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BioMed Research International 2020The oral cavity is one of the most complex microbial environments; however, the complex nature of the salivary microbiota and the level of inorganic anions in the saliva...
Comparison of the Microbiota and Inorganic Anion Content in the Saliva of Patients with Gastroesophageal Reflux Disease and Gastroesophageal Reflux Disease-Free Individuals.
The oral cavity is one of the most complex microbial environments; however, the complex nature of the salivary microbiota and the level of inorganic anions in the saliva of subjects with and without gastroesophageal reflux disease (GERD) are poorly understood. The primary goals of this pilot research were to assess differences in salivary bacterial community composition and inorganic anion concentrations between patients with GERD and GERD-free people. Thus, the salivary microbiota within both groups was dominated by these genera: Streptococcus, Prevotella, Porphyromonas, Veillonella, Neisseria, Haemophilus, Fusobacterium, Rothia, and Leptotrichia. However, the relative abundances of the genera Actinomyces, Atopobium, Stomatobaculum, Ruminococcaceae_[G-2], Veillonella, and Leptotrichia were significantly higher in the saliva samples of patients with GERD, while the genera Porphyromonas, Gemella, Peptostreptococcus, and Neisseria were less abundant in this group. The concentrations of chloride, phosphate, and sulphate ions in the human saliva varied among all subjects and sampling time. These results broaden our knowledge of the salivary microbial community composition and chemistry of saliva of patients with GERD and GERD-free individuals.
Topics: Adult; Anions; Bacteria; Female; Gastroesophageal Reflux; Humans; Male; Microbiota; Pilot Projects; Saliva; Young Adult
PubMed: 32509854
DOI: 10.1155/2020/2681791 -
BMC Microbiology Jul 2020The possibility that smokeless tobacco may contribute to oral carcinogenesis by influencing the oral microbiome has not been explored. This preliminary cross-sectional...
BACKGROUND
The possibility that smokeless tobacco may contribute to oral carcinogenesis by influencing the oral microbiome has not been explored. This preliminary cross-sectional study sought to assess the effect of using shammah, a form of smokeless tobacco prevalent in Arabia, on the tongue microbiome. Tongue scarping samples were obtained from 29 shammah users (SU; 27.34 ± 6.9 years) and 23 shammah non-users (SNU; 27.7 ± 7.19 years) and analyzed with 16S rRNA gene sequencing (V1-V3). Species-level taxonomy assignment of the high-quality, merged reads was obtained using a previously described BLASTn-based algorithm. Downstream analyses were performed with QIIME, LEfSe, and R.
RESULTS
A total of 178 species, belonging to 62 genera and 8 phyla were identified. Genera Streptococcus, Leptotrichia, Actinomyces, Veillonella, Haemophilus, Prevotella and Neisseria accounted for more than 60% of the average microbiome. There were no differences between the two groups in species richness and alpha-diversity, but PCoA showed significant separation (P = 0.015, ANOSIM). LEfSe analysis identified 22 species to be differentially abundant between the SU and SNU. However, only 7 species maintained a false discovery rate of ≤0.2 and could cluster the two groups separately: Rothia mucilaginosa, Streptococcus sp. oral taxon 66, Actinomyces meyeri, Streptococcus vestibularis Streptococcus sanguinis and a potentially novel Veillonella species in association with SU, and Oribacterium asaccharolyticum with SNU.
CONCLUSION
These preliminary results indicate that shammah use induces tongue microbiome changes including enrichment of several species with high acetaldehyde production potential, which warrants further investigation.
Topics: Adult; Bacteria; Case-Control Studies; Cross-Sectional Studies; DNA, Bacterial; DNA, Ribosomal; Humans; Male; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Tobacco, Smokeless; Tongue; Young Adult
PubMed: 32640977
DOI: 10.1186/s12866-020-01883-8 -
World Journal of Gastroenterology Mar 2022Choledocholithiasis is a severe disorder that affects a significant portion of the world's population. Treatment using endoscopic sphincterotomy (EST) has become...
