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BMC Bioinformatics Feb 2023It seems that several members of intestinal gut microbiota like Streptococcus bovis, Bacteroides fragilis, Helicobacter pylori, Fusobacterium nucleatum, Enterococcus...
BACKGROUND
It seems that several members of intestinal gut microbiota like Streptococcus bovis, Bacteroides fragilis, Helicobacter pylori, Fusobacterium nucleatum, Enterococcus faecalis, Escherichia coli, Peptostreptococcus anaerobius may be considered as the causative agents of Colorectal Cancer (CRC). The present study used bioinformatics and immunoinformatics approaches to design a potential epitope-based multi-epitope vaccine to prevent CRC with optimal population coverage.
METHODS
In this study, ten amino acid sequences of CRC-related pathogens were retrieved from the NCBI database. Three ABCpred, BCPREDS and LBtope online servers were considered for B cells prediction and the IEDB server for T cells (CD4 and CD8) prediction. Then, validation, allergenicity, toxicity and physicochemical analysis of all sequences were performed using web servers. A total of three linkers, AAY, GPGPG, and KK were used to bind CTL, HTL and BCL epitopes, respectively. In addition, the final construct was subjected to disulfide engineering, molecular docking, immune simulation and codon adaptation to design an effective vaccine production strategy.
RESULTS
A total of 19 sequences of different lengths for linear B-cell epitopes, 19 and 18 sequences were considered as epitopes of CD4 T and CD8 cells, respectively. The predicted epitopes were joined by appropriate linkers because they play an important role in producing an extended conformation and protein folding. The final multi-epitope construct and Toll-like receptor 4 (TLR4) were evaluated by molecular docking, which revealed stable and strong binding interactions. Immunity simulation of the vaccine showed significantly high levels of immunoglobulins, helper T cells, cytotoxic T cells and INF-γ.
CONCLUSION
Finally, the results showed that the designed multi-epitope vaccine could serve as an excellent prophylactic candidate against CRC-associated pathogens, but in vitro and animal studies are needed to justify our findings for its use as a possible preventive measure.
Topics: Animals; Molecular Docking Simulation; Epitopes, T-Lymphocyte; Vaccines, Subunit; Epitopes, B-Lymphocyte; Colorectal Neoplasms; Computational Biology
PubMed: 36829112
DOI: 10.1186/s12859-023-05197-0 -
The Pan African Medical Journal 2022a large number of microbes colonizing the gut are highly diverse and complex in their structure, as this complex structure of gut microbiota acts as an indicator of a...
INTRODUCTION
a large number of microbes colonizing the gut are highly diverse and complex in their structure, as this complex structure of gut microbiota acts as an indicator of a diseased state. Recently, there is a need for improved biomarkers for colorectal cancer (CRC) and advanced adenoma. Among the CRC associated organisms, bacteria are the most common causes of serious disease and deaths. To understand the dynamic interaction among bacteria colonizing the gut, different approaches have been implicated.
METHODS
in this study, faecal microbial markers were evaluated for detecting CRC. As most of these organisms are anaerobic, different molecular tools are of great values for rapid detection of these bacteria. Samples from Tumor Hospital were screened for the presence of different pathogens by both usual polymerase chain reaction (PCR) and a real-time assay.
RESULTS
in a total of 34 samples, by PCR method, bifidobacterium, fusobacterium and Escherichia coli (E. coli) were mainly identified in almost all samples. However, a clear variation in bacterial composition could be observed in Porphyromonas gingivalis, Prevotella intermedia and Peptostreptococcus magnus, where positive results could be detected only in diseased samples. In addition, E. faecium and E. saphenum were mainly identified in diseased samples. In contrast, providencia could be detected mainly in control samples. In realtime assay, the relative abundance was higher for fusobacterium and bifidobacterium markers in CRC patients compared to control samples. However, such increased in abundance has never been observed in both fusobacterium and bifidobacterium in the same sample.
CONCLUSION
these results demonstrated increased abundance of fusobacterium or bifidobacterium can be considered as a sign for impairment or a diseased condition and the possibility of use of the faecal microbiotain CRC patients as a marker for detecting the disease.
Topics: Humans; Egypt; Escherichia coli; Gastrointestinal Microbiome; Feces; Colorectal Neoplasms
PubMed: 36721476
DOI: 10.11604/pamj.2022.43.119.30037 -
Research Square Jan 2023The 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-hour 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 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 and 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: 36711747
DOI: 10.21203/rs.3.rs-2475944/v1 -
Heliyon Jan 2023This study aimed at investigating the characteristics and correlation between oral (tongue coating) and fecal microbiota in patients with diarrheal irritable bowel...
