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Microbiology Spectrum Jun 2023IgA nephropathy (IgAN) is reportedly associated with microbial dysbiosis. However, the microbiome dysregulation of IgAN patients across multiple niches remains unclear....
IgA nephropathy (IgAN) is reportedly associated with microbial dysbiosis. However, the microbiome dysregulation of IgAN patients across multiple niches remains unclear. To gain a systematic understanding of microbial dysbiosis, we conducted large-scale 16S rRNA gene sequencing in IgAN patients and healthy volunteers across 1,732 oral, pharynx, gut, and urine samples. We observed a niche-specific increase of several opportunistic pathogens, including and in the oral and pharynx, whereas some beneficial commensals decreased in IgAN patients. Similar alterations were also observed in the early versus advanced stage of chronic kidney disease (CKD) progression. Moreover, , and in the oral and pharynx were positively associated with creatinine and urea, indicating renal lesions. Random forest classifiers were developed by using the microbial abundance to predict IgAN, achieving an optimal accuracy of 0.879 in the discovery phase and 0.780 in the validation phase. This study provides microbial profiles of IgAN across multiple niches and underlines the potential of these biomarkers as promising, noninvasive tools with which to differentiate IgAN patients for clinical applications.
Topics: Humans; Glomerulonephritis, IGA; RNA, Ribosomal, 16S; Dysbiosis; Biomarkers; Microbiota
PubMed: 37227280
DOI: 10.1128/spectrum.05202-22 -
Frontiers in Cellular and Infection... 2023Oral microbiota is closely related to the homeostasis of the oral cavity and lungs. To provide potential information for the prediction, screening, and treatment...
BACKGROUND
Oral microbiota is closely related to the homeostasis of the oral cavity and lungs. To provide potential information for the prediction, screening, and treatment strategies of individuals, this study compared and investigated the bacterial signatures in periodontitis and chronic obstructive pulmonary disease (COPD).
MATERIALS AND METHODS
We collected subgingival plaque and gingival crevicular fluid samples from 112 individuals (31 healthy controls, 24 patients with periodontitis, 28 patients with COPD, and 29 patients with both periodontitis and COPD). The oral microbiota was analyzed using 16S rRNA gene sequencing and diversity and functional prediction analysis were performed.
RESULTS
We observed higher bacterial richness in individuals with periodontitis in both types of oral samples. Using LEfSe and DESeq2 analyses, we found differentially abundant genera that may be potential biomarkers for each group. is the predominant genus in COPD. Ten genera, including , , and were predominant in periodontitis. and were the signature of the healthy controls. The significantly different pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) between healthy controls and other groups were concentrated in genetic information processing, translation, replication and repair, and metabolism of cofactors and vitamins.
CONCLUSIONS
We found the significant differences in the bacterial community and functional characterization of oral microbiota in periodontitis, COPD and comorbid diseases. Compared to gingival crevicular fluid, subgingival plaque may be more appropriate for reflecting the difference of subgingival microbiota in periodontitis patients with COPD. These results may provide potentials for predicting, screening, and treatment strategies for individuals with periodontitis and COPD.
Topics: Humans; Dysbiosis; RNA, Ribosomal, 16S; Periodontitis; Bacteria; Pulmonary Disease, Chronic Obstructive; Chronic Periodontitis
PubMed: 36844402
DOI: 10.3389/fcimb.2023.1121399 -
Microorganisms Jan 2022Users of prosthetic devices face the accumulation of potentially drug-resistant pathogenic bacteria on the skin/prosthesis interface. In this study, we took surface...
The Identification of Multidrug-Resistant Microorganisms including Acquired from the Skin/Prosthetic Interface of Amputees and Their Susceptibility to Medihoney™ and Garlic Extract (Allicin).
