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Journal of Proteome Research Jun 2024Gut microbiota-derived microbial compounds may link to the pathogenesis of colorectal cancer (CRC). However, the role of the host-microbiome in the incidence and...
Gut microbiota-derived microbial compounds may link to the pathogenesis of colorectal cancer (CRC). However, the role of the host-microbiome in the incidence and progression of CRC remains elusive. We performed 16S rRNA sequencing, metabolomics, and proteomic studies on samples from 85 CRC patients who underwent colonoscopy examination and found two distinct changed patterns of microbiome in CRC patients. The relative abundances of and continuously increased from intramucosal carcinoma to advanced stages, whereas , , , , , and were significantly altered only in intermediate lesions. Fecal metabolomics analysis exhibited consistent increases in bile acids, indoles, and urobilin as well as a decrease in heme. Serum metabolomics uncovered the highest levels of bilin, glycerides, and nucleosides together with the lowest levels of bile acids and amino acids in the stage of intermediate lesions. Three fecal and one serum dipeptides were elevated in the intermediate lesions. Proteomics analysis of colorectal tissues showed that oxidation and autophagy through the PI3K/Akt-mTOR signaling pathway contribute to the development of CRC. Diagnostic analysis showed multiomics features have good predictive capability, with AUC greater than 0.85. Our overall findings revealed new candidate biomarkers for CRC, with potentially significant diagnostic and prognostic capabilities.
Topics: Humans; Colorectal Neoplasms; Proteomics; Gastrointestinal Microbiome; Feces; Metabolomics; Male; RNA, Ribosomal, 16S; Female; Middle Aged; Aged; Signal Transduction; Biomarkers, Tumor; Multiomics
PubMed: 38634357
DOI: 10.1021/acs.jproteome.3c00894 -
Journal of Periodontal Research Oct 2023To investigate the existence of any association between new putative periodontal pathogens and periodontitis. Two independent reviewers conducted electronic literature... (Meta-Analysis)
Meta-Analysis Review
To investigate the existence of any association between new putative periodontal pathogens and periodontitis. Two independent reviewers conducted electronic literature searches in the MEDLINE (PubMed), EMBASE, DOSS and Google Scholar databases as well as a manual search to identify eligible clinical studies prior to November 2022. Studies comparing the prevalence of microorganisms other than the already-known periodontal pathogens in subgingival plaque and/or saliva samples between subjects with periodontitis and subject with periodontal health were included. Meta-analyses were performed on data provided by the included studies. Fifty studies including a total of 2739 periodontitis subjects and 1747 subjects with periodontal health were included. The Archaea domain and 25 bacterial species (Anaeroglobus geminatus, Bacteroidales [G-2] bacterium HMT 274, Desulfobulbus sp. HMT 041, Dialister invisus, Dialister pneumosintes, Eubacterium brachy, Enterococcus faecalis, Eubacterium nodatum, Eubacterium saphenum, Filifactor alocis, Fretibacterium sp. HMT 360, Fretibacterium sp. HMT 362, Mogibacterium timidum, Peptoniphilaceae sp. HMT 113, Peptostreptococcus stomatis, Porphyromonas endodontalis, Slackia exigua, Streptococcus gordonii, Selenomonas sputigena, Treponema amylovorum, Treponema lecithinolyticum, Treponema maltophilum, Treponema medium, Treponema parvum and Treponema socranskii) were found to be statistically significantly associated with periodontitis. Network studies should be conducted to investigate the role of these newly identified periodontitis-associated microorganisms through interspecies interaction and host-microbe crosstalk analyses.
Topics: Humans; Bacteria; Periodontitis; Dental Plaque; Bacteroides; Eubacterium
PubMed: 37572051
DOI: 10.1111/jre.13173 -
JDR Clinical and Translational Research Jul 2024Common oral diseases are known to be associated with dysbiotic shifts in the supragingival microbiome, yet most oral microbiome associations with clinical end points...
