Genomic Stability and Genetic Defense Systems in
            <i>Dolosigranulum pigrum</i>
            , a Candidate Beneficial Bacterium from the Human Microbiome

Ramos, Stephany Flores; Brugger, Silvio D.; Escapa, Isabel F.; Skeete, Chelsey A.; Cotton, Sean L.; Eslami, Sara M.; Gao, Wei; Bomar, Lindsey; Tran, Tommy H; Jones, Dakota S; Minot, Samuel S.; Roberts, Richard J.; Johnston, Christopher A.; Lemon, Katherine P.

doi:10.1128/msystems.00425-21

Cited by 15 publications

(15 citation statements)

References 133 publications

(154 reference statements)

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“…Furthermore, probiotic treatment with Streptococcus salivarius has been explored for children suffering from chronic otitis media. S. salivarius can inhibit growth of most pathogens known to cause otitis media infections, among others including S. pneumoniae, H. influenzae, M. catarrhalis [37,38]. However, it has not yet been shown that D. pigrum supplementation, in isolation or combined with Corynebacterium, can also effectuate short-term or long-term clinical improvement.…”

Section: Resultsmentioning

confidence: 99%

The microbiota in respiratory tract infections: from association to intervention

Koenen

Piters

Bogaert

et al. 2022

Current Opinion in Infectious Diseases

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Purpose of reviewThe respiratory microbiota has a role in respiratory tract infection (RTI) pathogenesis. On the mucosa, the respiratory microbiota interacts with potential pathogenic viruses, bacteria and the host immune system, including secretory IgA (sIgA). This review discusses the role of the respiratory microbiota and its interaction with the (mucosal) immune system in RTI susceptibility, as well as the potential to exploit the microbiota to promote health and prevent RTIs. Recent findingsRecent studies confirm that specific microbiota profiles are associated with RTI susceptibility and during susceptibility and found accompanying RTIs, although clear associations have not yet been found for SARS-CoV-2 infection. sIgA plays a central role in RTI pathogenesis: it stands under control of the local microbiota, while at the same time influencing bacterial gene expression, metabolism and defense mechanisms. Respiratory microbiota interventions are still newly emerging but promising candidates for probiotics to prevent RTIs, such as Corynebacterium and Dolosigranulum species, have been identified.

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Section: Resultsmentioning

confidence: 99%

The microbiota in respiratory tract infections: from association to intervention

Koenen

Piters

Bogaert

et al. 2022

Current Opinion in Infectious Diseases

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“…Dolosigranulum pigrum is gaining interest as a member of the upper respiratory tract microbial community that is potentially beneficial for the host 5,6,8,[13][14][15][16][17][18][19] . Efforts are being made to better understand its metabolic models and defense mechanisms 20 . There is a critical need to screen samples to detect the presence of D. pigrum or to verify the identity of the organism isolated through culture-based methods.…”

Section: Discussionmentioning

confidence: 99%

Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome

Aziz

Palmer

Iversen

et al. 2023

Sci Rep

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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 × 104D. 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.

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“…Although some concerns regarding the safety of probiotics targeting gut microbiome were raised by several clinical trials [44], studies based on the nasal application of probiotics only revealed minor side effects [38], and considered to be safe [29,[45][46][47]. On the contrary, application of antibiotics is quite detrimental to the overall microbial diversity [48], contributing to the emergence and spread of antibiotic resistance and thus jeopardizing the success of the future treatments that would be necessary [49].…”

Section: Discussionmentioning

confidence: 99%

Developing and optimizing a personalized probiotic treatment regime for nasal endogenous Staphylococcus aureus decolonization

Tepekule

Bergadà-Pijuan

Scheier

et al. 2022

Preprint

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Despite the increasing burden of antibiotic resistance, current approaches to eradicate pathobionts such as Staphylococcus aureus from the nasal cavity are based on the use of antibacterial agents. An alternative approach is the artificial inoculation of commensal bacteria, i.e., probiotic treatment, which is supported by the increasing evidence for commensal-mediated inhibition of pathogens. To systematically investigate the potential and the limitations of this approach, we developed a quantitative framework simulating the dynamics of the nasal bacterial microbiome by combining mathematical microbiome modeling with longitudinal metagenomic data. By inferring the structure and the magnitude of microbial interaction parameters using metagenomic data, and then simulating the nasal microbial dynamics of patients colonized with S. aureus, we could compare the decolonization performance of probiotic and antibiotic treatments under different assumptions on patients' bacterial community composition and susceptibility profile. To further compare the robustness of these treatments, we simulated a S. aureus challenge following each treatment and quantified the recolonization probability. Our results suggest that probiotic treatment clearly outperforms antibiotics in terms of decolonization performance, recolonization robustness, and leads to less collateral reduction of the microbiome diversity. Moreover, we find that recolonization robustness is highest in those patients that were not initially colonized by Dolosigranulum pigrum. Thus, probiotic treatment may provide a promising alternative to combat antibiotic resistance, with the additional advantage of personalized treatment options via using the patient's own metagenomic data to tailor the intervention. The in silico framework developed in this work is an important step forward to further investigate this alternative in clinical trials.

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Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum , a Candidate Beneficial Bacterium from the Human Microbiome

Abstract: 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.

Cited by 15 publications

References 133 publications

The microbiota in respiratory tract infections: from association to intervention

The microbiota in respiratory tract infections: from association to intervention

Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome

Developing and optimizing a personalized probiotic treatment regime for nasal endogenous Staphylococcus aureus decolonization

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