Dolosigranulum pigrum : A promising nasal probiotic candidate

Citation:Stubbendieck RM, Hurst JH, Kelly MS (2024) Dolosigranulum pigrum: A promising nasal probiotic candidate. PLoS Pathog 20(2): e1011955. https://doi.org/10.1371/journal.ppat.1011955

Editor:Mary Ann Jabra-Rizk, University of Maryland, Baltimore, UNITED STATES

Published: February 1, 2024

Copyright: © 2024 Stubbendieck et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding:JHH was supported by a National Institutes of Health Career Development Award (K01-AI173398). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Acute respiratory infections (ARIs) are a major cause of morbidity and mortality across the life span. Globally, an estimated 17 billion ARIs occur each year, accounting for 2.4 million deaths (>740,000 deaths among children) [1]. Although the majority of these ARIs are caused by respiratory viruses, most severe or fatal cases are caused by bacterial respiratory pathobionts. Increasingly, commensal microbes in the upper respiratory tract (URT) are recognized to influence the risk and severity of respiratory viral infections and resistance to colonization and infection by bacterial pathobionts. Consequently, there is growing interest in leveraging these microbe–microbe or microbe–host interactions to develop novel strategies for ARI prevention or treatment [2]. Although the modern history of probiotics dates back more than a century, intranasal administration of live bacterial strains would represent a shift in our approach to preventing and treating ARIs. Necessary characteristics of such nasal probiotics would include the ability to adhere to the epithelium and successfully colonize the human URT, a lack of cytotoxicity to respiratory epithelial cells, some degree of resistance to horizontal gene transfer and mobile genetic elements, a low propensity to invade host tissues, and susceptibility to commonly available antibiotics. Below, we describe an understudied bacterial species, Dolosigranulum pigrum, which is increasingly viewed as a keystone species within the human URT and a promising nasal probiotic candidate for ARI prevention or treatment.

What is D. pigrum?

Deriving its name from the Latin words dolosus (“crafty, deceitful”), granulum (“a small grain”), and pigrum (“lazy”), D. pigrum (phylum: Firmicutes, class: Bacilli, order: Lactobacillales, family: Carnobacteriaceae) is a gram-positive, lactic acid bacterium that was first described by Aguirre and colleagues in 1993 [3]. It is non-spore-forming, facultatively anaerobic, catalase-negative, and generally susceptible to beta-lactams, clindamycin, and other commonly used antibiotics [4,5]. D. pigrum is the only recognized species within the genus Dolosigranulum. Its nearest phylogenetic relative is the putative otopathogen Alloiococcus otitis; the genetic similarity of these 2 species frequently resulted in taxonomic misclassification in analyses using 16S ribosomal RNA gene sequences from older reference databases [6]. D. pigrum has a relatively small genome size (<2 Mb for most strains) and has predicted auxotrophies for several amino acids, polyamines, and enzymatic cofactors, suggesting that it relies on its host or other microbes to provide these nutrients [7]. A recent analysis of D. pigrum strains collected over a 20-year period reported that the genomes of these strains were remarkably stable over time and possessed highly conserved chromosomal synteny [8]. Further, these genomes were found to contain multiple genes encoding clustered regularly interspaced short palindromic repeats (CRISPRs) and restriction–modification systems that may serve to limit horizontal gene transfer and exclude mobile genetic elements [8].

What are the natural habitats of D. pigrum?

