Ribosomal RNA Gene Research Articles

Evidence of brain injury in fetuses of mothers with preterm labor with intact membranes and preterm premature rupture of membranes

Brain injury and poor neurodevelopment have been consistently reported in infants and adults born before term. These changes occur, at least in part, prenatally and are associated with intra-amniotic inflammation. The pattern of brain changes has been partially documented by magnetic resonance imaging but not by neurosonography along with amniotic fluid brain injury biomarkers. This study aimed to evaluate the prenatal features of brain remodeling and injury in fetuses from patients with preterm labor with intact membranes or preterm premature rupture of membranes and to investigate the potential influence of intra-amniotic inflammation as a risk mediator. In this prospective cohort study, fetal brain remodeling and injury were evaluated using neurosonography and amniocentesis in singleton pregnant patients with preterm labor with intact membranes or preterm premature rupture of membranes between 24.0 and 34.0 weeks of gestation, with (n=41) and without (n=54) intra-amniotic inflammation. The controls for neurosonography were outpatient pregnant patients without preterm labor or preterm premature rupture of membranes matched 2:1 by gestational age at ultrasound. Amniotic fluid controls were patients with an amniocentesis performed for indications other than preterm labor or preterm premature rupture of membranes without brain or genetic defects whose amniotic fluid was collected in our biobank for research purposes matched by gestational age at amniocentesis. The group with intra-amniotic inflammation included those with intra-amniotic infection (microbial invasion of the amniotic cavity and intra-amniotic inflammation) and those with sterile inflammation. Microbial invasion of the amniotic cavity was defined as a positive amniotic fluid culture and/or positive 16S ribosomal RNA gene. Inflammation was defined by amniotic fluid interleukin 6 concentrations of >13.4 ng/mL in preterm labor and >1.43 ng/mL in preterm premature rupture of membranes. Neurosonography included the evaluation of brain structure biometric parameters and cortical development. Neuron-specific enolase, protein S100B, and glial fibrillary acidic protein were selected as amniotic fluid brain injury biomarkers. Data were adjusted for cephalic biometrics, fetal growth percentile, fetal sex, noncephalic presentation, and preterm premature rupture of membranes at admission. Fetuses from mothers with preterm labor with intact membranes or preterm premature rupture of membranes showed signs of brain remodeling and injury. First, they had a smaller cerebellum. Thus, in the intra-amniotic inflammation, non-intra-amniotic inflammation, and control groups, the transcerebellar diameter measurements were 32.7 mm (interquartile range, 29.8-37.6), 35.3 mm (interquartile range, 31.2-39.6), and 35.0 mm (interquartile range, 31.3-38.3), respectively (P=.019), and the vermian height measurements were 16.9 mm (interquartile range, 15.5-19.6), 17.2 mm (interquartile range, 16.0-18.9), and 17.1 mm (interquartile range, 15.7-19.0), respectively (P=.041). Second, they presented a lower corpus callosum area (0.72 mm2 [interquartile range, 0.59-0.81], 0.71 mm2 [interquartile range, 0.63-0.82], and 0.78 mm2 [interquartile range, 0.71-0.91], respectively; P=.006). Third, they showed delayed cortical maturation (the Sylvian fissure depth-to-biparietal diameter ratios were 0.14 [interquartile range, 0.12-0.16], 0.14 [interquartile range, 0.13-0.16], and 0.16 [interquartile range, 0.15-0.17], respectively [P<.001], and the right parieto-occipital sulci depth ratios were 0.09 [interquartile range, 0.07-0.12], 0.11 [interquartile range, 0.09-0.14], and 0.11 [interquartile range, 0.09-0.14], respectively [P=.012]). Finally, regarding amniotic fluid brain injury biomarkers, fetuses from mothers with preterm labor with intact membranes or preterm premature rupture of membranes had higher concentrations of neuron-specific enolase (11,804.6 pg/mL [interquartile range, 6213.4-21,098.8], 8397.7 pg/mL [interquartile range, 3682.1-17,398.3], and 2393.7 pg/mL [interquartile range, 1717.1-3209.3], respectively; P<.001), protein S100B (2030.6 pg/mL [interquartile range, 993.0-4883.5], 1070.3 pg/mL [interquartile range, 365.1-1463.2], and 74.8 pg/mL [interquartile range, 44.7-93.7], respectively; P<.001), and glial fibrillary acidic protein (1.01 ng/mL [interquartile range, 0.54-3.88], 0.965 ng/mL [interquartile range, 0.59-2.07], and 0.24 mg/mL [interquartile range, 0.20-0.28], respectively; P=.002). Fetuses with preterm labor with intact membranes or preterm premature rupture of membranes had prenatal signs of brain remodeling and injury at the time of clinical presentation. These changes were more pronounced in fetuses with intra-amniotic inflammation.

