-
Nutrients Nov 2023The objective of this study was to examine the correlation between gut microbiota and both age-related macular degeneration (AMD) and glaucoma. Mendelian randomization...
The objective of this study was to examine the correlation between gut microbiota and both age-related macular degeneration (AMD) and glaucoma. Mendelian randomization studies were conducted utilizing the data sourced from the genome-wide association study (GWAS) database for the gut microbiome, AMD, and glaucoma. Single nucleotide polymorphism (SNP) estimates were summarized through five Mendelian randomization (MR) methods. We utilized Cochran's Q statistic to evaluate the heterogeneity of the instrumental variables (IVs). Additionally, we employed a "leave-one-out" approach to verify the stability of our findings. Inverse variance weighted (IVW) suggests that Eubacterium (oxidoreducens group) and Parabacteroides had a protective effect on AMD. Both weighted median and IVW suggest that Lachnospiraceae (NK4A136 group) and Ruminococcaceae (UCG009) had a protective effect on AMD. However, both weighted median and IVW suggest that Dorea had a risk effect on AMD. Similarly, The IVW of Eubacterium (ventriosum group) showed a risk effect on AMD. The weighted median of Eubacterium (nodatum group), Lachnospiraceae (NC2004 group), and Roseburia had a risk effect on glaucoma. IVW suggested that Ruminococcaceae (UCG004) had a risk effect on glaucoma. Reverse MR analysis found a causal link between Eubacterium (nodatum group) and glaucoma. No causal relationships were found between AMD or glaucoma and the other mentioned bacterial groups. No significant heterogeneity or evidence of horizontal pleiotropy was detected. This study found that certain gut bacteria had protective effects on AMD, while others may be risk factors for AMD or glaucoma. Likewise, reverse MR found that glaucoma led to an increased abundance of certain gut bacteria. Further trials are needed to clarify the specific mechanisms involved.
Topics: Humans; Gastrointestinal Microbiome; Genome-Wide Association Study; Mendelian Randomization Analysis; Glaucoma; Macular Degeneration; Clostridiales; Lactobacillales
PubMed: 37960299
DOI: 10.3390/nu15214646 -
The Western Journal of Medicine Nov 1974The bacteriology of the gastrointestinal tract is rapidly changing in laboratory techniques and clinical correlations. The flora is found to be very complex,... (Review)
Review
The bacteriology of the gastrointestinal tract is rapidly changing in laboratory techniques and clinical correlations. The flora is found to be very complex, predominantly anaerobic, and importantly dependent on diet. An etiologic role for colon bacteria in colon cancer is suggested by correlations between epidemiologic data and prevalent dietary patterns and stool culture findings. Cultures from aspiration pneumonia, subphrenic abscess, and other intra-abdominal sepsis all yield anaerobes, and for best results antibiotic therapy should combat them as well as aerobes.
Topics: Adolescent; Adult; Aged; Anaerobiosis; Anti-Bacterial Agents; Bacteria; Child; Clostridium; Colonic Neoplasms; Diet; Eubacterium; Feces; Female; Humans; Intestines; Japan; Jejunum; Lung Abscess; Male; Middle Aged; Pneumonia, Aspiration; Sepsis; Stomach Neoplasms; Streptococcus; Subphrenic Abscess; United States
PubMed: 4617971
DOI: No ID Found -
Journal of Clinical Microbiology Aug 1987Three new species, Eubacterium nodatum, Eubacterium timidum, and Eubacterium brachy, were described, primarily from subgingival samples taken from patients with moderate...
