Ribosomal RNA Gene Research Articles

Identification of genetic markers of resistance to macrolide class antibiotics in Mannheimia haemolytica isolates from a Saskatchewan feedlot.

Mannheimia haemolytica is a major contributor to bovine respiratory disease (BRD), which causes substantial economic losses to the beef industry, and there is an urgent need for rapid and accurate diagnostic tests to provide evidence for treatment decisions and support antimicrobial stewardship. Diagnostic sequencing can provide information about antimicrobial resistance genes in M. haemolytica more rapidly than conventional diagnostics. Realizing the full potential of diagnostic sequencing requires a comprehensive understanding of the genetic markers of antimicrobial resistance. We identified genetic markers of resistance in M. haemolytica to macrolide class antibiotics commonly used for control of BRD. Genome sequences were determined for 99 M. haemolytica isolates with six different susceptibility phenotypes collected over 2 years from a feedlot in Saskatchewan, Canada. Known macrolide resistance genes estT, msr(E), and mph(E) were identified in most resistant isolates within predicted integrative and conjugative elements (ICEs). ICE sequences lacking antibiotic resistance genes were detected in 10 of 47 susceptible isolates. No resistance-associated polymorphisms were detected in ribosomal RNA genes, although previously unreported mutations in the L22 and L23 ribosomal proteins were identified in 12 and 27 resistant isolates, respectively. Pangenome analysis led to the identification of 79 genes associated with resistance to gamithromycin, of which 95% (75 of 79) had no functional annotation. Most of the observed phenotypic resistance was explained by previously identified antibiotic resistance genes, although resistance to the macrolides gamithromycin and tulathromycin was not explained in 39 of 47 isolates, demonstrating the need for continued surveillance for novel determinants of macrolide resistance.IMPORTANCEBovine respiratory disease is the costliest disease of beef cattle in North America and the most common reason for injectable antibiotic use in beef cattle. Metagenomic sequencing offers the potential to make economically significant reductions in turnaround time for diagnostic information for evidence-based selection of antibiotics for use in the feedlot. The success of diagnostic sequencing depends on a comprehensive catalog of antimicrobial resistance genes and other genome features associated with reduced susceptibility. We analyzed the genome sequences of isolates of Mannheimia haemolytica, a major bovine respiratory disease pathogen, and identified both previously known and novel genes associated with reduced susceptibility to macrolide class antimicrobials. These findings reinforce the need for ongoing surveillance for markers of antimicrobial resistance to support improved diagnostics and antimicrobial stewardship.

Key aspects of papillomavirus infection influence the host cervicovaginal microbiome in a preclinical murine papillomavirus (MmuPV1) infection model.

Human papillomaviruses (HPVs) are the most common sexually transmitted infection in the United States and are a major etiological agent of cancers in the anogenital tract and oral cavity. Growing evidence suggests changes in the host microbiome are associated with the natural history and ultimate outcome of HPV infection. We sought to define changes in the host cervicovaginal microbiome during papillomavirus infection, persistence, and pathogenesis using the murine papillomavirus (MmuPV1) cervicovaginal infection model. Cervicovaginal lavages were performed over a time course of MmuPV1 infection in immunocompetent female FVB/N mice and extracted DNA was analyzed by qPCR to track MmuPV1 viral copy number. 16S ribosomal RNA (rRNA) gene sequencing was used to determine the composition and diversity of microbial communities throughout this time course. We also sought to determine whether specific microbial communities exist across the spectrum of MmuPV1-induced neoplastic disease. We, therefore, performed laser-capture microdissection to isolate regions of disease representing all stages of neoplastic disease progression (normal, low- and high-grade dysplasia, and cancer) from female reproductive tract tissue sections from MmuPV1-infected mice and performed 16S rRNA sequencing. Consistent with other studies, we found that the natural murine cervicovaginal microbiome is highly variable across different experiments. Despite these differences in initial microbiome composition between experiments, we observed that MmuPV1 persistence, viral load, and severity of disease influenced the composition of the cervicovaginal microbiome. These studies demonstrate that papillomavirus infection can alter the cervicovaginal microbiome.IMPORTANCEHuman papillomaviruses (HPVs) are the most common sexually transmitted infection in the United States. A subset of HPVs that infect the anogenital tract (cervix, vagina, anus) and oral cavity cause at least 5% of cancers worldwide. Recent evidence indicates that the community of microbial organisms present in the human cervix and vagina, known as the cervicovaginal microbiome, plays a role in HPV-induced cervical cancer. However, the mechanisms underlying this interplay are not well-defined. In this study, we infected the female reproductive tract of mice with a murine papillomavirus (MmuPV1) and found that key aspects of papillomavirus infection and disease influence the host cervicovaginal microbiome. This is the first study to define changes in the host microbiome associated with MmuPV1 infection in a preclinical animal model of HPV-induced cervical cancer. These results pave the way for using MmuPV1 infection models to further investigate the interactions between papillomaviruses and the host microbiome.

