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Translational Psychiatry Jan 2024The causal effects of gut microbiome and the development of posttraumatic stress disorder (PTSD) are still unknown. This study aimed to clarify their potential causal...
BACKGROUND
The causal effects of gut microbiome and the development of posttraumatic stress disorder (PTSD) are still unknown. This study aimed to clarify their potential causal association using mendelian randomization (MR).
METHODS
The summary-level statistics for gut microbiome were retrieved from a genome-wide association study (GWAS) of the MiBioGen consortium. As to PTSD, the Freeze 2 datasets were originated from the Psychiatric Genomics Consortium Posttraumatic Stress Disorder Working Group (PGC-PTSD), and the replicated datasets were obtained from FinnGen consortium. Single nucleotide polymorphisms meeting MR assumptions were selected as instrumental variables. The inverse variance weighting (IVW) method was employed as the main approach, supplemented by sensitivity analyses to evaluate potential pleiotropy and heterogeneity and ensure the robustness of the MR results. We also performed reverse MR analyses to explore PTSD's causal effects on the relative abundances of specific features of the gut microbiome.
RESULTS
In Freeze 2 datasets from PGC-PTSD, eight bacterial traits revealed a potential causal association between gut microbiome and PTSD (IVW, all P < 0.05). In addition, Genus.Dorea and genus.Sellimonas were replicated in FinnGen datasets, in which eight bacterial traits revealed a potential causal association between gut microbiome and the occurrence of PTSD. The heterogeneity and pleiotropy analyses further supported the robustness of the IVW findings, providing additional evidence for their reliability.
CONCLUSION
Our study provides the potential causal impact of gut microbiomes on the development of PTSD, shedding new light on the understanding of the dysfunctional gut-brain axis in this disorder. Our findings present novel evidence and call for investigations to confirm the association between their links, as well as to illuminate the underlying mechanisms.
Topics: Humans; Gastrointestinal Microbiome; Stress Disorders, Post-Traumatic; Genome-Wide Association Study; Reproducibility of Results; Dietary Supplements
PubMed: 38296956
DOI: 10.1038/s41398-024-02765-7 -
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 -
PloS One 2022This study analyzes and compares the structure and diversity of gut microbiota in patients with primary Sjögren's syndrome (pSS) in Northern China to healthy...
This study analyzes and compares the structure and diversity of gut microbiota in patients with primary Sjögren's syndrome (pSS) in Northern China to healthy individuals to identify clinical features associated with dysbiosis. We included 60 Chinese pSS patients and 50 age- and gender-matched healthy controls. DNA was extracted from stool samples and subjected to 16S ribosomal RNA gene analysis (V3-V4) for intestinal dysbiosis. In addition, patients were examined for laboratory and serological pSS features. A Spearman's correlation analysis was performed to assess correlations between individual bacteria taxa and clinical characteristics. The alpha-diversity (Chao1 and Shannon Index) and beta-diversity (unweighted UniFrac distances) of the gut microbiota differed significantly between pSS patients and healthy controls. Further analysis showed that several gut opportunistic pathogens (Bacteroides, Megamonas, and Veillonella) were significantly more abundant in pSS patients and positively correlated with their clinical indicators. In contrast, some probiotic genera (Collinsella, unidentified_Ruminococcaceae, Romboutsia, and Dorea) were significantly decreased in pSS patients and negatively correlated with their clinical indicators. Therefore, pSS patients in Northern China showed a dysbiotic intestinal microbiome enriched for potentially pathogenic genera that might be associated with autoimmune disease.
Topics: Humans; Gastrointestinal Microbiome; Dysbiosis; Sjogren's Syndrome; RNA, Ribosomal, 16S; Bacteria; Clostridiaceae; China
PubMed: 36355832
DOI: 10.1371/journal.pone.0277270 -
Scientific Reports Dec 2021Weaning is a critical period in the life of pigs with repercussions on their health and welfare and on the economy of the swine industry. This study aimed to assess the...
Weaning is a critical period in the life of pigs with repercussions on their health and welfare and on the economy of the swine industry. This study aimed to assess the effect of the commercial early weaning on gut microbiota, intestinal gene expression and serum metabolomic response via an integrated-omic approach combining 16S rRNA gene sequencing, the OpenArray gene expression technology and H-NMR spectroscopy. Fourteen piglets from different litters were sampled for blood, jejunum tissue and caecal content two days before (- 2d), and three days after (+ 3d) weaning. A clearly differential ordination of caecal microbiota was observed. Higher abundances of Roseburia, Ruminococcus, Coprococcus, Dorea and Lachnospira genera in weaned piglets compared to prior to weaning showed the quick microbial changes of the piglets' gut microbiota. Downregulation of OCLN, CLDN4, MUC2, MUC13, SLC15A1 and SLC13A1 genes, also evidenced the negative impact of weaning on gut barrier and digestive functions. Metabolomic approach pinpointed significant decreases in choline, LDL, triglycerides, fatty acids, alanine and isoleucine and increases in 3-hydroxybutyrate after weaning. Moreover, the correlation between microbiota and metabolome datasets revealed the existence of metabolic clusters interrelated to different bacterial clusters. Our results demonstrate the impact of weaning stress on the piglet and give insights regarding the associations between gut microbiota and the animal gene activity and metabolic response.
