The clinical importance of microbiomes to the chronicity of wounds is widely appreciated, yet little is understood about patient-specific processes shaping wound microbiome composition. Here, a ...two-cohort microbiome-genome wide association study is presented through which patient genomic loci associated with chronic wound microbiome diversity were identified. Further investigation revealed that alternative TLN2 and ZNF521 genotypes explained significant inter-patient variation in relative abundance of two key pathogens, Pseudomonas aeruginosa and Staphylococcus epidermidis. Wound diversity was lowest in Pseudomonas aeruginosa infected wounds, and decreasing wound diversity had a significant negative linear relationship with healing rate. In addition to microbiome characteristics, age, diabetic status, and genetic ancestry all significantly influenced healing. Using structural equation modeling to identify common variance among SNPs, six loci were sufficient to explain 53% of variation in wound microbiome diversity, which was a 10% increase over traditional multiple regression. Focusing on TLN2, genotype at rs8031916 explained expression differences of alternative transcripts that differ in inclusion of important focal adhesion binding domains. Such differences are hypothesized to relate to wound microbiomes and healing through effects on bacterial exploitation of focal adhesions and/or cellular migration. Related, other associated loci were functionally enriched, often with roles in cytoskeletal dynamics. This study, being the first to identify patient genetic determinants for wound microbiomes and healing, implicates genetic variation determining cellular adhesion phenotypes as important drivers of infection type. The identification of predictive biomarkers for chronic wound microbiomes may serve as risk factors and guide treatment by informing patient-specific tendencies of infection.
Chronic wound infections are increasingly recognized to be dynamic and polymicrobial in nature, necessitating the development of wound models which reflect the complexities of infection in a ...non-healing wound. Wound slough isolated from human chronic wounds and transferred to mice was recently shown to create polymicrobial infection in mice, and there is potential this tool may be improved by cryogenic preservation. The purpose of this study was to investigate the application of cryogenic preservation to transferring polymicrobial communities, specifically by quantifying the effects of cryopreservation and wound microbiome transplantation. Slough from an established murine polymicrobial surgical excision model and five patients were subjected to three preservation strategies: refrigeration until infection, freezing in liquid nitrogen, or freezing in liquid nitrogen with glycerol solution prior to infection in individual mice. Four days following inoculation onto mice, wound microbiota were quantified using either culture isolation or by 16s rRNA gene community profiling and quantitative PCR. Cryogenic preservation did not significantly reduce bacterial viability. Reestablished microbial communities were significantly associated with patient of origin as well as host context (i.e., originally preserved from a patient versus mouse infection). Whereas preservation treatment did not significantly shape community composition, the transfers of microbiomes from human to mouse were characterized by reduced diversity and compositional changes. These findings indicated that changes should be expected to occur to community structure after colonization, and that compositional change is likely due to the rapid change in infection context as opposed to preservation strategy. Furthermore, species that were present in higher relative abundance in wound inoculate were more likely to colonize subsequent wounds, and wound inoculate with higher bacterial load established wound communities that were more compositionally similar. Results inform expectations for the complementation of chronic wound in vivo modeling with cryogenic preservation archives.
Background
Information regarding the microbiome in sinusitis using genetic sequencing is lacking and more‐in‐depth understanding of the microbiome could improve antimicrobial selection and treatment ...outcomes for cases of primary sinusitis.
Objectives
To describe sinus microbiota in samples from horses with sinusitis and compare microbiota and the presence of antimicrobial resistance genes between primary, dental‐related and other secondary causes of sinusitis.
Study design
Retrospective case series.
Methods
Records of equine sinusitis from 2017 to 2021 were reviewed and historical microbial amplicon sequence data were obtained from clinical diagnostic testing of sinus secretions. Following bioinformatic processing of bacterial and fungal sequence data, the sinus microbiota and importance of sinusitis aetiology among other factors were investigated from the perspectives of alpha diversity (e.g., number of operational taxonomic units OTUs, Hill1 Diversity), beta diversity, and differentially abundant taxa. Quantitative PCR allowed for comparisons of estimated bacterial abundance and detection rate of common antibiotic resistance‐associated genes. In a smaller subset, longitudinal analysis was performed to evaluate similarity in samples over time.
Results
Of 81 samples analysed from 70 horses, the bacterial microbiome was characterised in 66, and fungal in five. Only sinusitis aetiology was shown to significantly influence microbiome diversity and composition (p < 0.05). Dental‐related sinusitis (n = 44) was associated with a significantly higher proportion of obligate anaerobic bacteria, whereas primary sinusitis (n = 12) and other (n = 10) groups were associated with fewer bacteria and higher proportions of facultative anaerobic and aerobic genera. Antimicrobial resistance genes and fungal components were exclusively identified in dental‐related sinusitis.