First report of Sclerotium hydrophilum causing leaf spot on Brasenia schreberi in central China.

Brasenia schreberi, commonly known as watershield and referred to as 'Chun Cai' in Chinese, is a worldwide aquatic vegetable. It has long been regarded as health- promoting vegetable due to production of mucilage in young shoots, and thus has gained popularity in China. In September 2022, a leaf spot disease was observed at the National Aquatic Vegetable Germplasm Resource Nursery located in Wuhan, Hubei province, China. The disease occurred on watershield leaves. It started with the formation of leaf spots surrounded by halos.These spots ranged in color from yellow to brown and in diameter from 1 to 10 mm. Subsequently, the smaller spots merged, ultimately causing the entire leaves to turn black. Small brown- to black-colored sclerotia were produced on the underside of the diseased leaves. Disease incidence was 30% on average, and yield loss was approximately 15% on average. To isolate the pathogen, leaf tissues at the disease-healthy border area were excised into 5 × 5 mm pieces, these segments were immersed in 75% ethanol for 30 s, followed by immersion in 0.5% sodium hypochlorite for 30 s, and then rinsed twice in sterile water. After air-drying, the leaf pieces were incubated on potato dextrose agar (PDA) in darkness at 28°C for 3 d. Mycelia from the leaf pieces were transferred to new PDA plates for purification, three sclerotia-forming fungal isolates (Whcc-1, Whcc-3, Whcc-4) were finally obtained. They were incubated on PDA at 28°C for 4 to 14 d for observation of colony morphology. At 4 d after incubation (DAI), they grew rapidly with the average growth rate of 2.2 cm/d and formed colonies with whitish substrate mycelia and well-developed aerial mycelia and small white to light brown-colored sclerotia. At 10 to 14 DAI, the sclerotia gradually turned to black, 0.2 to 0.4 mm in diameter (0.26 mm on average, n = 50). These morphological characteristics matched description of Sclerotium hydrophilum (Bashyal et al. 2021). Molecular identification was done to further clarify the species identity of this fungus. Genomic DNA was extracted from isolates Whcc-1, Whcc-3, and Whcc-4. The internal transcribed spacer region of the ribosomal DNA (ITS-5.8S rDNA) and the small subunit ribosomal RNA gene (ssrRNA) were amplified using universal primers ITS1/ITS4 and NS1/NS6, as described by White et al. (1990). Sequence analysis revealed a high degree of similarity between the ITS-5.8S rDNA sequences from Whcc-1, Whcc-3, and Whcc-4 (GenBank Acc. No. OP782030, PP035994, and PP035995, respectively) and those of S. hydrophilum strain CBS201.27 (GenBank Acc. No. FJ231396), with similarities of 99.25%, 99.4%, and 99.25%, respectively. The ssrRNA sequences from Whcc-1, Whcc-3, and Whcc-4 (GenBank Acc. No. PP238401, PP261342 and PP261345) were found to be identical, displaying 100% similarity to the ssrRNA sequences of S. hydrophilum strain ZH11 (GenBank Acc. No. KC354147). Based on both morphological and molecular evidence, it can be inferred that Whcc-1, Whcc-3, and Whcc-4 belong to the species S. hydrophilum. Pathogenicity tests were conducted by inoculation of the mycelial agar plugs of Whcc-1, Whcc-3 or agar plugs of fresh PDA (control) on floating leaves of two watershield plants, 4 leaves (replicates) for each treatment. After inoculation, the treated leaves were sealed in plastic bags to maintain humidity, and grown under natural conditions (18°C to 28°C, with 8 hours of light daily). At 7 DAI, while control leaves remained healthy, the leaves inoculated with Whcc-1 and Whcc-3 leaves formed yellow- to brown-colored spots similar to those observed in the field surveys. S. hydrophilum was re-isolated from the leaf spots, thus verifing Koch's postulates. S. hydrophilum has a wide host range, infecting at least 19 genera of plants, including common rice and wild rice (Johnson et al. 1976), and water lily (Kernkamp et al. 1977). Moreover, it has been reported to infect rice in China (Punter et al. 1984; Zhong et al. 2018). To our knowledge, this is the first report of S. hydrophilum on watershield leaves in central China.