Topics: Animals; Bacteria; Cecum; Feces; Gastrointestinal Microbiome; Host Microbial Interactions; Jejunum; Metabolome; RNA, Ribosomal, 16S; Swine; Weaning
PubMed: 34873196
DOI: 10.1038/s41598-021-02754-6 -
Molecules (Basel, Switzerland) Feb 2020The allicin diallyldisulfid--oxide, a major garlic organosulfur compound (OSC) in crushed garlic ( L.), possesses antibacterial effects, and influences gut bacteria. In...
The allicin diallyldisulfid--oxide, a major garlic organosulfur compound (OSC) in crushed garlic ( L.), possesses antibacterial effects, and influences gut bacteria. In this study, we made allicin-free garlic (AFG) extract and investigated its effects on gut microbiome. C57BL/6N male mice were randomly divided into 6 groups and fed normal diet (ND) and high-fat diet (HFD) supplemented with or without AFG in concentrations of 1% and 5% for 11 weeks. The genomic DNAs of feces were used to identify the gut microbiome by sequencing 16S rRNA genes. The results revealed that the ratio of p- to p- increased by aging and HFD was reduced by AFG. In particular, the f-, g-, and g- decreased by aging and HFD was enhanced by AFG. The g- increased by aging and HFD decreased by AFG. In addition, the ratio of glutamic-pyruvic transaminase to glutamic-oxaloacetic transaminase (GPT/GOT) in serum was significantly increased in the HFD group and decreased by AFG. In summary, our data demonstrated that dietary intervention with AFG is a potential way to balance the gut microbiome disturbed by a high-fat diet.
Topics: Alanine Transaminase; Animals; Anti-Bacterial Agents; Aspartate Aminotransferases; Bacteroidetes; Diet, High-Fat; Dietary Supplements; Disulfides; Firmicutes; Garlic; Gastrointestinal Microbiome; Male; Mice; Mice, Inbred C57BL; Plant Extracts; Sulfinic Acids; Verrucomicrobia
PubMed: 32033507
DOI: 10.3390/molecules25030682 -
Frontiers in Pharmacology 2022Fonte Essenziale® water is a bicarbonate-sulfate-calcium-magnesium water, low in sodium, recognized by the Italian health care system in hydropinotherapy and...
Fonte Essenziale® water is a bicarbonate-sulfate-calcium-magnesium water, low in sodium, recognized by the Italian health care system in hydropinotherapy and hepatobiliary dyspepsia therapy. We wanted to explore its effects on the gut-liver axis and microbiota in non-alcoholic fatty liver disease patients. We considered enrollment for 70 patients, of which four were excluded. We finally enrolled 55 patients with ultrasound-documented steatosis (SPs+) and 11 patients without it (SPs-). They then drank 400 ml of water for 6 months in the morning on an empty stomach. Routine hematochemical and metabolic parameters, oxidative stress parameters, gastrointestinal hormone levels, and fecal parameters of the gut microbiota were evaluated at three different assessment times, at baseline (T0), after 6 months (T6), and after a further 6 months of water washout (T12). We lost, in follow-up, 4 (T6) and 22 (T12) patients. Between T0-T6, we observed a significant Futuin A and Selenoprotein A decrease and a GLP-1 and PYY increase in SPs+ and the same for Futuin A and GLP-1 in SPs-. Effects were lost at T12. In SPs+, between T0-T12 and T6-12, a significant reduction in Blautia was observed; between T0-T12, a reduction of Collinsella unc. was observed; and between T0-T12 and T6-12, an increase in Subdoligranulum and Dorea was observed. None of the bacterial strains we analyzed varied significantly in the SPs- population. These results indicate beneficial effects of water on gastrointestinal hormones and hence on the gut-liver axis in the period in which subjects drank water both in SPs- and in SPs+.
PubMed: 35837275
DOI: 10.3389/fphar.2022.869446 -
Investigative Ophthalmology & Visual... May 2024To identify compositional differences in the gut microbiome of nonmyopes (NM) and myopes using 16S ribosomal RNA sequencing and to investigate whether the microbiome may...
