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Saudi Journal of Biological Sciences Jul 2022The diversity of oral microbiota is affected by diets habits, gender, age, ethnic group, and environment. The acquisition of oral microbiota and the role of family on...
The diversity of oral microbiota is affected by diets habits, gender, age, ethnic group, and environment. The acquisition of oral microbiota and the role of family on oral microbiota development is poorly understood. This study aims to characterize and compare the oral bacterial microbiota among families using 16S rRNA gene sequencing. This work was conducted in Jeddah city from 2020 to 2021, in which four families composed of 20 members of different ethnicity and lifestyle were recruited. After the collection of saliva samples, the DNA was extracted and processed for 16S rRNA gene metagenomics sequencing. Among 378 OUTs generated, 39 (10.3%) were unique in group A, 13 (3.4%) unique in group B, and 11 (2.9%) were unique in groups C and D. We observed a significant variation at the level of top abundance phylum (14), families (23), genera (24), and species (22) of bacteria among family members. Within family groups, different bacterial species were reported to be more dominant among certain family members than the other; and and were more dominant in parents of some families than the other family member. In summary, this study highlights the precise and perceptible association of oral microbial between family members. Our findings documented the clustering of certain bacterial species in family groups, supporting the role of community in the development of oral microbiota.
PubMed: 35677897
DOI: 10.1016/j.sjbs.2022.103317 -
Gut Microbes 2021The need for alternative treatments for multiple sclerosis (MS) has triggered copious amounts of research into microbial therapies focused on manipulating the... (Comparative Study)
Comparative Study
The need for alternative treatments for multiple sclerosis (MS) has triggered copious amounts of research into microbial therapies focused on manipulating the microbiota-gut-brain axis. This comprehensive review was intended to present and systematically evaluate the current clinical and preclinical evidence for various probiotic and commensal gut microbial therapies as treatments for MS, using the Bradford Hill criteria (BHC) as a multi-parameter assessment rubric. Literature searches were performed to identify a total of 37 relevant studies (6 human, 31 animal), including 28 probiotic therapy and 9 commensal therapy studies. In addition to presenting qualitative summaries of these findings, therapeutic evidence for each bacterial formulation was assessed using the BHC to generate summative scores. These scores, which encompassed study quality, replication, and other considerations, were used to rank the most promising therapies and highlight deficiencies. Several therapeutic formulations, including VSL#3, Nissle 1917, and , emerged as the most promising. In contrast, a number of other therapies were hindered by limited evidence of replicable findings and other criteria, which need to be addressed by future studies in order to harness gut microbial therapies to ultimately provide cheaper, safer, and more durable treatments for MS.
Topics: Animals; Disease Models, Animal; Gastrointestinal Microbiome; Humans; Multiple Sclerosis; Probiotics; Symbiosis; Treatment Outcome
PubMed: 34264791
DOI: 10.1080/19490976.2021.1943289 -
Frontiers in Pediatrics 2022Persistent pulmonary interstitial emphysema (PPIE) is known to be related to mechanical ventilation and preterm. However, PPIE is also reported rarely in non-ventilated...
Persistent Pulmonary Interstitial Emphysema With Respiratory Infection: A Clinicopathological Analysis of Six Cases and Detection of Infectious Pathogens by Metagenomic Next-Generation Sequencing (mNGS).
BACKGROUND
Persistent pulmonary interstitial emphysema (PPIE) is known to be related to mechanical ventilation and preterm. However, PPIE is also reported rarely in non-ventilated and full-term infants. Its relationship with respiratory infection is rarely reported in the literature. PPIE is difficult to diagnose and always mimics other congenital thoracic malformations (CTMs), such as congenital cystic adenomatoid malformation (CCAM).
OBJECTIVE
The objective of this study was to evaluate clinicopathological and radiographic features of PPIE with respiratory infection and to detect the possible infectious pathogens.
METHODS
From January 2011 to December 2019, six cases were confirmed pathologically with PPIE from a large cohort of 477 resected CTMs in West China Hospital of Sichuan University. Clinical and radiographic features were obtained from patients' medical records and follow-up. The present study aimed to analyze clinicopathological and radiographic features and to detect the infectious pathogens by metagenomic next-generation sequencing (mNGS).