D. pigrum is highly adapted to the human nasal passages. In an analysis of 8,184 samples from 6 human body sites, Dolosigranulum sequencing reads were identified in 41% of nasal samples, 15% of skin samples, and <1% of fecal and oral cavity samples [9]. Moreover, in samples in which Dolosigranulum was detected, the organism was far more abundant in nasal samples (18% mean relative abundance) than in samples from other body sites (<2% mean relative abundance) [9]. Analyses of data from the Earth Microbiome Project revealed that Dolosigranulum reads were rarely identified in environmental sources (e.g., water, soil) but were identified in samples from a variety of animal species, including rodents, fish, birds, dogs, and primates [9]. Notably, Dolosigranulum was generally of low abundance in the microbiomes of these animals, although relative abundances approaching 50% were observed in some dogs [9]. Within humans, the prevalence and abundance of D. pigrum in the URT varies markedly across the life span. The mean relative abundance of Dolosigranulum in the nasal passages increases progressively during infancy (from approximately 1% in the days after birth to 10% to 20% by 12 months of age), remains largely stable during childhood, and declines during adolescence, coinciding with pubertal development [10–12]. Although comparatively few studies of the URT microbiota have been conducted among healthy adults and the elderly, nasal abundances of Dolosigranulum in these populations have generally been reported to be lower than those observed in children [12,13].

Is D. pigrum a human pathogen or pathobiont?

The original description of D. pigrum included 2 strains, one of which was isolated from postmortem human spinal cord tissue and the second of which was cultivated from eye and contact lens cultures from a woman with blurred vision and eye pain [3]. This description, along with several subsequent reports that similarly described instances in which D. pigrum was cultivated from patients with infections, suggested that this bacterium may have a role as a pathobiont [5,14]. However, more recent studies suggest that D. pigrum has limited pathogenicity in humans. The bacterium is now recognized to be almost ubiquitously present in the human URT, particularly during infancy and early childhood, and yet has only rarely been implicated in human infections, typically among elderly adults with compromised immunity [3,14–18]. Moreover, on many of the occasions when D. pigrum has been cultured from patients with infections, it has often grown in mixed cultures with established pathobionts, making its role in these infections uncertain [3,9]. Notably, none of the 34 D. pigrum genomes currently available in GenBank harbor genes encoding proteins that are closely related to known virulence factors, and D. pigrum has not been found to be cytotoxic to human respiratory epithelial cells in ex vivo experiments [9,19].

Is D. pigrum beneficial to human respiratory health?

Recent studies suggest that the presence or abundance of D. pigrum in the URT microbiota is associated with various states of respiratory health (Table 1). Compared to healthy controls, lower URT abundances of D. pigrum have been observed among infants and children with ARIs, children with acute otitis media, and adults with chronic rhinosinusitis [9,20–23]. Moreover, D. pigrum has been associated with the absence of URT colonization by bacterial respiratory pathobionts. Most notably, lower relative abundances of D. pigrum are found in the nasal cavities of Staphylococcus aureus carriers [4,24–27], and a prospective study found that higher nasal abundances of D. pigrum were associated with a lower risk of Staphylococcus aureus acquisition during infancy [28]. D. pigrum may also influence the outcome of efforts to decolonize Staphylococcus aureus carriers. Use of nasal mupirocin can eliminate both Staphylococcus aureus and D. pigrum from the nasal microbiota, while recolonization with Staphylococcus aureus after stopping mupirocin is associated with delayed recolonization by D. pigrum [4]. Several cross-sectional studies also reported lower relative abundances of D. pigrum among children colonized by Streptococcus pneumoniae, a bacterial pathobiont that is among the most common bacterial causes of pneumonia, acute otitis media, and acute bacterial rhinosinusitis [20,29]. Finally, compared to other nasal microbiome profiles, a profile codominated by Corynebacterium and Dolosigranulum was associated with a lower risk of respiratory viral infections during infancy [30].

[Figure omitted. See PDF.]