Characterization of the complete chloroplast genome sequence of &lt;i&gt;Hypericum petiolulatum&lt;/i&gt; (Hypericaceae)

&lt;i&gt;Hypericum&lt;/i&gt; L. (Hypericaceae) is one of the best-selling herbal medicines in the world comprising ca. 500 species of herbs, shrubs, and small trees. &lt;i&gt;Hypericum petiolulatum&lt;/i&gt; Hook. f. &amp; Thomson ex Dyer is widely distributed in China, Vietnam, Myanmar, Nepal, India, Malaysia, and Bhutan and is used as a traditional herb to treat hemoptysis and inflammation. In this study, we sequenced and assembled the complete chloroplast (cp) genome of &lt;i&gt;H. petiolulatum&lt;/i&gt;. The complete plastome of &lt;i&gt;H. petiolulatum&lt;/i&gt; was 136,105 bp in length, with a large single copy region (LSC) of 93,709 bp, a small single copy region (SSC) of 11088 bp and two identical inverted repeats (IRs) of 15,654 bp. The overall GC content of the plastome was 37.0%, while GC contents of the LSC, SSC, and each IR were 35.5%, 31.0%, and 43.8%, respectively. In addition, 116 genes consisting of 76 protein-coding genes, six ribosomal RNA genes, and 34 transfer RNA genes were identified. A phylogenetic analysis of 14 taxa inferred based on cp genome sequences revealed a close relationship between &lt;i&gt;H. petiolulatum&lt;/i&gt; and &lt;i&gt;H. perforatum&lt;/i&gt;. The complete cp genome sequence of &lt;i&gt;H. petiolulatum&lt;/i&gt; reported in this paper will facilitate population and phylogenomics studies of this medicinal plant group.

The first complete chloroplast genome of &lt;i&gt;Polygonatum hirtellum&lt;/i&gt;: Genome features and phylogenetic relationships

&lt;i&gt;Polygonatum hirtellum&lt;/i&gt; is a perennial herb within the family Asparagaceae. In the present study, the chloroplast (cp) genome of &lt;i&gt;P. hirtellum&lt;/i&gt; is reported for the first time, and its phylogenetic relationships are also investigated. The findings revealed that the cp genome was 155,697 bp and exhibited a typical quadripartite structure, consisting of a large single copy (84,468 bp), a small single copy (18,491 bp), and a pair of invert repeat sequences (26,369 bp). The GC content of the cp genomes amounted to 37.7%; 130 genes were identified, consisting of 84 protein-coding genes, 38 transfer RNA genes, and eight ribosomal RNA genes. A phylogenetic analysis based on the cp genome and coding sequence showed that &lt;i&gt;P. hirtellum&lt;/i&gt; was a member of section &lt;i&gt;Verticillata&lt;/i&gt; and could be distinguished from other species of the genus &lt;i&gt;Polygonatum&lt;/i&gt; used in the analysis.

Exploring the Microbiome Landscape of Dental Plaque: A Cross-Sectional Analysis in Periodontal Health and Disease.

This study aimed to comprehensively analyze the microbiome of dental plaque in individuals with varying periodontal statuses, encompassing both periodontal health and disease. The primary objectives were to identify microbial markers associated with different clinical conditions, explore variations in microbial diversity, and investigate potential correlations between the oral microbiome and clinical parameters. A cross-sectional design was employed, involving 164 participants aged 18 to 65 years. Inclusion criteria comprised individuals with good oral and systemic health for the periodontal health group and those diagnosed with various stages of periodontal disease for the periodontal disease group. Dental plaque samples were meticulously collected from diverse tooth surfaces, and clinical examinations were conducted to assess periodontal health status. High-throughput sequencing of the 16S ribosomal RNA (rRNA) gene was utilized for microbiome analysis. Demographic characteristics revealed a balanced distribution between the periodontal health and disease groups. Clinical parameters, including probing depth, clinical attachment loss, and bleeding on probing, exhibited significant differences between the two groups (p < 0.001). Microbial diversity indices indicated a higher diversity in the periodontal health group compared to the disease group (p < 0.001). Analysis of relative abundance of bacterial phyla identified significant variations, with Firmicutes, Bacteroidetes, and Actinobacteria showing differential prevalence between health and disease (p < 0.05). Differentially abundant taxa analysis highlighted specific species associated with each clinical condition, including Prevotella intermedia and Porphyromonas gingivalis. Network analysis revealed complex microbial interactions within the oral microbiome. Functional predictions indicated variations in metabolic capabilities between health and disease, with potential implications for virulence and antibiotic resistance. This study provides a comprehensive analysis of the oral microbiome in periodontal health and disease, revealing significant associations between microbial composition and clinical parameters. The identification of microbial markers and functional insights enhances our understanding of the complex interplay within the oral ecosystem. These findings hold promise for advancing diagnostic and therapeutic approaches tailored to individual microbial profiles.

