16S RNA Research Articles

Gut microbiota might influence the risk of rejection after liver transplantation

IntroductionLiver transplantation is the only radical treatment option available for patients with end-stage chronic liver disease. However, severe post-transplant complications remain relevant, including acute graft rejection and infection. Thus, the impact of gut microbiota on the frequency of these complications is highly promising. Materials and methodsThis prospective, cohort, closed-label study included 24 adults who underwent liver transplantation. The mean age was 49.2 ± 13.4 years; Child-Turcotte-Pugh A, B, and C classes were distributed as follows: A: 8 (33.3%); B: 11 (45.8%); C: 5 (20.8%). Gut microbiota was evaluated using 16S RNA new-generation sequencing. Study registrationNCT04281797. ResultsAccording to etiological distribution, significant differences were observed in the number of Firmicutes (p = 0.03) and Chlorobi (p = 0.009) harbored by the patients of alcoholic liver disease. Similarly, the severity of hepatic decompensation varied significantly for patients harboring Chlorobi (p = 0.01) and coprothermobacterota (p = 0.03). The association between sarcopenia and the microbiota was not significant among all taxa (p>0.1). Acute graft rejection differences between groups were found: Protobacteria (p = 0.001); Chlamydiae (p = 0.02); Gammaproteobacteria (p = 0.01); Chloroflexia (p = 0.004); Chlamydiia (p = 0.01); Enterobacteriaceae (p = 0.001); and Candidatus Saccharibacteria (p = 0.04), the median of which was found to be lower in patients with an acute graft rejection episode. ConclusionsObtained results prove a reliable interaction between gut microbiota and the incidence of acute liver graft rejection in dominant taxa and Candidatus Saccharibacteria that had not yet been observed in patients with rejection episodes.

Molecular characterization of Spodoptera litura Nucleopolyhedrovirus (SpltNPV) from Bogor using late expression factor-8 gene

Spodoptera litura Nucleopolyhedrovirus (SpltNPV) is a biological agent successfully developed as a bio insecticide to control S. litura. NPV is host-specific. Therefore, it only infects particular insects. NPV identification is needed so its use can be right on target. Molecular Identification by PCR has been used to characterise Baculovirus. Ac17, lef-2, polh, p35, and 16s RNA, are genes that are often used to identify NPVs. However, the lef-8 gene is the most conserved gene for NPV identification. We conducted this research to study SpltNPV molecular characterisation through nucleotide and amino acid using the lef-8 gene. The NPV isolate was propagated in the Insect Pathology Laboratory. We use the CTAB method to purify the NPV DNA. Forward TCCAAACGTCGATTACG and reverse GACAGGCAGGTTTCTAA primers were used to amplify the lef-8 gene of SpltNPV. The molecular character was used to describe the relationship of SpltNPV isolate with the other NPV reported in GenBank. The lef-8 gene can be used to identify SpltNPV. Based on nucleotides and amino acids sequence of the lef-8 gene, the homology of SpltNPV Bogor has the highest similarity to SpltNPV of German isolates of 99% and 94%. Based on the left-8 gene sequence phylogeny, the Bogor SpltNPV isolate is a member of the same group as the NPV on Spodoptera and Amsacta.

Microbiome of therapeutic muds used in Tatarstan

To characterize the microbiome of therapeutic muds, used in the Tatarstan Republic, by identifying spectrum of cultivated microorganisms, using molecular analysis of bacterial communities, and by determining their biodiversity and functional potential based on revealed genetic determinants. The study design of 5 peloids samples (local sapropels and peat deposits of swamp; 3 samples of Crimean sulfide muds) included three main techniques: isolation and taxonomic determination of cultivated microorganisms by time-of-flight mass-spectrometry; molecular analysis of peloids bacterial communities by 16S RNA high-throughput sequencing; identification of functional profiles of communities by their genetic determinant using Global Mapper tool on iVikodak platform. Experimental studies have confirmed the safety of examined peloids, where non-pathogenic cultivated bacteria belonging mainly to Bacillus and Rhodococcus genera were dominant. Metagenomic analysis showed that Firmicutes, Proteobacteria and Actinobacteria were predominant in all samples in different ratios. It has been established, that there is both the internal biodiversity of each sample and difference between them. The functional profile of microbial communities was determined based on the identification of bacterial genes. It has been revealed that all communities have an ability to synthesize antibiotics, as well as to decompose dangerous xenobiotics - polyaromatic hydrocarbons, cyclic compounds, and dioxins. Various microbial communities, which were identified in the therapeutic muds, contribute both to the clearance of toxicants in the peloids and to the antibacterial properties of the latter. The obtained priority results create a fundamental basis for the subsequent study of the role of peloids' microbiome of different origin in their healing action.