Users of prosthetic devices face the accumulation of potentially drug-resistant pathogenic bacteria on the skin/prosthesis interface. In this study, we took surface swabs of the skin/prosthesis interface of eleven disabled athletes to identify microorganisms present. In addition to determining their antimicrobial resistance profile, we assessed their sensitivity to Manuka honey and Garlic extract (allicin). Eleven volunteers were directed to swab the skin at the skin/prosthesis interface. After initial isolation of microorganisms, we employed the following general microbiological methods: Gram stain, Catalase test, Oxidase test, lactose fermenting capability, haemolytic capability, Staphaurex, mannitol fermenting capability, Streptex; API Staph, 20E, Candida, and BBL crystal identification system tests. Once identified, isolates were analysed for their sensitivity to penicillin, erythromycin, ampicillin, vancomycin, ceftazidime, ciprofloxacin, gentamicin, and colistin-sulphate. Isolates were also analysed for their sensitivity to allicin (Garlic Extract (GE)) and Manuka honey (Medihoney™) (MH). Eleven isolates were identified spp., spp., , and . All isolates were resistant to 1 unit of penicillin and 10 μg of ampicillin was observed to have the widest range of resistance with observed resistance against five of the eight antimicrobials employed in this study. This study highlights the prevalence of uncommon drug-resistant microorganisms on the skin within a vulnerable population, highlighting the potential for MH or GE intervention.
PubMed: 35208754
DOI: 10.3390/microorganisms10020299 -
Genome Research Jun 2022The oral microbiome is linked to oral and systemic health, but its fluctuation under frequent daily activities remains elusive. Here, we sampled saliva at 10- to 60-min...
The oral microbiome is linked to oral and systemic health, but its fluctuation under frequent daily activities remains elusive. Here, we sampled saliva at 10- to 60-min intervals to track the high-resolution microbiome dynamics during the course of human activities. This dense time series data showed that eating activity markedly perturbed the salivary microbiota, with tongue-specific and and dental plaque-specific , , and increased after every meal in a temporal order. The observation was reproducible in multiple subjects and across an 11-mo period. The microbiome composition showed significant diurnal oscillation patterns at different taxonomy levels with / increased at night and slowly increased during the daytime. We also identified microbial co-occurring patterns in saliva that are associated with the intricate biogeography of the oral microbiome. Microbial source tracking analysis showed that the contributions of distinct oral niches to the salivary microbiome were dynamically affected by daily activities, reflecting the role of saliva in exchanging microbes with other oral sites. Collectively, our study provides insights into the temporal microbiome variation in saliva and highlights the need to consider daily activities and diurnal factors in design of oral microbiome studies.
Topics: Humans; Microbiota; Prevotella; RNA, Ribosomal, 16S; Saliva
PubMed: 35688483
DOI: 10.1101/gr.276482.121 -
Journal of Animal Science Jul 2021Microbiota plays a prominent role in periodontal disease, but the canine oral microbiota and how dental chews may affect these populations have been poorly studied. We...
