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BMC Oral Health May 2024Patients with cleft lip and palate (CLP) have an oronasal communication differed from the closed state in healthy individuals, leading to a unique oral microbiome. This... (Comparative Study)
Comparative Study
BACKGROUND
Patients with cleft lip and palate (CLP) have an oronasal communication differed from the closed state in healthy individuals, leading to a unique oral microbiome. This study aimed to determine if variances in the oral microbiota persist among CLP patients who have received treatments for the closure of these fistulas compared to the microbiota of healthy individuals.
METHODS
Saliva samples were collected from a cohort comprising 28 CLP patients (CLP group) and 30 healthy controls (HC group). Utilizing 16S rRNA sequencing on the Illumina NovaSeq platform, we conducted a comprehensive analysis of the diversity and composition of the oral microbiota.
RESULTS
The analysis of the microbiota in the saliva samples revealed a total of 23 microbial phyla, 38 classes, 111 orders, 184 families, 327 genera and 612 species. The alpha diversity with microbial abundance and evenness indicated the significant difference between the CLP and HC groups. Principal coordinate analysis (PCoA) and the ADONIS test further supported the presence of distinct microorganisms between the two groups. The CLP group displayed elevated abundances of Neisseria, Haemophilus, Porphyromonas, and Granulicatella, as indicated by LefSe analysis. Conversely, Rothia, Veillonella, and Pauljensenia exhibited significant reductions in abundance in the CLP group. The results of the PICRUSt analysis indicated significant differences in the relative abundance of 25 KEGG pathways within the CLP group. Through Spearman correlation analysis, strong associations between Rothia, Veillonella, and Pauljensenia and 25 functional pathways linked to CLP were identified.
CONCLUSION
Findings of this study offer a thorough comprehension of the microbiome profiles of CLP patients after the restoration of oronasal structure and are anticipated to present innovative concepts for the treatment of CLP.
Topics: Humans; Cleft Palate; Cleft Lip; Microbiota; Male; Female; Saliva; Case-Control Studies; RNA, Ribosomal, 16S; Adolescent; Adult; Mouth; Child; Young Adult
PubMed: 38807164
DOI: 10.1186/s12903-024-04387-3 -
PLoS Pathogens May 2024The role of bacteria in the etiology of dental caries is long established, while the role of fungi has only recently gained more attention. The microbial invasion of...
The role of bacteria in the etiology of dental caries is long established, while the role of fungi has only recently gained more attention. The microbial invasion of dentin in advanced caries especially merits additional research. We evaluated the fungal and bacterial community composition and spatial distribution within carious dentin. Amplicon 16S rRNA gene sequencing together with quantitative PCR was used to profile bacterial and fungal species in caries-free children (n = 43) and 4 stages of caries progression from children with severe early childhood caries (n = 32). Additionally, healthy (n = 10) and carious (n = 10) primary teeth were decalcified, sectioned, and stained with Grocott's methenamine silver, periodic acid Schiff (PAS) and calcofluor white (CW) for fungi. Immunolocalization was also performed using antibodies against fungal β-D-glucan, gram-positive bacterial lipoteichoic acid, gram-negative endotoxin, Streptococcus mutans, and Candida albicans. We also performed field emission scanning electron microscopy (FESEM) to visualize fungi and bacteria within carious dentinal tubules. Bacterial communities observed included a high abundance of S. mutans and the Veillonella parvula group, as expected. There was a higher ratio of fungi to bacteria in dentin-involved lesions compared to less severe lesions with frequent preponderance of C. albicans, C. dubliniensis, and in one case C. tropicalis. Grocott's silver, PAS, CW and immunohistochemistry (IHC) demonstrated the presence of fungi within carious dentinal tubules. Multiplex IHC revealed that fungi, gram-negative, and gram-positive bacteria primarily occupied separate dentinal tubules, with rare instances of colocalization. Similar findings were observed with multiplex immunofluorescence using anti-S. mutans and anti-C. albicans antibodies. Electron microscopy showed monomorphic bacterial and fungal biofilms within distinct dentin tubules. We demonstrate a previously unrecognized phenomenon in which fungi and bacteria occupy distinct spatial niches within carious dentin and seldom co-colonize. The potential significance of this phenomenon in caries progression warrants further exploration.
