bacillus cereus 103PB, Providencia vermicola 104PB, Klebsiella pneumoniae 105PB, Bacillus subtilis 106PB, Aspergillus fumigatus 107PF, Aspergillus nomius 108PF, Aspergillus niger 109PF and Meyerozyma guilliermondii 110PF. Results revealed that the population of total heterotrophic bacteria (THB) ranged from 9.5 × 105 - 7.9 × 106 cfu/mL. The total heterotrophic fungi (THF) ranged from 2.1 × 104 - 6.4 × 104 cfu/mL. Total viable heterotrophic indigenous microbial population on CMC agar ranged from 8.2 × 105 - 9.1 × 106 cfu/mL and 1.4 × 103 - 3.4 × 103 cfu/mL for bacteria and fungi respectively. The microbial population of oil degrading bacteria (ODB) ranged from 6.4 × 105 - 4.8 × 106 cfu/mL and the oil degrading fungi (ODF) ranged from 2.8 × 103 - 4.7 × 104 cfu/mL. The findings revealed that microorganisms flourish well in POME. Therefore, this denotes that isolating native microorganisms from POME is imperative for effectual bioremediation, biotreatment and biodegradation of industrial wastewaters.

Matched MeSH terms: RNA, Ribosomal, 16S; RNA, Ribosomal, 18S
Description and characterization of questing hard tick, Dermacentor steini (Acari: Ixodidae) in Malaysia based on phenotypic and genotypic traits

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
Fulltext Nodosilinea signiensis sp. nov. (Leptolyngbyaceae, Synechococcales), a new terrestrial cyanobacterium isolated from mats collected on Signy Island, South Orkney Islands, Antarctica

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
Genome-based analyses reveal the presence of 12 heterotypic synonyms in the genus Streptomyces and emended descriptions of Streptomyces bottropensis, Streptomyces celluloﬂavus, Streptomyces fulvissimus, Streptomyces glaucescens, Streptomyces murinus, and Streptomyces variegatus

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
Exploring the fermentation characteristics of a newly isolated marine bacteria strain, Gordonia terrae TWRH01 for carotenoids production

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
Microbiota composition of captive bluestreak cleaner wrasse Labroides dimidiatus (Valenciennes, 1839)

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
Molecular evidence of Anaplasma infection in naturally affected domestic cats of Pakistan

Ahmed A, Ijaz M, Ghauri HN, Aziz MU, Ghaffar A, Naveed M, et al.

Comp Immunol Microbiol Infect Dis, 2020 Oct;72:101524.
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
Unusually high genetic diversity in the Bornean Limnonectes kuhlii-like fanged frogs (Anura: Dicroglossidae)

Matsui M, Kuraishi N, Eto K, Hamidy A, Nishikawa K, Shimada T, et al.

Mol Phylogenet Evol, 2016 09;102:305-19.
PMID: 27374495 DOI: 10.1016/j.ympev.2016.06.009

A fanged frog Limnonectes kuhlii was once thought to be wide-ranging in Southeast Asia, but is now confined to its type locality Java through recent phylogenetic studies, which clarified heterospecific status of non-Javanese populations, and monophyly of Bornean populations. However, large genetic differences among Bornean populations suggest occurrence of cryptic species, which we test using dense geographic sampling. We estimated the phylogenetic relationships among samples of Bornean populations together with their putative relatives from the continental Southeast Asia, using 2517bp sequences of the 12S rRNA, tRNA(val), and 16S rRNA of mitochondrial DNA, and 2367bp sequences of the NCX1, POMC, and RAG1 of nuclear genes. In the mtDNA trees, Bornean L. kuhlii-like frogs formed a monophyletic group split into 18 species lineages including L. hikidai, with the deepest phylogenetic split separating L. cintalubang from the remaining species. Almost all of these lineages co-occur geographically, and two to three lineages were found syntopically in each locality. Co-occurrence of more than one lineage may be maintained by differential morphology and microhabitat selection. These syntopic lineages should be regarded as distinct species. Our results clearly indicate that taxonomic revision is urgent to clarify many evolutionary problems of Bornean L. kuhlii-like frogs.

Matched MeSH terms: RNA, Ribosomal/genetics; RNA, Ribosomal/metabolism; RNA, Ribosomal/chemistry; RNA, Ribosomal, 16S/genetics; RNA, Ribosomal, 16S/metabolism; RNA, Ribosomal, 16S/chemistry
Sphingopyxis microcysteis sp. nov., a novel bioactive exopolysaccharides-bearing Sphingomonadaceae isolated from the Microcystis phycosphere

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
Bacterial endosymbiont inhabiting Leucaena leucocephala leaves and their antioxidant and antidiabetic potential

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
Flea-borne pathogens in the cat flea Ctenocephalides felis and their association with mtDNA diversity of the flea host

Azrizal-Wahid N, Sofian-Azirun M, Low VL

Comp Immunol Microbiol Infect Dis, 2021 Apr;75:101621.
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
Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users

Gopinath D, Wie CC, Banerjee M, Thangavelu L, Kumar R P, Nallaswamy D, et al.

