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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 -
Veterinary Journal (London, England :... Apr 2018The aim of this study was to characterise bacteria in the genus Bergeyella isolated from the nasal passages of healthy piglets. Nasal swabs from 3 to 4 week-old piglets...
The aim of this study was to characterise bacteria in the genus Bergeyella isolated from the nasal passages of healthy piglets. Nasal swabs from 3 to 4 week-old piglets from eight commercial domestic pig farms and one wild boar farm were cultured under aerobic conditions. Twenty-nine Bergeyella spp. isolates were identified by partial 16S rRNA gene sequencing and 11 genotypes were discriminated by enterobacterial repetitive intergenic consensus (ERIC)-PCR. Bergeyella zoohelcum and Bergeyella porcorum were identified within the 11 genotypes. Bergeyella spp. isolates exhibited resistance to serum complement and phagocytosis, poor capacity to form biofilms and were able to adhere to epithelial cells. Maneval staining was consistent with the presence of a capsule. Multiple drug resistance (resistance to three or more classes of antimicrobial agents) was present in 9/11 genotypes, including one genotype isolated from wild boar with no history of antimicrobial use. In conclusion, Bergeyella spp. isolates from the nasal cavities of piglets showed some in vitro features indicative of a potential for virulence. Further studies are necessary to identify the role of Bergeyella spp. in disease and within the nasal microbiota of pigs.
Topics: Animals; Anti-Bacterial Agents; Bacterial Typing Techniques; Flavobacteriaceae; Genotype; Microbiota; Nasal Cavity; RNA, Ribosomal, 16S; Swine
PubMed: 29680378
DOI: 10.1016/j.tvjl.2018.01.004 -
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 -
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 -
Journal of Applied Microbiology Mar 1998Eighty-five catalase- and oxidase-positive Gram-negative rods and cocci susceptible to penicillin G were isolated from a variety of food sources. The phenotypic... (Comparative Study)
Comparative Study
Eighty-five catalase- and oxidase-positive Gram-negative rods and cocci susceptible to penicillin G were isolated from a variety of food sources. The phenotypic relationships of these isolates with reference cultures of Bergeyella-like, Chryseobacterium, Empedobacter, Myroides, Moraxella, Sphingobacterium and Weeksella-like strains were examined by numerical taxonomy. Seventy-three isolates were recovered in five groups; 80% of the isolates clustered in groups 1, 2 and 3 and produced indole, bearing a strong resemblance to Weeksella and Bergeyella. They could not, however, be regarded as belonging to the known species of W. virosa and B. zoohelcum. It is suggested that three species may be necessary to accommodate the environmental Weeksella- or Bergeyella-like bacteria. The isolates in groups 4 and 5 had white colonies and were unable to produce indole, in this way resembling the Moraxella genus.
Topics: Bacterial Typing Techniques; Food Microbiology; Gram-Negative Aerobic Rods and Cocci; Gram-Negative Bacteria; Moraxella
PubMed: 9721639
DOI: 10.1046/j.1365-2672.1998.00346.x -
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 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 -
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 -
Journal of the Formosan Medical... Jul 2007Bergeyella zoohelcum is a rod-shaped, aerobic, Gram-negative, non-motile and non-saccharolytic bacterium. It is frequently isolated from the upper respiratory tract of... (Review)
Review
Bergeyella zoohelcum is a rod-shaped, aerobic, Gram-negative, non-motile and non-saccharolytic bacterium. It is frequently isolated from the upper respiratory tract of dogs, cats and other mammals. Clinically, B. zoohelcum has been known to cause cellulitis, leg abscess, tenosynovitis, septicemia, pneumonia and meningitis, and is associated with animal bites. In addition, food-borne transmission was considered in a recent case report. We report a 73-year-old man with liver cirrhosis who had no history of dog bite but had dog exposure, who developed cellulitis of the left lower leg and B. zoohelcum was isolated from blood culture. This patient, without evidence of polymicrobial infection, was treated with cefazolin and gentamicin with a good outcome. B. zoohelcum is a zoonotic pathogen that may cause bacteremia in patients with underlying disease such as liver cirrhosis; it can be treated with a beta-lactam or quinolone.
Topics: Aged; Animals; Bacteremia; Cellulitis; Dogs; Gram-Negative Aerobic Rods and Cocci; Humans; Male; Zoonoses
PubMed: 17660147
DOI: 10.1016/S0929-6646(07)60008-4 -
Open Forum Infectious Diseases Apr 2019is a new species in the family Flavobacteriaceae that was recently described in 3 cases of native valve infective endocarditis. We report the first case of prosthetic...
is a new species in the family Flavobacteriaceae that was recently described in 3 cases of native valve infective endocarditis. We report the first case of prosthetic valve endocarditis, provide the first draft genome of this species, and review the microbiologic characteristics of this emerging pathogen.
PubMed: 31024974
DOI: 10.1093/ofid/ofz134