Association between gut microbiota and CpG island methylator phenotype in colorectal cancer

ABSTRACT The intestinal microbiota is an important environmental factor implicated in CRC development. Intriguingly, modulation of DNA methylation by gut microbiota has been reported in preclinical models, although the relationship between tumor-infiltrating bacteria and CIMP status is currently unexplored. In this study, we investigated tumor-associated bacteria in 203 CRC tumor cases and validated the findings using The Cancer Genome Atlas datasets. We assessed the abundance of Bacteroides fragilis, Escherichia coli, Fusobacterium nucleatum, and Klebsiella pneumoniae through qPCR analysis and observed enrichment of all four bacterial species in CRC samples. Notably, except for E. coli, all exhibited significant enrichment in cases of CIMP. This enrichment was primarily driven by a subset of cases distinguished by high levels of these bacteria, which we labeled as “Superhigh”. The bacterial Superhigh status showed a significant association with CIMP (odds ratio 3.1, p-value = 0.013) and with MLH1 methylation (odds ratio 4.2, p-value = 0.0025). In TCGA CRC cases (393 tumor and 45 adj. normal), bacterial taxa information was extracted from non-human whole exome sequencing reads, and the bacterial Superhigh status was similarly associated with CIMP (odds ratio 2.9, p < 0.001) and MLH1 methylation (odds ratio 3.5, p < 0.001). Finally, 16S ribosomal RNA gene sequencing revealed high enrichment of Bergeyella spp. C. concisus, and F. canifelinum in CIMP-Positive tumor cases. Our findings highlight that specific bacterial taxa may influence DNA methylation, particularly in CpG islands, and contribute to the development and progression of CIMP in colorectal cancer.

Molecular characterization of Cryptosporidium spp. in Bactrian camels (Camelus bactrianus) from Yili Kazak Autonomous Prefecture of Xinjiang, China.

Cryptosporidium spp. is a significant zoonotic parasite. The prevalence and infection characteristics of Cryptosporidium spp. in Bactrian camels in Yili Kazak Autonomous Prefecture have yet to be fully understood. Thus, the molecular epidemiology of cryptosporidiosis in camels was investigated in this region. A total of 1,455 fecal samples were collected from 6 counties in three regions (Altay, Tacheng, and Yili) in Yili Prefecture. Nested PCR targeting the small subunit ribosomal RNA (ssu rRNA) gene was used to identify the species or genotypes of Cryptosporidium infection in camels. For C. parvum positive samples, the subtypes were identified using the 60-kDa glycoprotein (gp60) gene. The overall infection rate was 8.7% (126/1,455), ranging from 5.6% to 11.7% in different regions, and 4.2% to 15.8% in different counties. A significant difference was observed amongst the counties (p < 0.001). Three species were detected, namely C. andersoni (65.1%, 82/126), C. parvum (34.1%, 43/126), and C. occultus (0.8%, 1/126). Three C. parvum subtypes, If-like-A15G2 (n = 29), IIdA15G1 (n = 4), and IIdA19G1(n = 1) were detected, with If-like-A15G2 being the most prevalent subtype. Camels aged 3-12 months exhibited the highest infection rate (11.4%, 44/387), with no significant difference among age groups (p > 0.05). C. parvum was predominant in camels under 3 months, while C. andersoni prevailed in camels over 3 months. There was an extremely significant difference observed among seasons (p < 0.001), summer had the highest infection rates (16.9%, 61/360). This study collected nearly 1,500 samples and, for the first time, investigated Cryptosporidium spp. infection in camels based on different age groups and seasons. All three Cryptosporidiumspecies identified were zoonotic, posing a potential threat to human health and requiring close attention.

