Frontiers in Microbiology最新文献

The soybean mosaic disease-caused by the soybean mosaic virus (SMV)-significantly impacts soybean quality and yield. Among its various strains, SMV-SC7 is prevalent in China. Therefore, rapid and accurate diagnosis is deemed critical to mitigate the spread of SMV-SC7. In this study, a simple and rapid magnetic bead-based RNA extraction method was optimized. Furthermore, a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay that requires no specialized equipment such as PCR Amplifier was proposed, employing a lateral flow device (LFD) for visual interpretation of SMV-SC7. The RT-LAMP-LFD approach facilitated specificity testing of SMV-SC7. Moreover, the limit of detection (LOD) of this method was as low as 10^-5 ng (2.4 copies). The sensitivity of RT-LAMP-LFD was 10-fold higher than that of the colorimetric RT-LAMP method. In 194 field samples tested, the RT-LAMP-LFD detection of the SMV-SC7 had accuracy of 98.45% in comparison to RT-qPCR. In conclusion, the assay exhibited high specificity, sensitivity, and rapidity, enabling economical and portable detection of SMV-SC7 and providing technical support to identify SMV-SC7-infected soybeans.

Background: Periprosthetic joint infection (PJI) is a devastating complication following arthroplasty of the hip or knee joint and can be challenging to treat, depending on the underlying pathogen. There is still a debate whether streptococcal PJI are more difficult to treat than those caused by staphylococci. We aimed to investigate if the treatment results after PJI caused by Staphylococci aureus (S. aureus), Coagulase-negative Staphylococci spp. (CoNS) or Streptococci differ.

Patients and methods: This study was designed as a retrospective observational study on patients with PJI caused by either streptococci or staphylococci in the hip or knee treated at a tertiary referral center between 1998 and 2021. Patients were identified in the local PJI register and data were collected by medical chart review performed minimum 1 year after the index PJI. Patients with polymicrobial infections or incomplete data were excluded, leaving 299 patients with streptococcal or staphylococcal PJI for final analysis. These patients were categorized according to the underlying pathogen: 114 were S. aureus 121 were CoNS, and 64 Streptococci. Infection-free survival was defined as the absence of (1) further surgery to the index joint due to PJI, (2) suppressive antibiotic therapy, and (3) death due to PJI and was assessed using the Kaplan-Meier method. Cox regression models were fitted to estimate the risk of infection relapse adjusted for relevant confounders.

Results: We found no statistically or clinically significant difference in unadjusted survival between the three groups. Infection-free survival at 2 years was 71% (95%CI: 63-80) for S. aureus, 75% (95%CI: 67-84) for CoNS, and 60% (95%CI: 60-84) for Streptococci. The adjusted hazard ratios (HR) for the risk of infection relapse with S. aureus as the reference were 1.2 (95%CI: 0.7-2.0) for CoNS and 1.1 (95%CI: 0.6-2.0) for Streptococci. For all three groups of bacteria, survival was lower when DAIR was performed in comparison to exchange surgery.

Discussion: In our cohort, there was no difference in infection-free survival between the three groups. Albeit limitations due to the study design, it seems that streptococcal PJI do not have to be considered more difficult to treat than their staphylococcal counterparts. Exchange surgery shows favorable results in all groups compared to DAIR.

Aim: This study aims to comprehensively and systematically review the current status of research on probiotics and HIV/AIDS, while also exploring future research hotspots and trends in this domain.

Methods: The Web of Science (WoS) Core Collection database was queried up until May 13, 2024, to retrieve relevant literature on probiotics and HIV/AIDS. Utilizing CiteSpace, VOSviewers, and Bibliometrix software, scientific achievements and research frontiers in this field were analyzed.

Results: As of May 14, 2024, a total of 90 articles was included in. The publication output in this area peaked in 2017, with a subsequent decline in the number of articles post-2019. The United States emerged as the leading country in terms of article count (32 articles), with The University of Western Ontario being the institution with the highest publication output. Dr. Reid G contributed the most articles (12 articles). In addition to key terms, high-frequency keywords included immune activation, inflammation, and microbial translocation. The burst analysis of keywords suggests that vaccines may become a focal point of future research.

Conclusion: Future research hotspots and trends should focus on elucidating the types of probiotics, intervention timing, and optimal strains (in terms of mixing ratios) in the context of HIV/AIDS. Furthermore, exploration into the role of probiotic metabolites, such as short-chain fatty acids, in vaccine development is warranted.

