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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 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 -
Kidney360 Oct 2023, , , and are the most common genera in the anterior nares. The nasal abundance of is inversely correlated with the nasal abundance of . Peritoneal dialysis patients...
KEY POINTS
, , , and are the most common genera in the anterior nares. The nasal abundance of is inversely correlated with the nasal abundance of . Peritoneal dialysis patients have a distinctly diverse representation of and in their anterior nares.
BACKGROUND
The nasal passages harbor both commensal and pathogenic bacteria that can be associated with infectious complications. The nasal microbiome in peritoneal dialysis (PD) patients, however, has not been well characterized. In this study, we sought to characterize the anterior nasal microbiota in PD patients and assess its association with PD peritonitis.
METHODS
In this study, we recruited 32 PD patients, 37 kidney transplant (KTx) recipients, and 22 living donor/healthy control (HC) participants and collected their anterior nasal swabs at a single point in time. We followed the PD patients for future development of peritonitis. We performed 16S ribosomal RNA (rRNA) gene sequencing of the V4–V5 hypervariable region to determine the nasal microbiota. We compared nasal abundance of common genera among the three groups using Wilcoxon rank-sum test with Benjamini–Hochberg adjustment. DESeq2 was also used to compare the groups at the amplicon sequence variant levels.
RESULTS
In the entire cohort, the most abundant genera in the nasal microbiota included , , , and . Correlational analyses revealed a significant inverse relationship between the nasal abundance of and that of . PD patients have a higher nasal abundance of than KTx recipients and HC participants. PD patients have a more diverse representation of and than KTx recipients and HC participants. PD patients who concurrently have or who developed future peritonitis had a numerically higher nasal abundance of than PD patients who did not develop peritonitis.
CONCLUSIONS
We find a distinct nasal microbiota signature in PD patients compared with KTx recipients and HC participants. Given the potential relationship between the nasal pathogenic bacteria and infectious complications, further studies are needed to define the nasal microbiota associated with these infectious complications and to conduct studies on the manipulation of the nasal microbiota to prevent such complications.
Topics: Humans; Nose; Peritoneal Dialysis; Microbiota
PubMed: 37642987
DOI: 10.34067/KID.0000000000000249 -
Germs Sep 2023The annual incidence of infective endocarditis (IE) is 3-9 cases per 100000 in developed countries and most cases are due to staphylococci and streptococci. IE due to...
INTRODUCTION
The annual incidence of infective endocarditis (IE) is 3-9 cases per 100000 in developed countries and most cases are due to staphylococci and streptococci. IE due to Gram-positive anaerobic cocci (GPAC) is very rare.
CASE REPORT
We present a case of a 38-year-old female with bacteremia and infective endocarditis of the native mitral valve. She presented with fever, chills, and abdominal pain. A computed tomographic scan of the abdomen showed splenic abscesses. Blood cultures and broad-range PCR from the splenic abscess sample were negative. Transthoracic echocardiography showed a mobile filamentous structure on the atrial side of the anterior mitral leaflet which was suggestive for infective endocarditis. Karius test (cell-free microbial DNA testing) showed Gram-positive anaerobic cocci She was successfully treated with antibiotics.
CONCLUSIONS
In cases of infection with fastidious organisms like GPACs, the use of next-generation sequencing (NGS) can allow the correct identification of culprit pathogens and streamlined treatment.
PubMed: 38146378
DOI: 10.18683/germs.2023.1396 -
Nature Medicine May 2024Despite substantial progress in cancer microbiome research, recognized confounders and advances in absolute microbiome quantification remain underused; this raises...
