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Frontiers in Microbiology 2022Dental caries remains the most common chronic disease in children, and the respective etiology is not fully understood. Though is an important factor in the initiation...
Dental caries remains the most common chronic disease in children, and the respective etiology is not fully understood. Though is an important factor in the initiation and progression of caries, its presence is not always associated with the disease. The existence of caries discordant populations, in which counts do not correlate with caries experience, poses a challenging problem. This study explored the possible correlation of S. and other microorganism levels on caries-associated ecology of caries-concordant and discordant populations. A total of forty-seven children were analyzed in this study and stratified into four clinical groups based on their levels in saliva (HS/LS: High/low ) and caries experience. levels were determined by culture-based selective plating. The salivary microbiome of caries concordant and discordant populations was investigated by 16S rRNA gene sequencing and downstream bioinformatics analysis. The salivary microbial communities significantly clustered based on levels and independent of their caries experience. In addition to levels, significant differences in the abundance of other species were observed between HS and LS groups. Interestingly, disease-associated species such as spp., and spp. were significantly increased in HS groups and may contribute, in combination with , to the caries progression. Furthermore, health-associated species exhibited higher abundance in the LS groups, such as sp., and spp. but their possible contribution to the caries process remains to be elucidated. This study provides evidence that may play a role in shaping the salivary microbial community. Our results highlight that future caries research should consider additional species as health/disease microbial markers in conjunction with to improve diagnosis and caries management of the caries-discordant population.
PubMed: 35250921
DOI: 10.3389/fmicb.2022.782825 -
Microbiology Spectrum Mar 2023spp. are obligate, anaerobic, Gram-negative bacteria found in the human oral cavity and gut. Recent studies have indicated that gut promote human homeostasis by...
spp. are obligate, anaerobic, Gram-negative bacteria found in the human oral cavity and gut. Recent studies have indicated that gut promote human homeostasis by producing beneficial metabolites, specifically short-chain fatty acids (SCFAs), by lactate fermentation. The gut lumen is a dynamic environment with fluctuating nutrient levels, so the microbes present shifting growth rates and significant variations of gene expression. The current knowledge of lactate metabolism by has focused on log phase growth. However, the gut microbes are mainly in the stationary phase. In this study, we investigated the transcriptomes and major metabolites of Veillonella dispar ATCC 17748 during growth from log to stationary phases with lactate as the main carbon source. Our results revealed that reprogrammed its lactate metabolism during the stationary phase. Lactate catabolic activity and propionate production were significantly decreased during the early stationary phase but were partially restored during the stationary phase. The propionate/acetate production ratio was lowered from 1.5 during the log phase to 0.9 during the stationary phase. Pyruvate secretion was also greatly decreased during the stationary phase. Furthermore, we have demonstrated that the gene expression of is reprogrammed during growth, as evidenced by the distinct transcriptomes present during the log, early stationary, and stationary phases. In particular, propionate metabolism (the propanediol pathway) was downregulated during the early stationary phase, which explains the decrease in propionate production during the stationary phase. The fluctuations in lactate fermentation during the stationary phase and the associated gene regulation expand our understanding of the metabolism of commensal anaerobes in changing environments. Short-chain fatty acids produced by gut commensal bacteria play an important role in human physiology. Gut and the metabolites acetate and propionate, produced by lactate fermentation, are associated with human health. Most gut bacteria in humans are in the stationary phase. Lactate metabolism by spp. during the stationary phase is poorly understood and was therefore the focus of the study. To this end, we used a commensal anaerobic bacterium and explored its short-chain fatty acid production and gene regulation in order to provide a better understanding of lactate metabolism dynamics during nutrient limitation.
PubMed: 36975840
DOI: 10.1128/spectrum.03558-22 -
Scientific Reports Nov 2023Limited data exist on longitudinal changes in the sputum bacterial microbiome during treatment in nontuberculous mycobacterial pulmonary disease (NTM-PD) patients. We...
