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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 -
MSystems Feb 2023With growing awareness that what we put in and on our bodies affects our health and wellbeing, little is still known about the impact of textiles on the human skin....
With growing awareness that what we put in and on our bodies affects our health and wellbeing, little is still known about the impact of textiles on the human skin. Athletic wear often uses silver threading to improve hygiene, but little is known about its effect on the body's largest organ. In this study, we investigated the impact of such clothing on the skin's chemistry and microbiome. Samples were collected from different body sites of a dozen volunteers over the course of 12 weeks. The changes induced by the antibacterial clothing were specific for individuals, but more so defined by gender and body site. Unexpectedly, the microbial biomass on skin increased in the majority of the volunteers when wearing silver-threaded T-shirts. Although the most abundant taxa remained unaffected, silver caused an increase in diversity and richness of low-abundant bacteria and a decrease in chemical diversity. Both effects were mainly observed for women. The hallmark of the induced changes was an increase in the abundance of various monounsaturated fatty acids (MUFAs), especially in the upper back. Several microbe-metabolite associations were uncovered, including , detected in the upper back area, which was correlated with the distribution of MUFAs, and spp. found in the underarms, which were associated with a series of different bile acids. Overall, these findings point to a notable impact of the silver-threaded material on the skin microbiome and chemistry. We observed that relatively subtle changes in the microbiome result in pronounced shifts in molecular composition. The impact of silver-threaded material on human skin chemistry and microbiome is largely unknown. Although the most abundant taxa remained unaffected, silver caused an increase in diversity and richness of low-abundant bacteria and a decrease in chemical diversity. The major change was an increase in the abundance of various monounsaturated fatty acids that were also correlated with . Additionally, spp., found in the underarms, were associated with different bile acids in the armpit samples. Overall, the impact of the silver-threaded clothing was gender and body site specific.
Topics: Humans; Female; Silver; Clothing; Skin; Textiles; Microbiota; Bacteria; Propionibacteriaceae
PubMed: 36722970
DOI: 10.1128/msystems.00922-22 -
Digestive Diseases and Sciences Nov 2020Acute pancreatitis (AP) has a wide spectrum of severity and can be associated with considerable morbidity and mortality. Whether gut microbiota dysbiosis is associated...
BACKGROUND
Acute pancreatitis (AP) has a wide spectrum of severity and can be associated with considerable morbidity and mortality. Whether gut microbiota dysbiosis is associated with AP severity remains obscure.
AIMS
We aim to investigate the differences in the alterations of gut microbiota in different grades of AP severity.
METHODS
We collected clinical information and rectal swab samples from 80 individuals. The gut microbiota was tested by 16S rRNA gene sequencing, gut microbiota species composition analysis, difference analysis, random forest model prediction analysis, and gut microbiota species correlation network analysis.
RESULTS
There was a different microbiota profile in different severity grades. Bacteroides, Escherichis-Shigella, and Enterococcus were dominant species in mild, moderately severe, and severe AP, respectively. Finegoldia was the most significantly increased and Blautia the most decreased species in mild AP. Anaerococcus was the most significantly increased and Eubacterium hallii the most decreased species in moderately severe AP. Enterococcus was the most significantly increased and Eubacterium hallii the most decreased species in severe AP. Finegoldia, Eubacterium_hallii, and Lachnospiraceae were potential diagnostic biomarkers for mild AP and Eubacterium_hallii and Anaerococcus for moderately severe AP. There was a positive interaction between Firmicutes and Bacteroidetes in mild AP.
CONCLUSIONS
The disturbed gut microbiota is different among grades of AP, suggesting their potential role in the progression of disease severity. There was a different microbiota profile in different severity grades. Bacteroides, Escherichis-Shigella, and Enterococcus were dominant gut microbiota species in MAP, MSAP, and SAP, respectively. Finegoldia was the most significantly increased and Blautia the most decreased gut microbiota species in MAP. Anaerococcus was the most significantly increased and Eubacterium hallii the most decreased species in MSAP. Enterococcus was the most significantly increased and Eubacterium hallii the most decreased species in SAP. Finegoldia, Eubacterium_hallii, and Lachnospiraceae were potential diagnostic biomarkers for MAP and Eubacterium_hallii and Anaerococcus for MSAP. There was a positive interaction between Firmicutes and Bacteroidetes in MAP.