Table 1. Associative microbiome studies supporting the role of Dolosigranulum pigrum as a mutualist in the human upper respiratory tract.

https://doi.org/10.1371/journal.ppat.1011955.t001

Relatively little is known regarding the mechanisms by which D. pigrum promotes human respiratory health and interacts with other microbes and host cells within the human URT. Consistent with findings from epidemiological studies, some D. pigrum strains demonstrate in vitro growth inhibition of Staphylococcus aureus, although efforts to identify the underlying inhibitory mechanisms have thus far been unsuccessful [7,9,25]. D. pigrum may also act in concert with other URT commensals. While growth of S. pneumoniae is not inhibited on solid medium conditioned with D. pigrum or Corynebacterium pseudodiphtheriticum alone, inhibition is observed on medium conditioned by cocultivation of these species [7]. Similar to other lactic acid bacteria, D. pigrum produces L-lactic acid in millimolar concentrations in vitro, spurring interest in determining the extent to which lactic acid production by D. pigrum contributes to its interactions with other URT microbes [7,9]. Notably, the concentrations of lactic acid produced by D. pigrum are insufficient to inhibit in vitro growth of Staphylococcus aureus or S. pneumoniae, although similar concentrations have been reported to inhibit growth of the respiratory pathobiont Moraxella catarrhalis [35]. Ex vivo and in vivo models have provided additional insights into D. pigrum and its interactions with the host that may mediate protection from infections by respiratory pathobionts. Exposing human airway epithelial cells to D. pigrum reduced up-regulation of genes encoding the proinflammatory cytokines interleukin (IL)-1β and IL-8 in response to Staphylococcus aureus exposure, suggesting that D. pigrum reduces the tissue-damaging inflammation induced by this pathobiont [9]. Similarly, larvae of the greater wax moth died rapidly following injection of Staphylococcus aureus, whereas improved survival was observed when D. pigrum was coinjected with Staphylococcus aureus [9]. In mice, intranasal administration of D. pigrum prior to S. pneumoniae challenge reduced lung pneumococcal cell counts, promoted earlier recruitment of innate immune cells, and resulted in lower alveolar levels of proinflammatory cytokines and markers of tissue injury [36]. Finally, nasally administered D. pigrum altered respiratory and systemic cytokine profiles and lowered alveolar viral loads in mice experimentally infected with RSV [37].

Future directions

In conclusion, D. pigrum is an understudied lactic acid bacterium that is increasingly viewed as a mutualist in the human URT. Although early reports suggested that this species may act as a pathobiont, more recent studies demonstrate that it is a highly prevalent member of the URT microbiota that has only rarely been cultivated from individuals with infections, often in mixed cultures with established human pathobionts. D. pigrum appears to exert its beneficial effects in the human respiratory tract through both direct interactions with bacterial respiratory pathobionts and modulation of host immune and inflammatory responses. Given its multiple predicted auxotrophies and potential dependence on interactions with other commensal bacteria to produce some antimicrobial factors, D. pigrum may not be effective as a single-strain probiotic but rather may require administration in a probiotic consortium to confer health benefits. Regardless, though further research is needed, D. pigrum possesses several key characteristics that make it a highly promising nasal probiotic candidate for the prevention or treatment of ARIs and the promotion of human respiratory health.

References

1. 1. Jin X, Ren J, Li R, Gao Y, Zhang H, Li J, et al. Global burden of upper respiratory infections in 204 countries and territories, from 1990 to 2019. EClinicalMedicine. 2021;37:100986. pmid:34386754

* View Article

* PubMed/NCBI

* Google Scholar

2. 2. Hurst JH, Kelly MS. Leveraging the human microbiota to target bacterial respiratory pathogens: new paths toward an expanded antimicrobial armamentarium. mBio. 2023;14(4):e0085423. pmid:37338299

* View Article

* PubMed/NCBI

* Google Scholar

3. 3. Aguirre M, Morrison D, Cookson B, Gay F, Collins M. Phenotypic and phylogenetic characterization of some Gemella-like organisms from human infections: description of Dolosigranulum pigrum gen. nov., sp. nov. J Appl Bacteriol. 1993;75(6):608–612.

* View Article

* Google Scholar

4. 4. Baede VO, Barray A, Tavakol M, Lina G, Vos MC, Rasigade J-P. Nasal microbiome disruption and recovery after mupirocin treatment in Staphylococcus aureus carriers and noncarriers. Sci Rep. 2022;12(1):19738. pmid:36396730

* View Article

* PubMed/NCBI

* Google Scholar

5. 5. Laclaire L, Facklam R. Antimicrobial susceptibility and clinical sources of Dolosigranulum pigrum cultures. Antimicrob Agents Chemother. 2000;44(7):2001–2003.