Limited data exist on longitudinal changes in the sputum bacterial microbiome during treatment in nontuberculous mycobacterial pulmonary disease (NTM-PD) patients. We prospectively collected serial sputum samples from 14 NTM-PD patients during treatment, at the start (n = 14) and at 1 (n = 10), 3 (n = 10), 6 (n = 12), and 12 (n = 7) months. The bacterial microbiome changes were analyzed using 16S rRNA sequences (V3-V4 regions). Subgroup analysis included culture conversion (n = 9) and treatment refractory (n = 5) groups. In all patients, sputum alpha-diversity (ACE, Chao1, and Jackknife) significantly decreased during antibiotic treatment at 1, 3, 6, and 12 months compared to treatment initiation levels. Within the culture conversion group, genus/species-level beta-diversity showed differences at 1, 3, 6, and 12 months compared to treatment initiation (all p < 0.05). However, in the refractory group, there were no differences in beta-diversity at the genus/species levels in the sputum at any time point. In the linear discriminant analysis (LDA) effect sizes (LEfSe) analysis, the culture conversion group exhibited decreasing taxa at various levels (phylum/genus/species), but no significant increase in taxa was observed. LEfSe analysis of the refractory patient group revealed multiple taxa decreased during treatment. However, proportions of Veillonella dispar (LDA = 4.78), Fusobacterium periodonticum (LDA = 4.35), and Pseudomonas aeruginosa (LDA = 2.92) increased as the treatment period progressed in the refractory group. Sputum microbiota diversity decreases during NTM-PD treatment. In the culture conversion group, most taxa decrease, while some increase in the refractory group. These findings suggest that a distinct respiratory microbial community may exist in refractory NTM-PD patients compared to responsive antibiotic-treated patients.
Topics: Humans; Sputum; RNA, Ribosomal, 16S; Mycobacterium Infections, Nontuberculous; Microbiota; Anti-Bacterial Agents; Bacteria; Lung Diseases
PubMed: 37957253
DOI: 10.1038/s41598-023-47230-5 -
Scientific Reports Nov 2023Crohn's disease (CD) is a chronic inflammatory bowel disease. An imbalanced microbiome (dysbiosis) can predispose to many diseases including CD. The role of oral...
Crohn's disease (CD) is a chronic inflammatory bowel disease. An imbalanced microbiome (dysbiosis) can predispose to many diseases including CD. The role of oral dysbiosis in CD is poorly understood. We aimed to explore microbiome signature and dysbiosis of the salivary microbiome in CD patients, and correlate microbiota changes to the level of inflammation. Saliva samples were collected from healthy controls (HC) and CD patients (n = 40 per group). Salivary microbiome was analyzed by sequencing the entire 16S rRNA gene. Inflammatory biomarkers (C-reactive protein and calprotectin) were measured and correlated with microbiome diversity. Five dominant species were significantly enriched in CD, namely Veillonella dispar, Megasphaera stantonii, Prevotella jejuni, Dolosigranulum pigrum and Lactobacillus backii. Oral health had a significant impact on the microbiome since various significant features were cariogenic as Streptococcus mutans or periopathogenic such as Fusobacterium periodonticum. Furthermore, disease activity, duration and frequency of relapses impacted the oral microbiota. Treatment with monoclonal antibodies led to the emergence of a unique species called Simonsiella muelleri. Combining immunomodulatory agents with monoclonal antibodies significantly increased multiple pathogenic species such as Salmonella enterica, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa. Loss of diversity in CD was shown by multiple diversity indices. There was a significant negative correlation between gut inflammatory biomarkers (particularly calprotectin) and α-diversity, suggesting more inflammation associated with diversity loss in CD. Salivary dysbiosis was evident in CD patients, with unique microbiota signatures and perturbed species that can serve as disease biomarkers or potential targets for microbiota modulation. The interplay of various factors collectively contributed to dysbiosis, although each factor probably had a unique effect on the microbiome. The emergence of pathogenic bacteria in the oral cavity of CD patients is alarming since they can disturb gut homeostasis and induce inflammation by swallowing, or hematogenous spread of microbiota, their metabolites, or generated inflammatory mediators.
Topics: Humans; Crohn Disease; Dysbiosis; RNA, Ribosomal, 16S; Gastrointestinal Microbiome; Microbiota; Inflammation; Biomarkers; Antibodies, Monoclonal; Leukocyte L1 Antigen Complex
PubMed: 37932491
DOI: 10.1038/s41598-023-46714-8 -
MSystems Apr 2023Human gut dysbiosis is associated with type 2 diabetes mellitus (T2DM); however, the gut microbiome in pregnant women with pregestational type 2 diabetes mellitus (PGDM)...