Main limitations
Retrospective nature, incomplete prior antimicrobial administration data.
Conclusions
Molecular characterisation in sinusitis identifies microbial species which may be difficult to isolate via culture, and microbiome profiling can differentiate sinusitis aetiology, which may inform further treatment, including antimicrobial therapy.
Zusammenfassung
Hintergrund
Es fehlen Informationen über das Mikrobiom bei Sinusitis, die durch genetische Sequenzierung gewonnen wurden, und ein tieferes Verständnis des Mikrobioms könnte die Auswahl antimikrobieller Mittel und die Behandlungsergebnisse bei primärer Sinusitis verbessern.
Ziele
Beschreibung der Sinus‐Mikrobiota in Proben von Pferden mit Sinusitis und Vergleich der Mikrobiota und des Vorhandenseins antimikrobieller Resistenzgene zwischen primären, zahnbedingten und anderen sekundären Ursachen der Sinusitis.
Studiendesign
Retrospektive Betrachtung.
Methoden
Aufzeichnungen über Sinusitis bei Pferden aus den Jahren 2017–2021 wurden überprüft und historische mikrobielle Amplikon‐Sequenzdaten aus klinischen diagnostischen Tests von Sinus‐Sekreten gewonnen. Nach der bioinformatischen Verarbeitung von Bakterien‐ und Pilzsequenzdaten wurden die Mikrobiota der Nasennebenhöhlen und die Bedeutung der Ätiologie der Sinusitis unter anderem unter dem Gesichtspunkt der Alpha‐Diversität (z. B. Anzahl der operativen taxonomischen Einheiten OTUs, Hill1‐Diversität), der Beta‐Diversität und der unterschiedlich häufigen Taxa untersucht. Die quantitative PCR ermöglichte einen Vergleich der geschätzten Bakterienhäufigkeit und der Nachweisrate von Genen, die mit der Antibiotikaresistenz in Verbindung stehen. Bei einer kleineren Untergruppe wurde eine Längsschnittanalyse durchgeführt, um die Ähnlichkeit der Proben im Laufe der Zeit zu bewerten.
Ergebnisse
Von 81 analysierten Proben von 70 Pferden wurde das bakterielle Mikrobiom von 66 und das Pilzmikrobiom von fünf Pferden charakterisiert. Nur die Ätiologie der Sinusitis zeigte einen signifikanten Einfluss auf die Diversität und Zusammensetzung des Mikrobioms (p < 0,05). Zahnbedingte Sinusitis (n = 44) war mit einem signifikant höheren Anteil an obligat anaeroben Bakterien verbunden, während primäre Sinusitis (n = 12) und andere (n = 10) Gruppen mit weniger Bakterien und einem höheren Anteil an fakultativ anaeroben und aeroben Gattungen verbunden waren. Antimikrobielle Resistenzgene und Pilzkomponenten wurden ausschließlich bei zahnbedingter Sinusitis identifiziert. Serielle Proben ähnelten den Ausgangsproben tendenziell mehr als Proben von anderen Pferden.
Hauptlimitationen
Retrospektiver Charakter, unvollständige Daten über die vorherige Verabreichung antimikrobieller Mittel.
Schlussfolgerungen
Durch die molekulare Charakterisierung der Sinusitis werden Mikrobenarten identifiziert, die sich möglicherweise nur schwer über eine Kultur isolieren lassen, und durch die Erstellung von Mikrobiomprofilen kann die Ätiologie der Sinusitis differenziert werden, was wiederum Aufschluss über die weitere Behandlung, einschließlich einer antimikrobiellen Therapie, geben kann.
There has recently been an explosion of studies implicating the human microbiome in playing a critical role in many disease and wellness states. The etiology of abnormal semen analysis (SA) ...parameters is not identified in 30% of cases; investigations involving the semen microbiome may bridge this gap. Here, we explore the relationship between the semen microbiome and alterations of sperm parameters. We recruited men presenting for fertility evaluation or vasectomy consultation with proven biological paternity. SA and next generation sequencing was performed. Differential abundance testing using Analysis of composition of Microbiota with Bias Correction (ANCOM-BC) was performed along with canonical correlational analysis for microbial community profiling. Men with abnormal (N = 27) sperm motility showed a higher abundance of Lactobacillus iners compared to those with normal (N = 46) sperm motility (mean proportion 9.4% versus 2.6%, p = 0.046). This relationship persisted on canonical correlational analysis (r = 0.392, p = 0.011). Men with abnormal sperm concentration (N = 20) showed a higher abundance of Pseudomonas stutzeri (2.1% versus 1.0%, p = 0.024) and Pseudomonas fluorescens (0.9% versus 0.7%, p = 0.010), but a lower abundance of Pseudomonas putida (0.5% versus 0.8%, p = 0.020), compared to those with normal sperm concentration (N = 53). Major limitations are related to study design (cross-sectional, observational). Our results suggest that a small group of microorganisms may play a critical role in observed perturbations of SA parameters. Some of these microbes, most notably Lactobacillus iners, have been described extensively within other, fertility-related, contexts, whereas for others, this is the first report where they have potentially been implicated. Advances in our understanding of the semen microbiome may contribute to potentially new therapeutic avenues for correcting impairments in sperm parameters and improving male fertility.