BACKGROUND
Choledocholithiasis is a severe disorder that affects a significant portion of the world's population. Treatment using endoscopic sphincterotomy (EST) has become widespread; however, recurrence post-EST is relatively common. The bile microbiome has a profound influence on the recurrence of choledocholithiasis in patients after EST; however, the key pathogens and their functions in the biliary tract remain unclear.
AIM
To investigate the biliary microbial characteristics of patients with recurrent choledocholithiasis post-EST, using next-generation sequencing.
METHODS
This cohort study included 43 patients, who presented with choledocholithiasis at the Guangdong Second Provincial General Hospital between May and June 2020. The patients had undergone EST or endoscopic papillary balloon dilation and were followed up for over a year. They were divided into either the stable or recurrent groups. We collected bile samples and extracted microbial DNA for analysis through next-generation sequencing. Resulting sequences were analyzed for core microbiome and statistical differences between the diagnosis groups; they were examined using the Kyoto Encyclopedia of Genes and Genomes pathway hierarchy level using analysis of variance. Correlation between the key genera and metabolic pathways in bile, were analyzed using Pearson's correlation test.
RESULTS
The results revealed distinct clustering of biliary microbiota in recurrent choledocholithiasis. Higher relative abundances (RAs) of and (56.61% ± 14.81% 3.47% ± 1.10%, 8.95% ± 3.42% 0.69% ± 0.32%, respectively) and the absence of were observed in the bile of patients with recurrent disease, compared to that in stable patients. Construction of a microbiological co-occurrence network revealed a mutual relationship among , , and , and an antagonistic relationship among , and . Functional prediction of biliary microbiome revealed that the loss of transcription and metabolic abilities may lead to recurrent choledocholithiasis. Furthermore, the prediction model based on the RA of in the bile was effective in identifying the risk of recurrent choledocholithiasis ( = 0.03).
CONCLUSION
We demonstrated differences in the bile microbiome of patients with recurrent choledocholithiasis compared to that in patients with stable disease, thereby adding to the current knowledge on its microbiologic etiology.
Topics: Cholangiopancreatography, Endoscopic Retrograde; Choledocholithiasis; Cohort Studies; Humans; Risk Factors; Sphincterotomy, Endoscopic; Treatment Outcome
PubMed: 35431509
DOI: 10.3748/wjg.v28.i12.1257 -
NPJ Biofilms and Microbiomes Oct 2022Perturbations in the gut microbiome have been associated with colorectal cancer (CRC), with the colonic overabundance of Fusobacterium nucleatum shown as the most...
Perturbations in the gut microbiome have been associated with colorectal cancer (CRC), with the colonic overabundance of Fusobacterium nucleatum shown as the most consistent marker. Despite its significance in the promotion of CRC, genomic studies of Fusobacterium is limited. We enrolled 43 Vietnamese CRC patients and 25 participants with non-cancerous colorectal polyps to study the colonic microbiomes and genomic diversity of Fusobacterium in this population, using a combination of 16S rRNA gene profiling, anaerobic microbiology, and whole genome analysis. Oral bacteria, including F. nucleatum and Leptotrichia, were significantly more abundant in the tumour microbiomes. We obtained 53 Fusobacterium genomes, representing 26 strains, from the saliva, tumour and non-tumour tissues of six CRC patients. Isolates from the gut belonged to diverse F. nucleatum subspecies (nucleatum, animalis, vincentii, polymorphum) and a potential new subspecies of Fusobacterium periodonticum. The Fusobacterium population within each individual was distinct and in some cases diverse, with minimal intra-clonal variation. Phylogenetic analyses showed that within four individuals, tumour-associated Fusobacterium were clonal to those isolated from non-tumour tissues. Genes encoding major virulence factors (Fap2 and RadD) showed evidence of horizontal gene transfer. Our work provides a framework to understand the genomic diversity of Fusobacterium within the CRC patients, which can be exploited for the development of CRC diagnostic and therapeutic options targeting this oncobacterium.
