Ribosomal RNA Sequences Research Articles

Altered Endometrial Microbiota Profile Is Associated With Poor Endometrial Receptivity of Repeated Implantation Failure.

To gain insight into the endometrial pathophysiology of unexplained repeated implantation failure (RIF), we examined the characteristics of genital tract microbiota and explored the correlation between the microbiota and endometrial receptivity. Vaginal secretion (VS) and endometrial biopsy (EB) samples were collected from patients with RIF (RIF group, n=32) and those with infertility who had achieved pregnancy during their initial embryo transfer cycle (control group, n=18). 16S ribosomal RNA sequencing and quantitative PCR were performed to characterize the microbiota of the two groups. Spearman's correlation analysis was performed to determine the relationship between endometrial receptivity markers and endometrial microbiota. Endometrial microbiota exhibited distinct characteristics from vaginal microbiota, with a higher alpha-diversity. Alpha-diversity of the endometrial microbiota was higher in the RIF group than in the control group. Compared with the control group, the RIF group had a significant decrease in endometrial Lactobacillus abundance and an increase in Gardnerella and Acinetobacter abundances. The expression levels of endometrial receptivity markers, including homeobox A11, integrin αvβ3, leukemia inhibitor factor, matrix metalloproteinase-9, and vascular endothelial growth factor, were lower in the RIF group than in the control group. Moreover, the expression levels of these markers were correlated with endometrial Lactobacillus, Gardnerella, and Acinetobacter abundances. RIF is characterized by endometrial microbiota dysbiosis and poor endometrial receptivity. Moreover, abnormal endometrial microbiota is associated with impaired endometrial receptivity, which may be a potential cause of unexplained RIF.

Sauerkraut‐derived LAB strains as potential probiotic candidates for modulating carbohydrate digestion attributing bacterial organic acid profiling to antidiabetic activity

AbstractSauerkraut‐derived lactic acid bacterial (LAB) strains have gained attention due to their potential health benefits. This study focuses on evaluating seven Sauerkraut‐derived RAMULAB strains isolated from sauerkraut, aiming to identify promising candidates for modulating α‐glucosidase (AG) and α‐amylase (AM) enzymatic functions. RAMULAB strains with remarkable probiotic potential can contribute to the digestive health and manage conditions like diabetes. Identifying robust candidates from sauerkraut, a fermented food, holds promise for natural and cost‐effective probiotic sources. The RAMULAB strains underwent extensive characterization, including identification through 16S ribosomal RNA (rRNA) sequencing. Their tolerance to harsh conditions, adherence properties, antimicrobial activity, antioxidant potential, and inhibition of AG and AM were assessed. In silico analyses explored their molecular interactions, particularly with hydroxycitric acid, a potential antidiabetic compound. Among the RAMULAB strains, RAMULAB48 emerged as a standout candidate. It displayed exceptional resilience to acidic bile (≥97%), and simulated gastrointestinal conditions (≥95%), highlighting its suitability for probiotic applications. RAMULAB48 exhibited robust adherence properties, including cell‐surface hydrophobicity (80%), autoaggregation (42%), coaggregation with pathogens (≥33%), and adhesion to epithelial cells. Additionally, all seven isolates demonstrated gamma‐hemolysis and resistance to antibiotics (Kanamycin, Methicillin, and Vancomycin), while displaying strong antibacterial properties against foodborne pathogens. These RAMULAB strains also exhibited varying degrees of antioxidant activity, with RAMULAB48 displaying the highest potential (≥41%). In terms of antidiabetic activity, cell‐free supernatant (CS) obtained from RAMULAB48 expressed the highest inhibition levels, notably inhibiting yeast AG by an impressive 59.55% and AM being by a remarkable 67.42%. RAMULAB48 produced organic acids, including hydroxycitric acid (28.024 mg/mL), which showed promising antidiabetic properties through in silico analyses, indicating favorable interactions with the target enzymes. This study identifies Lacticaseibacillus paracasei RAMULAB48, a Sauerkraut‐derived RAMULAB strain, as a promising probiotic candidate with exceptional tolerance, adherence properties, antimicrobial activity, antioxidant potential, and antidiabetic effects. The presence of hydroxycitric acid further underscores its potential in managing diabetes.

Microbiome of the Middle Meatus, Tonsils, and Adenoids in Pediatric Chronic Rhinosinusitis.

