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PloS One 2024Crohn's disease (CD) entails intricate interactions with gut microbiome diversity, richness, and composition. The relationship between CD and gut microbiome is not...
Crohn's disease (CD) entails intricate interactions with gut microbiome diversity, richness, and composition. The relationship between CD and gut microbiome is not clearly understood and has not been previously characterized in Saudi Arabia. We performed statistical analysis about various factors influencing CD activity and microbiota dysbiosis, including diagnosis, treatment, and its impact on their quality of life as well as high-throughput metagenomic V3-V4 16S rRNA encoding gene hypervariable region of a total of eighty patients with CD, both in its active and inactive state with healthy controls. The results were correlated with the demographic and lifestyle information, which the participants provided via a questionnaire. α-diversity measures indicated lower bacterial diversity and richness in the active and inactive CD groups compared to the control group. Greater dysbiosis was observed in the active CD patients compared to the inactive form of the disease, showed by a reduction in microbial diversity. Specific pathogenic bacteria such as Filifactor, Peptoniphilus, and Sellimonas were identified as characteristic of CD groups. In contrast, anti-inflammatory bacteria like Defluviitalea, Papillibacter, and Petroclostridium were associated with the control group. Among the various factors influencing disease activity and microbiota dysbiosis, smoking emerged as the most significant, with reduced α-diversity and richness for the smokers in all groups, and proinflammatory Fusobacteria was more present (p<0.05). Opposite to the control group, microbial diversity and richness were lower in CD participants of older age compared to younger ones, and male CD participants showed less diversity compared to women participants from the same groups. Our results describe the first report on the relationship between microbiota and Crohn's disease progress in Saudi Arabia, which may provide a theoretical basis for the application of therapeutic methods to regulate gut microbes in CD.
Topics: Humans; Crohn Disease; Gastrointestinal Microbiome; Saudi Arabia; Male; Female; Adult; RNA, Ribosomal, 16S; Middle Aged; Dysbiosis; Young Adult; Bacteria; Case-Control Studies; Quality of Life
PubMed: 38656971
DOI: 10.1371/journal.pone.0299749 -
Frontiers in Microbiology 2024Human papilloma virus (HPV) is the most common sexually transmitted infection worldwide. Cervicovaginal microbiota plays an important role in HPV infection and is...
INTRODUCTION
Human papilloma virus (HPV) is the most common sexually transmitted infection worldwide. Cervicovaginal microbiota plays an important role in HPV infection and is associated with the development of squamous intraepithelial lesions (SIL). The natural history of cervical cancer involves reversible changes in the cervical tissue from a normal state, in which no neoplastic changes are detected in the squamous epithelium, to varying states of cellular abnormalities that ultimately lead to cervical cancer. Low-grade SIL (LSIL), like another cytological category - atypical squamous cells of undetermined significance (ASCUS), may progress to high-grade SIL (HSIL) and invasive cervical cancer or may regress to a normal state.
METHODS
In this work, we studied cervical canal microbiome in 165 HPV-positive and HPV-negative women of a reproductive age with ASCUS [HPV(+) = 29; HPV(-) = 11], LSIL [HPV(+) = 32; HPV(-) = 25], HSIL [HPV(+) = 46], and the control group with negative for intraepithelial lesion malignancy (NILM) [HPV(-) = 22].
RESULTS AND DISCUSSION
HPV16 is the most prevalent HPV type. We have not found any differences between diversity in studied groups, but several genus [like Prevotella (-value = 0.026), Gardnerella (-value = 0.003), Fannyhessea (-value = 0.024)] more often occurred in HSIL group compared by NILM or LSIL regardless of HPV. We have found statistically significant difference in occurrence or proportion of bacterial genus in studied groups. We also identified that increasing of the ratio of or age of patient lead to higher chance to HSIL, while increasing of the ratio of lead to higher chance to LSIL. Patients with a moderate dysbiosis equally often had either of three types of vaginal microbial communities (CST, Community State Type) with the prevalence of (CST I), (CST II), and (CST III); whereas severe dysbiosis is linked with CST IV involving the microorganisms genera associated with bacterial vaginosis and aerobic vaginitis: , , and .
