Ribosomal Ribonucleic Acid Research Articles

Disease-associated gut microbiome and metabolome changes in rats with chronic hypoxia-induced pulmonary hypertension.

Pulmonary hypertension (PH) is a progressive disease affecting the lung vasculature that is characterized by sustained vasoconstriction and leads to vascular remodeling. The lung microbiome contributes to PH progression, but the function of the gut microbiome and the correlation between the gut microbiome and metabolome remain unclear. We have analyzed whether chronic hypoxia-induced PH alters the rat fecal microbiota. We explored hypoxia-induced pulmonary hypertension model rats to find out the characteristic changes of intestinal microorganisms and metabolites of hypoxia-induced pulmonary hypertension, and provide a theoretical basis for clinical treatment. In the current study, a chronic hypoxia-induced PH rat model was used to investigate the role of the gut microbiome and metabolome as a potential mechanism contributing to the occurrence and development of PH. 16S ribosomal ribonucleic acid (16S rRNA), short-chain fatty acid (SCFA) measurements, mass spectrometry (MS) metabolomics analysis and metatranscriptome were performed to analyze stool samples. The datasets were analyzed individually and integrated for combined analysis using bioinformatics approaches. Our results suggest that the gut microbiome and metabolome of chronic hypoxia-induced PH rats are distinct from those of normoxic rats and may thus aid in the search for new therapeutic or diagnostic paradigms for PH. The gut microbiome and metabolome are altered as a result of chronic hypoxia-induced PH. This imbalanced bacterial ecosystem might play a pathophysiological role in PH by altering homeostasis.

Состояние микробиома десневой борозды детей с бронхиальной астмой

Aim. To compare the microbiome of the healthy gingival sulcus of children with bronchial asthma (BA) and different dental conditions. Design. Open comparative clinical and laboratory study. Materials and methods. Gingival substrate was obtained from 19 children aged 3–6 years with exacerbation of BA; the results of sequencing the genes of 16 subunits of ribosomal ribonucleic acid (16S rRNA) on the MiSeq platform (Illumina) were analyzed. Results. Five major phyla have been identified in the gingival sulcus: Firmicutes, Proteobacteria, Actinobacteria, Fusobacterium and Bacteroidetes and the dominant genus, Streptococcus. A significantly high relative prevalence of the species Neisseria oralis (p = 0.0073), Hemophilic massiliensis (p = 0.046), Hemophilic paraphrohaemolyticus (p = 0.05) and Lautropia mirabilis (p = 0.05) in children with asthma without caries was established. The level of immunoglobulin E (IgE) is significantly higher in children with asthma and caries compared to children without caries (461.79 ± 60.58 and 276.97 ± 81.15 IU/ml). Conclusion. The predominance of opportunistic and “healthy” bacterial species of the phylum Proteobacteria in the healthy gingival sulcus of children with BA may be an indicator of oral dysbiosis in BA. Overproduction of IgE in children with caries may be due to cariogenic flora, which requires further study. Keywords: sequencing, gingival crevicular microbiome, children, bronchial asthma, caries.

Short term antibiotic effects on gut microbiome in Indian preschoolers: A 16S rRNA analysis

Objectives: Antibiotic use is associated with dysbiosis of the gut microbiome. The objective of this study is to investigate the effect of antibiotics on gut composition in children aged 3–5 years receiving antibiotics compared to children who did not receive antibiotics. Materials and Methods: A total of 54 participants aged 3–5 years were included in this multi-centric cohort study. Participants were divided into two equal groups, that is the treatment-experienced group (Group 1, n = 27, antibiotic) and the treatment-not-experienced group (Group 2, n = 27, non-antibiotic). Stool samples of study participants were collected on days 0 and 5 (± 1 day) and analyzed using 16Svedberg ribosomal ribonucleic acid (16S rRNA) gene sequencing. Statistical Analysis: The Kruskal-Wallis H-test and Benjamini-Hochberg FDR correction were applied to determine the differentially abundant pathways across the zones using Statistical Analysis of Metagenomic Profiles (STAMP) (v2.1.3). Results: A non-significant increase in the mean abundance of the Phyla Bacteroidota, Proteobacteria, Actinobacteria, and Verrucomicrobiota was observed in both groups from day 0 to day 5. An alteration in the Firmicutes/Bacteroidetes ratio was observed. A significant (P < 0.05) abundance of genus Enterobacteriaceae, Enterococcaceae, and Lactobacillaceae was observed in the participants with antibiotic treatment. The relative abundance of families Enterococcus, Lactobacillus, Sellimonas, Ruminococcus, Torques, and Eggerthella groups was observed to be significantly higher (P < 0.05) in participants with antibiotic treatment. Beta-diversity indices revealed significant differences at group and subgroup levels regarding the bacterial counts. Conclusions: It was observed that a short-term course of 5 days of antibiotic usage is associated with altered microbial abundance and diversity.