Phylogeny and evolutionary timescales of the tribes Tagiadini and Celaenorrhinini (Hesperiidae, Pyrginae) inferred from mitochondrial genome and nuclear genes

AbstractTagiadini and Celaenorrhinini, two closely related groups of skippers in the subfamily Pyrginae, are mainly distributed across the Oriental, Palaearctic and African regions. While some efforts have been made to explore the phylogenetic relationships within Tagiadini and Celaenorrhinini, several unresolved issues still persist. In this study, we sequenced 13 complete mitochondrial genomes from Tagiadini and Celaenorrhinini. Additionally, we extracted nuclear genes CAD, EF‐1α, IDH, MDH, RPS5 and Wingless from the public database. Through comparative analysis, we gained insights into the structure of these newly sequenced mitogenomes. Furthermore, we constructed a comprehensive phylogenetic tree for Tagiadini and Celaenorrhinini, integrating the newly obtained mitochondrial genomes and nuclear genes with previously published mitogenomes and data from the sequence read archive (SRA). The total length of the mitochondrial genomes of the 13 skipper species ranged from 15,228 bp (Seseria sambara indosinica) to 15,431 bp (Pseudocoladenia festa). The newly sequenced genomes featured the standard set of 13 protein‐coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a non‐coding A + T‐rich region implicated in replication initiation. The phylogenetic analysis encompassing all mitochondrial and nuclear gene data consistently upheld the monophyly of genera within the tribes Tagiadini and Celaenorrhinini. Most of the intergeneric relationships identified in our study agreed with recent genomic discoveries, showing enhanced nodal support values in some cases. Lastly, we estimated the divergence of the Tagiadini + Celaenorrhinini branch at approximately 44.06 million years ago (Ma) during the middle Eocene epoch. The crown ages of Tagiadini and Celaenorrhinini were estimated at approximately 41.69 Ma and 38.49 Ma, respectively.

Assembly and comparative analysis of the first complete mitochondrial genome of Setaria italica.

In this study, we assembled the first complete mitochondrial genome of Setaria italica and confirmed the multi-branched architecture. The foxtail millet (Setaria italica) holds significant agricultural importance, particularly in arid and semi-arid regions. It plays a pivotal role in diversifying dietary patterns and shaping planting strategies. Although the chloroplast genome of S. italica has been elucidated in recent studies, the complete mitochondrial genome remains largely unexplored. In this study, we employed PacBio HiFi sequencing platforms to sequence and assemble the complete mitochondrial genome. The mitochondrial genome spans a total length of 446,614 base pairs and harbors a comprehensive set of genetic elements, including 33 unique protein-coding genes (PCGs), encompassing 24 unique mitochondrial core genes and 9 variable genes, along with 20 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. Our analysis of mitochondrial PCGs revealed a pronounced codon usage preference. For instance, the termination codon exhibits a marked preference for UAA, while alanine (Ala) exhibits a preference for GCU, and glutamine (Gln) favors CAA. Notably, the maximum Relative Synonymous Codon Usage (RSCU) values for cysteine (Cys) and phenylalanine (Phe) are both below 1.2, indicating a lack of strong codon usage preference for these amino acids. Phylogenetic analyses consistently place S. italica in close evolutionary proximity to Chrysopogon zizanioides, relative to other Panicoideae plants. Collinearity analysis showed that a total of 39 fragments were identified to display homology with both the mitochondrial and chloroplast genomes. A total of 417 potential RNA-editing sites were discovered across the 33 mitochondrial PCGs. Notably, all these editing events involved the conversion of cytosine (C) to uracil (U). Through the employment of PCR validation coupled with Sanger sequencing for the anticipated editing sites of these codons, RNA-editing events were conclusively identified at two specific loci: nad4L-2 and atp6-1030. The results of this study provide a pivotal foundation for advanced genomic breeding research in foxtail millet. Furthermore, they impart essential insights that will be instrumental for forthcoming investigations into the evolutionary and molecular dynamics of Panicoideae species.

Phylogenetic relationships and systematics of tapeworms of the family Davaineidae (Cestoda, Cyclophyllidea), with emphasis on species in rodents.