Alteration of Intestinal Microbiota and Hydrogen Sulfide Metabolism in Patients with Hashimoto's Thyroiditis.

To analyze the intestinal microbiota and H2S levels in patients with HT. Twenty euthyroid HT patients and twenty healthy control individuals were recruited. Fecal samples were collected, and the microbiota was examined using 16S RNA gene sequencing. We also collected serum samples to examine the H2S levels. Compared with patients with HT, the ACE and Chao indices were significantly lower in healthy controls (P=0.04, 0.03, respectively). The microbial composition of the HT group differed significantly from that of the healthy group. We observed a significant increase in the proportions of Bacteroides, Fusobacterium, Sutterella, and Veillonella in patients with HT (P < 0.05). Linear discriminant analysis and effect size analysis also revealed that Bacteroides and Ralstonia were enriched in patients with HT. Additionally, patients with HT had significantly lower H2S levels than healthy controls (P < 0.005). The enrichment of H2S anabolism was linked to the alteration of intestinal microbiota in patients with HT. We demonstrated that patients with HT have aberrant intestinal microbiome and that H2S anabolism may contribute to HT pathogenesis.

Microbial community composition and environmental response characteristics of typical brackish groundwater in the North China Plain

(Objective)To reveal the microbial community composition of regional shallow porous brackish groundwater and its response characteristics to groundwater environment, (Method)the first and second aquifers in Taocheng District, Hengshui City were selected, and 10 groundwater source samples were collected for hydrochemical analysis and microbial 16S RNA gene V4-V5 regional sequencing. (Results)The results showed that the shallow brackish groundwater in the study area is weakly alkaline and has high ion content. The spatial zonation of the abundance and diversity of groundwater microorganisms is obvious. The number of endemic bacteria in groundwater from upstream, midstream to downstream is 11, 135 and 22 respectively, with a total of 22 bacteria. Proteobacteria is the most dominant in groundwater level, and there are obvious differences in different sections. At the genus level, the main dominant species in each group and sample are Pseudomonas and Hydrogenophaga. In terms of composition difference, Pseudohongiella, Pseudorhodobacter and Limnohabitans are the representatives of UR, MR and LR. (Conclusion)On the whole, the composition of flora in groundwater is sensitive and closely related to hydrochemical processes. Species abundance is affected by alkaline and high salinity environmental indicators, while species diversity is related to depth and DO in weak reduction environment.

Characterization of bacterial pathogens involved in pneumonia of sheep and Goats

A study was conducted with the objectives to isolate, identify and characterize bacterial pathogens from pneumonia suspected samples of sheep and goats collected from veterinary clinic and slaughterhouses in and around Hyderabad, Telangana. A total of 112 bacterial isolates were recovered from 101 lung and nasal discharge samples of sheep and goats. The maximum prevalent bacteria were Staphylococcus aureus (49.10%), followed by Klebsiella pneumoniae (37.51%) and Pseudomonas aeruginosa (13.39%). Further, virulence-associated spa gene was detected in 72.7% of Staphylococcus isolates while uge gene of Klebsiella was detected in 61.9% of the isolates. The spa gene, uge gene, 16S RNA sequence of S. aureus, K. pneumonia and P. aeruginosa isolates showed high identities with United Kingdom isolates of S. aureus, United Kingdom isolates of K. pneumonia and Sudan isolates of P. aeruginosa, respectively. It was concluded that pneumonia is a multifactoral disease and the presence of various virulent associated genes among the isolates indicates their potential to resist the host immune to cause the disease.

Comparison of different PCR amplification targets for molecular diagnosis of Strongyloides stercoralis.