Pediatric chronic rhinosinusitis (PCRS) is a common condition with a significant impact on quality of life. This study compares the microbiome of pediatric patients with and without chronic rhinosinusitis. Single-center, prospective, quantitative case-control. Metropolitan. Patients undergoing adenoidectomy for PCRS (subjects, n = 20) or obstructive sleep apnea (controls, n = 20) were recruited. 16S ribosomal RNA sequencing was performed on the right middle meatus (MM), adenoid, and palatine tonsil samples from each patient. Alpha diversity was measured by the Simpson's diversity index, beta diversity was measured by the Bray-Curtis dissimilarity index, and the differential abundance of bacteria genera was analyzed. There were 40 adenoid, 40 tonsil, and 37 MM samples analyzed. There was no significant difference in alpha diversity between controls and subjects. Tonsils were significantly more diverse than the adenoids, which were more diverse than the MM (P < .001). There was no difference in bacterial composition between controls and subjects, but the composition of the 3 sites were significantly different (P < .001). The dissimilarity in bacterial composition between the adenoid and MM sites was larger in the control group than in the subject group. There were significant differences in alpha diversity and bacterial composition between the anatomic 3 sites; however, there was no difference between the controls and subjects. The larger dissimilarity in bacterial composition between adenoid and MM sites in controls compared to subjects suggests there may be colonization of the MM by the adenoid in PCRS patients.

Mechanisms of Electroacupuncture in Alleviating Visceral Hypersensitivity in Post-Infectious Irritable Bowel Syndrome Mice: The Role of GDNF Signaling Pathway and Gut Microbiota.

Post-infectious irritable bowel syndrome (PI-IBS) is a functional bowel disease that develops following an acute gastrointestinal infection. Electroacupuncture (EA) can regulate the gut microbiota and alleviate visceral hypersensitivity. Glial cell-derived neurotrophic factor (GDNF) is a potential factor in visceral hypersensitivity reactions. The aim of this study was to explore whether EA could alleviate visceral hypersensitivity in PI-IBS by regulating gut microbiota through GDNF signaling. 2,4,6-trinitrobenzene sulfonic acid (TNBS) was used to induce visceral hypersensitivity in PI-IBS mice. Assessment of intestinal visceral sensitivity using the abdominal withdrawal reflex (CRD). 16S ribosomal RNA (16S rRNA) sequencing to profile the gut microbiome community. GDNF can exacerbate the imbalances of the gut microbiota and increase visceral hypersensitivity compared with the model group. Whereas EA treatment increases the richness and diversity of the gut microbiota, decreases differences among species and alleviates visceral sensitivity. EA can alleviate visceral hypersensitivity in PI-IBS by regulating the gut microbiota via GDNF signaling, providing new insights for mechanistic research on EA in PI-IBS treatment.

Oral Microbiome and CPT1A Function in Fatty Acid Metabolism in Oral Cancer.

The oral microbiome is crucial for human health. Although oral dysbiosis may contribute to oral cancer (OC), the detailed relationships between the microbiome and OC remain unclear. In this case-control study, we aimed to elucidate the connection between the oral microbiome and mechanisms potentially involved in oral cancer. The study analyzed 1022 oral saliva samples, including 157 from oral cancer patients and 865 from healthy controls, using 16S ribosomal RNA (16S rRNA) sequencing and a Light Gradient Boosting Machine (LightGBM) model to identify four bacterial genera significantly associated with oral cancer. In patients with oral cancer, the relative abundance of Streptococcus and Parvimonas was higher; Corynebacterium and Prevotella showed decreased relative abundance; and levels of fatty acid oxidation enzymes, including Carnitine palmitoyltransferase 1A (CPT1A), long-chain acyl-CoA synthetase, acyl-CoA dehydrogenase, diacylglycerol choline phosphotransferase, and H+-transporting ATPase, were significantly higher compared to controls. Conversely, healthy controls exhibited increased levels of short-chain fatty acids (SCFAs) and CD4+T-helper cell counts. Survival analysis revealed that higher abundance of Streptococcus and Parvimonas, which correlated positively with interleukin-6, tumor necrosis factor-alpha, and CPT1A, were linked to poorer disease-free survival (DFS) and overall survival (OS) rates, while Prevotella and Corynebacterium were associated with better outcomes. These findings suggest that changes in these bacterial genera are associated with alterations in specific cytokines, CPT1A levels, SCFAs in oral cancer, with lower SCFA levels in patients reinforcing this link. Overall, these microbiome changes, along with cytokine and enzyme alterations, may serve as predictive markers, enhancing diagnostic accuracy for oral cancer.