INTRODUCTION
Common oral diseases are known to be associated with dysbiotic shifts in the supragingival microbiome, yet most oral microbiome associations with clinical end points emanate from cross-sectional studies. Orthodontic treatment is an elective procedure that can be exploited to prospectively examine clinically relevant longitudinal changes in the composition and function of the supragingival microbiome.
METHODS
A longitudinal cohort study was conducted among 24 adolescent orthodontic patients who underwent saliva and plaque sampling and clinical examinations at time points: before fixed appliance bonding and at 1, 6, and 12 wk thereafter. Clinical indices included bleeding on probing (BOP), mean gingival index (GI), probing depths (PDs), and plaque index (PI). To study the biologically (i.e., transcriptionally) active microbial communities, RNA was extracted from plaque and saliva for RNA sequencing and microbiome bioinformatics analysis. Longitudinal changes in microbiome beta diversity were examined using PERMANOVA tests, and the relative abundance of microbial taxa was measured using Kruskal-Wallis tests, Wilcoxon rank-sum tests, and negative binomial and zero-inflated mixed models.
RESULTS
Clinical measures of oral health deteriorated over time-the proportion of sites with GI and PI ≥1 increased by over 70% between prebonding and 12 wk postbonding while the proportion of sites with PD ≥4 mm increased 2.5-fold. , a health-associated species that antagonizes cariogenic pathogens, showed a lasting decrease in relative abundance during orthodontic treatment. Contrarily, caries- and periodontal disease-associated taxa, including , , and , increased in abundance after bonding. Relative abundances of and in prebonding saliva predicted elevated BOP 12 wk postbonding, whereas was associated with lower BOP.
CONCLUSIONS
This study offers insights into longitudinal community and species-specific changes in the supragingival microbiome transcriptome during fixed orthodontic treatment, advancing our understanding of microbial dysbioses and identifying targets of future health-promoting clinical investigations.
KNOWLEDGE TRANSFER STATEMENT
Bonding braces was associated with subsequent changes in the oral microbiome characterized by increases in disease-associated species, decreases in health-associated species, and worsened clinical measures of oral health.
Topics: Humans; Longitudinal Studies; Adolescent; Male; Biofilms; Female; Microbiota; Saliva; Transcriptome; Dental Plaque; Orthodontics; Gingiva; Child
PubMed: 37876206
DOI: 10.1177/23800844231199393 -
Journal of Clinical Periodontology Nov 2023Since blood metabolomic profiles of obese individuals are known to be altered, our objective was to examine the association between obesity-related metabolic patterns...
AIM
Since blood metabolomic profiles of obese individuals are known to be altered, our objective was to examine the association between obesity-related metabolic patterns and subgingival microbial compositions in obese and non-obese periodontally healthy individuals.
MATERIALS AND METHODS
Thirty-nine periodontally healthy subjects were enrolled. Based on body mass index scores, 20 subjects were categorized as lean and 19 as obese. A comprehensive periodontal examination was performed. Subgingival plaque and blood samples were collected. Plaque samples were analysed for bacteria using 16S rDNA sequencing. Untargeted metabolomic profiling (mass spectrometry) was used to quantify metabolites in serum.
RESULTS
Obese subjects were statistically associated with several periodontopathic taxa including Dialister invisus, Prevotella intermedia, Prevotella denticola, Fusobacterium nucleatum_subsp.vincentii, Mogibacterium diversum, Parvimonas micra and Shuttleworthia satelles. In obese individuals, an amino acid-related metabolic pattern was elevated; however, there was a decrease in metabolic patterns related to lipids and cofactor/vitamins. These metabolic perturbations were associated with multiple subgingival bacterial species that differentiated lean from obese individuals.
CONCLUSIONS
Obesity-related perturbations in circulating blood metabolites are associated with the development of periodontopathic bacterial colonization in the subgingival microbiome and consequently may increase the risk for periodontal disease in obese individuals.
PubMed: 37536958
DOI: 10.1111/jcpe.13860 -
PloS One 2024Osteomyelitis of the jaw is a severe inflammatory disorder that affects bones, and it is categorized into two main types: chronic bacterial and nonbacterial...