RESULTS
The six PPIE cases included four girls and two boys, ranging from 2 months to 5 years; 100% (5/5) of the available cases were full-term and without mechanical ventilation. CCAM were suspected in 66.7% (4/6) patients; 66.7% (4/6) cases affected a single lobe, and 33.3% (2/6) cases affected both lung lobes. Clinically, all six PPIEs were presented with symptoms of respiratory infection and diagnosed with pneumonia. All six patients were treated by surgery after anti-infective treatment. The pathologic characteristics showed lung cysts with variable size along the bronchovascular bundles, the cysts had a discontinuous fibrotic wall with a smooth inner surface lined with uninucleated and/or multinucleated macrophages. was detected in patient No. 1. Human beta-herpesvirus 5 was detected in patient No. 2. , and were detected in patient No. 5, and no infectious pathogen was detected in 50% (3/6, No. 3, No. 4, and No. 6) of cases.
CONCLUSION
Six rare cases of PPIE with respiratory infection were treated by surgery after anti-infective treatment. All five available cases were full-term infants without mechanical ventilation. The histological characteristics of PPIE were the wall of cysts composed of a thin layer of discontinuous fibrous tissue and lined with uninucleated or/and multinucleated macrophages.
PubMed: 35463878
DOI: 10.3389/fped.2022.836276 -
Frontiers in Cellular and Infection... 2021Untreated tooth decays affect nearly one third of the world and is the most prevalent disease burden among children. The disease progression of tooth decay is...
Untreated tooth decays affect nearly one third of the world and is the most prevalent disease burden among children. The disease progression of tooth decay is multifactorial and involves a prolonged decrease in pH, resulting in the demineralization of tooth surfaces. Bacterial species that are capable of fermenting carbohydrates contribute to the demineralization process by the production of organic acids. The combined use of machine learning and 16s rRNA sequencing offers the potential to predict tooth decay by identifying the bacterial community that is present in an individual's oral cavity. A few recent studies have demonstrated machine learning predictive modeling using 16s rRNA sequencing of oral samples, but they lack consideration of the multifactorial nature of tooth decay, as well as the role of fungal species within their models. Here, the oral microbiome of mother-child dyads (both healthy and caries-active) was used in combination with demographic-environmental factors and relevant fungal information to create a multifactorial machine learning model based on the LASSO-penalized logistic regression. For the children, not only were several bacterial species found to be caries-associated (, and ) but also detection and lower toothbrushing frequency were also caries-associated. Mothers enrolled in this study had a higher detection of and and a higher plaque index. This proof-of-concept study demonstrates the significant impact machine learning could have in prevention and diagnostic advancements for tooth decay, as well as the importance of considering fungal and demographic-environmental factors.
Topics: Child; Dental Caries; Dental Caries Susceptibility; Female; Humans; Machine Learning; Mothers; Prevotella; RNA, Ribosomal, 16S; Streptococcus mutans
PubMed: 34490147
DOI: 10.3389/fcimb.2021.727630 -
Frontiers in Immunology 2022Multiple sclerosis (MS) is an inflammatory and demyelinating disease of the CNS. The etiology of MS is complex, and results from the interaction of multiple...
BACKGROUND
Multiple sclerosis (MS) is an inflammatory and demyelinating disease of the CNS. The etiology of MS is complex, and results from the interaction of multiple environmental and genetic factors. Although human leukocyte antigen-HLA alleles such as HLA-DR2 and -DR3 are considered the strongest genetic factors, the environmental factors responsible for disease predisposition are not well understood. Recently, diet and gut microbiota have emerged as an important environmental factors linked to the increased incidence of MS. Especially, western diets rich inprotein and fat have been linked to the increased incidence of obesity. Numerous clinical data indicate a role of obesity and gut microbiota in MS; however, the mechanistic link between gut microbiota and obesity in the pathobiology of MS remains unclear. The present study determines the mechanisms driving MS severity in the context of obesity utilizing a high-fat diet (HFD) induced obese HLA-DR3 class-II transgenic mouse model of MS.
METHODS
HLA-DR3 transgenic mice were kept on a standard HFD diet or Normal Chow (NC) for eight weeks. Gut microbiota composition and functional analysis were performed from the fecal DNA of mice. Experimental autoimmune encephalomyelitis-EAE (an animal model of MS) was induced by immunization with the proteolipid protein-PLP peptide in complete Freud's Adjuvant (CFA) and pertussis toxin.