* View Article

* Google Scholar

6. 6. Lappan R, Jamieson SE, Peacock CS. Reviewing the pathogenic potential of the otitis-associated bacteria Alloiococcus otitidis and Turicella otitidis. Front Cell Infect Microbiol. 2020;10:51.

* View Article

* Google Scholar

7. 7. Brugger SD, Eslami SM, Pettigrew MM, Escapa IF, Henke MT, Kong Y, et al. Dolosigranulum pigrum cooperation and competition in human nasal microbiota. mSphere. 2020;5(5):e00852–e00820.

* View Article

* Google Scholar

8. 8. Flores Ramos S, Brugger SD, Escapa IF, Skeete CA, Cotton SL, Eslami SM, et al. Genomic stability and genetic defense systems in Dolosigranulum pigrum, a candidate beneficial bacterium from the human microbiome. Msystems. 2021;6(5):e00425–e00421.

* View Article

* Google Scholar

9. 9. De Boeck I, Wittouck S, Martens K, Spacova I, Cauwenberghs E, Allonsius CN, et al. The nasal mutualist Dolosigranulum pigrum AMBR11 supports homeostasis via multiple mechanisms. Iscience. 2021;24(9):102978.

* View Article

* Google Scholar

10. 10. Hurst JH, McCumber AW, Aquino JN, Rodriguez J, Heston SM, Lugo DJ, et al. Age-related changes in the nasopharyngeal microbiome are associated with SARS-CoV-2 infection and symptoms among children, adolescents, and young adults. Clin Infect Dis. 2022;75(1):e928–e937.

* View Article

* Google Scholar

11. 11. Oh J, Conlan S, Polley EC, Segre JA, Kong HH. Shifts in human skin and nares microbiota of healthy children and adults. Genome Med. 2012;4(10):77. pmid:23050952

* View Article

* PubMed/NCBI

* Google Scholar

12. 12. Kelly MS, Plunkett C, Yu Y, Aquino JN, Patel SM, Hurst JH, et al. Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy. ISME J. 2022;16(3):655–665.

* View Article

* Google Scholar

13. 13. Pereira PA, Aho VT, Paulin L, Pekkonen E, Auvinen P, Scheperjans F. Oral and nasal microbiota in Parkinson’s disease. Parkinsonism Relat Disord. 2017;38:61–67. pmid:28259623

* View Article

* PubMed/NCBI

* Google Scholar

14. 14. Hall G, Gordon S, Schroeder S, Smith K, Anthony K, Procop G. Case of synovitis potentially caused by Dolosigranulum pigrum. J Clin Microbiol. 2001;39(3):1202–1203.

* View Article

* Google Scholar

15. 15. Lécuyer H, Audibert J, Bobigny A, Eckert C, Janniere-Nartey C, Buu-Hoï A, et al. Dolosigranulum pigrum causing nosocomial pneumonia and septicemia. J Clin Microbiol. 2007;45(10):3474–3475.

* View Article

* Google Scholar

16. 16. Lin J-C, Hou S-J, Huang L-U, Sun J-R, Chang W-K, Lu J-J. Acute cholecystitis accompanied by acute pancreatitis potentially caused by Dolosigranulum pigrum. J Clin Microbiol. 2006;44(6):2298–2209.

* View Article

* Google Scholar

17. 17. Sampo M, Ghazouani O, Cadiou D, Trichet E, Hoffart L, Drancourt M. Dolosigranulum pigrum keratitis: a three-case series. BMC Ophthalmol. 2013;13(1):1–4.

* View Article

* Google Scholar

18. 18. Schanz CC, Layden MP, DeSimone DC, Stevens RW, Clement J. Native mitral valve infective endocarditis due to Dolosigranulum pigrum. IDCases. 2023;33:e01818.