Microbiota plays a prominent role in periodontal disease, but the canine oral microbiota and how dental chews may affect these populations have been poorly studied. We aimed to determine the differences in oral microbiota of adult dogs consuming dental chews compared with control dogs consuming only a diet. Twelve adult female beagle dogs (mean age = 5.31 ± 1.08 yr) were used in a replicated 4 × 4 Latin square design consisting of 28-d periods. Treatments (n = 12/group) included: diet only (CT); diet + Bones & Chews Dental Treats (BC; Chewy, Inc., Dania Beach, FL); diet + Dr. Lyon's Grain-Free Dental Treats (DL; Dr. Lyon's, LLC, Dania Beach, FL); and diet + Greenies Dental Treats (GR; Mars Petcare US, Franklin, TN). Each day, one chew was provided 4 h after mealtime. On day 27, breath samples were analyzed for total volatile sulfur compound concentrations using a Halimeter. On day 0 of each period, teeth were cleaned by a veterinary dentist blinded to treatments. Teeth were scored for plaque, calculus, and gingivitis by the same veterinary dentist on day 28 of each period. After scoring, salivary (SAL), subgingival (SUB), and supragingival (SUP) samples were collected for microbiota analysis using Illumina MiSeq. All data were analyzed using SAS (version 9.4) using the Mixed Models procedure, with P < 0.05 considered significant. All dogs consuming chews had lower calculus coverage and thickness, pocket depth and bleeding, plaque thickness, and halitosis compared with CT. In all sites of collection, CT dogs had a higher relative abundance of one or more potentially pathogenic bacteria (Porphyromonas, Anaerovorax, Desulfomicrobium, Tannerella, and Treponema) and lower relative abundance of one or more genera associated with oral health (Neisseria, Corynebacterium, Capnocytophaga, Actinomyces, Lautropia, Bergeyella, and Moraxella) than those fed chews. DL reduced Porphyromonas in SUP and SUB samples. DL and GR reduced Treponema in SUP samples. DL increased Corynebacterium in all sites of collection. BC increased Corynebacterium in SAL samples. DL and GR increased Neisseria in SAL samples. DL increased Actinomyces in the SUB sample. GR increased Actinomyces in SAL samples. Our results suggest that the dental chews tested in this study may aid in reducing periodontal disease risk in dogs by beneficially shifting the microbiota inhabiting plaque and saliva of a dog's oral cavity. These shifts occurred over a short period of time and were correlated with improved oral health scores.
Topics: Animals; Dog Diseases; Dogs; Female; Gingivitis; Halitosis; Microbiota; Saliva; Tooth
PubMed: 33780530
DOI: 10.1093/jas/skab100 -
Frontiers in Cellular and Infection... 2020In order to improve our understanding on the microbial complexity associated with Grade C/molar-incisor pattern periodontitis (GC/MIP), we surveyed the oral and fecal...
In order to improve our understanding on the microbial complexity associated with Grade C/molar-incisor pattern periodontitis (GC/MIP), we surveyed the oral and fecal microbiomes of GC/MIP and compared to non-affected individuals (Control). Seven Afro-descendants with GC/MIP and seven age/race/gender-matched controls were evaluated. Biofilms from supra/subgingival sites (OB) and feces were collected and submitted to sequencing. () JP2 clone genotyping and salivary nitrite levels were determined. Supragingival biofilm of GC/MIP presented greater abundance of opportunistic bacteria. was increased in subgingival healthy sites of GC/MIP compared to Control. and were more abundant whereas was reduced in OB of GC/MIP compared to controls. abundance was 50 times higher in periodontal sites with PD≥ 4 mm of GC/MIP than in controls. GC/MIP oral microbiome was characterized by a reduction in commensals such as , and and enrichment in periodontopathogens, especially and sulfate reducing . The oral microbiome of the JP2-like+ patient was phylogenetically distant from other GC/MIP individuals. GC/MIP presented a higher abundance of sulfidogenic bacteria in the feces, such as , and than controls. These preliminary data show that the dysbiosis of the microbiome in Afro-descendants with GC/MIP was not restricted to affected sites, but was also observed in supragingival and subgingival healthy sites, as well as in the feces. The understanding on differences of the microbiome between healthy and GC/MIP patients will help in developing strategies to improve and monitor periodontal treatment.