Osteomyelitis of the jaw is a severe inflammatory disorder that affects bones, and it is categorized into two main types: chronic bacterial and nonbacterial osteomyelitis. Although previous studies have investigated the association between these diseases and the oral microbiome, the specific taxa associated with each disease remain unknown. In this study, we conducted shotgun metagenome sequencing (≥10 Gb from ≥66,395,670 reads per sample) of bulk DNA extracted from saliva obtained from patients with chronic bacterial osteomyelitis (N = 5) and chronic nonbacterial osteomyelitis (N = 10). We then compared the taxonomic composition of the metagenome in terms of both taxonomic and sequence abundances with that of healthy controls (N = 5). Taxonomic profiling revealed a statistically significant increase in both the taxonomic and sequence abundance of Mogibacterium in cases of chronic bacterial osteomyelitis; however, such enrichment was not observed in chronic nonbacterial osteomyelitis. We also compared a previously reported core saliva microbiome (59 genera) with our data and found that out of the 74 genera detected in this study, 47 (including Mogibacterium) were not included in the previous meta-analysis. Additionally, we analyzed a core-genome tree of Mogibacterium from chronic bacterial osteomyelitis and healthy control samples along with a reference complete genome and found that Mogibacterium from both groups was indistinguishable at the core-genome and pan-genome levels. Although limited by the small sample size, our study provides novel evidence of a significant increase in Mogibacterium abundance in the chronic bacterial osteomyelitis group. Moreover, our study presents a comparative analysis of the taxonomic and sequence abundances of all genera detected using deep salivary shotgun metagenome data. The distinct enrichment of Mogibacterium suggests its potential as a marker to distinguish between patients with chronic nonbacterial osteomyelitis and chronic bacterial osteomyelitis, particularly at the early stages when differences are unclear.
Topics: Humans; Saliva; Osteomyelitis; Female; Microbiota; Male; Middle Aged; Metagenomics; Chronic Disease; Adult; Metagenome; Aged
PubMed: 38709734
DOI: 10.1371/journal.pone.0302569 -
Progress in Neuro-psychopharmacology &... Dec 2023Previous studies have reported a variety of gut microbiota alterations in patients with schizophrenia. However, none of these studies has investigated gut microbiota in...
BACKGROUND
Previous studies have reported a variety of gut microbiota alterations in patients with schizophrenia. However, none of these studies has investigated gut microbiota in patients with the deficit subtype of schizophrenia (D-SCZ) that can be characterized by primary and enduring negative symptoms. Therefore, in this study we aimed to profile gut microbiota of individuals with D-SCZ, compared to those with non-deficit schizophrenia (ND-SCZ) and healthy controls (HCs).
METHODS
A total of 115 outpatients (44 individuals with D-SCZ and 71 individuals with ND-SCZ) during remission of positive and disorganization symptoms as well as 120 HCs were enrolled. Gut microbiota was analyzed using the 16 rRNA amplicon sequencing. Additionally, the levels of C-reactive protein (CRP), glucose and lipid metabolism markers were determined in the peripheral blood samples.
RESULTS
Altogether 14 genera showed differential abundance in patients with D-SCZ compared to ND-SCZ and HCs, including Candidatus Soleaferrea, Eubacterium, Fusobacterium, Lachnospiraceae UCG-002, Lachnospiraceae UCG-004, Lachnospiraceae UCG-010, Libanicoccus, Limosilactobacillus, Mogibacterium, Peptococcus, Prevotella, Prevotellaceae NK3B31 group, Rikenellaceae RC9 gut group, and Slackia after adjustment for potential confounding factors. Observed alterations were significantly associated with cognitive performance in both groups of patients. Moreover, several significant correlations of differentially abundant genera with the levels of CRP, lipid profile parameters, glucose and insulin were found across all subgroups of participants.