Long COVID is an often-debilitating condition with severe, multisystem symptoms that can persist for weeks or months and increase the risk of various diseases. Currently, there is a lack of diagnostic tools for Long COVID in clinical practice. Therefore, this study utilizes plasma proteomics and metabolomics technologies to understand the molecular profile and pathophysiological mechanisms of Long COVID, providing clinical evidence for the development of potential biomarkers. This study included three age- and gender-matched cohorts: healthy controls (n = 18), COVID-19 recovered patients (n = 17), and Long COVID patients (n = 15). The proteomics results revealed significant differences in proteins between Long COVID-19 patients and COVID-19 recovered patients, with dysregulation mainly focused on pathways such as coagulation, platelets, complement cascade reactions, GPCR cell signal transduction, and substance transport, which can participate in regulating immune responses, inflammation, and tissue vascular repair. Metabolomics results showed that Long COVID patients and COVID-19 recovered patients have similar metabolic disorders, mainly involving dysregulation in lipid metabolites and fatty acid metabolism, such as glycerophospholipids, sphingolipid metabolism, and arachidonic acid metabolism processes. In summary, our study results indicate significant protein dysregulation and metabolic abnormalities in the plasma of Long COVID patients, leading to coagulation dysfunction, impaired energy metabolism, and chronic immune dysregulation, which are more pronounced than in COVID-19 recovered patients.

Soil microbial communities are vulnerable to anthropogenic disturbances such as climate change and land management decisions, thus altering microbially-mediated ecosystem functions. Increasingly, multiple stressors are considered in investigations of ecological response to disturbances. Typically, these investigations involve concurrent stressors. Less studied is how historical stressors shape the response of microbial communities to contemporary stressors. Here we investigate how historical exposure to antibiotics drives soil microbial response to subsequent temperature change. Specifically, grassland plots were treated with 32-months of manure additions from cows either administered an antibiotic or control manure from cows not treated with an antibiotic. In-situ antibiotic exposure initially increased soil respiration however this effect diminished over time. Following the 32-month field portion, a subsequent incubation experiment showed that historical antibiotic exposure caused an acclimation-like response to increasing temperature (i.e., lower microbial biomass at higher temperatures; lower respiration and mass-specific respiration at intermediate temperatures). This response was likely driven by a differential response in the microbial community of antibiotic exposed soils, or due to indirect interactions between manure and soil microbial communities, or a combination of these factors. Microbial communities exposed to antibiotics tended to be dominated by slower-growing, oligotrophic taxa at higher temperatures. Therefore, historical exposure to one stressor is likely to influence the microbial community to subsequent stressors. To predict the response of soils to future stress, particularly increasing soil temperatures, historical context is necessary.

Introduction: Irritable bowel syndrome (IBS) is a common chronic disorder of gastrointestinal function with a high prevalence worldwide. Due to its complex pathogenesis and heterogeneity, there is urrently no consensus in IBS research.

Methods: We collected and uniformly reanalyzed 1167 fecal 16S rRNA gene sequencing samples (623 from IBS patients and 544 from healthy subjects) from 9 studies. Using both a random effects (RE) model and a fixed effects (FE) model, we calculated the odds ratios for metrics including bacterial alpha diversity, beta diversity, common genera and pathways between the IBS and control groups.

Results: Significantly lower alpha-diversity indexes were observed in IBS patients by random effects model. Twenty-six bacterial genera and twelve predicted pathways were identified with significant odds ratios and classification potentials for IBS patients. Based on these feature, we used transfer learning to enhance the predictive capabilities of our model, which improved model performance by approximately 10%. Moreover, through correlation network analysis, we found that Ruminococcaceae and Christensenellaceae were negatively correlated with vitamin B6 metabolism, which was decreased in the patients with IBS. Ruminococcaceae was also negatively correlated with tyrosine metabolism, which was decreased in the patients with IBS.

Discussion: This study revealed the dysbiosis of fecal bacterial diversity, composition, and predicted pathways of patients with IBS by meta-analysis and identified universal biomarkers for IBS prediction and therapeutic targets.

Objective: This study aimed to explore the changes in gut microbiota and its metabolites in different pathophysiological stages of doxorubicin (DOX)-induced heart failure (DIHF) and the relationship between gut microbiota and metabolites in various degrees of DIHF.

Materials and methods: C57BL/6 J mice were injected intraperitoneally with 5 mg/kg of DOX once a week for 5 consecutive weeks. At different times after injection, the cardiac function and histopathological analysis was conducted, the serum levels of creatine kinase (CK), CK-MB, lactic dehydrogenase, and cardiac troponin T were determined. 16S rRNA gene sequencing of feces and the nontargeted metabolomics analysis of serum were performed. Multi-omics analyses were used to explore the correlation between gut microbiota and serum metabolites.

