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Heliyon May 2024The respiratory tract harbors a variety of microbiota, whose composition and abundance depend on specific site factors, interaction with external factors, and disease....
BACKGROUND
The respiratory tract harbors a variety of microbiota, whose composition and abundance depend on specific site factors, interaction with external factors, and disease. The aim of this study was to investigate the relationship between COVID-19 severity and the nasopharyngeal microbiome.
METHODS
We conducted a prospective cohort study in Mexico City, collecting nasopharyngeal swabs from 30 COVID-19 patients and 14 healthy volunteers. Microbiome profiling was performed using 16S rRNA gene analysis. Taxonomic assignment, classification, diversity analysis, core microbiome analysis, and statistical analysis were conducted using R packages.
RESULTS
The microbiome data analysis revealed taxonomic shifts within the nasopharyngeal microbiome in severe COVID-19. Particularly, we observed a significant reduction in the relative abundance of and genera in critically ill COVID-19 patients (p < 0.001). In contrast, these patients exhibited a marked enrichment of , and genera (p < 0.01). Analysis of the core microbiome across all samples consistently identified the presence of , , and .
CONCLUSIONS
Our study suggests that the disruption of physicochemical conditions and barriers resulting from inflammatory processes and the intubation procedure in critically ill COVID-19 patients may facilitate the colonization and invasion of the nasopharynx by oral microorganisms.
PubMed: 38826746
DOI: 10.1016/j.heliyon.2024.e31562 -
Bioprocess and Biosystems Engineering Jul 2024A reactor with silicone tubes as support medium was used for glycerol fermentation. The experimental set-up consisted of three phases. In P1, the applied glycerol...
A reactor with silicone tubes as support medium was used for glycerol fermentation. The experimental set-up consisted of three phases. In P1, the applied glycerol loading rate (gly-LR) was in the range of 6-10 g.L.d at an influent pH of 7.9 ± 0.4. In P2, gly-LR was kept constant (18.0 ± 1.8 g.L.d) with different doses of NaHCO. Finally in P3, two different gly-LR (9 and 18 g.L.d) were evaluated, dosing 1 g-NaHCO per g-COD of glycerol. Glycerol consumption was close 90%. The main end-product was 1,3-propanediol (1,3-PDO) (0.40 mol.mol-gly), but ethanol was also generated, particularly at pH above 8 and low gly-LR (0.20 mol.mol-gly). After 1-year operation with glycerol as the only carbon source, a drastic shift in the bacterial community was observed. The 1,3-PDO producers Lacrimispora and Clostridium became dominant, although non-glycerol-degrading fermentative genera, e.g., Actinomyces and Eubacterium, thrived at the expense of cellular breakdown products.
Topics: Glycerol; Bioreactors; Hydrogen-Ion Concentration; Fermentation; Anaerobiosis; Propylene Glycols
PubMed: 38822157
DOI: 10.1007/s00449-024-03003-6 -
Journal of Gastroenterology May 2024Microbiota may be associated with esophageal squamous cell carcinoma (ESCC) development. However, it is not known the predictive value of microbial biomarkers combining...
BACKGROUND
Microbiota may be associated with esophageal squamous cell carcinoma (ESCC) development. However, it is not known the predictive value of microbial biomarkers combining epidemiological factors for the early detection of ESCC and precancerous lesions.
METHODS
A total of 449 specimens (esophageal swabs and saliva) were collected from 349 participants with different esophageal statuses in China to explore and validate ESCC-associated microbial biomarkers from genes level to species level by 16S rRNA sequencing, metagenomic sequencing and real-time quantitative polymerase chain reaction.
RESULTS
A bacterial biomarker panel including Actinomyces graevenitzii (A.g_1, A.g_2, A.g_3, A.g_4), Fusobacteria nucleatum (F.n_1, F.n_2, F.n_3), Haemophilus haemolyticus (H.h_1), Porphyromonas gingivalis (P.g_1, P.g_2, P.g_3) and Streptococcus australis (S.a_1) was explored by metagenomic sequencing to early detect the participants in Need group (low-grade intraepithelial neoplasia, high-grade intraepithelial neoplasia and ESCC) vs participants without these lesions as the Noneed group. Significant quantitative differences existed for each microbial target in which the detection efficiency rate was higher in saliva than esophageal swab. In saliva, the area under the curve (AUC) based on the microbial biomarkers (A.g_4 ∩ P.g_3 ∩ H.h_1 ∩ S.a_1 ∩ F.n_2) was 0.722 (95% CI 0.621-0.823) in the exploration cohort. Combining epidemiological factors (age, smoking, drinking, intake of high-temperature food and toothache), the AUC improved to 0.869 (95% CI 0.802-0.937) in the exploration cohort, which was validated with AUC of 0.757 (95% CI 0.663-0.852) in the validation cohort.
CONCLUSIONS
It is feasible to combine microbial biomarkers in saliva and epidemiological factors to early detect ESCC and precancerous lesions in China.
PubMed: 38819499
DOI: 10.1007/s00535-024-02117-8 -
BMC Microbiology May 2024Schaalia species are primarily found among the oral microbiota of humans and other animals. They have been associated with various infections through their involvement... (Comparative Study)
Comparative Study
Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity.
BACKGROUND
Schaalia species are primarily found among the oral microbiota of humans and other animals. They have been associated with various infections through their involvement in biofilm formation, modulation of host responses, and interaction with other microorganisms. In this study, two strains previously indicated as Actinomyces spp. were found to be novel members of the genus Schaalia based on their whole genome sequences.