Three new species, Eubacterium nodatum, Eubacterium timidum, and Eubacterium brachy, were described, primarily from subgingival samples taken from patients with moderate and severe adult periodontitis. Except for the isolation of E. brachy from a pleuropulmonary infection, these species have not been reported from other infected body sites. We report on the isolation of these species and an undescribed group (D-6) of asaccharolytic eubacteria also found in periodontal disease from numerous different sites of infection, mostly the head and neck. A similarity in cellular morphological properties of E. nodatum and Actinomyces sp. was noted previously. Additional similarities, particularly to Actinomyces israelii, that we found are the formation of molar tooth colonies and the isolation from cases of lumpy jaw and from the genital tract of women in association with the use of an intrauterine contraceptive device. E. timidum and E. brachy did not occur more often from any particular site outside of the head, neck, and respiratory tract. The group D-6 strains came from a variety of sites in the trunk and pelvis. These species are all obligately anaerobic, asaccharolytic, and generally nonreactive, and they grow poorly and slowly on media commonly used to isolate anaerobic bacteria. L-Lysine (0.5%) markedly stimulated the growth of E. nodatum and, to a lesser extent, another acetate- and butyrate-producing group, Eubacterium sp. group D-6, but we did not find comparable stimulants for the other species. We found the production of phenyl acetate to be a helpful marker in the identification of E. timidum and Eubacterium sp. group D-6. Although the isolation and identification of most of these species remain somewhat difficult, the evidence from dental infections and the present report suggests that these species are potential pathogens that are likely to be overlooked in infected clinical material without special attention to more prolonged incubation and use of enriched isolation media.
Topics: Bacterial Infections; Culture Media; Eubacterium; Female; Humans; Pelvic Inflammatory Disease; Periodontitis
PubMed: 3624445
DOI: 10.1128/jcm.25.8.1540-1545.1987 -
International Journal of Systematic and... Aug 2017Several strictly anaerobic bacteria that are Gram-stain-positive have the ability to use uric acid as the sole source of carbon and energy. The phylogeny of three such...
Proposal for the reclassification of obligately purine-fermenting bacteria Clostridium acidurici (Barker 1938) and Clostridium purinilyticum (Dürre et al. 1981) as Gottschalkia acidurici gen. nov. comb. nov. and Gottschalkiapurinilytica comb. nov. and of Eubacterium angustum (Beuscher and...
Several strictly anaerobic bacteria that are Gram-stain-positive have the ability to use uric acid as the sole source of carbon and energy. The phylogeny of three such species, Clostridium acidurici, Clostridium purinilyticum, and Eubacterium angustum, members of the Clostridium cluster XII that ferment purines, but not most amino acids or carbohydrates, has been re-examined, taking advantage of their recently sequenced genomes. Phylogenetic analyses, based on 16S rRNA gene sequences, protein sequences of RpoB and GyrB, and on a concatenated alignment of 50 ribosomal proteins, revealed tight clustering of C. acidurici and C. purinilyticum. Eubacterium angustum showed consistent association with C. acidurici and C. purinilyticum , but differed from these two in terms of the genome size, G+C content of its chromosomal DNA and its inability to form spores. We propose reassigning C. acidurici and C. purinilyticum to the novel genus Gottschalkia as Gottschalkia acidurici gen. nov. comb. nov. (the type species of the genus) and Gottschalkia purinilytica comb. nov., respectively. Eubacterium angustum is proposed to be reclassified as Andreesenia angusta gen. nov. comb. nov. Furthermore, based on the phylogenetic data and similar metabolic properties, we propose assigning genera Gottschalkia and Andreesenia to the novel family Gottschalkiaceae. Metagenomic sequencing data indicate the widespread distibution of organisms falling within the radiation of the proposed family Gottschalkiaceae in terrestrial and aquatic habitats from upstate New York to Antarctica, most likely due to their ability to metabolize avian-produced uric acid.
Topics: Bacterial Typing Techniques; Base Composition; Clostridium; DNA, Bacterial; DNA, Ribosomal; Eubacterium; Fatty Acids; Genes, Bacterial; Phylogeny; Purines; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 28853681
DOI: 10.1099/ijsem.0.002008 -
International Dental Journal Jun 2017The aim of this cross-sectional study was to evaluate the dental and periodontal health, as well as the microbiological and salivary conditions, of patients with and...
OBJECTIVE
The aim of this cross-sectional study was to evaluate the dental and periodontal health, as well as the microbiological and salivary conditions, of patients with and without diabetes mellitus (DM) who are receiving haemodialysis.
