16S Ribosomal RNA Gene Research Articles

Chest Computed Tomography Radiomics for Determining Macrolide Resistance-Associated Gene Mutation Status in Children with Mycoplasma pneumoniae Pneumonia: A Two-Center Study

Rationale and ObjectivesThe mutations in the 23S ribosomal RNA (rRNA) gene are associated with an increase in resistance to macrolides in children with Mycoplasma pneumoniae pneumonia (MPP). This study aimed to develop and validate a chest computed tomography (CT) radiomics model for determining macrolide resistance-associated gene mutation status in MPP. Materials and MethodsA total of 258 MPP patients were retrospectively included from two institutions (training set: 194 patients from the first institution; external test set: 64 patients from the second). The 23S rRNA gene mutation status was tested by nasopharyngeal swab polymerase chain reaction. Radiomics features were extracted from chest CT images of pulmonary lesions segmented with semi-automatic delineation. Subsequently, radiomics feature reduction was applied to identify the most relevant features. Logistic regression and random forest algorithms were employed to establish the radiomics models, which were five-fold cross-validated in the training set and validated in the external test set. ResultsThe radiomics feature selection resulted in eight features. After five-fold cross-validation in the training set, the mean areas under the receiver operating characteristic curve (AUCs) of the logistic regression and random forest models were 0.868 (95% confidence interval (CI): 0.813-0.923) and 0.941 (95% CI: 0.907-0.975), respectively. In the external test set, the corresponding AUCs were 0.855 (95% CI: 0.758-0.952) and 0.815 (95% CI: 0.705-0.925). ConclusionChest CT radiomics is a promising diagnostic tool for determining macrolide resistance gene mutation status in MPP. Availability of data and materialThe datasets generated or analyzed during the study are available from the corresponding author on reasonable request.

Helicobacter pylori infection in infant rhesus macaque monkeys is associated with an altered lung and oral microbiome

It is estimated that more than half of the world population has been infected with Helicobacter pylori. Most newly acquired H. pylori infections occur in children before 10 years of age. We hypothesized that early life H. pylori infection could influence the composition of the microbiome at mucosal sites distant to the stomach. To test this hypothesis, we utilized the infant rhesus macaque monkey as an animal model of natural H. pylori colonization to determine the impact of infection on the lung and oral microbiome during a window of postnatal development. From a cohort of 4–7 month-old monkeys, gastric biopsy cultures identified 44% of animals infected by H. pylori. 16S ribosomal RNA gene sequencing of lung washes and buccal swabs from animals showed distinct profiles for the lung and oral microbiome, independent of H. pylori infection. In order of relative abundance, the lung microbiome was dominated by the phyla Proteobacteria, Firmicutes, Bacteroidota, Fusobacteriota, Campilobacterota and Actinobacteriota while the oral microbiome was dominated by Proteobacteria, Firmicutes, Bacteroidota, and Fusobacteriota. In comparison to the oral cavity, the lung was composed of more genera and species that significantly differed by H. pylori status, with a total of 6 genera and species that were increased in H. pylori negative infant monkey lungs. Lung, but not plasma IL-8 concentration was also associated with gastric H. pylori load and lung microbial composition. We found the infant rhesus macaque monkey lung harbors a microbiome signature that is distinct from that of the oral cavity during postnatal development. Gastric H. pylori colonization and IL-8 protein were linked to the composition of microbial communities in the lung and oral cavity. Collectively, these findings provide insight into how H. pylori infection might contribute to the gut-lung axis during early childhood and modulate future respiratory health.

Gut Microbiota Profiles in Myopes and Nonmyopes.

