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International Journal of Molecular... Nov 2022Genome sequencing facilitates the study of bacterial taxonomy and allows the re-evaluation of the taxonomic relationships between species. Here, we aimed to analyze the...
Genome sequencing facilitates the study of bacterial taxonomy and allows the re-evaluation of the taxonomic relationships between species. Here, we aimed to analyze the draft genomes of four commensal clinical isolates from the semen of infertile Lebanese men. To determine the phylogenetic relationships among these strains and other spp. and to confirm their identity at the genomic level, we compared the genomes of these four isolates with the complete genome sequences of and and the draft genomes of , , , and that are available in the NCBI Genbank database. Our findings revealed that the WGS analysis accurately identified and corroborated the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) species identities of the isolates. The combination of three well-established genome-based taxonomic tools (in silico DNA-DNA Hybridization, Ortho Average Nucleotide identity, and pangenomic studies) proved to be relatively the best identification approach. Notably, we also discovered that some strains that are deposited in databases contain many taxonomical errors. The latter is very important and must be addressed to prevent misdiagnosis and missing emerging etiologies. We also highlight the need for robust cut-offs to delineate the species using genomic tools.
Topics: Male; Humans; Phylogeny; Neisseria; Neisseria gonorrhoeae; Neisseria meningitidis; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; DNA; Genome, Bacterial
PubMed: 36362240
DOI: 10.3390/ijms232113456 -
International Journal of Cancer Mar 2022Evidence suggests that Helicobacter pylori plays a role in gastric cancer (GC) initiation. However, epidemiologic studies on the specific role of other bacteria in the...
Evidence suggests that Helicobacter pylori plays a role in gastric cancer (GC) initiation. However, epidemiologic studies on the specific role of other bacteria in the development of GC are lacking. We conducted a case-control study of 89 cases with gastric intestinal metaplasia (IM) and 89 matched controls who underwent upper gastrointestinal endoscopy at three sites affiliated with NYU Langone Health. We performed shotgun metagenomic sequencing using oral wash samples from 89 case-control pairs and antral mucosal brushing samples from 55 case-control pairs. We examined the associations of relative abundances of bacterial taxa and functional pathways with IM using conditional logistic regression with and without elastic-net penalty. Compared with controls, oral species Peptostreptococcus stomatis, Johnsonella ignava, Neisseria elongata and Neisseria flavescens were enriched in cases (odds ratios [ORs] = 1.29-1.50, P = .004-.01) while Lactobacillus gasseri, Streptococcus mutans, S parasanguinis and S sanguinis were under-represented (ORs = 0.66-0.76, P = .006-.042) in cases. Species J ignava and Filifactor alocis in the gastric microbiota were enriched (ORs = 3.27 and 1.43, P = .005 and .035, respectively), while S mutans, S parasanguinis and S sanguinis were under-represented (ORs = 0.61-0.75, P = .024-.046), in cases compared with controls. The lipopolysaccharide and ubiquinol biosynthesis pathways were more abundant in IM, while the sugar degradation pathways were under-represented in IM. The findings suggest potential roles of certain oral and gastric microbiota, which are correlated with regulation of pathways associated with inflammation, in the development of gastric precancerous lesions.
Topics: Aged; Case-Control Studies; Female; Gastric Mucosa; Gastrointestinal Microbiome; Helicobacter pylori; Humans; Male; Metagenomics; Metaplasia; Middle Aged; Mouth Mucosa; Precancerous Conditions; Stomach Neoplasms
PubMed: 34664721
DOI: 10.1002/ijc.33848 -
Clinical Chemistry and Laboratory... Feb 2020Our body is inhabited by a variety of microbes (microbiota), mainly bacteria, that outnumber our own cells. Until recently, most of what we knew about the human... (Review)
Review
Our body is inhabited by a variety of microbes (microbiota), mainly bacteria, that outnumber our own cells. Until recently, most of what we knew about the human microbiota was based on culture methods, whereas a large part of the microbiota is uncultivable, and consequently previous information was limited. The advent of culture-independent methods and, particularly, of next-generation sequencing (NGS) methodology, marked a turning point in studies of the microbiota in terms of its composition and of the genes encoded by these microbes (microbiome). The microbiome is influenced predominantly by environmental factors that cause a large inter-individual variability (~20%) being its heritability only 1.9%. The gut microbiome plays a relevant role in human physiology, and its alteration ("dysbiosis") has been linked to a variety of inflammatory gut diseases, including celiac disease (CD). CD is a chronic, immune-mediated disorder that is triggered by both genetic (mainly HLA-DQ2/DQ8 haplotypes) and environmental factors (gluten), but, in recent years, a large body of experimental evidence suggested that the gut microbiome is an additional contributing factor to the pathogenesis of CD. In this review, we summarize the literature that has investigated the gut microbiome associated with CD, the methods and biological samples usually employed in CD microbiome investigations and the putative pathogenetic role of specific microbial alterations in CD. In conclusion, both gluten-microbe and host-microbe interactions drive the gluten-mediated immune response. However, it remains to be established whether the CD-associated dysbiosis is the consequence of the disease, a simple concomitant association or a concurring causative factor.