The present study aims at clarifying the poorly known phylogenetic relationships and systematics of cestodes of the family Davaineidae Braun, 1900 (Cyclophyllidea), primarily the genus Raillietina Fuhrmann, 1920 and of the subfamily Inermicapsiferinae (Anoplocephalidae) from mammals (mostly rodents, 31 new isolates) and birds (eight new isolates). Phylogenetic analyses are based on sequences of the large subunit ribosomal RNA gene (28S) and mitochondrial NADH dehydrogenase subunit 1 gene (nad1). The main phylogenetic pattern emerging from the present analysis is the presence of three independent lineages within the main clade of the subfamily Davaineinae, one of which is almost entirely confined to species from rodents and the other two show a mixture of species from birds and mammals. It is suggested that the major diversification of the main clade took place in birds, possibly in galliforms. The subsequent diversification included repeated host shifts from birds to mammals and to other birds, and from rodents to other mammals, showing that colonisation of new host lineages has been the main driver in the diversification of davaineine cestodes. It is also shown that all isolates of Inermicapsifer Janicki, 1910, mainly from rodents, form a monophyletic group positioned among Raillietina spp. in the "rodent lineage", indicating that the genus Inermicapsifer is a member of the family Davaineidae. This means that the subfamily Inermicapsiferinae and the family Inermicapsiferidae should be treated as synonyms of the Davaineidae, specifically the subfamily Davaineinae. Three additional genera generally included in the Inermicapsiferinae, i.e. Metacapsifer Spasskii, 1951, Pericapsifer Spasskii, 1951 and Thysanotaenia Beddard, 1911, are also assigned here to the Davaineidae (subfamily Davaineinae). Raillietina spp. were present in all three main lineages and appeared as multiple independent sublineages from bird and mammalian hosts, verifying the non-monophyly of the genus Raillietina and suggesting a presence of multiple new species and genera.

First identification of Cytauxzoon manul in Eurasian lynx (Lynx lynx) in northwestern China

BackgroundMultiple species of the genera Cytauxzoon and Hepatozoon can infect wild felines, but the diversity of these and other apicomplexan parasites in Eurasian lynx is scarcely known. The aim of this study was to detect Cytauxzoon and Hepatozoon species with molecular methods in Eurasian lynxes and their ticks in northwestern China.MethodsDNA was extracted from the heart, liver, spleen, lung, and kidney samples of three Eurasian lynxes as well as from their five ixodid ticks. These DNA samples were screened with polymerase chain reactions (PCRs) for Cytauxzoon with the partial cytochrome b gene (CytB), cytochrome c oxidase subunit I gene (COI), and small subunit ribosomal RNA gene (18S rRNA), and Hepatozoon with three different fragments of small subunit ribosomal RNA gene (18S rRNA). PCR products were sequenced, aligned, and phylogenetically analyzed.ResultsOne adult female of Eurasian lynx (#1, adult female) was co-infected with Cytauxzoon manul and Hepatozoon felis genotype I, while an adult male lynx (#2) was infected with C. manul. Interestingly, H. felis genotype I was both detected in a male cub (#3) and two out of five infesting Hyalomma asiaticum ticks.ConclusionsFor the first time, Cytauxzoon manul is reported here from Eurasian lynx. In addition, H. felis has not been known to occur in this host species in China and Central Asia. Thus, the findings of this study extend our knowledge on the geographical distribution and host range of these haemoprotozoan parasites. Moreover, this is also the first evidence of C. manul and H. felis co-infection in Eurasian lynx.Graphical

CHARACTERIZATION OF THE CHLOROPLAST GENOME OF AQUILARIA CRASSNA PIERRE EX LECOMTE DISTRIBUTED IN VIETNAM USING LONG-READ DATA (OXFORD NANOPORE TECHNOLOGIES)

Aquilaria crassna Pierre ex Lecomte is a critically endangered species that is famous for its fragrance compounds for perfume and incense production. In this study, the complete chloroplast genome of A. crassna was sequenced using a long-read sequencing method of Oxford Nanopore Technologies. The complete chloroplast genome of A. crassna was 174,766 bp in length, which comprised a large single copy region of 87,231 bp, a small single copy region of 3,343 bp, and two inverted repeat regions of 42,096 bp. This genome contained 95 protein-coding genes, 38 transfer RNA genes, and eight ribosomal RNA genes. The analysis ofsmall single repeats revealed 39 mononucleotide and seven dinucleotide repeats, which are located mainly in non-coding regions. Comparative genomic analysis exhibited high conservation of the chloroplast genome within the Aquilaria genus regarding gene content, gene order, and genomic structure. This study provides useful genomic data for further studies examining the genetic population, genetic conservation, molecular markers, and phylogeny of Aquilaria crassna and related species within Thymelaeaceae.