Microbial coalbed gas and its geological formation process in the Jimsar region of the southern Junggar Basin, NW China

The southern Junggar Basin is abundant in coalbed gas (CBG) resources, with the Jimsar region in the southern part of the basin emerging as a potential CBG development demonstration area. However, further development of the CBG in this region is restricted by the lack of understanding of the genesis and gas reservoir formation mechanisms of the CBG. This study systematically collected CBG samples and associated water samples from the Jimsar region. Stable isotope, hydrogeochemical, and 16S ribosomal ribonucleic acid (rRNA) sequencing studies were carried out. The results demonstrate that the CBG is the primary microbial gas, and CO2 reduction is its formation pathway. Hydrogeochemical analysis shows that the coalbed water receives recharge from meteoric or surface water. The water environment is relatively active (open system). The total dissolved organic carbon (TDOC) in the coalbed water is primarily from coal, and the supply and consumption of the total dissolved nitrogen (TDN) may be relatively balanced. The dissolution of CO2 is the main source of the dissolved inorganic carbon (DIC). Furthermore, the positive δ13CDIC values and high alkalinity indicate microbial methanogenesis. Microbial community structure analysis revealed that the archaea are hydrogenotrophic methanogens in the Jimsar region. The microbial basis for the production of microbial gas is provided by the existence of hydrolytic, acidogenic, and hydrogen-producing acetogenic bacteria as well as methanogenic archaea. Natural gas genetic identification diagrams and detection of methane-oxidizing bacteria (Methylomicrobium) reveal that the CBG may be affected by slight oxidation. In addition, the methanogenic effect is much greater than the methane oxidation. Finally, based on these results and the regional tectonic background, the CBG enrichment and accumulation mode in the Jimsar region was established. This mode can be divided into three geological stages: burial and coalification, surface water recharge and microbial gas generation after uplift and denudation, and CBG accumulation controlled by reverse faults and hydrodynamic sealing. This study enriches the geological theory of CBG accumulation in the Jimsar region and provides guidance for the subsequent exploration and development of the CBG.

Ocular surface microbiota in patients with varying degrees of dry eye severity.

To elucidate the profiles of commensal bacteria on the ocular surfaces of patients with varying severity of dry eye (DE). The single-center, prospective, case-control, observational study categorized all participants into three distinct groups: 1) control group (n=61), 2) mild DE group (n=56), and 3) moderate-to-severe DE group (n=82). Schirmer's tear secretion strips were used, and the bacterial microbiota was analyzed using 16S ribosomal ribonucleic acid gene sequencing. The three groups had significant differences in alpha diversity: the control group had the highest richness (Chao1, Faith's phylogenetic diversity), the mild DE group showed the highest diversity (Shannon, Simpson), and the moderate-to-severe DE group had the lowest of the above-mentioned indices. DE severity was positively correlated with a reduction in beta diversity of the microbial community, with the moderate-to-severe DE group exhibiting the lowest beta diversity. Linear discriminant analysis effect size presented distinct dominant taxa that significantly differed between each. Furthermore, the exacerbation of DE corresponded with the enrichment of certain pathogenic bacteria, as determined by random forest analysis. As DE severity worsens, microbial community diversity tends to decrease. DE development corresponds with changes in microbial constituents, primarily characterized by reduced microbial diversity and a more homogenous species composition.

Disseminated nocardiosis including cerebral nocardiosis caused by Nocardia farcinica: a case report

Background: As nocardiosis presents with nonspecific symptoms, its diagnosis is often difficult, resulting in high mortality. Here, we report a rare case of disseminated Nocardia farcinica infection that was successfully managed with a combination of antibiotic therapies. Case report: A 71-year-old man with idiopathic thrombocytopenia purpura presented with sudden-onset motor aphasia, motor weakness of the right limb, and fever. Brain magnetic resonance imaging revealed multiple scattered diffusion-restricted lesions. Multiple cutaneous and peritoneal nodules were also identified. We performed full-length 16S ribosomal ribonucleic acid (rRNA) sequencing and obtained basic local alignment search tool results against the National Center for Biotechnology Information 16S rRNA database, which showed the best match to be N. farcinica. After maintaining the antibiotics for approximately 56 days, the patient recovered full consciousness, and the motor weakness of the right limb improved.Conclusion: Timely diagnosis of disseminated or cerebral nocardiosis and treatment with appropriate antibiotics are crucial for a desirable clinical outcome.