Bivalve microbiomes are shaped by host species, size, parasite infection, and environment.

Many factors affect an organism's microbiome including its environment, proximity to other organisms, and physiological condition. As filter feeders, bivalves have highly plastic microbiomes that are especially influenced by the surrounding seawater, yet they also maintain a unique core set of microbes. Using 16S ribosomal RNA sequencing, we characterized the bacterial microbiomes of four species of bivalves native to the Mid-Atlantic East Coast of North America: Crassostrea virginica, Macoma balthica, Ameritella mitchelli, and Ischadium recurvum and assessed the impact of their external environment, internal parasites, and size on their microbial communities. We found significant differences in bacterial amplicon sequence variants (ASVs) across species, with each species harboring a core ASV present across all individuals. We further found that some C. virginica co-cultured with I. recurvum had high abundances of the I. recurvum core ASV. We identified ASVs associated with infection by the parasites Perkinsus marinus and Zaops ostreum as well others associated with bivalve size. Several of these ASV are candidates for further investigation as potential probiotics, as they were found positively correlated with bivalve size and health. This research represents the first description of the microbiomes of A. mitchelli, I. recurvum, and M. balthica. We document that all four species have highly plastic microbiomes, while maintaining certain core bacteria, with important implications for growth, health, and adaptation to new environments.

Wastewater-based intestinal protozoa monitoring in Shanghai, China.

Intestinal protozoa Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi have been implicated in serious waterborne outbreaks worldwide. Wastewater-based epidemiology (WBE) is a promising approach for evaluating the disease prevalence in a catchment population in that it monitors the contamination level of the intestinal pathogens in wastewater. We collected 48 urban wastewater samples (24 from influents and 24 from effluents) from the Yangpu Wastewater Treatment Plant (YPWTP) in Shanghai, China. We identified Cryptosporidium spp., G. duodenalis, and E. bieneusi by nested polymerase chain reaction (PCR) amplification. Cryptosporidium hominis and subtype IdA14 were identified in two samples by analyzing the sequences of small subunit ribosomal RNA (SSU rRNA) and 60-kDa glycoprotein (gp60) genes, respectively. The G. duodenalis sub-assemblage AII (n = 8) and assemblage C (n = 4) in 12 samples were determined by analyzing triosephosphate isomerase (tpi) gene sequences. The E. bieneusi genotype A was identified in one sample by analyzing the sequence of the internal transcribed spacer (ITS) region of the rRNA gene. These findings suggest that improving wastewater treatment and monitoring the virility of pathogens in effluents is critical. We observed similar prevalence and genotypes/subtypes of the three intestinal protozoa in our wastewater samples as those reported in previous studies, providing evidence that WBE can be used as an effective epidemic management tool.IMPORTANCECryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi are common intestinal protozoa causing diarrhea. The infective oocysts, cysts, and spores released in feces can survive in different environments, including multiple types of water bodies. Humans can acquire these intestinal protozoan infections via the fecal-oral route as in waterborne transmission. Wastewater-based epidemiology can rapidly and reliably detect and monitor the emergence and spread of waterborne diseases. We detected Cryptosporidium spp., G. duodenalis, and E. bieneusi in a wastewater treatment plant in Shanghai, China, reflecting the occurrence and genetic characterizations of the three intestinal pathogens from community members served by the wastewater treatment plant.

Bioreduction potential of Providencia sp. and microbial consortium for hexavalent molybdenum: Isolation, identification, characterization, and optimization by response surface methodology

Molybdenum, a heavy metal with industrial applications, poses global toxicity concerns at concentrations exceeding 0.07 mg/L. This study aimed to isolate, characterize and optimize the molybdenum (Mo) reduction potential of bacterial strain and a mixed consortia. We used low phosphate media (LPM) for the isolation and optimization, employing one-factor-at-a-time (OFAT) and Response Surface Methodology (RSM) approaches. Molecular identification based on 16S ribosomal RNA sequencing of the Mo-reducing bacterial isolate revealed Providencia sp. Optimization via OFAT showed that this isolate effectively reduced 60 mM molybdate with optimal conditions of 2 mM phosphate and 10 mM fructose. The mixed consortium achieved remarkable reduction of molybdate at concentration up to 100 mM, the highest reported concentration to date. The RSM optimization of Providencia sp. revealed that the best reduction was supported by a pH of 6.50 and 60 mM molybdate. However, RSM was not successful with the consortium using the Plackett-Burman Design, suggesting that alternative designs should be explored for future optimization. This study advances understanding of Mo-reduction and highlights significant achievements in handling high molybdate concentrations.