* View Article

* Google Scholar

19. 19. Islam MA, Albarracin L, Melnikov V, Andrade BGN, Cuadrat RRC, Kitazawa H, et al. Dolosigranulum pigrum modulates immunity against SARS-CoV-2 in respiratory epithelial cells. Pathogens. 2021;10(6).

* View Article

* Google Scholar

20. 20. Laufer AS, Metlay JP, Gent JF, Fennie KP, Kong Y, Pettigrew MM. Microbial communities of the upper respiratory tract and otitis media in children. mBio. 2011;2(1):e00245–e00210. pmid:21285435

* View Article

* PubMed/NCBI

* Google Scholar

21. 21. Teo SM, Mok D, Pham K, Kusel M, Serralha M, Troy N, et al. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host Microbe. 2015;17(5):704–715. pmid:25865368

* View Article

* PubMed/NCBI

* Google Scholar

22. 22. Kelly MS, Surette MG, Smieja M, Pernica JM, Rossi L, Luinstra K, et al. The nasopharyngeal microbiota of children with respiratory infections in Botswana. Pediatr Infect Dis J. 2017;36(9):e211. pmid:28399056

* View Article

* PubMed/NCBI

* Google Scholar

23. 23. Lappan R, Imbrogno K, Sikazwe C, Anderson D, Mok D, Coates H, et al. A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera. BMC Microbiol. 2018;18(1):1–20.

* View Article

* Google Scholar

24. 24. Liu CM, Price LB, Hungate BA, Abraham AG, Larsen LA, Christensen K, et al. Staphylococcus aureus and the ecology of the nasal microbiome. Science Adv. 2015;1(5):e1400216.

* View Article

* Google Scholar

25. 25. Wagner Mackenzie B, Zoing M, Clow F, Waite DW, Radcliff FJ, Taylor MW, et al. Characterising clinical Staphylococcus aureus isolates from the sinuses of patients with chronic rhinosinusitis. Sci Rep. 2021;11(1):21940. pmid:34753993

* View Article

* PubMed/NCBI

* Google Scholar

26. 26. Khamash DF, Mongodin EF, White JR, Voskertchian A, Hittle L, Colantuoni E, et al. The association between the developing nasal microbiota of hospitalized neonates and Staphylococcus aureus colonization. Open Forum. Infect Dis. 2019;6(4).

* View Article

* Google Scholar

27. 27. Escapa IF, Chen T, Huang Y, Gajare P, Dewhirst FE, Lemon KP. New insights into human nostril microbiome from the expanded human oral microbiome database (eHOMD): a resource for the microbiome of the human aerodigestive tract. Msystems. 2018;3(6):e00187–e00118. pmid:30534599

* View Article

* PubMed/NCBI

* Google Scholar

28. 28. Accorsi EK, Franzosa EA, Hsu T, Cordy RJ, Maayan-Metzger A, Jaber H, et al. Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome. Genome Biol. 2020;21(1):1–24.

* View Article

* Google Scholar

29. 29. Patel SM, Farirai J, Patel MZ, Boiditswe S, Tawe L, Lekalake S, et al. Alterations of the upper respiratory microbiome among children living with HIV infection in Botswana. medRxiv 2022.12.19. https://doi.org/10.1101/2022.12.19.22283664

* View Article

* Google Scholar

30. 30. de Steenhuijsen Piters WAA, Watson RL, de Koff EM, Hasrat R, Arp K, Chu MLJN, et al. Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections. Nat Microbiol. 2022;7(2):224–237. pmid:35058634

* View Article

* PubMed/NCBI

* Google Scholar

31. 31. Hasegawa K, Linnemann RW, Mansbach JM, Ajami NJ, Espinola JA, Petrosino JF, et al. Nasal airway microbiota profile and severe bronchiolitis in infants: a case-control study. Pediatr Infect Dis J. 2017;36(11):1044–1051. pmid:28005692