Despite substantial progress in cancer microbiome research, recognized confounders and advances in absolute microbiome quantification remain underused; this raises concerns regarding potential spurious associations. Here we study the fecal microbiota of 589 patients at different colorectal cancer (CRC) stages and compare observations with up to 15 published studies (4,439 patients and controls total). Using quantitative microbiome profiling based on 16S ribosomal RNA amplicon sequencing, combined with rigorous confounder control, we identified transit time, fecal calprotectin (intestinal inflammation) and body mass index as primary microbial covariates, superseding variance explained by CRC diagnostic groups. Well-established microbiome CRC targets, such as Fusobacterium nucleatum, did not significantly associate with CRC diagnostic groups (healthy, adenoma and carcinoma) when controlling for these covariates. In contrast, the associations of Anaerococcus vaginalis, Dialister pneumosintes, Parvimonas micra, Peptostreptococcus anaerobius, Porphyromonas asaccharolytica and Prevotella intermedia remained robust, highlighting their future target potential. Finally, control individuals (age 22-80 years, mean 57.7 years, standard deviation 11.3) meeting criteria for colonoscopy (for example, through a positive fecal immunochemical test) but without colonic lesions are enriched for the dysbiotic Bacteroides2 enterotype, emphasizing uncertainties in defining healthy controls in cancer microbiome research. Together, these results indicate the importance of quantitative microbiome profiling and covariate control for biomarker identification in CRC microbiome studies.
Topics: Humans; Colorectal Neoplasms; Middle Aged; Feces; Female; Aged; Male; RNA, Ribosomal, 16S; Adult; Gastrointestinal Microbiome; Aged, 80 and over; Young Adult; Microbiota; Leukocyte L1 Antigen Complex
PubMed: 38689063
DOI: 10.1038/s41591-024-02963-2 -
International Wound Journal Nov 2023Identifying the microbiome within chronic diabetic foot ulcers is essential if effective antimicrobial therapies are to be administered. Using culture and 16S rRNA gene...
Identifying the microbiome within chronic diabetic foot ulcers is essential if effective antimicrobial therapies are to be administered. Using culture and 16S rRNA gene sequencing, the aim of this study was to compare the microbiome of paired tissue scraping samples with swab samples, collected from participants during attendance at a high-risk foot clinic. The mean richness of cultured swab and tissue scraping samples was consistent, with anaerobes infrequently isolated from both sample types. Comparing percentage frequencies of detection of selected genera of known and potential pathogens namely Staphylococcus, Streptococcus, Enterococcus, Corynebacterium, Enterobacteriaceae and Pseudomonas from cultured and sequenced swab and tissue scrapings indicated that both collection methods captured varying percentages of all the selected genera. The mean abundance of sequenced samples was not significantly different between swabs and tissue scrapings. The mean richness or number of distinct operational taxonomic units (OTUs) and Shannon's H diversity index were not significantly different between the two collection methods. The mean relative abundance of the selected genera of known and potential pathogens, including anaerobes Anaerococcus and Finegoldia, was higher in swabs compared with tissue scrapings and significantly so in Staphylococcus and Pseudomonas genera. Multivariate analyses confirmed no significant differences between the bacterial community compositions of the paired samples. These results suggest that tissue scrapings and swabs can effectively capture the microbiome of chronic DFUs using culture and 16S rRNA gene sequencing.
Topics: Humans; Diabetic Foot; RNA, Ribosomal, 16S; Bacteria; Microbiota; Foot; Staphylococcus; Pseudomonas; Diabetes Mellitus
PubMed: 37501084
DOI: 10.1111/iwj.14267 -
Journal of Translational Medicine Apr 2024The aim of this study was to assess the microbial variations and biomarkers in the vaginal and oral environments of patients with human papillomavirus (HPV) and cervical...
BACKGROUND
The aim of this study was to assess the microbial variations and biomarkers in the vaginal and oral environments of patients with human papillomavirus (HPV) and cervical cancer (CC) and to develop novel prediction models.
MATERIALS AND METHODS
This study included 164 samples collected from both the vaginal tract and oral subgingival plaque of 82 women. The participants were divided into four distinct groups based on their vaginal and oral samples: the control group (Z/KZ, n = 22), abortion group (AB/KAB, n = 17), HPV-infected group (HP/KHP, n = 21), and cervical cancer group (CC/KCC, n = 22). Microbiota analysis was conducted using full-length 16S rDNA gene sequencing with the PacBio platform.