Optimizing waste molasses utilization to enhance electron transfer via micromagnetic carriers: Mechanisms and high-nitrate wastewater denitrification performance

The biological denitrification of high-nitrate wastewater (HNW) is primarily hindered by insufficient carbon sources and excessive nitrite accumulation. In this study, micromagnetic carriers with varying micromagnetic field (MMF) strengths (0.0, 0.3, 0.6, 0.9 mT) were employed to enhance the denitrification of HNW using waste molasses (WMs) as a carbon source. The results revealed that 0.6 mT MMF significantly improved the total nitrogen removal (TN) efficiency at 96.3%. A high nitrate (NO3−-N) removal efficiency at 99.3% with a low nitrite (NO2−-N) accumulation at 25.5 mg/L was achieved at 0.6 mT MMF. The application of MMF facilitated the synthesis of adenosine triphosphate (ATP) and stimulated denitrifying enzymes (e.g., nitrate reductase (NAR), nitrite reductase (NIR), and nitric oxide reductase (NOR)), which thereby promoting denitrification. Moreover, the effluent chemical oxygen demand (COD), tryptophan and fulvic-like substances exhibited their lowest levels at 0.6 mT MMF. Analysis through 16S ribosomal ribonucleic acid gene sequencing indicated a significant enrichment of denitrifying bacteria including Castellaniella Klebsiella under the influence of MMF. Besides, the proliferation of Acholeplasma, Klebsiella and Proteiniphilum at 0.6 mT MMF promoted the hydrolysis and acidification of WMs. This study offers new insights into the enhanced utilization of WMs and the denitrification of HNW through the application of MMF.

Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance.

Combination antiretroviral therapy (cART) effectively controls HIV; however, chronic low-level viremia and gut microbiota dysbiosis remain significant drivers of gut and systemic inflammation. In this study, we explored the relationship between gut microbiota composition, intestinal inflammation, microbial translocation, and systemic inflammation in women on cART in Sub-Saharan Africa. We conducted a study in HIV-infected and HIV-uninfected lactating women followed up at 6 weeks and 6 months postpartum in Harare, Zimbabwe. We used 16S ribosomal Ribonucleic Acid (rRNA) sequencing and MesoScale Discovery V-Plex assays to examine the gut microbiome and to quantify plasma inflammatory biomarkers, respectively. In addition, we measured fecal calprotectin, plasma lipopolysaccharide-binding protein (LBP), and soluble cluster of differentiation 14 (sCD14) by enzyme-linked immunosorbent assay to assess gut inflammation, microbial translocation, and monocyte/macrophage activation. A group of 77 lactating women were studied, of which 35% were HIV-infected. Fecal calprotectin levels were similar by HIV status at both follow-up time points. In the HIV-infected group at 6 weeks postpartum, fecal calprotectin was elevated: median (interquartile range) [158.1 µg/g (75.3-230.2)] in women who had CD4+ T-lymphocyte counts <350 cells/µL compared with those with ≥350 cells/µL [21.1 µg/g (0-58.4)], p = 0.032. Plasma sCD14 levels were significantly higher in the HIV-infected group at both 6 weeks and 6 months postpartum, p < 0.001. Plasma LBP levels were similar, but higher levels were observed in HIV-infected women with elevated fecal calprotectin. We found significant correlations between fecal calprotectin, LBP, and sCD14 with proinflammatory cytokines. Gut microbial alpha diversity was not affected by HIV status and was not affected by use of antibiotic prophylaxis. HIV significantly affected microbial beta diversity, and significant differences in microbial composition were noted. The genera Slackia and Collinsella were relatively more abundant in the HIV-infected group, whereas a lower relative abundance of Clostriduim sensu_stricto_1 was observed. Our study also found correlations between gut microbial taxa abundance and systemic inflammatory biomarkers. HIV-infected lactating women had increased immune activation and increased microbial translocation associated with increased gut inflammation. We identified correlations between the gut inflammation and microbial composition, microbial translocation, and systemic inflammation. The interplay of these parameters might affect the health of this vulnerable population.

