Bacterial 16S rRNA Sequencing Research Articles

Effect of intestinal microbiota on duck short-beak and dwarf syndrome caused by novel goose parvovirus

Short-beak and dwarf syndrome (SBDS) is caused by infection with novel goose parvovirus (NGPV), which leads to intestinal dysbiosis, developmental delay, short beak, lameness, and paralysis in ducks and is the cause of skeletal health problems. NGPV infection can cause intestinal microbial disturbances, but it is still unclear whether the intestinal microbiota affects the pathogenicity of NGPV. Here, the effects of intestinal microbiota on NGPV-induced SBDS in Cherry Valley ducks were assessed by establishing a duck model for gut microflora depletion/reestablishment through antibiotics (ABX) treatment/fecal microbiota transplanted (FMT). By measuring body weight, beak length, beak width and tarsal length, we found that SBDS clinical symptoms were alleviated in ducks treated with ABX, but not in FMT ducks. Next, we conducted a comprehensive analysis of bone metabolism, gut barrier integrity, and inflammation levels using quantitative real-time PCR (qPCR), enzyme linked immunosorbent assay (ELISA), biochemical analysis and histological analysis. The results showed that ABX treatment improved bone quality reduced bone resorption, mitigated tissue lesions, protected intestinal barrier integrity, and inhibited systemic inflammation in NGPV-infected ducks. Moreover, cecal microflora composition and short-chain fatty acids (SCFAs) production were examined by bacterial 16S rRNA sequencing and gas chromatography. The results revealed that ABX treatment mitigated the decreased abundance of Firmicutes and Bacteroidota in NGPV-infected ducks, as well as increased SCFAs production. Furthermore, ABX treatment reduced the mucosa-associated lymphoid tissue lymphoma translocation protein 1 (Malt1) and nuclear factor κB (NF-κB) expression, which are correlated with systemic inflammation in SBDS ducks. These findings suggested that intestinal microflora depletion alleviated NGPV-induced SBDS by maintaining intestinal homeostasis, inhibiting inflammatory response and alleviating bone resorption. These results provide evidence for the pivotal role of intestinal microbiota in the process of SBDS and contribute a theoretical basis for the feasibility of microecological preparation as a method to control SBDS.

Probiotic Compounds Enhanced Recovery after Surgery for Patients with Distal Gastric Cancer: A Prospective, Controlled Clinical Trial.

Enhanced recovery after surgery (ERAS) for radical distal gastrectomy needs to be improved urgently. We investigated the effects of probiotic compounds (including Lactobacillus plantarum, L. rhamnosus, L. acidophilus, and Bifidobacterium animalis subsp.lactis) on enhance recovery after gastrectomy. The patients in this prospective study were divided into probiotic group (PG group, n = 36) and placebo group (CG group, n = 38), taking corresponding capsule according to the protocol during the perioperative period. We compared the trends in perioperative hematologic findings and the postoperative outcomes. Patients' feces were collected for bacterial 16S rRNA sequencing. Patients were followed up at 1 month postoperatively. After the application of probiotics, the patients' postoperative inflammatory response level was reduced, and the trend of postoperative NLR decrease was significantly faster in the patients of the PG group than in the CG group (P = 0.047, partial η2 = 0.054). The trend of postoperative increase in serum albumin concentration in the patients of the PG group was significantly better than that in the CG group (P = 0.016, partial η2 = 0.078). In addition, patients in the PG group met discharge criteria earlier postoperatively and had fewer medical expenses. The quality of life of PG group was improved postoperatively. Postoperative inflammation-related markers, including the ratio of Firmicutes/Bacteroidetes, were increasing in untreated patients. In addition, the postoperative microbial diversity and abundance in the PG group remained stable. Probiotic compounds can reduce the inflammatory response after gastrectomy and enhance the recovery of the DGC patients by maintaining the stability of the gut microbiota.

Discovery of Bacterial Key Genes from 16S rRNA-Seq Profiles That Are Associated with the Complications of SARS-CoV-2 Infections and Provide Therapeutic Indications.

