Partial 16S rDNA Sequencing Research Articles

Biological control of Paecilomyces formosus, the causal agent of dieback and canker diseases of pistachio by two strains of Streptomyces misionensis

Dieback and canker of pistachio shoots and limbs is a commercially significant disease in Iran. Paecilomyces formosus (Sakag., May., Inoue and Tada) Houbraken & Samson is considered as the major causal agent of this malady. Actinomycetes and particularly members of the genus Streptomyces are well known as biocontrol agents for many plant diseases; they achieve this by production of bioactive metabolites and hydrolytic enzymes. The present study aimed to exploit Streptomyces isolates to biologically control P. formosus in vitro and in greenhouse experiments. Fifty two actinomycetes isolates were evaluated for their antagonistic effect against P. formosus isolated from diseased orchards. Considering their in vitro antagonistic performance, two isolates, designated as BH4-1 and BH4-3 were selected for molecular identification and in vivo experiment to be evaluated for biocontrol efficacy. Partial sequences of 16S rDNA unveiled their identity as two strains of Streptomyces misionensis with 99.9% sequence homology. For in vivo greenhouse experiments, inoculation of artificially made wounds on pistachio young trees stems performed with spore suspensions and culture extracts of either of the two bioactive S. misionensis Cercos et al. strains alone and/or together with P. formosus spore suspensions. Cupravit® was used as fungicide control. To evaluate the effect of the biocontrol test agents on the development of disease symptoms and severity, after about nine months, canker severity score, length and width of internal discolored lesions and frequency of P. formosus re-isolation from lesion margins were measured. The recorded disease criteria for treatments receiving S. misionensis strains were significantly in favor of bio-controlling the disease compared to the controls.

New evidence of nematode-endosymbiont bacteria coevolution based on one new and one known dagger nematode species of Xiphinema americanum-group (Nematoda, Longidoridae).

Three populations of Xiphinema primum n. sp. and two populations of X. pachtaicum were recovered from natural forests and cultural regions of northern Iran. Both species belong to the X. americanum-group and were characterized by their morphological, morphometric and molecular data. The new species, which was recovered in three locations, belongs to the X. brevicolle-complex and is characterized by 2124–2981 μm long females with a widely rounded lip region separated from the rest of the body by a depression, 103–125 μm long odontostyle, two equally developed genital branches with endosymbiont bacteria inside the ovary, which are visible under light microscope (LM), vulva located at 51.8–58.0%, the tail is 26–37 μm long with a bluntly rounded end and four juvenile developmental stages. It was morphologically compared with nine similar species viz. X. brevicolle, X. diffusum, X. incognitum, X. himalayense, X. luci, X. parabrevicolle, X. paramonovi, X. parataylori and X. taylori. The second species, X. pachtaicum, was recovered in two geographically distant points close to city of Amol. Molecular phylogenetic studies of the new species were performed using partial sequences of the D2-D3 expansion segments of the large subunit ribosomal RNA gene (LSU rDNA D2-D3), the internal-transcribed spacer rDNA (ITS = ITS1+5.8S+ITS2), and the mitochondrial cytochrome c oxidase I gene (COI mtDNA) regions. The Iranian population of X. pachtaicum was also phylogenetically studied based upon its LSU rDNA D2-D3 sequences. Both species were also inspected for their putative endosymbiont bacteria. Candidatus Xiphinematobacter sp. was detected from two examined populations of the new species, whereas the second endosymbiont bacterium, detected from three examined isolates of X. pachtaicum, was related to the plant and fungal endosymbionts of the family Burkholderiaceae. The phylogenetic analyses of the two endosymbiont bacteria were performed using partial sequences of 16S rDNA. In cophylogenetic analyses, significant levels of cophylogenetic signal were observed using both LSU rDNA D2-D3 and COI mtDNA markers of the host nematodes and 16S rDNA marker of the endosymbiont bacteria.

Occurrence, characterization, and antibiogram of Staphylococcus aureus in meat, meat products, and some seafood from Libyan retail markets.