Gut-Brain-axis: effect of basil oil on the gut microbiota and its contribution to the anticonvulsant properties

BackgroundEpilepsy is a chronic neurological condition that disrupts the normal functioning of the brain and it is characterized by seizures. Research suggests the involvement of the Gut-Brain axis in epilepsy. This study seeks to determine the role of the gut microbiota in the anticonvulsant effect of basil oil (BO) using antibiotic-depleted and altered germ-free mice against naïve mice in Pentylenetetrazole (PTZ) induced seizure model. There is an ever growing interest in improvement of treatment outcomes in epilepsy and also in the development of newer therapeutic options, especially in the population of patients that do not attain seizure relief from available antiseizure medications (ASMs). According to research, gut microbiota can alter brain function and development. Increasing evidence suggests disrupting the delicate symbiotic balance existing between the gut and brain results in disease conditions. Also, the oil from Ocimum basilicum L., (BO) has been proven scientifically to significantly block clonic seizures induced by PTZ and picrotoxin in seizure models.MethodsThe microbiota of mice were depleted or altered by administering cocktail antibiotics and individual antibiotics respectively. DNA was isolated from mouse stool, and then the 16S ribosomal ribonucleic acid (16S rRNA) gene was quantitatively amplified using reverse transcription-polymerase chain reaction (RT-PCR). Amplicons were sequenced to determine the phylogenetic make-up of the bacteria involved. Metabolic profiles of the serum and stool of mice were determined using Proton (1H) Nuclear Magnetic Resonance (NMR) spectroscopy.ResultsCocktail antibiotic pre-treatment significantly reversed the anticonvulsant effect of BO by increasing frequency and duration of seizures but did not affect latency to seizure. In mice pre-treated with single antibiotics, the anticonvulsant effect of BO was lost as latency to seizures, frequency and duration of seizures increased compared to mice that received only BO. Assessment of the phylogenetic make-up of the microbiota in antibiotic pre-treated mice showed a distorted composition of the microbiota compared to the control group.ConclusionDepletion of the microbiota significantly reversed the anticonvulsant actions of BO. The concentrations of short chain fatty acids (SCFAs) was higher in stool than in the serum of the mice. Administration of BO probably does not influence the microbial composition within the mouse microbiota. The elevated ratio of Firmicutes to Bacteroidetes in microbiota-depleted groups might have contributed to the reversal of anticonvulsant actions of BO.

Antimicrobial mechanism and biocontrol effect of Bacillus cereus XZ30-2 on Aspergillus niger

Aspergillus niger is a major mold-causing spoilage in cereals, fruits and vegetables. Controlling of mold in stored grains is essential for safety of food. Currently, application of microorganisms to control A. niger is a safer and more effective method. In this study, strain XZ30-2 against A. niger was isolated and identified as Bacillus cereus according to morphological and biochemical characteristics as well as 16 Svedberg ribosomal ribonucleic acid (16S rRNA) gene sequence analysis. The investigation of action mechanism showed XZ30-2 culture filtrate caused the mycelia inflated or contract, increasing the membrane permeability, leading to the intracellular leakage and nucleic acids release, disrupting the proton pump, decreasing the ergosterol content, inducing the membrane lipid peroxidation and reactive oxygen species (ROS) accumulation in A. niger. Moreover, B. cereus XZ30-2 culture filtrate could produce hydrolases and lipopeptides, including iturin, surfactin and fengycin. This work also evaluated the control effect of XZ30-2 on A. niger in wheat grains, and indicated that 40 μL/g of culture filtrate significantly controlled the infection of A. niger. Therefore, B. cereus XZ30-2 can be developed as a biological agent for controlling A. niger in stored grains.

Soil Microbial Community Composition and Diversity Are Insusceptible to Nitrogen Addition in a Semi-Arid Grassland in Northwestern China

Human-caused nitrogen (N) deposition is a global environmental issue that can change community composition, functions, and ecosystem services. N deposition affects plants, soil, and microorganisms regionally and is linked to ecosystem, soil, and climate factors. We examined the effects of six N addition levels (0, 2.34 g, 4.67, 9.34,18.68, and 37.35 g N m−2 yr−1) on aboveground vegetation, surface soil properties, and microbial community. Alterations in microbial communities in response to N addition were monitored using 16S rRNA (16S ribosomal ribonucleic acid, where S donates a sedimentation coefficient) and ITS (internal transcribed spacer) regions for bacterial and fungal communities, respectively. N addition positively affected aboveground vegetation traits, such as biomass and community weighted mean of leaf nitrogen. N addition also limited phosphorus (P) availability and altered the microbial community assembly process from random processes to deterministic processes. The microbial community diversity and composition, however, were not sensitive to N addition. Partial least squares structural equation models showed that the composition of bacterial communities was mainly driven by the composition of plant communities and total nitrogen, while the composition of fungal communities was driven by soil pH and community weighted mean of leaf nitrogen. Taken together, the results of this research improved our understanding of the response of grassland ecosystems to N deposition and provided a theoretical basis for grassland utilization and management under N deposition.

