BACKGROUND: Colorectal carcinogenesis and progression are related to the gut microbiota and the tumor immune microenvironment. Our previous clinical trial demonstrated that berberine (BBR) hydrochloride might reduce the recurrence and canceration of colorectal adenoma (CRA). The present study aimed to further explore the mechanism of BBR in preventing colorectal cancer (CRC). METHODS: We performed metagenomics sequencing on fecal specimens obtained from the BBR intervention trial, and the differential bacteria before and after medication were validated using quantitative polymerase chain reaction. We further performed ApcMin/+ animal intervention tests, RNA sequencing, flow cytometry, immunohistochemistry, and enzyme-linked immunosorbent assays. RESULTS: The abundance of fecal Veillonella parvula ( V . parvula ) decreased significantly after BBR administration ( P = 0.0016) and increased through the development from CRA to CRC. Patients with CRC with a higher V. parvula abundance had worse tumor staging and a higher lymph node metastasis rate. The intestinal immune pathway of Immunoglobulin A production was activated, and the expression of TNFSF13B (Tumor necrosis factor superfamily 13b, encoding B lymphocyte stimulator [BLyS]), the representative gene of this pathway, and the genes encoding its receptors (interleukin-10 and transforming growth factor beta) were significantly upregulated. Animal experiments revealed that V. parvula promoted colorectal carcinogenesis and increased BLyS levels, while BBR reversed this effect. CONCLUSION: BBR might inhibit V. parvula and further weaken the immunomodulatory effect of B cells induced by V. parvula , thereby blocking the development of colorectal tumors. TRIAL REGISTRAION ClinicalTrials.gov, No. NCT02226185.
Animals ; Humans ; Berberine/therapeutic use* ; Carcinogenesis ; Veillonella ; Colorectal Neoplasms/genetics* ; Tumor Microenvironment

PURPOSE: Different characteristics of airway microbiome in asthmatics may lead to differential immune responses, which in turn cause eosinophilic or neutrophilic airway inflammation. However, the relationships among these factors have yet to be fully elucidated.METHODS: Microbes in induced sputum samples were subjected to sequence analysis of 16S rRNA. Airway inflammatory phenotypes were defined as neutrophils (>60%) and eosinophils (>3%), and inflammation endotypes were defined by levels of T helper (Th) 1 (interferon-γ), Th2 (interleukin [IL]-5 and IL-13), Th-17 (IL-17), and innate Th2 (IL-25, IL-33, and thymic stromal lymphopoietin) cytokines, inflammasomes (IL-1β), epithelial activation markers (granulocyte-macrophage colony-stimulating factor and IL-8), and Inflammation (IL-6 and tumor necrosis factor-α) cytokines in sputum supernatants was assessed by enzyme-linked immunosorbent assay.RESULTS: The numbers of operational taxonomic units were significantly higher in the mixed (n = 21) and neutrophilic (n = 23) inflammation groups than in the paucigranulocytic inflammation group (n = 19; p < 0.05). At the species level, Granulicatella adiacens, Streptococcus parasanguinis, Streptococcus pneumoniae, Veillonella rogosae, Haemophilus parainfluenzae, and Neisseria perflava levels were significantly higher in the eosinophilic inflammation group (n = 20), whereas JYGU_s levels were significantly higher in the neutrophilic inflammation group compared to the other subtypes (P < 0.05). Additionally, IL-5 and IL-13 concentrations were correlated with the percentage of eosinophils (P < 0.05) and IL-13 levels were positively correlated with the read counts of Porphyromonas pasteri and V. rogosae (P < 0.05). IL-1β concentrations were correlated with the percentage of neutrophils (P < 0.05). had a tendency to be positively correlated with the read count of JYGU_s (P = 0.095), and was negatively correlated with that of S. pneumoniae (P < 0.05).CONCLUSIONS: Difference of microbial patterns in airways may induce distinctive endotypes of asthma, which is responsible for the neutrophilic or eosinophilic inflammation in asthma.
Asthma ; Colony-Stimulating Factors ; Cytokines ; Enzyme-Linked Immunosorbent Assay ; Eosinophils ; Haemophilus parainfluenzae ; Inflammasomes ; Inflammation ; Interleukin-13 ; Interleukin-33 ; Interleukin-5 ; Microbiota ; Necrosis ; Neisseria ; Neutrophils ; Phenotype ; Pneumonia ; Porphyromonas ; Sequence Analysis ; Sputum ; Streptococcus ; Streptococcus pneumoniae ; Veillonella