Topics: Aggregatibacter actinomycetemcomitans; Desulfovibrio; Erysipelothrix; Feces; Humans; Incisor; Microbiota; Molar; Peptostreptococcus; Periodontitis; RNA, Ribosomal, 16S
PubMed: 33117737
DOI: 10.3389/fcimb.2020.583761 -
Journal of Translational Medicine Dec 2022Cardiovascular disease is a leading cause of morbidity and mortality. Oral health is associated with smoking and cardiovascular outcomes, but there are gaps in knowledge... (Review)
Review
Cardiovascular disease is a leading cause of morbidity and mortality. Oral health is associated with smoking and cardiovascular outcomes, but there are gaps in knowledge of many mechanisms connecting smoking to cardiovascular risk. Therefore, the aim of this review is to synthesize literature on smoking and the oral microbiome, and smoking and cardiovascular risk/disease, respectively. A secondary aim is to identify common associations between the oral microbiome and cardiovascular risk/disease to smoking, respectively, to identify potential shared oral microbiome-associated mechanisms. We identified several oral bacteria across varying studies that were associated with smoking. Atopobium, Gemella, Megasphaera, Mycoplasma, Porphyromonas, Prevotella, Rothia, Treponema, and Veillonella were increased, while Bergeyella, Haemophilus, Lautropia, and Neisseria were decreased in the oral microbiome of smokers versus non-smokers. Several bacteria that were increased in the oral microbiome of smokers were also positively associated with cardiovascular outcomes including Porphyromonas, Prevotella, Treponema, and Veillonella. We review possible mechanisms that may link the oral microbiome to smoking and cardiovascular risk including inflammation, modulation of amino acids and lipids, and nitric oxide modulation. Our hope is this review will inform future research targeting the microbiome and smoking-related cardiovascular disease so possible microbial targets for cardiovascular risk reduction can be identified.
Topics: Humans; RNA, Ribosomal, 16S; Cardiovascular Diseases; Risk Factors; Bacteria; Smoking; Heart Disease Risk Factors
PubMed: 36503487
DOI: 10.1186/s12967-022-03785-x -
Frontiers in Endocrinology 2022This study aimed at investigating the association between testosterone levels and gut microbiota in male patients with type 2 diabetes mellitus (T2DM) and providing a... (Observational Study)
Observational Study
OBJECTIVE
This study aimed at investigating the association between testosterone levels and gut microbiota in male patients with type 2 diabetes mellitus (T2DM) and providing a new strategy to elucidate the pathological mechanism of testosterone deficiency in T2DM patients.
METHODS
In an observational study including 46 T2DM male patients, the peripheral venous blood and fecal samples of all subjects were collected. The V3-V4 regions of bacterial 16S rDNA were amplified and sequenced. Alpha and beta diversities were calculated by QIIME software. The possible association between gut microbial community and clinical indicators was assessed using the Spearman correlation coefficient. The association between the relative abundance of bacteria and testosterone levels was discovered using linear regression analysis in R language.
RESULTS
There was no substantial difference in alpha and beta diversity. and were significantly much higher in the testosterone deficiency group. Linear regression analysis showed that the abundance of at the phylum level and at the order level were negatively correlated with testosterone level. After correcting for C-reactive protein (CRP) and homeostatic model assessment of insulin resistance (HOMA-IR), the relative abundance of still had a significant negative correlation with testosterone level. Meanwhile, at the genus level, , , and had a statistically significant negative association with testosterone level, respectively. was positively associated with FPG and total cholesterol level. was found positively associated with insulin, connecting peptide, and index of homeostatic model assessment of insulin resistance.
CONCLUSION
T2DM patients with testosterone deficiency have different gut microbiota compositions compared with T2DM patients alone. Low serum testosterone patients tend to have an increased abundance of opportunistic pathogens, which may be related to the occurrence and development of testosterone deficiency.
Topics: Diabetes Mellitus, Type 2; Gastrointestinal Microbiome; Humans; Insulin Resistance; Male; Microbiota; Testosterone
PubMed: 35399957
DOI: 10.3389/fendo.2022.836485 -
Frontiers in Cellular and Infection... 2021Microbial infections have been shown to contribute to gastric carcinogenesis, the knowledge of gastric microbiota alteration in this process may provide help in early...
OBJECTIVE
Microbial infections have been shown to contribute to gastric carcinogenesis, the knowledge of gastric microbiota alteration in this process may provide help in early diagnosis of gastric cancer. The aim of this study was to characterize the microbial changes and identify taxonomic biomarkers across stages of gastric carcinogenesis.