SARS-CoV-2 infections, commonly referred to as COVID-19, remain a critical risk to both human life and global economies. Particularly, COVID-19 patients with weak immunity may suffer from different complications due to the bacterial co-infections/super-infections/secondary infections. Therefore, different variants of alternative antibacterial therapeutic agents are required to inhibit those infection-causing drug-resistant pathogenic bacteria. This study attempted to explore these bacterial pathogens and their inhibitors by using integrated statistical and bioinformatics approaches. By analyzing bacterial 16S rRNA sequence profiles, at first, we detected five bacterial genera and taxa (Bacteroides, Parabacteroides, Prevotella Clostridium, Atopobium, and Peptostreptococcus) based on differentially abundant bacteria between SARS-CoV-2 infection and control samples that are significantly enriched in 23 metabolic pathways. A total of 183 bacterial genes were found in the enriched pathways. Then, the top-ranked 10 bacterial genes (accB, ftsB, glyQ, hldD, lpxC, lptD, mlaA, ppsA, ppc, and tamB) were selected as the pathogenic bacterial key genes (bKGs) by their protein-protein interaction (PPI) network analysis. Then, we detected bKG-guided top-ranked eight drug molecules (Bemcentinib, Ledipasvir, Velpatasvir, Tirilazad, Acetyldigitoxin, Entreatinib, Digitoxin, and Elbasvir) by molecular docking. Finally, the binding stability of the top-ranked three drug molecules (Bemcentinib, Ledipasvir, and Velpatasvir) against three receptors (hldD, mlaA, and lptD) was investigated by computing their binding free energies with molecular dynamic (MD) simulation-based MM-PBSA techniques, respectively, and was found to be stable. Therefore, the findings of this study could be useful resources for developing a proper treatment plan against bacterial co-/super-/secondary-infection in SARS-CoV-2 infections.

Oral administration of Manuka honey induces IFNγ-dependent resistance to tumor growth that correlates with beneficial modulation of gut microbiota composition.

To investigate the potential of Manuka honey (MH) as an immunomodulatory agent in colorectal cancer (CRC) and dissect the underlying molecular and cellular mechanisms. MH was administered orally over a 4 week-period. The effect of MH treatment on microbiota composition was studied using 16S rRNA sequencing of fecal pellets collected before and after treatment. Pretreated mice were implanted with CRC cells and followed for tumor growth. Tumors and lymphoid organs were analyzed by flow cytometry (FACS), immunohistochemistry and qRT-PCR. Efficacy of MH was also assessed in a therapeutic setting, with oral treatment initiated after tumor implantation. We utilized IFNγ-deficient mice to determine the importance of interferon signaling in MH-induced immunomodulation. Pretreatment with MH enhanced anti-tumor responses leading to suppression of tumor growth. Evidence for enhanced tumor immunogenicity included upregulated MHC class-II on intratumoral macrophages, enhanced MHC class-I expression on tumor cells and increased infiltration of effector T cells into the tumor microenvironment. Importantly, oral MH was also effective in retarding tumor growth when given therapeutically. Transcriptomic analysis of tumor tissue highlighted changes in the expression of various chemokines and inflammatory cytokines that drive the observed changes in tumor immunogenicity. The immunomodulatory capacity of MH was abrogated in IFNγ-deficient mice. Finally, bacterial 16S rRNA sequencing demonstrated that oral MH treatment induced unique changes in gut microbiota that may well underlie the IFN-dependent enhancement in tumor immunogenicity. Our findings highlight the immunostimulatory properties of MH and demonstrate its potential utilization in cancer prevention and treatment.

Detailed Characterization of the Lung-Gut Microbiome Axis Reveals the Link between PD-L1 and the Microbiome in Non-Small-Cell Lung Cancer Patients.