RESULTS
The vaginal bacterial community in the Z and AB groups exhibited a relatively simple structure predominantly dominated by Lactobacillus. However, CC group shows high abundances of anaerobic bacteria and alpha diversity. Biomarkers such as Bacteroides, Mycoplasma, Bacillus, Dialister, Porphyromonas, Anaerococcus, and Prevotella were identified as indicators of CC. Correlations were established between elevated blood C-reactive protein (CRP) levels and local/systemic inflammation, pregnancy, childbirth, and abortion, which contribute to unevenness in the vaginal microenvironment. The altered microbial diversity in the CC group was confirmed by amino acid metabolism. Oral microbial diversity exhibited an inverse pattern to that of the vaginal microbiome, indicating a unique relationship. The microbial diversity of the KCC group was significantly lower than that of the KZ group, indicating a link between oral health and cancer development. Several microbes, including Fusobacterium, Campylobacter, Capnocytophaga, Veillonella, Streptococcus, Lachnoanaerobaculum, Propionibacterium, Prevotella, Lactobacillus, and Neisseria, were identified as CC biomarkers. Moreover, periodontal pathogens were associated with blood CRP levels and oral hygiene conditions. Elevated oral microbial amino acid metabolism in the CC group was closely linked to the presence of pathogens. Positive correlations indicated a synergistic relationship between vaginal and oral bacteria.
CONCLUSION
HPV infection and CC impact both the vaginal and oral microenvironments, affecting systemic metabolism and the synergy between bacteria. This suggests that the use of oral flora markers is a potential screening tool for the diagnosis of CC.
Topics: Humans; Female; Microbiota; Vagina; Uterine Cervical Neoplasms; Papillomavirus Infections; Mouth; Adult; Middle Aged; Papillomaviridae; RNA, Ribosomal, 16S; Human Papillomavirus Viruses
PubMed: 38685022
DOI: 10.1186/s12967-024-05124-8 -
PloS One 2024Multiple inflammatory mechanisms dynamically interact in the development of chronic rhinosinusitis with nasal polyps (CRSwNP). Disruption of the relationship between...
OBJECTIVE
Multiple inflammatory mechanisms dynamically interact in the development of chronic rhinosinusitis with nasal polyps (CRSwNP). Disruption of the relationship between host and environmental factors on the mucosal surface leads to the development of inflammation. Microorganisms constitute the most important part of environmental factors.
METHODS
28 volunteers (18 CRSwNP patients and 10 healthy individuals) were included in the study. Eight patients were recurrent nasal polyposis cases, and the remaining were primary cases. Swab samples were taken from the middle meatus under endoscopic examination from all participants. After DNA extraction, a library was created with the Swift Amplicon 16S + ITS kit and sequenced with Illumina Miseq. Sequence analysis was performed using QIIME, UNITE v8.2 database for ITS and Silva v138 for 16S rRNA.
RESULTS
The predominant bacteria in all groups were Firmicutes, Proteobacteria, Actinobacteria as phyla and Staphylococcus, Corynebacterium, Sphingomonas as genera. Comparison of bacterial communities of CRSwNP patients and control group highlighted Corynebacterium, as the differentiating taxa for control group and Streptococcus, Moraxella, Rothia, Micrococcus, Gemella, and Prevotella for CRSwNP patients. The predominant fungal genus in all groups was Malassezia. Staphylococcus; showed a statistically significant negative correlation with Dolosigranulum. Corynebacterium had a positive correlation with Anaerococcus, and a negative correlation with Neisseria, Prevotella, Fusobacterium and Peptostreptococcus.
CONCLUSION
Nasal microbiome of CRSwNP patients shows greater inter-individual variation than the control group. Corynebacterium is less abundant in patients with CRSwNP compared to the control group. Malassezia is the predominant fungus in the nasal cavity and paranasal sinuses and correlates positively with the abundance of Corynebacterium.
Topics: Humans; Sinusitis; Nasal Polyps; Female; Male; Adult; Chronic Disease; Middle Aged; Bacteria; Rhinitis; Fungi; RNA, Ribosomal, 16S; Microbiota; Case-Control Studies; Rhinosinusitis
PubMed: 38820284
DOI: 10.1371/journal.pone.0304634 -
Gut Pathogens Dec 2023Critical illness and care within the intensive care unit (ICU) leads to profound changes in the composition of the gut microbiome. The impact of such changes on the...