Aim:The aim of the current investigation was to screen the presence of Staphylococci spp., especially S. aureus in meat, meat products of different animal species, and some seafood sold in some retail markets in Libya using cultural and molecular techniques, and to study their antibiotics resistance profiles.Materials and Methods:A total of 139 samples from red meat, meat products, and seafood were collected from many areas in Libya. Enumeration and isolation of Staphylococci spp. and S. aureus by normal cultural methods followed by molecular identification using molecular techniques by bacterial DNA extraction and partial sequencing of 16S rDNA.Results:Out of 139 samples, 112 (80.6%) were contaminated with different species of Staphylococci based on cultural characteristics of Staphylococci on Baird-Parker medium, for which S. aureus was detected in only 32 samples (23%). However, only six out of 18 (33.3%) isolates sent for sequencing were confirmed to be S. aureus using the molecular technique. The six identified isolates of S. aureus were tested for antimicrobial resistance against 24 most commonly used antibiotics. All isolates were resistant to only two antibiotics (cefotaxime and clindamycin). Among these six isolates, only one confirmed to be Methicillin-resistant Staphylococcus aureus.Conclusion:Results of this study suggest that food of animal origin could be a source of S. aureus with antimicrobial resistance characteristics that can be spread through the food chain, and raise the importance of these results for public health.

Four species of Mazocraeoides Price, 1936 (Monogenea: Mazocraeidae), including two new species from clupeiform fishes off Visakhapatnam coast, Bay of Bengal.

Four species of Mazocraeoides Price, 1936 including two new species are recorded from clupeiform fishes collected from Visakhapatnam Coast, Bay of Bengal: M. rotundus n. sp. from Ilisha filigera, M. fusiformes n. sp. from Stolephorus indicus, M. prashadi Chauhan, 1950 from Sardinella longiceps and M. dussumieri Mamaev, 1975 from Dussumieria hasselti. Mazocraeoides rotundus n. sp. is differentiated from the previously described species of Mazocraeoides by possessing the following combination of characters: the small pot-like body, the distribution of clamps in the posterior half of body and the genital complex consisting of five pairs of hooks arranged in two vertical rows. It differs from M. prashadi in the body shape and the much smaller size of the genital complex. Mazocraeoides fusiformes n. sp. differs from all the other species of the genus in the distribution of the clamps embracing only the posterior part of the testis and the genital complex consisting of one pair of needle-like lateral hooks and five pairs of median hooks. Mazocraeoides prashadi is redescribed to fill the gaps existing in the earlier description. Mazocraeoides dussumieri recorded earlier from South China Sea is reported for the first time from the Bay of Bengal. The validity of various species of Mazocraeoides is discussed and a key for the separation of valid species is provided. A host-parasite list is presented which gives details of the hosts, the geographic distribution and the validity status for each species. A partial 28S rDNA sequence was generated for M. dussumieri and deposited in GenBank.

A New Species of Pentaloculum (Cestoda: “Tetraphyllidea”) from the Taiwan Saddled Carpetshark, Cirrhoscyllium formosanum (Orectolobiformes: Parascylliidae)

Collection of cestodes from the Taiwan saddled carpetshark, Cirrhoscyllium formosanum, for the first time led to the discovery of Pentaloculum hoi n. sp. This species provided important insights into the identity of the heretofore monotypic Pentaloculum-known previously only from the blind electric ray, Typhlonarke aysoni, in New Zealand. The new species differs from Pentaloculum macrocephalum in testis number, vitelline follicle and cirrus sac configuration, and in that it is hyperapolytic rather than euapolytic. Maximum-likelihood analysis of sequence data generated for the D1-D3 region of the 28S rDNA gene not only confirmed this generic placement but also confirmed the close affinities between both species of Pentaloculum and specimens previously referred to in the literature as new genus 7 n. sp. 1. Examination of limited material of the latter, including that of a second specimen from which partial 28S rDNA sequence data were generated here, led to the realization that new genus 7 n. sp. 1 represents an undescribed species of Pentaloculum, referred to here as Pentaloculum n. sp. 2. All 3 species share bothridia divided into 1 anterior and 2 consecutive pairs of loculi. Given that Pentaloculum n. sp. 2 parasitizes a member of the second and only other genus of parascylliid sharks (i.e., Parascyllium), we predict that the 4 other species of Parascyllium and the 2 other species of Cirrhoscyllium are likely to host other species of Pentaloculum. The factors that might account for the eclectic host associations of Pentaloculum, which include a torpediniform ray and 2 species of orectilobiform sharks, are currently unclear. The compilation of diet data for these elasmobranchs and determination of the final intermediate hosts for these cestodes would be interesting avenues of further investigation given that cestodes are trophically transmitted between their intermediate and definitive hosts. The phylogenetic affinities of Pentaloculum among elasmobranch cestodes remain unresolved.