Next-generation sequencing technologies have started a new era of respiratory tract research in recent years. Alterations in the respiratory microbiome between healthy and malignant conditions have been revealed. However, the composition of the microbiome varies among studies, even in similar medical conditions. Also, there is a lack of complete knowledge about lung-gut microbiome interactions in lung cancer patients. The aim of this study was to explore the lung-gut axis in non-small-cell lung cancer (NSCLC) patients and the associations between lung-gut axis microbiota and clinical parameters (CRP, NLR, LPS, CD8, and PD-L1). Lung tissue and fecal samples were used for bacterial 16S rRNA sequencing. The results revealed, for the first time, that the bacterial richness in lung tumor tissue gradually decreased with an increase in the level of PD-L1 expression (p < 0.05). An analysis of β-diversity indicated a significant positive correlation between the genera Romboutsia and Alistipes in both the lung tumor biopsies and stool samples from NSCLC patients (p < 0.05). Survival analysis showed that NSCLC patients with higher bacterial richness in their stool samples had prolonged overall survival (HR: 2.06, 95% CI: 1.025-4.17, p = 0.0426).

The recovery of intestinal barrier function and changes in oral microbiota after radiation therapy injury.

Colorectal cancer (CRC) is the third most common malignant tumor, and neoadjuvant chemo-radiotherapy is usually recommended for advanced stage colorectal cancer. Radiotherapy can cause damage to intestinal mucosal barrier, which may be related to perioperative complications. Intestinal microbiota is one of the constituents of the intestinal mucosal biological barrier, and literature reports that patients with CRC have changes in corresponding oral microbiota. This study aims to analyze the levels of immunoglobulin SIgA, inflammatory factors, lymphocyte subsets quantity, and proportion in surgical specimens of intestinal mucosa at different time intervals after radiotherapy, in order to seek investigation for the optimal surgical time after radiotherapy and to provide evidence for finding probiotics or immunomodulators through high-throughput sequencing of bacterial 16s rRNA in patients' saliva microbiota. Ultimately, this may provide new ideas for reducing perioperative complications caused by radiotherapy-induced intestinal damage. We selected intestinal mucosal tissue and saliva samples from over 40 patients in our center who did not undergo radiotherapy and underwent surgery at different time intervals after radiotherapy. Detection of SIgA was performed using ELISA assay. Western Blotting was used to detect IL-1β, IL-6, and IL-17 in the intestinal mucosal tissue. Flow cytometry was used to detect CD4 and CD8. And the microbial community changes in saliva samples were detected through 16s rRNA sequencing. After radiotherapy, changes in SIgA, various cytokines, CD4CD8 lymphocyte subsets, and oral microbiota in the intestinal mucosal tissue of rectal cancer patients may occur. Over time, this change may gradually recover. In colorectal cancer, oncological aspects often receive more attention, while studies focusing on the intestinal mucosal barrier are less common. This study aims to understand the repair mechanisms of the intestinal mucosal barrier and reduce complications arising from radiotherapy-induced damage. The relationship between oral microbiota and systemic diseases has gained interest in recent years. However, the literature on the oral microbiota after radiotherapy for rectal cancer remains scarce. This study addresses this gap by analysing changes in the salivary microbiota of rectal cancer patients before and after radiotherapy, shedding light on microbiota changes. It aims to lay the groundwork for identifying suitable probiotics or immunomodulators to alleviate perioperative complications and improve the prognosis of CRC.

Detection of Staphylococcus Isolates and Their Antimicrobial Resistance Profiles and Virulence Genes from Subclinical Mastitis Cattle Milk Using MALDI-TOF MS, PCR and Sequencing in Free State Province, South Africa.