Biological and Synthetic Surfactants Increase Class I Integron Prevalence in Ex Situ Biofilms.

The role of biocides in the spread of antimicrobial resistance (AMR) has been addressed but only a few studies focus on the impact of surfactants on microbial diversity and AMR, although they are common constituents of cleaners, disinfectants, and personal care products and are thus released into the environment in large quantities. In this study, we used a static ex situ biofilm model to examine the development of four biofilms exposed to surfactants and analyzed the biofilms for their prevalence of class I integrons as a proxy for the overall abundance of AMR in a sample. We furthermore determined the shift in bacterial community composition by high-resolution melt analysis and 16S ribosomal RNA (16S rRNA) gene sequencing. Depending on the initial intrinsic prevalence of class I integrons in the respective ex situ biofilm, benzalkonium chloride, alkylbenzene sulfonate, and cocamidopropyl betaine increased its prevalence by up to 6.5× on average. For fatty alcohol ethoxylate and the biosurfactants sophorolipid and rhamnolipid, the mean increase did not exceed 2.5-fold. Across all surfactants, the increase in class I integrons was accompanied by a shift in bacterial community composition. Especially benzalkonium chloride, cocamidopropyl betaine, and alkylbenzene sulfonate changed the communities, while fatty alcohol ethoxylate, sophorolipid, and rhamnolipid had a lower effect on the bacterial biofilm composition.

First Discovery of Stereostratum corticioides Causing Rust on the Culm of the Bamboo Pseudosasa japonica

A fungus strain &lt;i&gt;Stereostratum corticioides&lt;/i&gt; PKVL1, belonging to the family &lt;i&gt;Pucciniaceae&lt;/i&gt; that causes rust in plants, was discovered on the sheath of the bamboo &lt;i&gt;Pseudosasa japonica&lt;/i&gt; leading to the death of the infected bamboo in the following year. Microscopic observation of the yellow fungal mass revealed teliospores with an oval, one-septate (two-celled) structure. The average length and width of teliospores were 31.83±3.57 μm and 20.74±1.72 μm, respectively. The large-subunit ribosomal RNA gene was amplified using the LR0R and LR7 primers, showing that the strain PKVL1 had a similarity of 99.34% to previously reported &lt;i&gt;S. corticioides&lt;/i&gt;. In particular, the two &lt;i&gt;Stereostratum&lt;/i&gt; strains form a separate cluster among the fungi in the family &lt;i&gt;Pucciniaceae&lt;/i&gt;. This is the first report in the Republic of Korea of fungal rust occurring on the culm of bamboo rather than on the leaves.

Analysis of the Overlength Main Noncoding Region in Metacarcinus magister (Decapoda: Brachyura) and a Phylogenetic Study of the Cancroidea Species.

Complete mitochondrial genomes (mitogenomes) can provide important information regarding the molecular evolution and phylogenetic relationships of marine invertebrates, especially in Brachyura. Only one Cancroidea species of mitogenomes has been sequenced before; in this research, the mitogenomic characteristics of Metacarcinus magister (Cancridae: Cancroidea) are newly studied. The length of the M. magister mitogenome was 48,820 bp, and it contained the typical 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. We performed a series of analyses on the characteristics of the mNCR of M. magister. The phylogenetics, life circumstances, and selective pressures were all analyzed to explain the formation of this length, which revealed the length of the M. magister mitogenome to be approximately three times greater than the normal length of Brachyuran mitogenomes. Phylogenetic analyses based on a dataset of 215 Decapodan mitogenomes indicated that all Eriphioidea crabs were clustered together as a group. Moreover, the rearrangement mechanism of the Cancroidea species was predicted to provide stronger evidence for the phylogenetic analysis. In general, the results obtained in this study will contribute to a better understanding of the cause of the unusual length of the M. magister mitogenome and provide new insights into the phylogeny of Brachyura.

