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Journal of Cachexia, Sarcopenia and... Oct 2022Several studies have examined gut microbiota and sarcopenia using 16S ribosomal RNA amplicon sequencing; however, this technique may not be able to identify altered... (Observational Study)
Observational Study
BACKGROUND
Several studies have examined gut microbiota and sarcopenia using 16S ribosomal RNA amplicon sequencing; however, this technique may not be able to identify altered specific species and functional capacities of the microbes. We performed shotgun metagenomic sequencing to compare the gut microbiome composition and function between individuals with and without sarcopenia.
METHODS
Participants were from a community-based observational study conducted among the residents of rural areas in China. Appendicular skeletal muscle mass was assessed using direct segmental multi-frequency bioelectrical impedance and grip strength using a Jamar Hydraulic Hand dynamometer. Physical performance was evaluated using the Short Physical Performance Battery, 5-time chair stand test and gait speed with the 6 m walk test. Sarcopenia and its severity were diagnosed according to the Asian Working Group for Sarcopenia 2019 algorithm. The gut microbiome was profiled by shotgun metagenomic sequencing to determine the microbial composition and function. A gut microbiota-based model for classification of sarcopenia was constructed using the random forest model, and its performance was assessed using the area under receiver-operating characteristic curve (AUC).
RESULTS
The study sample included 1417 participants (women: 58.9%; mean age: 63.3 years; sarcopenia prevalence: 10.0%). β-diversity indicated by Bray-Curtis distance (genetic level: P = 0.004; taxonomic level of species: P = 0.020), but not α-diversity indicated by Shannon index (genetic level: P = 0.962; taxonomic level of species: P = 0.922), was significantly associated with prevalent sarcopenia. After adjusting for potential confounders, participants with sarcopenia had higher relative abundance of Desulfovibrio piger (P = 0.003, Q = 0.090), Clostridium symbiosum (P < 0.001, Q = 0.035), Hungatella effluvii (P = 0.003, Q = 0.090), Bacteroides fluxus (P = 0.002, Q = 0.089), Absiella innocuum (P = 0.002, Q = 0.072), Coprobacter secundus (P = 0.002, Q = 0.085) and Clostridium citroniae (P = 0.001, Q = 0.060) than those without sarcopenia. The relative abundance of six species (Desulfovibrio piger, Clostridium symbiosum, Hungatella effluvii, Bacteroides fluxus, Absiella innocuum, and Clostridium citroniae) was also positively associated with sarcopenia severity. A differential species-based model was constructed to separate participants with sarcopenia from controls. The value of the AUC was 0.852, suggesting that model has a decent discriminative performance. Desulfovibrio piger ranked the highest in this model. Functional annotation analysis revealed that the phenylalanine, tyrosine, and tryptophan biosynthesis were depleted (P = 0.006, Q = 0.071), while alpha-Linolenic acid metabolism (P = 0.008, Q = 0.094), furfural degradation (P = 0.001, Q = 0.029) and staurosporine biosynthesis (P = 0.006, Q = 0.072) were enriched in participants with sarcopenia. Desulfovibrio piger was significantly associated with staurosporine biosynthesis (P < 0.001).
CONCLUSIONS
This large population-based observational study provided empirical evidence that alterations in the gut microbiome composition and function were observed among individuals with sarcopenia.
Topics: Bacteroides; Clostridiaceae; Clostridiales; Desulfovibrio; Female; Furaldehyde; Gastrointestinal Microbiome; Humans; Middle Aged; Phenylalanine; RNA, Ribosomal, 16S; Sarcopenia; Staurosporine; Tryptophan; Tyrosine; alpha-Linolenic Acid
PubMed: 35851765
DOI: 10.1002/jcsm.13037 -
Journal of Clinical Microbiology Jul 2006One hundred eight isolates were previously identified in our laboratory as Clostridium clostridioforme by colonial and cellular morphology, as well as biochemical tests....
One hundred eight isolates were previously identified in our laboratory as Clostridium clostridioforme by colonial and cellular morphology, as well as biochemical tests. Recent studies have indicated that there are actually three different species in this C. clostridioforme group: C. hathewayi, C. bolteae, and C. clostridioforme. Our isolates were reexamined using biochemical and enzymatic tests and molecular methods. Forty-six isolates were reidentified as C. hathewayi, 34 as C. bolteae, five as C. clostridioforme, and one as C. symbiosum. Twenty-two strains were identified only to the genus level by 16S rRNA gene sequencing, and although they are microscopically and morphologically indistinguishable from the above-mentioned three species, they are phenotypically different and only 96 to 98% similar by gene sequencing. Twenty of these 22 strains were indole positive and formed two novel species. We propose Clostridium aldenense sp. nov. and Clostridium citroniae sp. nov. as names for these new species. They are differentiated from each other by results for raffinose, rhamnose, alpha-galactosidase, and beta-galactosidase: positive, negative, positive, and positive, respectively, for the former species and negative, positive, negative, and negative, respectively, for the latter species. The type strain of C. aldenense is RMA 9741 (ATCC BAA-1318; CCUG 52204), and the type strain of C. citroniae is RMA 16102 (ATCC BAA-1317; CCUG 52203).
