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PloS One 2020The study of oral disease progression, in relation to the accumulation of subgingival biofilm in gingivitis and periodontitis is limited, due to either the ability to...
The study of oral disease progression, in relation to the accumulation of subgingival biofilm in gingivitis and periodontitis is limited, due to either the ability to monitor plaque in vitro. When compared, optical spectroscopic techniques offer advantages over traditional destructive or biofilm staining approaches, making it a suitable alternative for the analysis and continued development of three-dimensional structures. In this work, we have developed a confocal Raman spectroscopy analysis approach towards in vitro subgingival plaque models. The main objective of this study was to develop a method for differentiating multiple oral subgingival bacterial species in planktonic and biofilm conditions, using confocal Raman microscopy. Five common subgingival bacteria (Fusobacterium nucleatum, Streptococcus mutans, Veillonella dispar, Actinomyces naeslundii and Prevotella nigrescens) were used and differentiated using a 2-way orthogonal Partial Least Square with Discriminant Analysis (O2PLS-DA) for the collected spectral data. In addition to planktonic growth, mono-species biofilms cultured using the 'Zürich Model' were also analyzed. The developed method was successfully used to predict planktonic and mono-species biofilm species in a cross validation setup. The results show differences in the presence and absence of chemical bands within the Raman spectra. The O2PLS-DA model was able to successfully predict 100% of all tested planktonic samples and 90% of all mono-species biofilm samples. Using this approach we have shown that Confocal Raman microscopy can analyse and predict the identity of planktonic and mono-species biofilm species, thus enabling its potential as a technique to map oral multi-species biofilm models.
Topics: Actinomyces; Bacteria; Bacteriological Techniques; Biofilms; Culture Media; Fusobacterium nucleatum; Gingiva; Gingivitis; Microbial Viability; Microbiota; Microscopy, Confocal; Nonlinear Optical Microscopy; Periodontitis; Plankton; Prevotella intermedia; Streptococcus mutans; Veillonella
PubMed: 32392236
DOI: 10.1371/journal.pone.0232912 -
Microorganisms May 2020Oral bacteria possess the ability to form biofilms on solid surfaces. After the penetration of oral bacteria into the pulp, the contact between biofilms and pulp tissue...
Oral bacteria possess the ability to form biofilms on solid surfaces. After the penetration of oral bacteria into the pulp, the contact between biofilms and pulp tissue may result in pulpitis, pulp necrosis and/or periapical lesion. Depending on the environmental conditions and the availability of nutrients in the pulp chamber and root canals, mainly Gram-negative anaerobic microorganisms predominate and form the intracanal endodontic biofilm. The objective of the present study was to investigate the role of different substrates on biofilm formation as well as the separate and collective incorporation of six endodontic pathogens, namely and into a nine-species "basic biofilm". This biofilm was formed in vitro as a standard subgingival biofilm, comprising and The resulting endodontic-like biofilms were grown 64 h under the same conditions on hydroxyapatite and dentin discs. After harvesting the endodontic-like biofilms, the bacterial growth was determined using quantitative real-time PCR, were labeled using fluorescence in situ hybridization (FISH) and analyzed by confocal laser scanning microscopy (CLSM). The addition of six endodontic pathogens to the "basic biofilm" induced a decrease in the cell number of the "basic" species. Interestingly, counts increased in biofilms containing and respectively, both on hydroxyapatite and on dentin discs, whereas counts increased only on dentin discs by addition of . The growth of on hydroxyapatite discs and of and on dentin discs were significantly higher in the biofilm containing all species than in the "basic biofilm". Contrarily, the counts of , and on hydroxyapatite discs as well as counts of and on dentin discs decreased in the all-species biofilm. Overall, all bacterial species associated with endodontic infections were successfully incorporated into the standard multispecies biofilm model both on hydroxyapatite and dentin discs. Thus, future investigations on endodontic infections can rely on this newly established endodontic-like multispecies biofilm model.
PubMed: 32384777
DOI: 10.3390/microorganisms8050674 -
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 -
NPJ Biofilms and Microbiomes Mar 2020Cigarette smoking affects the oral microbiome, which is related to various systemic diseases. While studies that investigated the relationship between smoking and the...
Cigarette smoking affects the oral microbiome, which is related to various systemic diseases. While studies that investigated the relationship between smoking and the oral microbiome by 16S rRNA amplicon sequencing have been performed, investigations involving metagenomic sequences are rare. We investigated the bacterial species composition in the tongue microbiome, as well as single-nucleotide variant (SNV) profiles and gene content of these species, in never and current smokers by utilizing metagenomic sequences. Among 234 never smokers and 52 current smokers, beta diversity, as assessed by weighted UniFrac measure, differed between never and current smokers (pseudo-F = 8.44, R = 0.028, p = 0.001). Among the 26 species that had sufficient coverage, the SNV profiles of Actinomyces graevenitzii, Megasphaera micronuciformis, Rothia mucilaginosa, Veillonella dispar, and one Veillonella sp. were significantly different between never and current smokers. Analysis of gene and pathway content revealed that genes related to the lipopolysaccharide biosynthesis pathway in Veillonella dispar were present more frequently in current smokers. We found that species-level tongue microbiome differed between never and current smokers, and 5 species from never and current smokers likely harbor different strains, as suggested by the difference in SNV frequency.
