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BMC Biology Dec 2023Berberine (BBR) is a commonly used anti-intestinal inflammation drug, and its anti-cancer activity has been found recently. BBR can intervene and control malignant...
BACKGROUND
Berberine (BBR) is a commonly used anti-intestinal inflammation drug, and its anti-cancer activity has been found recently. BBR can intervene and control malignant colorectal cancer (CRC) through intestinal microbes, but the direct molecular target and related mechanism are unclear. This study aimed to identify the target of BBR and dissect related mechanisms against the occurrence and development of CRC from the perspective of intestinal microorganisms.
RESULTS
Here, we found that BBR inhibits the growth of several CRC-driving bacteria, especially Peptostreptococcus anaerobius. By using a biotin-conjugated BBR derivative, we identified the protein FtfL (formate tetrahydrofolate ligase), a key enzyme in C1 metabolism, is the molecular target of BBR in P. anaerobius. BBR exhibits strong binding affinity and potent inhibition on FtfL. Based on this, we determined the crystal structure of PaFtfL (P. anaerobius FtfL)-BBR complex and found that BBR can not only interfere with the conformational flexibility of PaFtfL tetramer by wedging the tetramer interface but also compete with its substrate ATP for binding within the active center. In addition, the enzymatic activities of FtfL homologous proteins in human tumor cells can also be inhibited by BBR.
CONCLUSIONS
In summary, our study has identified FtfL as a direct target of BBR and uncovered molecular mechanisms involved in the anti-CRC of BBR. BBR interferes with intestinal pathogenic bacteria by targeting FtfLs, suggesting a new means for controlling the occurrence and development of CRC.
Topics: Humans; Berberine; Neoplasms; Intestines; Bacteria
PubMed: 38049785
DOI: 10.1186/s12915-023-01778-w -
American Journal of Translational... 2024The prevalence of allergic rhinitis (common allergies) has increased in the last fifty years, from less than one percent to more than twenty-six percent of the...
The prevalence of allergic rhinitis (common allergies) has increased in the last fifty years, from less than one percent to more than twenty-six percent of the population. Today, more than one hundred million people in the US suffer seasonal or yearlong allergies. The hygiene hypothesis was proposed 30 years ago as a potential explanation for this phenomenon, and we built on it with the specific oral hygiene hypothesis. Our longitudinal pilot study suggested that oral probiotic deficiency is the cause of allergic rhinitis. This clinical trial served to verify our theory and evaluate the effectiveness of AllerPops for allergy relief. We carried out a phase II, randomized, double-blind, controlled, single-center 21-day study to investigate the efficacy of AllerPops to reduce nasal symptoms in 72 adult volunteers with seasonal/year-long nasal allergies and its impact on oral microbiome using amplicon sequencing of 16S ribosome RNA genes. The volunteers were randomly separated into two equally sized groups: a control group and an investigational group. Both groups were given at least three doses of AllerPops, taken every other day, and asked to answer questions about observed allergy symptoms. Volunteers in the investigational group cleaned their mouths before taking a dose and slowly dissolve the lozenge, while those in the control did not. Through this trial, we show that AllerPops prebiotic supplements are effective in providing sustained allergy relief (P = 0.002) and can modulate oral beneficial bacteria that produce short-chain fatty acids (SCFA), such as Fusobacteria, Butyrivibrio, and Peptostreptococcus. The clinical improvements correlated with changes in the relative abundance of probiotics significantly: Fusobacteria (R = 0.32, P = 0.009), Butyrivibrio (R = 0.25, P = 0.044), and Peptostreptococcus (R = 0.34, P = 0.005). These results point to the root cause of allergic rhinitis: the lack of oral probiotics that produce SCFA to pacify the immune systems. Future study of AllerPops' theory will help society redefine the best oral hygiene practice to protect oral probiotics so that we may prevent allergic and autoimmune diseases and dental/gum infections. The trial was retrospectively registered at clinicaltrials.com, with registration number NCT05956691, on 21/07/2023.
