Molecular Detection and Characterization of Blastocystis sp. and Enterocytozoon bieneusi in Cattle in Northern Spain

Some enteric parasites causing zoonotic diseases in livestock have been poorly studied or even neglected. This is the case in stramenopile Blastocystis sp. and the microsporidia Enterocytozoon bieneusi in Spain. This transversal molecular epidemiological survey aims to estimate the prevalence and molecular diversity of Blastocystis sp. and E. bieneusi in cattle faecal samples (n = 336) in the province of Álava, Northern Spain. Initial detection of Blastocystis and E. bieneusi was carried out by polymerase chain reaction (PCR) and Sanger sequencing of the small subunit (ssu) rRNA gene and internal transcribed spacer (ITS) region, respectively. Intra-host Blastocystis subtype diversity was further investigated by next generation amplicon sequencing (NGS) of the ssu rRNA gene in those samples that tested positive by conventional PCR. Amplicons compatible with Blastocystis sp. and E. bieneusi were observed in 32.1% (108/336, 95% CI: 27.2–37.4%) and 0.6% (2/336, 95% CI: 0.0–1.4%) of the cattle faecal samples examined, respectively. Sanger sequencing produced ambiguous/unreadable sequence data for most of the Blastocystis isolates sequenced. NGS allowed the identification of 10 Blastocystis subtypes including ST1, ST3, ST5, ST10, ST14, ST21, ST23, ST24, ST25, and ST26. All Blastocystis-positive isolates involved mixed infections of 2–8 STs in a total of 31 different combinations. The two E. bieneusi sequences were confirmed as potentially zoonotic genotype BEB4. Our data demonstrate that Blastocystis mixed subtype infections are extremely frequent in cattle in the study area. NGS was particularly suited to discern underrepresented subtypes or mixed subtype infections that were undetectable or unreadable by Sanger sequencing. The presence of zoonotic Blastocystis ST1, ST3, and ST5, and E. bieneusi BEB4 suggest cross-species transmission and a potential risk of human infection/colonization.

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Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea)

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004936 ◽

2021 ◽

Vol 71 (8) ◽

Author(s):

Ran Li ◽

Wenbao Zhuang ◽

Congcong Wang ◽

Hamed El-Serehy ◽

Saleh A. Al-Farraj ◽

...

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Small Subunit ◽

The Yellow Sea ◽

Rrna Gene ◽

Ssu Rrna ◽

Gene Trees ◽

Ssu Rrna Gene ◽

Anaerobic Ciliate ◽

Pr China

The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.

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Taxonomy, morphology and molecular systematics of three oligotrich ciliates, including a description of Apostrombidium parakielum spec. nov. (Ciliophora, Oligotrichia)

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.048314-0 ◽

2013 ◽

Vol 63 (Pt_3) ◽

pp. 1179-1191 ◽

Cited By ~ 14

Author(s):

Wen Song ◽

Jiamei Li ◽

Weiwei Liu ◽

Jiamei Jiang ◽

Khaled A. S. Al- Rasheid ◽

...

Keyword(s):

Sequence Data ◽

Novel Species ◽

Small Subunit ◽

Rrna Gene ◽

Ssu Rrna ◽

The Novel ◽

Small Subunit Rrna ◽

Ssu Rrna Gene ◽

Single Clade ◽

Ssu Rrna Gene Sequence

Three oligotrich ciliates, Apostrombidium parakielum spec. nov., Novistrombidium apsheronicum (Alekperov & Asadullayeva, 1997) Agatha, 2003 and Novistrombidium testaceum (Anigstein, 1914) Song & Bradbury, 1998 were collected from the coastal waters of China and their morphology and small-subunit rRNA (SSU rRNA) gene sequences were studied. The novel species can be recognized by the combination of its obconical body shape, 14–16 anterior and 6–8 ventral membranelles, somatic kinety in three parts and conspicuously long dorsal cilia. Based on the data obtained for this novel species, an improved diagnosis of the genus Apostrombidium is supplied. Descriptions of the population of N. apsheronicum and N. testaceum collected in this study are also provided and compared with the existing descriptions. In addition, the phylogenetic positions of these three species are inferred from their SSU rRNA gene sequence data. The results indicate that the genus Apostrombidium, the systematics of which has not previously been discussed using molecular information, clusters with Varistrombidium kielum and Omegastrombidium elegans, whereas N. testaceum and N. apsheronicum form a single clade.

