scholarly journals Metataxonomic investigation of the microbial community in the trachea and oropharynx of healthy controls and diabetic patients using endotracheal tubes

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259596
Author(s):  
Sun Young Cho ◽  
Jeong-Hyun Choi ◽  
Seung Hyeun Lee ◽  
Yong-Sung Choi ◽  
Sung Wook Hwang ◽  
...  
Keyword(s):  
Endotracheal Tube ◽  
Amplicon Sequencing ◽  
Diabetic Patients ◽  
Healthy Controls ◽  
Additional Risk ◽  
Endotracheal Tubes ◽  
Operational Taxonomic Units ◽  
16S Amplicon Sequencing ◽  
Healthy Control ◽  
Respiratory Microbiota

Background Although the study of respiratory microbiota has been an active field of research, obtaining the appropriate respiratory samples for healthy controls remains to be a challenge. As such, this study aims to evaluate the use of endotracheal tube washing as a viable control for sputum samples. Methods A total of 14 subjects, including 8 healthy respiratory controls and 6 diabetic patients without any respiratory disease, were enrolled in this study, during which the endotracheal tubes used in their scheduled routine surgery were collected. Pre-operative oral gargles were also collected from non-diabetic subjects. Results 16S amplicon sequencing revealed similar taxa composition in endotracheal tube washings and oral gargles in the healthy control subjects, although the relative abundance of 11 genus level operational taxonomic units was significantly different between the two sample sources. The diabetic subjects showed relatively lower diversity than those of non-diabetic subjects. The proportion range of the most abundant taxa detected in each endotracheal tube washings were 10.1–33.2%. Conclusion Endotracheal tube washing fluid may provide healthy control samples for upper respiratory investigations without incurring any additional risk to the subject.

scholarly journals Sarcopenia in diabetic nephropathy: a cross-sectional study

2018 ◽  
Vol 56 (2) ◽  
pp. 102-108 ◽  
Author(s):  
Meral Çeliker ◽  
Mustafa Yavuz Selçuk ◽  
Serdar Olt
Keyword(s):  
Diabetic Nephropathy ◽  
Cross Sectional Study ◽  
Control Group ◽  
Diabetic Patients ◽  
Healthy Controls ◽  
Diabetes Group ◽  
Cross Sectional ◽  
Hand Grip ◽  
European Working ◽  
Healthy Control

Abstract Objective. To investigate the relationship between sarcopenia and diabetic nephropathy. Methods. 56 diabetic patients without complications, 50 diabetic patients with nephropathy, 53 healthy controls included in this present study. Demographic characteristics such as sex, age, anthropometric measurements such as weight, body mass index [BMI], hip circumference, waist circumference and upper arm circumference were measured. Sarcopenia diagnosis was based on European Working Group on Sarcopenia in Older People [EWGSOP] criteria which consist of hand grip strength, 6-meter walking test and muscle mass. Results. The frequency of sarcopenia increased gradually from 15.1% in healthy control group to 21.4% in the diabetes group, and 34% in diabetic nephropathy group (X2 for trend, p = 0.029). The frequency of sarcopenia was similar in diabetes and diabetic nephropathy group. However, the frequency of sarcopenia was higher in diabetic nephropathy than healthy controls (OR = 2.89, CI [1.11-7.51] in logistic regression). Conclusion: In the present study, the prevalence of sarcopenia was higher in patients with diabetic nephropathy compared to healthy controls.

scholarly journals Colorectal Cancer Stage-Specific Fecal Bacterial Community Fingerprinting of the Taiwanese Population and Underpinning of Potential Taxonomic Biomarkers

2021 ◽  
Vol 9 (8) ◽  
pp. 1548
Author(s):  
Chuan-Yin Fang ◽  
Jung-Sheng Chen ◽  
Bing-Mu Hsu ◽  
Bashir Hussain ◽  
Jagat Rathod ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Control Group ◽  
Healthy Controls ◽  
Genus Level ◽  
16S Rrna Amplicon Sequencing ◽  
Microbial Dysbiosis ◽  
Cancer Group ◽  
Healthy Control

