The New Human Babesia sp. FR1 Is a European Member of the Babesia sp. MO1 Clade

In Europe, Babesia divergens is responsible for most of the severe cases of human babesiosis. In the present study, we describe a case of babesiosis in a splenectomized patient in France and report a detailed molecular characterization of the etiological agent, named Babesia sp. FR1, as well as of closely related Babesia divergens, Babesia capreoli and Babesia sp. MO1-like parasites. The analysis of the conserved 18S rRNA gene was supplemented with the analysis of more discriminant markers involved in the red blood cell invasion process: rap-1a (rhoptry-associated-protein 1) and ama-1 (apical-membrane-antigen 1). The rap-1a and ama-1 phylogenetic analyses were congruent, placing Babesia sp. FR1, the new European etiological agent, in the American cluster of Babesia sp. MO1-like parasites. Based on two additional markers, our analysis confirms the clear separation of B. divergens and B. capreoli. Babesia sp. MO1-like parasites should also be considered as a separate species, with the rabbit as its natural host, differing from those of B. divergens (cattle) and B. capreoli (roe deer). The natural host of Babesia sp. FR1 remains to be discovered.

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Molecular Characterization of Ciliate Diversity in Stream Biofilms

Applied and Environmental Microbiology ◽

10.1128/aem.01438-07 ◽

2008 ◽

Vol 74 (6) ◽

pp. 1740-1747 ◽

Cited By ~ 52

Author(s):

Andrew Dopheide ◽

Gavin Lear ◽

Rebecca Stott ◽

Gillian Lewis

Keyword(s):

18S Rrna ◽

Pcr Primers ◽

18S Rrna Gene ◽

Sequence Diversity ◽

Rrna Genes ◽

Rrna Gene ◽

Sequencing Analysis ◽

Specific Pcr ◽

Stream Biofilms

ABSTRACT Free-living protozoa are thought to be of fundamental importance in aquatic ecosystems, but there is limited understanding of their diversity and ecological role, particularly in surface-associated communities such as biofilms. Existing eukaryote-specific PCR primers were used to survey 18S rRNA gene sequence diversity in stream biofilms but poorly revealed protozoan diversity, demonstrating a need for protozoan-targeted primers. Group-specific PCR primers targeting 18S rRNA genes of the protozoan phylum Ciliophora were therefore designed and tested using DNA extracted from cultured protozoan isolates. The two most reliable primer combinations were applied to stream biofilm DNA, followed by cloning and sequencing analysis. Of 44 clones derived from primer set 384F/1147R, 86% were of probable ciliate origin, as were 25% of 44 clones detected by primer set 121F/1147R. A further 29% of 121F/1147R-detected clones matched sequences from the closely related phylum Apicomplexa. The highly ciliate-specific primer set 384F/1147R was subsequently used in PCRs on biofilm DNA from four streams exhibiting different levels of human impact, revealing differences in ciliate sequence diversity in samples from each site. Of a total of 240 clones, 73% were of probable ciliate origin; 54 different putative ciliate sequences were detected from throughout seven taxonomic ciliate classes. Sequences from Oligohymenophorea were most commonly detected in all samples, followed by either Spirotrichea or Phyllopharyngea. Restriction fragment length polymorphism profile-based analysis of clones suggested a potentially higher level of diversity than did sequencing. Nevertheless, newly designed PCR primers 384F/1147R were considered to provide an effective molecular basis for characterization of ciliate diversity in stream biofilms.

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Steinernema borjomiense n. sp. (Rhabditida: Steinernematidae), a new entomopathogenic nematode from Georgia

Nematology ◽

10.1163/15685411-00003167 ◽

2018 ◽

Vol 20 (7) ◽

pp. 653-669 ◽

Cited By ~ 4

Author(s):

Oleg Gorgadze ◽

Elena Fanelli ◽

Manana Lortkhipanidze ◽

Alberto Troccoli ◽

Medea Burjanadze ◽

...

Keyword(s):

New Species ◽

18S Rrna ◽

Entomopathogenic Nematode ◽

Phylogenetic Analyses ◽

Tail Length ◽

Morphological Characters ◽

18S Rrna Gene ◽

The Body ◽

Rrna Gene ◽

A New Species

Summary A new species of entomopathogenic nematode, Steinernema borjomiense n. sp., was isolated from the body of the host insect, Oryctes nasicornis (Coleoptera: Scarabaeidae), in Georgia, in the territory of Borjomi-Kharagauli. Morphological characters indicate that the new species is closely related to species of the feltiae-group. The infective juveniles are characterised by the following morphological characters: body length of 879 (777-989) μm, distance between the head and excretory pore = 72 (62-80) μm, pharynx length = 132 (122-142) μm, tail length = 70 (60-80) μm, ratio a = 26.3 (23.0-29.3), H% = 45 (40-51), D% = 54 (47-59), E% = 102 (95-115), and lateral fields consisting of seven ridges (eight incisures) at mid-body. Steinernema borjomiense n. sp. was molecularly characterised by sequencing three ribosomal regions (the ITS, the D2-D3 expansion domains and the 18S rRNA gene) and the mitochondrial COI gene. Phylogenetic analyses revealed that S. borjomiense n. sp. differs from all other known species of Steinernema and is a member of the monticolum-group.