Bacteria and methanogen community in the rumen fed different levels of grass-legume silages

Abstract. Ridwan R, Rusmana I, Widyastuti Y, Wiryawan KG, Prasetya B, Sakamoto M, Ohkuma M. 2019. Bacteria and methanogen community in the rumen fed different levels of grass-legume silages. Biodiversitas 20: 1055-1062. This study aimed to investigate the effects of dietary grass-legume silages on the microbial community by using a culture-independent approach. Treatments consisted of R0: 50% Pennisetum purpureum and 50 % concentrate; R1: 20% P. purpureum, 50 % concentrate, and 30% grass-legumes silage; R2: 20% P. purpureum, 35 % concentrate, and 45% grass-legumes silage; and R3; 20% P. purpureum, 20 % concentrate, and 60% grass-legumes silage. The rumen fluid obtained from fistulated cattle was used for T-RFLP, 16S rDNA clone library, and qPCR analyses. The results indicated that bacterial diversity was dominated by Bacteroidetes, Firmicutes, and methanogen by Methanobacteriales, based on partial 16S rDNA sequences. The microbial communities were dominated by Prevotella brevis, P. ruminicola, Succiniclasticum ruminis, and Methanobrevibacter ruminantium, M. smithi, M. thueri, and M. millerae. The increasing silage diet in a rumen suppressed methanogenesis by reducing population distribution of Methanobacteriales, directly or indirectly, by reducing the diversity of bacterial populations. Generally, the increase silage in the diet changed the bacterial and methanogen community. Grass-legume silage diets of less than 45% are potential for ruminant diet to reduce methane production by a decrease of 4% in the relative distribution of methanogens in the rumen.

Four new monorchiids from the golden trevally, Gnathanodon speciosus (Forsskål) (Perciformes: Carangidae), in Moreton Bay, Australia.

Four new monorchiid trematodes are reported from Moreton Bay, Australia; three new species of Provitellus Dove & Cribb, 1998 and one species of Ovipusillus Dove & Cribb, 1998, are described from Gnathanodon speciosus (Forsskål) (Carangidae), the golden trevally. Provitellus chaometra n. sp., Provitellus infrequens n. sp. and Provitellus infibrova n. sp. differ significantly from the only other species of this genus, Provitellus turrum Dove & Cribb, 1998, in the structure of the eggs, vitelline follicles and terminal organ. The four species are united, however, in the possession of short caeca and a long genital atrium, a combination not reported previously. Ovipusillus geminus n. sp. strongly resembles its only congener, Ovipusillus mayu Dove & Cribb, 1998, but differs in the morphology of the diverticulum in the cirrus-sac and the shape of the pharynx. Complete ITS2 and partial 28S rDNA sequence data were generated for all four species, as well as for two known species of Hurleytrematoides Yamaguti, 1953, Hurleytrematoides galzini McNamara & Cribb, 2011 and Hurleytrematoides loi McNamara & Cribb, 2011. These sequences were analysed with those for other monorchiids available on GenBank, and phylogenetic analyses showed that the four species of Provitellus and two species of Ovipusillus each form strongly supported clades. As with previous monorchiid phylogenetic studies, however, the overall resolution of the phylogeny of the Monorchiidae is poor.