Topics: Bacterial Proteins; Bacterial Typing Techniques; Clostridium; Clostridium Infections; DNA, Bacterial; DNA, Ribosomal; Enzymes; Genes, rRNA; Humans; Indoles; Microscopy; Molecular Sequence Data; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 16825358
DOI: 10.1128/JCM.00116-06 -
Oxidative Medicine and Cellular... 2022Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic stem cell disorders. Studies have shown the involvement of an abnormal immune system in...
Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic stem cell disorders. Studies have shown the involvement of an abnormal immune system in MDS pathogenesis. The gut microbiota are known to influence host immunity and metabolism, thereby contributing to the development of hematopoietic diseases. In this study, we performed gut microbiome and plasma metabolomic analyses in patients with MDS and healthy controls. We found that patients with MDS had a different gut microbial composition compared to controls. The gut microbiota in MDS patients showed a continuous evolutionary relationship from the phylum to the species level. At the species level, the abundance of , , , and increased, while that of decreased in MDS patients compared to controls. Moreover, abundance of bacterial genera correlated with the percentage of lymphocyte subsets in patients with MDS. Metabolomic analysis showed that the concentrations of hypoxanthine and pyroglutamic acid were increased, while that of 3a,7a-dihydroxy-5b-cholestan was decreased in MDS patients compared to controls. In conclusion, gut microbiome and plasma metabolomics are altered in patients with MDS, which may be involved in the immunopathogenesis of the disease.
Topics: Bacteria; Feces; Gastrointestinal Microbiome; Humans; Metabolomics; Myelodysplastic Syndromes; Plasma
PubMed: 35585879
DOI: 10.1155/2022/1482811 -
Diabetes Care Apr 2022To examine the previously unknown long-term association between gut microbiome composition and incident type 2 diabetes in a representative population cohort.
OBJECTIVE
To examine the previously unknown long-term association between gut microbiome composition and incident type 2 diabetes in a representative population cohort.
RESEARCH DESIGN AND METHODS
We collected fecal samples from 5,572 Finns (mean age 48.7 years; 54.1% women) in 2002 who were followed up for incident type 2 diabetes until 31 December 2017. The samples were sequenced using shotgun metagenomics. We examined associations between gut microbiome composition and incident diabetes using multivariable-adjusted Cox regression models. We first used the eastern Finland subpopulation to obtain initial findings and validated these in the western Finland subpopulation.
RESULTS
Altogether, 432 cases of incident diabetes occurred over the median follow-up of 15.8 years. We detected four species and two clusters consistently associated with incident diabetes in the validation models. These four species were Clostridium citroniae (hazard ratio [HR] 1.21; 95% CI 1.04-1.42), C. bolteae (HR 1.20; 95% CI 1.04-1.39), Tyzzerella nexilis (HR 1.17; 95% CI 1.01-1.36), and Ruminococcus gnavus (HR 1.17; 95% CI 1.01-1.36). The positively associated clusters, cluster 1 (HR 1.18; 95% CI 1.02-1.38) and cluster 5 (HR 1.18; 95% CI 1.02-1.36), mostly consisted of these same species.
CONCLUSIONS
We observed robust species-level taxonomic features predictive of incident type 2 diabetes over long-term follow-up. These findings build on and extend previous mainly cross-sectional evidence and further support links between dietary habits, metabolic diseases, and type 2 diabetes that are modulated by the gut microbiome. The gut microbiome can potentially be used to improve disease prediction and uncover novel therapeutic targets for diabetes.
Topics: Adult; Cohort Studies; Cross-Sectional Studies; Diabetes Mellitus, Type 2; Female; Finland; Gastrointestinal Microbiome; Humans; Male; Middle Aged
PubMed: 35100347
DOI: 10.2337/dc21-2358 -
Computational and Structural... 2020Visceral fat is an independent risk factor for metabolic and cardiovascular disease. The study aimed to investigate the associations between gut microbiome and visceral...
PURPOSE
Visceral fat is an independent risk factor for metabolic and cardiovascular disease. The study aimed to investigate the associations between gut microbiome and visceral fat.
METHODS
We recruited 32 obese adults and 30 healthy controls at baseline. Among the obese subjects, 14 subjects underwent laparoscopic sleeve gastrectomy (LSG) and were followed 6 months after surgery. Abdominal visceral fat area (VFA) and subcutaneous fat area (SFA) were measured by magnetic resonance imaging. Waist, hipline, waist-to-hip ratio (WHR) and body mass index (BMI) were included as simple obese parameters. Gut microbiome was analyzed by metagenomic sequencing.
