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MSphere Sep 2020Multiple epidemiological studies identify as a candidate beneficial bacterium based on its positive association with health, including negative associations with...
Multiple epidemiological studies identify as a candidate beneficial bacterium based on its positive association with health, including negative associations with nasal/nasopharyngeal colonization by the pathogenic species and Using a multipronged approach to gain new insights into function, we observed phenotypic interactions and predictions of genomic capacity that support the idea of a role for microbe-microbe interactions involving in shaping the composition of human nasal microbiota. We identified community-level and phenotypic cooperation by specific nasal species. Also, inhibited growth , whereas robust inhibition of required both and a nasal together. l-lactic acid production was insufficient to account for these inhibitions. Genomic analysis of 11 strains revealed that has a small genome (average 1.86 Mb) and multiple predicted auxotrophies consistent with relying on its human host and on cocolonizing bacteria for key nutrients. Further, the accessory genome of harbored a diverse repertoire of biosynthetic gene clusters, some of which may have a role in microbe-microbe interactions. These new insights into 's functions advance the field from compositional analysis to genomic and phenotypic experimentation on a potentially beneficial bacterial resident of the human upper respiratory tract and lay the foundation for future animal and clinical experiments. and infections cause significant morbidity and mortality in humans. For both, nasal colonization is a risk factor for infection. Studies of nasal microbiota identify as a benign bacterium present when adults are free of or when children are free of Here, we validated these associations with functional assays. We found that inhibited and, together with a specific nasal species, also inhibited Furthermore, genomic analysis of indicated that it must obtain key nutrients from other nasal bacteria or from humans. These phenotypic interactions support the idea of a role for microbe-microbe interactions in shaping the composition of human nasal microbiota and implicate as a mutualist of humans. These findings support the feasibility of future development of microbe-targeted interventions to reshape nasal microbiota composition to exclude and/or .
Topics: Bacteria; Carnobacteriaceae; Child, Preschool; Genomics; Humans; Infant; Microbial Interactions; Microbiota; Nasopharynx; Pneumococcal Infections; Staphylococcus aureus; Streptococcus pneumoniae
PubMed: 32907957
DOI: 10.1128/mSphere.00852-20 -
Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome.Scientific Reports Apr 2023Dolosigranulum pigrum-a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and...
Dolosigranulum pigrum-a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and low-cost options for confirming D. pigrum isolates and detecting D. pigrum in clinical specimens. Here we describe the design and validation of a novel PCR assay targeting D. pigrum that is both sensitive and specific. We designed a PCR assay targeting murJ, a single-copy core species gene identified through the analysis of 21 D. pigrum whole genome sequences. The assay achieved 100% sensitivity and 100% specificity against D. pigrum and diverse bacterial isolates and an overall 91.1% sensitivity and 100% specificity using nasal swabs, detecting D. pigrum at a threshold of 1.0 × 10 D. pigrum 16S rRNA gene copies per swab. This assay adds a reliable and rapid D. pigrum detection tool to the microbiome researcher toolkit investigating the role of generalist and specialist bacteria in the nasal environment.
Topics: Humans; RNA, Ribosomal, 16S; Gram-Positive Bacterial Infections; Gram-Positive Cocci; Polymerase Chain Reaction; DNA Primers; DNA, Bacterial
PubMed: 37059715
DOI: 10.1038/s41598-023-32709-y -
MSystems Oct 2021Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of...
Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into 's chromosomal structure, pangenome, and genomic stability, we compared the genomes of 28 strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites, including one RM system hot spot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of strains colonizing people in the United States across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation, and defenses against MGEs. Finally, these strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for as a therapeutic bacterium.
PubMed: 34546072
DOI: 10.1128/mSystems.00425-21 -
Frontiers in Cellular and Infection... 2022The human nose harbors various microbes that decisively influence the wellbeing and health of their host. Among the most threatening pathogens in this habitat is ....
The human nose harbors various microbes that decisively influence the wellbeing and health of their host. Among the most threatening pathogens in this habitat is . Multiple epidemiological studies identify as a likely beneficial bacterium based on its positive association with health, including negative associations with . Carefully curated GEMs are available for both bacterial species that reliably simulate their growth behavior in isolation. To unravel the mutual effects among bacteria, building community models for simulating co-culture growth is necessary. However, modeling microbial communities remains challenging. This article illustrates how applying the fosters our understanding of two microbes' joint growth conditions in the nasal habitat and their intricate interplay from a metabolic modeling perspective. The resulting community model combines the latest available curated GEMs of and . This uses case illustrates how to incorporate genuine GEM of participating microorganisms and creates a basic community model mimicking the human nasal environment. Our analysis supports the role of negative microbe-microbe interactions involving examined experimentally in the lab. By this, we identify and characterize metabolic exchange factors involved in a specific interaction between and as an candidate factor for a deep insight into the associated species. This method may serve as a blueprint for developing more complex microbial interaction models. Its direct application suggests new ways to prevent disease-causing infections by inhibiting the growth of pathogens such as through microbe-microbe interactions.