Description of the snail-eating flatworm in marine aquaria, Pericelis tectivorum sp. nov. (Polycladida, Platyhelminthes)

We describe a new marine snail-eating flatworm, Pericelis tectivorum sp. nov., found in coral-bearing marine aquaria. Pericelis tectivorum sp. nov. is characterised by several differential characters of the external and internal morphology like 1) a long line of frontal eyes extending anteriorly; 2) the length of the penis papilla; 3) the spherical seminal vesicle; 4) the lack of the enlargements of the ejaculatory duct; 5) the uterine vesicles, which start posterior of the female genital at the level of the sucker and 6) the distinct sucker. The combination of these characters in one species is unique and therefore the studied specimens are recognised by us as a new species. We additionally present a phylogenetic reconstruction using partial 28S rDNA sequences including three congeners. Our analysis demonstrates that P. tectivorum sp. nov. differs also genetically from other Pericelis species included in this analysis.

Longitudinal study of Amphibiocystidium sp. infection in a natural population of the Italian stream frog (Rana italica).

Mesomycetozoean-induced infections (order Dermocystida, genus Amphibiocystidium) in European and North American amphibians are causing alarm. To date, the pathogenicity of these parasites in field conditions has been poorly studied, and demographic consequences on amphibian populations have not been explored. In this study, an Amphibiocystidium sp. infection is reported in a natural population of the Italian stream frog (Rana italica) of Central Italy, over a 7-year period from 2008 to 2014. Light and electron microscope examinations, as well as partial 18S rDNA sequence analysis were used to characterize the parasite. Moreover, a capture-mark-recapture study was conducted to assess the frog demographics in response to infection. Negative effects of amphibiocystidiosis on individual survival and population fitness were absent throughout the sampling period, despite the high estimates of disease prevalence. This might have been due to resistance and/or tolerance strategies developed by the frogs in response to the persistence of Amphibiocystidium infection in this system. We hypothesized that in the examined R. italica population, amphibiocystidiosis is an ongoing endemic/epidemic infection. However, ecological and host-specific factors, interacting in a synergistic fashion, might be responsible for variations in the susceptibility to Amphibiocystidium infection of both conspecific populations and heterospecific individuals of R. italica.

Two new species of Mazocraes Hermann (Monogenea: Mazocraeidae) from clupeoid fishes off Visakhapatnam, Bay of Bengal.

Two new species of Mazocraes Hermann (Monogenea: Mazocraeidae) are described infecting clupeoid fishes of Visakhapatnam coast, Bay of Bengal: Mazocraes bengalensis n. sp. from Opisthopterus tardoore Cuvier and M. stolephorusi n. sp. from Stolephorus indicus van Hasselt and S. commersoni Lacepede. L. bengalensis n.sp. is distinguished from the most closely related species (M. gussevi, M. australis, M. alosae, M. mamaevi) by the combination of following characters: Body size, extent of caeca, number and arrangement of testes, size and structure of the clamps and the armature of genital complex. M. stolephorusi n. sp. differs from all the other species of Mazocraes in the pedunculate nature and the sizes of the haptoral clamps and the structure of the genital complex. A detailed analysis of the species of the genus Mazocraes is presented. The partial 28SrDNa sequences of M. bengalensis was generated and deposited in the GenBank.

A New Species of the Acanthocephalan Genus Filisoma (Cavisomidae) from Perciform Fishes in Rio de Janeiro, Brasil

