Microbiome analysis of the midguts of different developmental stages of Argas persicus in China

Argas persicus is an ectoparasite of poultry. The bacterial community structure and the pathogenic bacteria associated with different developmental stages of A. persicus have implications for control. Argas persicus were collected from chickens in the city of Jiuquan in Gansu, China. Bacterial DNA was extracted from the midgut contents of blood engorged larvae, nymphs and adult females. The V3-V4 hypervariable regions of 16S rRNA genes were sequenced using the IonS5?XL platform. Identification of Rickettsia spp. and detection of Coxiella burnetii were performed using PCR on target genes. The bacterial diversity within larvae was the highest and the bacterial diversity within nymphs was greater than that of adults. At different classification levels, seven bacterial phyla were common phyla, 27 genera were common genera, and 18 species were common species in the three samples. At the phylum level, Proteobacteria showed a marked predominance in all samples. Rickettsia, Stenotrophomonas, Spiroplasma, and Coxiella were the dominant bacteria at the genus level. The Rickettsia species in A. persicus was identified as Rickettsia hoogstraalii and the Coxiella species was identified as a Coxiella-like endosymbiont. Additionally, some bacterial species such as Pseudomonas geniculata, Sphingomonas koreensis, and Acinetobacter haemolyticus were reported here for the first time in A. persicus.     

Culicoides Latreille (Diptera: Ceratopogonidae) taxonomy: Current challenges and future directions

Culicoides Latreille biting midges (Diptera: Ceratopogonidae) cause a significant biting nuisance to humans, livestock and equines, and are the biological vectors of a range of internationally important pathogens of both veterinary and medical importance. Despite their economic significance, the delimitation and identification of species and evolutionary relationships between species within this genus remains at best problematic. To date no phylogenetic study has attempted to validate the subgeneric classification of the genus and the monophyly of many of the subgenera remains doubtful. Many informal species groupings are also known to exist but few are adequately described, further complicating accurate identification. Recent contributions to Culicoides taxonomy at the species level have revealed a high correlation between morphological and molecular analyses although molecular analyses are revealing the existence of cryptic species. This review considers the methods for studying the systematics of Culicoides using both morphological and genetic techniques, with a view to understanding the factors limiting our current understanding of Culicoides biology and hence arbovirus epidemiology. In addition, we examine the global status of Culicoides identification, highlighting areas that are poorly addressed, including the potential implementation of emerging technologies.     

Controversies in bacterial taxonomy: The example of the genus Borrelia

In this paper we survey key issues in bacterial taxonomy and review the literature regarding the recent genus separation proposed for the genus Borrelia. We discuss how information on members of the genus Borrelia is increasing but detailed knowledge on the relevant features is available only for a small subset of species. The data accumulated here show that there is considerable overlap in ecology, clinical aspects and molecular features between clades that argue against splitting of the genus Borrelia.     

Characterization of the Rothia spp. and their role in human clinical infections

The genus Rothia are emerging as opportunistic pathogens associated with various infections in immunocompromised and immunocompetent individuals. This review describes the taxonomy, cell wall structure, pathogenesis, phenotypic and molecular characteristics, clinical diseases, treatment and, as well as, the related genera that may be misidentified by Rothia species.     

Current understanding of the genetic diversity of Brucella,an expanding genus of zoonotic pathogens

Brucella species are responsible for brucellosis, one of the world's most widespread zoonotic diseases causing abortion in domestic animals and a potentially debilitating infection of man. Despite the identification of a number of distinct species within the genus with differing host preferences and pathogenicity it has been known for many years that members of the genus are genetically homogeneous. However, since the start of the millennium the application of new technologies to the group has resulted in rapid advances in the understanding of Brucella diversity and, after many years of inactivity, a process of expansion of the genus is underway. This review summarises the current state of knowledge in this area and outlines how this informs understanding of the taxonomy and evolution of the group and is enabling the development of increasingly sophisticated molecular typing tools.     