PubMed: 38550866
DOI: 10.3389/fmicb.2024.1334502 -
Journal of Medical Microbiology Mar 2024There is growing evidence that altered microbiota abundance of a range of specific anaerobic bacteria are associated with cancer, including spp., spp., spp., spp.,... (Review)
Review
There is growing evidence that altered microbiota abundance of a range of specific anaerobic bacteria are associated with cancer, including spp., spp., spp., spp., spp., spp spp and spp. linked to multiple cancer types. In this review we explore these pathogenic associations. The mechanisms by which bacteria are known or predicted to interact with human cells are reviewed and we present an overview of the interlinked mechanisms and hypotheses of how multiple intracellular anaerobic bacterial pathogens may act together to cause host cell and tissue microenvironment changes associated with carcinogenesis and cancer cell invasion. These include combined effects on changes in cell signalling, DNA damage, cellular metabolism and immune evasion. Strategies for early detection and eradication of anaerobic cancer-associated bacterial pathogens that may prevent cancer progression are proposed.
Topics: Humans; Bacteria, Anaerobic; Carcinogenesis; Immune Evasion; Porphyromonas; Signal Transduction; Tumor Microenvironment
PubMed: 38535967
DOI: 10.1099/jmm.0.001817 -
Scientific Reports Mar 2024Acne is a prevalent dermatological disease, with high global incidence, and is a health menace. The current study aimed to isolate and characterize the anaerobic...
Acne is a prevalent dermatological disease, with high global incidence, and is a health menace. The current study aimed to isolate and characterize the anaerobic bacteria responsible for the condition. Causes of a total of 70 acne-based bacterium isolates obtained from patients of mild, moderate, and severe acne, 24 were Clostridium innocuum, 21 were Lactobacillus plantarum, 13 were Anaerococcus prevotii, and 12 were Peptoniphilus asaccharolyticus. Nearly 69% of males were suffering, while the rest were females at 31%. The 15-30 years old age group was the most affected. The gold/alginate nanoparticles' nanopreparation (GANPs) produced from chloroauric acid and sodium alginate was an effective treatment against the acne conditions under the experimental conditions. The nanopreparation exhibited significant inhibitory activity against anaerobic bacterial isolates, with a minimum inhibitory concentration of 200 µg/ml for A. prevotii and P. asaccharolyticus, and 400 µg/ml for C. innocuum and L. plantarum. The in vitro efficacy of the GANPs on human blood parameters was also assessed. The concurrent results suggested potential antibacterial activity and hemocompatibility of the product, which has promise to be used as a successful antibacterial agent for acne.
Topics: Male; Female; Humans; Adolescent; Young Adult; Adult; Bacteria, Anaerobic; Alginates; Anti-Bacterial Agents; Acne Vulgaris; Microbial Sensitivity Tests
PubMed: 38523189
DOI: 10.1038/s41598-024-57643-5 -
Systematic and Applied Microbiology May 2024To clarify the evolutionary relationships among Peptoniphilus species, whose members show association with increased risk for prostate cancer, detailed phylogenomic and...
Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus.
To clarify the evolutionary relationships among Peptoniphilus species, whose members show association with increased risk for prostate cancer, detailed phylogenomic and comparative analyses were conducted on their genome sequences. In phylogenetic trees based on core genome proteins and 16S rRNA gene sequences, Peptoniphilus species formed eight distinct clades, with Aedoeadaptatus and Anaerosphaera species branching between them. The observed clades designated as Peptoniphilus sensu stricto (encompassing its type species), Harei, Lacrimalis, Duerdenii, Mikwangii, Stercorisuis, Catoniae and Aedoeadaptatus, show genus level divergence based on 16S rRNA similarity and average amino acid identity (AAI). The Genome Taxonomy Database also assigns most of these clades to distinct taxa. Several Peptoniphilus species (viz. P. coxii, P. ivorii, P. nemausensis and some non-validly published species) grouped reliably with the type species of Aedoeadaptatus (A. acetigenes) and are affiliated to this genus based on 16S rRNA similarity, AAI, and multiple uniquely shared molecular signatures. Hence, we are proposing the transfer of these species into the emended genus Aedoeadaptatus. Our analyses on protein sequences from Peptoniphilus genomes have also identified 54 novel molecular markers consisting of conserved signature indels (CSIs), which are specific for different Peptoniphilus species clades and provide reliable means for their demarcation in molecular terms. Lastly, we also show that based on the shared presence of these CSIs in the genomes of uncharacterized Peptoniphilus spp. (cultured and uncultured), their affiliations to the specific Peptoniphilus clades can be accurately predicted. These results should prove useful in understanding the potential involvement of Peptoniphilus-related species in diseases.
Topics: Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; DNA, Bacterial; Genome, Bacterial; Evolution, Molecular; Genetic Markers
PubMed: 38428338
DOI: 10.1016/j.syapm.2024.126499 -
Current Microbiology Feb 2024The strains Marseille-Q7072 (= CSUR Q7072 = CECT 30604) and Marseille-Q7826 (= CSUR Q7826 = CECT 30727) were isolated from vaginal samples. As MALDI-TOF mass...