RESULTS
Among the obese parameters, VFA had the largest number of correlations with the species that were differentially enriched between obese and healthy subjects, following by waist, WHR, BMI, hipline, and SFA. Within the species negatively correlated with VFA, had the strongest correlation, following by , , , , , , etc. and were increased after LSG. Functional analyses showed that among all the obese parameters, VFA had strongest correlation coefficients with the obesity-related microbial pathways. Microbial pathways involved in carbohydrate fermentation and biosynthesis of L-glutamate and L-glutamine might contribute to visceral fat accumulation.
CONCLUSIONS
Visceral fat was more closely correlated with gut microbiome compared with subcutaneous fat, suggesting an intrinsic connection between gut microbiome and metabolic cardiovascular diseases. Specific microbial species and pathways which were closely associated with visceral fat accumulation might contribute to new targeted therapies for metabolic disorders.
PubMed: 33033580
DOI: 10.1016/j.csbj.2020.09.026 -
Frontiers in Cell and Developmental... 2021Aplastic anemia results from bone marrow failure caused by an autoimmune abnormality, but the pathogenesis of severe aplastic anemia (SAA) is not well characterized. To...
Aplastic anemia results from bone marrow failure caused by an autoimmune abnormality, but the pathogenesis of severe aplastic anemia (SAA) is not well characterized. To identify potential metabolic markers of SAA and to further elucidate the pathogenetic mechanisms of SAA, we performed a metabolomic study of plasma samples and characterized the intestinal microbiota of patients with SAA and healthy controls. Patients with SAA had more Enterobacteriales and Lactobacillales, but fewer Bacteroidales, Clostridiales, and Erysipelotrichales than healthy controls. At the species level, the abundances of and others including were higher, whereas those of , , and were lower. Eight metabolites showed significantly different plasma concentrations in the SAA and healthy control groups. Coumaric acid, L-phenylalanine, and sulfate were present at higher concentrations in the SAA group; whereas L-glutamic γ-semialdehyde, theobromine, 3a, 7a-dihydroxy-5b-cholestane, γ-δ-dioxovaleric acid, and (12Z)-9, 10-dihydroxyoctadec-12-enoic acid were present at lower concentrations. In conclusion, patients with SAA show abnormalities in both their plasma metabolomes and intestinal microbial compositions. These differences might reflect the molecular mechanisms involved in the defective immunity that characterizes SAA.
PubMed: 34497802
DOI: 10.3389/fcell.2021.669887 -
Nutrients Nov 2022(1) Background: Pregnancy-induced hypertension (PIH) is associated with obvious microbiota dysbiosis in the third trimester of pregnancy. However, the mechanisms behind...
(1) Background: Pregnancy-induced hypertension (PIH) is associated with obvious microbiota dysbiosis in the third trimester of pregnancy. However, the mechanisms behind these changes remain unknown. Therefore, this study aimed to explore the relationship between the gut microbiome in early pregnancy and PIH occurrence. (2) Methods: A nested case-control study design was used based on the follow-up cohort. Thirty-five PIH patients and thirty-five matched healthy pregnant women were selected as controls. The gut microbiome profiles were assessed in the first trimester using metagenomic sequencing. (3) Results: Diversity analyses showed that microbiota diversity was altered in early pregnancy. At the species level, eight bacterial species were enriched in healthy controls: , , , , , , and . Conversely, , and were enriched in PIH patients. The results of functional analysis showed that the changes in these different microorganisms may affect the blood pressure of pregnant women by affecting the metabolism of vitamin K, sphingolipid, lipid acid and glycine. (4) Conclusion: Microbiota dysbiosis in PIH patients begins in the first trimester of pregnancy, and this may be associated with the occurrence of PIH. Bacterial pathway analyses suggest that the gut microbiome might lead to the development of PIH through the alterations of function modules.
Topics: Humans; Female; Pregnancy; Gastrointestinal Microbiome; Dysbiosis; Case-Control Studies; Hypertension, Pregnancy-Induced; Blood Pressure; Bacteria
PubMed: 36364844
DOI: 10.3390/nu14214582 -
Frontiers in Microbiology 2021Metabolic syndrome (MetS) is a wide-ranging disorder, which includes insulin resistance, altered glucose and lipid metabolism, and increased blood pressure and visceral...