The diversity of the orthoreoviruses: Molecular taxonomy and phylogentic divides

The family Reoviridae is a diverse group of viruses with double-stranded RNA genomes contained within icosahedral, non-enveloped, double-layered protein capsids. Within the Reoviridae, the Orthoreovirus genus includes viruses that infect reptiles, birds and mammals (including humans). Recent sequencing efforts have produced a great deal of new molecular data for the fusogenic orthoreoviruses, a group of reoviruses that induce cell–cell fusion during an infection. This new data has allowed a fresh look at the phylogenetic relationships among the members of the Orthoreovirus genus, and has provided insight into the evolution of orthoreovirus species and species groups. This review mainly focuses on the molecular taxonomy of the fusogenic orthoreoviruses, and aims to provide insight into their relationships with the non-fusogenic orthoreoviruses and other selected Reoviridae genera.     

The rhabdoviruses: Biodiversity,phylogenetics, and evolution

Rhabdoviruses (family Rhabdoviridae) include a diversity of important pathogens of animals and plants. They share morphology and genome organization. The understanding of rhabdovirus phylogeny, ecology and evolution has progressed greatly during the last 30 years, due to enhanced surveillance and improved methodologies of molecular characterization. Along with six established genera, several phylogenetic groups at different levels were described within the Rhabdoviridae. However, comparative relationships between viral phylogeny and taxonomy remains incomplete, with multiple representatives awaiting further genetic characterization. The same is true for rhabdovirus evolution. To date, rather simplistic molecular clock models only partially describe the evolutionary dynamics of postulated viral lineages. Ongoing progress in viral evolutionary and ecological investigations will provide the platform for future studies of this diverse family.     

山西省五台山地区有瓣蝇类名录

目的对山西省五台山地区有瓣蝇类进行系统分类研究。方法采用昆虫分类学原理和方法。结果五台山地区有瓣蝇类7科69属111种,包括粪蝇科（Scathophagidae）1属1种,花蝇科（Anthomyiidae）8属12种,厕蝇科（Fanniidae）1属6种,蝇科（Musicidae）24属41种,丽蝇科（Calliphoridae）9属15种,麻蝇科（Sarcophagidae）13属19种,寄蝇科（Tachinidae）13属17种。其中,2种五台山地区产模式种。结论五台山地区有瓣蝇类昆虫具有物种丰富、多样性及特有性等特点。     

Modulation of trypanosome establishment in Glossina palpalis palpalis by its microbiome in the Campo sleeping sickness focus,Cameroon

The purpose of this study was to investigate factors involved in vector competence by analyzing whether the diversity and relative abundance of the different bacterial genera inhabiting the fly's gut could be associated with its trypanosome infection status. This was investigated on 160 randomly selected G. p. palpalis flies - 80 trypanosome-infected, 80 uninfected - collected in 5 villages of the Campo trypanosomiasis focus in South Cameroon. Trypanosome species were identified using specific primers, and the V4 region of the 16S rRNA gene of bacteria was targeted for metabarcoding analysis in order to identify the bacteria and determine microbiome composition.A total of 261 bacterial genera were identified of which only 114 crossed two barriers: a threshold of 0.01% relative abundance and the presence at least in 5 flies. The secondary symbiont Sodalis glossinidius was identified in 50% of the flies but it was not considered since its relative abundance was much lower than the 0.01% relative abundance threshold. The primary symbiont Wigglesworthia displayed 87% relative abundance, the remaining 13% were prominently constituted by the genera Spiroplasma, Tediphilus, Acinetobacter and Pseudomonas. Despite a large diversity in bacterial genera and in their abundance observed in micobiome composition, the statistical analyzes of the 160 tsetse flies showed an association with flies' infection status and the sampling sites. Furthermore, tsetse flies harboring Trypanosoma congolense Savanah type displayed a different composition of bacterial flora compared to uninfected flies. In addition, our study revealed that 36 bacterial genera were present only in uninfected flies, which could therefore suggest a possible involvement in flies' refractoriness; with the exception of Cupriavidus, they were however of low relative abundance. Some genera, including Acinetobacter, Cutibacterium, Pseudomonas and Tepidiphilus, although present both in infected and uninfected flies, were found to be associated with uninfected status of tsetse flies. Hence their effective role deserves to be further evaluated in order to determine whether some of them could become targets for tsetse control of fly vector competence and consequently for the control of the disease. Finally, when comparing the bacterial genera identified in tsetse flies collected during 4 epidemiological surveys, 39 genera were found to be common to flies from at least 2 sampling campaigns.     