To identify compositional differences in the gut microbiome of nonmyopes (NM) and myopes using 16S ribosomal RNA sequencing and to investigate whether the microbiome may contribute to the onset or progression of the condition. Faecal samples were collected from 52 adult participants, of whom 23 were NM, 8 were progressive myopes (PM), and 21 were stable myopes (SM). The composition of the gut microbiota in each group was analysed using 16S ribosomal RNA gene sequencing. There were no significant differences in alpha and beta diversity between the three groups (NM, PM, and SM). However, the distributions of Bifidobacterium, Bacteroides, Megamonas, Faecalibacterium, Coprococcus, Dorea, Roseburia, and Blautia were significantly higher in the myopes (SM and PM combined) when compared with emmetropes. The myopes exhibited significantly greater abundance of bacteria that are linked to the regulation of dopaminergic signalling, such as Clostridium, Ruminococcus, Bifidobacterium, and Bacteroides. Individuals with stable myopia were found to have a significantly higher proportion of Prevotella copri than those with progressive myopia. Bifidobacterium adolescentis, a gamma-aminobutyric acid (GABA)-producing bacterium, was significantly higher in all myopes than in NM and, in the comparison between SM and PM, it is significantly higher in SM. B. uniformis and B. fragilis, both GABA-producing Bacteroides, were present in relatively high abundance in all myopes and in SM compared with PM, respectively. The presence of bacteria related to dopamine effect and GABA-producing bacteria in the gut microbiome of myopes may suggest a role of these microorganisms in the onset and progression of myopia.

Plants attacked above-ground by leaf-mining flies change below-ground microbiota to enhance plant defense.

Root-associated microbiomes play a crucial role in plant responses to biotic and abiotic stresses. Plants can enrich beneficial microbes to increase their stress-relieving ability. Above-ground insect herbivory is among the most detrimental stresses for plants, especially to crop production. However, few studies have explored how root-associated microbiomes respond to herbivores and influence plant-defense functions under herbivory stress. We investigate the changes and functional role of root-associated microbial communities under herbivory stress using leafminer (Liriomyza trifolii) and cowpea (Vigna unguiculata) as a focal system. We did this by using a combination of 16S ribosomal RNA gene profiling and metagenomic sequencing to test for differences in co-occurrence networks and functions between cowpea plants infested and noninfested with leafminers. The results demonstrated that leafminer infestation caused a shift in the rhizosphere microbiome, which was characterized by a significant variation in microbiome community structure and composition, the selection of hub microbes involved in nitrogen (N) metabolism, and functional enrichment related to N metabolism. Notably, nitrogen-fixing bacteria Bradyrhizobium species were actively enriched and selected to be hubs in the rhizosphere. Inoculation with Bradyrhizobium enhanced cowpea performance under leafminer stress and increased protease inhibitor levels to decrease leafminer fitness. Overall, our study characterized the changes of root-associated microbiota between leafminer-infested and noninfested cowpea plants and revealed the mechanisms underlying the rhizosphere microbiome shift that enhance plant performance and defense against herbivory. Our findings provide further support for the notion that plants enrich rhizosphere microbes to counteract aboveground insect herbivores.

Genetic Diversity Analysis of Rhynocoris marginatus Fabricius Based on 18S Ribosomal RNA Gene (Heteroptera: Reduviidae)

The R. marginatus are essential components of ecosystem, but also important in the biological control of insect pest, infesting a varity of agro ecosystem and medicine. The present investigation was carried out in the insect molecular genetic variation of 18S Ribosomal RNA gene from R. marginatus. The study was represent by the reduviid insect R. marginatus nucleotide gene sequences were translate amino acid sequence and obtained hydropathy, Domain, Transmembranes of proteins were calculated. The multiple gene sequence alignment of in-silico translated amino acid sequence of the partial ribosomal genes protein of R. marginatus were generated and the phylogenetic relationships were observed.

Molecular detection and characterization of prevailing Theileria equi genotype in equine from northern India

Equine piroplasmosis caused by Theileria equi is a febrile, tick-borne disease of equids. However, there is limited literature about the genotyping of T. equi in India. Blood samples were collected from 202 horses and subjected to microscopy and PCR to detect T. equi. Initially, a universal screening primer pair targeting 18S ribosomal RNA genes common for Babesia caballi and T. equi was employed to amplify the DNA of both parasites. Thereafter additional primers were employed for species-specific detection resulting in amplification of approximately 435 bp specific for T. equi. T.equi was detected in 9.9% and 20.79% of horses screened by microscopy and PCR, respectively. The representative samples confirmed positive by PCR were sequenced, submitted to NCBI (OR651254, OR687254, OR685656, OR650830, OR650834), and used for genotype characterization and phylogenetic analysis. Employing Genetool and MEGA X software, the T. equi Indian isolates and across the globe were compared, and the results demonstrated 99.05–100% and 95.86–100% homologies, respectively. All the T. equi Indian isolates belonged to genotype A. Phylogeny based on the EMA-1 gene of five isolates (OR731831, OR731833, OR731829, OR731830, OR731832) were also characterized by sequencing and support the previous findings. Genotypes C and D, as well as genotypes B and E, exhibited lower levels of evolutionary divergence compared to other genotypes. The EMA-1 gene exhibited limited diversity and might not be the most suitable target for assessing variability within T. equi populations. The findings also reveal a significant association (p < 0.01) between T. equi infection and the presence of ticks.