RESULTS
We observed that HFD-induced obesity caused gut dysbiosis and severe disease compared to mice on NC. Amelioration of disease severity in mice depleted of gut microbiota suggested an important role of gut bacteria in severe EAE in obese mice. Fecal microbiota analysis in HFD mice shows gut microbiota alterations with an increase in the abundance of and bacteria and modulation of various bacterial metabolic pathways including bacterial hydrogen sulfide biosynthetic pathways. Finally, mice on HFD showed increased gut permeability and systemic inflammation suggesting a role gut barrier modulation in obesity induced disease severity.
CONCLUSIONS
This study provides evidence for the involvement of the gut microbiome and associated metabolic pathways plus gut permeability in obesity-induced modulation of EAE disease severity. A better understanding of the same will be helpful to identify novel therapeutic targets to reduce disease severity in obese MS patients.
Topics: Animals; Diet, High-Fat; Disease Models, Animal; Dysbiosis; Encephalomyelitis, Autoimmune, Experimental; HLA-DR2 Antigen; HLA-DR3 Antigen; Humans; Hydrogen Sulfide; Mice; Mice, Obese; Mice, Transgenic; Multiple Sclerosis; Obesity; Pertussis Toxin; Proteolipids; Severity of Illness Index
PubMed: 36164343
DOI: 10.3389/fimmu.2022.966417 -
International Journal of Systematic and... Nov 2013Five obligately anaerobic, Gram-stain-negative, saccharolytic and proteolytic, non-spore-forming bacilli (strains CD3 : 27, CD3 : 28(T), CD3 : 33,...
Five obligately anaerobic, Gram-stain-negative, saccharolytic and proteolytic, non-spore-forming bacilli (strains CD3 : 27, CD3 : 28(T), CD3 : 33, CD3 : 32 and CD3 : 34) are described. All five strains were isolated from the small intestine of a female child with coeliac disease. Cells of the five strains were short rods or coccoid cells with longer filamentous forms seen sporadically. The organisms produced acetic acid and succinic acid as major metabolic end products. Phylogenetic analysis based on comparative 16S rRNA gene sequence analysis revealed close relationships between CD3 : 27, CD3 : 28(T) and CD3 : 33, between CD3 : 32 and Prevotella histicola CCUG 55407(T), and between CD3 : 34 and Prevotella melaninogenica CCUG 4944B(T). Strains CD3 : 27, CD3 : 28(T) and CD3 : 33 were clearly different from all recognized species within the genus Prevotella and related most closely to but distinct from P. melaninogenica. Based on 16S rRNA, RNA polymerase β-subunit (rpoB) and 60 kDa chaperonin protein subunit (cpn60) gene sequencing, and phenotypic, chemical and biochemical properties, strains CD3 : 27, CD3 : 28(T) and CD3 : 33 are considered to represent a novel species within the genus Prevotella, for which the name Prevotella jejuni sp. nov. is proposed. Strain CD3 : 28(T) ( = CCUG 60371(T) = DSM 26989(T)) is the type strain of the proposed novel species. All five strains were able to form homologous aggregates, in which tube-like structures were connecting individual bacteria cells. The five strains were able to bind to human intestinal carcinoma cell lines at 37 °C.