Supragingival Plaque Microbiomes in a Diverse South Florida Population.

Trillions of microbes comprise the human oral cavity, collectively acting as another bodily organ. Although research is several decades into the field, there is no consensus on how oral microbiomes differ in underrepresented groups such as Hispanic, Black, and Asian populations living in the United States. Here, using 16S ribosomal RNA sequencing, we examine the bacterial ecology of supragingival plaque from four quadrants of the mouth along with a tongue swab from 26 healthy volunteers from South Florida (131 total sequences after filtering). As an area known to be a unique amalgamation of diverse cultures from across the globe, South Florida allows us to address the question of how supragingival plaque microbes differ across ethnic groups, thus potentially impacting treatment regiments related to oral issues. We assess overall phylogenetic abundance, alpha and beta diversity, and linear discriminate analysis of participants based on sex, ethnicity, sampling location in the mouth, and gingival health. Within this cohort, we find the presence of common phyla such as Firmicutes and common genera such as Streptococcus. Additionally, we find significant differences across sampling locations, sex, and gingival health. This research stresses the need for the continued incorporation of diverse populations within human oral microbiome studies.

A new discovery of cryptic species in barred sand burrower Limnichthys fasciatus (Pisces: Creediidae) from the western Pacific, with evolutionary perspectives of anti-equatorial species.

Although the barred sand burrower, Limnichthys fasciatus, is widely distributed throughout the western Pacific, including Japan, Taiwan, and Australia, its morphology and genetics are poorly known. We discovered four cryptic species of Limnichthys from the western Pacific based on mtDNA cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (rRNA) sequences. Genetic distances showed remarkably large differences (12.7%-24.3% in COI and 7.9%-19.6% in 16S rRNA) between true L. fasciatus (type locality: southeastern Australia) and the others. A relaxed clock model with optimized selected substitution models showed that their deep divergence began in the middle Miocene epoch and subsequently diverged into the current cryptic species in the Plio-Pleistocene. A eurythermal common ancestor may have evolved independently in each region due to geographical events and paleoclimatic fluctuations, which made it possible for L. fasciatus complex to be an anti-equatorial species. Despite their deep genetic divergence, they showed marked phenotypic similarity, suggesting that they have experienced similar selective pressures related to their specific behavior.

Investigating the efficacy of acupuncture in treating patients with metabolic-associated fatty liver disease: a protocol for a randomised controlled clinical trial

IntroductionAcupuncture is widely used for metabolic-associated fatty liver disease (MAFLD) treatment; however, the clinical efficacy has not been confirmed due to the lack of high-level evidence-based clinical practice. The purpose...

Dietary inositol supplementation improves meat quality by modulating amino acid metabolism and gut microbiota composition of finishing pigs

Intramuscular fat (IMF) content influences various meat quality traits, including tenderness, flavor, juiciness and nutritional value. This study aimed to investigate the effects of dietary inositol supplementation on meat quality, metabolic profiles, and gut microbiota composition of finishing pigs. A total of 144 finishing pigs (initial body weight 70.41 ± 0.78 kg) were randomly divided into control, 0.075%, 0.15%, and 0.3% inositol groups. The data showed that inositol increased backfat thickness at the 6th to 7th rib and 10th rib, IMF content, and improved tenderness (P ≤ 0.05, n = 8). Paralleling an increase in fat deposition, 0.3% inositol also increased the protein level of PPARγ in the subcutaneous fat (P ≤ 0.05) and longissimus thoracis (LT) muscle (P = 0.062). Inositol elevated the content of amino acids in LT muscle and enhanced amino acid metabolism of finishing pigs, including lysine degradation, tyrosine metabolism, and arginine and proline metabolism. The 16S ribosomal RNA (rRNA) sequencing showed that 0.3% inositol supplementation altered the profiles of microbes in the colon, particularly decreasing the abundance of Firmicutes (P < 0.01) and increasing the abundance of Bacteroidota (P ≤ 0.05). Correlation analysis showed that differential microbes had strong correlation with differential metabolites in serum, including amino acids. In conclusion, this study demonstrated that dietary inositol supplementation could effectively improve IMF content and tenderness of pork, enhance amino acid metabolism, and regulate gut microbiota composition of finishing pigs.