Faecal microbiota study reveals specific dysbiosis in spondyloarthritis according to subtype, disease activity and treatment

To compare the diversity and composition of the gastrointestinal microbiome of patients with SpA. MiSeq sequencing of the V3-V4 region of the 16S ribosomal RNA gene was performed on DNA isolated from stool. Patients with concurrent SpA and IBD were excluded. Differences were assessed for richness and diversity indices by QIIME 2™. Differences between means >0,2% with a p-value<0,05 were assumed significant. Institutional Ethics Committee endorsement. 69 individuals included, 49 with SpA (ankylosing spondylitis-AS 72,9%, psoriatic arthritis-PsA 18,8%, reactive arthritis-ReA 8,3%) 5 positive controls-dysbiosis and 15 controls-eubiosis. Conventional treatment in 42,9%, anti-IL-17 16,3% and anti-TNF 40,8%. By subtype, statistically significant differences in favour of AS were found for the diversity indices. AS vs PsA there was a difference in favour of AS for Clostridium clostridioforme (p=0,002), Gemmiger formicilis (p=0,009), Roseburia inulivorans (p=0,008) and Lachnospira pectinoschiza. AS vs ReA there was a difference in favour of AS for L. pectinoschiza (p=0,009), Ruminococcus callidus (p=0.006), Clostridium ruminantium (p=0.031); G. formicilis (p=0,034). Diversity and richness showed differences in patients with high activity for Simpson's and Pielou's indices. In high activity, lower enrichment of Bacteroides eggerthii (p= 0,0003), C. ruminantium (p= 0,026) and Alistipes putredinis (p=0,035) was found. The number of ASV was higher in the anti-IL-17 vs conventional group (p=0.025) and a trend between anti-IL-17 vs anti-TNF (p=0.09). In anti-TNF there was a lower proportion for C. clostridioforme (p=0.023), G. formicilis (p=0.030) and R. callidus (p= 0.003). In anti IL-17, Alistipes indistinctus (p= 0.012) was decreased. There are differences in microbial diversity for SpA subtypes. The level of disease activity is plausible to influence the composition of the faecal microbiota. Anti-TNFα treatment may influence the microbiome environment favouring restoration of the gut microbiota, while anti-IL-17 may maintain an inflammatory environment.

Distinguishing bipolar depression, bipolar mania, and major depressive disorder by gut microbial characteristics.

Gut microbial disturbance has been widely confirmed in mood disorders. However, little is known about whether gut microbial characteristics can distinguish major depressive disorder (MDD), bipolar depression (BP-D), and bipolar mania (BP-M). This was a prospective case-control study. The composition of gut microbiota was profiled using 16S ribosomal RNA (rRNA) gene sequencing of fecal samples and compared between healthy controls (HC; n = 46), MDD (n = 51), BP-D (n = 44), and patients with BP-M (n = 45). Gut microbial compositions were remarkably changed in the patients with MDD, BP-D, and BP-M. Compared to HC, distinct gut microbiome signatures were found in MDD, BP-D, and BP-M, and some gut microbial changes were overlapping between the three mood disorders. Furthermore, we identified a signature of 7 operational taxonomic units (OUT; Prevotellaceae-related OUT22, Prevotellaceae-related OUT31, Prevotellaceae-related OTU770, Ruminococcaceae-related OUT70, Bacteroidaceae-related OTU1536, Propionibacteriaceae-related OTU97, Acidaminococcaceae-related OTU34) that can distinguish patients with MDD from those with BP-D, BP-M, or HC, with area under the curve (AUC) values ranging from 0.910 to 0.996. Our results provide the clinical rationale for the discriminative diagnosis of MDD, BP-D, and BP-M by characteristic gut microbial features.