BackgroundTwelve species of Filisoma Van Cleave, 1928 are recognized parasitizing tropical and subtropical fish. Four of these species were described from kyphosid fish and it has been suggested that a co-speciation may have occurred among species of Kyphosus Lacepède, 1801 and Filisoma, which could provide valuable information about the evolution history of this host–parasite system.PurposeDuring a survey of the helminth fauna of Kyphosus sectatrix (Linnaeus, 1758) and Kyphosus incisor (Cuvier, 1831) (Kyphosidae Jordan, 1887) off Rio de Janeiro coast, a new species of Filisoma was found and is described herein based on morphological, genetic, and ultrastructural data.MethodsFish were obtained off Rio de Janeiro coast, Brazil. The parasites found in the intestine were measured and drawings were made with a drawing tube. Type specimens were deposited at the Helminthological Collection of Oswaldo Cruz Institute (CHIOC). The ultrastructure was studied using scanning electron microscope. The genetic analysis included the study of the partial sequences of 18S, ITS1, 5.8S and 28S rDNA, and the mitochondrial cytochrome c oxidase 1 gene (cox 1), with phylogenetic reconstructions based on the maximum likelihood analysis.ResultsFilisoma caudata n. sp. is characterized by a proboscis with 16‒18 longitudinal rows of 38‒45 hooks each. Hooks are uniform in shape dorsoventrally, gradually decreasing in size towards the base of the proboscis. Anterior hooks are 30‒45 μ long, middle hooks 30‒35 μ long and 5 basal transversal hooks 20‒30 μ long. The new species is differentiated from the closest species Filisoma filiformis Weaver and Smales, 2013 by the size and distribution of hooks, apart from having a subterminal vulva and a curved posterior trunk end (tail) measuring 500‒1,000 long. Phylogenetic analysis based on 18S, 28S rDNA and mtDNA-cox1 markers grouped the new species with Filisoma bucerium Van Cleave, 1940 and Filisoma rizalinum Tubangui and Masiluñgan, 1946 showing a close relationship between these species of Cavisomidae Meyer, 1932 and Echinorhynchidae Cobbold, 1879; the latter represented by species of Acanthocephalus Koelreuther, 1771. The new species can be differentiated from others on morphological and molecular basis. A key to the 13 species of Filisoma Van Cleave, 1928 is provided.ConclusionFilisoma caudata n. sp. is described herein based on morphological, genetic, and ultrastructural data. The topologies of obtained phylogenies suggest that species of Echinorhynchidae should be reevaluated since the family is considered paraphyletic in all analyses conducted.

Morphological and molecular analyses of Pseudomazocraes sulamericana n. sp., Pseudomazocraes selene Hargis, 1957, Cemocotyle carangis (MacCallum, 1913) and Zeuxapta seriolae (Meserve, 1938) (Monogenea: Mazocraeidea) from carangid fishes in the south-western Atlantic Ocean.

An integrative taxonomy approach was followed to analyse morphological and molecular characters of the monogenean species Pseudomazocraes selene, Cemocotyle carangis and Zeuxapta seriolae; specimens were collected from the gills of the carangid fishes Selene vomer, Caranx latus and Seriola lalandi caught off the coasts of the states of Rio de Janeiro and Santa Catarina, Brazil. The research revealed the presence of Pseudomazocraes sulamericana n. sp., which can be differentiated from other congeners by the shape of clamps mid-sclerite possessing a ventral piece bifurcated at the end, with large and right-angled edges of almost the same length, and by the shape of larval hooks and rounded terminal lappet. New genetic sequences include partial 28S and 18S rDNA genes for all species, ITS1 and 5.8S rDNA for Zeuxapta seriolae and Cemocotyle carangis, and ITS2 and mtDNA cox1 for C. carangis. The phylogenetic concatenated analysis based on partial 28S rDNA and 18S rDNA sequences confirmed the position of C. carangis and Z. seriolae within the Heteraxinidae. The previous phylogenetic position of Chauhaneidae was discussed based on morphological studies and it is now confirmed by molecular data that Chauhaneidae is the sister group of Allodiscocotylidae and Protomicrocotylidae.