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Molecular Characterization of Blastocystis sp. in Camelus bactrianus in Northwestern China

Animals ◽

10.3390/ani11113016 ◽

2021 ◽

Vol 11 (11) ◽

pp. 3016

Author(s):

Xin Yang ◽

Yunhui Li ◽

Yuxin Wang ◽

Junwei Wang ◽

Peng Lai ◽

...

Keyword(s):

Northwestern China ◽

Rrna Gene ◽

Ssu Rrna ◽

Infection Rates ◽

Ssu Rrna Gene ◽

Worldwide Distribution ◽

Total Prevalence ◽

Faecal Samples ◽

Blastocystis Sp

Blastocystis sp. is an important zoonotic protist in humans and various animals with worldwide distribution. However, there have been no data on the occurrence of Blastocystis sp. in C. bactrianus, an important economic animal in northwestern China. In the present study, a PCR-sequencing tool based on the SSU rRNA gene was applied to investigate the prevalence and genetic diversity of Blastocystis sp. in 638 faecal samples from C. bactrianus in 21 sampling sites within three main breeding areas (Gansu, Inner Mongolia and Xinjiang) in northwestern China. The total prevalence of Blastocystis sp. was 21.8% (139/638) in C. bactrianus, with the infection rates of 29.5% (18/61), 50.0% (14/28) and 19.5% (107/549) for animals aged <2 years, 2–6 years and >6 years, respectively. Significant differences in prevalence were detected among C. bactrianus from three geographic areas (χ2 = 19.972, df = 2, p < 0.001) and all sampling sites (χ2 = 104.154, df = 20, p < 0.001). A total of 16 of 21 sampling sites were positive for Blastocystis sp., with the prevalence ranging from 7.7% to 70.6%. Sequence analysis of the SSU rRNA gene identified eight subtypes in C. bactrianus in the present study, including seven animal adapted subtypes (ST10, ST14, ST21, ST24, ST25, ST26 and ST30) and one potentially novel subtype, with ST10 being the dominant one. To the best of our knowledge, this study provides the first insight for the occurrence and genetic make-up of Blastocystis sp. in C. bactrianus and contributes to the understanding of the transmission of Blastocystis infection in C. bactrianus in China.

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Morphological and phylogenetic studies on three members of the genus Pseudochilodonopsis (Ciliophora, Cyrtophoria) isolated from brackish waters in China, including a novel species, Pseudochilodonopsis quadrivacuolata sp. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.000580 ◽

2015 ◽

Vol 65 (Pt_12) ◽

pp. 4323-4334 ◽

Cited By ~ 6

Author(s):