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Morphological redescription and molecular characterization of Trichodina matsu Basson & Van As, 1994 (Ciliophora, Mobilida, Trichodinidae) infecting Tachysurus fulvidraco (Richardson, 1846) from Chongqing, China

Zootaxa ◽

10.11646/zootaxa.4995.2.6 ◽

2021 ◽

Vol 4995 (2) ◽

pp. 334-344

Author(s):

QIAN ZHOU ◽

FAHUI TANG ◽

YUANJUN ZHAO

Keyword(s):

Phylogenetic Analyses ◽

Molecular Data ◽

18S Rrna Gene ◽

Rrna Gene ◽

Similar Species ◽

Sequence Alignments ◽

Multiple Sequence ◽

Multiple Sequence Alignments ◽

Morphological And Molecular Data ◽

Tachysurus Fulvidraco

During a survey of parasitic ciliates in Chongqing, China, Trichodina matsu Basson & Van As, 1994 was isolated from gills of Tachysurus fulvidraco. Furthermore, the 18S rRNA gene and ITS-5.8S rRNA region of T. matsu were sequenced for the first time and applied for the species identification and comparison with similar species in the present study. Based on the morphological and molecular comparisons, the results indicate that T. matsu is an ectoparasite specific for the Siluriformes catfish. Based on the analyses of genetic distance, multiple sequence alignments, and phylogenetic analyses, no obvious differentiation within populations of T. matsu was found. In addition, the ‘Trichodina hyperparasitis’ (KX904933) in GenBank is a misidentification and appears to be conspecific with T. matsu according to the comparison of morphological and molecular data.

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Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004977 ◽

2021 ◽

Vol 71 (9) ◽

Author(s):

Silvio Hering ◽

Moritz K. Jansson ◽

Michael E. J. Buhl

Keyword(s):

Type Species ◽

Throat Swab ◽

Novel Species ◽

Phylogenetic Analyses ◽

Routine Care ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

Bacterium Strain

A novel species within the genus Eikenella is described, based on the phenotypical, biochemical and genetic characterization of a strain of a facultatively anaerobic, Gram-negative rod-shaped bacterium. Strain S3360T was isolated from the throat swab of a patient sampled during routine care at a hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequences) placed the strain in the genus Eikenella , separate from all recognized species but with the closest relationship to Eikenella longinqua (NML 02-A-017T). Eikenella is one of the genera in the HACEK group known to be responsible for rare cases of endocarditis in humans. Until the recent descriptions of Eikenella exigua , Eikenella halliae and Eikenella longinqua , Eikenella corrodens had been the only validly published species in this genus since its description as Bacteroides corrodens in 1958. Unlike these species, strain S3360T is able to metabolize carbohydrates (glucose). The average nucleotide identities of strain S3360T with E. longinqua (NML 02-A-017T) and E. corrodens (NCTC 10596T), the type species of the genus, were 90.5 and 84.7 %, respectively, and the corresponding genome-to-genome distance values were 41.3 and 29.0 %, respectively. The DNA G+C content of strain S3360T was 58.4 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3360T is considered to represent a novel species within the genus Eikenella , for which the name Eikenella glucosivorans sp. nov. is proposed. The type strain is S3360T (DSM 110714T=CCOS 1935T=CCUG 74293T). In addition, an emendation of the genus Eikenella is proposed to include species which are saccharolytic.

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Redescription and phylogenetic analyses of Thaparocleidus gomtius and T. sudhakari (Monogenea: Dactylogyridae) from Wallago attu (Siluriformes: Siluridae) in India

Helminthologia ◽

10.1515/helm-2017-0008 ◽

2017 ◽

Vol 54 (1) ◽

pp. 87-96 ◽

Cited By ~ 1

Author(s):

C. Verma ◽

A. Chaudhary ◽

H. S. Singh

Keyword(s):

Phylogenetic Relationships ◽

18S Rrna ◽

Phylogenetic Analyses ◽

Uttar Pradesh ◽

18S Rrna Gene ◽

Morphometric Study ◽

Rrna Gene ◽

Molecular Analyses ◽

Wallago Attu ◽

Geographical Regions

Summary Two species of Thaparocleidus Jain (1952a) were found harboring W. attu from the Ganga River at two localities, Meerut and Farrukhabad, Uttar Pradesh, India, during the period of 2013-2015. Morphology and morphometric study of specimens identified as Thaparocleidus gomtius (Jain, 1952a) Lim, 1996 and T. sudhakari (Gusev, 1976) Lim, 1996. Molecular analyses using the 18S rRNA gene confirmed the validity of T. gomtius and T. sudhakari and demonstrated that both the species clustered with other Thaparocleidus species from different geographical regions. We aim at reassessing the taxonomy and establishing the phylogenetic relationships among these two redescribed species with other representatives of the genus Thaparocleidus.

