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Nursing ResearchNurse researchers are well poised to study the connection of the microbiome to health and disease. Evaluating published microbiome results can assist with study design...
BACKGROUND
Nurse researchers are well poised to study the connection of the microbiome to health and disease. Evaluating published microbiome results can assist with study design and hypothesis generation.
OBJECTIVES
This article aims to present and define important analysis considerations in microbiome study planning and to identify genera shared across studies despite methodological differences. This methods article will highlight a workflow that the nurse scientist can use to combine and evaluate taxonomy tables for microbiome study or research proposal planning.
METHODS
We compiled taxonomy tables from 13 published gut microbiome studies that had used Ion Torrent sequencing technology. We searched for studies that had amplified multiple hypervariable (V) regions of the 16S rRNA gene when sequencing the bacteria from healthy gut samples.
RESULTS
We obtained 15 taxonomy tables from the 13 studies, comprised of samples from four continents and eight V regions. Methodology among studies was highly variable, including differences in V regions amplified, geographic location, and population demographics. Nevertheless, of the 354 total genera identified from the 15 data sets, 25 were shared in all V regions and the four continents. When relative abundance differences across the V regions were compared, Dorea and Roseburia were statistically different. Taxonomy tables from Asian subjects had increased average abundances of Prevotella and lowered abundances of Bacteroides compared with the European, North American, and South American study subjects.
DISCUSSION
Evaluating taxonomy tables from previously published literature is essential for study planning. The genera found from different V regions and continents highlight geography and V region as important variables to consider in microbiome study design. The 25 shared genera across the various studies may represent genera commonly found in healthy gut microbiomes. Understanding the factors that may affect the results from a variety of microbiome studies will allow nurse scientists to plan research proposals in an informed manner. This work presents a valuable framework for future cross-study comparisons conducted across the globe.
Topics: Classification; Gastrointestinal Microbiome; Global Health; High-Throughput Nucleotide Sequencing; Humans; Sequence Analysis, DNA
PubMed: 34985847
DOI: 10.1097/NNR.0000000000000557 -
International Journal of Molecular... Jan 2023Dystonia is a movement disorder in which patients have involuntary abnormal movements or postures. Non-motor symptoms, such as psychiatric symptoms, sleep problems and...
Dystonia is a movement disorder in which patients have involuntary abnormal movements or postures. Non-motor symptoms, such as psychiatric symptoms, sleep problems and fatigue, are common. We hypothesise that the gut microbiome might play a role in the pathophysiology of the (non-)motor symptoms in dystonia via the gut-brain axis. This exploratory study investigates the composition of the gut microbiome in dystonia patients compared to healthy controls. Furthermore, the abundance of neuro-active metabolic pathways, which might be implicated in the (non-)motor symptoms, was investigated. We performed both metagenomic and 16S rRNA sequencing on the stool samples of three subtypes of dystonia (27 cervical dystonia, 20 dopa-responsive dystonia and 24 myoclonus-dystonia patients) and 25 controls. While microbiome alpha and beta diversity was not different between dystonia patients and controls, dystonia patients had higher abundances of and , and a lower abundance of compared to controls. For those with dystonia, non-motor symptoms and the levels of neurotransmitters in plasma explained the variance in the gut microbiome composition. Several neuro-active metabolic pathways, especially tryptophan degradation, were less abundant in the dystonia patients compared to controls. This suggest that the gut-brain axis might be involved in the pathophysiology of dystonia. Further studies are necessary to confirm our preliminary findings.
Topics: Humans; Dystonia; Gastrointestinal Microbiome; RNA, Ribosomal, 16S; Mental Disorders; Dystonic Disorders; Dyskinesias
PubMed: 36768705
DOI: 10.3390/ijms24032383 -
Clinical Nutrition Research Jul 2021Recently several studies have attempted to investigate the association between vitamin D and microbiota. However, studies have reported inconsistent results. This... (Review)
Review
Recently several studies have attempted to investigate the association between vitamin D and microbiota. However, studies have reported inconsistent results. This narrative review aimed to investigate the potential association between vitamin D and microbiota population in the gut by pooling together the results from observational studies and clinical trials. We considered animal and human studies in this field. Several studies have shown the correlation of vitamin D deficiency with microbiota. Furthermore, interventional studies were emerging that vitamin D change the microbiota composition in which leads to an increase in beneficial bacteria, such as , , , and while decreases in . Vitamin D could change the microbiota toward decreasing in and increasing in . At genera level, vitamin D may connect to some genera of family (e.g., , , , and ). It seems that adequate level of vitamin D is an important factor in improving the composition of the gut microbiota. More studies are needed to confirm possible underling mechanisms.