Molecular techniques are an alternative for the diagnosis of strongyloidiasis, produced by Strongyloides stercoralis. However, it is necessary to determine the best amplification target for the populations of this parasite present in a geographical area and standardize a polymerase chain reaction (PCR) protocol for its detection. The objectives of this work were the comparison of different PCR targets for molecular detection of S. stercoralis and the standardization of a PCR protocol for the selected target with the best diagnostic results. DNA extraction was performed from parasite larvae by saline precipitation. Three amplification targets of the genes encoding ribosomal RNA 18S (18S rDNA) and 5.8S (5.8S rDNA) and cytochrome oxidase 1 (COX1) of S. stercoralis were compared, and the PCR reaction conditions for the best target were standardized (concentration of reagents and template DNA, hybridization temperature, and number of cycles). The analytical sensitivity and specificity of the technique were determined. DNA extraction by saline precipitation made it possible to obtain DNA of high purity and integrity. The ideal target was the 5.8S rDNA, since the 18S rDNA yielded non-reproducible results and COX1 never amplified under any condition tested. The optimal conditions for the 5.8S rDNA-PCR were: 1.5 mM MgCl2, 100 μM dNTPs, 0.4 μM primers, and 0.75 U DNA polymerase, using 35 cycles and a hybridization temperature of 60 °C. The analytical sensitivity of the PCR was 1 attogram of DNA, and the specificity was 100%. Consequently, the 5.8S rDNA was shown to be highly sensitive and specific for the detection of S. stercoralis DNA.

ISOLATION AND CHARACTERIZATION OF BACTERIAL PATHOGENIC Bacillus sp. FROM THE Lethrinus lentjanin COASTAL AREA OF INDIA

India stands at the sixth-largest position in the sector of marine and freshwater fisheries and the second-largest in the production of aquaculture. In view of the economic benefits, this highlights the importance of controlling infectious fish diseases that pose threat to the production of aquaculture. It was hypothesized lesions found on the dorsal scales in the Lenthrinus lentjan, could be the reason for the massive morbidity and mortality. Live surface floating fish samples with pathological signs were collected from offshore areas of the Pallam fishing village, located in the Kanyakumari District of Tamil Nadu, India in August 2013. Detailed histological studies confirmed the presence of similar bacterial infections in the tissues adjacent to the lesion sites. The pathogen was isolated and it was subjected to a series of biochemical and 16S RNA sequencing and it was identified the causative bacterial pathogen as Bacillus sp. The pathogen possessed sub-terminal endospore-forming nature and also it has strong hemolytic activities. The organism was named as Bacillus sp. MSU1400. Furtherly, the study was complemented with the Pasteur method, performed on white carp fishes, in vitro, for the confirmation of the pathogen. The pathogen was sensitive to ampicillin, cephalexin, and gentamycin but it was resistant to tetracycline.

A novel narnavirus is widespread in Saccharomyces cerevisiae and impacts multiple host phenotypes.

RNA viruses are a widespread, biologically diverse group that includes the narnaviridiae, a family of unencapsidated RNA viruses containing a single ORF that encodes an RNA-dependent RNA polymerase. In the yeast Saccharomyces cerevisiae, the 20S and 23S RNA viruses are well-studied members of the narnaviridiae, which are present at low intracellular copy numbers, unless induced by stress or unfavorable growth conditions (Wickneret al. 2013), and are not known to affect host fitness. In this study, we describe a new Saccharomyces cerevisiae narnavirus that we designate as N1199. We show that N1199 is uniquely present as a double-stranded RNA at a high level relative to other known members of this family in one strain background, YJM1199, and is present as a single-stranded RNA at lower levels in 98 of the remaining 100-genomes strains. Further, we see a strong association between the presence of high level N1199 and host phenotype defects, including greatly reduced sporulation efficiency and growth on multiple carbon sources. Finally, we describe associations between N1199 abundance and host phenotype defects, including autophagy.