Identification of Leishmania species isolated from cutaneous leishmaniasis using molecular techniques in some provinces of Iraq

Objectives: To detect Leishmania species in selected regions in Iraq.Method: The cross-sectional study was conducted from December 2021 to March 2022 at Al-Hashimyah GeneralHospital in Babylon province, and Al Diwaniya Education Hospital in AL-Qadisiah province of Iraq. The samplecomprised patients with lesions suggestive of cutaneous leishmaniasis, as assessed by dermatologists. Direct smearwas used for parasitological examination by lesion aspiration. Molecular technique was used for the characterisationof parasite genus and species. Positive direct smear specimens were analysed by nested-polymerase chain reactionusing internal transcribed spacer-1 ribosomal ribonucleic acid gene.Results: Of the 120 specimens tested, 100(83.33%) tested positive; 59(59%) males and 41(41%) females. Most of theinfections were leishmania major 92(92%), followed by leishmania tropica 8(8%). There were 80(80%) dry lesions and20(20%) wet.Conclusions: Cutaneous leishmaniasis were mostly of tropica and major varieties in the studied areas.Keywords: Parasites, Dermatologists, Genes, rRNA, Cutaneous, Leishmania, Polymerase DNA.

Identification of a New Compound (4-Fluoro-2-Trifluoromethyl Imidazole) Extracted from a New Halophilic Bacillus aquimaris Strain Persiangulf TA2 Isolated from the Northern Persian Gulf with Broad-Spectrum Antimicrobial Effect.

The unique ecosystem of the Persian Gulf has made it a rich source of natural antimicrobial compounds produced by various microorganisms, especially bacteria, which can be used in the treatment of infectious diseases, especially those of drug-resistant microbes. This study aimed to identify antimicrobial compounds in the bacteria isolated from the northern region of the Persian Gulf in Abadan (Chavibdeh port), Iran, for the first time. Sampling was performed in the fall on November 15, 2019, from 10 different stations (water and sediment samples). The secondary metabolites of all isolates were extracted, and their antimicrobial effects were investigated. 16S ribosomal ribonucleic acid sequencing was used for the identification of the strains that showed the best inhibition against selected pathogens, and growth conditions were optimized for them. A fermentation medium in a volume of 5000 mL was prepared to produce the antimicrobial compound by the superior strain. The extracted antimicrobial compounds were identified using the gas chromatography-mass spectrometry technique. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined for the superior strain. The effects of salinity, pH, and temperature on the production of antimicrobial compounds were determined by measuring the inhibitory region (mm) of methicillin-resistant Staphylococcus aureus (MRSA). Four new strains with antimicrobial properties (i.e., Halomonas sp. strain Persiangulf TA1, Bacillus aquimaris strain Persiangulf TA2, Salinicoccus roseus strain Persiangulf TA4, and Exiguobacterium profundum strain Persiangulf TA9) were identified. The optimum growth temperatures were determined at 37-30, 37, and 40 °C for TA1 and TA2, TA4, and TA9 strains, respectively. The optimum pH values for the four strains were 7, 6-7, 7.5, and 6.5-7.5, respectively. The optimal salt concentrations for the four strains were 15%, 2.5-5%, 7.5%, and 5%, respectively. The ethyl acetate extract of strain Persiangulf TA2 showed extensive antimicrobial activity against human pathogens (75%) and MRSA. The most abundant compound identified in TA2 extract was the new compound 4-fluoro-2-trifluoromethyl imidazole. The MBC and MIC for the ethyl acetate extract of strain TA2 were 20 and 5 mg. mL-1 (Staphylococcus aureus), 40 and 20 mg. mL-1 (MRSA, Escherichia coli, and Enterococcus faecalis), 40 and 10 mg. mL-1 Acinetobacter baumannii), and 80 and 40 mg. mL-1 (Staphylococcus epidermidis, Shigella sp., Bacillus cereus, and Klebsiella pneumoniae), respectively. The optimal conditions for antibiotic production by TA2 strain were 5% salt concentration, pH of 7, and temperature of 35 °C. Newly detected natural compounds in TA2 strain due to superior antimicrobial activity even against MRSA strain can be clinically valuable in pharmacy and treatment.

Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis.