Clin Oral Investig, 2022 Feb;26(2):1647-1656.
PMID: 34436669 DOI: 10.1007/s00784-021-04137-7

INTRODUCTION: Smoked, and especially smokeless, tobacco are major causes of oral cancer globally. Here, we examine the oral bacteriome of smokers and of smokeless tobacco users, in comparison to healthy controls, using 16S rRNA gene sequencing.
METHODS: Oral swab samples were collected from smokers, smokeless tobacco users, and healthy controls (n = 44). Microbial DNA was extracted and the 16S rRNA gene profiled using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and taxonomical classification was performed using the phylogenetic placement method. Differentially abundant taxa were identified using DESeq2, while functional metagenomes based on KEGG orthology abundance were inferred using LIMMA.
RESULTS: A significantly higher microbial diversity was observed in smokeless tobacco users and smokers relative to controls (P 1.5; BH adj P

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Sulfitobacter alexandrii sp. nov., a new microalgae growth-promoting bacterium with exopolysaccharides bioflocculanting potential isolated from marine phycosphere

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
Taxonomic note on the family Pseudonocardiaceae based on phylogenomic analysis and descriptions of Allosaccharopolyspora gen. nov. and Halosaccharopolyspora gen. nov

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
The complete mitogenome of the cow tail ray Pastinachus atrus (Macleay, 1883) (Elasmobranchii; Myliobatiformes; Dasyatidae)

Austin CM, Tan MH, Lee YP, Croft LJ, Meekan MG, Gan HM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(2):1372-3.
PMID: 25103432 DOI: 10.3109/19401736.2014.947586

The complete mitogenome of the ray Pastinachus atrus was recovered from a partial genome scan using the HiSeq sequencing system. The P. atrus mitogenome has 18,162 base pairs (61% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 2516 bp non-coding AT-rich region. This mitogenome sequence is the first for a ray from Australian waters, the first for the Genus Pastinachus, and the 6th for the family Dasyatidae.

Matched MeSH terms: RNA, Ribosomal/genetics
Fulltext Molecular phylogeny of the bamboo sharks (Chiloscyllium spp.)

Masstor NH, Samat A, Nor SM, Md-Zain BM

Biomed Res Int, 2014;2014:213896.
PMID: 25013766 DOI: 10.1155/2014/213896

Chiloscyllium, commonly called bamboo shark, can be found inhabiting the waters of the Indo-West Pacific around East Asian countries such as Malaysia, Myanmar, Thailand, Singapore, and Indonesia. The International Union for Conservation of Nature (IUCN) Red List has categorized them as nearly threatened sharks out of their declining population status due to overexploitation. A molecular study was carried out to portray the systematic relationships within Chiloscyllium species using 12S rRNA and cytochrome b gene sequences. Maximum parsimony and Bayesian were used to reconstruct their phylogeny trees. A total of 381 bp sequences' lengths were successfully aligned in the 12S rRNA region, with 41 bp sites being parsimony-informative. In the cytochrome b region, a total of 1120 bp sites were aligned, with 352 parsimony-informative characters. All analyses yield phylogeny trees on which C. indicum has close relationships with C. plagiosum. C. punctatum is sister taxon to both C. indicum and C. plagiosum while C. griseum and C. hasseltii formed their own clade as sister taxa. These Chiloscyllium classifications can be supported by some morphological characters (lateral dermal ridges on the body, coloring patterns, and appearance of hypobranchials and basibranchial plate) that can clearly be used to differentiate each species.

Matched MeSH terms: RNA, Ribosomal/genetics*
Identification of Vibrio harveyi isolated from diseased Asian seabass Lates calcarifer by use of 16S ribosomal DNA sequencing

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*
Fulltext Phylogenetic relationships of leaf monkeys (Presbytis; Colobinae) based on cytochrome b and 12S rRNA genes

Vun VF, Mahani MC, Lakim M, Ampeng A, Md-Zain BM

Genet. Mol. Res., 2011;10(1):368-81.
PMID: 21365553 DOI: 10.4238/vol10-1gmr1048

Little is known about the classification and phylogenetic relationships of the leaf monkeys (Presbytis). We analyzed mitochondrial DNA sequences of cytochrome b (Cyt b) and 12S rRNA to determine the phylogenetic relationships of the genus Presbytis. Gene fragments of 388 and 371 bp of Cyt b and 12S rRNA, respectively, were sequenced from samples of Presbytis melalophos (subspecies femoralis, siamensis, robinsoni, and chrysomelas), P. rubicunda and P. hosei. The genus Trachypithecus (Cercopithecidae) was used as an outgroup. The Cyt b NJ and MP phylogeny trees showed P. m. chrysomelas to be the most primitive, followed by P. hosei, whereas 12S rRNA tree topology only indicated that these two species have close relationships with the other members of the genus. In our analysis, chrysomelas, previously classified as a subspecies of P. melalophos, was not included in either the P. m. femoralis clade or the P. m. siamensis clade. Whether or not there should be a separation at the species level remains to be clarified. The tree topologies also showed that P. m. siamensis is paraphyletic with P. m. robinsoni, and P. m. femoralis with P. rubicunda, in two different clades. Cyt b and 12S rRNA are good gene candidates for the study of phylogenetic relationships at the species level. However, the systematic relationships of some subspecies in this genus remain unclear.

Matched MeSH terms: RNA, Ribosomal/genetics*
Fulltext Erwinia mallotivora sp., a new pathogen of papaya (Carica papaya) in Peninsular Malaysia

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

Filters

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links