BACKGROUND: Diverse microbiota exist in the lower respiratory tract. Although next generation sequencing (NGS) is the most widely used microbiome analysis technique, it is difficult to implement NGS in clinical microbiology laboratories. Therefore, we evaluated the performance of conventional culture methods together with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in identifying microbiota in bronchoalveolar lavage (BAL) fluid. METHODS: BAL fluid samples (n=27) were obtained from patients undergoing diagnostic bronchoscopy for lung mass evaluation. Bacterial and fungal culture was performed with conventional media used in clinical microbiology laboratories. On an average, 20 isolated colonies were picked from each agar plate and identified by MALDI-TOF MS. Microbiome analysis using 16S rRNA NGS was conducted for comparison. RESULTS: Streptococcus spp. and Neisseria spp. were most frequently cultured from the BAL fluid samples. In two samples, Enterobacteriaceae grew predominantly on MacConkey agar. Actinomyces and Veillonella spp. were commonly identified anaerobes; gut bacteria, such as Lactobacillus, Bifidobacterium, and Clostridium, and fungi were also isolated. NGS revealed more diverse bacterial communities than culture, and Prevotella spp. were mainly identified solely by NGS. Some bacteria, such as Staphylococcus spp., Clostridium spp., and Bifidobacterium spp., were identified solely by culture, indicating that culture may be more sensitive for detecting certain bacteria. CONCLUSIONS: Culture and NGS of BAL fluid samples revealed common bacteria with some different microbial communities. Despite some limitations, culture combined with MALDI-TOF MS might play a complementary role in microbiome analysis using 16S rRNA NGS.
Actinomyces ; Agar ; Bacteria ; Bifidobacterium ; Bronchoalveolar Lavage Fluid* ; Bronchoalveolar Lavage* ; Bronchoscopy ; Clostridium ; Enterobacteriaceae ; Fungi ; Humans ; Lactobacillus ; Lung ; Mass Spectrometry ; Microbiota ; Neisseria ; Prevotella ; Respiratory System ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Staphylococcus ; Streptococcus ; Veillonella

For many years, developmental and physiological differences have been known to exist between anatomic segments of the colorectum. Because of different outcomes, prognoses, and clinical responses to chemotherapy, the distinction between right colon cancer (RCC) and left colon cancer (LCC) has gained attention. Furthermore, variations in the molecular features and gut microbiota between right and LCCs have recently been a hot research topic. CpG island methylator phenotype-high, microsatellite instability-high colorectal cancers are more likely to occur on the right side whereas tumors with chromosomal instability have been detected in approximately 75% of LCC patients and 30% of RCC patients. The mutation rates of oncogenes and tumor suppressor genes also differ between RCC and LCC patients. Biofilm is more abundant in RCC patients than LLC patients, as are Prevotella, Selenomonas, and Peptostreptococcus. Conversely, Fusobacterium, Escherichia/Shigella, and Leptotrichia are more abundant in LCC patients compared to RCC patients. Distinctive characteristics are apparent in terms of molecular features and gut microbiota between right and LCC. However, how or to what extent these differences influence diverging oncologic outcomes remains unclear. Further clinical and translational studies are needed to elucidate the causative relationship between primary tumor location and prognosis.
Biofilms ; Chromosomal Instability ; Colon* ; Colonic Neoplasms* ; Colorectal Neoplasms ; CpG Islands ; Drug Therapy ; Fusobacterium ; Gastrointestinal Microbiome* ; Genes, Tumor Suppressor ; Humans ; Leptotrichia ; Microsatellite Repeats ; Mutation Rate ; Oncogenes ; Peptostreptococcus ; Prevotella ; Prognosis ; Selenomonas ; Treatment Outcome

Recurrent aphthous stomatitis (RAS) is a common oral mucosal disorder for which no curative treatment is available. We previously reported that decreased Streptococcus salivarius and increased Acinetobacter johnsonii on the oral mucosa are associated with RAS risk. The purpose of this study was to identify antibiotics that selectively inhibit A. johnsonii but minimally inhibit oral mucosal commensals. S. salivarius KCTC 5512, S. salivarius KCTC 3960, A. johnsonii KCTC 12405, Rothia mucilaginosa KCTC 19862, and Veillonella dispar KCOM 1864 were subjected to antibiotic susceptibility test using amoxicillin, cefotaxime, gentamicin, clindamycin, and metronidazole in liquid culture. The minimal inhibitory concentration (MIC) was defined as the concentration that inhibits 90% of growth. Only gentamicin presented a higher MIC for A. johnsonii than MICs for S. salivarius and several oral mucosal commensals. Interestingly, the growth of S. salivarius increased 10~200% in the presence of sub-MIC concentrations of gentamicin, which was independent of development of resistance to gentamicin. In conclusion, gentamicin may be useful to restore RAS-associated imbalance in oral microbiota by selectively inhibiting the growth of A. johnsonii but enhancing the growth of S. salivarius.
Acinetobacter ; Amoxicillin ; Anti-Bacterial Agents* ; Cefotaxime ; Clindamycin ; Gentamicins ; Mass Screening* ; Metronidazole ; Microbiota ; Mouth Mucosa ; Stomatitis, Aphthous* ; Streptococcus ; Veillonella