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Cryptosporidium spp. in Domestic Dogs: the “Dog” Genotype

Applied and Environmental Microbiology ◽

10.1128/aem.66.5.2220-2223.2000 ◽

2000 ◽

Vol 66 (5) ◽

pp. 2220-2223 ◽

Cited By ~ 38

Author(s):

Una M. Morgan ◽

Lihua Xiao ◽

Paul Monis ◽

Abbie Fall ◽

Peter J. Irwin ◽

...

Keyword(s):

18S Rrna ◽

18S Rrna Gene ◽

Domestic Dogs ◽

Heat Shock Gene ◽

Valid Species ◽

Rrna Gene ◽

Phylogenetic Characterization ◽

Cryptosporidium Spp ◽

Shock Gene

ABSTRACT Genetic and phylogenetic characterization ofCryptosporidium isolates at two loci (18S rRNA gene and heat shock gene) from both Australian and United States dogs demonstrated that dog-derived Cryptosporidium isolates had a distinct genotype which is conserved across geographic areas. Phylogenetic analysis provided support for the idea that the “dog” genotype is, in fact, a valid species.

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Genotypic Characterization of Torymus sinensis (Hymenoptera: Torymidae) After Its Introduction in Tuscany (Italy) for the Biological Control of Dryocosmus kuriphilus (Hymenoptera: Cynipidae)

Journal of Insect Science ◽

10.1093/jisesa/iez080 ◽

2019 ◽

Vol 19 (4) ◽

Cited By ~ 1

Author(s):

Ambra Viviani ◽

Rodolfo Bernardi ◽

Andrea Cavallini ◽

Elisabetta Rossi

Keyword(s):

Biological Control ◽

18S Rrna ◽

18S Rrna Gene ◽

Its2 Region ◽

Rrna Gene ◽

Gall Wasp ◽

Dryocosmus Kuriphilus ◽

Torymus Sinensis ◽

The World

Abstract Torymus sinensis Kamijo (Hymenoptera: Torymidae) is an alien parasitoid that is used in many areas of the world for biological control the Asian chestnut gall wasp, Dryocosmus kuriphilus Yasumatsu (Hymenoptera: Cynipidae). In Italy, this parasitoid was imported from Japan in 2003 and subsequently multiplied and released throughout the country. In this study, a phylogenetic investigation was carried out on insects from three different sites in northern Tuscany (Italy). Moreover, the possible hybridization between T. sinensis and some native Torymus species was evaluated. The conserved region 18S rRNA gene and the hypervariable ITS2 (Internal Transcribed Spacer 2) region of the ribosomal cistrone were selected as molecular markers. Sequencing the amplified products, after cloning, ruled out any hybridization between T. sinensis and the native Torymus species, and also confirmed the presence of two haplotypes for the Tuscan population of T. sinensis both for the region of the 18S rRNA gene as well as for the ITS2 region. These results confirm that the environmental impact of the alien parasitoid T. sinensis in the study site is acceptable, although an extensive and repeated monitoring would be desirable.

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Blastococcus jejuensis sp. nov., an actinomycete from beach sediment, and emended description of the genus Blastococcus Ahrens and Moll 1970

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64268-0 ◽

2006 ◽

Vol 56 (10) ◽

pp. 2391-2396 ◽

Cited By ~ 27

Author(s):

Soon Dong Lee

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Rrna Gene ◽

The Novel ◽

Separate Species ◽

Beach Sediment ◽

Actinomycete Strain ◽

Type Strains

A novel actinomycete, strain KST3-10T, was isolated from sand sediment of a beach in Jeju, Korea, and was subjected to polyphasic taxonomic characterization. The organism produced circular, smooth, translucent, apricot-coloured colonies comprising coccoid- or rod-shaped cells. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the family Geodermatophilaceae and consistently formed a distinct sub-branch outside the radiation of the genus Blastococcus. The organism showed 16S rRNA gene sequence similarity values of 98.2 % with respect to Blastococcus aggregatus DSM 4725T and 98.1 % with respect to Blastococcus saxobsidens BC444T. The type strains of the two Blastococcus species shared 98.2 % sequence similarity with respect to each other, whereas the levels of sequence similarity between the novel organism and the type strains of the less closely related neighbours, Modestobacter multiseptatus and Geodermatophilus obscurus, were in the range 96.2–96.9 %. The physiological, biochemical and chemotaxonomic data revealed that the novel organism can be readily differentiated from members of the genus Blastococcus and that it merits separate species status. On the basis of the phenotypic and genotypic evidence, strain KST3-10T represents a novel species of the genus Blastococcus, for which the name Blastococcus jejuensis sp. nov. is proposed. The type strain is KST3-10T (=NRRL B-24440T=KCCM 42251T).