Chemical characterization of Thymus zygis L. (thyme) and Elettaria cardamomum L. (cardamom) essential oils and investigation of their inhibitory potentials against cervicovaginal Escherichia coli isolates

IntroductionThe cervicovaginal microbiota plays a crucial role in women's well-being and reproductive health. This study initially focuses on identifying the chemical components of the essential oils (EOs) from Elettaria cardamomum L. (cardamom) (Ec) and Thymus zygis L. (thyme) (Tz). Subsequently, this study aims to determine the antimicrobial and biofilm inhibitory effects of these EOs against both cervicovaginal mixed cultures and the microbial strains isolated from them. MethodsThe compositions of EOs were determined by GC–MS analysis using an Agilent 7890B GC/5977A Series MSD System. Cervicovaginal samples were obtained from two women presenting complaints of a strong odor and vaginal discharge. Samples were collected from the cervix using a sterile cytobrush, ensuring no contact with the urethra, rectum, or external parts of the vagina. The cytological examination was conducted using Papanicolaou staining. Isolated microorganisms were identified through 16S Ribosomal RNA Gene Sequence Analysis and characterized using antibiogram tests. Antimicrobial tests of the EOs were performed by broth microdilution and disc diffusion methods. Biofilm formation was assessed using a crystal violet binding assay. ResultsThe major components of Ec EO were α-terpinyl acetate (41.95 %) and eucalyptol (28.58 %), whereas Tz EO contained significant amounts of o-cymene (38.76 %), carvacrol (22.66 %), and thymol (20.69 %). Escherichia coli codes OR651248 and OR651249 were isolated from CV 6 and CV 7 mixed cultures, respectively. E. coli OR651248 demonstrated a higher antibiotic resistance level than E. coli OR651249. Biofilm formation by mixed cultures was significantly higher than that by E. coli isolates (P < 0.05). The Ec EO displayed minimal to no effect against both mixed cultures, showing zero inhibition zone, 500 μL/mL minimum inhibitory concentrations (MICs), and 500 μL/mL minimum microbicidal concentrations (MMCs). However, the Tz EO exhibited antimicrobial activity against both mixed cultures and the E. coli isolates, with inhibition zones > 15 mm and MICs/MMCs < 4 μL/mL (P < 0.05). In all microbial cultures, 0.5 MIC of both EOs inhibited biofilm formation by more than 80 %. ConclusionThe Tz EO exhibits promising potential as an antimicrobial and biofilm inhibitory agent for managing cervicovaginal E. coli infections.

Coprococcus eutactus screened from healthy adolescent attenuates chronic restraint stress-induced depression-like changes in adolescent mice: Potential roles in the microbiome and neurotransmitter modulation

The onset of depression commonly occurs in adolescence; therefore, depressive prevention and intervention are pivotal during this period. It is becoming evident that neurotransmitter imbalance and gut microbiota dysbiosis are prominent causes of depression. However, the underlying links and mechanisms remain poorly understood. In this study, with 16S ribosomal RNA gene sequencing, genus Coprococcus markedly differentiated between the healthy and unmedicated depressive adolescents. Based on this, transplantation of Coprococcus eutactus (C.e.) was found to dramatically ameliorate the chronic restraint stress (CRS) induced depression-like changes and prevent synaptic loss and glial-stimulated neuroinflammation in mice. The Ultra-high performance liquid chromatography tandem mass spectrometry analysis (UHPLC-MS/MS) further showed that neurotoxic neurotransmitters in kynurenine pathway (KP) such as 3-hydroxykynurenine (3−HK) and 3-hydroxyanthranilic acid (3-HAA) decreased in mouse brains, mechanistically deciphering the transfer of the tryptophan metabolic pathway to serotonin metabolic signaling in the brain after C.e. treatment, which was also verified in the colon. Molecularly, blockage of KP activities mediated by C.e. was ascribed to the restraint of the limit-step enzymes responsible for kynurenine, 3-HK, and quinolinic acid generation. In the colon, C.e. treatment significantly recovered goblet cells and mucus secretion in CRS mice which may ascribe to the rebalance of the disordered gut microbiota, especially Akkermansia, Roseburia, Rikenella, Blautia, and Alloprevotella. Taken together, the current study reveals for the first time the beneficial effects and potential mechanisms of C.e. in ameliorating CRS-induced depression, unraveling the direct links between C.e. treatment and neurotransmitter rebalance, which may provide efficacious therapeutic avenues for adolescent depressive intervention.