Topics: Humans; RNA, Ribosomal, 16S; Phylogeny; Fusobacterium; Genomics; Microbiota; Colorectal Neoplasms; Asian People
PubMed: 36307484
DOI: 10.1038/s41522-022-00351-7 -
Cancer Cell International Mar 2022Microbiome has been shown to substantially contribute to some cancers. However, the diagnostic implications of microbiome in head and neck squamous cell carcinoma...
BACKGROUND
Microbiome has been shown to substantially contribute to some cancers. However, the diagnostic implications of microbiome in head and neck squamous cell carcinoma (HNSCC) remain unknown.
METHODS
To identify the molecular difference in the microbiome of oral and non-oral HNSCC, primary data was downloaded from the Kraken-TCGA dataset. The molecular differences in the microbiome of oral and non-oral HNSCC were identified using the linear discriminant analysis effect size method.
RESULTS
In the study, the common microbiomes in oral and non-oral cancers were Fusobacterium, Leptotrichia, Selenomonas and Treponema and Clostridium and Pseudoalteromonas, respectively. We found unique microbial signatures that positively correlated with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in oral cancer and positively and negatively correlated KEGG pathways in non-oral cancer. In oral cancer, positively correlated genes were mostly found in prion diseases, Alzheimer disease, Parkinson disease, Salmonella infection, and Pathogenic Escherichia coli infection. In non-oral cancer, positively correlated genes showed Herpes simplex virus 1 infection and Spliceosome and negatively correlated genes showed results from PI3K-Akt signaling pathway, Focal adhesion, Regulation of actin cytoskeleton, ECM-receptor interaction and Dilated cardiomyopathy.
CONCLUSIONS
These results could help in understanding the underlying biological mechanisms of the microbiome of oral and non-oral HNSCC. Microbiome-based oncology diagnostic tool warrants further exploration.
PubMed: 35346218
DOI: 10.1186/s12935-022-02554-6 -
Revista Da Associacao Medica Brasileira... 2010The aim of this review is to update knowledge about the vaginal ecosystem, non-cultivation methods for bacterial identification (gene amplification), the Lactobacillus... (Review)
Review
The aim of this review is to update knowledge about the vaginal ecosystem, non-cultivation methods for bacterial identification (gene amplification), the Lactobacillus species that comprise normal vaginal flora and influence of host genetics on bacterial interactions with local innate and acquired immune defenses. A Medline (Pubmed) search from 1997-2009 for relevant articles was performed and the most informative articles were selected. Non-culture techniques (gene amplification) allow a comprehensive analysis of the vaginal ecosystem's composition. In the majority of women in the reproductive age there is a predominance of one or more species of Lactobacillus: L. crispatus, L. inners and L gasseri. However, in other apparently healthy women there is a deficiency or complete absence of Lactobacilli. Instead, there is a substitution by other lactic acid-producing bacteria: Atobium, Megasphaera and/or Leptotrichia species. The infectivity and/or proliferation of pathogenic bacteria in the vagina is suppressed by lactic acid production, by products of endogenous bacteria and by activation of local innate and acquired immunity. Vaginal epithelial cells produce several compounds with anti-microbial activity. These cells have Toll-like receptors on their membrane that recognize molecular patterns associated with pathogens. Recognition leads to production of pro-inflammatory cytokines and stimulation of antigen-specific immunity. The production of IgG and IgA antibodies is also triggered in the endocervix and vagina in response to infection. Vaginal flora composition and the immune mechanisms constitute important defenses. Criteria of normal and abnormal flora have to be reviewed and genetic polymorphism can explain variations in flora composition. This new knowledge should be included in the clinical practice of gynecologists and obstetricians to improve patients care.