Despite advances in the characterization of colorectal cancer (CRC), it still faces a poor prognosis. There is growing evidence that gut microbiota and their metabolites potentially contribute to the development of CRC. Thus, microbial dysbiosis and their metabolites associated with CRC, based on stool samples, may be used to advantage to provide an excellent opportunity to find possible biomarkers for the screening, early detection, prevention, and treatment of CRC. Using 16S rRNA amplicon sequencing coupled with statistical analysis, this study analyzed the cause–effect shift of the microbial taxa and their metabolites that was associated with the fecal gut microbiota of 17 healthy controls, 21 polyps patients, and 21 cancer patients. The microbial taxonomic shift analysis revealed striking differences among the healthy control, polyps and cancer groups. At the phylum level, Synergistetes was reduced significantly in the polyps group compared to the healthy control and cancer group. Additionally, at the genus level and in association with the cancer group, a total of 12 genera were highly enriched in abundance. In contrast, only Oscillosprira was significantly higher in abundance in the healthy control group. Comparisons of the polyps and cancer groups showed a total of 18 significantly enriched genera. Among them, 78% of the genera associated with the cancer group were in higher abundance, whereas the remaining genera showed a higher abundance in the polyps group. Additionally, the comparison of healthy control and polyp groups showed six significantly abundant genera. More than 66% of these genera showed a reduced abundance in the polyps group than in healthy controls, whereas the remaining genera were highly abundant in the polyps group. Based on tumor presence and absence, the abundance of Olsenella and Lactobacillus at the genus level was significantly reduced in the patient group compared to healthy controls. The significant microbial function prediction revealed an increase in the abundance of metabolites in the polyps and cancer groups compared to healthy controls. A correlation analysis revealed a higher contribution of Dorea in the predicted functions. This study showed dysbiosis of gut microbiota at the taxonomic level and their metabolic functions among healthy subjects and in two stages of colorectal cancer, including adenoma and adenocarcinoma, which might serve as potential biomarkers for the early diagnosis and treatment of CRC.

scholarly journals Accuracy of Age-Based Formula to Predict the Size and Depth of Cuffed Oral Preformed Endotracheal Tubes in Children Undergoing Tonsillectomy

2021 ◽  
pp. 014556132098051
Author(s):  
Matula Tareerath ◽  
Peerachatra Mangmeesri
Keyword(s):  
Body Mass Index ◽  
Endotracheal Tube ◽  
Body Mass ◽  
Normal Weight ◽  
Overweight And Obesity ◽  
The Body ◽  
Insertion Depth ◽  
Endotracheal Tubes ◽  
Endotracheal Tube Size ◽  
Actual Size

Objectives: To retrospectively investigate the reliability of the age-based formula, year/4 + 3.5 mm in predicting size and year/2 + 12 cm in predicting insertion depth of preformed endotracheal tubes in children and correlate these data with the body mass index. Patients and Methods: Patients were classified into 4 groups according to their nutritional status: thinness, normal weight, overweight, and obesity; we then retrospectively compared the actual size of endotracheal tube and insertion depth to the predicting age-based formula and to the respective bend-to-tip distance of the used preformed tubes. Results: Altogether, 300 patients were included. The actual endotracheal tube size corresponded with the Motoyama formula (64.7%, 90% CI: 60.0-69.1), except for thin patients, where the calculated size was too large (0.5 mm). The insertion depth could be predicted within the range of the bend-to-tip distance and age-based formula in 85.0% (90% CI: 81.3-88.0) of patients. Conclusion: Prediction of the size of cuffed preformed endotracheal tubes using the formula of Motoyama was accurate in most patients, except in thin patients (body mass index < −2 SD). The insertion depth of the tubes was mostly in the range of the age-based-formula to the bend-to-tip distance.

scholarly journals Risk of Typical Diabetes-Associated Complications in Different Clusters of Diabetic Patients: Analysis of Nine Risk Factors

2021 ◽  
Vol 11 (5) ◽  
pp. 328
Author(s):  
Michael Leutner ◽  
Nils Haug ◽  
Luise Bellach ◽  
Elma Dervic ◽  
Alexander Kautzky ◽  
...  
Keyword(s):  
Risk Factors ◽  
Liver Disease ◽  
Diabetic Patients ◽  
Complication Risk ◽  
Increased Risk ◽  
Icd 10 ◽  
Healthy Control ◽  
Design And Methods ◽  
The Relationship ◽  
Observation Period