Topics: Humans; Dental Caries; Dentin; Male; Child; Female; Child, Preschool; Bacteria; Fungi; RNA, Ribosomal, 16S
PubMed: 38805482
DOI: 10.1371/journal.ppat.1011865 -
Microbial Biotechnology May 2024The human gut hosts numerous ecological niches for microbe-microbe and host-microbe interactions. Gut lactate homeostasis in humans is crucial and relies on various...
Mutualistic interactions of lactate-producing lactobacilli and lactate-utilizing Veillonella dispar: Lactate and glutamate cross-feeding for the enhanced growth and short-chain fatty acid production.
The human gut hosts numerous ecological niches for microbe-microbe and host-microbe interactions. Gut lactate homeostasis in humans is crucial and relies on various bacteria. Veillonella spp., gut lactate-utilizing bacteria, and lactate-producing bacteria were frequently co-isolated. A recent clinical trial has revealed that lactate-producing bacteria in humans cross-feed lactate to Veillonella spp.; however, their interspecies interaction mechanisms remain unclear. Veillonella dispar, an obligate anaerobe commonly found in the human gut and oral cavity, ferments lactate into acetate and propionate. In our study, we investigated the interaction between V. dispar ATCC 17748 and three representative phylogenetically distant strains of lactic acid bacteria, Lactobacillus acidophilus ATCC 4356, Lacticaseibacillus paracasei subsp. paracasei ATCC 27216, and Lactiplantibacillus plantarum ATCC 10241. Bacterial growth, viability, metabolism and gene level adaptations during bacterial interaction were examined. V. dispar exhibited the highest degree of mutualism with L. acidophilus. During co-culture of V. dispar with L. acidophilus, both bacteria exhibited enhanced growth and increased viability. V. dispar demonstrated an upregulation of amino acid biosynthesis pathways and the aspartate catabolic pathway. L. acidophilus also showed a considerable number of upregulated genes related to growth and lactate fermentation. Our results support that V. dispar is able to enhance the fermentative capability of L. acidophilus by presumably consuming the produced lactate, and that L. acidophilus cross-feed not only lactate, but also glutamate, to V. dispar during co-culture. The cross-fed glutamate enters the central carbon metabolism in V. dispar. These findings highlight an intricate metabolic relationship characterized by cross-feeding of lactate and glutamate in parallel with considerable gene regulation within both L. acidophilus (lactate-producing) and V. dispar (lactate-utilizing). The mechanisms of mutualistic interactions between a traditional probiotic bacterium and a potential next-generation probiotic bacterium were elucidated in the production of short-chain fatty acids.
Topics: Lactic Acid; Fatty Acids, Volatile; Glutamic Acid; Veillonella; Symbiosis; Microbial Interactions; Humans; Lactobacillus acidophilus; Lactobacillus; Microbial Viability; Fermentation
PubMed: 38801349
DOI: 10.1111/1751-7915.14484 -
Journal of Translational Medicine May 2024Small intestinal bacterial overgrowth (SIBO) is the presence of an abnormally excessive amount of bacterial colonization in the small bowel. Hydrogen and methane breath...
BACKGROUND
Small intestinal bacterial overgrowth (SIBO) is the presence of an abnormally excessive amount of bacterial colonization in the small bowel. Hydrogen and methane breath test has been widely applied as a non-invasive method for SIBO. However, the positive breath test representative of bacterial overgrowth could also be detected in asymptomatic individuals.
METHODS
To explore the relationship between clinical symptoms and gut dysbiosis, and find potential fecal biomarkers for SIBO, we compared the microbial profiles between SIBO subjects with positive breath test but without abdominal symptoms (PBT) and healthy controls (HC) using 16S rRNA amplicon sequencing.
RESULTS
Fecal samples were collected from 63 SIBO who complained of diarrhea, distension, constipation, or abdominal pain, 36 PBT, and 55 HC. For alpha diversity, the Shannon index of community diversity on the genus level showed a tendency for a slight increase in SIBO, while the Shannon index on the predicted function was significantly decreased in SIBO. On the genus level, significantly decreased Bacteroides, increased Coprococcus_2, and unique Butyrivibrio were observed in SIBO. There was a significant positive correlation between saccharolytic Coprococcus_2 and the severity of abdominal symptoms. Differently, the unique Veillonella in the PBT group was related to amino acid fermentation. Interestingly, the co-occurrence network density of PBT was larger than SIBO, which indicates a complicated interaction of genera. Coprococcus_2 showed one of the largest betweenness centrality in both SIBO and PBT microbiota networks. Pathway analysis based on the Kyoto Encyclopedia of Genes and Genome (KEGG) database reflected that one carbon pool by folate and multiple amino acid metabolism were significantly down in SIBO.