Foliar spraying with a synthetic community of Bacillus increases the selenium content, quality, and contribution to phyllosphere microecology of pakchoi

Due to widespread selenium insufficiency worldwide, the human body's intake of selenium through foods has been a vital approach. Microorganisms have been widely used as a green and efficient tool for selenium biofortification of crops. However, most studies have focused on one type of PGPB, while the synergistic effects of multiple PGPBs have rarely been explored. In this study, a synthetic community was constructed by selenium absorption promotion strains, including Bacillus subtilis, Bacillus cereus, and Bacillus altitudinis, which were used instead of traditional single strain. The synthetic community was inoculated on leaves by foliar spraying under two exogenous selenomethionine treatments (10 mg L−1 and 20 mg L−1). Results showed that the synthetic community improved selenium absorption, growth, and quality of pakchoi largely. In contrast to the inoculation of Bacillus subtilis, Bacillus cereus, and Bacillus altitudinis respectively, the inoculation of the synthetic community increased the fresh weight (increased by 23.22 %, 14.55 % and 16.30 %), dry weight (increased by 13.91 %, 13.59 %, and 6.32 %) and selenium content (increased by 68.61 %, 54.37 %, and 12.46 %) in the treatments with the application of 10 mg L−1 selenium. The synthetic community inoculation enhanced the fresh weight (increased by 23.50 %, 26.35 %, and 15.63 %), dry weight (increased by 25.61 %, 20.72 %, and 15.77 %), selenium content (increased by 66.05 %, 90.20 %, and 38.90 %) in the treatments with the application of 20 mg L−1 selenium. Besides, the synthetic community also increased SPAD value, the contents of soluble protein, reducing sugar, vitamin C, and nitrogen content of pakchoi. And the nitrate content was significantly decreased. High-throughput sequencing of the 16S ribosomal RNA gene indicated that foliar spraying with synthetic community increased the relative abundance of Acinetobacter. This suggested that the composition of phyllosphere bacterial taxa was optimized by the synthetic community. This study demonstrated the potential of the synthetic community in the selenium biofortification of crops.

Microbiome studies in veterinary field: communities’ diversity measurements pitfalls

In recent years, the role of the microbiota has proved to be extremely important in medicine as one of the most important aspects for the characterization of living beings in both healthy and pathological conditions. Moreover, the development of shotgun technology, and in particular the cheaper 16S ribosomal RNA (rRNA) gene sequencing, made possible its wide diffusion. In veterinary sciences, microbiome studies have seen applications not only in medicine in the strict sense (e.g diagnosis) but also, for example, in food inspection (quality, fraud, etc.) and in animal feed preparation itself. However, focusing on microbial profiling by 16S rRNA sequencing, there are several crucial aspects to be considered: from the experimental design definition and the sample size problem to the data analysis steps. This latter involves several layers, e.g. which 16S rRNA databases to use, which metrics for alpha and beta diversity, etc. In this work, we want to present, as a case study, a critical discussion about the large number of alpha and beta diversity metrics and their impact in the statistical comparisons among groups.

Vaginal microbiomes of breast cancer survivors treated with aromatase inhibitors with and without vulvovaginal symptoms

Genitourinary syndrome of menopause (GSM) is the leading cause of vaginal symptoms in breast cancer survivors treated with aromatase inhibitors. However, there are currently no effective treatment options available for women with a history of breast cancer. Recent research has established that changes in the vaginal microbiome may be linked to GSM. Most studies have assessed the microbiome without accounting for the estrogen status. It remains unknown whether the vaginal microbiome differ among patients with a low estrogenic state with and without vulvovaginal symptoms. To address such research questions, our study compares the vaginal microbiomes among breast cancer survivors treated with aromatase inhibitors with and without vulvovaginal symptoms. A total of 50 breast cancer survivors treated with aromatase inhibitors were recruited, among whom 25 had vulvovaginal symptoms and 25 had no vulvovaginal symptoms. Vaginal swabs were collected. DNA extraction, followed by sequencing of the V3–V4 regions of the 16S ribosomal RNA gene, were performed. Differential abundance analysis was conducted by linear discriminant analysis effect size. Taxonomy assignment, alpha diversity and beta diversity were examined. The relative abundance of genus Sneathia and genus Gardnerella was significantly increased in vulvovaginal symptoms group with no differences in bacterial diversity and richness.