PURPOSE
To identify compositional differences in the gut microbiome of nonmyopes (NM) and myopes using 16S ribosomal RNA sequencing and to investigate whether the microbiome may contribute to the onset or progression of the condition.
METHODS
Faecal samples were collected from 52 adult participants, of whom 23 were NM, 8 were progressive myopes (PM), and 21 were stable myopes (SM). The composition of the gut microbiota in each group was analysed using 16S ribosomal RNA gene sequencing.
RESULTS
There were no significant differences in alpha and beta diversity between the three groups (NM, PM, and SM). However, the distributions of Bifidobacterium, Bacteroides, Megamonas, Faecalibacterium, Coprococcus, Dorea, Roseburia, and Blautia were significantly higher in the myopes (SM and PM combined) when compared with emmetropes. The myopes exhibited significantly greater abundance of bacteria that are linked to the regulation of dopaminergic signalling, such as Clostridium, Ruminococcus, Bifidobacterium, and Bacteroides. Individuals with stable myopia were found to have a significantly higher proportion of Prevotella copri than those with progressive myopia. Bifidobacterium adolescentis, a gamma-aminobutyric acid (GABA)-producing bacterium, was significantly higher in all myopes than in NM and, in the comparison between SM and PM, it is significantly higher in SM. B. uniformis and B. fragilis, both GABA-producing Bacteroides, were present in relatively high abundance in all myopes and in SM compared with PM, respectively.
CONCLUSIONS
The presence of bacteria related to dopamine effect and GABA-producing bacteria in the gut microbiome of myopes may suggest a role of these microorganisms in the onset and progression of myopia.
Topics: Humans; Male; Adult; Female; Gastrointestinal Microbiome; Feces; RNA, Ribosomal, 16S; Myopia; Bacteria; Young Adult; Middle Aged; DNA, Bacterial
PubMed: 38691091
DOI: 10.1167/iovs.65.5.2 -
Journal of Korean Medical Science Apr 2023Long coronavirus disease 2019 (COVID-19) in recovered patients (RPs) is gradually recognized by more people. However, how long it will last and the underlining mechanism...
BACKGROUND
Long coronavirus disease 2019 (COVID-19) in recovered patients (RPs) is gradually recognized by more people. However, how long it will last and the underlining mechanism remains unclear.
METHODS
We conducted a prospective follow-up study to evaluate the long-term symptoms and clinical indices of RPs at one-year after discharge from Union Hospital, Wuhan, China between December 2020 to May 2021. We also performed the 16S rRNA sequencing of stool samples from RPs and healthy controls (HCs) and analyzed the correlation between the gut microbiota and long COVID-19.
RESULTS
In total, 187 RPs were enrolled, among them, 84 (44.9%) RPs reported long COVID-19 symptoms at one-year after discharge. The most common long-term symptoms were cardiopulmonary symptoms, including chest tightness after activity (39/187, 20.9%), palpitations on exercise (27/187, 14.4%), sputum (21/187, 11.2%), cough (15/187, 8.0%) and chest pain (13/187, 7.0%), followed by systemic symptoms including fatigue (34/187, 18.2%) and myalgia (20/187, 10.7%), and digestive symptoms including constipation (14/187, 7.5%), anorexia (13/187, 7.0%), and diarrhea (8/187, 4.3%). Sixty-six (35.9%) RPs presented either anxiety or depression (42/187 [22.8%] and 53/187 [28.8%] respectively), and the proportion of anxiety or depression in the long symptomatic group was significantly higher than that in the asymptomatic group (41/187 [50.6%] vs. 25/187 [24.3%]). Compared with the asymptomatic group, scores of all nine 36-Item Short Form General Health Survey domains were lower in the symptomatic group (all < 0.05). One hundred thirty RPs and 32 HCs (non-severe acute respiratory syndrome coronavirus 2 infected subjects) performed fecal sample sequencing. Compared with HCs, symptomatic RPs had obvious gut microbiota dysbiosis including significantly reduced bacterial diversities and lower relative abundance of short-chain fatty acids (SCFAs)-producing salutary symbionts such as group, , , , , and group. Meanwhile, the relative abundance of _group, , and showed decreasing tendencies between HCs, the asymptomatic group, and the symptomatic group.
CONCLUSION
This study demonstrated the presence of long COVID-19 which correlates with gut microbiota dysbiosis in RPs at one-year after discharge, indicating gut microbiota may play an important role in long COVID-19.
Topics: Humans; COVID-19; Post-Acute COVID-19 Syndrome; Patient Discharge; Follow-Up Studies; Gastrointestinal Microbiome; Dysbiosis; RNA, Ribosomal, 16S; Prospective Studies; Feces
PubMed: 37069814
DOI: 10.3346/jkms.2023.38.e120 -
Gut Pathogens Dec 2022Emerging evidence suggests that gut microbiota plays a predominant role in Crohn's disease (CD). However, the microbiome alterations in the early stage of CD patients...