* View Article

* PubMed/NCBI

* Google Scholar

32. 32. de Koff EM, Man WH, van Houten MA, Vlieger AM, Chu MLJ, Sanders EA, et al. Microbial and clinical factors are related to recurrence of symptoms after childhood lower respiratory tract infection. ERJ Open Res. 2021;7(2):00939–02020. pmid:34195257

* View Article

* PubMed/NCBI

* Google Scholar

33. 33. Gan W, Yang F, Tang Y, Zhou D, Qing D, Hu J, et al. editors. The difference in nasal bacterial microbiome diversity between chronic rhinosinusitis patients with polyps and a control population. Int Forum Allergy Rhinol. 2019;9(6):582–592.

* View Article

* Google Scholar

34. 34. Tang HH, Lang A, Teo SM, Judd LM, Gangnon R, Evans MD, et al. Developmental patterns in the nasopharyngeal microbiome during infancy are associated with asthma risk. J Allergy Clin Immunol. 2021;147(5):1683–1691. pmid:33091409

* View Article

* PubMed/NCBI

* Google Scholar

35. 35. Van den Broek M, De Boeck I, Claes I, Nizet V, Lebeer S. Multifactorial inhibition of lactobacilli against the respiratory tract pathogen Moraxella catarrhalis. Benef Microbes. 2018;9(3):429–439.

* View Article

* Google Scholar

36. 36. Raya Tonetti F, Tomokiyo M, Ortiz Moyano R, Quilodrán-Vega S, Yamamuro H, Kanmani P, et al. The respiratory commensal bacterium Dolosigranulum pigrum 040417 improves the innate immune response to Streptococcus pneumoniae. Microorganisms. 2021;9(6):1324.

* View Article

* Google Scholar

37. 37. Ortiz Moyano R, Raya Tonetti F, Tomokiyo M, Kanmani P, Vizoso-Pinto MG, Kim H, et al. The ability of respiratory commensal bacteria to beneficially modulate the lung innate immune response Is a strain dependent characteristic. Microorganisms. 2020;8(5). pmid:32414154

* View Article

* PubMed/NCBI

* Google Scholar

Citation: Stubbendieck RM, Hurst JH, Kelly MS (2024) Dolosigranulum pigrum: A promising nasal probiotic candidate. PLoS Pathog 20(2): e1011955. https://doi.org/10.1371/journal.ppat.1011955

References

1. Jin X, Ren J, Li R, Gao Y, Zhang H, Li J, et al. Global burden of upper respiratory infections in 204 countries and territories, from 1990 to 2019. EClinicalMedicine. 2021;37:100986. pmid:34386754

2. Hurst JH, Kelly MS. Leveraging the human microbiota to target bacterial respiratory pathogens: new paths toward an expanded antimicrobial armamentarium. mBio. 2023;14(4):e0085423. pmid:37338299

3. Aguirre M, Morrison D, Cookson B, Gay F, Collins M. Phenotypic and phylogenetic characterization of some Gemella-like organisms from human infections: description of Dolosigranulum pigrum gen. nov., sp. nov. J Appl Bacteriol. 1993;75(6):608–612.

4. Baede VO, Barray A, Tavakol M, Lina G, Vos MC, Rasigade J-P. Nasal microbiome disruption and recovery after mupirocin treatment in Staphylococcus aureus carriers and noncarriers. Sci Rep. 2022;12(1):19738. pmid:36396730

5. Laclaire L, Facklam R. Antimicrobial susceptibility and clinical sources of Dolosigranulum pigrum cultures. Antimicrob Agents Chemother. 2000;44(7):2001–2003.

6. Lappan R, Jamieson SE, Peacock CS. Reviewing the pathogenic potential of the otitis-associated bacteria Alloiococcus otitidis and Turicella otitidis. Front Cell Infect Microbiol. 2020;10:51.