BACKGROUND
This study aimed at investigating the characteristics and correlation between oral (tongue coating) and fecal microbiota in patients with diarrheal irritable bowel syndrome (IBS-D).
METHODS
Fifty-two IBS-D patients were chosen, with ten healthy volunteers serving as the normal control group. Tongue coating samples and fecal samples of subjects were sequenced for the 16S rRNA gene (V4-V5). Bioinformatics analysis was done on the test data to investigate oral and fecal microbiota composition characteristics in IBS-D patients.
RESULTS
The microbial richness of tongue coating in IBS-D group was lower than that in the normal control group (P < 0.05). The beta diversity of tongue coating microbiota and fecal microbiota was significantly different in the IBS-D group compared to the normal control group (P < 0.05). ( and ), , , , and were considerably high in number the tongue coating samples of the IBS-D group in comparison to the normal control group. Similarly, the fecal samples from the IBS-D group were significantly enriched in , ( and ), , , , and compared to the normal control group.
CONCLUSIONS
The oral and fecal microbiotas of IBS-D patients differ from those of the control group; hence studying IBS-D from the perspective of the oral-gut microbiome axis is an interesting research avenue.
PubMed: 36711269
DOI: 10.1016/j.heliyon.2023.e13114 -
European Journal of Clinical... Mar 2023Accumulating evidence has related the gut microbiota to colorectal cancer (CRC). Fusobacterium nucleatum has repeatedly been linked to colorectal tumorigenesis. The aim...
Accumulating evidence has related the gut microbiota to colorectal cancer (CRC). Fusobacterium nucleatum has repeatedly been linked to colorectal tumorigenesis. The aim of this study was to investigate microbial composition in different sampling sites, in order to profile the microbial dynamics with CRC progression. Further, we characterized the tumor-associated F. nucleatum subspecies. Here, we conducted Illumina Miseq next-generation sequencing of the 16S rRNA V4 region in biopsy samples, to investigate microbiota alterations in cancer patients, patients with adenomatous polyp, and healthy controls in Norway. Further, Fusobacterium positive tumor biopsies were subjected to MinION nanopore sequencing of Fusobacterium-specific amplicons to characterize the Fusobacterium species and subspecies. We found enrichment of oral biofilm-associated bacteria, Fusobacterium, Gemella, Parvimonas, Granulicatella, Leptotrichia, Peptostreptococcus, Campylobacter, Selenomonas, Porphyromonas, and Prevotella in cancer patients compared to adenomatous polyp patients and control patients. Higher abundance of amplicon sequence variants (ASVs) classified as Phascolarctobacterium, Bacteroides vulgatus, Bacteroides plebeius, Bacteroides eggerthii, Tyzzerella, Desulfovibrio, Frisingicoccus, Eubacterium coprostanoligenes group, and Lachnospiraceae were identified in cancer and adenomatous polyp patients compared to healthy controls. F. nucleatum ssp. animalis was the dominating subspecies. F. nucleatum ssp. nucleatum, F. nucleatum ssp. vincentii, Fusobacterium pseudoperiodonticum, Fusobacterium necrophorum, and Fusobacterium gonidiaformans were identified in five samples. Several biofilm-associated bacteria were enriched at multiple sites in cancer patients. Another group of bacteria was enriched in both cancer and polyps, suggesting that they may have a role in polyp development and possibly early stages of CRC.
Topics: Humans; RNA, Ribosomal, 16S; Fusobacterium nucleatum; Bacteria; Carcinogenesis; Gastrointestinal Microbiome; Adenomatous Polyps; Colorectal Neoplasms
PubMed: 36703031
DOI: 10.1007/s10096-023-04551-7 -
Wounds : a Compendium of Clinical... Nov 2022HO with concurrent chronic osteomyelitis is extremely rare. To the authors' knowledge, this is the first case in the English-language literature with wound infection and...
INTRODUCTION
HO with concurrent chronic osteomyelitis is extremely rare. To the authors' knowledge, this is the first case in the English-language literature with wound infection and mature HO with chronic osteomyelitis caused by mixed infection of Pasteurella canis, Peptoniphilus coxii, Peptostreptococcus canis, and Fusobacterium nucleatum following licking of a wound by a domesticated dog.