High-Resolution Small RNAs Landscape Provides Insights into Alkane Adaptation in the Marine Alkane-Degrader Alcanivorax dieselolei B-5

Alkanes are widespread in the ocean, and Alcanivorax is one of the most ubiquitous alkane-degrading bacteria in the marine ecosystem. Small RNAs (sRNAs) are usually at the heart of regulatory pathways, but sRNA-mediated alkane metabolic adaptability still remains largely unknown due to the difficulties of identification. Here, differential RNA sequencing (dRNA-seq) modified with a size selection (~50-nt to 500-nt) strategy was used to generate high-resolution sRNAs profiling in the model species Alcanivorax dieselolei B-5 under alkane (n-hexadecane) and non-alkane (acetate) conditions. As a result, we identified 549 sRNA candidates at single-nucleotide resolution of 5'-ends, 63.4% of which are with transcription start sites (TSSs), and 36.6% of which are with processing sites (PSSs) at the 5'-ends. These sRNAs originate from almost any location in the genome, regardless of intragenic (65.8%), antisense (20.6%) and intergenic (6.2%) regions, and RNase E may function in the maturation of sRNAs. Most sRNAs locally distribute across the 15 reference genomes of Alcanivorax, and only 7.5% of sRNAs are broadly conserved in this genus. Expression responses to the alkane of several core conserved sRNAs, including 6S RNA, M1 RNA and tmRNA, indicate that they may participate in alkane metabolisms and result in more actively global transcription, RNA processing and stresses mitigation. Two novel CsrA-related sRNAs are identified, which may be involved in the translational activation of alkane metabolism-related genes by sequestering the global repressor CsrA. The relationships of sRNAs with the characterized genes of alkane sensing (ompS), chemotaxis (mcp, cheR, cheW2), transporting (ompT1, ompT2, ompT3) and hydroxylation (alkB1, alkB2, almA) were created based on the genome-wide predicted sRNA-mRNA interactions. Overall, the sRNA landscape lays the ground for uncovering cryptic regulations in critical marine bacterium, among which both the core and species-specific sRNAs are implicated in the alkane adaptive metabolisms.

Prevalence and associated risk factors of Schistosoma indicum infection in cattle of Assam, India

The hepato-intestinal schistosomosis, a chronic debilitating infection caused by Schistosoma indicum is one of the major helminthic problems which cause considerable reduction in production and productivity, and economic losses in Assam, India. Hence their accurate diagnosis by traditional and molecular methods is the key to its management. A total of 420 faecal samples and liver and intestinal mesenteries from different slaughter houses of Assam were collected and examined during March 2015 to February 2016 to record the prevalence of visceral schistosomosis. It was observed that prevalence rate of schistosomosis was found to be more in mesenteric and hepatic portal vein examination (12.38%) than the faecal examination (4.52%). The 28S RNA gene (28S) and mitochondrial cytochrome c oxidase subunit 1 (COI) gene of morphologically identified adult S. indicum was amplified with amplicon sizes 590 bp and 372 bp, respectively which could be used as molecular marker for diagnosis S. indicum infection. However, based on worm pair detection, the study showed an increasing incidence of schistosomosis from the month of May onward reached highest peak in July and gradually decline to lowest point in April, while coprological examination showed the highest peak in August and the lowest in March. The risk factors include age, breed and management systems of the cattle. Therefore, this study emphasizes on employing both conventional and molecular techniques to detect the various risk factors of S. indicum infection in cattle for successful control measures.

Transgenerational transfer of the microbiome is altered by ocean acidification in oyster larvae

Ocean acidification will affect marine molluscs, however, transgenerational plasticity (TGP) can ameliorate some effects. Marine molluscs acquire members of their microbiome via the egg, yet we know little about how the microbiome can be influenced by transgenerational exposure to ocean acidification. We exposed adult Sydney Rock oysters (Saccostrea glomerata) from four genotypes to elevated and ambient PCO2 for nine weeks. Larvae were then raised in the same ambient and elevated PCO2 conditions. The relative abundance of bacteria in eggs and larvae were characterised using 16S RNA amplicon sequencing. Parental exposure to elevated PCO2 significantly altered the bacterial community composition of both eggs and larvae, but this was dependent on genotype. Parental exposure to elevated PCO2 caused five core Rhodobacteraceae ASVs to increase in relative abundance, and three Rhodobacteraceae ASVs to decrease in relative abundance. These findings show transfer of maternal microbiomes to larvae is altered by exposure to ocean acidification and this may play a role in TGP.

Biogeographic Patterns and Community Assembly Processes of Bacterioplankton and Potential Pathogens in Subtropical Estuaries in China.

