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Journal of Clinical Microbiology Sep 2004Sixty-three clinical isolates of charcoal-black-pigmented, gram-positive coryneform rods were received for identification by the Centers for Disease Control and...
Identification of some charcoal-black-pigmented CDC fermentative coryneform group 4 isolates as Rothia dentocariosa and some as Corynebacterium aurimucosum: proposal of Rothia dentocariosa emend. Georg and Brown 1967, Corynebacterium aurimucosum emend. Yassin et al. 2002, and Corynebacterium...
Sixty-three clinical isolates of charcoal-black-pigmented, gram-positive coryneform rods were received for identification by the Centers for Disease Control and Prevention (CDC) and were provisionally designated CDC fermentative coryneform group 4 (FCG4). Forty-five of these were characterized by morphological, physiologic, antimicrobial susceptibility, cellular fatty acids, 16S rRNA gene sequencing, and DNA-DNA hybridization analyses. Nitrate reduction, cellular fatty acid analysis, 16S rRNA gene sequencing, and DNA-DNA hybridization studies segregated these strains into two groups: FCG4a (8 strains) and FCG4b (37 strains). The FCG4a strains, only one of which was from a female genitourinary source, produced cellular fatty acid and biochemical profiles similar to those observed with reference strains of Rothia dentocariosa and Rothia mucilaginosa, while the FCG4b strains were similar to Corynebacterium species. DNA-DNA hybridization analysis demonstrated species-level relatedness among six FCG4a tested strains and showed that they were a charcoal-black-pigmented variant of R. dentocariosa. Sixteen isolates of the FCG4b group, mainly from female genitourinary tract specimens, as well as the type strains of two recently named species, Corynebacterium aurimucosum and Corynebacterium nigricans, were shown by DNA-DNA hybridization analysis and the sequencing of the 16S rRNA gene to be related at the species level and unrelated to the type strain of R. dentocariosa; therefore, the Corynebacterium-like strains were classified as a charcoal-black-pigmented variant of C. aurimucosum, because this name has nomenclatural priority over C. nigricans. These findings indicate that FCG4 represents a heterogeneous group that contains pigmented variants of both R. dentocariosa and C. aurimucosum; hence, the descriptions of both R. dentocariosa and C. aurimucosum have been amended to include charcoal-black-pigmented variants, and C. nigricans is a pro synonym of C. aurimucosum.
Topics: Centers for Disease Control and Prevention, U.S.; Corynebacterium; Female; Genitalia, Female; Humans; Microbial Sensitivity Tests; Micrococcaceae; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S; United States
PubMed: 15365010
DOI: 10.1128/JCM.42.9.4189-4198.2004 -
Frontiers in Cellular and Infection... 2022In recent years, the role of gastric and duodenal microbiota has acquired increasing importance in the homeostasis of the host, although, to date, most evidence concern...
In recent years, the role of gastric and duodenal microbiota has acquired increasing importance in the homeostasis of the host, although, to date, most evidence concern the faecal microbiota. Indeed, the gastric, and duodenal microbiota are challenging to study, due to gastric acid, bile, digestive enzymes, and rapid transit time. Specifically, the gastric acid environment may influence their bacterial composition since the acid barrier protects against orally ingested microorganisms and leads to their inactivation before reaching the intestine. The aim of this study was to assess a correlation between intragastric pH and gastric as well as intestinal microbiota of patients with histologic gastric alterations. pH was measured in the gastric juice and the bacterial composition in gastric and duodenal biopsies and faecal samples, was investigated 16s rRNA gene sequencing. The main result is the direct correlation of duodenal microbiota biodiversity, alpha diversity measures, with intragastric pH values. In particular, patients with hypochlorhydria showed increased duodenal microbiota biodiversity, higher intragastric pH values being prevalent in patients with chronic atrophic gastritis. Lastly, the latter was also strongly associated to the presence of oral bacteria, like and , in the duodenal microbiota. In conclusions, our results suggest a low-acid gastric environment as a contributive factor for duodenal dysbiosis, potentially leading to the development of pathological conditions of the gastrointestinal tract.