Klossiella equi Infecting Kidneys of Ontario Horses: Life Cycle Features and Multilocus Sequence-Based Genotyping Confirm the Genus Klossiella Belongs in the Adeleorina (Apicomplexa: Coccidia)

Species in the genus Klossiella Smith and Johnson, 1902 are unique among the suborder Adeleorina because they are monoxenous in mammals exclusively, whereas all other reported members of the Adeleorina use invertebrates as definitive hosts. Unlike other coccidia, all members of the Adeleorina undergo syzygy, the association of microgamonts and macrogamonts before maturation to gametes and syngamy. After fertilization, many members of the Adeleorina produce thin-walled polysporocystic oocysts. Despite being biologically similar to other members of the Adeleorina, the phylogenetic placement of the genus Klossiella has been questioned based on its unique host affinity. In the present study, 2 cases of Klossiella equi were reported from the kidneys of horses in Ontario. Details of the life cycle as well as mitochondrial and nuclear 18S ribosomal DNA ( 18S rDNA) sequences were analyzed to provide both morphological and molecular evidence for the phylogenetic placement of K. equi. Initially, various stages of the life cycle were identified in histological slides prepared from the kidney tissue, and DNA was isolated from the infected tissue. Polymerase chain reaction and Sanger sequencing were used to generate a complete mitochondrial genome sequence (6,569 bp) and a partial 18S rDNA sequence (1,443 bp). The K. equi 18S rDNA sequence was aligned with various publicly available apicomplexan 18S rDNA sequences. This alignment was used to generate a phylogenetic tree based on Bayesian inference. Multiple K. equi stages were identified including meronts, microgamonts, and macrogamonts associating in syzygy as well as thin-walled oocysts in various stages of sporogonic development. The 18S rDNA sequence of K. equi positioned within the monophyletic Adeleorina clade. The mitochondrial genome of K. equi contained 3 coding sequences for cytochrome c oxidase I, cytochrome c oxidase III, and cytochrome b as well as various fragmented ribosomal sequences. These components were arranged in a unique order that has not been observed in other apicomplexan mitochondrial genomes sequenced to date. Overall, it was concluded that there were sufficient morphological and molecular data to confirm the placement of K. equi and the genus Klossiella among the Adeleorina. The biological and molecular data obtained from these cases may assist with future studies evaluating the prevalence and life history of this seemingly underreported parasite and better define the impact of K. equi on the health of domestic and wild equids.

Determination of enterotoxin genes in bacillus cereus from raw milk using multiplex polymerase chain reaction technique

A Gram-positive bacterium, which can usually be found in cultivating plants and soil, causing it commonly universal is regarded as Bacillus cereus. It is said that most strains present in B. cereus is specifically called the primary cause of food poisoning illnesses which is characterised by either emetic or diarrheal syndrome, the most essential purpose of the current research was, therefore, to isolate and identify the enterotoxin genes in B. cereus through using a multiplex polymerase chain reaction (mPCR)technique. To achieve this aim, thus B.cereus was isolated from raw milk then cultured on mannitol egg yolk polymyxin agar and chromogenic B. cereus agar. The samples were then examined using biochemical investigation then established using partial sequencing of 16SrDNA. Among 40 samples, 20 of them were found to contain hblC and hblD, a hemolytic enterotoxin (HBL) complex encoding genes. The total mean of contamination samples in the B. cereus was proved to be higher (1.4×105 – 3.2×105 CFU/mL) than the acceptable detection level of B. cereus in dairy products ~103 CFU/mL. The isolates (10%) were shown to express hblC gene whereas the isolates (20%) were shown to express the hblD gene. The findings suggested that the detected enterotoxin genes of B. cereus which were found in raw milk may create a potential danger to the health of the public.

Heterophyid trematodes (Digenea) from penguins: A new species of Ascocotyle Looss, 1899, first description of metacercaria of Ascocotyle (A.) patagoniensis Hernández-Orts et al. (2012), and first molecular data.