Microbial communities in coastal waters are diverse and dynamic and play important roles in ecosystem functions and services. Despite the ecological impact of bacterioplankton or pathogens, little is known about whether bacterioplankton and pathogen communities exhibit similar patterns. Here, using 16S RNA gene amplicon sequencing, the geographic patterns and assembly processes of bacterioplankton and pathogen communities in 30 subtropical estuaries were studied. Results showed that the estuarine bacterioplankton communities mainly consisted of Proteobacteria (49.06%), Actinobacteria (17.62%), and Bacteroidetes (16.33%), among which 31 pathogen genera (186 amplicon sequence variants [ASVs]) were identified. Under the influence of salinity, bacterioplankton and pathogens showed similar biogeographic patterns. Redundancy and correlation analyses indicated that the bacterioplankton communities were strongly correlated with estuarine environmental factors, but potential pathogens were less influenced. Co-occurrence network analysis revealed a close relationship between bacterioplankton and potential pathogens, with two pathogens identified as connectors (i.e., ASV340 [Clostridium perfringens] and ASV1624 [Brevundimonas diminuta]), implying potential impacts of pathogens on structure, function, and stability of estuarine bacterioplankton communities. Null-model analysis revealed that deterministic processes (heterogeneous selection) dominated bacterioplankton community assembly, while stochastic processes (undominated effect) shaped the potential pathogen community. Our findings illustrate the biogeographic patterns and community assembly mechanisms of bacterioplankton and pathogens in estuaries, which should provide guidance and a reference for the control of potential pathogenic bacteria. IMPORTANCE Bacterioplankton play an important role in estuarine ecosystem functions and services; however, potentially pathogenic bacteria may exhibit infectivity and pose a serious threat to environmental and human health. In this study, geographic patterns and assembly processes of bacterioplankton communities in 30 subtropical estuaries were explored, and potential pathogenic bacteria in the estuaries were detected and profiled. Our results demonstrate here that bacterioplankton and pathogens show similar biogeographic patterns under the influence of salinity. Interestingly, heterogeneous selection dominated bacterioplankton assembly, while stochasticity dominated pathogen assembly. This study provides important information for future risk assessment of potential pathogenic bacteria as well as management in estuarine ecosystems.

Bioactive Compounds from Endophytic Bacteria Bacillus subtilis Strain EP1 with Their Antibacterial Activities.

Endophytic bacteria boost host plant defense and growth by producing vital compounds. In the current study, a bacterial strain was isolated from the Boswellia sacra plant and identified as Bacillus subtilis strain EP1 (accession number: MT256301) through 16S RNA gene sequencing. From the identified bacteria, four compounds-1 (4-(4-cinnamoyloxy)phenyl)butanoic acid), 2 (cyclo-(L-Pro-D-Tyr)), 3 (cyclo-(L-Val-L-Phe)), and 4 (cyclo-(L-Pro-L-Val))-were isolated and characterized by 1D and 2D NMR and mass spectroscopy. Moreover, antibacterial activity and beta-lactam-producing gene inhibition (δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine synthetase (ACVS) and aminoadipate aminotransferase (AADAT)) assays were performed. Significant antibacterial activity was observed against the human pathogenic bacterial strains (E. coli) by compound 4 with a 13 ± 0.7 mm zone of inhibition (ZOI), followed by compound 1 having an 11 ± 0.7 mm ZOI. In contrast, the least antibacterial activity among the tested samples was offered by compound 2 with a 10 ± 0.9 mm ZOI compared to the standard (26 ± 1.2 mm). Similarly, the molecular analysis of beta-lactam inhibition determined that compounds 3 and 4 inhibited the two genes (2- to 4-fold) in the beta-lactam biosynthesis (ACVS and AADAT) pathway. From these results, it can be concluded that future research on these compounds could lead to the inhibition of antibiotic-resistant pathogenic bacterial strains.