CONCLUSIONS
This study provides valuable insights into the fecal microbiota composition and predicted metabolic functional changes in patients with SIBO. Butyrivibrio and Coprococcus_2, both renowned for their role in carbohydrate fermenters and gas production, contributed significantly to the symptoms of the patients. Coprococcus's abundance hints at its use as a SIBO marker. Asymptomatic PBT individuals show a different microbiome, rich in Veillonella. PBT's complex microbial interactions might stabilize the intestinal ecosystem, but further study is needed due to the core microbiota similarities with SIBO. Predicted folate and amino acid metabolism reductions in SIBO merit additional validation.
Topics: Humans; Feces; Female; Male; Intestine, Small; Middle Aged; Adult; Breath Tests; Case-Control Studies; Gastrointestinal Microbiome; RNA, Ribosomal, 16S
PubMed: 38796441
DOI: 10.1186/s12967-024-05316-2 -
BMC Oral Health May 2024The oral microbiome plays an essential role in maintaining oral homeostasis and health; smoking significantly affects it, leading to microbial dysbiosis. The study aims...
BACKGROUND
The oral microbiome plays an essential role in maintaining oral homeostasis and health; smoking significantly affects it, leading to microbial dysbiosis. The study aims to investigate changes in the oral microbiome composition of smokers in the Qatari population and establish a correlation with lipid biomarkers.
METHODS
The oral microbiota was profiled from saliva samples of 200 smokers and 100 non-smokers in the Qatari population, and 16s rRNA V3-V4 region were sequenced using the Illumina MiSeq platform. The operational taxonomic units (OTUs) were clustered using QIIME and the statistical analysis was performed by R.
RESULTS
Non-smokers exhibited a more diverse microbiome, with significant alpha and beta diversity differences between the non-smoker and smoker groups. Smokers had a higher abundance of Firmicutes, Bacteroidota, Actinobacteriota, Patescibacteria, and Proteobacteria at the phylum level and of Streptococcus, Prevotella, Veillonella, TM7x, and Porphyromonas at the genus level. In contrast, non-smokers had more Bacteroidota, Firmicutes, Proteobacteria, Fusobacteriota, and Patescibacteria at the phylum level, and Prevotella, Streptococcus, Veillonella, Porphromonas, and Neisseria at the genus level. Notably, Streptococcus was significantly positively correlated with LDL and negatively correlated with HDL. Additionally, Streptococcus salivarius, within the genus Streptococcus, was substantially more abundant in smokers.
CONCLUSION
This study highlights the significant influence of smoking on the composition of the oral microbiome by enriching anaerobic microbes and depleting aerobic microbes. Moreover, the observed correlation between Streptococcus abundance and the lipid biomarkers suggests a potential link between smokers-induced salivary microbiome dysbiosis and lipid metabolism. Understanding the impact of smoking on altering the oral microbiome composition and its correlation with chemistry tests is essential for developing targeted interventions and strategies to improve oral health and reduce the risk of diseases.
Topics: Humans; Saliva; Dysbiosis; Smoking; Male; Microbiota; Female; Biomarkers; Adult; Lipids; Middle Aged; RNA, Ribosomal, 16S
PubMed: 38796419
DOI: 10.1186/s12903-024-04340-4 -
Animals : An Open Access Journal From... May 2024The purpose of this study was to evaluate the effect of fermented mixed feed (FMF) (soybean meal-rapeseed meal-corn bran (6:3:1, //)) on the growth performance,...
The purpose of this study was to evaluate the effect of fermented mixed feed (FMF) (soybean meal-rapeseed meal-corn bran (6:3:1, //)) on the growth performance, intestinal microbial communities, and metabolomes of squabs. One hundred and eighty 1-day-old squabs were randomly allocated to two groups, each containing six replicates of fifteen squabs cared for by 60 pairs of breeding pigeons secreting crop milk. Each pair of breeding pigeons cared for three squabs. The control group was fed a basal diet, while the experimental group was fed the basal diet containing 5% FMF. The results showed that daily weight gain, carcass weight, villus height, and the mRNA level of in the ileum were increased in the birds fed FMF compared to the control squabs ( < 0.05). Greater abundances of beneficial bacteria such as , , and as well as fewer harmful bacteria (i.e., , , and ) in the ilea of squabs fed FMF. Six differential metabolites were identified in the FMF-treated squabs; one metabolite was increased (ω-salicoyisalicin) and five were decreased (3-benzoyloxy-6-oxo-12-ursen-28-oic acid, estradiol-17-phenylpropionate, aminotriazole, phosphatidyl ethanolamine (22:6/0:0), and 1-arachidonoylglycerophosphoinositol). Positive correlations were observed between the abundance of and villus height. Overall, FMF treatment improved both growth and intestinal health in pigeons, suggesting potential benefits for pigeon production.