The multi-batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature in recent years. The large amount of 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored in public repositories and information in taxonomic databases of the same gene far exceeds that related to complete genomes. This review is intended to guide researchers new to studying microbiota, particularly the oral microbiota, using 16S rRNA gene sequencing and those who want to expand and update their knowledge to optimise their decision-making and improve their research results. First, we describe the advantages and disadvantages of using the 16S rRNA gene as a phylogenetic marker and the latest findings on the impact of primer pair selection on diversity and taxonomic assignment outcomes in oral microbiome studies. Strategies for primer selection based on these results are introduced. Second, we identified the key factors to consider in selecting the sequencing technology and platform. The process and particularities of the main steps for processing 16S rRNA gene-derived data are described in detail to enable researchers to choose the most appropriate bioinformatics pipeline and analysis methods based on the available evidence. We then produce an overview of the different types of advanced analyses, both the most widely used in the literature and the most recent approaches. Several indices, metrics and software for studying microbial communities are included, highlighting their advantages and disadvantages. Considering the principles of clinical metagenomics, we conclude that future research should focus on rigorous analytical approaches, such as developing predictive models to identify microbiome-based biomarkers to classify health and disease states. Finally, we address the batch effect concept and the microbiome-specific methods for accounting for or correcting them.

First report of Nalanthamala vermoesenii causing pink rot of Phoenix canariensis in Mexico.

In Mexico City, the Canary Island date palm (Phoenix canariensis Chabaud) is an important plant forming part of its landscape identity. In February 2022, pink rot disease symptoms were observed on 16 P. canariensis plants in Mexico City (19°25'43.98"N, 99° 9'49.41"W). The incidence was 27%, while the severity 12%. External symptoms included necrotic lesions that advanced from the petiole towards the rachis. Internal symptoms were rotted, dark brown discoloration in bud, petiole, and rachis. Abundant conidial masses were developed on the infected tissues. Pieces of diseased tissues (5-mm cubes) were surface sterilized for 2 min in 3% sodium hypochlorite, rinsed with sterilized distilled water, plated onto potato dextrose agar (PDA), and incubated at 24°C and 12-h photoperiod, 20 pink fungal colonies were developed with sparse aerial mycelia on PDA. Conidiophores were hyaline, dimorphic, penicillate, and Acremonium-like. Conidia were dimorphic, typically with somewhat truncated ends, 4.5 to 5.7 × 1.9 to 2.3 μm (mean 4.99 × 2.15, n = 100), borne in long chains on penicillate conidiophores; on Acremonium-like conidiophores conidia were cylindrical, straight, and slightly curved, 4.55 to 10.1 × 1.2 to 2.35 μm (mean 8.2 × 1.7, n = 100). These morphological characteristics resembled those of Nalanthamala vermoesenii (Biourge) Schroers (Schroers et al. 2005). Genomic DNA was extracted from the mycelia of a representative isolate CP-SP53. The internal transcribed spacer (ITS) region and the large subunit of ribosomal ribonucleic acid (LSU) were amplified and sequenced. The sequences were deposited in GenBank with accession numbers OQ581472 (ITS) and OQ581465 (LSU). Phylogenetic trees based on ITS and LSU sequences of Nalanthamala species were reconstructed using maximum likelihood and Bayesian inference methods. Isolate CP-SP53 was placed in the clade of Nalanthamala vermoesenii. The pathogenicity test was carried out twice with isolate CP-SP53 on five 3-year-old P. canariensis plants. Four petioles per plant were surface disinfected with 75% ethanol, and wounded with a sterilized scalpel (shallow cuts 0.5 cm wide). A mycelial plug (5 mm in diam.) of a 1-week-old PDA culture was placed on each wounded site. Sterile PDA plugs were used for five non-inoculated control plants. All plants were maintained at 22 ± 2°C and a 12-h photoperiod. Twenty-five days after inoculation (dai), wounded petioles showed the same symptoms observed in the field, whereas control plants remained healthy. Forty-five dai, all inoculated plants died. Pink conidial masses developed on symptomatic tissues. To fulfill Koch's postulates, the pathogen was reisolated by placing the pink conidial masses onto PDA. The colony characteristics and morphometric measurements were identical to those of isolate CP-SP53. Nalanthamala vermoesenii has been reported on P. canariensis in Greece and United States (Feather et al. 1979; Ligoxigakis et al. 2013) and Syagrus romanzoffiana in Egypt (Mohamed et al. 2016). To our knowledge, this is the first report of Nalanthamala vermoesenii as the causal agent of pink rot on P. canariensis in Mexico. This plant is the most commonly planted ornamental palm in Mexico City. The spread of N. vermoesenii could be a threat for the estimated 15 thousand palms, therefore dramatically change the urban landscape.