Staphylococcus species are amongst the bacteria that cause bovine mastitis worldwide, whereby they produce a wide range of protein toxins, virulence factors, and antimicrobial-resistant properties which are enhancing the pathogenicity of these organisms. This study aimed to detect Staphylococcus spp. from the milk of cattle with subclinical mastitis using MALDI-TOF MS and 16S rRNA PCR as well as screening for antimicrobial resistance (AMR) and virulence genes. Our results uncovered that from 166 sampled cows, only 33.13% had subclinical mastitis after initial screening, while the quarter-level prevalence was 54%. Of the 50 cultured bacterial isolates, MALDI-TOF MS and 16S rRNA PCR assay and sequencing identified S. aureus as the dominant bacteria by 76%. Furthermore, an AMR susceptibility test showed that 86% of the isolates were resistant to penicillin, followed by ciprofloxacin (80%) and cefoxitin (52%). Antimicrobial resistance and virulence genes showed that 16% of the isolates carried the mecA gene, while 52% of the isolates carried the Lg G-binding region gene, followed by coa (42%), spa (40%), hla (38%), and hlb (38%), whereas sea and bap genes were detected in 10% and 2% of the isolates, respectively. The occurrence of virulence factors and antimicrobial resistance profiles highlights the need for appropriate strategies to control the spread of these pathogens.

Seasonal dynamics of gut microbiome: A study of multi-kingdom microbiota of earthworm gut in an urban park

Earthworms play an important role in maintaining terrestrial ecosystem function. In urban areas, earthworms mainly inhabit parks where they function through feeding and excretion of soil elements and nutrient turnover. Seasonal diet strongly alters the earthworm gut microbiome and thus affects this ecological process, but the seasonal variation of eukaryotes is still poorly described. In this study, we obtained earthworm samples from three seasons: summer, autumn and winter, assessing the gut microbiome of earthworms using bacterial 16S rRNA and eukaryotic 18S rRNA gene amplicon sequencing techniques. We identified biomarkers that significantly change with seasons and analyzed eukaryotic-bacterial interactions under seasonal variation through inter-kingdom networks. The results of this study showed that season significantly influenced the diversity of earthworm gut bacterial community, while the diversity of eukaryotic community was relatively stable. Inter-kingdom molecular ecological network analysis revealed high degree of positive or negative interactions between fungi and bacteria, protists and bacteria, and fungi and protists as keystone taxonomies divided the network into several modules. In summary, the gut eukaryotic community is more stable than the bacterial community throughout the seasons, and it has shown to maintain season-long homeostasis in the earthworm gut.

Transfusion‐dependent thalassemia patients develop cognitive impairment with gut dysbiosis

AbstractBackgroundThalassemia is an auto‐recessive hemoglobinopathy affecting populations worldwide. Although life expectancy of thalassemia patients has been increasing due to therapeutic advancements, neurocognitive complications have been continuously reported among transfusion‐dependent thalassemia (TDT). Interestingly, the relationships among cognitive decline, systemic iron burden, and gut microbial alterations in TDT patients remain to be determined.MethodTwenty‐eight participants, including 14 TDT patients and 14 heathy controls, were recruited to evaluate a cognitive function using the Mental State Examination T10 (MSET10) test. Serum ferritin was employed to reflect a severity of systemic iron burden. Stool was collected to determine a gut microbial profile using a next‐generation sequencing of bacterial 16s rRNA V3‐V4 regions.ResultTDT patients had the cognitive impairment, higher systemic iron burden, and gut dysbiosis when compared with the controls. TDT patients also had lower MSET10 scores than the controls (Figure 1A). In addition, an increase in serum ferritin was observed in the TDT, indicating that there was the iron burden in the TDT (Figure 1B). Moreover, gut dysbiosis in TDT patients as indicated by higher bacterial diversity and different microbial compositions in comparison with the controls were observed (Figure 1C and 1D). The MSET10 scores were negatively correlated with the levels of serum ferritin and gut microbial diversity (Figure 1E and 1F). Interestingly, the levels of serum ferritin were positively correlated with the gut microbial diversity (Figure 1G).ConclusionThese findings suggest that a systemic iron burden may involve in an alteration of gut microbiota, and the systemic iron burden together with the gut dysbiosis may concurrently deteriorate a cognitive function in TDT patients. Therefore, an iron reduction with a gut microbial manipulation, such as a combined usage of an iron chelator with a probiotic supplement, should provide benefits to prevent neurodegeneration as well as gut microbial disturbance in TDT patients.