Sex-dependent effects of carbohydrate source and quantity on caspase-1 activity in the mouse central nervous system

BackgroundMounting evidence links glucose intolerance and diabetes as aspects of metabolic dysregulation that are associated with an increased risk of developing dementia. Inflammation and inflammasome activation have emerged as a potential link between these disparate pathologies. As diet is a key factor in both the development of metabolic disorders and inflammation, we hypothesize that long term changes in dietary factors can influence nervous system function by regulating inflammasome activity and that this phenotype would be sex-dependent, as sex hormones are known to regulate metabolism and immune processes.Methods5-week-old male and female transgenic mice expressing a caspase-1 bioluminescent reporter underwent cranial window surgeries and were fed control (65% complex carbohydrates, 15% fat), high glycemic index (65% carbohydrates from sucrose, 15% fat), or ketogenic (1% complex carbohydrates, 79% fat) diet from 6 to 26 weeks of age. Glucose regulation was assessed with a glucose tolerance test following a 4-h morning fast. Bioluminescence in the brain was quantified using IVIS in vivo imaging. Blood cytokine levels were measured using cytokine bead array. 16S ribosomal RNA gene amplicon sequencing of mouse feces was performed to assess alterations in the gut microbiome. Behavior associated with these dietary changes was also evaluated.ResultsThe ketogenic diet caused weight gain and glucose intolerance in both male and female mice. In male mice, the high glycemic diet led to increased caspase-1 biosensor activation over the course of the study, while in females the ketogenic diet drove an increase in biosensor activation compared to their respective controls. These changes correlated with an increase in inflammatory cytokines present in the serum of test mice and the emergence of anxiety-like behavior. The microbiome composition differed significantly between diets; however no significant link between diet, glucose tolerance, or caspase-1 signal was established.ConclusionsOur findings suggest that diet composition, specifically the source and quantity of carbohydrates, has sex-specific effects on inflammasome activation in the central nervous system and behavior. This phenotype manifested as increased anxiety in male mice, and future studies are needed to determine if this phenotype is linked to alterations in microbiome composition.

Evolutionary and phylogenetic insights from the mitochondrial genomic analysis of Diceraeus melacanthus and D. furcatus (Hemiptera: Pentatomidae)

The mitochondrial genomes of D. melacanthus and D. furcatus were sequenced and used to investigate the phylogenetic relationships with 54 species of Pentatomidae. Their mitogenomes are 17,197 and 15,444 bp-long, respectively, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22/21 transfer RNA genes, with conserved gene arrangement. Leu, Lys, and Ser were the most common amino acids in their PCGs. PCGs evolutionary analysis indicated their mitogenomes are under purifying selection, and the most conserved genes are from the cytochrome complex, reinforcing their suitability as markers for molecular taxonomy. We identified 490 mtSSRs in 56 Pentatomidae species, with large variation and a positive correlation between mtSSR number and genome size. Three mtSSRs were identified in each Diceraeus species. Only the mtSSR in the nad6 (D. melacanthus) and nad4 (D. furcatus) appear to have application as molecular markers for species characterization. Phylogenetic analysis confirmed the monophyly of Pentatomidae. However, our analysis challenged the monophyly of Pentatominae and Podopinae. We also detected unexpected relationships among some tribes and genera, highlighting the complexity of the internal taxonomic structure of Pentatomidae. Both Diceraeus species were grouped in the same clade with the remaining Carpocorini analyzed.

