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BMC Bioinformatics Jun 2022Microbial communities in the human body, also known as human microbiota, impact human health, such as colorectal cancer (CRC). However, the different roles that...
BACKGROUND
Microbial communities in the human body, also known as human microbiota, impact human health, such as colorectal cancer (CRC). However, the different roles that microbial communities play in healthy and disease hosts remain largely unknown. The microbial communities are typically recorded through the taxa counts of operational taxonomic units (OTUs). The sparsity and high correlations among OTUs pose major challenges for understanding the microbiota-disease relation. Furthermore, the taxa data are structured in the sense that OTUs are related evolutionarily by a hierarchical structure.
RESULTS
In this study, we borrow the idea of super-variant from statistical genetics, and propose a new concept called super-taxon to exploit hierarchical structure of taxa for microbiome studies, which is essentially a combination of taxonomic units. Specifically, we model a genus which consists of a set of OTUs at low hierarchy and is designed to reflect both marginal and joint effects of OTUs associated with the risk of CRC to address these issues. We first demonstrate the power of super-taxon in detecting highly correlated OTUs. Then, we identify CRC-associated OTUs in two publicly available datasets via a discovery-validation procedure. Specifically, four species of two genera are found to be associated with CRC: Parvimonas micra, Parvimonas sp., Peptostreptococcus stomatis, and Peptostreptococcus anaerobius. More importantly, for the first time, we report the joint effect of Parvimonas micra and Parvimonas sp. (p = 0.0084) as well as that of Peptostrepto-coccus stomatis and Peptostreptococcus anaerobius (p = 8.21e-06) on CRC. The proposed approach provides a novel and useful tool for identifying disease-related microbes by taking the hierarchical structure of taxa into account and further sheds new lights on their potential joint effects as a community in disease development.
CONCLUSIONS
Our work shows that proposed approaches are effective to study the microbiota-disease relation taking into account for the sparsity, hierarchical and correlated structure among microbes.
Topics: Colorectal Neoplasms; Firmicutes; Humans; Microbiota; Peptostreptococcus
PubMed: 35729515
DOI: 10.1186/s12859-022-04786-9 -
Postepy Dermatologii I Alergologii Feb 2022Quantitative and qualitative changes in the microbiome of the skin affect the emergence and course of allergic diseases, in particular, of acute urticaria.
INTRODUCTION
Quantitative and qualitative changes in the microbiome of the skin affect the emergence and course of allergic diseases, in particular, of acute urticaria.
AIM
To investigate the taxonomic composition of the skin microbiota in children with acute urticaria and to study its effect on the course of the disease.
MATERIAL AND METHODS
In total, 75 children with diagnosed acute urticaria at the age of 7--14 years were examined. The average age of children was 10.83 ±0.95, of which 44 (58.7%) were boys, and 31 (41.3%) were girls. The control group consisted of 30 virtually healthy children of the appropriate age, of whom 16 (53.3%) were boys, and 13 (46.7%) were girls.
RESULTS
Regardless of the severity of the disease, the examined children suffering from acute urticaria had sensitization in history with a significant prevalence of food sensitization ( < 0.05). The occurrence of a severe episode of acute urticaria is associated with allergens of drug origin in 52.6% of cases and the action of unidentified triggers in 47.4% of cases. In children with acute urticaria, , bacteria of the genus , and dominated on a non-affected skin area, while for the affected skin area, the , bacteria of the genus , and were denoted as dominating.
CONCLUSIONS
High frequency of detection on affected and non- affected skin areas in children with acute urticaria is a predictor of the disease severity.
PubMed: 35369637
DOI: 10.5114/ada.2022.113808 -
Frontiers in Cellular and Infection... 2020In order to improve our understanding on the microbial complexity associated with Grade C/molar-incisor pattern periodontitis (GC/MIP), we surveyed the oral and fecal...