Comprehensive sampling of the lung microbiome in early-stage non–small cell lung cancer

ObjectivesData are scarce on whether the composition of the lung microbiome (extending from the nasopharynx to the peripheral lung tissue) varies according to histology or grade of non–small cell lung cancer. We hypothesized that the composition of the lung microbiome would vary according to the histology and the grade of non–small cell lung cancer. MethodsWe collected naso-oral and central lobar (cancer affected, ipsilateral unaffected, and contralateral unaffected) bronchoalveolar lavage fluid and brushing samples from patients with clinical early-stage lung cancer between July 2018 and February 2020 at a single academic center. We performed bacterial 16S rRNA sequencing and then compared clinical and pathologic findings with microbiome signatures. ResultsSamples were collected from 28 patients. Microbial composition in affected lobes displayed unique enrichment of oropharyngeal bacterial species that was significantly different compared with that from the unaffected contralateral lobes; patients with chronic obstructive pulmonary disease had similar diversity to those without chronic obstructive pulmonary disease (P = .1312). The lung microbiome diversity in patients with adenocarcinoma was similar to those with squamous cell cancer (P = .27). There were no differences in diversity or composition in the unaffected lobes of patients with adenocarcinoma versus squamous cell cancer. There was a trend toward lower lung microbial diversity in poorly differentiated adenocarcinomas compared with well-differentiated adenocarcinomas (P = .08). ConclusionsThe lung microbiota differs between cancer affected and unaffected lobes in the same patient. Furthermore, poorly differentiated lung cancers were associated with lower microbial diversity. Larger studies will be required to confirm these findings.

Effects of multiple N, P, and K fertilizer combinations on strawberry growth and the microbial community.

Nitrogen (N), phosphorus (P), and potassium (K) exert various effects on strawberry (Fragaria ananassa Duchesne) yields. In this study, we employed an orthogonal experimental design (T1-T9) with three fertilization treatments (N, P, and K) at three levels to identify an optimal fertilization scheme for strawberry cultivation. The effects of fertilizer combinations the rhizosphere soil microbial community were also explored by using bacterial full-length 16S rRNA and fungal ITS (internal transcribed spacer) sequencing (30 samples for each analysis). The results showed that the average plant height and leaf area of the fertilized groups were 24.6% and 41.6% higher than those of the non-fertilized group (T0). After 60 d of planting, the sucrase activity in the T6 group increased by 76.67% compared to the T0 group, with phosphate fertilizer exerting a more significant impact on sucrase activity. The T6 treatment group had the highest alpha diversity index among bacterial and fungal microorganisms, and had a different microbial community structure compared with the control group. The most abundant bacterial taxa in the strawberry rhizosphere soil were Proteobacteria, Bacteroidota, and Acidobacteriota, and the most abundant fungal phyla were Monoblepharomycota, Glomeromycota, and Mucoromycota. Application of the optimal combined fertilizer treatment (T6) significantly increased the abundance of Proteobacteria and altered the abundance of Gemmatimonas compared to other treatment groups. Notably, Gemmatimonas abundance positively correlated with strawberry plant height and soil N, P, and K levels. These findings indicated that the relative abundance of beneficial bacteria could be enhanced by the application of an optimal fertilizer ratio, ultimately improving strawberry agronomic traits.

Solitary Bees Host More Bacteria and Fungi on Their Cuticle than Social Bees.

Bees come into contact with bacteria and fungi from flowering plants during their foraging trips. The Western honeybee (Apis mellifera) shows a pronounced hygienic behavior with social interactions, while the solitary red mason bee (Osmia bicornis) lacks a social immune system. Since both visit the same floral resources, it is intriguing to speculate that the body surface of a solitary bee should harbor a more complex microbiome than that of the social honeybee. We compared the cuticular microbiomes of A. mellifera (including three European subspecies) and O. bicornis for the first time by bacterial 16S rRNA and fungal ITS gene-based high-throughput amplicon sequencing. The cuticular microbiome of the solitary O. bicornis was significantly more complex than that of the social A. mellifera. The microbiome composition of A. mellifera subspecies was very similar. However, we counted significantly different numbers of fungi and a higher diversity in the honeybee subspecies adapted to warmer climates. Our results suggest that the cuticular microbiome of bees is strongly affected by visited plants, lifestyle and adaptation to temperature, which have important implications for the maintenance of the health of bees under conditions of global change.