Metabolic syndrome (MetS) is a wide-ranging disorder, which includes insulin resistance, altered glucose and lipid metabolism, and increased blood pressure and visceral obesity. MetS symptoms combine to result in a significant increase in cardiovascular risk. It is therefore critical to treat MetS in the early stages of the disorder. In this study, 123 MetS patients and 304 controls were recruited to determine whether the gut microbiome plays a role in MetS development and progression. By using whole-genome shotgun sequencing, we found that the gut microbiomes of MetS patients were different from those of controls, with MetS patients possessing significantly lower gut microbiome diversity. In addition, 28 bacterial species were negatively correlated with waist circumstance, with showing the strongest correlation, followed by , , , , and . These species were also enriched in controls relative to MetS patients. In addition, pathways involved in the biosynthesis of carbohydrates, fatty acids, and lipids were enriched in the MetS group, indicating that microbial functions related to fermentation may play a role in MetS. We also found that microbiome changes in MetS patients may aggravate inflammation and contribute to MetS diseases by inhibiting the production of short-chain fatty acids (SCFAs). Taken together, these results indicate the potential utility of beneficial gut microbiota as a potential therapeutic to alleviate MetS.
PubMed: 34335505
DOI: 10.3389/fmicb.2021.682721 -
PloS One 2017The modern Western diet is rich in advanced glycation end products (AGEs). We have previously shown an association between dietary AGEs and markers of inflammation and... (Randomized Controlled Trial)
Randomized Controlled Trial
The modern Western diet is rich in advanced glycation end products (AGEs). We have previously shown an association between dietary AGEs and markers of inflammation and oxidative stress in a population of end stage renal disease (ESRD) patients undergoing peritoneal dialysis (PD). In the current pilot study we explored the effects of dietary AGEs on the gut bacterial microbiota composition in similar patients. AGEs play an important role in the development and progression of cardiovascular (CVD) disease. Plasma concentrations of different bacterial products have been shown to predict the risk of incident major adverse CVD events independently of traditional CVD risk factors, and experimental animal models indicates a possible role AGEs might have on the gut microbiota population. In this pilot randomized open label controlled trial, twenty PD patients habitually consuming a high AGE diet were recruited and randomized into either continuing the same diet (HAGE, n = 10) or a one-month dietary AGE restriction (LAGE, n = 10). Blood and stool samples were collected at baseline and after intervention. Variable regions V3-V4 of 16s rDNA were sequenced and taxa was identified on the phyla, genus, and species levels. Dietary AGE restriction resulted in a significant decrease in serum Nε-(carboxymethyl) lysine (CML) and methylglyoxal-derivatives (MG). At baseline, our total cohort exhibited a lower relative abundance of Bacteroides and Alistipes genus and a higher abundance of Prevotella genus when compared to the published data of healthy population. Dietary AGE restriction altered the bacterial gut microbiota with a significant reduction in Prevotella copri and Bifidobacterium animalis relative abundance and increased Alistipes indistinctus, Clostridium citroniae, Clostridium hathewayi, and Ruminococcus gauvreauii relative abundance. We show in this pilot study significant microbiota differences in peritoneal dialysis patients' population, as well as the effects of dietary AGEs on gut microbiota, which might play a role in the increased cardiovascular events in this population and warrants further studies.
Topics: Cardiovascular Diseases; Diet; Feces; Female; Gastrointestinal Microbiome; Glycation End Products, Advanced; Humans; Kidney Failure, Chronic; Male; Middle Aged; Peritoneal Dialysis; Pilot Projects
PubMed: 28931089
DOI: 10.1371/journal.pone.0184789 -
World Journal of Gastroenterology Apr 2012To characterize the colon microbiota in two women histologically diagnosed with collagenous colitis using a culture-independent method.
AIM
To characterize the colon microbiota in two women histologically diagnosed with collagenous colitis using a culture-independent method.
METHODS
Biopsies were taken from the ascending colon and the total DNA was extracted. Universal bacterial primers were used to amplify the bacterial 16S rRNA genes. The amplicons were then cloned into competent Escherichia coli cells. The clones were sequenced and identified by comparison to known sequences.
RESULTS
The clones could be divided into 44 different phylotypes. The microbiota was dominated by Firmicutes and Bacteroidetes. Seven phylotypes were found in both patients and constituted 47.5% of the total number of clones. Of these, the most dominating were clones similar to Bacteroides cellulosilyticus, Bacteroides caccae, Bacteroides thetaiotaomicron, Bacteroides uniformis and Bacteroides dorei within Bacteroidetes. Sequences similar to Faecalibacterium prausnitzii and Clostridium citroniae were also found in both patients.
CONCLUSION
A predominance of potentially pathogenic Bacteroides spp., and the presence of clones showing similarity to Clostridium clostridioforme were found but the overall colon microbiota showed similarities to a healthy one. Etiologies for collagenous colitis other than an adverse bacterial flora must also be considered.
Topics: Bacteria; Bacteroides; Clostridium; Colitis, Collagenous; Colon; DNA Primers; DNA, Bacterial; Female; Genes, rRNA; Humans; Metagenome; Middle Aged; Polymerase Chain Reaction; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 22529692
DOI: 10.3748/wjg.v18.i14.1628