RESULTS
Whole-genome sequencing revealed both strains with a genome size of 2.3 Mbp and GC contents of 65.5%. Phylogenetics analysis for taxonomic placement revealed strains NCTC 9931 and C24 as distinct species within the genus Schaalia. Overall genome-relatedness indices including digital DNA-DNA hybridization (dDDH), and average nucleotide/amino acid identity (ANI/AAI) confirmed both strains as distinct species, with values below the species boundary thresholds (dDDH < 70%, and ANI and AAI < 95%) when compared to nearest type strain Schaalia odontolytica NCTC 9935. Pangenome and orthologous analyses highlighted their differences in gene properties and biological functions compared to existing type strains. Additionally, the identification of genomic islands (GIs) and virulence-associated factors indicated their genetic diversity and potential adaptive capabilities, as well as potential implications for human health. Notably, CRISPR-Cas systems in strain NCTC 9931 underscore its adaptive immune mechanisms compared to strain C24.
CONCLUSIONS
Based on these findings, strain NCTC 9931 (= ATCC 17982 = DSM 43331 = CIP 104728 = CCUG 18309 = NCTC 14978 = CGMCC 1.90328) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24 (= NCTC 14980 = CGMCC 1.90329) represents a distinct novel subspecies, for which the name Schaalia dentiphila subsp. denticola. subsp. nov. is proposed. This study enriches our understanding of the genomic diversity of Schaalia species and paves the way for further investigations into their roles in oral health.
SIGNIFICANCE
This research reveals two Schaalia strains, NCTC 9931 and C24, as novel entities with distinct genomic features. Expanding the taxonomic framework of the genus Schaalia, this study offers a critical resource for probing the metabolic intricacies and resistance patterns of these bacteria. This work stands as a cornerstone for microbial taxonomy, paving the way for significant advances in clinical diagnostics.
Topics: Humans; Genome, Bacterial; Mouth; Phylogeny; Base Composition; Whole Genome Sequencing; DNA, Bacterial; Genomic Islands; Nucleic Acid Hybridization
PubMed: 38802738
DOI: 10.1186/s12866-024-03346-w -
Frontiers in Cellular and Infection... 2024Alveolar cleft (AC) is a common congenital defect in people with cleft lip and palate (CLP). Alveolar bone grafting (ABG) is typically performed during adolescence,...
INTRODUCTION
Alveolar cleft (AC) is a common congenital defect in people with cleft lip and palate (CLP). Alveolar bone grafting (ABG) is typically performed during adolescence, resulting in the fissure remaining in the mouth for a longer length of time. Patients with AC have a greater rate of oral diseases such as dental caries than the normal population, and the precise characteristics of the bacterial alterations caused by AC are unknown.
METHODS
We recruited a total of 87 subjects and collected dental plaque samples from AC adolescents (AAP), post-operative ABG adolescents (PAP), healthy control adolescents (CAP), AC young adults (AYP), post-operative ABG young adults (PYP), and healthy control young adults (CYP). The sequencing of 16S rRNA genes was performed.
RESULTS
The microbial composition of plaque from alveolar cleft patients differed significantly from age-matched healthy controls. Linear discriminant analysis effect size (LEfSe) analysis revealed that AAP was enriched for , and , whereas AYP was enriched for , and . There were phenotypic differences in facultatively anaerobic, Gram-negative, Gram-positive, and oxidative stress tolerance between the AYP group with longer alveolar cleft and the healthy control group according to Bugbase phenotypic predictions. Alveolar bone grafting did not alter the functional phenotype of alveolar cleft patients but reduced the number of differential genera between alveolar cleft patients and healthy controls at both ages.
CONCLUSIONS
Our study systematically characterized the supragingival plaque microbiota of alveolar cleft patients, post-alveolar bone grafting patients, and matched healthy controls in two ages to gain a better understanding of plaque ecology and microbiology associated with alveolar clefts.
Topics: Humans; Dental Plaque; Cleft Palate; Adolescent; Microbiota; RNA, Ribosomal, 16S; Female; Male; Cleft Lip; Young Adult; Bacteria; Alveolar Bone Grafting; Adult
PubMed: 38800834
DOI: 10.3389/fcimb.2024.1361206 -
New Microbes and New Infections Jun 2024
PubMed: 38799923
DOI: 10.1016/j.nmni.2024.101249 -
New Microbes and New Infections Jun 2024
Expression of Concern: Enterococcus timonensis' sp. nov., Actinomyces marseillensis' sp. nov., Leptotrichia massiliensis' sp. nov., Actinomyces pacaensis' sp. nov., Actinomyces oralis' sp. nov., Actinomyces culturomici' sp. nov. and Gemella massiliensis' sp. nov., new bacterial species isolated...
PubMed: 38799903
DOI: 10.1016/j.nmni.2024.101309 -
New Microbes and New Infections Jun 2024
Expression of Concern: Sanguibacter massiliensis sp. nov., Actinomyces minihominis sp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov. And Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples.
PubMed: 38799884
DOI: 10.1016/j.nmni.2024.101388 -
New Microbes and New Infections Jun 2024
Expression of Concern: Actinomyces ihuae, Actinomyces bouchesdurhonensis, Actinomyces urinae, Actinomyces marseillensis, Actinomyces mediterranea and Actinomyces oralis sp. nov. identified by culturomics.
PubMed: 38799873
DOI: 10.1016/j.nmni.2024.101247 -
New Microbes and New Infections Jun 2024
PubMed: 38799831
DOI: 10.1016/j.nmni.2024.101248