Topics: Acetic Acid; Bacterial Typing Techniques; Base Composition; Celiac Disease; Cell Line, Tumor; Child; DNA, Bacterial; DNA-Directed RNA Polymerases; Epithelial Cells; Fatty Acids; Female; Humans; Intestine, Small; Molecular Sequence Data; Phylogeny; Prevotella; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Succinic Acid; Sweden
PubMed: 23793857
DOI: 10.1099/ijs.0.052647-0 -
MSphere Feb 2023The tongue dorsum is colonized by a stable microbiota, mostly comprising common commensal taxa. However, the predominance of each taxon varies among individuals. We... (Observational Study)
Observational Study
The tongue dorsum is colonized by a stable microbiota, mostly comprising common commensal taxa. However, the predominance of each taxon varies among individuals. We hypothesized that equilibrium in the tongue microbiota is affected by exposure to butyrate in the oral fluid, which is reported to affect the growth of specific microorganisms. In this study, the bacterial composition of the tongue microbiotas of 69 male adults was determined via 16S rRNA gene sequencing to investigate its relationship to -butyric acid concentration in oral rinse samples. The tongue microbiotas of individuals with a higher -butyric acid level had higher relative abundances of Prevotella histicola, Veillonella atypica, and Streptococcus parasanguinis and lower relative abundances of Neisseria subflava and Porphyromonas pasteri. Subsequently, tongue microbiota samples collected from 12 adults were cultivated for 13 h in basal medium containing mucin and different concentrations of sodium butyrate (0, 0.8, 1.6, and 3.2 mM) to assess its effect on the growth of tongue microbiota organisms. The bacterial composition of the cultivated tongue microbiotas also demonstrated a significant gradual shift with an increase in sodium butyrate levels in beta-diversity analysis. was significantly less predominant in the microbiota after cultivation with an increased addition of sodium butyrate, although no statistical difference was observed in the other aforementioned taxa. These results suggest that butyrate in the oral fluid is partially involved in the dysbiotic shift of the tongue microbiota. Oral microbial populations that are always ingested with saliva have attracted increasing attention because more oral microorganisms than previously known reach distal organs, such as the lungs and intestinal tract, thereby affecting our health. However, although such organisms are predominately derived from the tongue dorsum, the dynamics and determinants of the tongue microbiota composition remain unclear. This study demonstrated that exposure to butyrate could lead to a dysbiotic shift in the tongue microbiota using an observational epidemiological and microbiota cultivation approach. This result adds a new dimension to tongue microbiota ecology.
Topics: Adult; Humans; Male; Butyric Acid; RNA, Ribosomal, 16S; Tongue; Microbiota; Saliva; Bacteria; Dysbiosis
PubMed: 36507724
DOI: 10.1128/msphere.00490-22 -
Dietary Isoflavones Alter Gut Microbiota and Lipopolysaccharide Biosynthesis to Reduce Inflammation.Gut Microbes 2022The etiopathogenesis of multiple sclerosis (MS) is strongly affected by environmental factors such as diet and the gut microbiota. An isoflavone-rich (ISO) diet was...
The etiopathogenesis of multiple sclerosis (MS) is strongly affected by environmental factors such as diet and the gut microbiota. An isoflavone-rich (ISO) diet was previously shown to reduce the severity of MS in the animal model experimental autoimmune encephalomyelitis (EAE). Translation of this concept to clinical trial where dietary isoflavones may be recommended for MS patients will require preliminary evidence that providing the isoflavone-rich diet to people with MS (PwMS) who lack phytoestrogen-metabolizing bacteria has beneficial effects. We have previously shown that the gut microbiota of PwMS resembles the gut microbiota of mice raised under a phytoestrogen-free (phyto-free) diet in that it lacks phytoestrogen-metabolizing bacteria. To investigate the effects of phytoestrogens on the microbiota inflammatory response and EAE disease severity we switched the diet of mice raised under a phyto-free (PF) diet to an isoflavone-rich diet. Microbiota analysis showed that the change in diet from one that is ISO to one that is PF reduces beneficial bacteria such as species. In addition we observed functional differences in lipopolysaccharide (LPS) biosynthesis pathways. Moreover LPS extracted from feces of mice fed an ISO diet induced increased production of anti-inflammatory cytokines from bone marrow-derived macrophages relative to fecal-LPS isolated from mice fed a PF diet. Eventually mice whose diet was switched from a PF diet to an ISO diet trended toward reduced EAE severity and mortality. Overall we show that an isoflavone-rich diet specifically modulates LPS biosynthesis of the gut microbiota imparts an anti-inflammatory response and decreases disease severity.
Topics: Animals; Cytokines; Diet; Encephalomyelitis, Autoimmune, Experimental; Gastrointestinal Microbiome; Inflammation; Isoflavones; Lipopolysaccharides; Mice; Mice, Inbred C57BL; Phytoestrogens
PubMed: 36179318
DOI: 10.1080/19490976.2022.2127446 -
Journal of Translational Medicine Mar 2021Chronic obstructive pulmonary disease (COPD) is a progressive, life-threatening lung disease with increasing prevalence and incidence worldwide. Increasing evidence...
BACKGROUND
Chronic obstructive pulmonary disease (COPD) is a progressive, life-threatening lung disease with increasing prevalence and incidence worldwide. Increasing evidence suggests that lung microbiomes might play a physiological role in acute exacerbations of COPD. The objective of this study was to characterize the association of the microbiota and exacerbation risk or airflow limitation in stable COPD patients.