The strains Marseille-Q7072 (= CSUR Q7072 = CECT 30604) and Marseille-Q7826 (= CSUR Q7826 = CECT 30727) were isolated from vaginal samples. As MALDI-TOF mass spectrometry failed to identify them, their genomes were directly sequenced to determine their taxogenomic identities. Both strains are anaerobic without any oxidase and catalase activity. C is the most abundant fatty acid for both strains. Strain Marseille-Q7072 is non-spore-forming, non-motile, Gram-stain-positive, and coccus-shaped, while strain Marseille-Q7826 is non-spore-forming, motile, Gram-stain-variable, and curved rod-shaped. The genomic comparison of the Marseille-Q7072 and Marseille-Q7826 strains showed that all digital DNA-DNA hybridisation (dDDH) and mean orthologous nucleotide identity (OrthoANI) values were below published species thresholds (70% and 95-96%, respectively) with other closely related species with standing in nomenclature. Thus, we conclude that both strains are new bacterial species. Strain Marseille-Q7072 is a new member of the Bacillota phylum, for which the name Peptoniphilus genitalis sp. nov. is proposed, while the Marseille-Q7826 strain is a new member of the Actinomycetota phylum, for which the name Mobiluncus massiliensis sp. nov. is proposed.
Topics: Female; Humans; Mobiluncus; Bacteria; Clostridiales; Microbiota; DNA
PubMed: 38372813
DOI: 10.1007/s00284-023-03584-7 -
International Forum of Allergy &... Feb 2024Dysregulation of the airway microbiota is thought to contribute to airway inflammation in both chronic rhinosinusitis (CRS) and asthma. However, the relationship between...
BACKGROUND
Dysregulation of the airway microbiota is thought to contribute to airway inflammation in both chronic rhinosinusitis (CRS) and asthma. However, the relationship between the upper and lower airway microbiome remains unclear.
METHODS
Sinus and lung brushes were collected from 29 CRS participants undergoing sinus surgery. DNA was extracted and submitted for 16s rRNA microbiome sequencing. Alpha and beta diversity metrics, taxonomic composition, and differences between individual taxa were compared for paired sinus and bronchial samples.
RESULTS
Twenty-three out of 29 participants had sufficient samples for analysis. The mean (standard deviation) age was 51.59 (14.57) years, and 10 (44%) patients were female. Twelve (52%) patients had comorbid asthma. Sinus brushes had significantly higher alpha diversity indexes (Shannon and Faith) compared to bronchial brushes (p < 0.001). Beta diversity metrics were significantly different between the sinus and bronchial samples. Principal coordinate analysis showed no clustering of paired nasal and bronchial samples. Sinus brushes had significantly more Lawsonella, Corynebacterium, and Staphylococcus compared to bronchia brushes, while the latter were enriched in Tropheryma and Sphingomonas, among others (false discovery rate [FDR]-adjusted p < 0.01). Finally, CRS patients with comorbid asthma had significantly higher Pseudomonas and Peptoniphilus in sinus brushes and lower Prevotella in bronchial brushes when compared to non-asthmatics (FDR-adjusted p < 0.01).
CONCLUSION
The sinus and bronchial bacterial microbiomes differ in important ways. Our study suggests that migration of bacteria from the sinus into the lower airways is unlikely in patients with CRS.
PubMed: 38343306
DOI: 10.1002/alr.23335 -
Reproduction, Fertility, and Development Feb 2024Little is known about the microbial composition of stallion semen.
CONTEXT
Little is known about the microbial composition of stallion semen.
AIMS
To describe the microbiota detected in equine semen of healthy miniature pony stallions.
METHODS
Semen specimens were collected using a Missouri artificial vagina at a single time point. PacBio (Pacific Biosciences) genomic DNA sequencing of the 16S rRNA gene was performed on these specimens, following which next-generation microbiome bioinformatics platform QIIME2 was used to process fastq files and analyse the amplicon data. The data were categorised into genus, family, class, order and phylum.
KEY RESULTS
Firmicutes and Bacteroidetes phyla predominated (76%), followed by Proteobacteria (15%). Bacteroidales, Clostridiales and Cardiobacteriales predominated the microbial rank of order (86%). Class was mainly composed of Bacteroidia, Clostridia and Gammaproteobacteria (87%), while family was mainly composed of Porphyromonadaceae , Family_XI and Cardiobacteriaceae (62%). At the level of genus, 80% of the abundance was composed of seven genera, namely Porphyromonas, Suttonella, Peptoniphilus, Fastidiosipila, Ezakiella, Petrimonas and an unknown taxon.
CONCLUSIONS
The findings indicate that specific microbiota may be characteristic of healthy miniature pony stallions' semen with some inter-individual variations observed.