Topics: Adult; Aged; Bacteria; Case-Control Studies; Cigarette Smoking; DNA, Bacterial; DNA, Ribosomal; Female; High-Throughput Nucleotide Sequencing; Humans; Male; Metagenomics; Middle Aged; Phylogeny; Polymorphism, Single Nucleotide; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Tongue
PubMed: 32170059
DOI: 10.1038/s41522-020-0121-6 -
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 -
BMC Oral Health Nov 2019The extent to which the composition and diversity of the oral microbiome varies with age is not clearly understood.
BACKGROUND
The extent to which the composition and diversity of the oral microbiome varies with age is not clearly understood.
METHODS
The 16S rRNA gene of subgingival plaque in 1219 women, aged 53-81 years, was sequenced and its taxonomy annotated against the Human Oral Microbiome Database (v.14.5). Composition of the subgingival microbiome was described in terms of centered log(2)-ratio (CLR) transformed OTU values, relative abundance, and prevalence. Correlations between microbiota abundance and age were evelauted using Pearson Product Moment correlations. P-values were corrected for multiple testing using the Bonferroni method.
RESULTS
Of the 267 species identified overall, Veillonella dispar was the most abundant bacteria when described by CLR OTU (mean 8.3) or relative abundance (mean 8.9%); whereas Streptococcus oralis, Veillonella dispar and Veillonella parvula were most prevalent (100%, all) when described as being present at any amount. Linear correlations between age and several CLR OTUs (Pearson r = - 0.18 to 0.18), of which 82 (31%) achieved statistical significance (P < 0.05). The correlations lost significance following Bonferroni correction. Twelve species that differed across age groups (each corrected P < 0.05); 5 (42%) were higher in women ages 50-59 compared to ≥70 (corrected P < 0.05), and 7 (48%) were higher in women 70 years and older.
CONCLUSIONS
We identified associations between several bacterial species and age across the age range of postmenopausal women studied. Understanding the functions of these bacteria could identify intervention targets to enhance oral health in later life.
Topics: Aged; Aged, 80 and over; Bacteria; Dental Plaque; Female; Humans; Microbiota; Middle Aged; Postmenopause; RNA, Ribosomal, 16S
PubMed: 31722703
DOI: 10.1186/s12903-019-0906-2 -
Frontiers in Microbiology 2019Fusobacteria are common obligately anaerobic Gram-negative bacteria of the oral cavity that may act as a bridge between early and late colonizing bacteria in dental...
Fusobacteria are common obligately anaerobic Gram-negative bacteria of the oral cavity that may act as a bridge between early and late colonizing bacteria in dental plaque and have a role in oral and extra-oral infections. has a crucial role in oral biofilm structure and ecology, as revealed in experimental and clinical biofilm models. The aim of this study was to investigate the impact of various species on biofilm formation and structure in three different oral biofilm models namely a supragingival, a supragingival "feeding", and a subgingival biofilm model. The standard six-species supragingival and "feeding" biofilm models employed contained , , , , , and sp. The subgingival biofilm model contained 10 species (, , ssp. , , , , , , , and ). Six different species or subspecies, respectively, were tested namely ssp. , ssp. , ssp. , ssp. , , and ). Biofilms were grown anaerobically on hydroxyapatite disks in 24-well culture dishes. After 64 h, biofilms were either harvested and quantified by culture analysis or proceeded to fluorescent hybridization (FISH) and confocal laser scanning microscopy (CLSM). All species tested established well in the biofilms, with CFUs ranging from 1.4E+04 ( ssp. ) to 5.6E+06 ( ssp. ). The presence of specific sp./ssp. induced a significant decrease in levels in the supragingival model and in levels in the "feeding" supragingival model. In the subgingival model, the counts of , , , , and significantly decreased in the presence of specific sp./ssp. Collectively, this study showed variations in the growing capacities of different fusobacteria within biofilms, affecting the growth of surrounding species and potentially the biofilm architecture. Hence, clinical or experimental studies need to differentiate between sp./ssp., as their biological properties may well vary.
PubMed: 31417514
DOI: 10.3389/fmicb.2019.01716 -
Journal of Gastrointestinal Surgery :... Aug 2020Recently, the link between obesity and gut microbiota has become a focus for research. This study shed some light on the modification of postoperative gut microbial...
BACKGROUND
Recently, the link between obesity and gut microbiota has become a focus for research. This study shed some light on the modification of postoperative gut microbial composition after bariatric surgery.
METHODS
A prospective longitudinal study on healthy lean subjects and patients who underwent bariatric surgery (Roux-en-Y gastric bypass and laparoscopic sleeve gastrectomy) was carried out. Anthropometric and metabolic data, smoking, food preferences data, and stool samples were collected from lean subjects and from obese patients before and 3 and 6 months after surgery (T0, T3, and T6, respectively).