Topics: Humans; Staphylococcus aureus; Methicillin-Resistant Staphylococcus aureus; Nose; Staphylococcal Infections; Bacteria; Microbiota
PubMed: 36605126
DOI: 10.3389/fcimb.2022.925215 -
Metabolites Apr 2021is a quite recently discovered Gram-positive coccus. It has gained increasing attention due to its negative correlation with , which is one of the most successful...
is a quite recently discovered Gram-positive coccus. It has gained increasing attention due to its negative correlation with , which is one of the most successful modern pathogens causing severe infections with tremendous morbidity and mortality due to its multiple resistances. As the possible mechanisms behind its inhibition of remain unclear, a genome-scale metabolic model (GEM) is of enormous interest and high importance to better study its role in this fight. This article presents the first GEM of , which was curated using automated reconstruction tools and extensive manual curation steps to yield a high-quality GEM. It was evaluated and validated using all currently available experimental data of . With this model, already predicted auxotrophies and biosynthetic pathways could be verified. The model was used to define a minimal medium for further laboratory experiments and to predict various carbon sources' growth capacities. This model will pave the way to better understand 's role in the fight against .
PubMed: 33918864
DOI: 10.3390/metabo11040232 -
Microbial Biotechnology May 2021Several studies have recently pointed towards an increased occurrence and prevalence of several taxa of the lactic acid bacteria (LAB) in the microbiota of the upper... (Review)
Review
Several studies have recently pointed towards an increased occurrence and prevalence of several taxa of the lactic acid bacteria (LAB) in the microbiota of the upper respiratory tract (URT) under healthy conditions versus disease. These include several species of the Lactobacillales such as Lacticaseibacillus casei, Lactococcus lactis and Dolosigranulum pigrum. In addition to physiological studies on their potential beneficial functions and their long history of safe use as probiotics in other human body sites, LAB are thus increasingly to be explored as alternative or complementary treatment for URT diseases. This review highlights the importance of lactic acid bacteria in the respiratory tract and their potential as topical probiotics for this body site. We focus on the potential probiotic properties and adaptation factors that are needed for a bacterial strain to optimally exert its beneficial activity in the respiratory tract. Furthermore, we discuss a range of in silico, in vitro and in vivo models needed to obtain better insights into the efficacy and adaptation factors specifically for URT probiotics. Such knowledge will facilitate optimal strain selection in order to conduct rigorous clinical studies with the most suitable probiotic strains. Despite convincing evidence from microbiome association and in vitro studies, the clinical evidence for oral or topical probiotics for common URT diseases such as chronic rhinosinusitis (CRS) needs further substantiation.
Topics: Carnobacteriaceae; Humans; Lactobacillales; Microbiota; Probiotics
PubMed: 33507624
DOI: 10.1111/1751-7915.13759 -
Pathogens (Basel, Switzerland) May 2021In a previous work, we demonstrated that nasally administered 040417 beneficially modulated the respiratory innate immune response triggered by the activation of...
In a previous work, we demonstrated that nasally administered 040417 beneficially modulated the respiratory innate immune response triggered by the activation of Toll-like receptor 3 (TLR3) and improved protection against Respiratory Syncytial Virus (RSV) in mice. In this work, we aimed to evaluate the immunomodulatory effects of 040417 in human respiratory epithelial cells and the potential ability of this immunobiotic bacterium to increase the protection against Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The respiratory commensal bacterium 040417 differentially modulated the production of IFN-β, IL-6, CXCL8, CCL5 and CXCL10 in the culture supernatants of Calu-3 cells stimulated with poly(I:C) or challenged with SARS-CoV-2. The differential cytokine profile induced by the 040417 strain was associated with a significant reduction in viral replication and cellular damage after coronavirus infection. Of note, 030918 was not able to modify the resistance of Calu-3 cells to SARS-CoV-2 infection, indicating a strain-specific immunomodulatory effect for respiratory commensal bacteria. The findings of this work improve our understanding of the immunological mechanisms involved in the modulation of respiratory immunity induced by respiratory commensal bacteria, by demonstrating their specific effect on respiratory epithelial cells. In addition, the results suggest that particular strains such as 040417 could be used as a promising alternative for combating SARS-CoV-2 and reducing the severity of COVID-19.