Zhishuai Qu ◽

Hongbo Pan ◽

Khaled A. S. Al-Rasheid ◽

Xiaozhong Hu ◽

Shan Gao

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Small Subunit ◽

Dorsal Side ◽

Rrna Gene ◽

Ssu Rrna ◽

Ssu Rrna Gene ◽

Ssu Rrna Gene Sequence

Three cyrtophorian ciliates isolated from brackish biotopes in China, Pseudochilodonopsis quadrivacuolata sp. nov., Pseudochilodonopsis fluviatilis Foissner, 1988 and Pseudochilodonopsis mutabilis Foissner, 1981, were investigated using living observation and protargol-staining methods. P. quadrivacuolata sp. nov. can be characterized as follows: cell size 50–70 × 30–40 μm in vivo; body oval with posterior end rounded; four tetragonally positioned contractile vacuoles; 12–15 nematodesmal rods; five right and six left somatic kineties; terminal fragment positioned apically on dorsal side, consisting of 11–14 basal bodies; four or five fragments in preoral kinety. P. fluviatilis and P. mutabilis were generally consistent with previous descriptions. In addition, a brief revision and a key to Pseudochilodonopsis are presented. The small-subunit (SSU) rRNA gene was also sequenced to support the identification of these species. Phylogenetic analyses based on molecular data indicate that the genera Pseudochilodonopsis and Chilodonella are closely related and both are well outlined; that is, all known congeners for which SSU rRNA gene sequence data are available group together, forming the core part of the family Chilodonellidae.

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Morphologic, Host Specificity, and Molecular Characterization of a Hungarian Cryptosporidium meleagridis Isolate

Applied and Environmental Microbiology ◽

10.1128/aem.66.2.735-738.2000 ◽

2000 ◽

Vol 66 (2) ◽

pp. 735-738 ◽

Cited By ~ 51

Author(s):

Tamás Sréter ◽

Gábor Kovács ◽

Alexandre J. da Silva ◽

Norman J. Pieniazek ◽

Zoltán Széll ◽

...

Keyword(s):

Sequence Data ◽

Variable Region ◽

Active Role ◽

Distinct Species ◽

Small Subunit ◽

Rrna Gene ◽

Broad Host Range ◽

Ssu Rrna ◽

Ssu Rrna Gene ◽

Bovine Strain

ABSTRACT This study was undertaken in order to characterizeCryptosporidium meleagridis isolated from a turkey in Hungary and to compare the morphologies, host specificities, organ locations, and small-subunit RNA (SSU rRNA) gene sequences of this organism and other Cryptosporidium species. The phenotypic differences between C. meleagridis andCryptosporidium parvum Hungarian calf isolate (zoonotic genotype) oocysts were small, although they were statistically significant. Oocysts of C. meleagridis were successfully passaged in turkeys and were transmitted from turkeys to immunosuppressed mice and from mice to chickens. The location ofC. meleagridis was the small intestine, like the location of C. parvum. A comparison of sequence data for the variable region of the SSU rRNA gene of C. meleagridisisolated from turkeys with other Cryptosporidium sequence data in the GenBank database revealed that the Hungarian C. meleagridis sequence is identical to a C. meleagridissequence recently described for a North Carolina isolate. Thus,C. meleagridis is a distinct species that occurs worldwide and has a broad host range, like the C. parvum zoonotic strain (also called the calf or bovine strain) andCryptosporidium felis. Because birds are susceptible toC. meleagridis and to some zoonotic strains of C. parvum, these animals may play an active role in contamination of surface waters not only with Cryptosporidium baileyi but also with C. parvum-like parasites.

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Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria

10.1101/258137 ◽

2018 ◽

Cited By ~ 8

Author(s):

Jeffrey S. McLean ◽

Batbileg Bor ◽

Thao T. To ◽

Quanhui Liu ◽

Kristopher A. Kerns ◽

...

Keyword(s):