Transposon insertion in Rothia dentocariosa

ObjectivesRothia spp. are emerging as significant bacteria associated with oral health, with Rothia dentocariosa being one of the most prevalent species. However, there is a lack of studies examining these properties at the genetic level. This study aimed to establish a genetic modification platform for R. dentocariosa. MethodsRothia spp. were isolated from saliva samples collected from healthy volunteers. Subsequently, R. dentocariosa strains were identified through colony morphology, species-specific polymerase chain reaction (PCR), and 16S ribosomal RNA gene sequencing. The identified strains were then transformed with plasmid pJRD215, and the most efficient strain was selected. Transposon insertion mutagenesis was performed to investigate the possibility of genetic modifications. ResultsA strain demonstrating high transforming ability, designated as R. dentocariosa LX16, was identified. This strain underwent transposon insertion mutagenesis and was screened for 5-fluoroorotic acid-resistant transposants. The insertion sites were confirmed using arbitrary primed PCR, gene-specific PCR, and Sanger sequencing. ConclusionThis study marks the first successful genetic modification of R. dentocariosa. Investigating R. dentocariosa at the genetic level can provide insights into its role within the oral microbiome.

Characterization of Lactococcus garvieae and Streptococcus agalactiae in cultured red tilapia Oreochromis sp. in Thailand.

Acute mortality with clinical symptoms of streptococcal-like infections was observed in red tilapia Oreochromis sp. cultured in floating cages in Prachin Buri Province, Thailand, during May 2023. Herein, we identified an emerging pathogen, Lactococcus garvieae, as the etiological agent. After bacterial isolation from the brain and kidney of diseased fish, identification was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and the VITEK 2 system. Sequencing of the 16S ribosomal RNA (rRNA) gene and phylogenetic analysis were applied to confirm bacterial species. Antimicrobial susceptibility testing was conducted. Histopathological findings in the brain, kidney, spleen, liver, and heart were evaluated. From 20 fish samples, L. garvieae (n = 18 isolates) and Streptococcus agalactiae (n = 2 isolates) were identified. A phylogenetic tree of the 16S rRNA gene revealed that Thai isolates of either L. garvieae or S. agalactiae clustered with reference piscine isolates from intercontinental locations. Our isolates showed resistance against quinolones while being susceptible to other antimicrobials. Histopathological changes demonstrated severe septicemic conditions, with more invasive lesions-especially in the heart and liver-being apparent in L. garvieae-infected fish compared to S. agalactiae-infected fish. This study represents the first reported outbreak of L. garvieae with a concurrent S. agalactiae infection in farmed red tilapia in Thailand.

The airway microbiome of persons with cystic fibrosis correlates with acquisition and microbiological outcomes of incident Stenotrophomonas maltophilia infection.

Chronic infection with Stenotrophomonas maltophilia in persons with cystic fibrosis (pwCF) has been linked to an increased risk of pulmonary exacerbations and lung function decline. We sought to establish whether baseline sputum microbiome associates with risk of S. maltophilia incident infection and persistence in pwCF. pwCF experiencing incident S. maltophilia infections attending the Calgary Adult CF Clinic from 2010-2018 were compared with S. maltophilia-negative sex, age (+/-2 years), and birth-cohort-matched controls. Infection outcomes were classified as persistent (when the pathogen was recovered in ≥50% of cultures in the subsequent year) or transient. We assessed microbial communities from prospectively biobanked sputum using V3-V4 16S ribosomal RNA (rRNA) gene sequencing, in the year preceding (Pre) (n = 57), at (At) (n = 22), and after (Post) (n = 31) incident infection. We verified relative abundance data using S. maltophilia-specific qPCR and 16S rRNA-targeted qPCR to assess bioburden. Strains were typed using pulse-field gel electrophoresis. Twenty-five pwCF with incident S. maltophilia (56% female, median 29 years, median FEV1 61%) with 33 total episodes were compared with 56 uninfected pwCF controls. Demographics and clinical characteristics were similar between cohorts. Among those with incident S. maltophilia infection, sputum communities did not cluster based on infection timeline (Pre, At, Post). Communities differed between the infection cohort and controls (n = 56) based on Shannon Diversity Index (SDI, p = 0.04) and clustered based on Aitchison distance (PERMANOVA, p = 0.01) prior to infection. At the time of incident S. maltophilia isolation, communities did not differ in SDI but clustered based on Aitchison distance (PERMANOVA, p = 0.03) in those that ultimately developed persistent infection versus those that were transient. S. maltophilia abundance within sputum was increased in samples from patients (Pre) relative to controls, measuring both relative (p = 0.004) and absolute (p = 0.001). Furthermore, S. maltophilia abundance was increased in sputum at incident infection in those who ultimately developed persistent infection relative to those with transient infection, measured relatively (p = 0.04) or absolute (p = 0.04), respectively. Microbial community composition of CF sputum associates with S. maltophilia infection acquisition as well as infection outcome. Our study suggests sputum microbiome may serve as a surrogate for identifying infection risk and persistence risk.