The microbiota gut-brain-axis is a bidirectional circuit that links the neural, endocrine, and immunological systems with gut microbial communities. The gut microbiome plays significant roles in ...human mind and behavior, specifically pain perception, learning capacity, memory, and temperament. Studies have shown that disruptions in the gut microbiota have been associated with substance use disorders. The interplay of gut microbiota in substance abuse disorders has not been elucidated; however, postmortem microbiome profiles may produce promising avenues for future forensic investigations. The goal of the current study was to determine gut microbiome composition in substance abuse disorder cases using transverse colon tissues of 21 drug overdose versus 19 non-overdose-related cases. We hypothesized that postmortem samples of the same cause of death will reveal similar microbial taxonomic relationships. We compared microbial diversity profiles using amplicon-based sequencing of the 16S rRNA gene V4 hypervariable region. The results demonstrated that the microbial abundance in younger-aged cases were found to have significantly more operational taxonomic units than older cases. Using weighted UniFrac analysis, the influence of substances in overdose cases was found to be a significant factor in determining microbiome similarity. The results also revealed that samples of the same cause of death cluster together, showing a high degree of similarity between samples and a low degree of similarity among samples of different causes of death. In conclusion, our examination of human transverse colon microflora in decomposing remains extends emerging literature on postmortem microbial communities, which will ultimately contribute to advanced knowledge of human putrefaction.
The microbiota gut-brain-axis is a bidirectional circuit that links the neural, endocrine, and immunological systems with gut microbial communities. The gut microbiome plays significant roles in ...human mind and behavior, specifically pain perception, learning capacity, memory, and temperament. Studies have shown that disruptions in the gut microbiota have been associated with substance use disorders. The interplay of gut microbiota in substance abuse disorders has not been elucidated; however, postmortem microbiome profiles may produce promising avenues for future forensic investigations. The goal of the current study was to determine gut microbiome composition in substance abuse disorder cases using transverse colon tissues of 21 drug overdose versus 19 non-overdose-related cases. We hypothesized that postmortem samples of the same cause of death will reveal similar microbial taxonomic relationships. We compared microbial diversity profiles using amplicon-based sequencing of the 16S rRNA gene V4 hypervariable region. The results demonstrated that the microbial abundance in younger-aged cases were found to have significantly more operational taxonomic units than older cases. Using weighted UniFrac analysis, the influence of substances in overdose cases was found to be a significant factor in determining microbiome similarity. The results also revealed that samples of the same cause of death cluster together, showing a high degree of similarity between samples and a low degree of similarity among samples of different causes of death. In conclusion, our examination of human transverse colon microflora in decomposing remains extends emerging literature on postmortem microbial communities, which will ultimately contribute to advanced knowledge of human putrefaction.
Polymicrobial bacterial infection is an important factor contributing to wound chronicity. Consequently, clinicians frequently adopt a biofilm‐based wound care approach, in which wounds are treated ...utilizing DNA sequencing information about microbial communities. While more successful than treatment not using community information, there is little information about temporal dynamics of wound communities and optimal approaches over the course of treatment. To characterize these dynamics, temporal analysis over three sampling points was conducted for 167 chronic wounds. Across sampling intervals, wound communities from the same patients changed in composition, and most commonly shared less than 50% of observed species. There was a significant relationship between community similarity and time between sampling. Classifying wounds into state types, we found that communities frequently transitioned from Pseudomonas or Staphylococcus dominated, into a highly variable state type. Although low abundance microbial species are typically disregarded due to uncertainty of biological importance, we found that 80% of wound microbiomes included common or dominant species at subsequent time points that were in low abundance in earlier samples. Moreover, these species were often those known to frequently infect wounds. Results document compositional shifts through the course of treatment and suggest that routine consideration of low abundance species may improve biofilm‐based wound care. Moreover, findings indicate that integrating ecological modeling to understand wound microbiome succession may lead to more informed therapy.
We investigated whether microbial DNA sequencing could improve the selection of antibiotics before kidney stone surgery in patients not known to have any bacteria in the urine on standard culture. We ...found that the use of microbe DNA to guide antibiotic choices decreased postoperative infection rate and may encourage individualized use of available antibiotics.
Next-generation sequencing (NGS) methods for microbial profiling have increased sensitivity to detect urinary pathogens.