Human gut dysbiosis is associated with type 2 diabetes mellitus (T2DM); however, the gut microbiome in pregnant women with pregestational type 2 diabetes mellitus (PGDM) remains unexplored. We investigated the alterations in the gut microbiota composition in pregnant women with or without PGDM. The gut microbiota was examined using 16S rRNA sequencing data of 234 maternal fecal samples that were collected during the first (T1), second (T2), and third (T3) trimesters. The PGDM group presented a reduction in the number of gut bacteria taxonomies as the pregnancies progressed. Linear discriminant analyses revealed that , , and Roseburia intestinalis were enriched in the PGDM group, whereas Bacteroides vulgatus, Faecalibacterium prausnitzii, Eubacterium rectale, Bacteroides uniformis, Eubacterium eligens, , Bacteroides fragilis, , , R-7, Roseburia inulinivorans, Streptococcus oralis, Prevotella melaninogenica, Neisseria perflava, Bacteroides ovatus, Bacteroides caccae, Veillonella dispar, and Haemophilus parainfluenzae were overrepresented in the control group. Correlation analyses showed that the PGDM-enriched taxa were correlated with higher blood glucose levels during pregnancy, whereas the taxonomic biomarkers of normoglycemic pregnancies exhibited negative correlations with glycemic traits. The microbial networks in the PGDM group comprised weaker microbial interactions than those in the control group. Our study reveals the distinct characteristics of the gut microbiota composition based on gestational ages between normoglycemic and PGDM pregnancies. Further longitudinal research involving women with T2DM at preconception stages and investigations using shotgun metagenomic sequencing should be performed to elucidate the relationships between specific bacterial functions and PGDM metabolic statuses during pregnancy and to identify potential therapeutic targets. The incidence of pregestational type 2 diabetes mellitus (PGDM) is increasing, with high rates of serious adverse maternal and neonatal outcomes that are strongly correlated with hyperglycemia. Recent studies have shown that type 2 diabetes mellitus is associated with gut microbial dysbiosis; however, the gut microbiome composition and its associations with the metabolic features of patients with PGDM remain largely unknown. In this study, we investigated the changes in the gut microbiota composition in pregnant women with and without PGDM. We identified differential taxa that may be correlated with maternal metabolic statuses during pregnancy. Additionally, we observed that the number of taxonomic and microbial networks of gut bacteria were distinctly reduced in women with hyperglycemia as their pregnancies progressed. These results extend our understanding of the associations between the gut microbial composition, PGDM-related metabolic changes, and pregnancy outcomes.
Topics: Infant, Newborn; Humans; Female; Pregnancy; Gastrointestinal Microbiome; Diabetes Mellitus, Type 2; Pregnant Women; Dysbiosis; RNA, Ribosomal, 16S; Pregnancy Outcome; Hyperglycemia
PubMed: 36853013
DOI: 10.1128/msystems.01146-22 -
JDR Clinical and Translational Research Jan 2024Describe associations between dental caries and dental plaque microbiome, by dentition and family membership.
OBJECTIVE
Describe associations between dental caries and dental plaque microbiome, by dentition and family membership.
METHODS
This cross-sectional analysis included 584 participants in the Center for Oral Health Research in Appalachia Cohort 1 (COHRA1). We sequenced the 16S ribosomal RNA gene (V4 region) of frozen supragingival plaque, collected 10 y prior, from 185 caries-active (enamel and dentinal) and 565 caries-free (no lesions) teeth using the Illumina MiSeq platform. Sequences were filtered using the R DADA2 package and assigned taxonomy using the Human Oral Microbiome Database.
RESULTS
Microbiomes of caries-active and caries-free teeth were most similar in primary dentition and least similar in permanent dentition, but caries-active teeth were significantly less diverse than caries-free teeth in all dentition types. Streptococcus mutans had greater relative abundance in caries-active than caries-free teeth in all dentition types ( < 0.01), as did in primary and mixed dentition ( < 0.01). sp. HMT 203 had significantly higher relative abundance in caries-free than caries-active teeth in all dentition types ( < 0.01). In a linear mixed model adjusted for confounders, the relative abundance of was significantly greater in plaque from caries-active than caries-free teeth ( < 0.001), and the relative abundance of sp. HMT 203 was significantly lower in plaque from caries-active than caries-free teeth ( < 0.001). Adding an effect for family improved model fit for sp. HMT 203 but not.
CONCLUSIONS
The diversity of supragingival plaque composition from caries-active and caries-free teeth changed with dentition, but was positively and sp. HMT 203 was negatively associated with caries regardless of dentition. There was a strong effect of family on the associations of sp. HMT 203 with the caries-free state, but this was not true for and the caries-active state.