Molecular investigation of Blastocystis in children and calves in Bangladesh

BackgroundBlastocystis, a widely distributed zoonotic protozoan infecting both humans and numerous animals, remains poorly understood with its potential medical and veterinary significance. This study examined the molecular occurrence and genetic variation of Blastocystis in children and calves in Bangladesh to explore cross-species transmission and disease burden.MethodsIn total, 998 DNA samples were investigated, comprising 299 stool DNA from children and 699 fecal DNA from calves, using polymerase chain reaction and sequencing of the small subunit ribosomal RNA (SSU rRNA) gene.ResultsThis study detected Blastocystis in 5.35% of the children and 14.74% of the calves. While slight variations in occurrence rates were observed across different study variables, none were statistically significant. The occurrence was highest among children under 5 years and calves aged 1–3 months. Regarding breed, the Holstein Friesian cross and the Jersey cross exhibited higher rates of infection. Conversely, occurrences were lower among children and calves in Gazipur district. The remaining parameters displayed nearly equivalent percentages of Blastocystis. The subtypes identified in children included ST1, ST3, and ST4, with ST1 comprising 50% of them. ST3 and ST4 were also found in calves, alongside ST10 (55.34%) being the most prevalent. Other subtypes found in calves were ST14, ST21, and ST24–ST26.ConclusionsThis study found that Blastocystis is more common in calves than in children in Bangladesh, with genetic diversity of nine subtypes. The common occurrence of identical variants of two subtypes in both populations suggests potential zoonotic transmission, highlighting the necessity for further molecular investigations and comprehensive measures within the One Health framework to mitigate public health risks.

Viromics reveals two novel viruses of the family Closteroviridae in Codiaeum variegatum plant with leaf variegation symptoms.

Codiaeum variegatum is a valuable ornamental plant with distinct bright yellowing and golden spots on dark green leaves, which resemble virus symptoms. To investigate the factors, especially viral agents, associated with the variegated leaf color of Codiaeum variegatum, we performed virome profiling of a single C. variegatum 'Gold Dust' leaf sample collected from Hainan, China using ribosomal RNA-depleted total RNA sequencing on an Illumina NovaSeq 6000 platform. Two novel viruses, with two variants each, belonging to the family Closteroviridae were detected and characterized: Croton golden spot-associated virus C variants 1 and 2 (CGSaVC-v1, and CGSaVC-v2) of the genus Crinivirus and Croton golden spot-associated virus A variants 1 and 2 (CGSaVA-v1 and CGSaVA-v2) of the genus Ampelovirus. Transmission electron microscopy showed long, flexuous, filamentous virus particles approximately 15 nm in diameter and 760-770 nm in length. Molecular screening of ninety-seven variegated individual plant leaves showed a high prevalence of CGSaVA-v1 (90.7%), CGSaVA-v2 (75.3 %), CGSaVC-v1 (70.1%), and CGSaVC-v2 (47.4%), while asymptomatic leaves near the meristem tip were mostly free of the target viruses. To our knowledge, this is the first study to demonstrate the significant association between closterovirids and the golden spots. The findings provide novel insights into the genetic diversity of the family Closteroviridae and inform future germplasm conservation and new cultivar development of Codiaeum Variegatum.

A dual ribosomal system in the zebrafish soma and germline.