Alterations in Gut Microbiota and Their Correlation with Brain Beta-Amyloid Burden Measured by 18F-Florbetaben PET in Mild Cognitive Impairment Due to Alzheimer's Disease.

(1) Background: This study investigated changes in the gut microbial composition of individuals with mild cognitive impairment (MCI) due to Alzheimer's disease (AD) and their relationship with positron emission tomography (PET) amyloid accumulation. (2) Methods: In total, 17 cognitively normal individuals without amyloid-beta (Aβ) accumulation (Aβ-NC) and 24 with Aβ-positive mild cognitive impairment (Aβ+MCI) who underwent 18F-florbetaben PET and fecal bacterial 16S ribosomal RNA gene sequencing were enrolled. The taxonomic compositions of the Aβ-NC and Aβ+MCI groups were compared. The abundance of taxa was correlated with the standardized uptake value ratio (SUVR), using generalized linear models. (3) Results: There were significant differences in microbiome richness (ACE, p = 0.034 and Chao1, p = 0.024), alpha diversity (Shannon, p = 0.039), and beta diversity (Bray-Curtis, p = 0.018 and Generalized UniFrac, p = 0.034) between the Aβ-NC and Aβ+MCI groups. The global SUVR was positively correlated with the genus Intestinibacter (q = 0.006) and negatively correlated with the genera Roseburia (q = 0.008) and Agathobaculum (q = 0.029). (4) Conclusions: In this study, we identified significant changes in the gut microbiota composition that occur in individuals with MCI due to AD. In particular, the correlation analysis results between PET amyloid burden and gut microbial abundance showed that amyloid deposition is associated with a reduction in specific taxa involved in butyrate production.

The complete mitochondrial genome of Leucoptera coffeella (Lepidoptera: Lyonetiidae) and phylogenetic relationships within the Yponomeutoidea superfamily

The coffee leaf miner (Leucoptera coffeella) is one of the major pests of coffee crops in the neotropical regions, and causes major economic losses. Few molecular data are available to identify this pest and advances in the knowledge of the genome of L. coffeella will contribute to improving pest identification and also clarify taxonomy of this microlepidoptera. L. coffeella DNA was extracted and sequenced using PacBio HiFi technology. Here we report the complete L. coffeella circular mitochondrial genome (16,407 bp) assembled using Aladin software. We found a total of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and an A + T rich-region and a D-loop. The L. coffeella mitochondrial gene organization is highly conserved with similarities to lepidopteran mitochondrial gene rearrangements (trnM-trnI-trnQ). We concatenated the 13 PCG to construct a phylogenetic tree and inferred the relationship between L. coffeella and other lepidopteran species. L. coffeella is found in the Lyonetiidae clade together with L. malifoliella and Lyonetia clerkella, both leaf miners. Interestingly, this clade is assigned in the Yponomeutoidea superfamily together with Gracillariidae, and both superfamilies displayed species with leaf-mining feeding habits.

Subtype Determination of Blastocystis Spp. Isolated from Poultry Tikrit City

Blastocystis spp. spread throughout the world, it is one of the intestinal parasites that settle in human’s gastrointestinal tract, as well as occurring in other hosts such as Aves, reptiles, cattle and insects. Gross stool samples collected from poultry were 221 samples. Blastocystis spp. and subtypes investigated by a PCR reaction which targeting the small subunit of ribosomal RNA (SSU rRNA) gene. Microscopic results and sequencing analysis results of SSU rRNA gene showed 2 sample were infected with Blastocystis with percentage 0.9% out of 221 poultry fecal samples. The poultry infected with Blastocystis consisted of chicken and turkey, as infected rate in chicken were 0.6% out of 163 chickens while infected rate in turkey were 1.7% out of 58 turkeys. The existence of subtype (ST6) of Blastocystis was confirmed via BLAST analysis.