Topics: Adult; Dysbiosis; Feces; Female; Gastrointestinal Microbiome; Humans; Male; Middle Aged; Pancreatitis; Severity of Illness Index
PubMed: 32076933
DOI: 10.1007/s10620-020-06061-4 -
New Microbes and New Infections May 2020sp. nov. strain Marseille-P3557 is a new species isolated from a stool of a Nigerian child with marasmus. The genome of Marseille-P3557 was 2 130 060 bp long (35.4%...
sp. nov. strain Marseille-P3557 is a new species isolated from a stool of a Nigerian child with marasmus. The genome of Marseille-P3557 was 2 130 060 bp long (35.4% G + C content). The closest species based on 16S ribosomal RNA sequence was strain 20548, with 97.6% sequence similarity. Considering phenotypic features and comparative genome studies, we propose the strain Marseille-P3557 as the type strain of sp. nov., a new species within the genus .
PubMed: 32211195
DOI: 10.1016/j.nmni.2020.100655 -
New Microbes and New Infections Sep 2020Using the culturomics method, two strains were isolated, identified and characterized following the taxonogenomics concept. sp. nov. strain Marseille-P4512 (=...
Using the culturomics method, two strains were isolated, identified and characterized following the taxonogenomics concept. sp. nov. strain Marseille-P4512 (= CSURP4512) and sp. nov. strain Marseille-P4857 (= CSURP4857) were isolated from the vagina of a French woman. The phylogenic tree, phenotypic criteria and genomic analysis described here clearly show that these two bacteria are different from previously known bacterial species with standing in nomenclature and new members of phylum.
PubMed: 32774867
DOI: 10.1016/j.nmni.2020.100706 -
MedRxiv : the Preprint Server For... Feb 2023The nasal passages harbor both commensal and pathogenic bacteria. In this study, we sought to characterize the anterior nasal microbiota in PD patients using 16S rRNA...
RATIONALE & OBJECTIVE
The nasal passages harbor both commensal and pathogenic bacteria. In this study, we sought to characterize the anterior nasal microbiota in PD patients using 16S rRNA gene sequencing.
STUDY DESIGN
Cross-sectional.
SETTING & PARTICIPANTS
We recruited 32 PD patients, 37 kidney transplant (KTx) recipients, 22 living donor/healthy control (HC) participants and collected anterior nasal swabs at a single point in time.
PREDICTORS
We performed 16S rRNA gene sequencing of the V4-V5 hypervariable region to determine the nasal microbiota.
OUTCOMES
Nasal microbiota profiles were determined at the genus level as well as the amplicon sequencing variant level.
ANALYTICAL APPROACH
We compared nasal abundance of common genera among the 3 groups using Wilcoxon rank sum testing with Benjamini-Hochberg adjustment. DESeq2 was also utilized to compare the groups at the ASV 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.
LIMITATIONS
16S RNA gene sequencing provides taxonomic information to the genus level.
CONCLUSIONS
We find a distinct nasal microbiota signature in PD patients compared to 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.
PubMed: 36865147
DOI: 10.1101/2023.02.23.23286379 -
Frontiers in Immunology 2023Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects gut luminal cells through the angiotensin-converting enzyme-2 receptor and disrupts the gut...
OBJECTIVES
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects gut luminal cells through the angiotensin-converting enzyme-2 receptor and disrupts the gut microbiome. We investigated whether the gut microbiome in the early stage of SARS-CoV-2 infection was associated with the prognosis of coronavirus disease (COVID-19).
METHODS
Thirty COVID-19 patients and 16 healthy controls were prospectively enrolled. Blood and stool samples and clinical details were collected on days 0 (enrollment), 7, 14, and 28. Participants were categorized into four groups by their clinical course.
RESULTS
Gut microbiota composition varied during the clinical course of COVID-19 and was closely associated with cytokine levels (=0.003). A high abundance of the genus (linear discriminant analysis [LDA] effect size: 3.97856, =0.004), species (LDA effect size: 4.00551, =0.020), and (LDA effect size: 4.00885, =0.007) was associated with a good prognosis. Starch, sucrose, and galactose metabolism was highly activated in the gut microbiota of the poor prognosis group. Glucose-lowering diets, including whole grains, were positively correlated with a good prognosis.
CONCLUSION
Gut microbiota may mediate the prognosis of COVID-19 by regulating cytokine responses and controlling glucose metabolism, which is implicated in the host immune response to SARS-CoV-2.