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Genetic characterization of Strongyloides spp. from captive, semi-captive and wild Bornean orangutans (Pongo pygmaeus) in Central and East Kalimantan, Borneo, Indonesia

Parasitology ◽

10.1017/s0031182011001284 ◽

2011 ◽

Vol 138 (11) ◽

pp. 1417-1422 ◽

Cited By ~ 17

Author(s):

E. M. LABES ◽

N. WIJAYANTI ◽

P. DEPLAZES ◽

A. MATHIS

Keyword(s):

18S Rrna ◽

Genetic Characterization ◽

18S Rrna Gene ◽

Rdna Locus ◽

Rrna Gene ◽

Fecal Material ◽

East Kalimantan ◽

The One ◽

Bornean Orangutans

SUMMARYOrangutans (Pongo spp.), Asia's only great apes, are threatened in their survival due to habitat loss, hunting and infections. Nematodes of the genus Strongyloides may represent a severe cause of death in wild and captive individuals. In order to better understand which Strongyloides species/subspecies infect orangutans under different conditions, larvae were isolated from fecal material collected in Indonesia from 9 captive, 2 semi-captive and 9 wild individuals, 18 captive groups of Bornean orangutans and from 1 human working with wild orangutans. Genotyping was done at the genomic rDNA locus (part of the 18S rRNA gene and internal transcribed spacer 1, ITS1) by sequencing amplicons. Thirty isolates, including the one from the human, could be identified as S. fuelleborni fuelleborni with 18S rRNA gene identities of 98·5–100%, with a corresponding published sequence. The ITS1 sequences could be determined for 17 of these isolates revealing a huge variability and 2 main clusters without obvious pattern with regard to attributes of the hosts. The ITS1 amplicons of 2 isolates were cloned and sequenced, revealing considerable variability indicative of mixed infections. One isolate from a captive individual was identified as S. stercoralis (18S rRNA) and showed 99% identity (ITS1) with S. stercoralis sequences from geographically distinct locations and host species. The findings are significant with regard to the zoonotic nature of these parasites and might contribute to the conservation of remaining orangutan populations.

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Cultivable bacterial flora of Indian oil reservoir: isolation, identification and characterization of the biotechnological potential

Biologia ◽

10.1515/biolog-2015-0017 ◽

2015 ◽

Vol 70 (1) ◽

pp. 1-10 ◽

Cited By ~ 3

Author(s):

Neha Saxena ◽

Soham Pore ◽

Preeti Arora ◽

Neelam Kapse ◽

Anupama Engineer ◽

...

Keyword(s):

Oil And Gas ◽

Produced Water ◽

Phylogenetic Analyses ◽

Bacterial Flora ◽

Oil Reservoirs ◽

Rrna Gene ◽

Oil Reservoir ◽

Biotechnological Potential ◽

Taxonomic Novelty

Abstract‘Produced water’ is a term used in oil industry to describe water produced along with oil and gas from oil reservoir. Microorganisms have been frequently isolated from produced water/oil reservoirs; however, there is paucity of information regarding the diversity and characterization of bacterial flora from Indian oil reservoirs. The present investigation was undertaken to study bacterial diversity associated with Indian oil reservoirs and to investigate their potential as a source of industrially valuable enzymes. A total of 103 strains were isolated from five oil reservoirs. PCR-based DNA fingerprinting grouped these strains into 72 genovars. These isolates were identified using morphological, phenotypical and phylogenetic analyses. Most of these isolates were thermophiles (growing at 45◦C or higher), halotolerant (growth at 5% salinity) and were distributed through a variety of genera including but not limited to Bacillus, Chelatococcus, Paenibacillus and Pseudomonas species. The 16S rRNA gene sequence of several strains shared less than 97% homology with the reference sequences in the GenBank database indicating taxonomic novelty of these strains. Assessment of the biotechnological potential of 72 genovars revealed that majority of strains produce one or many of the valuable enzymes including amylase, cellulase, xylanase, pectinase, inulinase, protease, alcohol dehydrogenase and urease. Most of the isolates also degraded crude oil or petroleum hydrocarbons. The vast pool of phenotypic, genetic and functional diversity of the strains retrieved in this study suggested oil reservoirs as yet largely untapped and potent source of taxonomically novel and biotechnologically valuable microorganisms.

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