PubMed: 38322553
DOI: 10.62347/JWOU4205 -
Journal of Advanced Veterinary and... Dec 2023This research aims to investigate the microbial diversity of Budu prepared from fresh and frozen fish from the Pariaman and Pasaman districts in West Sumatra Province,...
OBJECTIVE
This research aims to investigate the microbial diversity of Budu prepared from fresh and frozen fish from the Pariaman and Pasaman districts in West Sumatra Province, Indonesia, as well as provide basic information about Budu quality.
MATERIALS AND METHODS
To obtain the bacterial microbial composition, deoxyribonucleic acid extraction was carried out using amplicon-sequencing of the gene in the V3-V4 region from two types of Budu and carried out in duplicate.
RESULTS
Budu prepared with fresh (Pariaman) or frozen (Pasaman) fish was dominated by Firmicutes (78.455%-92.37%) and Proteobacteria (6.477%-7.23%) phyla. The total microbial species in Budu from Pariaman were higher (227 species) than in Pasaman (153 species). The bacterial species found are (1.878%-2.21%), (0.597%-0.70%), (0.00%-0.002%), (0.073%-0.09%), (0.00%-0.01%), (0.00%-0.001%), and (0.00%-0.003%). and are found in both Budu. and are found in Budu Pariaman. and were found in Budu Pasaman.
CONCLUSION
Metagenomic analysis of Budu from different fish, Pariaman (fresh fish) and Pasaman (frozen fish) showed that the biodiversity of bacteria was barely different. Both Budu found lactic acid bacteria from the family, genus and pathogenic bacteria, such as and . The discovery of various species of pathogenic bacteria indicates that development is still needed in the Budu production process to improve Budu quality.
PubMed: 38370893
DOI: 10.5455/javar.2023.j736 -
Acta Bio-medica : Atenei Parmensis Aug 2023Corynebacterium or diphtheroid's are gram-positive aerobic, pleomorphic skin and mucosal membrane components that are not pathogenic in nature. Peptostreptococcus...
Corynebacterium or diphtheroid's are gram-positive aerobic, pleomorphic skin and mucosal membrane components that are not pathogenic in nature. Peptostreptococcus indolicus belongs to the Peptostreptococcus genus and is a Gram-Positive Anaerobic Cocci (GPAC). Less than one percent of endocarditis is caused by gram-positive anaerobic bacteria. We report the first case of Peptoniphilus indolicus and Corynebacterium endocarditis in a patient with native valves and a pacemaker. In time, diagnosis of a Peptoniphilus indolicus infection can lead to early management of the infection and a decreased incidence of serious complications such as embolization or abscess formation. The combination of aggressive antibiotic administration and surgical intervention can significantly decrease morbidity and mortality. This case report will highlight the importance of Peptoniphilus infective endocarditis, ultimately leading to better diagnostic strategies and management.
Topics: Humans; Endocarditis; Endocarditis, Bacterial; Corynebacterium; Embolization, Therapeutic
PubMed: 37606054
DOI: 10.23750/abm.v94iS1.14614 -
Journal of Pharmacy & Bioallied Sciences Apr 2024Herbal extracts have evoked interest owing to the small number of terpenoids and phenolic compounds, which impart antimicrobial, antioxidant, and anti-inflammatory...
Herbal extracts have evoked interest owing to the small number of terpenoids and phenolic compounds, which impart antimicrobial, antioxidant, and anti-inflammatory properties. The minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and minimum fungicidal concentration (MFC) of four herbal extracts (lemon grass oil, basil oil, peppermint oil, and Obicure tea extract) against endodontic pathogens along with the MIC: MBC/MFC ratio were evaluated. The antimicrobial activity by detecting the MIC of three essential oils and tea extract was evaluated against eight common endodontic pathogens by the broth dilution method, while MBC was detected by subculturing onto blood agar from the first -three to five tubes from the MIC dilution tubes (showing no turbidity), which were plated on blood agar. All herbal extracts proved to be effective antimicrobials against tested endodontic pathogens. Basil oil had a bacteriostatic effect on all the organisms ( < 0.05). Mint oil showed bacteriostatic activity on and ( > 0.05). Tea extract had a bacteriostatic effect ( > 0.05) against all tested microbes except Actinomyces, Lactobacilli, , and . Lemon grass oil had a bactericidal effect against all the organisms and a bacteriostatic effect against ( > 0.05). It can be concluded that basil oil showed a strong bactericidal effect on the test organisms. The MIC for the organisms ranged from 0.2 to 50 μg/ml.