PubMed: 34386438
DOI: 10.7762/cnr.2021.10.3.181 -
Digestion 2023Fluoropyrimidines (FPs) are key drugs in many chemotherapy regimens; however, recipients are often prone to diarrhea due to gastrointestinal toxicity. Disruption of the... (Observational Study)
Observational Study
BACKGROUND AND AIM
Fluoropyrimidines (FPs) are key drugs in many chemotherapy regimens; however, recipients are often prone to diarrhea due to gastrointestinal toxicity. Disruption of the intestinal epithelial barrier function by FPs leads to dysbiosis, which may exacerbate intestinal epithelial cell damage as a secondary effect and trigger diarrhea. However, despite studies on chemotherapy-induced changes in the intestinal microbiome of humans, the relationship between dysbiosis and diarrhea is unclear. In this study, we aimed to investigate the relationship between chemotherapy-induced diarrhea and the intestinal microbiome.
METHODS
We conducted a single-center prospective observational study. Twenty-three patients who received chemotherapy, including FPs as first-line chemotherapy for colorectal cancer, were included. Stool samples were collected before the start of chemotherapy and after one cycle of treatment to analyze intestinal microbiome composition and perform PICRUSt predictive metagenomic analysis.
RESULTS
Gastrointestinal toxicity was observed in 7 of 23 patients (30.4%), diarrhea was observed in 4 (17.4%), and nausea and anorexia were observed in 3 (13.0%). In 19 patients treated with oral FPs, the α diversity of the microbial community decreased significantly following chemotherapy only in the diarrheal group. At the phylum level, the diarrheal group showed a significant decrease in the abundance of Firmicutes and a significant increase in the abundance of Bacteroidetes with chemotherapy (p = 0.013 and 0.011, respectively). In the same groups, at the genus level, Bifidobacterium abundance was significantly decreased (p = 0.019). In contrast, in the non-diarrheal group, Actinobacteria abundance increased significantly with chemotherapy at the phylum level (p = 0.011). Further, Bifidobacterium, Fusicatenibacter, and Dorea abundance significantly increased at the genus level (p = 0.006, 0.019, and 0.011, respectively). The PICRUSt predictive metagenomic analysis revealed that chemotherapy caused significant differences in membrane transport in KEGG pathway level 2 and in 8 KEGG pathway level 3, including transporters and oxidative phosphorylation in the diarrhea group.
CONCLUSION
Organic-acid-producing bacteria seem to be involved in diarrhea associated with chemotherapy, including FPs.
Topics: Humans; Gastrointestinal Microbiome; Dysbiosis; Diarrhea; Bacteria; Antineoplastic Agents; RNA, Ribosomal, 16S
PubMed: 37231829
DOI: 10.1159/000528282 -
Nutrients Feb 2023Roux-en-Y Gastric bypass (RYGB) promotes improvement in type 2 diabetes (T2D) shortly after surgery, with metabolic mechanisms yet to be elucidated. This study aimed to...
Roux-en-Y Gastric bypass (RYGB) promotes improvement in type 2 diabetes (T2D) shortly after surgery, with metabolic mechanisms yet to be elucidated. This study aimed to investigate the relationship between food intake, tryptophan metabolism, and gut microbiota on the glycemic control of obese T2D women after RYGB surgery. Twenty T2D women who underwent RYGB were evaluated before and three months after surgery. Food intake data were obtained by a seven-day food record and a food frequency questionnaire. Tryptophan metabolites were determined by untargeted metabolomic analysis, and the gut microbiota was determined by 16S rRNA sequencing. The glycemic outcomes were fasting blood glucose, HbA1C, HOMA-IR, and HOMA-beta. Linear regression models were applied to assess the associations between the changes in food intake, tryptophan metabolism, and gut microbiota on glycemic control after RYGB. All variables changed after RYGB ( < 0.05), except for tryptophan intake. Jointly, the variation in red meat intake, plasma indole-3-acetate, and was associated with postoperative HOMA-IR {R 0.80, R adj 0.74; < 0.01}. Red meat intake decreased three months after bariatric surgery while indole-3-acetate and increased in the same period. These combined variables were associated with better insulin resistance in T2D women after RYGB.