METHODS
One-hundred and fifty-nine haemodialysis patients were included and divided into groups according to the pre-existing diabetes status: DM or no DM. The oral examination included dental findings and assessment of the periodontal situation. The periodontal condition was classified as healthy/mild, moderate or severe periodontitis. Subgingival biofilm samples were analysed using the polymerase chain reaction. The salivary diagnostics included measurement of unstimulated and stimulated salivary flow, pH and buffer capacity. Statistical analyses used Fisher's test, the t-test and the Mann-Whitney U-test (α = 5%).
RESULTS
The dental findings showed no significant difference between patients with and without DM (P = 0.44). The prevalence of periodontitis was high (96% in patients with DM and 97% in patients who did not have DM) and there was no significant difference between the groups (P = 0.71). There was a higher prevalence of Porphyromonas gingivalis, Parvimonas micros, Eubacterium nucleatum and Capnocytophaga spp. in patients without DM (P < 0.05). The salivary pH was significantly higher in patients without DM (P < 0.01).
CONCLUSION
While differences in the prevalence of periodontal pathogenic bacteria and in the salivary pH were detected between the groups, the dental and periodontal status was comparable between patients with and without DM. Accordingly, DM appears to have no decisive influence on the oral health in patients treated with haemodialysis who have well-controlled diabetes.
Topics: Aged; Aged, 80 and over; Bacteria; Biofilms; Capnocytophaga; Cross-Sectional Studies; Dental Plaque; Diabetes Complications; Diabetes Mellitus; Eubacterium; Female; Germany; Gingival Hemorrhage; Health Status; Humans; Hydrogen-Ion Concentration; Male; Middle Aged; Oral Health; Periodontal Attachment Loss; Periodontal Diseases; Periodontal Index; Periodontal Pocket; Periodontitis; Porphyromonas gingivalis; Prevalence; Renal Dialysis; Saliva; Salivation
PubMed: 28547773
DOI: 10.1111/idj.12282 -
Frontiers in Cellular and Infection... 2022In this study, we examined the changes to the composition and function of the gut microbiota from patients with metabolic dysfunction-associated fatty liver disease...
PURPOSE
In this study, we examined the changes to the composition and function of the gut microbiota from patients with metabolic dysfunction-associated fatty liver disease (MAFLD).We compared patients in a case group (liver stiffness (LSM) ≥ 7.4 kPa) with a matched control group (LSM < 7.4 kPa) and investigated the correlation between characteristics of the microbiota and other biochemical indicators.
METHODS
The study looked at a total of 85 men with MAFLD, 17 of whom were in the case group and 68 of whom were in the control group. We measured waist circumference, blood pressure, and body mass index, as well as clinical parameters including liver stiffness, enzyme levels, cholesterol levels, and fat attenuation. Whole-genome shotgun sequencing technology and the MetaCyc database were then used to detect the composition and major pathways of the gut microbiota for each patient. Statistical analyses were performed, including the chi-square test, the student's t-test, the Wilcoxon rank-sum test, and the Mann-Whitney test.
RESULTS
Whole-genome sequencing showed that the composition of the gut microbiota in patients with an LSM of above 7.4 kPa was significantly different to that of the control group. There were seven bacterial species that were different between the two groups. Prevotella copri, Phascolarctobacterium succinatutens, Eubacterium biforme, and Collinsella aerofaciens were enriched in the case group (P < 0.05). Conversely, Bacteroides coprocola, Bacteroides stercoris and Clostridiales bacterium 1_7_47FAA were decreased in the case group (P < 0.05). Furthermore, after removing low abundance pathways, a total of 32 microbial pathways were found to be significantly different between the two groups. Most pathways enriched in the case group over the control were related to biosynthesis of metabolites including amino acids, vitamins, nucleosides, and nucleotides. Conclusion. The composition and function of the gut microbiota in patients with increased liver stiffness are significantly altered. This observation may provide new avenues to better understand the mechanism of liver fibrosis.