Two species of heterophyid trematodes were found in the Magellanic penguin, Spheniscus magellanicus (Forster), from Patagonia, Argentina. Ascocotyle (Ascocotyle) patagoniensis Hernández-Orts et al. (2012) is re-described based on new, properly fixed specimens (original material from South American sea lion, Otaria flavescens Shaw, was from frozen hosts). Metacercariae of this species are reported and described for the first time from the heart of the silversides, Odontesthes argentinensis (Valenciennes) and O. smitti (Lahille), from Patagonia. Ascocotyle (Phagicola) cameliae n. sp. is described from the intestine of S. magellanicus. The new species is placed into the subgenus Phagicola Faust, 1920 because of the presence of a single row of circumoral spines and uterine loops and vitelline follicles being confined posterior to the ventral sucker. However, it differs distinctly from other members of this subgenus by the number (19–24) and length (23–31 μm) of massive circumoral spines and by the morphology of the ventrogenital sac with a large, simple gonotyl devoid of refractile bodies. Molecular data (partial 28S rDNA sequences) for both species are also provided. Matching sequences from metacercarial and adult stages helped elucidate partially the life-cycle of A. (A.) patagoniensis. The interspecific relationships and phylogenetic position of Ascocotyle were further assessed on a broad phylogeny on the Opisthorchioidea Looss, 1899. Ascocotyle (P.) ornamentata Shalaby, Esposito, Riegler & Carratù (1993) described from decomposed worms (all circumoral spines were detached) found in a dog in Egypt, with no type-specimens of this species deposited in a repository collection, is considered to be species inquirenda.

A remarkable new opsiine leafhopper genus (Hemiptera: Cicadellidae: Deltocephalinae) from Southern China, with notes on its phylogenetic position

A remarkable new genus of tribe Opsiini (Deltocephalinae), Yinformibus gen. nov. including Yinformibus menglaensis sp. nov. is described from Yunnan of China. The new genus is placed in the tribe Opsiini based on male adults having a pair of aedeagal shafts, each with its own gonopore. Partial 28S rDNA and Histone H3 sequences are provided for the new species, and a phylogenetic analysis based on these markers for Deltocephalinae retrieved from GenBank suggests Opsiini is monophyletic and supports the placement of Yinformibus gen. nov. in Opsiini. The molecular results placed the new genus in a clade comprising Hishimonus Ishihara, Opsius Fieber, and an undescribed genus from Zambia. Additionally, we also analysed the relationships of Yinformibus gen. nov. with other genera based on morphology.http://www.zoobank.org/urn:lsid:zoobank.org:pub:85C23AC3-8B19-4F29-9F55-BFC392242B51

Molecular Characterization of Enterobacter and Escherichia coli Pathotypes Prevalent in the Popular Street Foods of Dhaka City and their Multidrug Resistance

Food borne pathogenic enteric bacteria are of great concern for global public health. Among them, Escherichia coli and Enterobacter spp. are the most prevalent in the street food. In this study, 23 strains of such enteric bacteria were isolated from multiple food samples by conventional cultural technique. Isolated strains were characterized molecularly into different genotypes using RAPD, amplified ribosomal DNA restriction analysis, and partial sequencing of 16S rDNA. RAPD represents 10 different types of strains whereas ARDRA clusters them into two separate groups. 16 out of the 23 isolates were identified as E. coli and the rest were as Enterobacter spp. by biochemical tests and were further confirmed by partial 16S rDNA sequencing. Significant level of virulence traits including stx1, stx2 and escV genes were identified in E. coli strains. Also, most of the isolates were found resistant to azithromycin and amoxicillin. This study revealed the presence of various pathogenic enteric bacteria in various street foods with multidrug resistance. Therefore, this study suggests that people consuming such street foods are at major risk of food borne illness.
 Bangladesh J Microbiol, Volume 34 Number 2 December 2017, pp 67-72