Oral Cavity ◽

De Novo ◽

Gc Content ◽

Single Copy ◽

Small Subunit ◽

Rrna Gene ◽

Ssu Rrna ◽

Ssu Rrna Gene ◽

Human Oral Cavity

ABSTRACTRecently, we discovered that a member of the Saccharibacteria/TM7 phylum (strain TM7x) isolated from the human oral cavity, has an ultra-small cell size (200-300nm), a highly reduced genome (705 Kbp) with limited de novo biosynthetic capabilities, and a very novel lifestyle as an obligate epibiont on the surface of another bacterium 1. There has been considerable interest in uncultivated phyla, particularly those that are now classified as the proposed candidate phyla radiation (CPR) reported to include 35 or more phyla and are estimated to make up nearly 15% of the domain Bacteria. Most members of the larger CPR group share genomic properties with Saccharibacteria including reduced genomes (<1Mbp) and lack of biosynthetic capabilities, yet to date, strain TM7x represents the only member of the CPR that has been cultivated and is one of only three CPR routinely detected in the human body. Through small subunit ribosomal RNA (SSU rRNA) gene surveys, members of the Saccharibacteria phylum are reported in many environments as well as within a diversity of host species and have been shown to increase dramatically in human oral and gut diseases. With a single copy of the 16S rRNA gene resolved on a few limited genomes, their absolute abundance is most often underestimated and their potential role in disease pathogenesis is therefore underappreciated. Despite being an obligate parasite dependent on other bacteria, six groups (G1-G6) are recognized using SSU rRNA gene phylogeny in the oral cavity alone. At present, only genomes from the G1 group, which includes related and remarkably syntenic environmental and human oral associated representatives1, have been uncovered to date. In this study we systematically captured the spectrum of known diversity in this phylum by reconstructing completely novel Class level genomes belonging to groups G3, G6 and G5 through cultivation enrichment and/or metagenomic binning from humans and mammalian rumen. Additional genomes for representatives of G1 were also obtained from modern oral plaque and ancient dental calculus. Comparative analysis revealed remarkable divergence in the host-associated members across this phylum. Within the human oral cavity alone, variation in as much as 70% of the genes from nearest oral clade (AAI 50%) as well as wide GC content variation is evident in these newly captured divergent members (G3, G5 and G6) with no environmental relatives. Comparative analyses suggest independent episodes of transmission of these TM7 groups into humans and convergent evolution of several key functions during adaptation within hosts. In addition, we provide evidence from in vivo collected samples that each of these major groups are ultra-small in size and are found attached to larger cells.

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Telonema antarcticum sp. nov., a common marine phagotrophic flagellate

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63652-0 ◽

2005 ◽

Vol 55 (6) ◽

pp. 2595-2604 ◽

Cited By ~ 26

Author(s):

Dag Klaveness ◽

Kamran Shalchian-Tabrizi ◽

Helge Abildhauge Thomsen ◽

Wenche Eikrem ◽

Kjetill S. Jakobsen

Keyword(s):

Molecular Phylogeny ◽

Small Subunit ◽

Food Vacuole ◽

Rrna Gene ◽

Ssu Rrna ◽

Small Subunit Rrna ◽

Ssu Rrna Gene ◽

Structural Identity ◽

Food Particles ◽

Ssu Rrna Gene Sequence

Telonema is a widely distributed group of phagotrophic flagellates with two known members. In this study, the structural identity and molecular phylogeny of Telonema antarcticum was investigated and a valid description is proposed. Molecular phylogeny was studied using small-subunit rRNA (SSU rRNA) gene sequences. The pear-shaped cell had two subequal flagella that emerged laterally on the truncated antapical tail. One flagellum had tripartite hairs. The cell was naked, but had subsurface vesicles containing angular paracrystalline bodies of an unknown nature. A unique complex cytoskeletal structure, the subcortical lamina, was found to be an important functional and taxonomic feature of the genus. Telonema has an antero-ventral depression where food particles are ingested and then transferred to a conspicuous anterior food vacuole. The molecular phylogeny inferred from the SSU rRNA gene sequence suggested that Telonema represents an isolated and deep branch among the tubulocristate protists.

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phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes

mSystems ◽

10.1128/msystems.00920-20 ◽

2020 ◽

Vol 5 (5) ◽

Cited By ~ 1

Author(s):

Harald R. Gruber-Vodicka ◽

Brandon K. B. Seah ◽

Elmar Pruesse

Keyword(s):