PubMed: 38882894
DOI: 10.4103/jpbs.jpbs_735_23 -
Molecular Oncology May 2024The incidence of colorectal cancer (CRC) has increased worldwide, and early diagnosis is crucial to reduce mortality rates. Therefore, new noninvasive biomarkers for CRC...
The incidence of colorectal cancer (CRC) has increased worldwide, and early diagnosis is crucial to reduce mortality rates. Therefore, new noninvasive biomarkers for CRC are required. Recent studies have revealed an imbalance in the oral and gut microbiomes of patients with CRC, as well as impaired gut vascular barrier function. In the present study, the microbiomes of saliva, crevicular fluid, feces, and non-neoplastic and tumor intestinal tissue samples of 93 CRC patients and 30 healthy individuals without digestive disorders (non-CRC) were analyzed by 16S rRNA metabarcoding procedures. The data revealed that Parvimonas, Fusobacterium, and Bacteroides fragilis were significantly over-represented in stool samples of CRC patients, whereas Faecalibacterium and Blautia were significantly over-abundant in the non-CRC group. Moreover, the tumor samples were enriched in well-known periodontal anaerobes, including Fusobacterium, Parvimonas, Peptostreptococcus, Porphyromonas, and Prevotella. Co-occurrence patterns of these oral microorganisms were observed in the subgingival pocket and in the tumor tissues of CRC patients, where they also correlated with other gut microbes, such as Hungatella. This study provides new evidence that oral pathobionts, normally located in subgingival pockets, can migrate to the colon and probably aggregate with aerobic bacteria, forming synergistic consortia. Furthermore, we suggest that the group composed of Fusobacterium, Parvimonas, Bacteroides, and Faecalibacterium could be used to design an excellent noninvasive fecal test for the early diagnosis of CRC. The combination of these four genera would significantly improve the reliability of a discriminatory test with respect to others that use a single species as a unique CRC biomarker.
Topics: Humans; Colorectal Neoplasms; Fusobacterium; Male; Female; Bacteroides; Middle Aged; Feces; Biomarkers, Tumor; Faecalibacterium; Aged; RNA, Ribosomal, 16S; Gastrointestinal Microbiome; Saliva; Adult
PubMed: 38366793
DOI: 10.1002/1878-0261.13604 -
Microorganisms Feb 2024Calf intestines are colonized by rich and complex microbial communities, playing a crucial role in animal physiology, metabolism, nutrition, and immune function. In this...
Differential Microbial Composition and Interkingdom Interactions in the Intestinal Microbiota of Holstein and German Simmental × Holstein Cross F1 Calves: A Comprehensive Analysis of Bacterial and Fungal Diversity.
Calf intestines are colonized by rich and complex microbial communities, playing a crucial role in animal physiology, metabolism, nutrition, and immune function. In this study, we provide insight into the composition of fecal microbial bacteria and fungi, respectively, as well as the cross-kingdom interactions. We investigated the intestinal microbiota of different breeds of calves by characterizing the bacterial and fungal communities in the rectal feces of Holstein calves and German Simmental × Holstein cross F1 generation (GXH) using 16S rRNA and ITS amplicon sequencing techniques. PICRUSt2 (version 2.2.0) were used to determine microbial diversity and function and explore the reasons why Holstein calves are more susceptible to diarrhea. The results revealed no significant difference in the diversity of fecal microbiota among the groups ( > 0.05). We identified and as the dominant bacterial phyla in the fecal bacterial communities of the two breeds of calves. and play important roles in the fungal community but differ in relative abundance. was the dominant genus at the group level for calf fecal microbiota in both breeds. The relative abundance of , -, , and was higher in Holstein calves, and the relative abundance of , , , and was lower than GXH group. and were the dominating genera of fecal fungi in both groups of calves. LEfSe analysis revealed 33 different bacteria and 23 different fungi between the two groups, with more differential strains found in GXH. In addition, the feces fungi-bacteria interkingdom interactions varied among breeds. Thus, the composition and structure of bacterial and fungal communities in calf feces varied by breed, indicating a potential association between breed and microbial communities. We also found differences in the network between bacterial-fungal kingdoms. We explain the reasons for Holstein calves being more prone to diarrhea. This indicated that breed makes differences in calf diarrhea rates by influencing gut microbial composition and interactions.