Recent evidence has indicated that bacteria-derived extracellular vesicles (EVs) are important for host–microbe communication. The aims of the present study were to evaluate whether bacteria-derived EVs are excreted via the urinary tract and to compare the composition of bacteria-derived EVs in the urine of pregnant and non-pregnant women. Seventy-three non-pregnant and seventy-four pregnant women were enrolled from Dankook University and Ewha Womans University hospitals. DNA was extracted from urine EVs after EV isolation using the differential centrifugation method. 16S ribosomal RNA (16S rRNA) gene sequencing was performed using high-throughput 454 pyrosequencing after amplification of the V1–V3 region of the 16S rDNA. The composition of 13 taxa differed significantly between the pregnant and non-pregnant women. At the genus level, Bacillus spp. EVs were more significantly enriched in the urine of the pregnant women than in that of the non-pregnant women (45.61% vs 0.12%, respectively). However, Pseudomonas spp. EVs were more dominant in non-pregnant women than in pregnant women (13.2% vs 4.09%, respectively). Regarding the compositional difference between pregnant women with normal and preterm delivery, EVs derived from Ureaplasma spp. and the family Veillonellaceae (including Megasphaera spp.) were more abundant in the urine of preterm-delivered women than in that of women with normal deliveries. Taken together, these data showed that Bacillus spp. EVs predominate in the urine of pregnant women, whereas Pseudomonas spp. EVs predominate in the urine of non-pregnant women; this suggests that Bacillus spp. EVs might have an important role in the maintenance of pregnancy.
Bacillus ; Centrifugation ; DNA ; DNA, Ribosomal ; Extracellular Vesicles* ; Female ; Hospitals, University ; Humans ; Megasphaera ; Metagenomics* ; Methods ; Pregnancy ; Pregnant Women ; Pseudomonas ; RNA, Ribosomal, 16S ; Ureaplasma ; Urinary Tract ; Veillonellaceae

The aim of this study was to identify the non-Aggregatibacter actinomycetemcomitans bacteria grown on the tryptic soy-serum-bacitracin-vancomycin (TSBV) medium, an A. actinomycetemcomitans selective medium. A total of 82 unidentified bacterial isolates from the oral cavities of a Korean population were kindly provide by the Korean Collection for Oral Microbiology. All the clinical isolates were grown on TSBV medium and bacterial DNA purified from each isolate was subjected to PCR with universal primers specific for bacterial 16S rRNA genes (16S rDNAs) sequence. The each bacterial 16S rDNA was amplified by PCR and the nucleotide sequences of it was determined by the dideoxynucleotide chain termination method. They were identified by 16S rDNA sequence comparison method at the specie-level. The data showed that Neisseria spp. (42 strains), Fusobacterium spp. (10 strains), Capnocytophaga spp. (8 strains), Propionibacterium acnes (5 strains), Aggregatibacter aprophilus (4 strains), Campylobacter spp. (5 strains), Veillonella dispar (3 strains), Streptococcus sp. (1 strain), Haemophilus parainfluenzae (1 strain), Leptotrichia wadei (1 strain), Morococcus sp./Neisseria sp. (1 strain), and Staphylococcus sp. (1 strain) were identified. These results could be used to develop a new A. actinomycetemcomitans-selective medium which is more effective than the TSBV medium in future studies.
Aggregatibacter ; Bacteria* ; Base Sequence ; Campylobacter ; Capnocytophaga ; DNA, Bacterial ; DNA, Ribosomal ; Fusobacterium ; Genes, rRNA ; Haemophilus parainfluenzae ; Leptotrichia ; Methods ; Neisseria ; Polymerase Chain Reaction ; Propionibacterium acnes ; Staphylococcus ; Streptococcus ; Veillonella