Detailed observations of the life history and phylogenetic placements of the freshwater green alga Oocystaenium elegans (Oocystaceae, Trebouxiophyceae), with an emended description

SUMMARYOocystaenium elegans Gonzalves &amp; Mehra (Oocystaceae, Trebouxiophyceae) was collected from a paddy field in Japan. Its life history was reexamined based on detailed observations of cultured material, and an emended description is given. This species is a large spindle‐shaped green alga that grows in puddles and paddy fields and has been reported in India, Nepal and Cuba. Reproduction occurs asexually via autospore formation and sexually via oogamy. Although this oogamy is considered to involve fertilization by globular egg cells and antherozoids, the results of the present study revealed that the egg cells (female cells) remained spindle‐shaped and became globular zygotes after fertilization. The place on the egg cells where the antherozoid attached swelled to become a receptive papilla, after which the antherozoid invaded. Phylogenetic analysis based on nuclear 18S small subunit ribosomal RNA gene sequences showed that O. elegans is included in the family Oocystaceae.

Genetic diversity and host specificity of Blastocystis in reptiles, Eastern Thailand

Blastocystis inhabits the digestive tracts of a diverse range of hosts. Transmission patterns, including host specificity, and the clinical and public health significance of Blastocystis in humans remain poorly understood. This study aimed to investigate the distribution and genetic diversity of Blastocystis in herbivorous and carnivorous reptiles in Eastern Thailand. A total of 501 faecal samples were collected from 363 iguanas, 79 bearded dragons, 50 tortoises, and nine snakes in an animal breeding farm in Chonburi Province, Eastern Thailand. Detection and differentiation of Blastocystis was based on amplification, sequencing, and phylogenetic analysis of specific small subunit (SSU) ribosomal RNA genes from faecal DNA extracted from the samples. Altogether 101/501 samples (20 %) were polymerase chain reaction (PCR) and sequencing-positive for Blastocystis, 90 (89 %) of which were from iguanas; the remaining positive samples were from African spurred tortoise (n=6), Bearded dragon (n=3), Leopard tortoise (n=1), and Red-footed tortoise (n=1). Phylogenetic analysis revealed that most of the Blastocystis sequences from iguanas were largely similar, and they were distinct from those of the tortoises. Subtype 17 was found in the three bearded dragons and likely reflected Blastocystis from prey animals. This is the largest survey of Blastocystis in reptiles to date. Remarkable differences in Blastocystis colonization rates and genetic diversity were observed between iguanas and other reptile orders, and what was considered Blastocystis colonization was only observed in herbivorous reptiles.

Comparative Mitogenomics and Phylogenetic Implications for Nine Species of the Subfamily Meconematinae (Orthoptera: Tettigoniidae).

Currently, the subfamily Meconematinae encompasses 1029 species, but whole-mitochondrial-genome assemblies have only been made available for 13. In this study, the whole mitochondrial genomes (mitogenomes) of nine additional species in the subfamily Meconematinae were sequenced. The size ranged from 15,627 bp to 17,461 bp, indicating double-stranded circular structures. The length of the control region was the main cause of the difference in mitochondrial genome length among the nine species. All the mitogenomes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (CR). The majority strand encoded 23 genes, and the minority strand encoded 14 genes. A phylogenetic analysis reaffirmed the monophyletic status of each subfamily, but the monophysitism of Xizicus, Xiphidiopsis and Phlugiolopsis was not supported.

New Haplotypes of Blastocystis sp. Identified in Faeces from Various Animal Groups in Algeria.

Blastocystis sp. is a single-celled, anaerobic, parasitic protozoan commonly found in the intestinal tract of animals and humans globally. Genetic analysis has revealed significant diversity within its species, leading to the identification of at least 40 subtypes (ST1-ST40). This study aimed to identify and differentiate Blastocystis in faeces samples from various animal hosts in Algeria. A total of 403 fecal samples, collected from both domestic and zoo animals, were subjected to PCR amplification and sequencing of Blastocystis-specific small subunit ribosomal RNA (SSU-RNA) gene. The overall prevalence of Blastocystis in animals was found to be 38.9%. Through comprehensive phylogenetic and phylogeographic analyses, we identified four distinct subtypes (ST1 in both domestic and zoo animals, and ST3, ST4, and ST5 exclusively in zoo animals), encompassing nine different haplotypes, including five that appear original to Algeria. This study represents the first epidemiological molecular investigation of Blastocystis sp. in animals in Algeria.