In order to improve our understanding on the microbial complexity associated with Grade C/molar-incisor pattern periodontitis (GC/MIP), we surveyed the oral and fecal microbiomes of GC/MIP and compared to non-affected individuals (Control). Seven Afro-descendants with GC/MIP and seven age/race/gender-matched controls were evaluated. Biofilms from supra/subgingival sites (OB) and feces were collected and submitted to sequencing. () JP2 clone genotyping and salivary nitrite levels were determined. Supragingival biofilm of GC/MIP presented greater abundance of opportunistic bacteria. was increased in subgingival healthy sites of GC/MIP compared to Control. and were more abundant whereas was reduced in OB of GC/MIP compared to controls. abundance was 50 times higher in periodontal sites with PD≥ 4 mm of GC/MIP than in controls. GC/MIP oral microbiome was characterized by a reduction in commensals such as , and and enrichment in periodontopathogens, especially and sulfate reducing . The oral microbiome of the JP2-like+ patient was phylogenetically distant from other GC/MIP individuals. GC/MIP presented a higher abundance of sulfidogenic bacteria in the feces, such as , and than controls. These preliminary data show that the dysbiosis of the microbiome in Afro-descendants with GC/MIP was not restricted to affected sites, but was also observed in supragingival and subgingival healthy sites, as well as in the feces. The understanding on differences of the microbiome between healthy and GC/MIP patients will help in developing strategies to improve and monitor periodontal treatment.
Topics: Aggregatibacter actinomycetemcomitans; Desulfovibrio; Erysipelothrix; Feces; Humans; Incisor; Microbiota; Molar; Peptostreptococcus; Periodontitis; RNA, Ribosomal, 16S
PubMed: 33117737
DOI: 10.3389/fcimb.2020.583761 -
Journal of Dental Research Jan 2016The oral microbiota was compared between Romanian adolescents with a high prevalence of caries and no dental care and Swedish caries-active and caries-free adolescents... (Comparative Study)
Comparative Study
The oral microbiota was compared between Romanian adolescents with a high prevalence of caries and no dental care and Swedish caries-active and caries-free adolescents in caries prevention programs and with a low prevalence of caries. Biofilm samples were analyzed by FLX+ pyrosequencing of the V1 to V4 hypervariable regions of the 16S rRNA gene and polymerase chain reaction (PCR)/quantitative PCR (qPCR) for Streptococcus mutans and Streptococcus sobrinus. Sequences obtained blasted to 9 phyla, 66 genera, and 401 human oral taxa (HOT) in the 16S rRNA Human Oral Microbiome Database, of which 295 were represented by ≥20 sequences. The Romanian adolescents had more sequences in Firmicutes and fewer in Actinobacteria phyla and more sequences in the genera Bacteroidetes [G-3], Porphyromonas, Abiotrophia, Filifactor, Peptostreptococcaceae [11][G-4], Pseudoramibacter, Streptococcus, and Neisseria and fewer in Actinomyces, Selenomonas, Veillonella, Campylobacter, and TM7 [G-1] than the Swedish groups. Multivariate modeling employing HOT, S. sobrinus and S. mutans (PCR/qPCR), and sugar snacks separated Romanian from Swedish adolescents. The Romanian adolescents' microbiota was characterized by a panel of streptococci, including S. mutans, S. sobrinus, and Streptococcus australis, and Alloprevotella, Leptotrichia, Neisseria, Porphyromonas, and Prevotella. The Swedish adolescents were characterized by sweet snacks, and those with caries activity were also characterized by Prevotella, Actinomyces, and Capnocytophaga species and those free of caries by Actinomyces, Prevotella, Selenomonas, Streptococcus, and Mycoplasma. Eight species including Streptococcus mitis and Streptococcus species HOT070 were prevalent in Romanian and Swedish caries-active subjects but not caries-free subjects. In conclusion, S. mutans and S. sobrinus correlated with Romanian adolescents with caries and with limited access to dental care, whereas S. mutans and S. sobrinus were detected infrequently in Swedish adolescents in dental care programs. Swedish caries-active adolescents were typically colonized by Actinomyces, Selenomonas, Prevotella, and Capnocytophaga. Hence, the role of mutans streptococci as a primary caries pathogen appears less pronounced in populations with prevention programs compared to populations lacking caries treatment and prevention strategies.