Variability of Human rDNA and Transcription Activity of the Ribosomal Genes

Human ribosomal DNA is represented by hundreds of repeats in each cell. Every repeat consists of two parts: a 13 kb long 47S DNA with genes encoding 18S, 5.8S, and 28S RNAs of ribosomal particles, and a 30 kb long intergenic spacer (IGS). Remarkably, transcription does not take place in all the repeats. The transcriptionally silent genes are characterized by the epigenetic marks of the inactive chromatin, including DNA hypermethylation of the promoter and adjacent areas. However, it is still unknown what causes the differentiation of the genes into active and silent. In this study, we examine whether this differentiation is related to the nucleotide sequence of IGS. We isolated ribosomal DNA from the nucleoli of human-derived HT1080 cells, and separated methylated and non-methylated DNA by chromatin immunoprecipitation. Then, we used PCR to amplify a 2 kb long region upstream of the transcription start and sequenced the product. We found that six SNVs and a series of short deletions in a region of simple repeats correlated with the DNA methylation status. These data indicate that variability of IGS sequence may initiate silencing of the ribosomal genes. Our study also suggests a number of pathways to this silencing that involve micro-RNAs and/or non-canonical DNA structures.

Multi-Locus Sequencing Reveals Putative Novel Anaplasmataceae Agents, 'Candidatus Ehrlichia dumleri' and Anaplasma sp., in Ring-Tailed Coatis (Carnivora: Nasua nasua) from Urban Forested Fragments at Midwestern Brazil.

The Anaplasmataceae family encompasses obligate intracellular α-proteobacteria of human and veterinary medicine importance. This study performed multi-locus sequencing to characterize Ehrlichia and Anaplasma in coati's blood samples in Midwestern Brazil. Twenty-five samples (25/165-15.1%) were positive in the screening PCR based on the dsb gene of Ehrlichia spp. and were characterized using 16S rRNA, sodB, groEL, and gltA genes and the 23S-5S intergenic space region (ITS). Phylogenetic analyses based on all six molecular markers positioned the sequences into a new clade, with a common origin of Ehrlichia ruminantium. Haplotype analyses of 16S RNA sequences revealed the presence of two distinct Ehrlichia genotypes. Six samples (6/165, 3.6%) were positive in the screening nPCR for the 16S rRNA gene of Anaplasma spp. and were submitted to an additional PCR targeting the ITS for molecular characterization. Phylogenetic analyses based on both 16S rRNA gene and ITS positioned the Anaplasma sp. detected in the present study in a large clade with other Anaplasma sp. previously detected in ticks and wild animals and in a clade with 'Candidatus Anaplasma brasiliensis', respectively. Based on distinct molecular markers, the present work described a putative novel Anaplasmataceae agent, namely 'Candidatus Ehrlichia dumleri', and Anaplasma sp. closely related to the previously described 'Candidatus Anaplasma brasiliensis'.

An Integrated Analytical Approach for the Characterization of Probiotic Strains in Food Supplements

Research surrounding health benefits from probiotics is becoming popular because of the increasing demand for safer products with protective and therapeutic effects. Proven benefits are species- or genus-specific; however, no certified assays are available for their characterization and quantification at the strain level in the food supplement industry. The objective of this study was to develop a strain-specific Real-time quantitative polymerase chain reaction (RT-qPCR)-based method to be implemented in routine tests for the identification and quantification of Bifidobacterium longum, Bifidobacterium animalis spp. lactis, Lactobacillus paracasei, Lactobacillus rhamnosus, Lactobacillus casei, Bifidobacterium breve, Lactobacillus acidophilus, Lactobacillus plantarum, and Lactobacillus helveticus, starting from a powder mixture of food supplements. The method optimization was carried out in combination with flow cytometry to compare results between the two strategies and implement the analytical workflow with the information also regarding cell viability. These assays were validated in accordance with the International Council for Harmonization of Technical Requirements for Pharmaceuticals for Human Use (ICH) criteria using the plate count enumeration as the gold standard reference. Briefly, probiotic DNAs were extracted from two powder food supplements. Strain-specific primers targeting unique sequence regions of 16S RNA were identified and amplified by RT-qPCR. Primers were tested for specificity, sensitivity, and efficiency. Both RT-qPCR and flow-cytometry methods described in our work for the quantification and identification of Lactobacillus and Bifidobacterium strains were specific, sensitive, and precise, showing better performances with respect to the morphological colony identification. This work demonstrated that RT-qPCR can be implemented in the quality control workflow of commercial probiotic products giving more standardized and effective results regarding species discrimination.