IMPLICATIONS
Larger equine studies involving fertile and infertile subjects could be informed by this study and could explore the relationship of the semen microbiome to male fertility.
Topics: Female; Male; Horses; Humans; Animals; Semen; RNA, Ribosomal, 16S; Microbiota; Fertility
PubMed: 38331564
DOI: 10.1071/RD23117 -
Dermatology (Basel, Switzerland) 2024Darier disease is a rare inherited disease with dominant skin manifestations including keratotic papules and plaques on sebaceous and flexural areas. Secondary infection...
INTRODUCTION
Darier disease is a rare inherited disease with dominant skin manifestations including keratotic papules and plaques on sebaceous and flexural areas. Secondary infection of skin lesions is common, and Staphylococcus aureus commonly colonizes these lesions. The aim of the study was to characterize the bacterial microbiome of cutaneous Darier lesions compared to normal-looking skin and disease severity.
METHODS
All patients with a history of Darier followed up at Emek Medical Center were invited to participate in the study. Patients that did not use antibiotics in the past month and signed informed consent had four skin sites sampled with swabs: scalp, chest, axilla, and palm. All samples were analyzed for bacterial microbiome using 16S rDNA sequencing.
RESULTS
Two hundred and eighty microbiome samples obtained from lesional and non-lesional skin of the scalp, chest, axilla, and palm of 42 Darier patients were included in the analysis. The most abundant bacterial genera across all skin sites were Propionibacterium, Corynebacterium, Paracoccus, Micrococcus, and Anaerococcus. Scalp and chest lesions featured a distinct microbiome configuration that was mainly driven by an overabundance of Staphylococci species. Patients with more severe disease exhibited microbiome alterations in the chest, axilla, and palm compared with patients with only mild disease, driven by Peptoniphilus and Moryella genera in scalp and palmar lesions, respectively.
CONCLUSION
Staphylococci were significantly associated with Darier lesions and drove Darier-associated dysbiosis. Severity of the disease was associated with two other bacterial genera. Whether these associations also hold a causative role and may serve as a therapeutic target remains to be determined and requires further investigation.
Topics: Humans; Darier Disease; Male; Female; Dysbiosis; Adult; Middle Aged; Microbiota; Axilla; Skin; Corynebacterium; Young Adult; Propionibacterium; Micrococcus; Severity of Illness Index; Hand; Thorax; Scalp; Aged; Adolescent
PubMed: 38330926
DOI: 10.1159/000537714 -
Journal of Gastroenterology Mar 2024Recent evidence suggests that the presence of microbiome within human pancreatic ductal adenocarcinoma (PDAC) tissue potentially influences cancer progression and...
BACKGROUND
Recent evidence suggests that the presence of microbiome within human pancreatic ductal adenocarcinoma (PDAC) tissue potentially influences cancer progression and prognosis. However, the significance of tumor-resident microbiome remains unclear. We aimed to elucidate the impact of intratumoral bacteria on the pathophysiology and prognosis of human PDAC.
METHODS
The presence of intratumoral bacteria was assessed in 162 surgically resected PDACs using quantitative polymerase chain reaction (qPCR) and in situ hybridization (ISH) targeting 16S rRNA. The intratumoral microbiome was explored by 16S metagenome sequencing using DNA extracted from formalin-fixed paraffin-embedded tissues. The profile of intratumoral bacteria was compared with clinical information, pathological findings including tumor-infiltrating T cells, tumor-associated macrophage, fibrosis, and alterations in four main driver genes (KRAS, TP53, CDKN2A/p16, SMAD4) in tumor genomes.
RESULTS
The presence of intratumoral bacteria was confirmed in 52 tumors (32%) using both qPCR and ISH. The 16S metagenome sequencing revealed characteristic bacterial profiles within these tumors, including phyla such as Proteobacteria and Firmicutes. Comparison of bacterial profiles between cases with good and poor prognosis revealed a significant positive correlation between a shorter survival time and the presence of anaerobic bacteria such as Bacteroides, Lactobacillus, and Peptoniphilus. The abundance of these bacteria was correlated with a decrease in the number of tumor-infiltrating T cells positive for CD4, CD8, and CD45RO.
CONCLUSIONS
Intratumoral infection of anaerobic bacteria such as Bacteroides, Lactobacillus, and Peptoniphilus is correlated with the suppressed anti-PDAC immunity and poor prognosis.
Topics: Humans; RNA, Ribosomal, 16S; Pancreatic Neoplasms; Carcinoma, Pancreatic Ductal; Prognosis; Microbiota
PubMed: 38242997
DOI: 10.1007/s00535-023-02069-5