CONCLUSION
Findings from the present study indicate that individuals with D-SCZ show a distinct profile of gut microbiota alterations that is associated with cognitive performance, metabolic parameters and subclinical inflammation.
Topics: Humans; Gastrointestinal Microbiome; Schizophrenia; Case-Control Studies; Glucose; Clostridiales
PubMed: 37473955
DOI: 10.1016/j.pnpbp.2023.110834 -
Microorganisms Nov 2023During weaning, piglets experience various stressor events that disrupt their gut microbiota and immune balance, decrease growth parameters, and increase mortality...
During weaning, piglets experience various stressor events that disrupt their gut microbiota and immune balance, decrease growth parameters, and increase mortality rates. In this study, we assessed the efficacy of CACC616 as a probiotic supplement. We characterized this strain and evaluated its effect on improving growth performance, modulating gut microbiota composition, and reducing noxious odor components in weaned piglets compared to a non-supplementary diet (control). During the 26-day period, 40 crossbred weaned piglets were randomly assigned to pens with 20 animals each in two groups: control and treatment groups with CACC616. On day 26, the treatment group exhibited a lower feed conversion ratio (FCR) and a significant alteration in gut microbial composition, correlating with improved growth parameters and gut health ( < 0.05). The treatment group also exhibited significantly reduced digestibility- and intestinal-environment-related noxious odor components ( < 0.05). The CACC616 strain effectively reduced pathogenic genera numbers, including , , and spp., with the treatment group exhibiting lower fecal calprotectin levels than the control group ( < 0.05). Overall, this study revealed that the functional probiotic CACC616 contributes to enhanced FCR and effectively modulates weaned piglets' inflammation and intestinal microbiota.
PubMed: 38138034
DOI: 10.3390/microorganisms11122890 -
Medicine Aug 2023This study aimed to investigate the characteristics of intestinal flora in patients with chronic functional constipation before and after lactulose intervention....
This study aimed to investigate the characteristics of intestinal flora in patients with chronic functional constipation before and after lactulose intervention. Twenty-nine patients with constipation in the treatment group received oral lactulose (15 mL/d) for a month. Twenty healthy subjects served as controls. Stool specimens were collected before and after lactulose treatment. Fecal bacteria were examined by 16SrRNA gene sequencing and bioinformatics analysis. After lactulose treatment, most bacteria in the constipation group, including Bifidobacteria, Bacillus cereus, Prevotella, Bacillus, Anaerostipes, Oribacterium, and Mogibacterium increased as compared to those in the healthy control group. Anaerotruncus declined in the healthy control group after lactulose treatment. Our study shows lactulose can increase the abundance of probiotics, optimize the intestinal microenvironment, and alleviate constipation.
Topics: Humans; Lactulose; Gastrointestinal Microbiome; Constipation; Feces; Bacteria
PubMed: 37565923
DOI: 10.1097/MD.0000000000034703 -
International Endodontic Journal Aug 2024To investigate the bacteriome present in teeth with primary endodontic infection (PEI) and apical periodontitis (AP) and to determine quantitatively and qualitatively...
AIM
To investigate the bacteriome present in teeth with primary endodontic infection (PEI) and apical periodontitis (AP) and to determine quantitatively and qualitatively the impact of chemomechanical preparation (CMP) using 2.5% sodium hypochlorite NAOCl on the bacteriome found in PEI with AP using the Illumina MiSeq platform.
METHODOLOGY
Thirty-six paired samples from 18 patients were successfully sequenced and analysed. Samples were collected at two sampling times: before (s1) and after (s2) CMP using 2.5% NaOCl. The DNA was extracted from s1 and s2 samples and quantified using quantitative PCR (qPCR). All 36 samples were sequenced using the Illumina MiSeq platform. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants (ASVs). Alpha diversity metrics representing abundance (Chao1) and diversity and evenness (Shannon, Simpson) were computed. The paired-sample Wilcoxon's test was used to compare alpha diversity metrics and qPCR counts between s1 and s2. The PERMANOVA method (with 999 permutations) was applied to compare community composition between sample types (s1 versus s2) and between patient IDs. ALDEx2 (ANOVA-like differential expression tool for high-throughput sequencing data) to investigate differentially abundant taxa between s1 and s2. A paired-sample Wilcoxon's test was used to compare alpha diversity metrics and qPCR counts between s1 and s2.