A Survey of Zoonotic Bacteria in the Spleen of Six Species of Rodents in Panama

Emerging zoonotic diseases are one of the main threats to human and animal health. Among the agents with the potential for zoonoses, those of bacterial origin have great relevance in Public Health. Rodents are considered one of the main reservoirs of pathogens that represent a risk to human health or animal species. We used massive 16S ribosomal RNA gene amplicon sequencing to survey bacteria present in the spleen of six species of rodents in Panama in order to identify bacterial taxa with zoonotic potential in the country. We found 3352 bacterial Amplicon Sequence Variants (ASVs, i.e., phylogenetic species) in the spleen of six rodent species surveyed (Liomys adspersus, Melanomys caliginosus, Mus musculus, Proechimys semispinosus, Rattus rattus, Zygodontomys brevicauda). This bacterial community was represented by 25 phyla, 55 classes, 140 orders, 268 families, and 508 genera. The three predominant phyla were Actinobacteria, Firmicutes, and Proteobacteria, and the five predominant classes were Actinobacteria, Alpha- and Gammaproteobacteria, Bacilli, and Clostridia. There were seven high-abundance genera: Acinetobacter, Bartonella, Cutibacterium, Enterococcus, Sarcina, Staphylococcus, and Wolbachia. Genera found with less abundance included Bradyrhizobium, Chryseobacterium, Clostridium, Corynebacterium, Lactobacillus, Pseudonocardia, Rhodococcus, and Sphingomonas. Some of these genera (high or low abundance) have clinical importance. The identification of bacterial taxa with zoonotic potential in rodent species performed here allows us to have surveillance mechanisms for these pathogens and to be able to recognize localities to be prioritized for prevention of transmission and outbreaks, thus being of value for public health in Panama.

First Report of White Mucus Disease Caused by Fuligo gyrosa on Agrocybe chaxingu in China.

Agrocybe chaxingu is an edible and medicinal mushroom widely cultivated in China (Liu et al. 2021). Agrocybe chaxingu is extremely well-liked for the unique flavor and nutritional value. In May 2021, a serious white mucus disease was observed in the farms of A. chaxingu in the Ganxian district of Ganzhou City, Jiangxi Province, China, with an approximate disease incidence of 20%. In the years of 2022 and 2023, the same white mucus disease on A. chaxingu was observed in the farms in Nanchang City, Jiujiang City and Guangchang County, Jiangxi Province, China. The disease generally occurs on the media, stipe or pileus of A. chaxingu under condition of high humidity. The plasmodial slime molds migrated from the surface of culture media (78% hardwood sawdust, 15% wheat bran, 5% tea seed shell, 1% lime, and 1% gypsum) to the base of fruiting bodies, stipes and finally to pilei, showing as moist, sticky, and white reticulated structures. The infected fruiting bodies of A. chaxingu were completely covered by reticulated plasmodia, displaying a white or pale-yellow color. This resulted in the growth cessation, wilting and eventual death of fruiting body. Microscopic observation found that the plasmodia of slime mold enveloped the hyphae of A. chaxingu, resulting in the fragmentation of the hyphae. The disease can spread quickly, resulting in a 30% reduction in production. Slime mold cultures were isolated by transferring diseased fruiting bodies of A. chaxingu onto oat-agar medium (2% agar and 1% oatmeal) at 25 ℃. The isolates can be obtained after being subcultured for two to three generations. Purified plasmodia were placed on the semi-defined medium (1% tryptone, 1% glucose, 0.15% yeast extract, chick embryo extract and a balanced salt solution) to confirm the absence of bacteria (Daniel et al. 1964) and thus obtained the pure culture. Specimen of the voucher has been deposited in the Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences as number IAAM-W0002. The vegetative plasmodia have a large and well-developed scalloped structure that were white or milky white in colour. The white plasmodium became opaque pale yellow when exposed to light before fruiting. The veins merged and thickened. Fruiting bodies can be formed on the lid or side of the Petri dish under light condition. The fruiting bodies formed papillae with irregular shape, and then the color changed from translucent yellow to greyish black. Spores were usually spherical or subglobose, free, greyish brown in mass, purplish brown, 7-12 μm in diameter under light microscopy. These morphological characteristics were found to be consistent with those of Fuligo gyrosa (Synonym: Physarum gyrosum) (Kim et al. 2009; Shi et al. 2005; Jahn 1902). The identity of the isolates was further confirmed by sequence analysis of the 18S ribosomal RNA gene with primer SMNUR101/NS4 (Rusk et al. 1995; White et al. 1990). Using BLASTn searches, the sequence of 18S rRNA gene (GenBank accession number OR186216) matched the sequence of F. gyrosa (GenBank accession number LC744593) with the identity of 99.91% and coverage of 97%. A phylogenetic tree based on the 18S rRNA gene also demonstrated that the slime mold clustered with F. gyrosa. Over ten isolates have been obtained from the diseased A. chaxingu samples in different factories and identified as F. gyrosa. To test the pathogenicity of F. gyrosa, five healthy young fruiting bodies (three to five days of primordium) of A. chaxingu cultivated in mushroom-growing room were gently inoculated by a 12 mm diameter oat-agar medium with plasmodia at 24 ± 2 ℃ and then were kept with relative humidity of 90%-95%. Five fruiting bodies inoculated with a 12 mm oat-agar medium served as controls. After 5 days, white mucus characteristics and three fifths of death symptoms were observed on the fruiting bodies inoculated with the plasmodia, while the controls remained asymptomatic. The slime mold on the inoculated fruiting bodies was morphologically identical to F. gyrosa that was observed on the initial diseased fruiting bodies. It was also observed the envelopment A. chaxingu hyphae by the plasmodia of slime mold and fragmentation of the hyphae, and the fragmentation was not observed in the controls. Reisolations were prepared from the inoculated fruiting bodies and confirmed to be F. gyrosa based on morphological characteristics and 18S rRNA sequence, thus fulfilling Koch's postulates. Fuligo gyrosa has been reported to cause severe disease in oriental melon in Korea (Kim et al. 2009). This is the first report of F. gyrosa causing white mucus disease in cultivated A. chaxingu. The findings will provide important information on prevention and control of the disease, and be helpful for the development of A. chaxingu industry.