Molecular epidemiology,phylogeny and evolution of dermatophytes

Dermatophytes are fungi that invade and propagate in the keratinized skin of mammals, including humans, often causing contagious infections. The species of medical concern belong to the genera Microsporum, Trichophyton, Epidermophyton (in their anamorphic state) and Arthroderma (in their telomorphic state), which were traditionally identified based on their morphology and biochemical characters. Nonetheless, limitations linked to the differentiation of closely related agents at species and strains level have been recently overcome by molecular studies. Indeed, an accurate identification of dermatophytes is pivotal for the establishment of effective control and prevention programs as well as for determining the most appropriate and effective antifungal therapies to be applied. This article reviews the DNA techniques and the molecular markers used to identify and to characterize dermatophyte species, as well as aspects of their phylogeny and evolution. The applications of typing molecular strain to both basic and applied research (e.g., taxonomy, ecology, typing of infection, antifungal susceptibility) have also been discussed.     

Hybridization in Phlebotominae (Diptera: Psychodidae): A mini-review

Taxonomy based only on morphology, although extremely important for the classification of sandflies, has been shown to be insufficient for the delimitation of some taxa. Thus, integrative taxonomy could play a fundamental role in clarifying these and other taxonomic issues, since data from different areas are used to aggregate greater reliability in species classification. Experimental crosses are important taxonomic tools, since the presence of reproductive barriers when associated with divergence between two evolutionary lineages, confirms the specific status of taxa based on the biological species concept. In the subfamily Phlebotominae, experimental crosses were mostly focused on the study of the Lutzomyia longipalpis complex, which helped to identify different evolutionary lineages for that group of vectors. Considering the difficulty of classifying some Phlebotominae species and the importance of hybridization studies for taxonomy, we grouped all the information associated with experimental crosses in sandflies in a mini-review. In view of the results grouped in this review, it is evident that i) experimental crossings are important tools to aggregate studies of integrative taxonomy in the Phlebotominae subfamily; ii) these analyses should be applied in the taxonomic studies of cryptic species; iii) Lu longipalpis populations have pre and/or post-zygotic reproductive barriers; iv) Lu. longipalpis represents more than one species and efforts must be applied to differentiate the taxa of the Lu. longipalpis complex; v) Phlebotomus populations do not present intraspecific reproductive barriers; vi) the absence of reproductive barriers between Ph. sergenti from Israel and Turkey (representing populations of the same evolutionary lineage) does not rule out the possible existence of cryptic species, it being necessary to perform experimental crosses between the different strains indicated by the molecular markers; and finally, vii) different species of Phlebotomus have post-zygotic barriers, confirming the specific status of Ph. duboscqi, Ph. papatasi, and Ph. bergeroti.     

Mosquito and sand fly gregarines of the genus Ascogregarina and Psychodiella (Apicomplexa: Eugregarinorida,Aseptatorina) – Overview of their taxonomy,life cycle,host specificity and pathogenicity

Mosquitoes and sand flies are important blood-sucking vectors of human diseases such as malaria or leishmaniasis. Nevertheless, these insects also carry their own parasites, such as gregarines; these monoxenous pathogens are found exclusively in invertebrates, and some of them have been considered useful in biological control. Mosquito and sand fly gregarines originally belonging to a single genus Ascogregarina were recently divided into two genera, Ascogregarina comprising parasites of mosquitoes, bat flies, hump-backed flies and fleas and Psychodiella parasitizing sand flies. Currently, nine mosquito Ascogregarina and five Psychodiella species are described. These gregarines go through an extraordinarily interesting life cycle; the mosquito and sand fly larvae become infected by oocysts, the development continues transtadially through the larval and pupal stages to adults and is followed by transmission to the offspring by genus specific mechanisms. In adult mosquitoes, ascogregarines develop in the Malpighian tubules, and oocysts are defecated, while in the sand flies, the gregarines are located in the body cavity, their oocysts are injected into the accessory glands of females and released during oviposition. These life history differences are strongly supported by phylogenetical study of SSU rDNA proving disparate position of Ascogregarina and Psychodiella gregarines. This work reviews the current knowledge about Ascogregarina and Psychodiella gregarines parasitizing mosquitoes and sand flies, respectively. It gives a comprehensive insight into their taxonomy, life cycle, host specificity and pathogenicity, showing a very close relationship of gregarines with their hosts, which suggests a long and strong parasite-host coevolution.     