Genetic Relatedness among Escherichia coli Isolated from Clinical Samples

A common member of the intestinal microbiota in humans and animals is Escherichia coli. Based on the presence of virulence factors, E. coli can be potentially pathogenic. The focus of this study was to determine genotypic diversity among clinical strains of E. coli. Test isolates were identified by biochemical, culture-based and molecular tests. Partial sequence of 16s rDNA was determined by Polymerase Chain Reaction using universal primers. The sequences were used as input in Basic Local Alignment Search Tool (BLAST) to reconfirm the identity of the isolates. Sequences were edited in Chromas and aligned in Bioedit. Afterwards, sequences were fed into Mega 5 and a dendogram was constructed. We used three sequences deposited in GenBank for comparison with our test sequences. It was found that two of our sequences showed similarity to the reference sequences. One of the isolates was similar to a Uropathogenic and a commensal E. coli. The other isolate showed similarity to a UPEC strain. It is possible that both of these isolates were commensal bacteria that led to opportunistic infection in the patients. The rest of the nine strains were different from the reference sequences. These isolates may be opportunistic pathogens that have undergone mutation events leading to sufficiently different rDNA sequences from the reference bacteria. Or they may also be pathogenic strains that caused infection in patients. This study indicated that clinical isolates of E. coli show variation in terms of their rDNA sequences. In order to study their phylogeny, other supporting tools such as investigation for phylogenetic markers, RAPD, ARDRA, ERIC-PCR, ribotyping, etc. may be used to study variation among isolates to a more significant extent.
 Bangladesh J Microbiol, Volume 34 Number 2 December 2017, pp 97-101

Holocephalocotyle monstrosaen. gen. n. sp. (Monogenea, Monocotylidae) from the olfactory rosette of the rabbit fish,Chimaera monstrosa(Holocephali, Chimaeridae) in deep waters off Algeria

Based on a molecular and morphological study, a new monocotylid genus, Holocephalocotyle n. gen. is proposed to accommodate Holocephalocotyle monstrosae n. sp., found on the olfactory rosette of the rabbit fish, Chimaera monstrosa Linnaeus (Chondrichthyes, Chimaeridae), from the Mediterranean Sea off Algeria. Identification of fish hosts was confirmed by molecular barcoding of the COI gene. A partial 28S rDNA sequence (D1–D2 domain) of Holocephalocotyle monstrosae was obtained; it was distinct from all known monocotylid sequences (p-distance: 15.5–23%). A phylogenetic tree constructed from available monocotylid sequences showed that Holocephalocotyle monstrosae was included, and basal, in a robust group including species of Merizocotyle, Mycteronastes and Empruthotrema, confirming that the species is a member of the Merizocotylinae. The new genus is unique among the Merizocotylinae in having a distinctive pattern of haptoral loculi with one central, five peripheral and seven “interperipheral loculi” partially inserted between peripheral loculi and a compartmentalised sclerotised male copulatory organ. The diagnosis of the Merizocotylinae is amended to include this new genus. The new genus represents the second monocotylid genus recorded from holocephalans.

Holocarpic oomycete parasitoids of red algae are not Olpidiopsis.

Olpidiopsis is a genus of obligate holocarpic endobiotic oomycetes. Most of the species classified in the genus are known only from their morphology and life cycle, and a few have been examined for their ultrastructure or molecular phylogeny. However, the taxonomic placement of all sequenced species is provisional, as no sequence data are available for the type species, O. saprolegniae, to consolidate the taxonomy of species currently placed in the genus. Thus, efforts were undertaken to isolate O. saprolegniae from its type host, Saprolegnia parasitica and to infer its phylogenetic placement based on 18S rDNA sequences. As most species of Olpidiopsis for which sequence data are available are from rhodophyte hosts, we have also isolated the type species of the rhodophyte-parasitic genus Pontisma, P. lagenidioides and obtained partial 18S rDNA sequences. Phylogenetic reconstructions in the current study revealed that O. saprolegniae from Saprolegnia parasitica forms a monophyletic group with a morphologically similar isolate from S. ferax, and a morphologically and phylogenetically more divergent species from S. terrestris. However, they were widely separated from a monophyletic, yet unsupported clade containing P. lagenidioides and red algal parasites previously classified in Olpidiopsis. Consequently, all holocarpic parasites in red algae should be considered to be members of the genus Pontisma as previously suggested by some researchers. In addition, a new species of Olpidiopsis, O. parthenogenetica is introduced to accommodate the pathogen of S. terrestris.