Topics: Female; Humans; Lactobacillus; Vagina
PubMed: 20676549
DOI: 10.1590/s0104-42302010000300026 -
The Eurasian Journal of Medicine Feb 2023Common noncommunicable diabetes mellitus disease has many complications in several parts of the human body. The oral cavity is one of the areas affected by diabetes...
Common noncommunicable diabetes mellitus disease has many complications in several parts of the human body. The oral cavity is one of the areas affected by diabetes mellitus conditions. The most common complications of diabetes mellitus in oral areas include increased drying of the mouth and increased oral diseases resulting from either microbial activity, such as dental caries, periodontal diseases, and oral candidiasis, or physiological problems, such as oral cancer, burning mouth syndrome, and temporomandibular disorders. Diabetes mellitus also has an impact on the diversity and quantity of oral microbiota. Oral infections promoted by diabetes mellitus mainly result from disturbance of the balance between different species of oral microbiota. Some oral species may be positively or negatively correlated with diabetes mellitus, while others may not be affected at all. The most numerous species in the presence of diabetes mellitus are those of phylum Firmicutes of bacteria such as hemolytic Streptococci, Staphylococcus spp., Prevotella spp., Leptotrichia spp., and Veillonella and species of the fungus Candida. Proteobacteria spp. and Bifidobacteria spp. are common microbiota that are negatively impacted by diabetes mellitus. In general, the effect of diabetes mellitus could include all types of oral microbiota, whether it is bacteria or fungi. The 3 types of association between diabetes mellitus and oral microbiota that will be illustrated in this review are increase, decrease, or lack of impact. As final inclusion, a great number of oral microbiota have increased in the presence of diabetes mellitus.
PubMed: 36861873
DOI: 10.5152/eurasianjmed.2023.21164 -
PloS One 2022Although some human studies have reported gut microbiome changes in individuals with Alzheimer's disease (AD) dementia or mild cognitive impairment (MCI), gut microbiome...
BACKGROUND
Although some human studies have reported gut microbiome changes in individuals with Alzheimer's disease (AD) dementia or mild cognitive impairment (MCI), gut microbiome alterations in preclinical AD, i.e., cerebral amyloidosis without cognitive impairment, is largely unknown.
OBJECTIVE
We aimed to identify gut microbial alterations associated with preclinical AD by comparing cognitively normal (CN) older adults with cerebral Aβ deposition (Aβ+ CN) and those without cerebral Aβ deposition (Aβ- CN).
METHODS
Seventy-eight CN older participants (18 Aβ+ CN and 60 Aβ- CN) were included, and all participants underwent clinical assessment and Pittsburg compound B-positron emission tomography. The V3-V4 region of the 16S rRNA gene of genomic DNA extracted from feces was amplified and sequenced to establish the microbial community.
RESULTS
Generalized linear model analysis revealed that the genera Megamonas (B = 3.399, q<0.001), Serratia (B = 3.044, q = 0.005), Leptotrichia (B = 5.862, q = 0.024) and Clostridium (family Clostridiaceae) (B = 0.788, q = 0.034) were more abundant in the Aβ+ CN group than the Aβ- CN group. In contrast, genera CF231 (B = -3.237, q< 0.001), Victivallis (B = -3.447, q = 0.004) Enterococcus (B = -2.044, q = 0.042), Mitsuokella (B = -2.119, q = 0.042) and Clostridium (family Erysipelotrichaceae) (B = -2.222, q = 0.043) were decreased in Aβ+ CN compared to Aβ- CN. Notably, the classification model including the differently abundant genera could effectively distinguish Aβ+ CN from Aβ- CN (AUC = 0.823).
CONCLUSION
Our findings suggest that specific alterations of gut bacterial taxa are related to preclinical AD, which means these changes may precede cognitive decline. Therefore, examining changes in the microbiome may be helpful in preclinical AD screening.
