Prevalence and molecular characterization of Cryptosporidium spp. in Père David’s deer (Elaphurus davidianus) in Jiangsu, China

Abstract Cryptosporidium is a zoonotic parasite that causes diarrhea in a broad range of animals, including deer. Little is known about the prevalence and genotype of Cryptosporidium spp. in Père David’s deer. In this study, 137 fecal samples from Père David’s deer were collected between July 2017 and August 2018 in the Dafeng Reserve and analyzed for Cryptosporidium spp. by nested-PCR based on the small subunit ribosomal RNA (SSU rRNA) gene, followed by sequence analyses to determine the species. The 60 kDa glycoprotein (gp60) gene was used to characterize Cryptosporidium spp. Among 137 samples, 2 (1.46%) were positive for Cryptosporidium spp. according to SSU rRNA gene sequencing results. Both samples belonged to the Cryptosporidium deer genotype, with two nucleotide deletions and one nucleotide substitution. The prevalence data and molecular characterization of this study provide basic knowledge for controlling and preventing Cryptosporidium infections in Père David’s deer in this area.

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Prevalence and Genetic Characterization of Cryptosporidium Infection in Java Sparrows (Lonchura oryzivora) in Northern China

BioMed Research International ◽

10.1155/2017/2318476 ◽

2017 ◽

Vol 2017 ◽

pp. 1-4 ◽

Cited By ~ 2

Author(s):

Qiu-Xia Yao ◽

Xiao-Xuan Zhang ◽

Kai Chen ◽

Jian-Gang Ma ◽

Wen-Bin Zheng ◽

...

Keyword(s):

Pcr Amplification ◽

Northern China ◽

Small Subunit ◽

Rrna Gene ◽

Ssu Rrna ◽

Ssu Rrna Gene ◽

Wide Range ◽

Baseline Information ◽

And Control

Cryptosporidiosis is a cosmopolitan parasitosis that affects a wide range of hosts including birds. As information concerning Cryptosporidium in birds is limited, the present study examined the prevalence and genotypes of Cryptosporidium in Java sparrows in Beijing and Shangqiu, northern China. Three hundred and fifty fecal samples were collected from Java sparrows (Lonchura oryzivora, 225 white Java sparrows and 125 gray Java sparrows) in Beijing and Shangqiu in October 2015, and the samples were examined by PCR amplification of the small subunit ribosomal RNA (SSU rRNA) gene. The overall Cryptosporidium prevalence is 13.42% (47/350), with 16.44% (37/225) in white Java sparrows and 8.00% (10/125) in gray Java sparrows. Cryptosporidium prevalence was 9.82% (16/163) in Java sparrows from Beijing and 16.58% (31/187) in Java sparrows from Shangqiu. The prevalence of Cryptosporidium in females and males was 40.63% (26/64) and 7.34% (21/286), respectively. The Cryptosporidium prevalence in Java sparrows of different ages varied from 10.47% to 16.33%. Sequence analysis of the SSU rRNA gene revealed that all the samples represented C. baileyi. This is the first report of Cryptosporidium in gray Java sparrows in China, which extend the host range for C. baileyi. These results provide baseline information for further studies of molecular epidemiology and control of Cryptosporidium infection in poultry in China.

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Prevalence and Characterization of Cryptosporidium Species in Tibetan Antelope (Pantholops hodgsonii)

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.713873 ◽

2021 ◽

Vol 11 ◽

Author(s):

Si-Yuan Qin ◽

He-Ting Sun ◽

Chuang Lyu ◽

Jun-Hui Zhu ◽

Zhen-Jun Wang ◽

...

Keyword(s):

Pcr Amplification ◽

Small Subunit ◽

Rrna Gene ◽

Ssu Rrna ◽

Ssu Rrna Gene ◽

Tibet Autonomous Region ◽

Ssu Rrna Gene Sequence ◽

And Control ◽

Tibetan Antelope

Cryptosporidium is an enteric apicomplexan parasite, which can infect multiple mammals including livestock and wildlife. Tibetan Antelope (Pantholops hodgsonii) is one of the most famous wildlife species, that belongs to the first class protected wild animals in China. However, it has not been known whether Tibetan Antelope is infected with Cryptosporidium so far. The objective of the present study was to determine the prevalence and characterization of Cryptosporidium species infection in Tibetan Antelope and the corresponding species by using molecular biological method. In the current study, a total of 627 fecal samples were randomly collected from Tibetan Antelope in the Tibet Autonomous Region (2019–2020), and were examined by PCR amplification of the small subunit ribosomal RNA (SSU rRNA) gene. Among 627 samples, 19 (3.03%, 19/627) were examined as Cryptosporidium-positive, with 7 (2.33%, 7/300) in females and 12 (3.67%, 12/327) in males. The analysis of SSU rRNA gene sequence suggested that only two Cryptosporidium species, namely, C. xiaoi and C. ubiquitum, were identified in this study. This is the first evidence for an existence of Cryptosporidium in Tibetan Antelope. These findings extend the host range for Cryptosporidium spp. and also provide important data support for prevention and control of Cryptosporidium infection in Tibetan Antelope.

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Molecular Characterization of the Host-Adapted Pathogen Verticillium longisporum on the Basis of a Group-I Intron Found in the Nuclear SSU-rRNA Gene

Current Microbiology ◽

10.1007/s0028403380 ◽

2001 ◽

Vol 42 (3) ◽

pp. 217-224 ◽

Cited By ~ 8

Author(s):

Vassiliki K. Karapapa ◽

Milton A. Typas

Keyword(s):

Molecular Characterization ◽

Group I Intron ◽

Rrna Gene ◽

Ssu Rrna ◽

Ssu Rrna Gene ◽

Verticillium Longisporum ◽

Group I

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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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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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New insights into the phylogeny of the Acantharea based on SSU rRNA gene sequencing

European Journal of Protistology ◽

10.1016/s0932-4739(00)80020-6 ◽

2000 ◽

Vol 36 (1) ◽

pp. 34-39 ◽

Cited By ~ 6

Author(s):

Linda A. Amaral Zettler ◽

David A. Caron

Keyword(s):

Gene Sequencing ◽

Rrna Gene ◽

Ssu Rrna ◽

Ssu Rrna Gene ◽

Rrna Gene Sequencing

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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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