Prevalence of Escherichia coli O157 isolated from marketed raw cow milk in Kwara State, Nigeria

Escherichia coli (E. coli) is a common cause of poor milk microbial quality, often resulting from unhygienic milk handling. Here, a cross-sectional study was performed to determine the prevalence and antibiotic susceptibility profile of E. coli O157 in raw cow milk sold in Kwara State. Raw cow milk (n = 1225) samples from 11 selected markets within the agro-ecological zones of Kwara State (known for vending milk) were collected across rainy (n = 548) and dry (n = 677) seasons. Isolation and identification of E. coli were done using standard procedures. The Polymerase Chain Reaction was utilized to detect E. coli O157 targeting 16S RNA and its virulence (eaeAO157) and toxigenic (Shiga-toxin 1 (stx1)) genes. The antimicrobial susceptibility profile of E. coli O157 isolates was determined by multi-disc diffusion. The total prevalence of E. coli was 48.9% (n = 599), of which 2.3% (n = 28) were E. coli O157. The prevalence of E. coli was significantly higher during the dry (58.8%) than during the rainy (36.7%) season. Twenty-six E. coli O157 isolates possessed the eaeAO157 gene, while all the 28 isolates carried the stx1. E. coli O157 were susceptible to nitrofurantoin (50.0%) and ciprofloxacin (46.5%), but resistant to cefotaxime (96.4%), ampicillin (89.3%), gentamicin (89.3%) and chloramphenicol (71.4%). This study established the presence of E. coli O157 with virulence, toxigenic genes, and antimicrobial resistance in raw cow milk in Kwara State. Improved hygienic practices during milk handling are recommended.

Chromatin localization of nucleophosmin organizes ribosome biogenesis

Ribosome biogenesis takes place in the nucleolus, a nuclear membrane-less organelle. Although well studied, it remains unknown how nascent ribosomal subunits separate from the central chromatin compartment and move to the outer granular component, where maturation occurs. We find that the Schizosaccharomyces pombe nucleophosmin-like protein Fkbp39 localizes to rDNA sites encoding the 60S subunit rRNA, and this localization contributes to its specific association with nascent 60S subunits. Fkbp39 dissociates from chromatin to bind nascent 60S subunits, causing the latter to partition away from chromatin and from nascent 40S subunits through liquid-liquid phase separation. Invivo, Fkbp39 binding directs the translocation of nascent 60S subunits toward the nucleophosmin-rich granular component. This process increases the efficiency of 60S subunit assembly, facilitating the incorporation of 60S RNA domain III. Thus, chromatin localization determines the specificity of nucleophosmin in sorting nascent ribosomal subunits and coordinates their movement into specialized assembly compartments within the nucleolus.

Gut microbiota in hypertensive patients with versus without obstructive sleep apnea.

We investigated the alteration of gut microbiota and the associated metabolic risks in hypertensive patients with obstructive sleep apnea (OSA) comorbidity. Fecal and blood samples were collected from 52 hypertensive patients, who were divided into three groups: A (controls, apnea-hypopnea index[AHI]<5, n=15), B (mild OSA, 5<AHI<20, n=17), and C (moderate-to-severe OSA, AHI>20, n=20). The composition of the gut microbiota was studied through 16s RNA sequencing of variable regions 3-4. Analysis of the results revealed that group C had a significant higher concentration of total cholesterol, low-density lipoprotein, and IL-1β compared with group A. The Shannon index showed that bacterial biodiversity was lower in OSA patients. At the phylum level, the ratio of Firmicutes to Bacteroidetes (F/B) was significantly higher in group C than in groups A and B. At the genus level, the relative abundance of short-chain fatty acids (SCFA)-producing bacteria (e.g., Bacteroides and Prevotella) was lower while the number of inflammation-related bacteria (e.g., Lactobacillus) was increased in patients with OSA. We found that the IL-1β level was negatively correlated with Bacteroidetes. The area under the receiver operating characteristic curve was .672 for F/B ratio in determining hypertensive patients with OSA. In patients with hypertension, OSA was associated with worse gut dysbiosis, as evidenced by decreased levels of short-chain fatty acids-producing bacteria and increased number of inflammation-related bacteria. The differences in gut microbiota discriminate hypertensive patients with OSA from those without and may result in an enhanced inflammatory response and increase the risk of metabolic diseases.