Topics: Celiac Disease; Gastrointestinal Microbiome; Humans; Mouth
PubMed: 31494628
DOI: 10.1515/cclm-2019-0657 -
Journal of Thoracic Disease May 2014Neisseria flavescens is an uncommon pathogen of human infection, pneumonia and empyema caused by N. flavescens is rarely reported. Herein, we report a 56-year-old...
Neisseria flavescens is an uncommon pathogen of human infection, pneumonia and empyema caused by N. flavescens is rarely reported. Herein, we report a 56-year-old diabetic patient presenting necrotising pneumonia and empyema due to N. flavescens infection. The main clinical manifestation of this patient was high fever, sticky pus and gradually aggravating dyspnea. The chest computed tomography (CT) scan showed there are mass of high density areas around hilus of the left lung, hollow sign with inflammation also appeared. A biopsy specimen was taken from the left principal bronchus by lung puncture biopsy and showed necrosis and inflammation. Microscopic examination of direct smear and culture of sticky pus, much more gram-negative diplococcus was present, pathogen was further identified by Vitek NH card, Vitek MS and confirmed as N. flavescens by 16S rRNA gene sequencing finally. Anti-infection therapy following the antimicrobial susceptibility test results was effectively. To our knowledge, this is the first report of pulmonary infection caused by N. flavescens.
PubMed: 24822118
DOI: 10.3978/j.issn.2072-1439.2014.02.16 -
Scientific Reports Jul 2018We previously profiled duodenal microbiome in active (a-), gluten-free diet (GFD) celiac disease (CD) patients and controls finding higher levels of the Proteobacterium...
We previously profiled duodenal microbiome in active (a-), gluten-free diet (GFD) celiac disease (CD) patients and controls finding higher levels of the Proteobacterium Neisseria flavescens in a-CD patients than in the other two groups. Here, we investigate the oropharyngeal microbiome in CD patients and controls to evaluate whether this niche share microbial composition with the duodenum. We characterized by 16S rRNA gene sequencing the oropharyngeal microbiome in 14 a-CD, 22 GFD patients and 20 controls. Bacteroidetes, Proteobacteria and Firmicutes differed significantly between the three groups. In particular, Proteobacteria abounded in a-CD and Neisseria species mostly accounted for this abundance (p < 0.001), whereas Bacteroidetes were more present in control and GFD microbiomes. Culture-based oropharyngeal microbiota analysis confirmed the greater abundance of Proteobacteria and of Neisseria species in a-CD. Microbial functions prediction indicated a greater metabolic potential for degradation of aminoacids, lipids and ketone bodies in a-CD microbiome than in control and GFD microbiomes, in which polysaccharide metabolism predominated. Our results suggest a continuum of a-CD microbial composition from mouth to duodenum. We may speculate that microbiome characterization in the oropharynx, which is a less invasive sampling than the duodenum, could contribute to investigate the role of dysbiosis in CD pathogenesis.