7. Brugger SD, Eslami SM, Pettigrew MM, Escapa IF, Henke MT, Kong Y, et al. Dolosigranulum pigrum cooperation and competition in human nasal microbiota. mSphere. 2020;5(5):e00852–e00820.

8. Flores Ramos S, Brugger SD, Escapa IF, Skeete CA, Cotton SL, Eslami SM, et al. Genomic stability and genetic defense systems in Dolosigranulum pigrum, a candidate beneficial bacterium from the human microbiome. Msystems. 2021;6(5):e00425–e00421.

9. De Boeck I, Wittouck S, Martens K, Spacova I, Cauwenberghs E, Allonsius CN, et al. The nasal mutualist Dolosigranulum pigrum AMBR11 supports homeostasis via multiple mechanisms. Iscience. 2021;24(9):102978.

10. Hurst JH, McCumber AW, Aquino JN, Rodriguez J, Heston SM, Lugo DJ, et al. Age-related changes in the nasopharyngeal microbiome are associated with SARS-CoV-2 infection and symptoms among children, adolescents, and young adults. Clin Infect Dis. 2022;75(1):e928–e937.

11. Oh J, Conlan S, Polley EC, Segre JA, Kong HH. Shifts in human skin and nares microbiota of healthy children and adults. Genome Med. 2012;4(10):77. pmid:23050952

12. Kelly MS, Plunkett C, Yu Y, Aquino JN, Patel SM, Hurst JH, et al. Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy. ISME J. 2022;16(3):655–665.

13. Pereira PA, Aho VT, Paulin L, Pekkonen E, Auvinen P, Scheperjans F. Oral and nasal microbiota in Parkinson’s disease. Parkinsonism Relat Disord. 2017;38:61–67. pmid:28259623

14. Hall G, Gordon S, Schroeder S, Smith K, Anthony K, Procop G. Case of synovitis potentially caused by Dolosigranulum pigrum. J Clin Microbiol. 2001;39(3):1202–1203.

15. Lécuyer H, Audibert J, Bobigny A, Eckert C, Janniere-Nartey C, Buu-Hoï A, et al. Dolosigranulum pigrum causing nosocomial pneumonia and septicemia. J Clin Microbiol. 2007;45(10):3474–3475.

16. Lin J-C, Hou S-J, Huang L-U, Sun J-R, Chang W-K, Lu J-J. Acute cholecystitis accompanied by acute pancreatitis potentially caused by Dolosigranulum pigrum. J Clin Microbiol. 2006;44(6):2298–2209.

17. Sampo M, Ghazouani O, Cadiou D, Trichet E, Hoffart L, Drancourt M. Dolosigranulum pigrum keratitis: a three-case series. BMC Ophthalmol. 2013;13(1):1–4.

18. Schanz CC, Layden MP, DeSimone DC, Stevens RW, Clement J. Native mitral valve infective endocarditis due to Dolosigranulum pigrum. IDCases. 2023;33:e01818.

19. Islam MA, Albarracin L, Melnikov V, Andrade BGN, Cuadrat RRC, Kitazawa H, et al. Dolosigranulum pigrum modulates immunity against SARS-CoV-2 in respiratory epithelial cells. Pathogens. 2021;10(6).

20. Laufer AS, Metlay JP, Gent JF, Fennie KP, Kong Y, Pettigrew MM. Microbial communities of the upper respiratory tract and otitis media in children. mBio. 2011;2(1):e00245–e00210. pmid:21285435

21. Teo SM, Mok D, Pham K, Kusel M, Serralha M, Troy N, et al. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host Microbe. 2015;17(5):704–715. pmid:25865368

22. Kelly MS, Surette MG, Smieja M, Pernica JM, Rossi L, Luinstra K, et al. The nasopharyngeal microbiota of children with respiratory infections in Botswana. Pediatr Infect Dis J. 2017;36(9):e211. pmid:28399056

23. Lappan R, Imbrogno K, Sikazwe C, Anderson D, Mok D, Coates H, et al. A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera. BMC Microbiol. 2018;18(1):1–20.