Biogeochemical characterization of four depleted gas reservoirs for conversion into underground hydrogen storage.

Depleted gas reservoirs are a valuable option for underground hydrogen storage (UHS). However, different classes of microorganisms, which are capable of using free H2 as a reducing agent for their metabolism, inhabit deep underground formations and can potentially affect the storage. This study integrates metagenomics based on Illumina-NGS sequencing of bacterial and archaeal 16S rRNA and dsrB and mcrA functional genes to unveil the composition and the variability of indigenous microbial populations of four Italian depleted reservoirs. The obtained mcrA sequences allow us to implement the existing taxonomic database for mcrA gene sequences with newly classified sequences obtained from the Italian gas reservoirs. Moreover, the KEGG and COG predictive functional annotation was used to highlight the metabolic pathways potentially associated with hydrogenotrophic metabolisms. The analyses revealed the specificity of each reservoir microbial community, and taxonomic and functional data highlighted the presence of an enriched number of taxa, whose activity depends on both reservoir hydrochemical composition and nutrient availability, of potential relevance in the context of UHS. This study is the very first to address the profiling of the microbial population and allowed us to perform a preliminary assessment of UHS feasibility in Italy.

О микробиоме глазной поверхности

The latest molecular biology methods, in particular, bacterial 16S rRNA sequencing, makes it possible to reveal the diversity of the ocular surface microbiota and expand the list of the most common types identified by cultural methods. Most metagenomic sequencing results confirm that Corynebacterium, Propionibacterium, and Staphylococcus are dominant on the healthy ocular surface. However, the obtained data point to differences in the microbial spectrum among people. Factors explaining this variability are currently unknown, in particular, to what extent it is related to people and their environment, and to what extent they are artificial, i.e. brought in from outside. Describing the microorganisms on the ocular surface is not easy due to the possible risk of bacterial contamination. More research is needed, including better experimental studies, to avoid bias in the study of the role of the ocular surface microbiome in relation to healthy and pathological conditions. In particular, the study of strain heterogeneity, overlaps, taxonomic composition and functional profile of the healthy eye surface microbiome are important for drug development, especially those based on probiotics, for the treatment of eye diseases. Key words: ocular surface of a healthy person, ocular microbiome, ocular microbiota, microbial flora, cultural method, identification by the 16S rRNA marker gene, metagenomic sequencing

SAT046 Canagliflozin Leads To Less Weight Gain, Confers Changes In The Gut Microbiota And Extends Life Span In Male C57BL6 Mice