Topics: Humans; Animals; Aged; Gastrointestinal Microbiome; Alzheimer Disease; RNA, Ribosomal, 16S; Tomography, X-Ray Computed; Cognitive Dysfunction
PubMed: 36445883
DOI: 10.1371/journal.pone.0278276 -
PloS One 2021The objective of this pilot study was to describe the microbial profiles present in the plaque and saliva of children who continued to develop new carious lesions...
The objective of this pilot study was to describe the microbial profiles present in the plaque and saliva of children who continued to develop new carious lesions following treatment with silver diamine fluoride ("nonresponders") compared to caries active, caries-free, and children immediately receiving SDF treatment for untreated caries in order to identify potential microbial differences that may relate to a re-incidence of caries. Saliva and plaque samples from infected and contralateral sites were obtained from twenty children who were either caries free, had active carious lesions, were caries active and received SDF treatment immediately before sampling, or had previously received SDF treatment and developed new caries. In total, 8,057,899 Illumina-generated sequence reads from 60 samples were obtained. Reads were processed using the Quantitative Insights Into Microbial Ecology pipeline. Group differences were assessed using Analysis of Variance Models and Tukey Honest Significant Differences. To identify significant taxa between treatment groups, Linear discriminant analysis Effect Size (LefSe) and Analysis of Differential Abundance Taking Sample Variation Into Account were used. Differential abundant analysis indicated that members of the Lachnospiraceae family were significantly enriched in non-responders and the genus Tannerella and species Granulicatella adiances were also highly abundant in this group. LefSe analysis between non-responders and SDF-treated groups revealed that genera Leptotrichia and Granulicatella were enriched in non-responders. We observed the highest abundance of phosphotransferase system and lowest abundance of lipopolysaccharide synthesis in non-responders. The microbiome in dental biofilms is responsible for initiation and progression of dental caries. SDF has been shown to be effective in arresting the progression carious lesions, in part due to its antimicrobial properties. Findings suggest that the differential abundance of select microbiota and specific pathway functioning in individuals that present with recurrent decay after SDF treatment may contribute to a potential failure of silver diamine fluoride to arrest dental caries. However, the short duration of sample collection following SDF application and the small sample size emphasize the need for further data and additional analysis.
Topics: Carnobacteriaceae; Child; Cross-Sectional Studies; DNA, Bacterial; Dental Caries; Dental Plaque; Discriminant Analysis; Fluorides, Topical; Humans; Leptotrichia; Microbiota; Pilot Projects; Principal Component Analysis; Quaternary Ammonium Compounds; Saliva; Sequence Analysis, DNA; Silver Compounds; Treatment Failure
PubMed: 33720954
DOI: 10.1371/journal.pone.0242396 -
Molecular Cell Jun 2022CRISPR systems are prokaryotic adaptive immune systems that use RNA-guided Cas nucleases to recognize and destroy foreign genetic elements. To overcome CRISPR immunity,...
CRISPR systems are prokaryotic adaptive immune systems that use RNA-guided Cas nucleases to recognize and destroy foreign genetic elements. To overcome CRISPR immunity, bacteriophages have evolved diverse families of anti-CRISPR proteins (Acrs). Recently, Lin et al. (2020) described the discovery and characterization of 7 Acr families (AcrVIA1-7) that inhibit type VI-A CRISPR systems. We detail several inconsistencies that question the results reported in the Lin et al. (2020) study. These include inaccurate bioinformatics analyses and bacterial strains that are impossible to construct. Published strains were provided by the authors, but MS2 bacteriophage plaque assays did not support the published results. We also independently tested the Acr sequences described in the original report, in E. coli and mammalian cells, but did not observe anti-Cas13a activity. Taken together, our data and analyses prompt us to question the claim that AcrVIA1-7 reported in Lin et al. are type VI anti-CRISPR proteins.
Topics: Animals; Bacteriophages; CRISPR-Associated Proteins; CRISPR-Cas Systems; Escherichia coli; Leptotrichia; Mammals; Prophages; Ribonucleases
PubMed: 35623354
DOI: 10.1016/j.molcel.2022.05.002