Comprehensive Assessment of the Intrinsic Pancreatic Microbiome.

We sought to comprehensively profile tissue and cyst fluid in patients with benign, precancerous, and cancerous conditions of the pancreas to characterize the intrinsic pancreatic microbiome. Small studies in pancreatic ductal adenocarcinoma (PDAC) and intraductal papillary mucinous neoplasm (IPMN) have suggested that intra-pancreatic microbial dysbiosis may drive malignant transformation. Pancreatic samples were collected at the time of resection from 109 patients. Samples included tumor tissue (control, n=20; IPMN, n=20; PDAC, n=19) and pancreatic cyst fluid (IPMN, n=30; SCA, n=10; MCN, n=10). Assessment of bacterial DNA by quantitative PCR and 16S ribosomal RNA gene sequencing was performed. Downstream analyses determined the relative abundances of individual taxa between groups and compared intergroup diversity. Whole-genome sequencing data from 140 patients with PDAC in the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) were analyzed to validate findings. Sequencing of pancreatic tissue yielded few microbial reads regardless of diagnosis, and analysis of pancreatic tissue showed no difference in the abundance and composition of bacterial taxa between normal pancreas, IPMN, or PDAC groups. Low-grade dysplasia (LGD) and high-grade dysplasia (HGD) IPMN were characterized by low bacterial abundances with no difference in tissue composition and a slight increase in Pseudomonas and Sediminibacterium in HGD cyst fluid. Decontamination analysis using the CPTAC database confirmed a low-biomass, low-diversity intrinsic pancreatic microbiome that did not differ by pathology. Our analysis of the pancreatic microbiome demonstrated very low intrinsic biomass that is relatively conserved across diverse neoplastic conditions and thus unlikely to drive malignant transformation.

Bloodstream Infection caused by Corynebacterium striatum in COVID-19 patient

Objectives: Recent research recognized coryneform bacteria as emerging opportunistic pathogens. Corynebacterium striatum appears as a significant pathogen in immunocompromised and immunocompetent patients. Methods: In this paper, we report a case of an adult COVID-19 patient with C. striatum bloodstream infection. In addition, we reviewed clinical cases of bloodstream infection caused by Corynebacterium spp, mainly C. striatum. Results: We present a 43-year-old patient hospitalized due to bilateral pneumonia caused by a SARS-CoV-2 infection. During hospitalization, the patient was connected to a veno-venous extracorporeal membrane oxygenation (ECMO) circuit. C. striatum was isolated in seven sets of blood cultures sampled over seven consecutive days. Based on identification done by MALDI- ToF, empirical therapy with vancomycin was initiated. Identification was confirmed by 16S ribosomal RNA gene sequencing. Although central venous catheter was replaced, C. striatum was persistently isolated in blood cultures in the following days. Although replacement of the ECMO cannula would be recommended, the procedure was not performed due to the severe patient's condition. Fosfomycin was added to vancomycin as salvage therapy in order to reorganize the structure of the biofilm and enable better penetration and efficacy of vancomycin which resulted in sterile blood cultures in the following days. Conclusion: During the last decades, there have been many examples of bloodstream infections caused by skin contaminants. Although the central venous catheter is most commonly described as a route of entry of the skin microbiota in the bloodstream, other catheters such as pleural catheter and ECMO system, should not be neglected. It is well known that bacterial cells often form a biofilm on the surface of different medical devices such as central venous catheters, endoscopes, and urinary catheters. Fosfomycin has the potential to penetrate the biofilm, transform the biofilm structure and potentially increase the concentration of other antimicrobial agents in the biofilm.