Topics: Humans; COVID-19; Gastrointestinal Microbiome; SARS-CoV-2; Cytokines; Prognosis; Disease Progression
PubMed: 37051240
DOI: 10.3389/fimmu.2023.1079277 -
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 -
Frontiers in Cell and Developmental... 2022The development of new biomarkers for human male infertility is crucial to improve the diagnosis and the prognosis of this disease. Recently, seminal microbiota was...
The development of new biomarkers for human male infertility is crucial to improve the diagnosis and the prognosis of this disease. Recently, seminal microbiota was shown to be related to sperm quality parameters, suggesting an effect in human fertility and postulating it as a biomarker candidate. However, its relationship to sperm DNA integrity has not been studied yet. The aim of the present study is to characterize the seminal microbiota of a western Mediterranean population and to evaluate its relationship to sperm chromatin integrity parameters, and oxidative stress. For that purpose, 14 samples from sperm donors and 42 samples from infertile idiopathic patients were obtained and were analyzed to assess the composition of the microbiota through full-length gene sequencing (Illumina MiSeq platform). Microbial diversity and relative abundances were compared to classic sperm quality parameters (macroscopic semen parameters, motility, morphology and concentration), chromatin integrity (global DNA damage, double-stranded DNA breaks and DNA protamination status) and oxidative stress levels (oxidation-reduction potential). The seminal microbiota observed of these samples belonged to the phyla , , and . The most abundant genera were , , , , , , , , , and . To our knowledge, this is the first detection of genus in seminal samples. Two clusters of microbial profiles were built based on a clustering analysis, and specific genera were found with different frequencies in relation to seminal quality defects. The abundances of several bacteria negatively correlate with the sperm global DNA fragmentation, most notably , and . The latter two were also associated with higher sperm motility and additionally with lower oxidative-reduction potential. , and correlated with reduced chromatin protamination status and increased double-stranded DNA fragmentation. These effects on DNA integrity coincide in many cases with the metabolism or enzymatic activities of these genera. Significant differences between fertile and infertile men were found in the relative presence of the family and the , and genera, which supports its possible involvement in male fertility. Our findings sustain the hypothesis that the seminal microbiome has an effect on male fertility.
PubMed: 35837328
DOI: 10.3389/fcell.2022.937157 -
The Journal of Allergy and Clinical... Apr 2021Little is known about the relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the respiratory virus responsible for the ongoing...
BACKGROUND
Little is known about the relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the respiratory virus responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic, and the upper respiratory tract (URT) microbiome.
OBJECTIVE
We sought to compare the URT microbiome between SARS-CoV-2-infected and -uninfected adults and to examine the association of SARS-CoV-2 viral load with the URT microbiome during COVID-19.
METHODS
We characterized the URT microbiome using 16S ribosomal RNA sequencing in 59 adults (38 with confirmed, symptomatic, mild to moderate COVID-19 and 21 asymptomatic, uninfected controls). In those with COVID-19, we measured SARS-CoV-2 viral load using quantitative reverse transcription PCR. We then examined the association of SARS-CoV-2 infection status and its viral load with the ⍺-diversity, β-diversity, and abundance of bacterial taxa of the URT microbiome. Our main models were all adjusted for age and sex.
RESULTS
The observed species index was significantly higher in SARS-CoV-2-infected than in -uninfected adults (β linear regression coefficient = 7.53; 95% CI, 0.17-14.89; P = .045). In differential abundance testing, 9 amplicon sequence variants were significantly different in both of our comparisons, with Peptoniphilus lacrimalis, Campylobacter hominis, Prevotella 9 copri, and an Anaerococcus unclassified amplicon sequence variant being more abundant in those with SARS-CoV-2 infection and in those with high viral load during COVID-19, whereas Corynebacterium unclassified, Staphylococcus haemolyticus, Prevotella disiens, and 2 Corynebacterium_1 unclassified amplicon sequence variants were more abundant in those without SARS-CoV-2 infection and in those with low viral load during COVID-19.
CONCLUSIONS
Our findings suggest complex associations between SARS-CoV-2 and the URT microbiome in adults. Future studies are needed to examine how these viral-bacterial interactions can impact the clinical progression, severity, and recovery of COVID-19.
Topics: Adult; Biodiversity; COVID-19; Case-Control Studies; Female; Host Microbial Interactions; Humans; Male; Microbiota; Middle Aged; Pandemics; RNA, Ribosomal, 16S; Respiratory System; SARS-CoV-2; Species Specificity; Viral Load
PubMed: 33577896
DOI: 10.1016/j.jaci.2021.02.001