BACKGROUND
Emerging evidence suggests that gut microbiota plays a predominant role in Crohn's disease (CD). However, the microbiome alterations in the early stage of CD patients still remain unclear. The present study aimed to identify dysbacteriosis in patients with early CD and explore specific gut bacteria related to the progression of CD.
METHODS
This study was nested within a longitudinal prospective Chinese CD cohort, and it included 18 early CD patients, 22 advanced CD patients and 30 healthy controls. The microbiota communities were investigated using high-throughput Illumina HiSeq sequencing targeting the V3-V4 region of 16S ribosomal DNA (rDNA) gene. The relationship between the gut microbiota and clinical characteristics of CD was analyzed.
RESULTS
Differential microbiota compositions were observed in CD samples (including early and advanced CD samples) and healthy controls samples. Notably, Lachnospiracea_incertae_sedis and Parabacteroides were enriched in the early CD patients, Escherichia/Shigella, Enterococcus and Proteus were enriched in the advanced CD patients, and Roseburia, Gemmiger, Coprococcus, Ruminococcus 2, Butyricicoccus, Dorea, Fusicatenibacter, Anaerostipes, Clostridium IV were enriched in the healthy controls [LDA score (log10) > 2]. Furthermore, Kruskal-Wallis Rank sum test results showed that Blautia, Clostridium IV, Coprococcus, Dorea, Fusicatenibacter continued to significantly decrease in early and advanced CD patients, and Escherichia/Shigella and Proteus continued to significantly increase compared with healthy controls (P < 0.05). The PICRUSt analysis identified 16 remarkably different metabolic pathways [LDA score (log10) > 2]. Some genera were significantly correlated with various clinical parameters, such as fecal calprotectin, erythrocyte sedimentation rate, C-reactive protein, gland reduce, goblet cells decreased, clinical symptoms (P < 0.05).
CONCLUSIONS
Dysbacteriosis occurs in the early stage of CD and is associated with the progression of CD. This data provides a foundation that furthers the understanding of the role of gut microbiota in CD's pathogenesis.
PubMed: 36517872
DOI: 10.1186/s13099-022-00521-0 -
Kidney & Blood Pressure Research 2023Numerous research works have shown that serum Gal-deficient (Gd) IgA1 levels are increased in IgA nephropathy (IgAN) patients and these levels are a dangerous risk...
INTRODUCTION
Numerous research works have shown that serum Gal-deficient (Gd) IgA1 levels are increased in IgA nephropathy (IgAN) patients and these levels are a dangerous risk factor for IgAN. A relationship between the gut microbiota and IgAN has been reported. Whether the gut microbiota participates in the pathogenesis of IgAN was still controversial.
METHODS
We evaluated changes in the gut flora and the levels of Gd-IgA1 in IgAN patients and healthy controls (HCs). We investigated the Gd-IgA1 levels in both blood and urine specimens. C57BL/6 mice were given a broad-spectrum antibiotic cocktail to deplete the endogenous gut flora. We established a model of IgAN in pseudosterile mice and investigated the expression of the markers of intestinal permeability, inflammation, and local immune responses.
RESULTS
Studies have shown that the levels of certain gut flora differ between IgAN patients and HCs. Moreover, elevated Gd-IgA1 levels were found in both the serum and urine. Interestingly, Coprococcus, Dorea, Bifidobacterium, Blautia, and Lactococcus, selected from 10 candidate biomarkers to predict risk in IgAN patients according to random forest analysis, were inversely associated with urinary Gd-IgA1 levels. Notably, the urine level of Gd-IgA1 could best distinguish IgAN patients from HCs. Additionally, the degree of kidney damage in pseudosterile mice with IgAN was more severe than that in mice with IgAN. Furthermore, the markers of intestinal permeability were significantly elevated in pseudosterile IgAN mice. Moreover, the inflammation responses (TLR4, MyD88, and NF-κB in intestinal and renal tissues; TNF-α and IL-6 in serum) and local immune responses (BAFF and APRIL in intestinal tissue) were upregulated in pseudosterile IgAN mice.
CONCLUSIONS
The urine Gd-IgA1 level may be as a biomarker for the early screening of potential IgAN, and gut microbiota dysbiosis was demonstrated in IgAN, which might involve the dysfunction of the mucosal barrier, inflammation, and local immune responses.
Topics: Humans; Animals; Mice; Glomerulonephritis, IGA; Gastrointestinal Microbiome; Mice, Inbred C57BL; Immunoglobulin A; Inflammation; Biomarkers; Immunity
PubMed: 36878203
DOI: 10.1159/000528973