Topics: Achlorhydria; Dysbiosis; Gastric Mucosa; Helicobacter Infections; Helicobacter pylori; Humans; RNA, Ribosomal, 16S
PubMed: 35521214
DOI: 10.3389/fcimb.2022.854904 -
MSystems 2018Clinical interventions in the stomach have been linked to fecal microbiota alterations, suggesting a function of the stomach in gastrointestinal (GI) homeostasis. We...
Clinical interventions in the stomach have been linked to fecal microbiota alterations, suggesting a function of the stomach in gastrointestinal (GI) homeostasis. We sought to determine the taxonomic bacterial biogeography of the upper GI tract, including different sites within the human stomach (cardia, corpus, and antrum), adjacent upstream (esophagus) and downstream (duodenum) locations, and luminal contents (aspirate), as well as whole-stomach samples from mice and gerbils. Qualitative and quantitative DNA- and RNA-based taxonomic microbiota analyses were combined to study the relationship of relative and absolute bacterial abundances and transcriptionally active bacterial microbiota components in the stomach of humans and mice. Stomach microbiota compositions resembled those of esophagus and duodenum. However, along the descending GI tract, the relative abundances of specific oropharyngeal commensals decreased () or increased (Rothia mucilaginosa, , and ). Furthermore, the compositional similarity (weighted UniFrac) between stomach aspirates and esophageal biopsy samples increased with gastric relative abundance. In both human aspirate and mouse stomach samples, were more abundant among transcriptionally active bacteria than . The relative abundance of in the stomach was negatively correlated and that of was positively correlated with absolute bacterial abundance, suggesting a disproportionate increase of over at higher bacterial densities. Human, mouse, and gerbil stomach samples showed similarities at higher taxonomic levels but differences at lower taxonomic levels. Our findings suggest selective enrichment and depletion of specific bacterial taxa in the stomach and being transcriptionally more active than that increase in relative abundance with total bacterial load. Clinical stomach interventions, such as acid inhibition or bypass surgery, have been linked to fecal microbiota alterations. We demonstrate that the stomach microbiota largely overlaps those of adjacent gastrointestinal locations and identify gradual decreases and increases in the relative abundances of specific bacteria within the stomach, suggesting selective enrichment and depletion. Moreover, similarities between stomach and esophagus samples are proportional to the concentrations of () in the stomach. The relative abundance of in the stomach, compared to that of , is increased in RNA relative to DNA, indicating higher transcriptional activity. Moreover, increased absolute bacterial loads are associated with decreased relative abundance of and higher relative abundance of . Our findings characterize the stomach microbiota as influenced by influx against a background of transcriptionally more active Human, mouse, and gerbil stomach microbiotas differ at lower taxonomic levels, which might affect the utility of these model organisms.
PubMed: 30505943
DOI: 10.1128/mSystems.00262-18 -
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 -
International Journal of Infectious... May 2024Non-tuberculous mycobacteria (NTM) frequently colonize the airways of patients with bronchiectasis; however, there has been limited research into airway microbiota...
OBJECTIVES
Non-tuberculous mycobacteria (NTM) frequently colonize the airways of patients with bronchiectasis; however, there has been limited research into airway microbiota composition and predisposing factors for NTM detection during acute bronchiectasis exacerbations.
METHODS
This study enrolled 34 patients with bronchiectasis experiencing acute exacerbations. Metagenomic next-generation sequencing was used to detect microbiota in bronchoalveolar lavage fluid (BALF), and bioinformatics methods were used for the comparative analysis of meaningful microbiota in the BALF of patients with acute exacerbations of bronchiectasis. A correlation analysis was conducted to identify susceptibility factors for NTM in patients with bronchiectasis.
