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International Journal of Systematic and... Mar 2024A Gram-stain-positive, non-spore-forming, and obligate anaerobic bacteria designated strain CBA3647 was isolated from a horse faecal sample in Jeju, Republic of Korea....
A Gram-stain-positive, non-spore-forming, and obligate anaerobic bacteria designated strain CBA3647 was isolated from a horse faecal sample in Jeju, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBA3647 formed a distinct phyletic lineage from closely related species within the genus . Based on comparative analysis of 16S rRNA gene sequences, ATCC 27337 is most closely related to strain CBA3647 with a 16S rRNA gene similarity of 98.31 %, while similarity to other type strains is below 98.0 %. The genomic DNA G+C content of strain CBA3647 was 30.0 mol%. The digital DNA-DNA hybridization values between strain CBA3647 and the six species were equal to or less than 24 %. Cells were non-motile and oval-shaped cocci with catalase-positive and oxidase-negative activities. Growth occurred at 20-40 °C (optimum, 35 °C), pH 6-8 (optimum, pH 7), and in the presence of 0-2 % (w/v) NaCl (optimum, 1 %). Strain CBA3647 contained C iso and C as major fatty acids. Phenotypic, chemotaxonomic, and molecular properties of strain CBA3647 suggest that it represents a novel species in the genus , which has been named sp. nov. The type strain is CBA3647 (=KACC 22891= JCM 35846).
Topics: Animals; Horses; Base Composition; Fatty Acids; Peptostreptococcus; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; Feces
PubMed: 38536087
DOI: 10.1099/ijsem.0.006295 -
Nature Communications Mar 2024Multi-omic studies of the human gut microbiome are crucial for understanding its role in disease across multiple functional layers. Nevertheless, integrating and...
Multi-omic studies of the human gut microbiome are crucial for understanding its role in disease across multiple functional layers. Nevertheless, integrating and analyzing such complex datasets poses significant challenges. Most notably, current analysis methods often yield extensive lists of disease-associated features (e.g., species, pathways, or metabolites), without capturing the multi-layered structure of the data. Here, we address this challenge by introducing "MintTea", an intermediate integration-based approach combining canonical correlation analysis extensions, consensus analysis, and an evaluation protocol. MintTea identifies "disease-associated multi-omic modules", comprising features from multiple omics that shift in concord and that collectively associate with the disease. Applied to diverse cohorts, MintTea captures modules with high predictive power, significant cross-omic correlations, and alignment with known microbiome-disease associations. For example, analyzing samples from a metabolic syndrome study, MintTea identifies a module with serum glutamate- and TCA cycle-related metabolites, along with bacterial species linked to insulin resistance. In another dataset, MintTea identifies a module associated with late-stage colorectal cancer, including Peptostreptococcus and Gemella species and fecal amino acids, in line with these species' metabolic activity and their coordinated gradual increase with cancer development. This work demonstrates the potential of advanced integration methods in generating systems-level, multifaceted hypotheses underlying microbiome-disease interactions.
Topics: Humans; Multiomics; Microbiota; Bacteria; Gastrointestinal Microbiome
PubMed: 38521774
DOI: 10.1038/s41467-024-46888-3 -
Gut Pathogens Mar 2024The gut microbiota is associated with risk for colorectal cancer (CRC), a chronic disease for which racial disparities persist with Black Americans having a higher risk...
BACKGROUND
The gut microbiota is associated with risk for colorectal cancer (CRC), a chronic disease for which racial disparities persist with Black Americans having a higher risk of CRC incidence and mortality compared to other groups. Given documented racial differences, the gut microbiota may offer some insight into previously unexplained racial disparities in CRC incidence and mortality. A case-control analysis comparing 11 women newly diagnosed with CRC with 22 cancer-free women matched on age, BMI, and race in a 1:2 ratio was conducted. Information about participants' diet and perceived stress levels were obtained via 24-h Dietary Recall and Perceived Stress Scale-10 survey, respectively. Participants provided stool samples from which microbial genomic DNA was extracted to reveal the abundance of 26 genera chosen a priori based on their previously observed relevance to CRC, anxiety symptoms, and diet.
RESULTS
Significantly lower alpha diversity was observed among cancer-free Black women compared to all other race-cancer status combinations. No group differences were observed when comparing beta diversity. Non-Hispanic White CRC cases tended to have higher relative abundance of Fusobacteria, Gemellaceae, and Peptostreptococcus compared to all other race-cancer combination groups. Perceived stress was inversely associated with alpha diversity and was associated with additional genera.
CONCLUSIONS
Our findings suggest that microbiome-CRC associations may differ by racial group. Additional large, racially diverse population-based studies are needed to determine if previously identified associations between characteristics of the gut microbiome and CRC are generalizable to Black women and other racial, ethnic, and gender groups.
PubMed: 38468325
DOI: 10.1186/s13099-024-00608-w -
The Laryngoscope Mar 2024This study aimed to elucidate the bacterial profile of chronic rhinosinusitis (CRS) in patients with end-stage renal disease (ESRD) and chronic kidney disease (CKD)...