KNOWLEDGE TRANSFER STATEMENT
Patients' and dentists' concerns about transmission of bacteria within families causing caries should be tempered by the evidence that some shared bacteria may contribute to good oral health.
Topics: Humans; Dental Caries; Dentition; Adenosine Deaminase; Cross-Sectional Studies; Dental Caries Susceptibility; Intercellular Signaling Peptides and Proteins; Microbiota; Streptococcus mutans
PubMed: 36154330
DOI: 10.1177/23800844221121260 -
GigaScience Apr 2020Changes to human respiratory tract microbiome may contribute significantly to the progression of respiratory diseases. However, there are few studies examining the...
BACKGROUND
Changes to human respiratory tract microbiome may contribute significantly to the progression of respiratory diseases. However, there are few studies examining the relative abundance of microbial communities at the species level along the human respiratory tract.
FINDINGS
Bronchoalveolar lavage, throat swab, mouth rinse, and nasal swab samples were collected from 5 participants. Bacterial ribosomal operons were sequenced using the Oxford Nanopore MinION to determine the relative abundance of bacterial species in 4 compartments along the respiratory tract. More than 1.8 million raw operon reads were obtained from the participants with ∼600,000 rRNA reads passing quality assurance/quality control (70-95% identify; >1,200 bp alignment) by Discontiguous MegaBLAST against the EZ BioCloud 16S rRNA gene database. Nearly 3,600 bacterial species were detected overall (>750 bacterial species within the 5 dominant phyla: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria. The relative abundance of bacterial species along the respiratory tract indicated that most microbes (95%) were being passively transported from outside into the lung. However, a small percentage (<5%) of bacterial species were at higher abundance within the lavage samples. The most abundant lung-enriched bacterial species were Veillonella dispar and Veillonella atypica while the most abundant mouth-associated bacterial species were Streptococcus infantis and Streptococcus mitis.
CONCLUSIONS
Most bacteria detected in lower respiratory samples do not seem to colonize the lung. However, >100 bacterial species were found to be enriched in bronchoalveolar lavage samples (compared to mouth/nose) and may play a substantial role in lung health.
Topics: Bacteria; Bronchoalveolar Lavage Fluid; Humans; Lung; Microbiota; RNA, Ribosomal, 16S
PubMed: 32298431
DOI: 10.1093/gigascience/giaa038 -
Frontiers in Oncology 2019Nasopharyngeal carcinoma (NPC) is a malignant nasopharyngeal disease with a complicated etiology that occurs mostly in southern China. Intestinal flora imbalance is...
Nasopharyngeal carcinoma (NPC) is a malignant nasopharyngeal disease with a complicated etiology that occurs mostly in southern China. Intestinal flora imbalance is believed to be associated with a variety of organ malignancies. Current studies revealed that the destruction of intestinal flora is associated with NPC, and many studies have shown that intestinal flora can be used as a biomarker for many cancers and to predict cancer. To compare the differences in intestinal flora compositions and biological functions among 8 patients with familial NPC (NPC_F), 24 patients with sporadic NPC (NPC_S), and 27 healthy controls (NOR), we compared the intestinal flora DNA sequencing and hematological testing results between every two groups using bioinformatic methods. Compared to the NOR group, the intestinal flora structures of the patients in the NPC_F and NPC_S groups showed significant changes. In NPC_F, spp., spp., and spp. were significantly increased, and and spp. were significantly reduced. In NPC_S, , and spp. were significantly increased, and was significantly reduced. A beta diversity analysis showed significant difference compared NPC_F with NOR based on Bray Curtis ( = 0.012) and Unweighted UniFrac ( = 0.0045) index, respectively. The areas under the ROC curves plotted were all 1. Additionally, the concentrations of 5-hydroxytryptamine (5-HT) in NPC_F and NPC_S were significantly higher than those of NOR. was positively correlated with 5-HT (rcm: 0.85, < 0.001). A functional analysis of the intestinal flora showed that NPC_F was associated with Neurodegenerative Diseases ( = 0.023) and that NPC_S was associated with Neurodegenerative Diseases ( = 0.045) as well. We found that NPC was associated with structural imbalances in the intestinal flora, with that promoted the elevation of 5-HT and opportunistic pathogens being significantly increased, while probiotics significantly decreased. can be used as a novel biomarker and disease prediction models should be established for NPC. The new biomarkers and disease prediction models may be used for disease risk prediction and the screening of high-risk populations, as well as for the early noninvasive diagnosis of NPC.