Re-evaluation of the systematic position of the order Prostomatida (Protista: Ciliophora), with the establishment of two new genera and two new species

Abstract Prostomatean ciliates inhabit a wide range of aquatic environments and serve as a trophic link in food webs. However, the biodiversity and molecular phylogeny of the Prostomatea, especially the order Prostomatida, is poorly known owing to undersampling and the paucity of molecular data. Here, three prostomatid ciliates, Platina marina gen. nov., sp. nov., Parametacystis pulchra gen. nov., sp. nov. and Apsiktrata gracilis, were studied based on morphological data and small subunit ribosomal ribonucleic acid (SSU rRNA) gene sequences. The two new genera show a close relationship with the class Plagiopylea but a distant relationship with Metacystis, which bears a strong morphological similarity to the two new genera. The simplified oral ciliature can be regarded as a synapomorphy of the two new genera. The SSU rRNA gene of a representative of the family Apsiktratidae was sequenced for the first time. Morphological and phylogenetic analyses suggest that Apsiktratidae might be more closely related to Prorodontida than to Prostomatida, and the oral basket might be more phylogenetically informative than the brosse in distinguishing Prorodontida and Prostomatida. Supplementation with rare taxa reveals a close association between the Prostomatida and Trimyemidae. The putative secondary structure of the SSU rRNA V9 region suggests a sister relationship between the order Prostomatida and the class Plagiopylea.

Hemorrhagic transformation in patients with large-artery atherosclerotic stroke is associated with the gut microbiota and lipopolysaccharide.

Abstract JOURNAL/nrgr/04.03/01300535-202407000-00032/figure1/v/2023-11-20T171125Z/r/image-tiff Hemorrhagic transformation is a major complication of large-artery atherosclerotic stroke (a major ischemic stroke subtype) that worsens outcomes and increases mortality. Disruption of the gut microbiota is an important feature of stroke, and some specific bacteria and bacterial metabolites may contribute to hemorrhagic transformation pathogenesis. We aimed to investigate the relationship between the gut microbiota and hemorrhagic transformation in large-artery atherosclerotic stroke. An observational retrospective study was conducted. From May 2020 to September 2021, blood and fecal samples were obtained upon admission from 32 patients with first-ever acute ischemic stroke and not undergoing intravenous thrombolysis or endovascular thrombectomy, as well as 16 healthy controls. Patients with stroke who developed hemorrhagic transformation (n = 15) were compared to those who did not develop hemorrhagic transformation (n = 17) and with healthy controls. The gut microbiota was assessed through 16S ribosomal ribonucleic acid sequencing. We also examined key components of the lipopolysaccharide pathway: lipopolysaccharide, lipopolysaccharide-binding protein, and soluble CD14. We observed that bacterial diversity was decreased in both the hemorrhagic transformation and non-hemorrhagic transformation group compared with the healthy controls. The patients with ischemic stroke who developed hemorrhagic transformation exhibited altered gut microbiota composition, in particular an increase in the relative abundance and diversity of members belonging to the Enterobacteriaceae family. Plasma lipopolysaccharide and lipopolysaccharide-binding protein levels were higher in the hemorrhagic transformation group compared with the non-hemorrhagic transformation group. lipopolysaccharide, lipopolysaccharide-binding protein, and soluble CD14 concentrations were associated with increased abundance of Enterobacteriaceae. Next, the role of the gut microbiota in hemorrhagic transformation was evaluated using an experimental stroke rat model. In this model, transplantation of the gut microbiota from hemorrhagic transformation rats into the recipient rats triggered higher plasma levels of lipopolysaccharide, lipopolysaccharide-binding protein, and soluble CD14. Taken together, our findings demonstrate a noticeable change in the gut microbiota and lipopolysaccharide-related inflammatory response in stroke patients with hemorrhagic transformation. This suggests that maintaining a balanced gut microbiota may be an important factor in preventing hemorrhagic transformation after stroke.

Transcriptomic, 16S ribosomal ribonucleic acid and network pharmacology analyses shed light on the anticoccidial mechanism of green tea polyphenols against Eimeria tenella infection in Wuliangshan black-boned chickens