RESULTS
The qPCR counts were significantly higher in s1 compared to s2 (p = .0007). The Chao1 index indicated no difference in alpha diversity (p < .7019); whereas Shannon (p = .0056) and Simpson (p = .02685) indexes showed higher values in s2. The PERMANOVA test using Adonis2 showed a significant effect of sample time on community composition (R = .0630, p = .012). Patient ID also showed a significant effect on community composition (R = .6961, p = .001). At the genus level, Dialister, Mogibacterium, Prevotella, and Olsenella were differentially enriched at s1, while Actinomyces, Stenotrophomonas_unclassified, Enterococcus_unclassified, and Actinomyces_unclassified were differentially enriched in s2.
CONCLUSION
The bacteriome present in teeth with PEI with AP is complex and diverse. CMP using 2.5% NaOCl showed a high quantitatively and qualitatively disinfectant impact on the bacteriome present in PEI with AP.
Topics: Humans; Periapical Periodontitis; High-Throughput Nucleotide Sequencing; Sodium Hypochlorite; Root Canal Preparation; Adult; Disinfection; Dental Pulp Cavity; Male; Female; Root Canal Irrigants; DNA, Bacterial; Middle Aged; Microbiota; Root Canal Therapy; Bacteria
PubMed: 38700876
DOI: 10.1111/iej.14074 -
Anais Brasileiros de Dermatologia 2023Psoriasis is a chronic inflammatory disease associated with systemic inflammation and comorbidities. Changes in the composition of the intestinal microbiome are involved...
BACKGROUND
Psoriasis is a chronic inflammatory disease associated with systemic inflammation and comorbidities. Changes in the composition of the intestinal microbiome are involved in the pathogenesis of inflammatory diseases and metabolic syndrome. Characterizing the intestinal microbiome of patients with psoriasis may be relevant for the understanding of its clinical course and comorbidity prevention.
OBJECTIVE
To characterize the intestinal microbiome of men with psoriasis compared to omnivore and vegetarian controls (without psoriasis).
METHOD
Cross-sectional study of 42 adult males: 21 omnivores with psoriasis; and controls: 14 omnivores and 7 vegetarian individuals. The characterization of the intestinal microbiome was performed by metagenomic analysis. Serum levels of lipopolysaccharide-binding protein (LPB) and C-reactive protein (CRP) were evaluated.
RESULTS
The groups differed from each other regarding nutritional aspects and microbiome; individuals with psoriasis had a higher consumption of protein and lower consumption of fibers. Levels of LPB, CRP, and the Firmicutes/Bacteroidetes ratio were higher in the group with psoriasis than in the vegetarian group (p<0.05). The genera Prevotella, Mogibacterium, Dorea, Bifidobacterium and Coprococcus, differed in the group with psoriasis compared to vegetarians; the genera Mogibacterium, Collinsella and Desulfovibrio differed from omnivores. A microbiome pattern linked to psoriasis (plsPSO) was identified, which was associated with higher LPB levels (rho=0.39; p=0.02), and lower dietary fiber intake (rho=-0.71; p<0.01).
STUDY LIMITATIONS
Only adult men were evaluated.
CONCLUSION
A difference was identified in the intestinal microbiome of adult men with psoriasis when compared to healthy omnivores and vegetarian controls. The identified microbiome pattern was correlated with dietary fiber intake and serum levels of LPB.
Topics: Male; Humans; Adult; Diet; Diet, Vegetarian; Gastrointestinal Microbiome; Cross-Sectional Studies; Brazil; Vegetarians; Dietary Fiber; Psoriasis
PubMed: 37156688
DOI: 10.1016/j.abd.2022.08.008