High Throughput ◽

Small Subunit ◽

General Purpose ◽

Reference Database ◽

Rrna Gene ◽

Ssu Rrna ◽

Small Subunit Rrna ◽

Ssu Rrna Gene ◽

Domains Of Life ◽

Environmental Microbes

ABSTRACT The small-subunit rRNA (SSU rRNA) gene is the key marker in molecular ecology for all domains of life, but it is largely absent from metagenome-assembled genomes that often are the only resource available for environmental microbes. Here, we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning of full metagenomic assemblies. We show that a cleanup of artifacts is pivotal even with a curated reference database. With such a filtered database, the general-purpose mapper BBmap extracts SSU rRNA reads five times faster than the rRNA-specialized tool SortMeRNA with similar sensitivity and higher selectivity on simulated metagenomes. Reference-based targeted assemblers yielded either highly fragmented assemblies or high levels of chimerism, so we employ the general-purpose genomic assembler SPAdes. Our optimized implementation is independent of reference database composition and has satisfactory levels of chimera formation. phyloFlash quickly processes Illumina (meta)genomic data, is straightforward to use, even as part of high-throughput quality control, and has user-friendly output reports. The software is available at https://github.com/HRGV/phyloFlash (GPL3 license) and is documented with an online manual. IMPORTANCE To track organisms across all domains of life, the SSU rRNA gene is the gold standard. Many environmental microbes are known only from high-throughput sequence data, but the SSU rRNA gene, the key to visualization by molecular probes and link to existing literature, is often missing from metagenome-assembled genomes (MAGs). The easy-to-use phyloFlash software suite tackles this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based linking to MAGs. Starting from a cleaned reference database, phyloFlash profiles the taxonomic diversity and assembles the sorted SSU rRNA reads. The phyloFlash design is domain agnostic and covers eukaryotes, archaea, and bacteria alike. phyloFlash also provides utilities to visualize multisample comparisons and to integrate the recovered SSU rRNAs in a metagenomics workflow by linking them to MAGs using assembly graph parsing.

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Morphological and Genetic Evidence that the Cyanobacterium Lyngbya wollei (Farlow ex Gomont) Speziale and Dyck Encompasses at Least Two Species

Applied and Environmental Microbiology ◽

10.1128/aem.02645-07 ◽

2008 ◽

Vol 74 (12) ◽

pp. 3710-3717 ◽

Cited By ~ 16

Author(s):

Jennifer J. Joyner ◽

R. Wayne Litaker ◽

Hans W. Paerl

Keyword(s):

Phylogenetic Analysis ◽

Habitat Degradation ◽

Sequence Similarity ◽

Inorganic Nitrogen ◽

Small Subunit ◽

Morphological Data ◽

Rrna Gene ◽

Ssu Rrna ◽

Lyngbya Wollei ◽

Ssu Rrna Gene

ABSTRACT Dense blooms of the cyanobacterium Lyngbya wollei are increasingly responsible for declining water quality and habitat degradation in numerous springs, rivers, and reservoirs. This research represents the first molecular phylogenetic analysis of L. wollei in comparison with the traditional morphological characterization of this species. Specimens were collected from several springs in Florida and a reservoir in North Carolina. Segments of the small-subunit (SSU) rRNA and nifH genes were PCR amplified, cloned, and sequenced. The phylogenetic analysis of the SSU rRNA gene revealed sequences that fell into three distinct subclusters, each with >97% sequence similarity. These were designated operational taxonomic unit 1 (OTU1), OTU2, and OTU3. Similarly, the nifH sequences fell into three distinct subclusters named S1, S2, and S3. When either bulk samples or individual filaments were analyzed, we recovered OTU1 with S1, OTU2 with S2, and OTU3 with S3. The coherence between the three SSU rRNA gene and nifH subclusters was consistent with genetically distinct strains or species. Cells associated with subclusters OTU3 and S3 were significantly wider and longer than those associated with other subclusters. The combined molecular and morphological data indicate that the species commonly identified as L. wollei in the literature represents two or possibly more species. Springs containing OTU3 and S3 demonstrated lower ion concentrations than other collection sites. Geographical locations of Lyngbya subclusters did not correlate with residual dissolved inorganic nitrogen or phosphorus concentrations. This study emphasizes the need to complement traditional identification with molecular characterization to more definitively detect and characterize harmful cyanobacterial species or strains.

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