RESULTS
Compared with patients with community-acquired pneumonia, patients with bronchiectasis had higher detection rates of NTM (38.2%), Pseudomonas aeruginosa, and Haemophilus influenzae. Patients with NTM-positive bronchiectasis had lower body mass index and lipid profiles than patients who were NTM-negative. Metagenomic next-generation sequencing of BALF revealed patients who were NTM-positive had increased relative abundance of Rothia and other anaerobic genera compared with patients who were NTM-negative. Patients who were NTM-positive also showed higher levels of Streptococcus parasanguinis at the species level. Elevated Rothia mucilaginosa and S. parasanguinis correlated with decreased percentages of clusters of differentiation 3+ T lymphocytes and clusters of differentiation 3+ T-cell subgroups in peripheral blood.
CONCLUSIONS
NTM colonization increases the risk of acute bronchiectasis exacerbations. Low body mass index, lipid levels, and isolation of R. mucilaginosa and S. parasanguinis in BALF are susceptibility factors for NTM colonization in patients with bronchiectasis.
PubMed: 38821186
DOI: 10.1016/j.ijid.2024.107120 -
Revista Chilena de Infectologia :... Apr 2022Rothia mucilaginosa is a bacterium derived from the upper respiratory tract microbiota, which is rarely associated with infections in immunocompromised patients...
Rothia mucilaginosa is a bacterium derived from the upper respiratory tract microbiota, which is rarely associated with infections in immunocompromised patients suffering chronic lung diseases, mainly pneumonia and bacteremia. Its treatment is generally based on the use of β-lactams. The case study of a kidney transplant patient using immunosuppressive drugs, who developed a disseminated Cryptococcus neoformans infection, is described. After starting antifungal therapy, he presented with fever, appearance of new radiological infiltrates and acute respiratory failure, demonstrating a positive culture for R. mucilaginosa in a study with bronchoalveolar lavage, ruling out other etiologies. He evolved favorably after the use of meropenem, with good clinical response and resolution of radiological infiltrates.
Topics: Humans; Immunocompromised Host; Kidney Transplantation; Male; Micrococcaceae; Pneumonia, Bacterial
PubMed: 35856995
DOI: 10.4067/S0716-10182022000200210 -
Biomedical Reports Jun 2024Phototherapy is the most commonly used treatment for neonatal hyperbilirubinemia (NH). Gut microbiota is involved in bilirubin metabolism; however, it is uncertain...
Phototherapy is the most commonly used treatment for neonatal hyperbilirubinemia (NH). Gut microbiota is involved in bilirubin metabolism; however, it is uncertain whether this is affected by phototherapy. The present study included 43 newborns with hyperbilirubinemia and collected fecal samples for high-throughput sequencing before and after phototherapy. Selection α diversity analysis was used to determine the differences in diversity and abundance between the two groups, whereas similarity was determined using β diversity analysis. Linear discriminant analysis effect size analysis was used to screen for markedly different bacteria. The structure of the gut microbiota in newborns with hyperbilirubinemia changed after phototherapy, with a significant decrease in abundance and diversity. The changes in the key bacterial species were characterized by an increase in the abundance of and a decrease in the abundance of , , and . These changes mainly manifested as an increase in beneficial bacteria and a decrease in opportunistic bacteria, which may not be related to the side effects of phototherapy. These results can provide theoretical assistance for microbiological research on the later stages of NH.
PubMed: 38765854
DOI: 10.3892/br.2024.1789 -
Frontiers in Genetics 2023Biological material from the oral cavity is an excellent source of samples for genetic diagnostics. This is because collection is quick, easy-to-access, and...