RESULTS
We collected stool samples from 25 obese patients before surgery and 3 and 6 months thereafter and from 25 normal weight patients. After Roux-en-Y gastric bypass, Yokenella regensburgei (p < 0.05), Fusobacterium varium (p < 0.05), Veillonella dispar/atypica (p < 0.05), and Streptococcus australis/gordonii (p < 0.05) were transiently identified in the gut at T3. Roux-en-Y gastric bypass patients had a permanent increase in Akkermansia muciniphila (p < 0.05), which is associated with healthy metabolism, both at T3 and T6. There were no significant changes in gut microbiota in laparoscopic sleeve gastrectomy patients.
CONCLUSIONS
In our study, Roux-en-Y gastric bypass induced major microbial differences and greater weight loss compared with laparoscopic sleeve gastrectomy. Analyzing the microbiota composition, a proliferation of potential pathogens and the onset of beneficial bacteria was observed. The effects of these bacteria on human health are still far from clear. Understanding the mechanisms of action of these bacteria could be the keystone in developing new therapeutic strategies for obesity.
Topics: Bariatric Surgery; Enterobacteriaceae; Fusobacterium; Gastrectomy; Gastric Bypass; Gastrointestinal Microbiome; Humans; Laparoscopy; Longitudinal Studies; Obesity, Morbid; Prospective Studies; Streptococcus; Veillonella
PubMed: 31388884
DOI: 10.1007/s11605-019-04321-x -
Journal of Clinical Medicine May 2019Cystic fibrosis (CF) is a systemic genetic disease that leads to pulmonary and digestive disorders. In the majority of CF patients, the intestine is the site of chronic...
Cystic fibrosis (CF) is a systemic genetic disease that leads to pulmonary and digestive disorders. In the majority of CF patients, the intestine is the site of chronic inflammation and microbiota disturbances. The link between gut inflammation and microbiota dysbiosis is still poorly understood. The main objective of this study was to assess gut microbiota composition in CF children depending on their intestinal inflammation. We collected fecal samples from 20 children with CF. Fecal calprotectin levels were measured and fecal microbiota was analyzed by 16S rRNA sequencing. We observed intestinal inflammation was associated with microbiota disturbances characterized mainly by increased abundances of , and , along with decreased abundances of , , and . Those changes exhibited similarities with that of Crohn's disease (CD), as evidenced by the elevated CD Microbial-Dysbiosis index that we applied for the first time in CF. Furthermore, the significant over-representation of in children with intestinal inflammation appears to be specific to CF and raises the issue of gut-lung axis involvement. Taken together, our results provide new arguments to link gut microbiota and intestinal inflammation in CF and suggest the key role of the gut-lung axis in the CF evolution.
PubMed: 31083321
DOI: 10.3390/jcm8050645 -
BJOG : An International Journal of... Jan 2020To evaluate the potential impact of intrapartum antibiotics, and their specific classes, on the infant gut microbiota in the first year of life.
OBJECTIVE
To evaluate the potential impact of intrapartum antibiotics, and their specific classes, on the infant gut microbiota in the first year of life.
DESIGN
Prospective study of infants in the New Hampshire Birth Cohort Study (NHBCS).
SETTINGS
Rural New Hampshire, USA.
POPULATION OR SAMPLE
Two hundred and sixty-six full-term infants from the NHBCS.
METHODS
Intrapartum antibiotic use during labour and delivery was abstracted from medical records. Faecal samples collected at 6 weeks and 1 year of age were characterised by 16S rRNA sequencing, and metagenomics analysis in a subset of samples.
EXPOSURES
Maternal exposure to antibiotics during labour and delivery.
MAIN OUTCOME MEASURE
Taxonomic and functional profiles of faecal samples.
RESULTS
Infant exposure to intrapartum antibiotics, particularly to two or more antibiotic classes, was independently associated with lower microbial diversity scores as well as a unique bacterial community at 6 weeks (GUnifrac, P = 0.02). At 1 year, infants in the penicillin-only group had significantly lower α diversity scores than infants not exposed to intrapartum antibiotics. Within the first year of life, intrapartum exposure to penicillins was related to a significantly lower increase in several taxa including Bacteroides, use of cephalosporins was associated with a significantly lower rise over time in Bifidobacterium and infants in the multi-class group experienced a significantly higher increase in Veillonella dispar.
CONCLUSIONS
Our findings suggest that intrapartum antibiotics alter the developmental trajectory of the infant gut microbiome, and specific antibiotic types may impact community composition, diversity and keystone immune training taxa.
TWEETABLE ABSTRACT
Class of intrapartum antibiotics administered during delivery relates to maturation of infant gut microbiota.
Topics: Antibiotic Prophylaxis; Bacteroides; Bacteroidetes; Bifidobacterium; Feces; Female; Gastrointestinal Microbiome; Humans; Infant, Newborn; Lactobacillus; Maternal Exposure; Mothers; Pregnancy; Prospective Studies; RNA, Ribosomal, 16S; Sequence Analysis, RNA; Term Birth; Vagina; beta-Lactamases
PubMed: 31006170
DOI: 10.1111/1471-0528.15799