PubMed: 34064210
DOI: 10.3390/pathogens10060634 -
Zhejiang Da Xue Xue Bao. Yi Xue Ban =... Dec 2021To explore the application value of nanopore sequencing technique in the diagnosis and treatment of secondary infections in patients with severe coronavirus disease 2019...
To explore the application value of nanopore sequencing technique in the diagnosis and treatment of secondary infections in patients with severe coronavirus disease 2019 (COVID-19). A total of 77 clinical specimens from 3 patients with severe COVID-19 were collected. After heat inactivation, all samples were subjected to total nucleic acid extraction based on magnetic bead enrichment. The extracted DNA was used for DNA library construction, then nanopore real-time sequencing detection was performed. The sequencing data were subjected to Centrifuge software database species matching and R program differential analysis to obtain potential pathogen identification. Nanopore sequencing results were compared with respiratory pathogen qPCR panel screening and conventional microbiological testing results to verify the effectiveness of nanopore sequencing detection. Nanopore sequencing results showed that positive pathogen were obtained in 44 specimens (57.1%). The potential pathogens identified by nanopore sequencing included , , and , et al. , , were also detected in clinical microbiological culture-based detection; was detected in respiratory pathogen screening qPCR panel; was only detected by the nanopore sequencing technique. Comprehensive considerations with the clinical symptoms, the patient was treated with antibiotics against , and the infection was controlled. Nanopore sequencing may assist the diagnosis and treatment of severe COVID-19 patients through rapid identification of potential pathogens.
Topics: COVID-19; Coinfection; Humans; Nanopore Sequencing; Nanopores; Sequence Analysis, DNA
PubMed: 35347908
DOI: 10.3724/zdxbyxb-2021-0158 -
Revista Argentina de Microbiologia 2022Dolosigranulum pigrum is a gram-positive, facultatively anaerobic coccus, which is part of the oral and upper respiratory tract microbiota. Although reports of...
Dolosigranulum pigrum is a gram-positive, facultatively anaerobic coccus, which is part of the oral and upper respiratory tract microbiota. Although reports of infections by this microorganism are scarce, it has been associated with a wide spectrum of infectious diseases. The case of an elderly man with a lower corneal abscess, in which Dolosigranulum pigrum was isolated, is described. The microorganism was identified by mass spectrometry (MALDI-TOF MS) and by the sequencing of the 16S rRNA gene. Furthermore, the presumptive identification of the causative agent was achieved by using key phenotypic tests such as the cluster arrangement in Gram stain, the negative catalase test, the production of pyrrolidonyl arylamidase and leucine aminopeptidase activity, the growth in 6.5% NaCl and esculin hydrolysis. The data from the literature (and the present case) support the association of the microorganism with ocular infections, which often take a destructive course, mainly in elderly patients.
Topics: Abscess; Aged; Carnobacteriaceae; Gram-Positive Bacterial Infections; Gram-Positive Cocci; Humans; Male; RNA, Ribosomal, 16S
PubMed: 34895780
DOI: 10.1016/j.ram.2021.10.002 -
IScience Sep 2021Comparing the nasal microbiome of healthy individuals and chronic rhinosinusitis (CRS) patients revealed as a species clearly associated with nasal health, although...
Comparing the nasal microbiome of healthy individuals and chronic rhinosinusitis (CRS) patients revealed as a species clearly associated with nasal health, although isolates obtained from healthy individuals are scarce. In this study, we explored the properties of this understudied lactic acid bacterium by integrating comparative genomics, habitat mining, cultivation, and functional characterization of interaction capacities. Mining 10.000 samples from the Earth Microbiome Project of 17 habitat types revealed that is mainly associated with the human nasal cavity. AMBR11 isolated from the nose of a healthy individual exerted antimicrobial activity against , decreased proinflammatory cytokine production in airway epithelial cells, and larvae mortality induced by this important nasal pathobiont. Furthermore, the strain protected the nasal barrier function in a mouse model using interleukin-4 as disruptive cytokine. Hence, AMBR11 is a mutualist with high potential as topical live biotherapeutic product.
PubMed: 34485860
DOI: 10.1016/j.isci.2021.102978