Topics: Celiac Disease; Computational Biology; Female; Humans; Male; Microbiota; Neisseria; Oropharynx; RNA, Ribosomal, 16S
PubMed: 30038321
DOI: 10.1038/s41598-018-29443-1 -
A Review on Microbial Species for Forensic Body Fluid Identification in Healthy and Diseased Humans.Current Microbiology Jul 2023Microbial communities present in body fluids can assist in distinguishing between types of body fluids. Metagenomic studies have reported bacterial genera which are core... (Review)
Review
Microbial communities present in body fluids can assist in distinguishing between types of body fluids. Metagenomic studies have reported bacterial genera which are core to specific body fluids and are greatly influenced by geographical location and ethnicity. Bacteria in body fluids could also be due to bacterial infection; hence, it would be worthwhile taking into consideration bacterial species associated with diseases. The present review reports bacterial species characteristic of diseased and healthy body fluids across geographical locations, and bacteria described in forensic studies, with the aim of collating a set of bacteria to serve as the core species-specific markers for forensic body fluid identification. The most widely reported saliva-specific bacterial species are Streptococcus salivarius, Prevotella melaninogenica, Neisseria flavescens, with Fusobacterium nucleatum associated with increased diseased state. Lactobacillus crispatus and Lactobacillus iners are frequently dominant in the vaginal microbiome of healthy women. Atopobium vaginae, Prevotella bivia, and Gardnerella vaginalis are more prevalent in women with bacterial vaginosis. Semen and urine-specific bacteria at species level have not been reported, and menstrual blood bacteria are indistinguishable from vaginal fluid. Targeting more than one bacterial species is recommended for accurate body fluid identification. Although metagenomic sequencing provides information of a broad microbial profile, the specific bacterial species could be used to design biosensors for rapid body fluid identification. Validation of microbial typing methods and its application in identifying body fluids in a mixed sample would allow regular use of microbial profiling in a forensic workflow.
Topics: Humans; Female; Vaginosis, Bacterial; Vagina; Body Fluids; Gardnerella vaginalis; Saliva; Bacteria
PubMed: 37491404
DOI: 10.1007/s00284-023-03413-x -
Frontiers in Microbiology 2022The relationship between oral squamous cell carcinoma (OSCC) development and the microbiome has attracted increasing attention. The depth of invasion (DOI) is an...
The relationship between oral squamous cell carcinoma (OSCC) development and the microbiome has attracted increasing attention. The depth of invasion (DOI) is an important indicator of tumor progression, staging and prognosis, and the change in the oral microbiome based on the DOI is unclear. This report describes the use of metagenomic analyses to investigate the relationship between the oral microbiome and the DOI. Forty patients in different DOI categories were recruited; 10 healthy people served as the control group. Swab samples collected from the participants were subjected to metagenomic analyses, and the oral microbial communities and their functions were investigated. The abundances of , , , and were significantly increased in the patients compared with the controls. The abundances of some bacteria exhibited a stage-related trend. The abundances of , and increased with increasing DOI. In contrast, the abundances of and decreased with increasing DOI. Based on receiver operating characteristic (ROC) curve analysis, eight species were found to have predictive value: , , , and in the healthy control group and , , and in the high DOI group. In the functional analysis, several metabolic pathways were decreased, whereas flagellar assembly and bacterial chemotaxis showed an increasing trend as the disease progressed. Biofilm formation, flagella, lipopolysaccharide (LPS) and other virulence factors exhibited staging-related changes. These pathogenic pathways and factors had a clear correlation with specific pathogens. In particular, when OSCC progressed to the late stage, microbial diversity and functional potential changed greatly.
PubMed: 35222330
DOI: 10.3389/fmicb.2022.795777 -
Frontiers in Cellular and Infection... 2020While extensive literature exists about the role of oral bacterial pathogens like and in oral squamous cell carcinoma (OSCC), the role of health-associated species has...
While extensive literature exists about the role of oral bacterial pathogens like and in oral squamous cell carcinoma (OSCC), the role of health-associated species has been largely unexplored. In this study, we assessed the effect of , and on proliferation and expression of marker genes (IL-6, TNF-α, MMP3, CD36, CCD1, and NANOG) in OSCC cell lines CAL27, SCC25, and SCC4. was included as a pathogenic control. Both bacterial lysates (3 concentrations) and live cells (3 MOIs) were tested. , and resulted in substantial, dose-dependent reduction of proliferation, which was found to be mediated by HO for the former and intracellular infection in the latter two species. However, only showed differential antiproliferative effect against the cancer cell lines vs. the normal control (TIGKs). In the gene expression assays, the health-associated species mostly downregulated CD36, a gene that plays an important role in tumor growth and metastasis, while upregulated it. IL6 and TNF expression, on the other hand, was upregulated by almost all species, particularly the Gram-negatives including . The effect on other genes was less evident and varied significantly by cell line. This exploratory study is the first insight into how health-associated bacteria may interact with OSCC. Further studies to explore whether the observed effects may have implications for the prevention or treatment of oral cancer are warranted.