Topics: Bacteria; Clostridiales; Eubacterium; Gastrointestinal Microbiome; Humans; Liver; Male
PubMed: 35992168
DOI: 10.3389/fcimb.2022.873048 -
IDCases 2024species are a group of obligated anaerobic gram-positive bacilli that are recognized as commensals of the gastrointestinal tract flora. Cases of bacteremia mediated by...
species are a group of obligated anaerobic gram-positive bacilli that are recognized as commensals of the gastrointestinal tract flora. Cases of bacteremia mediated by are rare. This report describes a case of bacteremia caused by in an 82-year-old female with a history of a cecal perforation secondary to an obstructing sigmoid stricture. The results showed the utility of using whole genome sequencing to identify the causative agent and underlined the significance to identify anaerobic organisms in diagnostic microbiology practice and to perform antimicrobial susceptibility testing to guide therapy and enhance patient outcomes.
PubMed: 38774153
DOI: 10.1016/j.idcr.2024.e01989 -
Journal of Dental Research Jan 2016The oral microbiota was compared between Romanian adolescents with a high prevalence of caries and no dental care and Swedish caries-active and caries-free adolescents... (Comparative Study)
Comparative Study
The oral microbiota was compared between Romanian adolescents with a high prevalence of caries and no dental care and Swedish caries-active and caries-free adolescents in caries prevention programs and with a low prevalence of caries. Biofilm samples were analyzed by FLX+ pyrosequencing of the V1 to V4 hypervariable regions of the 16S rRNA gene and polymerase chain reaction (PCR)/quantitative PCR (qPCR) for Streptococcus mutans and Streptococcus sobrinus. Sequences obtained blasted to 9 phyla, 66 genera, and 401 human oral taxa (HOT) in the 16S rRNA Human Oral Microbiome Database, of which 295 were represented by ≥20 sequences. The Romanian adolescents had more sequences in Firmicutes and fewer in Actinobacteria phyla and more sequences in the genera Bacteroidetes [G-3], Porphyromonas, Abiotrophia, Filifactor, Peptostreptococcaceae [11][G-4], Pseudoramibacter, Streptococcus, and Neisseria and fewer in Actinomyces, Selenomonas, Veillonella, Campylobacter, and TM7 [G-1] than the Swedish groups. Multivariate modeling employing HOT, S. sobrinus and S. mutans (PCR/qPCR), and sugar snacks separated Romanian from Swedish adolescents. The Romanian adolescents' microbiota was characterized by a panel of streptococci, including S. mutans, S. sobrinus, and Streptococcus australis, and Alloprevotella, Leptotrichia, Neisseria, Porphyromonas, and Prevotella. The Swedish adolescents were characterized by sweet snacks, and those with caries activity were also characterized by Prevotella, Actinomyces, and Capnocytophaga species and those free of caries by Actinomyces, Prevotella, Selenomonas, Streptococcus, and Mycoplasma. Eight species including Streptococcus mitis and Streptococcus species HOT070 were prevalent in Romanian and Swedish caries-active subjects but not caries-free subjects. In conclusion, S. mutans and S. sobrinus correlated with Romanian adolescents with caries and with limited access to dental care, whereas S. mutans and S. sobrinus were detected infrequently in Swedish adolescents in dental care programs. Swedish caries-active adolescents were typically colonized by Actinomyces, Selenomonas, Prevotella, and Capnocytophaga. Hence, the role of mutans streptococci as a primary caries pathogen appears less pronounced in populations with prevention programs compared to populations lacking caries treatment and prevention strategies.
Topics: Abiotrophia; Actinobacteria; Actinomyces; Adolescent; Bacteroidetes; Biofilms; Campylobacter; Capnocytophaga; DMF Index; Dental Care; Dental Caries; Eubacterium; Fusobacteria; Gram-Negative Bacteria; Humans; Microbiota; Neisseria; Peptostreptococcus; Porphyromonas; Prevotella; Selenomonas; Snacks; Streptococcus; Streptococcus mutans; Streptococcus sobrinus; Veillonella
PubMed: 26442950
DOI: 10.1177/0022034515609554 -
Antioxidants (Basel, Switzerland) Nov 2022To systematically evaluate the effect of Gandankang (GDK) aqueous extract in alleviating acute and chronic liver injury. Forty-one chemical compounds were identified by...