Topics: Humans; Female; Gastric Bypass; Insulin Resistance; Diabetes Mellitus, Type 2; RNA, Ribosomal, 16S; Tryptophan; Red Meat; Acetates; Indoles; Blood Glucose; Insulin; Obesity, Morbid
PubMed: 36904185
DOI: 10.3390/nu15051185 -
Microorganisms Sep 2023Depression is a leading cause of disease worldwide. The association between gut microbiota and depression has barely been investigated in the Japanese population. We...
Depression is a leading cause of disease worldwide. The association between gut microbiota and depression has barely been investigated in the Japanese population. We analyzed Iwaki health check-up data collected from 2017 to 2019 and constructed generalized linear mixed models. The independent variable was the relative abundance of each of the 37 gut microbiota genera that were reported to be associated with depression. The dependent variable was the presence of depression assessed by the Center for Epidemiologic Studies Depression Scale. Potential confounders, including grip strength, gender, height, weight, smoking, and drinking habits, were adjusted in the regression models. Nine genera's regression coefficients (, , , , , , , , and ) showed statistical significance after multiple comparisons adjustment. Among these nine gut bacteria genera, , , , , , and were reported to be associated with butyrate production in the intestine. Our results indicate that gut microbiotas may influence the depression condition of the host via the butyrate-producing process.
PubMed: 37764129
DOI: 10.3390/microorganisms11092286 -
Frontiers in Microbiology 2023Recent studies have suggested that the composition of gut microbiota (GM) may change after intracerebral hemorrhage. However, the causal inference of GM and hemorrhagic...
BACKGROUND
Recent studies have suggested that the composition of gut microbiota (GM) may change after intracerebral hemorrhage. However, the causal inference of GM and hemorrhagic stroke is unknown. Mendelian Randomization (MR) is an effective research method that removes confounding factors and investigates the causal relationship between exposure and outcome. This study intends to explore the causal relationship between GM and hemorrhagic stroke with the help of MR.
METHODS
Univariable and multivariable MR analyses were performed using summary statistics of the GM ( = 18,340) in the MiBioGen consortium vs. the FinnGen consortium R9 summary statistics (intracerebral hemorrhage, subarachnoid hemorrhage, and nontraumatic intracranial hemorrhage). Causal associations between gut microbiota and hemorrhagic stroke were analyzed using inverse variance weighted, MR-Egger regression, weighted median, weighted mode, simple mode, and MR-PRESSO. Cochran's statistic, MR-Egger regression, and leave-one-out analysis were used to test for multiplicity and heterogeneity of instrumental variables. Separate reverse MR analyses were performed for microbiota found to be causally associated with hemorrhagic stroke in the forward MR analysis. Also, multivariate MR analyses were conducted after incorporating common confounders.
RESULTS
Based on the results of univariable and multivariate MR analyses, (OR, 0.80; 95%CI, 0.66-0.97; = 0.025) had a protective effect against hemorrhagic stroke, while (OR, 0.81; 95%CI, 0.67-0.99; = 0.039) had a potential protective effect. Furthermore, (OR, 1.77; 95%CI, 1.27-2.46; = 0.001), (OR, 1.24; 95%CI, 1.05-1.48; = 0.013) and (OR, 1.28; 95%CI, 1.01-1.62; = 0.041) acted as potential risk factors for hemorrhagic stroke. The abundance of (β, 0.05; 95%CI, 0.002 ~ 0.101; = 0.041) may increase, and that of (β, -0.072; 95%CI, -0.137 ~ -0.007; = 0.030) decreased after hemorrhagic stroke according to the results of reverse MR analysis. No significant pleiotropy or heterogeneity was detected in any of the MR analyses.
CONCLUSION
There is a significant causal relationship between GM and hemorrhagic stroke. The prevention, monitoring, and treatment of hemorrhagic stroke through GM represent a promising avenue and contribute to a deeper understanding of the mechanisms underlying hemorrhagic stroke.
PubMed: 38188561
DOI: 10.3389/fmicb.2023.1290909 -
Nutrients Jul 2023Western diet (WD) intake, aging, and inactivation of farnesoid X receptor (FXR) are risk factors for metabolic and chronic inflammation-related health issues ranging...