Topics: Burkholderiaceae; Carcinoma, Squamous Cell; Fusobacterium nucleatum; Humans; Hydrogen Peroxide; Micrococcaceae; Mouth Neoplasms; Neisseria; Porphyromonas gingivalis; Veillonella
PubMed: 33123499
DOI: 10.3389/fcimb.2020.575656 -
Cellular Microbiology Aug 2019We previously identified a Neisseria flavescens strain in the duodenum of celiac disease (CD) patients that induced immune inflammation in ex vivo duodenal mucosal...
Celiac disease-associated Neisseria flavescens decreases mitochondrial respiration in CaCo-2 epithelial cells: Impact of Lactobacillus paracasei CBA L74 on bacterial-induced cellular imbalance.
We previously identified a Neisseria flavescens strain in the duodenum of celiac disease (CD) patients that induced immune inflammation in ex vivo duodenal mucosal explants and in CaCo-2 cells. We also found that vesicular trafficking was delayed after the CD-immunogenic P31-43 gliadin peptide-entered CaCo-2 cells and that Lactobacillus paracasei CBA L74 (L. paracasei-CBA) supernatant reduced peptide entry. In this study, we evaluated if metabolism and trafficking was altered in CD-N. flavescens-infected CaCo-2 cells and if any alteration could be mitigated by pretreating cells with L. paracasei-CBA supernatant, despite the presence of P31-43. We measured CaCo-2 bioenergetics by an extracellular flux analyser, N. flavescens and P31-43 intracellular trafficking by immunofluorescence, cellular stress by TBARS assay, and ATP by bioluminescence. We found that CD-N. flavescens colocalised more than control N. flavescens with early endocytic vesicles and more escaped autophagy thereby surviving longer in infected cells. P31-43 increased colocalisation of N. flavescens with early vesicles. Mitochondrial respiration was lower (P < .05) in CD-N. flavescens-infected cells versus not-treated CaCo-2 cells, whereas pretreatment with L. paracasei-CBA reduced CD-N. flavescens viability and improved cell bioenergetics and trafficking. In conclusion, CD-N. flavescens induces metabolic imbalance in CaCo-2 cells, and the L. paracasei-CBA probiotic could be used to correct CD-associated dysbiosis.
Topics: Adenosine Triphosphate; Autophagosomes; Autophagy; Caco-2 Cells; Celiac Disease; Culture Media, Conditioned; Dysbiosis; Gene Expression; Gliadin; Host-Pathogen Interactions; Humans; Lacticaseibacillus paracasei; Lysosomal-Associated Membrane Protein 2; Microtubule-Associated Proteins; Mitochondria; Neisseria; Oxidative Phosphorylation; Peptide Fragments; Probiotics; Thiobarbituric Acid Reactive Substances; Transport Vesicles; Vesicular Transport Proteins
PubMed: 31042331
DOI: 10.1111/cmi.13035 -
Journal of Oral Microbiology Jun 2021: A few recent studies have characterized the salivary microbiome in association with Autism Spectrum Disorder (ASD). Here, we sought to assess if there is an...
: A few recent studies have characterized the salivary microbiome in association with Autism Spectrum Disorder (ASD). Here, we sought to assess if there is an association between the tongue microbiome and ASD. : Tongue scrapping samples were obtained from 25 children with ASD and 38 neurotypical controls. The samples were sequenced for the gene (V1-V3) and the resultant high-quality reads were assigned to the species-level using our previously described BLASTn-based algorithm. Downstream analyses of microbial profiles were conducted using QIIME, LEfSe, and R. : Independent of grouping, and accounted for > 60% of the average microbiome. and were the most abundant species. Species richness and diversity did not significantly differ between the study groups. Thirteen species and three genera were differentially abundant between the two groups, e.g. enrichment of and and depletion of and in the ASD group. However, none of them withstood adjustment for multiple comparisons. : The tongue microbiome of children with ASD was not significantly different from that of healthy control children, which is largely consistent with results from the literature.
PubMed: 34211637
DOI: 10.1080/20002297.2021.1936434