Comprehensive Effect of Carbon Tetrachloride and Reversal of Gandankang Formula in Mice Liver: Involved in Oxidative Stress, Excessive Inflammation, and Intestinal Microflora.
To systematically evaluate the effect of Gandankang (GDK) aqueous extract in alleviating acute and chronic liver injury. Forty-one chemical compounds were identified by ultra-high performance liquid chromatography-linear trap quadrupole-orbitrap-tandem mass spectrometry (UHPLC-LTQ-Orbitrap-MS) from GDK. All dosages of GDK and Biphenyl diester (BD) improved CCl-induced acute and chronic liver injury. GDK curbed liver fibrosis and blocked the NF-κB pathway to effectively inhibit the hepatic inflammatory response. Additionally, GDK treatment reduced the abundance of , , , , and , in comparison with those in the CCl mice and elevated the abundance of and as evident from 16S rDNA sequencing. Correlation analysis showed that the abundance of and was positively correlated with inflammation, fibrosis, and oxidation indexes. This indicates that GDK ameliorates chronic liver injury by mitigating fibrosis and inflammation. Nrf2 pathway is the key target of GDK in inhibiting liver inflammation and ferroptosis. and played a vital role in attenuating liver fibrosis.
PubMed: 36421420
DOI: 10.3390/antiox11112234 -
PloS One 2022No microbiological criteria were included in the 2018 EFP-AAP classification of periodontal diseases that could be used to differentiate between stages and grades....
No microbiological criteria were included in the 2018 EFP-AAP classification of periodontal diseases that could be used to differentiate between stages and grades. Furthermore, differences in the subgingival microbiome depending on stage and grade have not been established. Sixty subgingival biofilm samples were collected in Spain (n = 30) and Colombia (n = 30) from three distinct patient categories: those with periodontal health/gingivitis (n = 20), those with stage I-II periodontitis (n = 20), and those with stage III-IV periodontitis (n = 20). Patients were evaluated by 16S rRNA gene amplification sequencing. Amplicon sequence variants were used to assign taxonomic categories compared to the Human Oral Microbiome Database (threshold ≥97% identity). Alpha diversity was established by Shannon and Simpson indices, and principal coordinate analysis, ANOSIM, and PERMANOVA of the UNIFRAC distances were performed using QIIME2. Although differences in the alpha diversity were observed between samples according to country, Filifactor alocis, Peptostreptococcaceae [XI][G-4] bacterium HMT 369, Fretibacterium fastidiosum, Lachnospiraceae [G-8] bacterium HMT 500, Peptostreptococcaceae [XI][G-5] [Eubacterium] saphenum, Peptostreptococcus stomatis, and Tannerella forsythia were associated with periodontitis sites in all stages. However, only F. alocis, Peptostreptococcaceae [XI][G-4] bacterium HMT 369, Peptostreptococcaceae [XI][G-9] [Eubacterium] brachy, Peptostreptococcaceae [XI][G-5] [Eubacterium] saphenum, and Desulfobulbus sp. HMT 041 were consistent in stage III-IV periodontitis in both countries. Porphyromonas gingivalis and Tannerella forsythia were differentially expressed in severe lesions in the countries studied. Although some non-cultivable microorganisms showed differential patterns between the different stages of periodontitis, they were not the same in the two countries evaluated. Further studies using larger samples with advanced next-generation techniques for high-throughput sequencing of phyla and non-cultivable bacteria within the subgingival microbiome could provide more insight into the differences between stages of periodontitis.
Topics: Eubacterium; Gingivitis; Humans; Microbiota; Periodontitis; Porphyromonas gingivalis; RNA, Ribosomal, 16S
PubMed: 35998186
DOI: 10.1371/journal.pone.0273523