24. Liu CM, Price LB, Hungate BA, Abraham AG, Larsen LA, Christensen K, et al. Staphylococcus aureus and the ecology of the nasal microbiome. Science Adv. 2015;1(5):e1400216.

25. Wagner Mackenzie B, Zoing M, Clow F, Waite DW, Radcliff FJ, Taylor MW, et al. Characterising clinical Staphylococcus aureus isolates from the sinuses of patients with chronic rhinosinusitis. Sci Rep. 2021;11(1):21940. pmid:34753993

26. Khamash DF, Mongodin EF, White JR, Voskertchian A, Hittle L, Colantuoni E, et al. The association between the developing nasal microbiota of hospitalized neonates and Staphylococcus aureus colonization. Open Forum. Infect Dis. 2019;6(4).

27. Escapa IF, Chen T, Huang Y, Gajare P, Dewhirst FE, Lemon KP. New insights into human nostril microbiome from the expanded human oral microbiome database (eHOMD): a resource for the microbiome of the human aerodigestive tract. Msystems. 2018;3(6):e00187–e00118. pmid:30534599

28. Accorsi EK, Franzosa EA, Hsu T, Cordy RJ, Maayan-Metzger A, Jaber H, et al. Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome. Genome Biol. 2020;21(1):1–24.

29. Patel SM, Farirai J, Patel MZ, Boiditswe S, Tawe L, Lekalake S, et al. Alterations of the upper respiratory microbiome among children living with HIV infection in Botswana. medRxiv 2022.12.19. https://doi.org/10.1101/2022.12.19.22283664

30. de Steenhuijsen Piters WAA, Watson RL, de Koff EM, Hasrat R, Arp K, Chu MLJN, et al. Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections. Nat Microbiol. 2022;7(2):224–237. pmid:35058634

31. Hasegawa K, Linnemann RW, Mansbach JM, Ajami NJ, Espinola JA, Petrosino JF, et al. Nasal airway microbiota profile and severe bronchiolitis in infants: a case-control study. Pediatr Infect Dis J. 2017;36(11):1044–1051. pmid:28005692

32. de Koff EM, Man WH, van Houten MA, Vlieger AM, Chu MLJ, Sanders EA, et al. Microbial and clinical factors are related to recurrence of symptoms after childhood lower respiratory tract infection. ERJ Open Res. 2021;7(2):00939–02020. pmid:34195257

33. Gan W, Yang F, Tang Y, Zhou D, Qing D, Hu J, et al. editors. The difference in nasal bacterial microbiome diversity between chronic rhinosinusitis patients with polyps and a control population. Int Forum Allergy Rhinol. 2019;9(6):582–592.

34. Tang HH, Lang A, Teo SM, Judd LM, Gangnon R, Evans MD, et al. Developmental patterns in the nasopharyngeal microbiome during infancy are associated with asthma risk. J Allergy Clin Immunol. 2021;147(5):1683–1691. pmid:33091409

35. Van den Broek M, De Boeck I, Claes I, Nizet V, Lebeer S. Multifactorial inhibition of lactobacilli against the respiratory tract pathogen Moraxella catarrhalis. Benef Microbes. 2018;9(3):429–439.

36. Raya Tonetti F, Tomokiyo M, Ortiz Moyano R, Quilodrán-Vega S, Yamamuro H, Kanmani P, et al. The respiratory commensal bacterium Dolosigranulum pigrum 040417 improves the innate immune response to Streptococcus pneumoniae. Microorganisms. 2021;9(6):1324.

37. Ortiz Moyano R, Raya Tonetti F, Tomokiyo M, Kanmani P, Vizoso-Pinto MG, Kim H, et al. The ability of respiratory commensal bacteria to beneficially modulate the lung innate immune response Is a strain dependent characteristic. Microorganisms. 2020;8(5). pmid:32414154