Biological material from the oral cavity is an excellent source of samples for genetic diagnostics. This is because collection is quick, easy-to-access, and non-invasive. We have set-up clinical whole genome sequence testing for patients with suspected hereditary disease. Beside the excellent quality of human DNA that can be isolated from such samples, we observed the presence of non-human DNA sequences at varying percentages. We investigated the proportion of non-human mapped reads (NHMR) sequenced from buccal swabs and saliva, the type of microbial genomes from which they were derived, and impact on molecular classification. Read sequences that did not map to the human reference genome were aligned to complete reference microbial reference sequences from the National Center for Biotechnology Information's (NCBI) RefSeq database using Kraken2. Out of 765 analyzed samples over 80% demonstrated more than 5% NHMRs. The majority of NHMRs were from bacterial genomes (average 69%, buccal swabs and 54% saliva), while the proportion of viruses was low, averaging 0.32% (buccal swabs) and 0.07% (saliva). We identified more than 30 different bacterial families of which and were the most common species. Importantly, the level of contamination did not impact the diagnostic yield.
PubMed: 36824435
DOI: 10.3389/fgene.2023.1081424 -
Frontiers in Microbiology 2021Oral microbiota dysbiosis is associated with the occurrence and progression of oral cancer. To investigate the association between the microbiota and risk of oral...
Oral microbiota dysbiosis is associated with the occurrence and progression of oral cancer. To investigate the association between the microbiota and risk of oral squamous cell carcinoma (OSCC), we identified the microbial composition of paired tumor (TT)/normal paracancerous tissues (NPT) and saliva (TS) samples in OSCC patients through 16S rRNA gene sequencing. A total of 22 phyla, 321 genera, and 869 species were identified in the oral samples. Paired comparisons revealed significant differences between TT, NPT, and TS groups, with the genus significantly enriched in TT. The phylum Actinobacteria; genus ; and species , , and were significantly enriched in NPT, while the phylum Bacteroidetes; genera , , and ; and seven species, including sp., sp., and sp., were significantly enriched in TS. In TTs, the abundance of was profoundly higher in the gingiva, while and were enriched in the lining mucosa and tongue. Increasing in abundance from the early tumor stage to the late stage, in TT and sp. in TS were positively correlated with OSCC development, suggesting that bacteria were selected by different microenvironments. The correlation between 11 microbial species and 17 pathway abundances was revealed, indicating the potential function of low-abundance bacteria. Overall, our analysis revealed that multiple oral bacterial taxa are associated with a subsequent risk of OSCC and may be used as biomarkers for risk prediction and intervention in oral cancers.
PubMed: 34712209
DOI: 10.3389/fmicb.2021.719601 -
Anales Del Sistema Sanitario de Navarra Dec 2017Rothia mucilaginosa (R. mucilaginosa), formerly named Stomatococcus mucilaginosus, is a facultatively anaerobic, encapsulated gram-positive coccus, which forms part of...
Rothia mucilaginosa (R. mucilaginosa), formerly named Stomatococcus mucilaginosus, is a facultatively anaerobic, encapsulated gram-positive coccus, which forms part of the normal oropharyngeal and is rarely considered to be a pathogen in immunocompetent patients, although it can produce, on rare occasions, serious infections like bacteremia, endocarditis and respiratory infections; such as pneumonia, pleural empyema or superinfection of bronchiectasis. We present the case of a 74-year-old male diagnosed with right basal pneumonia of torpid evolution with a poor initial response to different antibiotics, with clinical and radiological worsening and the appearance of bilateral bronchopneumonia with pseudonodular images. R. mucilaginosa in pure culture was isolated in three sputum cultures and in bronchial suction. The patient was finally treated with Linezolid with a good clinical response and normalisation of the thorax radiography, confirming the disappearance of R. mucilaginosa in subsequent sputum cultures. As there are few documented cases of pneumonia due to R. mucilaginosa, we believe that presenting this case will be of interest.
Topics: Aged; Bronchopneumonia; Gram-Positive Bacterial Infections; Humans; Male; Micrococcaceae
PubMed: 29149111
DOI: 10.23938/ASSN.0090