CASE REPORT
A 49-year-old female with a painful, swollen, and purulent wound with bone exposure, measuring 2.5 cm × 1.5 cm, on the right leg was referred after an unsuccessful 3-month treatment regimen for an open wound resulting from a motorcycle accident. The patient's dog licked the wound several times 1 week after the accident. Sequestrectomy and debridement were performed after a 3-week OPD treatment. Postoperative treatment included NPWT applied for 6 days, 1 week of open wound care, STSG 2 weeks after the first operation, and IV antibiotics for 3 weeks. Pathologic examination was positive for HO with chronic osteomyelitis. The patient was discharged 3 weeks after admission under stable condition followed by OPD treatment. Wound healing was achieved 2 months after discharge.
CONCLUSIONS
Repeated licking of the patient's wound by her dog caused the colonization of pathogens from the dog's saliva, and inappropriate wound care by the patient herself resulted in HO with chronic osteomyelitis, which was successfully treated with a regimen of NPWT, open wound care, STSG, and IV antibiotics.
Topics: Female; Dogs; Animals; Anti-Bacterial Agents; Wound Healing; Osteomyelitis; Wound Infection; Ossification, Heterotopic
PubMed: 36608841
DOI: 10.25270/wnds/21096 -
Indian Journal of Ophthalmology Jan 2023Orbital cellulitis is a serious condition with potentially severe complications. Treatment requires interdisciplinary care and early introduction of antimicrobial...
PURPOSE
Orbital cellulitis is a serious condition with potentially severe complications. Treatment requires interdisciplinary care and early introduction of antimicrobial therapy. In our tertiary center, a team of pediatricians, pediatric ophthalmologists, and otorhinolaryngologists successfully participated in the management of pediatric periorbital/orbital cellulitis. This study aimed to demonstrate our interdisciplinary approach and to investigate clinical profile and management of pediatric periorbital/orbital cellulitis.
METHODS
A retrospective chart review was performed of all pediatric patients hospitalized for periorbital and orbital cellulitis in a tertiary hospital center from September 15, 2016, to March 15, 2020.
RESULTS
A total of 26 children-median age 2.7 years (range 0.5-12)-were treated during the study period. Disease presentation was unilateral, mainly during winter (n = 12) and autumn (n = 12), without ophthalmoplegia/proptosis. Seven patients had orbital cellulitis (Chandler classification of ≥III) and were older (6.5 years, P = 0.011) with sinusitis (P < 0.001), required surgery (P = 0.004), underwent longer antimicrobial treatment (13 days, P < 0.001), and had a longer length of hospital stay (13.43 days, P = 0.001). Orbital cellulitis occurred in a median of three days (range 1-12) of acute rhinosinusitis. Radiological survey was performed in 11 patients, whereas six patients were treated surgically. All intraoperatively collected cultures (sinus swabs) were positive, whereas Streptococcus pyogenes and Peptostreptococcus were isolated in five cases. All patients fully recovered. No recurrence was documented.
CONCLUSION
Sinusitis is associated with severe orbital cellulitis and surgical management. Orbital cellulitis occurred early in the course of acute rhinosinusitis, as a distinctive presentation of rhinosinusitis. Interdisciplinary care and early management are crucial in treatment of pediatric periorbital/orbital cellulitis.
Topics: Child; Humans; Infant; Child, Preschool; Orbital Cellulitis; Retrospective Studies; Sinusitis; Acute Disease; Exophthalmos; Eye Diseases; Anti-Bacterial Agents; Orbital Diseases
PubMed: 36588244
DOI: 10.4103/ijo.IJO_798_22 -
Gut Pathogens Dec 2022Colorectal cancer (CRC) is a multifactorial disease with genetic and environmental factors. Regional differences in risk factors are an important reason for the...
BACKGROUND
Colorectal cancer (CRC) is a multifactorial disease with genetic and environmental factors. Regional differences in risk factors are an important reason for the different incidences of CRC in different regions.
OBJECTIVE
The goal was to clarify the intestinal microbial composition and structure of CRC patients in different regions and construct CRC risk prediction models based on regional differences.
METHODS
A metagenomic dataset of 601 samples from 6 countries in the GMrepo and NCBI databases was collected. All whole-genome sequencing (WGS) data were annotated for species by MetaPhlAn2. We obtained the relative abundance of species composition at the species level and genus level. The MicrobiotaProcess package was used to visualize species composition and PCA. LEfSe analysis was used to analyze the differences in the datasets in each region. Spearman correlation analysis was performed for CRC differential species. Finally, the CRC risk prediction model was constructed and verified in each regional dataset.