Objectives: Diabetic patients are often diagnosed with several comorbidities. The aim of the present study was to investigate the relationship between different combinations of risk factors and complications in diabetic patients. Research design and methods: We used a longitudinal, population-wide dataset of patients with hospital diagnoses and identified all patients (n = 195,575) receiving a diagnosis of diabetes in the observation period from 2003–2014. We defined nine ICD-10-codes as risk factors and 16 ICD-10 codes as complications. Using a computational algorithm, cohort patients were assigned to clusters based on the risk factors they were diagnosed with. The clusters were defined so that the patients assigned to them developed similar complications. Complication risk was quantified in terms of relative risk (RR) compared with healthy control patients. Results: We identified five clusters associated with an increased risk of complications. A combined diagnosis of arterial hypertension (aHTN) and dyslipidemia was shared by all clusters and expressed a baseline of increased risk. Additional diagnosis of (1) smoking, (2) depression, (3) liver disease, or (4) obesity made up the other four clusters and further increased the risk of complications. Cluster 9 (aHTN, dyslipidemia and depression) represented diabetic patients at high risk of angina pectoris “AP” (RR: 7.35, CI: 6.74–8.01), kidney disease (RR: 3.18, CI: 3.04–3.32), polyneuropathy (RR: 4.80, CI: 4.23–5.45), and stroke (RR: 4.32, CI: 3.95–4.71), whereas cluster 10 (aHTN, dyslipidemia and smoking) identified patients with the highest risk of AP (RR: 10.10, CI: 9.28–10.98), atherosclerosis (RR: 4.07, CI: 3.84–4.31), and loss of extremities (RR: 4.21, CI: 1.5–11.84) compared to the controls. Conclusions: A comorbidity of aHTN and dyslipidemia was shown to be associated with diabetic complications across all risk-clusters. This effect was amplified by a combination with either depression, smoking, obesity, or non-specific liver disease.

scholarly journals SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tzipi Braun ◽  
Shiraz Halevi ◽  
Rotem Hadar ◽  
Gilate Efroni ◽  
Efrat Glick Saar ◽  
...  
Keyword(s):  
Clinical Microbiology ◽  
Amplicon Sequencing ◽  
Viral Disease ◽  
Nasopharyngeal Swab ◽  
Microbial Composition ◽  
16S Amplicon Sequencing ◽  
The World ◽  
Health And Disease ◽  
Longitudinal Sampling ◽  
Potential Interactions

AbstractThe coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.

scholarly journals Raised TSH is associated with endothelial dysfunction in Metabolic Syndrome: A case control study

2017 ◽  
Vol 55 (4) ◽  
pp. 212-221 ◽  
Author(s):  
Ashok Kumar Ahirwar ◽  
Archana Singh ◽  
Anju Jain ◽  
Surajeet Kumar Patra ◽  
Binita Goswami ◽  
...  
Keyword(s):  
Metabolic Syndrome ◽  
Endothelial Dysfunction ◽  
Subclinical Hypothyroidism ◽  
Serum Insulin ◽  
Binary Logistic Regression ◽  
Binary Logistic Regression Analysis ◽  
Healthy Controls ◽  
Healthy Control ◽  
Study Population ◽  
Serum Tsh

AbstractIntroduction. Endothelial dysfunction has been considered as one of the important factors in pathogenesis of Metabolic Syndrome (Met S). Subclinical hypothyroidism (SCH) has also been reported to be associated with Met S. The aim of our study is to evaluate the association of raised TSH with mediators of endothelial dysfunction in Met S with Subclinical hypothyroidism as compared to healthy controls.Methods. Study population consisted of 100 subjects, out of which 50 were cases of Met S and 50 were healthy controls. Met S group were further divided into two, based on the presence & absence of SCH. Serum insulin, T3, T4, TSH were measured by chemiluminescence based immunoassay (CLIA). Serum nitric oxide (NO) levels were measured by Modified Griess’s method and serum endothelin-1 (ET-1) levels were measured by ELISA.Results. Out of 50 cases of Met S, SCH was diagnosed in 22. The mean serum TSH levels were significantly higher in Met S cases as compared to healthy controls (5.7 ± 1.2 μIU/mL vs. 2.3 ± 1.6 μIU/mL, P <0.0001). Mean serum NO levels were significantly lower in Met S cases as compared to healthy control (15.4 ± 10 μM vs. 21 ± 10 μM, p = 0.009). Mean serum ET-1 levels were significantly higher in Met S cases as compared to healthy controls (2.68 ± 1.7 fmol/mL vs. 2.1 ± 0.84 fmol/mL, p = 0.011). On Pearson’s correlation analysis, TSH showed positive correlation with ET-1 (r = 0.341, p = 0.001) and negative correlation with NO (r = −0.331, p = 0.001). Binary logistic regression analysis showed that TSH, NO and ET-1 has significant odd’s ratio for predicting Met S.Conclusion. Met S cases were screened for thyroid abnormalities and found to have 44% of SCH along with co-existing endothelial dysfunction. Raised TSH in SCH could cause endothelial dysfunction which may lead to Met S and associated co-morbidities. Present study gives new insight in linking endothelial dysfunction and raised TSH in Met S. Therefore, Met S cases should be screened for SCH and treated appropriately to attenuate endothelial dysfunction and associated comorbidities in Met S.