Morphology,genetic characterization and phylogeny of Aplectana dayaoshanensis n. sp. (Nematoda: Ascaridida) from frogs

Cosmocercoid nematodes are common parasites in the digestive tract of amphibians. However, our knowledge of the species diversity, genetic data and molecular phylogeny of the superfamily Cosmocercoidea are far from being well understood. In the present study, large numbers of cosmocercoid nematodes were collected from the fine-spined frog Sylvirana spinulosa (Smith) (Anura: Ranidae) and the white-spotted thigh tree-frog Polypedates megacephalus (Hallowell) (Anura: Rhacophoridae) in Guangxi Province, China. Integrated morphological and genetic evidence reveals these nematode specimens to be a new species of the genus Aplectana, A. dayaoshanensis n. sp. (Cosmocercoidea: Cosmocercidae). The molecular characterization of small ribosomal DNA (18S), internal transcribed spacer (ITS) and large ribosomal DNA (28S) of A. dayaoshanensis n. sp., together with the 28S of A. chamaeleonis (Baylis, 1929) (collected from Hyperolius kivuensis Ahl in Rwanda), were reported for the first time. Moreover, phylogenetic analyses using maximum likelihood (ML) inference based on 18S + 28S and ITS sequence data, respectively, both supported the family Cosmocercidae to be a monophyletic group and the family Kathlaniidae to be a paraphyletic group. Our phylogenetic results rejected the monophyly of the genus Aplectana. The present results contribute to the knowledge of the species diversity and genetic data of cosmocercoid nematodes, and preliminarily revealed the phylogenetic relationships of the major families and some genera in the Cosmocercoidea.     

Cryptic diversity and habitat partitioning in an economically important aphid species complex

Cardamom Bushy Dwarf Virus (CBDV) is an aphid-borne nanovirus which infects large cardamom, Amomum subulatum (Zingiberaceae family), in the Himalayan foothills of Northeast India, Nepal and Bhutan. Two aphid species have been reported to transmit CBDV, including Pentalonia nigronervosa and Micromyzus kalimpongensis (also described as Pentalonia kalimpongensis). However, P. nigronervosa was recently split into two species which exhibit different host plant affiliations. Whilst P. nigronervosa primarily feeds on banana plants, Pentalonia caladii (previously considered a ‘form’ of P. nigronervosa) typically feeds on plants belonging to the Araceae, Heliconiaceae and Zingiberaceae families. This raises the possibility that CBDV vectors that were originally described as P. nigronervosa correspond to P. caladii. Accurate identification of vector species is important for understanding disease dynamics and for implementing management strategies. However, closely related species can be difficult to distinguish based on morphological characteristics. In this study, we used molecular markers (two mitochondrial loci and one nuclear locus) and Bayesian phylogenetic analyses to identify aphid specimens collected from 148 CBDV infected plants at a range of locations and elevations throughout Sikkim and the Darjeeling district of West Bengal (Northeast India). Our results revealed the presence of a diversity of lineages, comprising up to six distinct species in at least two related genera. These included the three species mentioned above, an unidentified Pentalonia species and two lineages belonging to an unknown genus. Surprisingly, P. caladii was only detected on a single infected plant, indicating that this species may not play an important role in CBDV transmission dynamics. Distinct elevation distributions were observed for the different species, demonstrating that the community composition of aphids which feed on large cardamom plants changes across an elevation gradient. This has implications for understanding how competent vector species could influence spatial and temporal transmission patterns of CBDV.     

Health significance of Gram‐negative bacteria associated with waste‐fed tropical aquaculture system

Commercially important freshwater fish species, Cyprinus carpio, Oreochromia niloticus, Sarother‐odon galilaeus and Clarias anguillaris grown in aquaculture ponds receiving untreated sewage and animal faecal waste and in an untreated concrete tank were sampled to determine the presence of potentially pathogenic Gram negative bacteria to man. The resistance of some representative bacterial isolates to some commonly used antibacterial drugs were also determined. Fourteen bacterial species from nine genera, namely, Escherichia, Citrobacter, Enterobacter, Proteus, Salmonella, Serratia, Klebsiella, Pseudomonas and Aeromonas from both fish intestinal tracts and culture water samples were identified. Escherichia coli predominated in the sewage and animal manure‐treated ponds, while fluorescent Pseudomonas were common in the untreated pond. Pathogenic Salmonella spp. were isolated at a low frequency (1.32%) in fish from the sewage pond. Of the 577 bacterial isolates identified, 199 (34.49%) were resistant to at least one antibacterial drug.     