INTRODUCTION
This study aimed to elucidate the bacterial profile of chronic rhinosinusitis (CRS) in patients with end-stage renal disease (ESRD) and chronic kidney disease (CKD) compared with nonrenal patients, guiding antibiotic selection for clinicians.
METHODS
We retrospectively analyzed 13,906 inpatients from the Chang Gung Research Database who underwent sinus surgery (2004-2018). Patients were categorized into ESRD-CRS, CKD-CRS, and non-CKD-CRS based on the estimated glomerular filtration rate. Bacterial cultures from surgical samples were classified as facultative anaerobes or aerobes (e.g., Klebsiella pneumoniae [KP], Pseudomonas aeruginosa [Ps.a]), anaerobes, and fungi and ranked by prevalence.
RESULTS
Data from 47 ESRD-CRS, 230 CKD-CRS, and 13,123 non-CKD-CRS patients were analyzed. In ESRD-CRS, the predominant species were KP (31.6%), Ps.a (21.1%), and Coagulase-negative Staphylococcus (CoNS, 15.8%). CKD-CRS showed Staphylococcus epidermidis (27.7%), CoNS (20.5%), and Ps.a (20.5%). Non-CKD-CRS had Staphylococcus epidermidis (29.8%), CoNS (25.0%), and Staphylococcus aureus (15.5%). For anaerobes, ESRD-CRS was dominated by Fusobacterium nucleatum (10.5%) and Peptostreptococcus micros (10.5%), whereas CKD-CRS and non-CKD-CRS showed Propionibacterium acnes as a primary strain (14.5% and 28.7%, respectively).
CONCLUSION
For CRS in ESRD, antibiotics targeting KP and Fusobacterium nucleatum are recommended. In CKD-CRS, a focus on Staphylococcus epidermidis and Propionibacterium acnes is suggested.
LEVEL OF EVIDENCE
4 Laryngoscope, 2024.
PubMed: 38459950
DOI: 10.1002/lary.31389 -
Indian Journal of Otolaryngology and... Feb 2024Brain abscess is a serious clinical condition caused by a localized collection of pus within the brain tissue. This typically occurs as a result of an infection that...
Brain abscess is a serious clinical condition caused by a localized collection of pus within the brain tissue. This typically occurs as a result of an infection that originates from a nearby area, such as an ear, sinus, or dental infection, or an infection in the bloodstream. and species are the most common organisms implicated in brain abscesses. Apart from aerobic growth, cases of mixed infections of both aerobic and anaerobic organisms are also commonly reported in the literature. Herein we report a 23-year-old immunocompetent female with chronic otitis media who presented with cerebellar abscess where the aerobic growth was sterile and anaerobic culture revealed pure growth of dual anaerobes viz… and This case highlights the importance of prompt diagnosis and management of polymicrobial anaerobic infection in cases of brain abscess.
PubMed: 38440584
DOI: 10.1007/s12070-023-04218-x -
Frontiers in Microbiology 2024Colorectal cancer (CRC) is a type of tumor caused by the uncontrolled growth of cells in the mucosa lining the last part of the intestine. Emerging evidence underscores...
BACKGROUND
Colorectal cancer (CRC) is a type of tumor caused by the uncontrolled growth of cells in the mucosa lining the last part of the intestine. Emerging evidence underscores an association between CRC and gut microbiome dysbiosis. The high mortality rate of this cancer has made it necessary to develop new early diagnostic methods. Machine learning (ML) techniques can represent a solution to evaluate the interaction between intestinal microbiota and host physiology. Through explained artificial intelligence (XAI) it is possible to evaluate the individual contributions of microbial taxonomic markers for each subject. Our work also implements the Shapley Method Additive Explanations (SHAP) algorithm to identify for each subject which parameters are important in the context of CRC.
RESULTS
The proposed study aimed to implement an explainable artificial intelligence framework using both gut microbiota data and demographic information from subjects to classify a cohort of control subjects from those with CRC. Our analysis revealed an association between gut microbiota and this disease. We compared three machine learning algorithms, and the Random Forest (RF) algorithm emerged as the best classifier, with a precision of 0.729 ± 0.038 and an area under the Precision-Recall curve of 0.668 ± 0.016. Additionally, SHAP analysis highlighted the most crucial variables in the model's decision-making, facilitating the identification of specific bacteria linked to CRC. Our results confirmed the role of certain bacteria, such as , and , whose abundance appears notably associated with the disease, as well as bacteria whose presence is linked to a non-diseased state.
DISCUSSION
These findings emphasizes the potential of leveraging gut microbiota data within an explainable AI framework for CRC classification. The significant association observed aligns with existing knowledge. The precision exhibited by the RF algorithm reinforces its suitability for such classification tasks. The SHAP analysis not only enhanced interpretability but identified specific bacteria crucial in CRC determination. This approach opens avenues for targeted interventions based on microbial signatures. Further exploration is warranted to deepen our understanding of the intricate interplay between microbiota and health, providing insights for refined diagnostic and therapeutic strategies.