To determine whether NGS microbial profiling can be used to guide antibiotic prophylaxis and reduce infection compared with the standard of care.
A prospective randomized controlled clinical trial of patients undergoing urologic stone interventions at an academic health center from December 2019 to January 2022 was conducted. Urine was collected at the preoperative visit for standard culture and intervention NGS diagnostics. Evaluable patients were culture negative, met 2-wk follow-up, and did not cancel surgery. Of 240 individuals (control = 121, intervention = 119), 83 control and 74 intervention patients were evaluable.
Microbial findings (paired quantitative polymerase chain reaction and NGS) were sent to an infectious disease pharmacist to recommend prophylactic antimicrobial regimen.
The primary outcome was postoperative urinary infection within the follow-up period (Fisher’s exact test). The primary outcome was analyzed by modified intent-to-treat (mITT) and per-protocol analyses. Secondary endpoints considered included positive culture concordance, antibiotic use, and adverse events. Additional post hoc analyses investigated factors contributing to infection (univariate logistic regression).
The intervention significantly reduced postsurgical urinary infection risk by 7.1% (–0.73%, 15%) compared with the standard of care in the mITT analysis (1.4% vs 8.4%, p = 0.045) or by 8.5% (0.88%, 16%) compared with the per-protocol analysis (0% vs 8.5%, p = 0.032). NGS-guided treatment altered the distribution of antibiotics used (p = 0.025), and antibiotics poorly matched with NGS findings were associated with increased infection odds (odds ratio OR = 5.9, p = 0.046). Women were at greater odds to develop infection (OR = 10, p = 0.03) and possessed differentiated microbial profiles (p < 0.001).
Urinary microbial NGS-guided antibiotic prophylaxis before endoscopic urologic stone lithotripsy improves antibiotic selection to reduce healthcare-associated urinary infections; however, treatment efficacy may be limited by the ability to adhere to the recommended protocol.
We investigated whether microbial DNA sequencing could improve the selection of antibiotics before kidney stone surgery in patients not known to have any bacteria in the urine on standard culture. We found that using microbe DNA to guide antibiotic choices decreased postoperative infection rate and may encourage individualized use of available antibiotics.
Although pre/pro/postbiotics have become more prevalent in dermatologic and cosmetic fields, the mode of action when topically applied is largely unknown. A multi-omic approach was applied to ...decipher the impact of the skincare products with pre/postbiotics on skin microbiome and metabolome.
Subjects with dry skin applied a body wash and body lotion with or without pre/postbiotics for 6 weeks. Skin hydration was measured at baseline, 3 and 6 weeks. Skin swabs were collected for 16S rRNA gene sequencing, metagenomics and metabolomics analysis.
Skin hydration significantly increased in both groups. The prebiotic group significantly reduced opportunistic pathogens, e.g.,
and
, and increased the commensals, e.g.,
,
. Bacterial sugar degradation pathways were enriched in the prebiotic group, while fatty acid biosynthesis pathways were reduced in control. The changes on skin metabolome profiles by the products were more prominent. The prebiotic group performed greater modulation on many clinically-relevant metabolites compared to control. Correlation analysis showed
and
positively correlated with skin hydration,
and
negatively correlated with the metabolites that are positively associated with skin hydration improvement.
This holistic study supported a hypothesis that the pre/postbiotics increased skin hydration through the modulation of skin microbiome, metabolic pathways and metabolome.
Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for treatment by identifying microbial ...and molecular biomarkers. This study investigates the skin microbiome and metabolome of healthy adult subjects and lesion (ADL) and non-lesion (ADNL) of AD patients by 16S rRNA gene sequencing and mass spectrometry, respectively. Samples from AD patients showed alterations in the diversity and composition of the skin microbiome, with ADL skin having the greatest divergence.
species, especially
, were significantly increased in AD patients. Metabolomic profiles were also different between the groups. Dipeptide derivatives are more abundant in ADL, which may be related to skin inflammation. Co-occurrence network analysis of the microbiome and metabolomics data revealed higher co-occurrence of metabolites and bacteria in healthy ADNL compared to ADL.
co-occurred with dipeptide derivatives in ADL, while phytosphingosine-derived compounds showed co-occurrences with commensal bacteria, for example
sp.,
sp.,
,
,
sp.,
sp.,
,
,
, and
, in healthy and ADNL groups. Therefore, these findings provide valuable insights into how AD affects the human skin metabolome and microbiome.IMPORTANCEThis study provides valuable insight into changes in the skin microbiome and associated metabolomic profiles in an adult population with mild to moderate atopic dermatitis. It also identifies new therapeutic targets that may be useful for developing personalized treatments for individuals with atopic dermatitis based on their unique skin microbiome and metabolic profiles.
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