RESULTS
The composition of the intestinal bacterial community varied in different regions. Differential intestinal bacteria of CRC in different regions are inconsistent. There was a common diversity of bacteria in all six countries, such as Peptostreptococcus stomatis and Fusobacterium nucleatum at the species level. Peptostreptococcus stomatis (species level) and Peptostreptococcus (genus level) are important CRC-related bacteria that are related to other bacteria in different regions. Region has little influence on the accuracy of the CRC risk prediction model. Peptostreptococcus stomatis is an important variable in CRC risk prediction models in all regions.
CONCLUSION
Peptostreptococcus stomatis is a common high-risk pathogen of CRC worldwide, and it is an important variable in CRC risk prediction models in all regions. However, regional differences in intestinal bacteria had no significant impact on the accuracy of the CRC risk prediction model.
PubMed: 36578080
DOI: 10.1186/s13099-022-00524-x -
International Journal of Hygiene and... Mar 2023Firefighters are frequently exposed to high temperatures, environmental toxicants, and strenuous physical demands. The health impacts of these occupational exposures on...
BACKGROUND
Firefighters are frequently exposed to high temperatures, environmental toxicants, and strenuous physical demands. The health impacts of these occupational exposures on processes including inflammation and kidney function as well as on the gut microbiota are poorly understood. A firefighter training course may provide a controlled environment to assess these health risks.
METHODS
Basic health measures, stool, and blood samples were obtained from 24 firefighters participating in a one-week, heat-intensive training course. Indicators of inflammation, gut permeability, kidney health, and stool microbiota composition were measured before and after the training course in 18 participants. Urine specific gravity was measured before and after a heat-intensive training day to evaluate dehydration.
RESULTS
The majority of firefighters in this cohort were categorized as hypertensive and experienced multiple heat-related illness symptoms during the training week and dehydration after the heat-intensive training day. While plasma IL-1β, CXCL8, and NGAL decreased over the training week, other indicators of inflammation and acute kidney injury increased, and estimated kidney function declined. Microbiota composition shifted over the course of the training week, with changes in Peptostreptococcus anaerobius and Streptococcus.
CONCLUSIONS
This pilot study conducted in a controlled field setting suggests that the occupational environment of firefighters may increase their risk for systemic inflammation and kidney disease.
Topics: Humans; Gastrointestinal Microbiome; Firefighters; Dehydration; Pilot Projects; Inflammation; Kidney
PubMed: 36577282
DOI: 10.1016/j.ijheh.2022.114107 -
Gut Pathogens Dec 2022Previous evidence has shown that the gut microbiota plays a role in the development and progression of colorectal cancer (CRC). This study aimed to provide quantitative...
BACKGROUND
Previous evidence has shown that the gut microbiota plays a role in the development and progression of colorectal cancer (CRC). This study aimed to provide quantitative analysis and visualization of the interaction between the gut microbiota and CRC in order to establish a more precise microbiota panel for CRC diagnosis.
METHOD
A paired-sample study was designed by retrieving original metagenomic data from the GMrepo database. The differences in the distribution of the gut microbiota between CRCs and controls were analysed at the species level. A co-occurrence network was established, and the microbial interactions with environmental factors were assessed. Random forest models were used to determine significant biomarkers for differentiating CRC and control samples.
RESULTS
A total of 709 metagenomic samples from 6 projects were identified. After matching, 86 CRC patients and 86 matched healthy controls from six countries were enrolled. A total of 484 microbial species and 166 related genera were analysed. In addition to previously recognized associations between Fusobacterium nucleatum and species belonging to the genera Peptostreptococcus, Porphyromonas, and Prevotella and CRC, we found new associations with the novel species of Parvimonas micra and Collinsella tanakaei. In CRC patients, Bacteroides uniformis and Collinsella tanakaei were positively correlated with age, whereas Dorea longicatena, Adlercreutzia equolifaciens, and Eubacterium hallii had positive associations with body mass index (BMI). Finally, a random forest model was established by integrating different numbers of species with the highest model-building importance and lowest inner subcategory bias. The median value of the area under the receiver operating characteristic curve (AUC) was 0.812 in the training cohort and 0.790 in the validation set.
CONCLUSIONS
Our study provides a novel bioinformatics approach for investigating the interaction between the gut microbiota and CRC using an online free database. The identification of key species and their associated genes should be further emphasized to determine the relative causality of microbial organisms in the development of CRC.
PubMed: 36564826
DOI: 10.1186/s13099-022-00527-8