Topics: Abiotrophia; Actinobacteria; Actinomyces; Adolescent; Bacteroidetes; Biofilms; Campylobacter; Capnocytophaga; DMF Index; Dental Care; Dental Caries; Eubacterium; Fusobacteria; Gram-Negative Bacteria; Humans; Microbiota; Neisseria; Peptostreptococcus; Porphyromonas; Prevotella; Selenomonas; Snacks; Streptococcus; Streptococcus mutans; Streptococcus sobrinus; Veillonella
PubMed: 26442950
DOI: 10.1177/0022034515609554 -
International Endodontic Journal Feb 2023To evaluate the root canal microbiome composition in cases of primary and secondary apical periodontitis.
AIM
To evaluate the root canal microbiome composition in cases of primary and secondary apical periodontitis.
METHODOLOGY
Thirty-nine samples from patients with primary root canal infections obtained before root canal treatment, and 40 samples obtained during root-end resection procedures from previously filled cases with apical periodontitis were evaluated using 16S rRNA next-generation sequencing analysis (NGS). Demographic and clinical factors included age, sex, infection type, percussion sensitivity, and presence of pain. Differences in abundances of genera were evaluated using Kruskal-Wallis test. Alpha and beta diversity indices were calculated using mothur. The Shannon and Chao1 indices were used to measure alpha diversity. The Bray-Curtis dissimilarity was used to measure beta diversity. Differences in community composition were evaluated using analysis of similarity (ANOSIM) with Bonferroni correction for multiple comparisons.
RESULTS
Significantly fewer operational taxonomic units values were observed from samples from secondary infections (p < .0001). While no significant differences were observed in the Chao 1 index between primary and secondary infections, the Shannon alpha diversity was significantly lower in secondary relative to primary infections (p = .008). Among samples, sex, age (adult vs. older adult), percussion sensitivity, and presence of pain all showed no significant effects on community composition via an analysis of similarity (ANOSIM). However, community composition was significantly different depending on whether the sample was from a primary or secondary infection (R = .051, p = .03). Nine microbial genera comprised the predominant taxa observed among samples (>3.3%) and included Parvimonas, Fusobacterium, Campylobacter, Arachnia, Eubacterium, Prevotella, Peptostreptococcus, Fretibacterirum, and Pseudoramibacter. Significantly greater relative abundances of Prevotella, Peptostreptococcus, Veillonella, Lactucaseibacillus, and Dialister were observed in primary infections.
CONCLUSIONS
Primary endodontic infections are more diverse than secondary infections. The microbial composition is not associated with the clinical manifestations of apical periodontitis.
Topics: Aged; Humans; Bacteria; Coinfection; Dental Pulp Cavity; Pain; Periapical Periodontitis; RNA, Ribosomal, 16S
PubMed: 36334085
DOI: 10.1111/iej.13864 -
Frontiers in Cellular and Infection... 2021Oral cancer is the most common malignant tumor in the oral and maxillofacial region, of which more than 90% is squamous cell carcinoma. The incidence of oral cancer is...
Oral cancer is the most common malignant tumor in the oral and maxillofacial region, of which more than 90% is squamous cell carcinoma. The incidence of oral cancer is on the rise worldwide. An imbalance between the microorganism composition and its host may lead to the occurrence of oral malignant tumors. Accumulating evidence suggests that the oral microbiota plays an important role in oral cancer; however, the association between oral microbiota and oral cancer has not yet been comprehensively studied. In this study, metagenomic sequencing was used to compare the microbial composition of three groups of samples from Chinese patients with oral cancer, patients with precancerous lesion, and normal individuals. In terms of microbiota richness, the oral microbiota of patients with precancerous lesions was richer than that of oral cancer patients and healthy controls, whereas in terms of microbiota diversity, there was little difference between the three groups. The three groups of samples exhibited statistically significant differences in microbiota composition and metabolic function at the family, genus, and species levels ( < 0.05). The differentially enriched phylum in oral cancer samples was Bacteroidetes ( < 0.05). At the genus level, the main differentially enriched taxa were , and ( < 0.05). The species level was differentially enriched in and (p < 0.05). The prediction of microbiota function shows that oral cancer is mainly associated with coenzyme A biosynthesis, phosphopantothenic acid biosynthesis, inosine 5'-phosphate degradation, and riboflavin biosynthesis. Furthermore, the increase in C-reactive protein level in oral cancer patients was found to be closely related to . Overall, oral bacterial profiles showed significant differences between the oral cancer group and normal group. Hence, microbes can be employed as diagnostic markers and treatment targets for oral cancer.