PubMed: 38543537
DOI: 10.3390/microorganisms12030486 -
BioRxiv : the Preprint Server For... Jan 2024The human gut microbiome is a complex ecosystem with profound implications for health and disease. This recognition has led to a surge in multi-omic microbiome studies,...
The human gut microbiome is a complex ecosystem with profound implications for health and disease. This recognition has led to a surge in multi-omic microbiome studies, employing various molecular assays to elucidate the microbiome's role in diseases across multiple functional layers. However, despite the clear value of these multi-omic datasets, rigorous integrative analysis of such data poses significant challenges, hindering a comprehensive understanding of microbiome-disease interactions. Perhaps most notably, multiple approaches, including univariate and multivariate analyses, as well as machine learning, have been applied to such data to identify disease-associated markers, namely, specific features (e.g., species, pathways, metabolites) that are significantly altered in disease state. These methods, however, often yield extensive lists of features associated with the disease without effectively capturing the multi-layered structure of multi-omic data or offering clear, interpretable hypotheses about underlying microbiome-disease mechanisms. Here, we address this challenge by introducing an intermediate integration-based method for analyzing multi-omic microbiome data. MintTea combines a canonical correlation analysis (CCA) extension, consensus analysis, and an evaluation protocol to robustly identify disease-associated multi-omic modules. Each such module consists of a set of features from the various omics that both shift in concord, and collectively associate with the disease. Applying MintTea to diverse case-control cohorts with multi-omic data, we show that this framework is able to capture modules with high predictive power for disease, significant cross-omic correlations, and alignment with known microbiome-disease associations. For example, analyzing samples from a metabolic syndrome (MS) study, we found a MS-associated module comprising of a highly correlated cluster of serum glutamate- and TCA cycle-related metabolites, as well as bacterial species previously implicated in insulin resistance. In another cohort, we identified a module associated with late-stage colorectal cancer, featuring and species and several fecal amino acids, in agreement with these species' reported role in the metabolism of these amino acids and their coordinated increase in abundance during disease development. Finally, comparing modules identified in different datasets, we detected multiple significant overlaps, suggesting common interactions between microbiome features. Combined, this work serves as a proof of concept for the potential benefits of advanced integration methods in generating integrated multi-omic hypotheses underlying microbiome-disease interactions and a promising avenue for researchers seeking systems-level insights into coherent mechanisms governing microbiome-related diseases.
PubMed: 37461534
DOI: 10.1101/2023.07.03.547607 -
DEN Open Apr 2024Although prednisolone treatment is effective in Cronkhite-Canada syndrome (CCS), its mechanisms of action are poorly understood. We performed analyses of cytokine...
Although prednisolone treatment is effective in Cronkhite-Canada syndrome (CCS), its mechanisms of action are poorly understood. We performed analyses of cytokine expression and fecal microbiota in a patient with the concurrent occurrence of CCS and rectal cancer, in whom regression of polyposis was achieved by prednisolone. Regression of CCS polyps was accompanied by downregulation of proinflammatory cytokine expression and alterations in microbiota composition; a decrease in and with the promotion of inflammation. We could not completely exclude the possibility that alterations in fecal microbiota composition might be influenced by the presence of advanced cancer. However, this case suggests that the administration of PSL might lead to the regression of CCS polyps through alterations in gut microbiota composition and suppression of proinflammatory cytokine responses.
PubMed: 37168272
DOI: 10.1002/deo2.222 -
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