Abstract Disclosure: E.E. Habeos: None. F. Filippopoulou: None. M. Kanakis: None. G.I. Habeos: None. N. Belmokhtar: None. P. Stathopoulou: None. G. Tsiamis: None. S. Taraviras: None. G. Lagoumintzis: None. D.V. Chartoumpekis: None. Introduction: SGLT2 inhibitors (SGLT2i) are widely prescribed drugs for the treatment of diabetes. Their beneficial health effects appear to be pleiotropic and are not limited to the amelioration of glycemic profile. The SGLT2i-induced glycosuria is suggested to provoke a metabolic shift that mimics the fasting response. Since calorie restriction has been shown to enhance longevity in mice, we hypothesized that treating mice with SGLT2i would also increase their life span. Methods: To this end, 4-months old male C57BL6 mice were fed with a standard chow diet (Control, n=83) or a diet supplemented with 200 mg/kg canagliflozin (Cana, n=92) and were observed up to the natural end of their life. Results: The canagliflozin-treated mice gained less weight over time. For instance, at the age of 10 months, the body weight of control mice was higher (means ± SEM: 33.1 ± 0.26 g) than the body weight of their canagliflozin-treated counterparts (means ± SEM: 31.4± 0.21 g; p&amp;lt;0.01). The development and severity of age-related cataracts were also examined at the age of 14 months, but no statistically significant difference was found in the severity score between the 2 groups. The survival curves of the control and the Cana mice diverged significantly, with the median survival of the control being 107.5 weeks versus 112.5 weeks of the Cana group (p=0.011). As the gut microbiome is known to change with age and be associated with the development of age-related diseases, feces were collected from 17-month-old mice (n=10 per group) and analysis of fecal bacterial 16S rRNA sequences was performed. Differences in beta diversity (diversity of bacterial species across samples) and relative abundance of bacterial species were noted between the Control and the Cana groups. Conclusions-Discussion: Our study highlights the effect of SGLT2i on longevity in a widely used mouse model (C57BL6). The underlying mechanisms leading to the enhancement of longevity are not clear yet. Some microbiota changes associated with the SGLT2i treatment, as described in other mouse models with enhanced longevity, warrant further investigation and analysis. It would be useful to extend these studies employing various SGLT2i with different potencies and selectivity against SGLT so as to determine if the observed effect on longevity is independent of the type of the drug. Presentation: Saturday, June 17, 2023

Impact of Elevational Gradients and Chemical Parameters on Changes in Soil Bacterial Diversity Under Semiarid Mountain Region.

Elevation gradients, often regarded as "natural experiments or laboratories", can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We obtained bacterial sequences using MiSeq sequencing and clustered them into operational taxonomic units (OTUs). The total number of reads obtained by the bacterial 16S rRNA sequencing analysis was 1,090,555, with an average of approximately 45,439 reads per sample collected from various elevations. The current study observed inconsistent bacterial diversity patterns in samples from the lowest to highest elevations. 983 OTUs were found common among all the elevations. The most unique OTUs were found in the soil sample from elevation_2, followed by elevation_1. Soil sample collected at elevation_6 had the least unique OTUs. Actinobacteria, Protobacteria, Chloroflexi were found most abundant bacterial phyla in current study. Ammonium nitrogen (NH4+-N), and total phosphate (TP) are the main factors influencing bacterial diversity at elevations_1. pH was the main factor influencing the bacterial diversity at elevations_2, elevation_3 and elevation_4. Our results provide new visions on forming and maintaining soil microbial diversity along an elevational gradient and have implications for microbial responses to environmental change in semiarid mountain ecosystems.

Skin Microbiome Composition is Associated with Radiation Dermatitis in Breast Cancer Patients Undergoing Radiation after Reconstructive Surgery: A Prospective, Longitudinal Study

Approximately 95% of breast cancer (BC) patients receiving radiotherapy (RT) develop varying degrees of radiation dermatitis (RD), which can greatly affect the patient's quality of life and aesthetics. Severe acute RD can lead to interruption or delay of RT. Currently, there is no consensus on the prevention and management of RD. The skin microbiota (SM), which are mainly composed of bacteria and fungi, are essential for skin homeostasis and microbial dysbiosis is correlated with the onset and progression of many common skin diseases. However, to date, research on the role of the SM in RD remains scarce. This prospective, longitudinal study aims to analyze the association of SM with RD. We collected 200 SM samples both before and after RT from the region in the irradiated chest wall of 100 BC patients receiving RT after reconstructive surgery and samples from the corresponding region in the contralateral breast for bacterial 16S and fungal ITS (internal transcribed spacer) rRNA sequencing. Acute RD was graded according to the Toxicity Criteria of the Radiation Therapy Oncology Group (RTOG). Patients were divided into no or mild dermatitis (N/MD, RTOG grade 0 or 1) and severe dermatitis (SD, RTOG grade 2 and above). The compositional differences across groups were compared using STAMP and high-dimensional class comparisons by linear discriminant analysis of effect size (LEfSe). Differences in metabolic function between groups were predicted by the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) method. Significant differences were observed in the diversity and composition of the SM between N/MD and SD both before and after RT. Analysis of bacterial 16S sequencing (n = 89, 63 N/MD, 26 SD) showed significantly higher relative abundance of particular taxa such as Ralstonia, Truepera, Methyloversatilis genera and lower abundance of particular taxa including Staphylococcus, Corynebacterium genera in N/MD patients. Besides, analysis of fungal ITS sequencing (n = 71, 53 N/MD, 18 SD) showed significantly higher relative abundance of particular taxa such as Hypocreaceae family and lower abundance of particular taxa such as Sporidiobolus genus in N/MD patients. Pathways including fatty acid synthesis were predicted to be enriched in N/MD patients. The SM and pathway markers were identified in this study to be associated with the severity of acute RD in BC patients undergoing RT after reconstructive surgery. More patient data is needed to verify the current findings and the results of metagenomic, metatranscriptomic, and metabolomic analyses will further mine key biomarkers at the compositional and functional level.