Complete mitogenome and phylogenetic analysis of Hyalinocerus flavoscutatus Cai and Shen 1998 (Hemiptera: Eurymelinae: Idiocerini)

This study presents the initial sequencing and characterization of the complete mitochondrial genome (mitogenome) of Hyalinocerus flavoscutatus, making the first comprehensive exploration of the mitogenome in the Hyalinocerus. Utilizing next-generation sequencing techniques, we identified a circular DNA molecule spanning 15,307 bp. The mitogenome comprises 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a primary non-coding region. Maximum likelihood phylogenetic evaluation, based on 13 protein-coding genes and two ribosomal RNA genes, robustly supports H. flavoscutatus as the basal group within Idiocerini. This research unveils valuable insights into the mitogenome of H. flavoscutatus and enhances our understanding of phylogenetic placement within the broader context of related tribes.

The first mitochondrial genome of Meroplius fukuharai (Diptera: Sepsidae)

Meroplius fukuharai is an important sanitary and ecological resource insect. We sequenced and annotated the mitogenome of Meroplius fukuharai which is the first representative of the genus Meroplius with nearly complete mitochondrial data. This mitogenome is 14,803 bp long, which consists of 22 transfer RNA genes, 13 protein-coding genes (PCGs), and two ribosomal RNA genes. All genes have a conservational arrangement with other published species of Sepsidae. Our results also supported the monophyly of Sepsidae, and the genus Meroplius is more closely related to genus Sepsis, Microsepsis, and Archisepsis.

The complete chloroplast genome sequence of Olea dioica Roxb, 1820 (Oleaceae)

Olea dioica Roxb, 1820 is a very important ethnomedicinal tree because of its medicinal properties and it belongs to the Oleaceae family. It is mainly distributed in evergreen and semi-evergreen forests. However, the chloroplast genome of O. dioica has not yet been reported. In this study, the chloroplast genome sequence of O. dioica was sequenced using next-generation sequencing technologies. The complete chloroplast genome of O. dioica was 155,138 bp in length (GenBank accession no. PP048999), comprising a large single-copy (LSC) region of 86,048 bp, a small single-copy (SSC) region of 17,816 bp, and two inverted repeat (IR) regions 25,637 bp each. The overall GC content was 37.8%. The complete chloroplast genome of O. dioica contains 131 complete genes, which are 88 protein-coding genes, 35 transfer RNA genes, and eight ribosomal RNA genes. A maximum-likelihood (ML) tree of O. dioica and 14 other species in the family Oleaceae suggested that O. dioica showed a close relationship with Olea brachiata.