Longitudinal evaluation of the cutaneous and rectal microbiota of German shepherd dogs with perianal fistulas undergoing therapy with ciclosporin and ketoconazole.

Perianal fistulas are painful ulcers or sinus tracts that disproportionately affect German shepherd dogs and are proposed as a spontaneous animal model of fistulising Crohn's disease. To characterise the rectal and cutaneous microbiota in German shepherd dogs with perianal fistulas and to investigate longitudinal shifts with lesion resolution during immunomodulatory therapy. Eleven German shepherd dogs with perianal fistulas and 15 healthy German shepherd dogs. Affected dogs were evaluated and swabbed at three visits, 30 days apart, while undergoing treatment with ciclosporin and ketoconazole. Healthy German shepherd dogs were contemporaneously sampled. Sites included the rectum, perianal skin and axilla. The microbiome was evaluated following sequencing of the V4 hypervariable region of the 16S ribosomal RNA (rRNA) gene. Alpha diversity was not significantly different between healthy and affected dogs at each of the three body sites (p > 0.5), yet rectal and perianal beta diversities from affected dogs differed significantly from those of healthy dogs at Day 0 (p = 0.004). Rectal and perianal relative abundance of Prevotella spp. increased and perianal Staphylococcus spp. relative abundance decreased in affected dogs over time, coincident with lesion resolution. Changes in lesional cutaneous and rectal microbiota occur in German shepherd dogs with perianal fistulas and shift over time with lesion resolution during immunomodulatory therapy. Further investigations of the role of cutaneous and enteric microbiota in the pathogenesis of perianal fistulas, and whether manipulation of microbial populations may ameliorate disease, are needed.

A lipidome landscape of aging in mice.

Understanding the molecular mechanisms of aging is crucial for enhancing healthy longevity. We conducted untargeted lipidomics across 13 biological samples from mice at various life stages (2, 12, 19 and 24 months) to explore the potential link between aging and lipid metabolism, considering sex (male or female) and microbiome (specific pathogen-free or germ-free) dependencies. By analyzing 2,704 molecules from 109 lipid subclasses, we characterized common and tissue-specific lipidome alterations associated with aging. For example, the levels of bis(monoacylglycero)phosphate containing polyunsaturated fatty acids increased in various organs during aging, whereas the levels of other phospholipids containing saturated and monounsaturated fatty acids decreased. In addition, we discovered age-dependent sulfonolipid accumulation, absent in germ-free mice, correlating with Alistipes abundance determined by 16S ribosomal RNA gene amplicon sequencing. In the male kidney, glycolipids such as galactosylceramides, galabiosylceramides (Gal2Cer), trihexosylceramides (Hex3Cer), and mono- and digalactosyldiacylglycerols were detected, with two lipid classes-Gal2Cer and Hex3Cer-being significantly enriched in aged mice. Integrated analysis of the kidney transcriptome revealed uridine diphosphate galactosyltransferase 8A (UGT8a), alkylglycerone phosphate synthase and fatty acyl-coenzyme A reductase 1 as potential enzymes responsible for the male-specific glycolipid biosynthesis in vivo, which would be relevant to sex dependency in kidney diseases. Inhibiting UGT8 reduced the levels of these glycolipids and the expression of inflammatory cytokines in the kidney. Our study provides a valuable resource for clarifying potential links between lipid metabolism and aging.

Attenuation of inflammatory bowel disease by oral administration of mucoadhesive polydopamine-coated yeast β-glucan via ROS scavenging and gut microbiota regulation