Predacious bacteria, Bdellovibrio with potential for biocontrol

Bacteria of the genus of Bdellovibrio are highly motile Gram-negative predators of other Gram-negative bacteria causing lysis of their prey. Here we report results of studies on the interactions of Bdellovibrio with species of Alcaligenes, Campylobacter, Erwinia, Escherichia, Helicobacter, Pseudomonas, Legionella, and Shigella in agar lower, liquid media and cells attached to a surface. Helicobacter pylori was studied employing both actively growing and viable but nonculturable (VBNC) cells. The majority of the bacterial strains tested were found to be susceptible to Bdellovibrio. A significant observation was that Bdellovibrio attacked both actively growing and VBNC H. pylori, that phenomenon has never been reported. The results indicate that bdellovibrios have potential as biocontrol agents.     

Nontuberculous mycobacteria: Insights on taxonomy and evolution

Seventy years have passed since Ernest H. Runyon presented a phenotypic classification approach for nontuberculous mycobacteria (NTM), primarily as a starting point in trying to understand their clinical relevance. From numerical taxonomy (biochemical testing) to 16S rRNA gene sequencing to whole genome sequencing (WGS), our understanding of NTM has also evolved. Novel species are described at a rapid pace, while taxonomical relationships are re-defined in large part due to the accessibility of WGS. The evolutionary course of clonal complexes within species is better known for some NTM and less for others. In contrast with M. tuberculosis, much is left to learn about NTM as a whole.     

Integrative taxonomy of Mesocriconema onoense (Tylenchida: Criconematidae) from Vietnam highly suggests the synonymization of Mesocriconema brevistylus and related species

The genus Mesocriconema is one of the most diverse genera within the family Criconematidae, known as ring nematodes, with more than 90 species. Although species in this genus usually show distinct morphological characterizations, the identification based only on morphology can lead to misidentification in many studies resulted in a number of synonymizations in the genus over time. In this study, an integrated approach has been applied in characterizing Mesocriconema onoense from Vietnam. The molecular data of 28S rRNA, ITS, 18S rRNA regions were analyzed and discussed to confirm the correct names on GenBank. Besides, phylogenetic analyses of 28S rRNA, ITS, and 18S rRNA regions of Mesocriconema species revealed that Mesocriconema brevistylus should be considered as a junior synonym of M. onoense. Consequently, M. helicus, M. onostris, and M. paronostris should also be considered as the synonyms of M. onoense.     

Morphological and genetic characterization of Syphabulea tjanschani () (Nematoda: Oxyuridae), with phylogenetic position of Syphabulea in Oxyuridae

Pinworms are important parasitic nematodes in animals and humans, and many species are of medical and veterinary importance. The genus Syphabulea is a poorly known group of pinworms. The systematic position of Syphabulea in Oxyuridae remains unclear. Moreover, there is still a paucity of detailed information on some morphological aspects of the type species S. tjanschani (Ablasov, 1962). In the present study, the detailed morphology of S. tjanschani was studied using light microscopy and, for the first time, scanning electron microscopy. The results revealed three traits useful for the characterization of the species including: cuticular depression around excretory pore, non-prominent labial teeth and number of adhesive ridges in three ventral mammelons. The ribosomal [small ribosomal DNA (18S), internal transcribed spacer (ITS) and large ribosomal DNA (28S)] and mitochondrial [cytochrome c oxidase subunit 1 (cox1)] target regions of S. tjanschani were also firstly amplified and sequenced for future use in the molecular identification of this poorly known species. In addition, in order to investigate the systematic position of Syphabulea in Oxyuridae, the phylogenetic analyses of representatives of the Oxyuridae were performed using maximum likelihood (ML) and maximum parsimony (MP) methods based on 18S, 28S and 18S + 28S + cox1 sequence data, respectively. The phylogenetic results based on different sequence data all supported the genus Syphabulea to be a member of the subfamily Syphaciinae. The phylogenetic analysis based on 28S sequence data also showed Syphabulea as sister to the genus Syphatineria. Our present study represents the first attempt to resolve the systematic position of the genus Syphabulea using phylogenetic analyses based on molecular data.