PubMed: 38791629
DOI: 10.3390/ani14101411 -
Scientific Reports May 2024Objectives were to assess differences in uterine microbiome associated with clinical cure and pregnancy outcomes in dairy cows treated for metritis. Cows with metritis...
Objectives were to assess differences in uterine microbiome associated with clinical cure and pregnancy outcomes in dairy cows treated for metritis. Cows with metritis (reddish-brownish, watery, and fetid vaginal discharge) were paired with cows without metritis based on parity and days postpartum. Uterine contents were collected through transcervical lavage at diagnosis, five days later following antimicrobial therapy (day 5), and at 40 days postpartum. Uterine microbiome was assessed by sequencing the V4 hypervariable region of the 16S rRNA gene. Although alpha-diversity based on Chao1, Shannon, and inverse Simpson indexes at diagnosis did not differ between cows with and without metritis, disease was associated with differences in beta-diversity. Prevalence of Porphyromonas, Bacteroides, and Veillonella was greater in cows with metritis. Streptococcus, Sphingomonas, and Ureaplasma were more prevalent in cows without metritis. Differences in beta-diversity between cows with and without metritis persisted on day 5. Uterine microbiome was not associated with clinical cure. Richness and alpha-diversity, but not beta-diversity, of uterine microbiome 40 days postpartum were associated with metritis and pregnancy. No relationship between uterine microbiome and pregnancy outcomes was observed. Results indicate that factors other than changes in intrauterine bacterial community underlie fertility loss and clinical cure in cows with metritis.
Topics: Female; Animals; Cattle; Pregnancy; Uterus; Microbiota; Pregnancy Outcome; Endometritis; Cattle Diseases; RNA, Ribosomal, 16S; Bacteria
PubMed: 38789554
DOI: 10.1038/s41598-024-61704-0 -
Frontiers in Immunology 2024Increasing evidence indicates the microbial ecology of chronic obstructive pulmonary disease (COPD) is intricately associated with the disease's status and severity, and... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Increasing evidence indicates the microbial ecology of chronic obstructive pulmonary disease (COPD) is intricately associated with the disease's status and severity, and distinct microbial ecological variations exist between COPD and healthy control (HC). This systematic review and meta-analysis aimed to summarize microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota of different stages of COPD and HC to make comparisons.
METHODS
A comprehensive systematic literature search was conducted in PubMed, Embase, the Web of Science, and the Cochrane Library databases to identify relevant English articles on the oral, airway, and intestine microbiota in COPD published between 2003 and 8 May 2023. Information on microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota was collected for comparison between different stages of COPD and HC.
RESULTS
A total of 20 studies were included in this review, involving a total of 337 HC participants, 511 COPD patients, and 154 AECOPD patients. We observed that no significant differences in alpha diversity between the participant groups, but beta diversity was significantly different in half of the included studies. Compared to HC, , , , and of oral microbiota in SCOPD were reduced at the genus level. Most studies supported that , , and were increased, but , , , , and were decreased at the genus level in the airway microbiota of SCOPD. However, the abundance of , and genera exhibited an increase, whereas and showed a decrease in the airway microbiota of AECOPD compared to HC. And of intestine microbiota in SCOPD was reduced at the genus level.
CONCLUSION
The majority of published research findings supported that COPD exhibited decreased alpha diversity compared to HC. However, our meta-analysis does not confirm it. In order to further investigate the characteristics and mechanisms of microbiome in the oral-airway- intestine axis of COPD patients, larger-scale and more rigorous studies are needed.
SYSTEMATIC REVIEW REGISTRATION
PROSPERO (https://www.crd.york.ac.uk/prospero/), identifier CRD42023418726.