Protein synthesis during vertebrate embryogenesis is driven by ribosomes of two distinct origins: maternal ribosomes synthesized during oogenesis and stored in the egg, and somatic ribosomes, produced by the developing embryo after zygotic genome activation (ZGA). In zebrafish, these two ribosome types are expressed from different genomic loci and also differ in their ribosomal RNA (rRNA) sequence. To characterize this dual ribosome system further, we examined the expression patterns of maternal and somatic rRNAs during embryogenesis and in adult tissues. We found that maternal rRNAs are not only expressed during oogenesis but are continuously produced in the zebrafish germline. Proteomic analyses of maternal and somatic ribosomes unveiled differences in core ribosomal protein composition. Most nucleotide differences between maternal and somatic rRNAs are located in the flexible, structurally not resolved expansion segments. Our in vivo data demonstrated that both maternal and somatic ribosomes can be translationally active in the embryo. Using transgenically tagged maternal or somatic ribosome subunits, we experimentally confirm the presence of hybrid 80S ribosomes composed of 40S and 60S subunits from both origins and demonstrate the preferential in vivo association of maternal ribosomes with germline-specific transcripts. Our study identifies a distinct type of ribosomes in the zebrafish germline and thus presents a foundation for future explorations into possible regulatory mechanisms and functional roles of heterogeneous ribosomes.

Effects of Compound Probiotics on Pharmacokinetics of Cytochrome 450 Probe Drugs in Rats.

Compound probiotics have been widely used and commonly coadministered with other drugs for treating various chronic illnesses, yet their effects on drug pharmacokinetics remain underexplored. This study elucidated the impact of VSL#3 on the metabolism of probe drugs for cytochrome P450 enzymes (P450s), specifically omeprazole, tolbutamide, midazolam, metoprolol, phenacetin, and chlorzoxazone. Male Wistar rats were administered drinking water containing VSL#3 or not for 14 days and then intragastrically administered a P450 probe cocktail; this was done to investigate the host P450's metabolic phenotype. Stool, liver/jejunum, and serum samples were collected for 16S ribosomal RNA sequencing, RNA sequencing, and bile acid profiling. The results indicated significant differences in both α and β diversity of intestinal microbial composition between the probiotic and vehicle groups in rats. In the probiotic group, the bioavailability of omeprazole increased by 269.9%, whereas those of tolbutamide and chlorpropamide decreased by 28.1% and 27.4%, respectively. The liver and jejunum exhibited 1417 and 4004 differentially expressed genes, respectively, between the two groups. In the probiotic group, most of P450 genes were upregulated in the liver but downregulated in the jejunum. The expression of genes encoding metabolic enzymes and drug transporters also changed. The serum-conjugated bile acids in the probiotic group were significantly reduced. Shorter duodenal villi and longer ileal villi were found in the probiotic group. In summary, VSL#3 administration altered the gut microbiota, host drug-processing gene expression, and intestinal structure in rats, which could be reasons for pharmacokinetic changes. SIGNIFICANCE STATEMENT: This study focused on the effects of the probiotic VSL#3 on the pharmacokinetic profile of cytochrome P450 probe drugs and the expression of host drug metabolism genes. Compared with previous studies, the present study provides a comprehensive explanation for the host drug metabolism profile modified by probiotics, combined here with the bile acid profile and histopathological analysis.

Probiotics‐Loaded Selenium Nanoparticles Effectively Alleviated DSS‐Induced Colitis by Scavenging ROS and Remodeling Intestinal Innate Immune and Microbiota

AbstractAlterations in the intestinal microenvironment, including increased levels of reactive oxygen species (ROS), abnormalities in intestinal mucosal immune regulation, and dysbiosis of the intestinal microbiota, are crucial to the development of inflammatory bowel disease (IBD). Herein, an oral colon‐targeting Se‐Probiotic@Alginate bead (BLSe) with ROS‐scavenging ability and gut immune‐microbiota microenvironment remodeling ability is developed using alginate as the primary outer shell encapsulated with probiotics Bacillus licheniformis (BL) and selenium nanoparticles stabilized by yeast glucan (SeNPs). In vitro studies have shown that SeNPs possess antioxidant activity and BLSe exhibits excellent stability in gastric fluids and are released in intestinal fluids. In vivo studies have also shown that BLSe significantly alleviated dextran sulphate sodium (DSS)‐induced colitis in mice by inhibiting colon shortening, enhancing antioxidant activity, reducing pro‐inflammatory cytokine secretion, and protecting the intestinal mucosal barrier. 16S ribosomal RNA sequencing shows that BLSe can remodel the composition of the gut microbiota by improving bacterial diversity and restoring the relative abundance of beneficial bacteria in the colon. Overall, this study advances a promising probiotic‐based nanomedicine for managing IBD.

CO2 protects cells from iron-Fenton oxidative DNA damage in E. coli and humans.