The purpose of this study was to isolate and identify bacteria from the 4 patients with non-odontogenic infectious lesions (mucormycosis, chronic inflammation from wound infection, and two actinomycosis) and determine their antimicrobial susceptibility against eight antibiotics. Bacterial culture was performed under three culture conditions (anaerobic, CO2, and aerobic incubator). The bacterial strains were identified by 16S rRNA gene (16S rDNA) sequence comparison analysis method. For investigating the antimicrobial susceptibility of the bacteria against eight antibiotics, penicillin G, amoxicillin, tetracycline, cefuroxime, erythromycin, clindamycin, vancomycin, and Augmentin(R) (amoxicillin + clavulanic acid), minimum inhibitory concentration (MIC) measurement was performed using broth microdilution assay. Nosocomial pathogens such as Enterococcus faecalis, Klebsiella pneumoniae, Bacillus subtilis, and Neisseria flavescens were isolated from mucormycosis. Veillonella parvula, Enterobacter hormaechei, and Acinetobacter calcoaceticus were isolated from chronic inflammatory lesion. Actinomyces massiliensis was isolated from actinomycosis in parotid gland. Capnocytophaga ochracea was isolated from actinomycosis in buccal region in anaerobic condition. There was no susceptible antibiotic to all bacteria in mucormycosis. Tetracycline was susceptible to all bacteria in chronic inflammation. C. ochracea was resistant to vancomycin and penicillin G; and other antibiotics showed susceptibility to all bacteria in actinomycosis. The results indicated that the combined treatment of two or more antibiotics is better than single antibiotic treatment in mucormycosis, and penicillin is the first recommended antibiotic to treat actinomycosis.
Acinetobacter calcoaceticus ; Actinomyces ; Actinomycosis ; Amoxicillin ; Anti-Bacterial Agents ; Bacillus subtilis ; Bacteria* ; Capnocytophaga ; Cefuroxime ; Clindamycin ; Enterobacter ; Enterococcus faecalis ; Erythromycin ; Genes, rRNA ; Humans ; Inflammation ; Klebsiella pneumoniae ; Microbial Sensitivity Tests ; Mucormycosis ; Neisseria ; Parotid Gland ; Penicillin G ; Penicillins ; Tetracycline ; Vancomycin ; Veillonella ; Wound Infection

The objective of this study was to investigate the compositional profiles and microbial shifts of oral microbiota during head-and-neck radiotherapy. Bioinformatic analysis based on 16S rRNA gene pyrosequencing was performed to assess the diversity and variation of oral microbiota of irradiated patients. Eight patients with head and neck cancers were involved in this study. For each patient, supragingival plaque samples were collected at seven time points before and during radiotherapy. A total of 147,232 qualified sequences were obtained through pyrosequencing and bioinformatic analysis, representing 3,460 species level operational taxonomic units (OTUs) and 140 genus level taxa. Temporal variations were observed across different time points and supported by cluster analysis based on weighted UniFrac metrics. Moreover, the low evenness of oral microbial communities in relative abundance was revealed by Lorenz curves. This study contributed to a better understanding of the detailed characterization of oral bacterial diversity of irradiated patients.
Actinomyces ; classification ; radiation effects ; Actinomycetaceae ; classification ; radiation effects ; Alcaligenaceae ; classification ; radiation effects ; Bacteria ; classification ; radiation effects ; Capnocytophaga ; classification ; radiation effects ; Carnobacteriaceae ; classification ; radiation effects ; Computational Biology ; Dental Plaque ; microbiology ; Follow-Up Studies ; Gemella ; classification ; radiation effects ; Head and Neck Neoplasms ; radiotherapy ; High-Throughput Nucleotide Sequencing ; Humans ; Middle Aged ; Neisseria ; classification ; radiation effects ; Prevotella ; classification ; radiation effects ; Propionibacteriaceae ; classification ; radiation effects ; RNA, Bacterial ; analysis ; RNA, Ribosomal, 16S ; analysis ; Streptococcus ; classification ; radiation effects ; Veillonella ; classification ; radiation effects

Xylitol is a five-carbon sugar alcohol that reduces the incidence of caries by inhibiting the growth of oral streptococci, including Streptococcus mutans. Since xylitol is transported via the fructose phosphotransferase system, we hypothesized that it could also affect the growth of other oral bacteria strains. We tested the effects of xylitol against non-periodontopathogenic oral bacteria frequently found in healthy subjects as well as periodontopathogens including Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia. With 5% xylitol, Streptococcus vestibularis and Gemella morbillorum showed marked growth inhibition. With 10% xylitol, all of the tested periodontopathogens and Actinomyces naeslundii showed marked growth inhibition, whereas the growth inhibition of Neisseria mucosa, Neisseria sicca and Veillonella parvula was mild only. Xylitol is a widely used sweetener and the concentration used in our experiment is easily achieved in the oral cavity. If xylitol reduces the growth of periodontopathogens more preferentially, it could also reduce the prevalence of these pathogens and have clinical utility in the prevention or treatment of periodontal disease.
Actinomyces ; Bacteria* ; Forsythia ; Fructose ; Gemella ; Incidence ; Mouth ; Neisseria mucosa ; Neisseria sicca ; Periodontal Diseases ; Porphyromonas gingivalis ; Prevalence ; Streptococcus ; Streptococcus mutans ; Sweetening Agents ; Treponema denticola ; Veillonella ; Xylitol*