Soil microbial biomass and community structure in response to agricultural use of deserts across northern China

Although desert reclamation efforts have been used for increased crop production, their impacts on the structure of soil microbial communities remain largely understudied. Here, six adjacent pairs of different native desert and newly reclaimed cropland soils across a 3300 km transect in northern China were selected to address how microbial biomass, community composition, biogeographic pattern and the relative importance of ecological processes responded to agricultural reclamation using qPCR and high-throughput amplicon sequencing of bacterial 16S rRNA and fungal ITS genes. Agricultural intensification generally increased bacterial and fungal biomasses compared to undisturbed desert soils, while most microbial α-diversities were not significantly changed across these sampling sites. The relative abundances of some dominant microbial phyla and families significantly changed in response to agricultural intensification, which was site-dependent. Bacterial and fungal communities showed similar biogeographic patterns predominantly dominated by community turnover rather than nestedness for both desert and cropland soils, while agricultural intensification made bacterial community compositions more dissimilar. Deterministic process and stochastic process dominated bacterial and fungal community assembly in both desert and cropland soils, respectively. Agricultural intensification slightly reduced the relative importance of deterministic process for bacterial community assembly, while it conversely increased the relative importance of deterministic process to fungal community assembly by shifting the contributions of different assembly components. These results suggest that short-term land-use transformation from native deserts to croplands impact desert soil microbial community structure by making bacterial community more stochastic and fungal community more deterministic.

Screening of Aptamers that Bind to the Multivalent Aminoglycoside Amikacin

Increased awareness of the multiple roles of RNA molecules has led to the realization that, in addition to their structural and functional roles, RNAs can be drug targets for small molecular therapy. Amikacin, a member of the aminoglycoside group of antibiotics, binds to specific sites in bacterial 16S ribosomal RNAs (rRNAs) and interferes with protein synthesis leading to cell death. Here, we used the systemic evolution of ligands by exponential enrichment (SELEX) method to isolate high affinity RNA fragments (aptamers) that bind to amikacin. After five rounds of SELEX selection, in which a linear N25 DNA template was used for the first selection cycle, the resulting RNA was cloned and sequenced. Among the 38 clones generated, five groups of sequences (groups A through E) containing nine conserved motifs were identified. The sequences of groups A and B were almost identical, indicating that the selected RNA was enriched. Subsequently, the Basic Local Alignment Search Tool program was used to search for the conserved motifs in bacterial 16S rRNA sequences. Strikingly, no sequence homology was observed, suggesting that the conserved sequences (motifs) identified in this studymay be novel target sites for amikacin. Bangladesh Pharmaceutical Journal 26(2): 134-143, 2023 (July)

Dithiotreitol and Next Generation Sequencing of Bacterial 16S rRNA Shows Similar Diagnostic Security as Periprosthetic Tissue Cultures to Diagnose PJI

Dithiotreitol and Next Generation Sequencing of Bacterial 16S rRNA Shows Similar Diagnostic Security as Periprosthetic Tissue Cultures to Diagnose PJI