BackgroundEimeria tenella is an obligate intracellular parasitic protozoan that invades the chicken cecum and causes coccidiosis, which induces acute lesions and weight loss. Elucidating the anticoccidial mechanism of action of green tea polyphenols could aid the development of anticoccidial drugs and resolve the problem of drug resistance in E. tenella.MethodsWe constructed a model of E. tenella infection in Wuliangshan black-boned chickens, an indigenous breed of Yunnan Province, China, to study the efficacy of green tea polyphenols against the infection. Alterations in gene expression and in the microbial flora in the cecum were analyzed by ribonucleic acid (RNA) sequencing and 16S ribosomal RNA (rRNA) sequencing. Quantitative real-time polymerase chain reaction was used to verify the host gene expression data obtained by RNA sequencing. Network pharmacology and molecular docking were used to clarify the interactions between the component green tea polyphenols and the targeted proteins; potential anticoccidial herbs were also analyzed.ResultsTreatment with the green tea polyphenols led to a reduction in the lesion score and weight loss of the chickens induced by E. tenella infection. The expression of matrix metalloproteinase 7 (MMP7), MMP1, nitric oxide synthase 2 and ephrin type-A receptor 2 was significantly altered in the E. tenella infection plus green tea polyphenol-treated group and in the E. tenella infection group compared with the control group; these genes were also predicted targets of tea polyphenols. Furthermore, the tea polyphenol (-)-epigallocatechin gallate acted on most of the targets, and the molecular docking analysis showed that it has good affinity with interferon induced with helicase C domain 1 protein. 16S ribosomal RNA sequencing showed that the green tea polyphenols had a regulatory effect on changes in the fecal microbiota induced by E. tenella infection. In total, 171 herbs were predicted to act on two or three targets in MMP7, MMP1, nitric oxide synthase 2 and ephrin type-A receptor 2.ConclusionsGreen tea polyphenols can directly or indirectly regulate host gene expression and alter the growth of microbiota. The results presented here shed light on the mechanism of action of green tea polyphenols against E. tenella infection in chickens, and have implications for the development of novel anticoccidial products.Graphical

Bioprospecting the potential of metabolites from a Saharan saline soil strain Nocardiopsis dassonvillei GSBS4.

Saharan soil samples collected in El-Oued province have been investigated for actinobacteria as a valuable source for the production of bioactive metabolites. A total of 273 isolates were obtained and subjected to antagonistic activity tests against human pathogenic germs. A strain with a broad-spectrum antimicrobial activity was selected and identified as Nocardiopsis dassonvillei GSBS4, with high sequence similarities to N. dassonvillei subsp. dassonvilleiT X97886.1 (99%) based on polyphasic taxonomy approach and 16S ribosomal ribonucleic acid gene sequence analysis. The GSBS4 ethyl acetate crude extract showed strong antibacterial activity towards pathogenic bacteria and Candida albicans. It inhibited biofilm formation by Staphylococcus aureus and methicillin-resistant S. aureus with minimum inhibitory concentrations estimated at 0.144 and 1.15 mg·mL-1 , respectively. A 44% biofilm reduction was obtained for S. aureus and 61% for Pseudomonas aeruginosa. Furthermore, phenols composition of the crude extract showed a significant dose-dependent antioxidant activity by α-diphenyl-β-picrylhydrazyl (57.21%) and 2,2'-azinobis (3-ethylbenzothiazoline-6-sulfonic acid) (64.29%) radicals scavenging assays. Although no inhibition was obtained on human coronavirus human coronavirus (HCoV) 229E and on model enterovirus (poliovirus 1) infection, a dose-dependent increase in cell viability of HCoV 229E-infected cells was noticed as the viability increased from 21% to 37%. Bioassay-guided fractionation of the crude extract gave a fraction showing antibacterial activity, which was analyzed by liquid chromatography-electrospray mass spectrometric technique, providing structural features on a major purple metabolite.

Heavy-metal tolerant bacterial strains isolated from industrial sites and scrap yards in Kashmir, India.

Heavy metal pollution has posed a severe danger to environmental stability due to its high toxicity and lack of biodegradability. The present study deals with the appraisement of tolerance shown by various bacteria in varied copper and iron concentrations. Among the 20 isolates, four isolates, GN2, SC5, SC8, and SC10, exhibiting more significant iron and copper tolerance, were selected and identified by 16 S ribosomal ribonucleic acid (rRNA) gene sequence analysis as Pantoea agglomerans strain GN2, Pantoea sp. strain SC5, Bacillus sp. strain SC8 and Priestia aryabhattaistrain SC10. The minimum inhibitory concentration of molecularly identified strains revealed that P. agglomerans strain GN2 showed tolerance to iron sulfate and copper sulfate upto 600 and 400 µg/mL, whereas Bacillus sp. SC8 (OQ202165) showed tolerance of 700 and 250 µg/mL were tolerant to iron sulfate and copper sulfate up to 700 and 150 µg/mL, respectively. Pantoea sp. strain SC5 showed significant tolerance to both heavy metals. The isolates were further studied for their ability to grow at varying temperatures and pH ranges. Most of the isolates showed optimal growth at 37°C and pH 7. However, Pantoea sp. SC5 was competent to have prominent growth at 45°C and pH 8.0. Microbial remediation, which is eco-friendly, has proven the most effective method for bioremediation of heavy metal-contaminated environments. Using heavy metal-resistant bacteria for microbial remediation of iron and copper-contaminated environments could be a viable and valuable strategy. These isolates could also be used to decontaminate heavy metal-polluted agricultural soils.