METHODS
The sputum microbiota from 78 COPD outpatients during periods of clinical stability was investigated using 16S rRNA V3-V4 amplicon sequencing. The microbiome profiles were compared between patients with different risks of exacerbation, i.e., the low risk exacerbator (LRE) or high risk exacerbator (HRE) groups, and with different airflow limitation severity, i.e., mild to moderate (FEV1 ≥ 50; PFT I) or severe to very severe (FEV1 < 50; PFT II).
RESULTS
The bacterial diversity (Chao1 and observed OTUs) was significantly decreased in the HRE group compared to that in the LRE group. The top 3 dominant phyla in sputum were Firmicutes, Actinobacteria, and Proteobacteria, which were similar in the HRE and LRE groups. At the genus level, compared to that in the LRE group (41.24%), the proportion of Streptococcus was slightly decreased in the HRE group (28.68%) (p = 0.007). However, the bacterial diversity and the proportion of dominant bacteria at the phylum and genus levels were similar between the PFT I and PFT II groups. Furthermore, the relative abundances of Gemella morbillorum, Prevotella histicola, and Streptococcus gordonii were decreased in the HRE group compared to those in the LRE group according to linear discriminant analysis effect size (LEfSe). Microbiome network analysis suggested altered bacterial cooperative regulation in different exacerbation phenotypes. The proportions of Proteobacteria and Neisseria were negatively correlated with the FEV1/FVC value. According to functional prediction of sputum bacterial communities through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis, genes involved in lipopolysaccharide biosynthesis and energy metabolism were enriched in the HRE group.
CONCLUSION
The present study revealed that the sputum microbiome changed in COPD patients with different risks of exacerbation. Additionally, the bacterial cooperative networks were altered in the HRE patients and may contribute to disease exacerbation. Our results provide evidence that sputum microbiome community dysbiosis is associated with different COPD phenotypes, and we hope that by understanding the lung microbiome, a potentially modifiable clinical factor, further targets for improved COPD therapies during the clinically stable state may be elucidated.
Topics: Gemella; Humans; Microbiota; Phenotype; Phylogeny; Prevotella; Pulmonary Disease, Chronic Obstructive; RNA, Ribosomal, 16S; Sputum
PubMed: 33757530
DOI: 10.1186/s12967-021-02788-4 -
Frontiers in Cellular and Infection... 2022Early childhood caries (ECC) is not only the most common chronic childhood disease but also disproportionately affects underserved populations. Of those, children living...
Early childhood caries (ECC) is not only the most common chronic childhood disease but also disproportionately affects underserved populations. Of those, children living in Thailand have been found to have high rates of ECC and severe ECC. Frequently, the cause of ECC is blamed on a handful of cariogenic organisms, such as and . However, ECC is a multifactorial disease that results from an ecological shift in the oral cavity from a neutral pH (~7.5) to an acidic pH (<5.5) environment influenced by the host individual's biological, socio-behavioral, and lifestyle factors. Currently, there is a lack of understanding of how risk factors at various levels influence the oral health of children at risk. We applied a statistical machine learning approach for multimodal data integration (parallel and hierarchical) to identify caries-related multiplatform factors in a large cohort of mother-child dyads living in Chiang Mai, Thailand (N=177). Whole saliva (1 mL) was collected from each individual for DNA extraction and 16S rRNA sequencing. A set of maternal and early childhood factors were included in the data analysis. Significantly, vaginal delivery, preterm birth, and frequent sugary snacking were found to increase the risk for ECC. The salivary microbial diversity was significantly different in children with ECC or without ECC. Results of linear discriminant analysis effect size (LEfSe) analysis of the microbial community demonstrated that , , and were significantly enriched in ECC children. Whereas was less abundant among caries-free children, suggesting its potential to be a candidate biomarker for good oral health. Based on the multimodal data integration and statistical machine learning models, the study revealed that the mode of delivery and snack consumption outrank salivary microbiome in predicting ECC in Thai children. The biological and behavioral factors may play significant roles in the microbial pathobiology of ECC and warrant further investigation.
Topics: Child, Preschool; Dental Caries; Dental Caries Susceptibility; Female; Humans; Infant, Newborn; Microbiota; Premature Birth; RNA, Ribosomal, 16S; Saliva; Snacks; Streptococcus mutans; Thailand
PubMed: 35677657
DOI: 10.3389/fcimb.2022.881899