BACKGROUND
Critical illness and care within the intensive care unit (ICU) leads to profound changes in the composition of the gut microbiome. The impact of such changes on the patients and their subsequent disease course remains uncertain. We hypothesized that specific changes in the gut microbiome would be more harmful than others, leading to increased mortality in critically ill patients.
METHODS
This was a prospective cohort study of critically ill adults in the ICU. We obtained rectal swabs from 52 patients and assessed the composition the gut microbiome using 16 S rRNA gene sequencing. We followed patients throughout their ICU course and evaluated their mortality rate at 28 days following admission to the ICU. We used selbal, a machine learning method, to identify the balance of microbial taxa most closely associated with 28-day mortality.
RESULTS
We found that a proportional ratio of four taxa could be used to distinguish patients with a higher risk of mortality from patients with a lower risk of mortality (p = .02). We named this binarized ratio our microbiome mortality index (MMI). Patients with a high MMI had a higher 28-day mortality compared to those with a low MMI (hazard ratio, 2.2, 95% confidence interval 1.1-4.3), and remained significant after adjustment for other ICU mortality predictors, including the presence of the acute respiratory distress syndrome (ARDS) and the Acute Physiology and Chronic Health Evaluation (APACHE II) score (hazard ratio, 2.5, 95% confidence interval 1.4-4.7). High mortality was driven by taxa from the Anaerococcus (genus) and Enterobacteriaceae (family), while lower mortality was driven by Parasutterella and Campylobacter (genera).
CONCLUSIONS
Dysbiosis in the gut of critically ill patients is an independent risk factor for increased mortality at 28 days after adjustment for clinically significant confounders. Gut dysbiosis may represent a potential therapeutic target for future ICU interventions.
PubMed: 38115015
DOI: 10.1186/s13099-023-00567-8 -
International Journal of Food Science 2024Indonesia has abundant traditional fermented food with various lactic acid bacteria (LAB), which can be developed into probiotics for pharmaceutical and functional food...
Indonesia has abundant traditional fermented food with various lactic acid bacteria (LAB), which can be developed into probiotics for pharmaceutical and functional food and feed products. This research is aimed at (1) obtaining and identifying LAB isolates and (2) studying the microbiome (bacterial diversity and abundance) of spontaneously-fermented traditional foods of Kalimantan Island, Cincalok, Tempoyak, and Mandai. To obtain LAB isolates, food samples were serially diluted and inoculated on MRS agar that contained 1% CaCO (MRSA). Isolates forming clear zones were purified and identified by DNA barcoding. The microbiome was studied using genomic-sequencing techniques and analysed for taxonomic composition. Seven pure isolates were obtained from Cincalok, two Tempoyak, and one Mandai. DNA barcoding revealed that the Cincalok seven isolates were (strain HSP-S16), (FSB201), , (SS1995), (S11-6), (C01), and (P3.1); two from Tempoyak, (E1D3BL1) and (UMCC-2996); and one from Mandai, (XAAS.x13; non-LAB). The , , , , and belong to LAB. The from Cincalok and non-LAB in these three fermented foods were the first documented report. The microbiome revealed the dominance of phyla in the fermented foods, with 93% in Cincalok, 89.94% in Tempoyak, and 60.32% in Mandai. On the genus level, Cincalok was dominated by 40.33%, 23.29%, 9.27%, and 6.84%. Meanwhile, Tempoyak was dominated only by 89.94%. Mandai were dominated by 31.97%, 17.14%, 16.85%, 15.15%, and 6.2%. However, Mandai's microbiome LAB was not culturable/isolated on MRSA. The plausibility is that those unculturable LAB require coculturing with other bacteria and additional media components to grow on MRSA. This study is the first report regarding the microbiome of Cincalok, Tempoyak, and Mandai, along with their culturable LAB isolates.
PubMed: 38715571
DOI: 10.1155/2024/6589766