PubMed: 38426064
DOI: 10.3389/fmicb.2024.1348974 -
Current Cancer Drug Targets Feb 2024It is a well-known fact that cancer is considered the second leading cause of mortality across the globe. Although the human oral cavity and intestine are the natural...
It is a well-known fact that cancer is considered the second leading cause of mortality across the globe. Although the human oral cavity and intestine are the natural habitat of thousands of microbes, dysbiosis results in malignancies, such as oral squamous cell carcinoma and colorectal cancer. Amongst the intestinal microbes, H. pylori is a deadly carcinogen. Also, causative pathogens for the development of pancreatic and colorectal cancer are found in the oral cavity, such as Fusobacterium nucleatum and Porphyromonas gingivalis. Many periodontopathic micro- organisms, like Streptococcus sp., Peptostreptococcus sp., Prevotella sp., Fusobacterium sp., Porphyromonas gingivalis, and Capnocytophaga gingivalis, strongly have an impact on the development of oral cancers. Three basic mechanisms are involved in pathogen-mediated cancer development, like chronic inflammation-mediated angiogenesis, inhibition of cellular apoptosis, and release of carcinogenic by-products. Microbiota has a dichotomous role to play in cancer, i.e., microbiota can be used for cancer management too. Shreds of evidence are there to support the fact that microbiota enhances the chemotherapeutic drug efficacy. This review presents the possible mechanism of the oncogenic effect of microbiota with emphasis on the oral microbiome and also attempts to explain the intricate role of microbiota in cancer management.
PubMed: 38409691
DOI: 10.2174/0115680096282503240124104029 -
Frontiers in Microbiology 2024Cervical cancer ranks among the most prevalent cancers globally with high-risk human papillomaviruses implicated in nearly 99% of cases. However, hidden players such as... (Review)
Review
Cervical cancer ranks among the most prevalent cancers globally with high-risk human papillomaviruses implicated in nearly 99% of cases. However, hidden players such as changes in the microbiota are now being examined as potential markers in the progression of this disease. Researchers suggest that changes in the vaginal microbiota might correlate with cervical cancer. This review provides a comprehensive look at the microbiota changes linked with the advancement of cervical cancer. It also scrutinizes the databases from past studies on the microbiota during healthy and cancerous stages, drawing connections between prior findings concerning the role of the microbiota in the progression of cervical cancer. Preliminary findings identify spp., spp., spp., and spp., as potential biomarkers for cervical cancer progression. spp., spp., and spp. were identified as potential biomarkers for HPVs (+), while spp. may be indicative of HPV (-). However, the study's limitations, including potential biases and methodological constraints, underscore the need for further research to validate these findings and delve deeper into the microbiota's role in HPV development. Despite these limitations, the review provides valuable insights into microbiota trends during cervical cancer progression, offering direction for future research. The review summarizes key findings from previous studies on microbiota during healthy and cancerous stages, as well as other conditions such as CIN, SIL, HPV (+), and HPV (-), indicating a promising area for further investigation. The consistent presence of HPV across all reported cervical abnormalities, along with the identification of distinct bacterial genera between cancerous and control samples, suggests a potential link that merits further exploration. In conclusion, a more profound understanding of the microbial landscape could elucidate the pathogenesis of cervical diseases and inform future strategies for diagnosis, prevention, and treatment.
PubMed: 38389527
DOI: 10.3389/fmicb.2024.1352778 -
Cell Reports. Medicine Mar 2024Obesity is a risk factor for colorectal cancer (CRC), and the involvement of gut microbiota in the pathogenesis of obesity and CRC is widely recognized. However, the...
Obesity is a risk factor for colorectal cancer (CRC), and the involvement of gut microbiota in the pathogenesis of obesity and CRC is widely recognized. However, the landscape of fecal microbiome and metabolome distinguishing patients with obesity-related CRC from obesity remains unknown. Here, we utilize metagenomic sequencing and metabolomics from 522 patients with CRC and healthy controls to identify the characteristics of obese CRC. Our integrated analysis reveals that obesity-related CRC is characterized by elevated Peptostreptococcus stomatis, dysregulated fatty acids and phospholipids, and altered Kyoto Encyclopedia of Genes and Genomes pathways involving glycerophospholipid metabolism and lipopolysaccharide synthesis. Correlation analysis unveils microbial interactions in obesity, where the probiotic Faecalibacterium prausnitzii and the tumor-promoting species P. stomatis may engage in cross-feeding, thereby promoting tumorigenesis. In vitro experiments affirm enhanced growth under cross-feeding conditions. The mutualistic microbe-microbe interaction may contribute to the association between obesity and elevated CRC risk. Additionally, diagnostic models incorporating BMI-specific microbial biomarkers display promise for precise CRC screening.
Topics: Humans; Metabolome; Microbiota; Obesity; Colorectal Neoplasms; Microbial Interactions
PubMed: 38378003
DOI: 10.1016/j.xcrm.2024.101429 -
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