METHODS
The gastric microbiota was investigated by 16S rRNA gene analysis in gastric mucosal specimens from 47 patients including superficial gastritis (SG), atrophic gastritis (AG), gastric intraepithelial neoplasia (GIN), and gastric cancer (GC). Differences in microbial composition across the disease stages, especially in GIN and GC were assessed using linear discriminant analysis effect size.
RESULTS
There was no gradual changing trend in the richness or diversity of the gastric microbiota across stages of gastric carcinogenesis. The relative abundance of dominant taxa at phylum and genus levels didn't show a gradual shift pattern, and the only four taxa that continuously enriched from SG to GC were , , , and , all of which were oral bacteria. The most representative taxa which were enriched in GC patients were oral bacteria including , and , and environmental bacteria including , , and . The gastric microbiota in GIN patients were characterized by enrichment of intestinal commensals including , , , and . Gastric cardia cancer and non-cardia cancer patients had significantly different microbiota profiles characterized by a higher abundance of in the cardia cancer patients.
CONCLUSIONS
Our results provide insights on potential taxonomic biomarkers for gastric cancer and precancerous stages, and suggest that gastric microbiota might play different roles in the carcinogenesis of cardia cancer and non-cardia cancer.
Topics: Helicobacter Infections; Helicobacter pylori; Humans; Microbiota; Precancerous Conditions; RNA, Ribosomal, 16S; Stomach Neoplasms
PubMed: 33747975
DOI: 10.3389/fcimb.2021.559148 -
Frontiers in Microbiology 2021Gliomas are the most prevalent form of primary malignant brain tumor, which currently have no effective treatments. Evidence from human studies has indicated that oral...
Gliomas are the most prevalent form of primary malignant brain tumor, which currently have no effective treatments. Evidence from human studies has indicated that oral microbiota is closely related to cancers; however, whether oral microbiota plays a role in glioma malignancy remains unclear. The present study aimed to investigate the association between oral microbiota and grade of glioma and examine the relationship between malignancy-related oral microbial features and the isocitrate dehydrogenase 1 (IDH1) mutation in glioma. High-grade glioma (HGG; =23) patients, low-grade glioma (LGG; =12) patients, and healthy control (HCs; =24) participants were recruited for this case-control study. Saliva samples were collected and analyzed for 16S ribosomal RNA (rRNA) sequencing. We found that the shift in oral microbiota β-diversity was associated with high-grade glioma (=0.01). The phylum Patescibacteria was inversely associated with glioma grade (LGG and HC: =0.035; HGG and HC: <0.01). The genera (LGG and HC: =0.043; HGG and HC: <0.01) and (LGG and HC: =0.044; HGG and HC: <0.01) were inversely associated with glioma grades. The genera and were significantly more positively correlated with the IDH1 mutation in gliomas when compared with the IDH1-wild-type group. We further identified five oral microbial features (, , , and ) that accurately discriminated HGG from LGG (area under the curve [AUC]: 0.63, 95% confidence interval [CI]: 0.44-0.83) and HCs (AUC: 0.79, 95% CI: 0.68-0.92). The functional prediction analysis of oral bacterial communities showed that genes involved in cell adhesion molecules (<0.001), extracellular matrix molecule-receptor interaction (<0.001), focal adhesion (<0.001), and regulation of actin cytoskeleton (<0.001) were associated with glioma grades, and some microbial gene functions involving lipid metabolism and the adenosine 5'-monophosphate-activated protein kinase signaling pathway were significantly more enriched in IDH1 mutant gliomas than compared with the IDH1-wild-type gliomas. In conclusion, our work revealed oral microbiota features and gene functions that were associated with glioma malignancy and the IDH1 mutation in glioma.
PubMed: 34733261
DOI: 10.3389/fmicb.2021.746568