Results: The results showed that DOX caused cardiac contractile dysfunction and left ventricular (LV) dilation. The levels of myocardial enzymes significantly increase in 3 and 5 weeks after DOX injection. DOX-treated mice showed significant differences in the composition and abundance of gut microorganisms, and the levels of serum metabolites at different times of treatment. Multi-omics analyses showed that intestinal bacteria were significantly correlated with the differential metabolites. Some bacteria and metabolites can be used as biomarkers of DIHF (AUC > 0.8). KEGG analyses showed the involvement of different metabolic pathways in various degrees of DIHF.

Conclusion: Marked differences were found in the composition and abundance of gut microorganisms, the levels of serum metabolites and metabolic pathways in different degrees of DIHF. The intestinal bacteria were significantly correlated with differential metabolites in different degrees of DIHF. The gut microbiota may serve as new targets for the treatment of DIHF.

Background: Colorectal cancer (CRC) is among the top three causes of global cancer mortality. In Vietnam, CRC is the third leading cause of death in women and the fourth cause of cancer mortality in men. A large number of metagenomic studies have reported the relationship between altered composition and function of the gut microbiota with CRC, but this relationship in low- and middle-income countries including Vietnam (with an estimated population of 100.3 million people in 2023, ranking 16th largest country by population in the world) is not well-explored.

Methods: We collected clinical data and fecal samples from 43 CRC patients and 44 healthy control subjects. The total community DNA of microorganisms was extracted from the fecal samples and analyzed for microbiota composition using Illumina MiSeq amplicon sequencing targeting the V3-V4 region of the 16S rRNA gene.

Results: We identified a significant difference in the overall fecal microbiota composition between CRC patients and healthy controls, and we detected several CRC-associated microbial signatures in fecal samples of Vietnamese patients with CRC, which overlapped with signatures from other countries and meta-analyses. Although patients with (n = 8) and without (n = 35) type 2 diabetes (T2D) exhibited distinct gut microbiota composition compared to healthy controls, increased relative abundances of putatively pathogenic species including Parvimonas micra, Peptostreptococcus stomatis, and Prevotella intermedia were consistent biomarkers for CRC. In contrast, several health-associated species were significantly depleted in CRC patients such as Lactobacillus johnsonii and Bifidobacterium longum in CRC/non-T2D patients, Ruminococcus species, Bacteroides uniformis, and Phascolarctobacterium faecium in CRC/T2D patients, and Butyricicoccus pullicaecorum in both CRC groups combined.

Conclusion: Our findings confirm alterations in gut microbiota composition in CRC in a pilot Vietnamese cohort and highlight several gut microbial taxa that may have inhibitory or driver roles in CRC. This and future studies will enable the development of cancer diagnostics and treatment strategies for CRC in Vietnam, with a focus on targeting the microbiota.

Introduction: The development of a hepatitis E virus (HEV) vaccine is critical, with ORF2 capsid protein as the main target. We previously demonstrated that oral coadministration of recombinant ORF2 with immunomodulatory bacterium-like-particles (IBLP) induces a specific immune response in mice, particularly using IBLP derived from Lacticaseibacillus rhamnosus IBL027 (IBLP027), which was effective in eliciting a local humoral response. IBLP are non-live bacteria with adjuvant and carrier properties, serving as a platform for exposing proteins or antigens fused to LysM (lysine motif) domains, protein modules that bind to cell wall polysaccharides like peptidoglycan.

Materials: We cloned the most immunogenic domain of ORF2 (O2P2) fused to five LysM domains (LysM₅O2P2) and displayed this chimeric protein on the surface of IBLP027 to create a prototype vaccine (IBLP027-LysM₅O2P2). We evaluated its capacity to induce an immune response in vivo by immunizing mice with three doses of either the experimental vaccine or the chimeric protein alone, using an oral or a combined schedule with subcutaneous priming followed by oral boosting. Control groups received IBLP027. Sera and small intestine fluid were analyzed for humoral response, while Peyer's patches and spleen immune cells were used for ex vivo stimulation with capsid protein to assess cellular response.

Results: The oral scheme failed to elicit an IgG response, but this was overcome by a subcutaneous priming dose followed by oral boosters, which led to increasing IgG titers in the combined scheme. The highest IgG titers were seen in the vaccine prototype group. Most groups produced significantly higher IgA levels in intestinal fluid, especially in those that received the oral scheme. Cellular response studies showed increased tumor necrosis factor (TNF)-α, interferon (IFN)-γ interleukin (IL)-4, and IL-17 levels in groups receiving the chimeric protein via oral or combined schedules.

Conclusion: Further and continuous research is needed to better understand both the needs and expectations of students and supervisors in different academic realities, including in Veterinary Medicine schools, from which the information available on the subject is scarce.