Western diet (WD) intake, aging, and inactivation of farnesoid X receptor (FXR) are risk factors for metabolic and chronic inflammation-related health issues ranging from metabolic dysfunction-associated steatotic liver disease (MASLD) to dementia. The progression of MASLD can be escalated when those risks are combined. Inactivation of FXR, the receptor for bile acid (BA), is cancer prone in both humans and mice. The current study used multi-omics including hepatic transcripts, liver, serum, and urine metabolites, hepatic BAs, as well as gut microbiota from mouse models to classify those risks using machine learning. A linear support vector machine with -fold cross-validation was used for classification and feature selection. We have identified that increased urine sucrose alone achieved 91% accuracy in predicting WD intake. Hepatic lithocholic acid and serum pyruvate had 100% and 95% accuracy, respectively, to classify age. Urine metabolites (decreased creatinine and taurine as well as increased succinate) or increased gut bacteria (, , and ) could predict FXR deactivation with greater than 90% accuracy. Human disease relevance is partly revealed using the metabolite-disease interaction network. Transcriptomics data were also compared with the human liver disease datasets. WD-reduced hepatic (cytochrome P450 family 39 subfamily a member 1) and increased (GRAM domain containing 1B) were also changed in human liver cancer and metabolic liver disease, respectively. Together, our data contribute to the identification of noninvasive biomarkers within the gut-liver axis to predict metabolic status.
Topics: Mice; Humans; Animals; Liver; Fatty Liver; Liver Neoplasms; Inflammation; Biomarkers; Bile Acids and Salts; Mice, Inbred C57BL
PubMed: 37571345
DOI: 10.3390/nu15153406 -
Frontiers in Microbiology 2024The objective of this study is to investigate the causal relationship between gut microbiota and juvenile idiopathic arthritis, and to identify and quantify the...
OBJECTIVE
The objective of this study is to investigate the causal relationship between gut microbiota and juvenile idiopathic arthritis, and to identify and quantify the potential role of plasma metabolites as mediators.
METHODS
Using summary-level data from genome-wide association studies, a two-sample Mendelian randomization was conducted involving 131 gut microbiota genus, 1,400 plasma metabolites, and juvenile idiopathic arthritis. Additionally, a two-step approach was employed to quantify the proportion of the effect of gut microbiota on juvenile idiopathic arthritis mediated by plasma metabolites. Effect estimation primarily utilized Inverse Variance Weighting, with further validation using Bayesian weighted Mendelian randomization.
RESULTS
In our MR analysis, a positive correlation was observed between and the risk of juvenile idiopathic arthritis, while showed a negative correlation with juvenile idiopathic arthritis risk. Mediation analysis indicated that Furaneol sulfate levels acted as a mediator between and juvenile idiopathic arthritis, with an indirect effect proportion of 19.94, 95% CI [8.86-31.03%].
CONCLUSION
Our study confirms a causal relationship between specific microbial genus and juvenile idiopathic arthritis, and computes the proportion of the effect mediated by plasma metabolites, offering novel insights for clinical interventions in juvenile idiopathic arthritis.
PubMed: 38605717
DOI: 10.3389/fmicb.2024.1363776 -
Journal of Microbiology and... Dec 2023Biochemical gut metabolism of dietary bioactive compounds is of great significance in elucidating health-related issues at the molecular level. In this study, a human...
Biochemical gut metabolism of dietary bioactive compounds is of great significance in elucidating health-related issues at the molecular level. In this study, a human gut bacterium cleaving C-C glycosidic bond was screened from puerarin conversion to daidzein, and a new, gram-positive -glycoside-deglycosylating strain, sp. MRG-IFC3, was isolated from human fecal sample under anaerobic conditions. Though MRG-IFC3 biotransformed isoflavone -glycoside, it could not metabolize other -glycosides, such as vitexin, bergenin, and aloin. As evident from the production of the corresponding aglycons from various 7--glucosides, MRG-IFC3 strain also showed 7--glycoside cleavage activity; however, flavone 3--glucoside icariside II was not metabolized. In addition, for mechanism study, -glycosyl bond cleavage of puerarin by MRG-IFC3 strain was performed in DO GAM medium. The complete deuterium enrichment on C-8 position of daidzein was confirmed by H NMR spectroscopy, and the result clearly proved for the first time that daidzein is produced from puerarin. Two possible reaction intermediates, the quinoids and 8-dehydrodaidzein anion, were proposed for the production of daidzein-8d. These results will provide the basis for the mechanism study of stable -glycosidic bond cleavage at the molecular level.
Topics: Humans; Bacteria; Glycosides; Isoflavones; Glucosides; Feces
PubMed: 37789701
DOI: 10.4014/jmb.2308.08021