scholarly journals Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 241-252
Author(s):  
Dyah Asri Handayani Taroepratjeka ◽  
Tsuyoshi Imai ◽  
Prapaipid Chairattanamanokorn ◽  
Alissara Reungsang
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
High Salinity ◽  
Amplicon Sequencing ◽  
Spatial Proximity ◽  
Lignocellulosic Waste ◽  
Evaporation Pond ◽  
Operational Taxonomic Units ◽  
Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

scholarly journals SAT0290 HIGH SERUM MYOSTATIN LEVELS SUGGEST ACCELERATED MUSCLE SENESCENCE IN ACTIVE IDIOPATHIC INFLAMMATORY MYOSITIS

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1089.2-1090
Author(s):  
A. Anuja ◽  
M. Singh ◽  
M. K. Rai ◽  
H. Singh ◽  
V. Agarwal ◽  
...  
Keyword(s):  
Young Adults ◽  
Elevated Serum ◽  
High Serum ◽  
Inactive Disease ◽  
Healthy Controls ◽  
Muscle Enzymes ◽  
Inflammatory Myositis ◽  
Idiopathic Inflammatory Myositis ◽  
Healthy Control ◽  
Accelerated Senescence

Background:Inflammation is the forerunner to fibrosis and premature ageing in various systemic diseases. Hence it seems plausible that idiopathic inflammatory myopathies (IIM) may exhibit accelerated senescence too.Objectives:Hence we investigated the Myostatin: Follistatin system in the serum as a reflection of early senescence in myositis as compared with healthy and diseased controls.Methods:Patients with inflammatory myositis (ACR/EULAR criteria) presenting to the wards and outpatient clinic between December 2017 to August 2019 were recruited. Those with active infection, pregnancy, renal dysfunction or chronic kidney disease were excluded. Apart from patient and disease variables, activity and damage were assessed using standard IMACS score set measures. Patients in inception cohort were additionally followed up at 1 and 6 months. Myostatin and Follistatin were estimated in sera using ELISA (R&D systems, USA). Juvenile myositis and young adults (18-40 years) were subsequently analyzed separately. Non-parametric tests were used for paired and unpaired analysis. Results expressed as median.Results:95 myositis (8 Juvenile myositis, 26 DM, 10 PM, 29 Overlap, 2 NAM 1 CAM and 19 ASS) patients (23 Male and 72 Female) with median age 38 (24.5-46.0) years and disease duration 0.9 (2.3-5.1) years were included. Serum Myostatin was lower in IIM than in healthy control (HC) (153.5 vs. 243.6 p<0.0001, Fig 1A) but higher in IIM as compared with disease controls (153.5 vs 86.1 p=0.0174 Fig. 1B). Serum myostatin was comparable between juvenile and adult myositis and in the various subsets of adult myositis (Fig. 1 C and D). Myostatin levels were higher in active as compared with inactive myositis in young adults (211.7 vs. 158.9, p=0.0149, Figure 1E). Serum Myostatin correlated with height (r 0.3, p=0.003) and weight (r 0.2, p=0.047) but not MMT8 or muscle enzymes.Figure 1.Serum Myostatin levels in IIM as compared with healthy controls (A) and disease controls (B). Levels in juvenile myositis as compared with adult IIM (C) and in various subsets of IIM (D). Serum Myostatin levels in active and inactive disease (E).Although Follistatin was lower in IIM than HC (198.4 vs 243.6, p=<0.0001), the neither Follistatin nor Myostatin: Follistatin ratios differ between subsets, and in active versus inactive disease Figure 2 A-D). On follow-up, the serial Myostatin estimation paralleled change in disease activity.Figure 2.Serum Follistatin levels in IIM as compared with healthy controls (A) and disease controls (C). Levels in juvenile and adult IIM (D) and in various subsets of IIM (D).Conclusion:Elevated serum Myostatin levels in active myositis raise the possibility of accelerated senescence in the inflamed muscle tissues which need further investigation.Acknowledgments: :Partly funded by APLAR and IRA research grants awarded to LG.Disclosure of Interests:None declared

scholarly journals Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gongchao Jing ◽  
Yufeng Zhang ◽  
Wenzhi Cui ◽  
Lu Liu ◽  
Jian Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Large Scale ◽  
Low Cost ◽  
Human Microbiome ◽  
Amplicon Sequencing ◽  
Training Sample ◽  
Rrna Gene ◽  
16S Amplicon Sequencing ◽  
Cross Platform ◽  
Functional Profiles

Abstract Background Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results. Results Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS. Conclusions This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.

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