PubMed: 31867274
DOI: 10.3389/fonc.2019.01346 -
Infection and Immunity Oct 2022Root caries in geriatric patients is a growing problem as more people are maintaining their natural teeth into advanced age. We determined the levels of various...
Root caries in geriatric patients is a growing problem as more people are maintaining their natural teeth into advanced age. We determined the levels of various bacterial species previously implicated in root caries disease or health using quantitative real-time PCR in a pilot study of 7 patients with 1 to 4 root caries lesions per person. Levels of 12 different species on diseased roots compared to healthy (contralateral control) roots were measured. Four species were found at significantly higher levels on diseased roots (Streptococcus mutans, Veillonella parvula/dispar, Actinomyces naeslundii/viscosus, and Capnocytophaga granulosa) compared across all plaque samples. The level of colonization by these species varied dramatically (up to 1,000-fold) between patients, indicating different patients have different bacteria contributing to root caries disease. Neither of the two species previously reported to correlate with healthy roots (C. granulosa and Delftia acidovorans) showed statistically significant protective roles in our population, although D. acidovorans showed a trend toward higher levels on healthy teeth (0.08). There was a significant positive correlation between higher levels of S. mutans and V. parvula/dispar on the same diseased teeth. mixed biofilm studies demonstrated that co-culturing S. mutans and V. parvula leads to a 50 to 150% increase in sucrose-dependent biofilm mass compared to S. mutans alone, depending on the growth conditions, while V. parvula alone did not form biofilms. The presence of V. parvula also decreased the acidification of S. mutans biofilms when grown in artificial saliva and enhanced the health of mixed biofilms.
Topics: Humans; Aged; Streptococcus mutans; Root Caries; Saliva, Artificial; Pilot Projects; Veillonella; Biofilms; Sucrose; Dental Caries
PubMed: 36129298
DOI: 10.1128/iai.00355-22 -
Frontiers in Cellular and Infection... 2020Efforts to map gingival tissue proteomes and microbiomes have been hampered by lack of sufficient tissue extraction methods. The pressure cycling technology (PCT) is an...
Efforts to map gingival tissue proteomes and microbiomes have been hampered by lack of sufficient tissue extraction methods. The pressure cycling technology (PCT) is an emerging platform for reproducible tissue homogenisation and improved sequence retrieval coverage. Therefore, we employed PCT to characterise the proteome and microbiome profiles in healthy and diseased gingival tissue. Healthy and diseased contralateral gingival tissue samples (total = 10) were collected from five systemically healthy individuals (51.6 ± 4.3 years) with generalised chronic periodontitis. The tissues were then lysed and digested using a Barocycler, proteins were prepared and submitted for mass spectrometric analysis and microbiome DNA for 16S rRNA profiling analysis. Overall, 1,366 human proteins were quantified (false discovery rate 0.22%), of which 69 proteins were differentially expressed (≥2 peptides and < 0.05, 62 up, 7 down) in periodontally diseased sites, compared to healthy sites. These were primarily extracellular or vesicle-associated proteins, with functions in molecular transport. On the microbiome level, 362 species-level operational taxonomic units were identified. Of those, 14 predominant species accounted for >80% of the total relative abundance, whereas 11 proved to be significantly different between healthy and diseased sites. Among them, sp. HMT253 and and were associated with disease sites and strongly interacted ( > 0.7) with 30 and 6 up-regulated proteins, respectively. Healthy-site associated strains sp. HMT478 and sp. HMT417 showed strong negative interactions ( < -0.7) with 31, 21, 9, and 18 up-regulated proteins, respectively. In contrast the down-regulated proteins did not show strong interactions with the regulated bacteria. The present study identified the proteomic and intra-tissue microbiome profile of human gingiva by employing a PCT-assisted workflow. This is the first report demonstrating the feasibility to analyse full proteome profiles of gingival tissues in both healthy and disease sites, while deciphering the tissue site-specific microbiome signatures.
Topics: Fusobacterium; Gingiva; Humans; Microbiota; Proteome; Proteomics; RNA, Ribosomal, 16S; Streptococcus; Veillonella
PubMed: 33117738
DOI: 10.3389/fcimb.2020.588155