Topics: Carcinoma, Squamous Cell; China; Humans; Microbiota; Mouth Neoplasms; RNA, Ribosomal, 16S
PubMed: 34956932
DOI: 10.3389/fcimb.2021.780067 -
Journal of Immunology Research 2022As a common female reproductive system malignancy, cervical cancer (CC) disturbs numerous women's health. This study demonstrates the role of the vaginal microbial...
As a common female reproductive system malignancy, cervical cancer (CC) disturbs numerous women's health. This study demonstrates the role of the vaginal microbial environment () in cervical cancer. Functional assays, including cell proliferation assay, tube formation assay, and immunofluorescence staining, revealed the effect of -treated macrophages on cell proliferation and the angiogenesis process. The tube formation assay disclosed the function of -treated macrophages on angiogenesis. In vivo assays were also established to explore the impact of -treated macrophages on tumor migration. The results revealed that -induced macrophages boosted cervical cancer migration and angiogenesis both in vitro and in vivo. Then, this study unveiled that -induced macrophage secreted VEGF to stimulate the angiogenesis in cervical cancer. As a whole, -induced macrophage facilitates cervical cancer development through modulation of VEGF expression.
Topics: Female; Humans; Macrophages; Peptostreptococcus; Uterine Cervical Neoplasms; Vascular Endothelial Growth Factor A
PubMed: 35983073
DOI: 10.1155/2022/3525735 -
BMC Microbiology Dec 2022Streptococcus agalactiae or group B Streptococcus (GBS) asymptomatically colonizes the genitourinary tracts of up to 30% of pregnant women. Globally, GBS is an important...
BACKGROUND
Streptococcus agalactiae or group B Streptococcus (GBS) asymptomatically colonizes the genitourinary tracts of up to 30% of pregnant women. Globally, GBS is an important cause of neonatal morbidity and mortality. GBS has recently been linked to adverse pregnancy outcomes. The potential interactions between GBS and the vaginal microbiome composition remain poorly understood. In addition, little is known about the vaginal microbiota of pregnant Egyptian women.
RESULTS
Using V3-V4 16S rRNA next-generation sequencing, we examined the vaginal microbiome in GBS culture-positive pregnant women (22) and GBS culture-negative pregnant women (22) during the third trimester in Ismailia, Egypt. According to the alpha-diversity indices, the vaginal microbiome of pregnant GBS culture-positive women was significantly more diverse and less homogenous. The composition of the vaginal microbiome differed significantly based on beta-diversity between GBS culture-positive and culture-negative women. The phylum Firmicutes and the family Lactobacillaceae were significantly more abundant in GBS-negative colonizers. In contrast, the phyla Actinobacteria, Tenericutes, and Proteobacteria and the families Bifidobacteriaceae, Mycoplasmataceae, Streptococcaceae, Corynebacteriaceae, Staphylococcaceae, and Peptostreptococcaceae were significantly more abundant in GBS culture-positive colonizers. On the genus and species levels, Lactobacillus was the only genus detected with significantly higher relative abundance in GBS culture-negative status (88%), and L. iners was the significantly most abundant species. Conversely, GBS-positive carriers exhibited a significant decrease in Lactobacillus abundance (56%). In GBS-positive colonizers, the relative abundance of the genera Ureaplasma, Gardnerella, Streptococcus, Corynebacterium, Staphylococcus, and Peptostreptococcus and the species Peptostreptococcus anaerobius was significantly higher. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to the metabolism of cofactors and vitamins, phosphatidylinositol signaling system, peroxisome, host immune system pathways, and host endocrine system were exclusively enriched among GBS culture-positive microbial communities. However, lipid metabolism KEGG pathways, nucleotide metabolism, xenobiotics biodegradation and metabolism, genetic information processing pathways associated with translation, replication, and repair, and human diseases (Staphylococcus aureus infection) were exclusively enriched in GBS culture-negative communities.