Topics: Pulmonary Disease, Chronic Obstructive; Humans; Gastrointestinal Microbiome; Mouth; Microbiota; Bacteria
PubMed: 38779669
DOI: 10.3389/fimmu.2024.1407439 -
Frontiers in Cellular and Infection... 2024Ulcerative colitis (UC) is a multifactorial chronic inflammatory bowel disease (IBD) that affects the large intestine with superficial mucosal inflammation. A dysbiotic...
BACKGROUND
Ulcerative colitis (UC) is a multifactorial chronic inflammatory bowel disease (IBD) that affects the large intestine with superficial mucosal inflammation. A dysbiotic gut microbial profile has been associated with UC. Our study aimed to characterize the UC gut bacterial, fungal, and metabolic fingerprints by omic approaches.
METHODS
The 16S rRNA- and ITS2-based metataxonomics and gas chromatography-mass spectrometry/solid phase microextraction (GC-MS/SPME) metabolomic analysis were performed on stool samples of 53 UC patients and 37 healthy subjects (CTRL). Univariate and multivariate approaches were applied to separated and integrated omic data, to define microbiota, mycobiota, and metabolic signatures in UC. The interaction between gut bacteria and fungi was investigated by network analysis.
RESULTS
In the UC cohort, we reported the increase of , , Enterobacteriaceae, TM7-3, , , , , , , Gemellaceae, and phenylethyl alcohol; and we also reported the decrease of ; Ruminococcaceae; ; ; ; ; ; ; ; ; ; hexadecane; cyclopentadecane; 5-hepten-2-ol, 6 methyl; 3-carene; caryophyllene; p-Cresol; 2-butenal; indole, 3-methyl-; 6-methyl-3,5-heptadiene-2-one; 5-octadecene; and 5-hepten-2-one, 6 methyl. The integration of the multi-omic data confirmed the presence of a distinctive bacterial, fungal, and metabolic fingerprint in UC gut microbiota. Moreover, the network analysis highlighted bacterial and fungal synergistic and/or divergent interkingdom interactions.
CONCLUSION
In this study, we identified intestinal bacterial, fungal, and metabolic UC-associated biomarkers. Furthermore, evidence on the relationships between bacterial and fungal ecosystems provides a comprehensive perspective on intestinal dysbiosis and ecological interactions between microorganisms in the framework of UC.
Topics: Humans; Colitis, Ulcerative; Gastrointestinal Microbiome; Male; Adult; Female; Bacteria; Middle Aged; Metabolomics; RNA, Ribosomal, 16S; Gas Chromatography-Mass Spectrometry; Feces; Fungi; Dysbiosis; Metabolome; Aged; Young Adult; Solid Phase Microextraction; Mycobiome; Multiomics
PubMed: 38779566
DOI: 10.3389/fcimb.2024.1366192 -
Research (Washington, D.C.) 2024The gut microbiota undergoes substantial changes in COVID-19 patients; yet, the utility of these alterations as prognostic biomarkers at the time of hospital admission,...
The gut microbiota undergoes substantial changes in COVID-19 patients; yet, the utility of these alterations as prognostic biomarkers at the time of hospital admission, and its correlation with immunological and hematological parameters, remains unclear. The objective of this study is to investigate the gut microbiota's dynamic change in critically ill patients with COVID-19 and evaluate its predictive capability for clinical outcomes alongside immunological and hematological parameters. In this study, anal swabs were consecutively collected from 192 COVID-19 patients (583 samples) upon hospital admission for metagenome sequencing. Simultaneously, blood samples were obtained to measure the concentrations of 27 cytokines and chemokines, along with hematological and biochemical indicators. Our findings indicate a significant correlation between the composition and dynamics of gut microbiota with disease severity and mortality in COVID-19 patients. Recovered patients exhibited a higher abundance of and denser interactions among gut commensal bacteria compared to deceased patients. Furthermore, the abundance of gut commensal bacteria exhibited a negative correlation with the concentration of proinflammatory cytokines and organ damage markers. The gut microbiota upon admission showed moderate prognostic prediction ability with an AUC of 0.78, which was less effective compared to predictions based on immunological and hematological parameters (AUC 0.80 and 0.88, respectively). Noteworthy, the integration of these three datasets yielded a higher predictive accuracy (AUC 0.93). Our findings suggest the gut microbiota as an informative biomarker for COVID-19 prognosis, augmenting existing immune and hematological indicators.
PubMed: 38779486
DOI: 10.34133/research.0389