Treatment for inflammatory bowel disease (IBD) is challenging since current anti-inflammatory and immunosuppressive therapies do not address the underlying causes of the illness, which include increased levels of reactive oxygen species (ROS) and dysbiosis of the gut commensal microbiota. Additionally, these treatments often have systemic off-target effects and adverse side effects. In this study, we have developed a prebiotic yeast β-glucan nanocomplex coated with bio-adhesive polydopamine (YBNs@PDA) to effectively prolong their retention time in the gastrointestinal (GI) tract. The oral administration of YBNs@PDA restored the epithelium barriers, reduced ROS levels, and minimized systemic drug exposure while improved therapeutic efficacy in an acute colitis mouse model. Furthermore, 16S ribosomal RNA genes sequencing demonstrated a higher richness and diversity in gut microflora composition following the treatments. In particular, YBNs@PDA markedly augmented the abundance of Lachnospiraceae NK4A136 and Bifidobacterium, both of which are probiotics with crucial roles in relieving colitis via retaining gut homeostasis. Cumulatively, these results demonstrate that the potential of YBNs@PDA as a novel drug-free, ROS-scavenging and gut microbiota regulation nanoplatform for the treatment of GI disorders.

Pulchinenoside B4 ameliorates oral ulcers in rats by modulating gut microbiota and metabolites

Pulchinenoside B4, a natural saponin monomer from the Pulsatilla plant, plays an important role as an immunomodulator in the treatment of acute inflammation. Oral ulcer (OU) is a common ulcerative injury disease that occurs in the oral mucosa, including mucosal ulceration and abnormalities of lips and tongue. A close correlation exists between gut microbiota and circulating metabolites in patients with OU. However, the correlation between gut microbiota and serum metabolomics is not clear. Therefore, this study aimed to explore the changes in gut microbiota and metabolites in OU. The 16S ribosomal RNA (16S rRNA) gene sequencing was used to detect the changes in the composition of gut microbiota in OU rat model. Moreover, the endogenous small metabolites were explored by collecting the non-targeted serum metabolomics data. A total of 34 OU-related biomarkers were identified, mainly related to fatty acid metabolism and inflammatory pathways. The administration of B4 effectively reduced the occurrence of OU and restored the levels of multiple endogenous biomarkers and key gut microbial species to the normal level. This study demonstrated that the gut microbiota and metabolites were altered in the OU rat model, which were significantly restored to the normal level by B4, thereby showing good application prospects in the treatment of OU.Key points• The first investigating the correlation between OU and gut microbiota.• A close correlation between metabolites and gut microbiota in OU disease was successfully identified.• Pulchinenoside B4 ameliorates oral ulcers in rats by modulating gut microbiota and metabolites.

The use of 18S rRNA for identification of the first record of Tadpole Shrimp Lepidurus apus (Linnaeus, 1758) from Jordan

Abstract. Abushattal S, Alnasarat H, Alnaimat SM, Eid E. 2024. The use of 18S rRNA for identification of the first record of Tadpole Shrimp Lepidurus apus (Linnaeus, 1758) from Jordan. Biodiversitas 25: 1223-1229. The tadpole shrimps are living fossils that survive in temporary water pools and are considered benthic organisms that swim and feed on tiny organisms. Two genera of tadpole shrimps exist worldwide: Triops and Lepidurus, which share similar ecological niches and habitats but never coincide. The occurrence of the tadpole shrimp Lepidurus apus in Jordan was confirmed for the first time using the 18S rRNA Gene-Based PCR Assay. The experimental approach encompassed the amplification of biological specimens utilizing a universal amplicon measuring approximately 1,500 base pairs (bp), specifically targeting the 18S ribosomal RNA (rRNA) gene. Subsequently, the acquired sequences underwent scrutiny through BlastN search against the GenBank database for validation and comparative analysis. Genetic analysis was needed to define the species accurately, especially with tadpole shrimp's generally high morphological variability. This species was recorded in a temporary freshwater pool in the desert of Al-Jafr in Ma’an governorate in southern Jordan. The DNA analysis showed a 100% identical sequence of the 18S rRNA gene with Lepidurus apus sequences. This record is important due to the ecological role of the tadpole shrimps as filter feeders, consuming algae, bacteria, and other small particles of organic matter, and as a food source for various fish, birds, and other aquatic animals. In addition, it will pave the way for future research to identify its economic importance, such as its role in mosquito control and its potential role in aquaculture. Finally, tadpole shrimp are sensitive to environmental changes and could be used to indicate climatic changes and habitat degradation. This is mainly due to their sensitivity to changes in water quality, including temperature, pH, and chemical composition, and their niche requirements for survival and reproduction. In addition, monitoring tadpole shrimp distribution and comparing it with historical records can reveal patterns of climate-induced range shifts.