CONCLUSIONS
Understanding how perturbations of the vaginal microbiome contribute to pregnancy complications may result in the development of alternative, targeted prevention strategies to prevent maternal GBS colonization. We hypothesized associations between inferred microbial function and GBS status that would need to be confirmed in larger cohorts.
Topics: Infant, Newborn; Female; Pregnancy; Humans; Pregnant Women; Pregnancy Trimester, Third; Streptococcus agalactiae; RNA, Ribosomal, 16S; Streptococcal Infections; Vagina; Streptococcus; Pregnancy Complications, Infectious; Lactobacillus; Microbiota
PubMed: 36544085
DOI: 10.1186/s12866-022-02730-8 -
Critical Care (London, England) Jun 2002This review describes the microbiology, diagnosis and management of bacteremia caused by anaerobic bacteria in children. Bacteroides fragilis, Peptostreptococcus sp.,... (Review)
Review
This review describes the microbiology, diagnosis and management of bacteremia caused by anaerobic bacteria in children. Bacteroides fragilis, Peptostreptococcus sp., Clostridium sp., and Fusobacterium sp. were the most common clinically significant anaerobic isolates. The strains of anaerobic organisms found depended, to a large extent, on the portal of entry and the underlying disease. Predisposing conditions include: malignant neoplasms, immunodeficiencies, chronic renal insufficiency, decubitus ulcers, perforation of viscus and appendicitis, and neonatal age. Organisms identical to those causing anaerobic bacteremia can often be recovered from other infected sites that may have served as a source of persistent bacteremia. When anaerobes resistant to penicillin are suspected or isolated, antimicrobial drugs such as clindamycin, chloramphenicol, metronidazole, cefoxitin, a carbapenem, or the combination of a beta-lactamase inhibitor and a penicillin should be administered. The early recognition of anaerobic bacteremia and administration of appropriate antimicrobial and surgical therapy play a significant role in preventing mortality and morbidity in pediatric patients.
Topics: Bacteremia; Bacteria, Anaerobic; Child; Humans; Incidence
PubMed: 12133179
DOI: 10.1186/cc1490 -
Molecular Oncology May 2024Oral and intestinal samples from a cohort of 93 colorectal cancer (CRC) patients and 30 healthy controls (non-CRC) were collected for microbiome analysis. Saliva (28...
Oral and intestinal samples from a cohort of 93 colorectal cancer (CRC) patients and 30 healthy controls (non-CRC) were collected for microbiome analysis. Saliva (28 non-CRC and 94 CRC), feces (30 non-CRC and 97 CRC), subgingival fluid (20 CRC), and tumor tissue samples (20 CRC) were used for 16S metabarcoding and/or RNA sequencing (RNAseq) approaches. A differential analysis of the abundance, performed with the ANCOM-BC package, adjusting the P-values by the Holm-Bonferroni method, revealed that Parvimonas was significantly over-represented in feces from CRC patients (P-value < 0.001) compared to healthy controls. A total of 11 Parvimonas micra isolates were obtained from the oral cavity and adenocarcinoma of CRC patients. Genome analysis identified a pair of isolates from the same patient that shared 99.2% identity, demonstrating that P. micra can translocate from the subgingival cavity to the gut. The data suggest that P. micra could migrate in a synergistic consortium with other periodontal bacteria. Metatranscriptomics confirmed that oral bacteria were more active in tumor than in non-neoplastic tissues. We suggest that P. micra could be considered as a CRC biomarker detected in non-invasive samples such as feces.
Topics: Humans; Colorectal Neoplasms; Male; Female; Adenocarcinoma; Middle Aged; Aged; Mouth; Feces; RNA, Ribosomal, 16S; Gingiva; Saliva; Peptostreptococcus; Firmicutes
PubMed: 37558206
DOI: 10.1002/1878-0261.13506