The complete mitochondrial genome of Chibiraga houshuaii (Lepidoptera, Limacodidae) and its phylogenetic implications

Chibiraga is a mall East Asian genus in the family Limacodidae (slug-moths). The latter includes many agricultural pests. Mitochondrial genome analysis is an important tool for studying insect molecular identification and phylogenetics. However, there are very few mitogenome sequences available for Limacodidae species, and none for the genus Chibiraga at all. To explore the mitogenome features of Chibiraga and verify its phylogenetic position, the complete mitogenome of Chibiraga houshuaii was sequenced and annotated. The complete 15,487 bp genome encoded 37 mitochondrial genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (CR). Most of the PCGs had typical ATN start codons and terminated with TAA or a single T residue. UUA (Leu2), AUU (Ile), UUU (Phe), AUA (Met) and AAU (Asn) were the five most frequently used codons. All tRNAs were folded into cloverleaf secondary structure, except for trnS1, which lacked the DHU arm. Phylogenetic analyses within the superfamily Zygaenoidea were performed based on multiple datasets from mitochondrial genes. The results showed that the families Phaudidae, Limacodidae and Zygaenidae were respectively recovered as monophyly; C. houshuaii was clustered in a clade with nettle type larvae in Limacodidae.

Phylogenetic evidence of a possible Trichuris globulosa species complex in Arabian camels from Kuwait.

During a 1-year study, Trichuris adults were obtained after necropsy of Arabian camels (Camelus dromedarius) from a slaughterhouse in Kuwait. Morphological and molecular identification was performed to confirm the identity of the Trichuris specimens obtained from C. dromedarius. Fifteen male Trichuris specimens were selected, and molecular identification was performed using mitochondrial cytochrome c oxidase subunit I, 12S ribosomal RNA, 16S ribosomal RNA genes and the nuclear internal transcribed spacer 2 (ITS2) region. Through phylogenetic analysis, 2 distinct groups were obtained using the mitochondrial genes, where group 1 showed a close relationship to Trichuris globulosa while group 2 showed a close relationship to Trichuris ovis, providing molecular evidence of a possible T. globulosa species complex. Additionally, the nuclear ITS2 region did not provide enough resolution to distinguish between the 2 groups of Trichuris specimens. Observation of morphological characters revealed variations in the shape of the male spicule sheath, where specimens present either a globular posteriorly truncated swelling or the absence of posteriorly truncated swelling. Moreover, the variations in male spicule sheath does not corroborate with the results of molecular data, suggesting the limited use of this character for identification of T. globulosa. In conclusion, molecular analysis suggests a possible species complex in T. globulosa, with the mitochondrial genetic markers successfully differentiating between the 2 groups. The limited use of the male spicule sheath as a diagnostic character for identification of T. globulosa is suggested.

Host-microbiome associations in saliva predict COVID-19 severity.

Established evidence indicates that oral microbiota plays a crucial role in modulating host immune responses to viral infection. Following severe acute respiratory syndrome coronavirus 2, there are coordinated microbiome and inflammatory responses within the mucosal and systemic compartments that are unknown. The specific roles the oral microbiota and inflammatory cytokines play in the pathogenesis of coronavirus disease 2019 (COVID-19) are yet to be explored. Here, we evaluated the relationships between the salivary microbiome and host parameters in different groups of COVID-19 severity based on their oxygen requirement. Saliva and blood samples (n = 80) were collected from COVID-19 and from noninfected individuals. We characterized the oral microbiomes using 16S ribosomal RNA gene sequencing and evaluated saliva and serum cytokines and chemokines using multiplex analysis. Alpha diversity of the salivary microbial community was negatively associated with COVID-19 severity, while diversity increased with health. Integrated cytokine evaluations of saliva and serum showed that the oral host response was distinct from the systemic response. The hierarchical classification of COVID-19 status and respiratory severity using multiple modalities separately (i.e. microbiome, salivary cytokines, and systemic cytokines) and simultaneously (i.e. multimodal perturbation analyses) revealed that the microbiome perturbation analysis was the most informative for predicting COVID-19 status and severity, followed by the multimodal. Our findings suggest that oral microbiome and salivary cytokines may be predictive of COVID-19 status and severity, whereas atypical local mucosal immune suppression and systemic hyperinflammation provide new cues to understand the pathogenesis in immunologically compromised populations.