Whereas hydroxyl radical is commonly named as the Fenton product responsible for DNA and RNA damage in cells, here we demonstrate that the cellular reaction generates carbonate radical anion due to physiological levels of bicarbonate. Analysis of the metabolome, transcriptome and, in human cells, the nuclear genome shows a consistent buffering of H2O2-induced oxidative stress leading to one common pathway, namely guanine oxidation. Particularly revealing are nanopore-based studies of direct RNA sequencing of cytosolic and mitochondrial ribosomal RNA along with glycosylase-dependent qPCR studies of oxidative DNA damage in telomeres. The focusing of oxidative modification on one pathway is consistent with the highly evolved base excision repair suite of enzymes and their involvement in gene regulation in response to oxidative stress.

Description of Bacterial RNA Transcripts Detected in Mycobacterium tuberculosis - Infected Cells from Peripheral Human Granulomas using Single Cell RNA Sequencing.

Mycobacterium tuberculosis (Mtb) remains a global human health threat and a significant cause of human morbidity and mortality. We document here the capture of Mtb transcripts in libraries designed to amplify eukaryotic mRNA. These reads are often considered spurious or nuisance and are rarely investigated. Because of early literature suggesting the possible presence of polyadenylated transcripts in Mtb RNA, we included the H37Rv Mtb reference genome when assembling scRNA seq libraries from fine needle aspirate samples from patients presenting at the TB clinic, Port Moresby General Hospital, Papua New Guinea. We used 10X Genomics single-cell RNA sequencing transcriptomics pipeline, which initiates mRNA amplification with poly-T primers on ~30-micron beads designed to capture, in this case, human mRNA associated with individual cells in the clinical samples. Utilizing the 10X Genomics Cell Ranger tool to align sequencing reads, we consistently detected bacterial small and large ribosomal subunit RNA sequences (rrs and rrl, respectively) and other bacterial gene transcripts in the cell culture and patient samples. We interpret Mtb reads associated with the host cell's unique molecular identifier (UMI) and transcriptome to indicate infection of that individual host cell. The Mtb transcripts detected showed frequent sequence variation from the reference genome, with greater than 90% of the rrs or rrl reads from many clinical samples having at least 1 sequence difference compared to the H37Rv reference genome. The data presented includes only bacterial sequences from patients with TB infections that were confirmed by the hospital pathology lab using acid-fast microscopy and/or GeneXpert analysis. The repeated, non-random nature of the sequence variations detected in Mtb rrs and rrl transcripts from multiple patients, suggests that, even though this appears to be a stochastic process, there is possibly some selective pressure that limits the types and locations of sequence variation allowed. The variation does not appear to be entirely artefactual, and it is hypothesized that it could represent an additional mechanism of adaptation to enhance bacterial fitness against host defenses or chemotherapy.

Treatment response of venlafaxine induced alterations of gut microbiota and metabolites in a mouse model of depression.

Antidepressants remain the first-line treatment for depression. However, the factors influencing medication response are still unclear. Accumulating evidence implicates an association between alterations in gut microbiota and antidepressant response. Therefore, the aim of this study is to investigate the role of the gut microbiota-brain axis in the treatment response of venlafaxine. After chronic social defeat stress and venlafaxine treatment, mice were divided into responders and non-responders groups. We compared the composition of gut microbiota using 16S ribosomal RNA sequencing. Meanwhile, we quantified metabolomic alterations in serum and hippocampus, as well as hippocampal neurotransmitter levels using liquid chromatography-mass spectrometry. We found that the abundances of 29 amplicon sequence variants (ASVs) were significantly altered between the responders and non-responders groups. These ASVs belonged to 8 different families, particularly Muribaculaceae. Additionally, we identified 38 and 39 differential metabolites in serum and hippocampus between the responders and non-responders groups, respectively. Lipid, amino acid, and purine metabolisms were enriched in both serum and hippocampus. In hippocampus, the concentrations of tryptophan, phenylalanine, gamma-aminobutyric acid, glutamic acid, and glutamine were increased, while the level of succinic acid was decreased in the responders group, compared with the non-responders group. Our findings suggest that the gut microbiota may play a role in the antidepressant effect of venlafaxine by modulating metabolic processes in the central and peripheral tissues. This provides a novel microbial and metabolic framework for understanding the impact of the gut microbiota-brain axis on antidepressant response.