Phylogenetic insights into the terrestrial snails Helicoidei (Gastropoda: Stylommatophora) with special emphasis on the Camaenidae

Abstract The superfamily Helicoidei are a widely distributed and diverse infraorder of land snails and slugs. Here, we constructed a phylogenetic tree based on sequences of the large subunit ribosomal RNA gene to investigate the relationships within the Helicoidei. Based on our phylogenetic tree, the family Camaenidae, as currently recognized, is not monophyletic, with the Polygyridae falling within the group. Likewise, the family Hygromiidae as currently defined is not monophyletic and incorporates the Geomitridae. The family Xanthoncyhidae form a monophyletic group that is sister to the Pleurodontidae. Likewise, the family Helicidae form a monophyletic group; it is sister to the branch incorporating Hygromiidae, Geomitridae, Pleurodontidae, Helicodontidae, and Xanthonychidae. The Solaropsidae are the sister group to a clade comprising other Sagdoidea. Our findings suggest that the Hygromiidae s.l. families should be restored to their previous name, Hygromiidae. A new genus of Bradybaeninae, Jiaoliaous Zhang gen. nov., is described here, with a simple genital system, single dart sac with multi-branched mucous glands, and a penis with a penial sheath.

Novel trypanosomatid species detected in Mongolian pikas (Ochotona pallasi) and their fleas in northwestern China

BackgroundIn the family Trypanosomatidae, the genus Trypanosoma contains protozoan parasites that infect a diverse range of hosts, including humans, domestic animals, and wildlife. Wild rodents, as natural reservoir hosts of various pathogens, play an important role in the evolution and emergence of Trypanosomatidae. To date, no reports are available on the trypanosomatid infection of pikas (Lagomorpha: Ochotonidae).MethodsIn this study, Mongolian pikas and their fleas were sampled at the China–Mongolia border, northwestern China. The samples were analyzed with polymerase chain reaction (PCR) and sequencing for the presence of Trypanosomatidae on the basis of both the 18S ribosomal RNA (18S rRNA) gene and the glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) gene. The morphology of trypomastigotes was also observed in peripheral blood smears by microscopy.ResultsMolecular and phylogenetic analyses revealed a new genotype of the Trypanosoma lewisi clade that was found both in pika blood and flea samples. This genotype, which probably represents a new species, was provisionally designated as “Trypanosoma sp. pika”. In addition, a novel genotype belonging to the genus Blechomonas of Trypanosomatidae was detected in fleas. On the basis of its molecular and phylogenetic properties, this genotype was named Blechomonas luni-like, because it was shown to be the closest related to B. luni compared with other flea-associated trypanosomatids.ConclusionsTo the best of our knowledge, this is the first study to report any trypanosomatid species in Mongolian pikas and their fleas. Further studies are needed to investigate the epidemiology of these protozoan parasites, as well as to evaluate their pathogenicity for humans or domestic animals.Graphical

Power law in species–area relationship overestimates bacterial diversity in grassland soils at larger scales

AbstractAimSpecies–area relationships (SAR) are widely utilized for estimating the species richness and its spatial turnover across various scales. Despite the prevalent characterization of SAR using the power law in many microbial community studies, its efficacy remains unvalidated. This study aims to characterize the microbial SAR and its mechanisms in alpine grassland soils on the Qinghai‐Tibet Plateau (QTP).LocationQinghai‐Tibet Plateau, China.Time PeriodAugust 2014.Major Taxa StudiedSoil bacteria.MethodsSoil samples were collected from five alpine grassland sites on the QTP. Employing a nested sampling strategy at each site, soil samples were collected in plot sizes ranging from 0.5 × 0.5 m2 to 2048 × 2048 m2. Soil bacterial communities were analysed by sequencing 16S ribosomal RNA gene amplicons using an Illumina MiSeq.ResultsThe bacterial SAR exhibited a logarithmic power law (R2: 0.952–0.999), outperforming the power law (R2: 0.701–0.852). Consequently, the most widely adopted power law led to an overestimation of species richness by up to 15.07% in areas &gt;256 × 256 m2, and the regional maximum theoretical richness based on Chao1 by up to 9.88%. Mechanistically, the passive sampling hypothesis was refuted through the rarefied species richness analysis, and the disproportionate effect hypothesis was rejected based on analyses of the effective numbers of species number conversions for the probability of interspecific encounters (SPIE). Notably, Pearson and multiple linear regression analyses indicated that the spatial turnover of bacterial richness was determined by the environmental heterogeneity (R2: 0.855–0.999), rather or better than environmental variables themselves, supporting the ‘environment heterogeneity hypothesis’.Main ConclusionsSoil bacterial SAR in alpine grasslands exhibited a logarithmic power relationship. Spatial turnover was primarily governed by the environmental heterogeneity. In contrast, the traditional power law leads to an overestimation of soil bacterial diversity at the regional scale.