Heidi Aarø Åmdal

• Brar, Navdeep Kaur; Dhariwal, Achal; Åmdal, Heidi Aarø; Junges, Roger; Salvadori, Gabriela & Baker, J.L. [Show all 8 contributors for this article] (2024). Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome. npj Biofilms and Microbiomes. 10(1). doi: 10.1038/s41522-024-00507-7. Full text in Research Archive Show summary

  Prolonged exposure to antibiotics at low concentration can promote processes associated with bacterial biofilm formation, virulence and antibiotic resistance. This can be of high relevance in microbial communities like the oral microbiome, where commensals and pathogens share a common habitat and where the total abundance of antibiotic resistance genes surpasses the abundance in the gut. Here, we used an ex vivo model of human oral biofilms to investigate the impact of ampicillin on biofilm viability. The ecological impact on the microbiome and resistome was investigated using shotgun metagenomics. The results showed that low concentrations promoted significant shifts in microbial taxonomic profile and could enhance biofilm viability by up to 1 to 2-log. For the resistome, low concentrations had no significant impact on antibiotic resistance gene (ARG) diversity, while ARG abundance decreased by up to 84%. A positive correlation was observed between reduced microbial diversity and reduced ARG abundance. The WHO priority pathogens Streptococcus pneumoniae and Staphylococcus aureus were identified in some of the samples, but their abundance was not significantly altered by ampicillin. Most of the antibiotic resistance genes that increased in abundance in the ampicillin group were associated with streptococci, including Streptococcus mitis, a well-known potential donor of ARGs to S. pneumoniae. Overall, the results highlight the potential of using the model to further our understanding of ecological and evolutionary forces driving antimicrobial resistance in oral microbiomes.

• Xavier-Queiroz, Mateus; Hamann, Pedro Ricardo Vieira; Åmdal, Heidi Aarø; Polikarpov, Igor; Petersen, Fernanda Cristina & Ricomini-Filho, Antônio Pedro (2024). Absence of inhibitory effects of two new glucanases on streptococcus mutans growth. Brazilian Journal of Oral Sciences. ISSN 1677-3217. 23. doi: 10.20396/BJOS.V23I00.8676163. Full text in Research Archive Show summary

  Glucanohydrolases have shown promise in degrading exopolysaccharides in cariogenic biofilms, making them a potential strategy for biofilm control without disrupting the oral microbiota. However, their direct antimicrobial effects remain unclear. Aim: To determine the antimicrobial activity on S. mutans of two newly discovered glucanases characterized by our group, PmGH87 (mutanase) from Prevotella melaninogenica and CoGH66 (dextranase) from Capnocytophaga ochracea, using a commercial dextranase from Penicillum sp. as a control. Methods: Their effects on growth were assessed using a luciferase reporter system coupled with the promoter of the ldh gene in Streptococcus mutans. Results: Quantification of optical density and luminescence over a 10-hour growth period revealed that the commercial dextranase exhibited inhibitory effects on S. mutans growth. However, these effects were neutralized by heat treatment, suggesting the presence of a heat-sensitive contaminant or an additional antimicrobial property associated with the commercial dextranase from Penicillum sp. On the other hand, the purified mutanase and dextranase enzymes had no inhibitory effect on S. mutans growth. Conclusion: In conclusion, the absence of inhibitory effects on S. mutans growth by the newly discovered enzymes emphasizes their potential for biofilm control while preserving the delicate balance of the oral microbiota and preventing the emergence of resistance.

• Dhariwal, Achal; Rajar, Polona; Silva, Gabriela Salvadori Da; Åmdal, Heidi Aarø; Berild, Dag & Saugstad, Ola Didrik [Show all 11 contributors for this article] (2024). Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants. Nature Communications. 15(1). doi: 10.1038/s41467-024-50433-7. Full text in Research Archive Show summary

  Respiratory pathogens, commonly colonizing nasopharynx, are among the leading causes of death due to antimicrobial resistance. Yet, antibiotic resistance determinants within nasopharyngeal microbial communities remain poorly understood. In this prospective cohort study, we investigate the nasopharynx resistome development in preterm infants, assess early antibiotic impact on its trajectory, and explore its association with clinical covariates using shotgun metagenomics. Our findings reveal widespread nasopharyngeal carriage of antibiotic resistance genes (ARGs) with resistomes undergoing transient changes, including increased ARG diversity, abundance, and composition alterations due to early antibiotic exposure. ARGs associated with the critical nosocomial pathogen Serratia marcescens persist up to 8–10 months of age, representing a long-lasting hospitalization signature. The nasopharyngeal resistome strongly correlates with microbiome composition, with inter-individual differences and postnatal age explaining most of the variation. Our report on the collateral effects of antibiotics and prolonged hospitalization underscores the urgency of further studies focused on this relatively unexplored reservoir of pathogens and ARGs.

• Dornelas-Figueira, Louise Morais; Filho, Antonio Pedro Ricomini; Junges, Roger; Åmdal, Heidi Aarø; Cury, Altair Antoninha Del Bel & Petersen, Fernanda Cristina (2023). In Vitro Impact of Fluconazole on Oral Microbial Communities, Bacterial Growth, and Biofilm Formation. Antibiotics. 12(9). doi: 10.3390/antibiotics12091433. Full text in Research Archive Show summary

  Antifungal agents are widely used to specifically eliminate infections by fungal pathogens. However, the specificity of antifungal agents has been challenged by a few studies demonstrating antibacterial inhibitory effects against Mycobacteria and Streptomyces species. Here, we evaluated for the first time the potential effect of fluconazole, the most clinically used antifungal agent, on a human oral microbiota biofilm model. The results showed that biofilm viability on blood and mitis salivarius agar media was increased over time in the presence of fluconazole at clinically relevant concentrations, despite a reduction in biomass. Targeted PCR revealed a higher abundance of Veillonella atypica, Veillonella dispar, and Lactobacillus spp. in the fluconazole-treated samples compared to the control, while Fusobacterium nucleatum was reduced and Streptococcus spp were not significantly affected. Further, we tested the potential impact of fluconazole using single-species models. Our results, using Streptococcus mutans and Streptococcus mitis luciferase reporters, showed that S. mutans planktonic growth was not significantly affected by fluconazole, whereas for S. mitis, planktonic growth, but not biofilm viability, was inhibited at the highest concentration. Fluconazole’s effects on S. mitis biofilm biomass were concentration and time dependent. Exposure for 48 h to the highest concentration of fluconazole was associated with S. mitis biofilms with the most increased biomass. Potential growth inhibitory effects were further tested using four non-streptococcal species. Among these, the planktonic growth of both Escherichia coli and Granulicatella adiacens was inhibited by fluconazole. The data indicate bacterial responses to fluconazole that extend to a broader range of bacterial species than previously anticipated from the literature, with the potential to disturb biofilm communities.

• Junges, Roger; Khan, Rabia; Tovpeko, Yanina; Åmdal, Heidi Aarø; Petersen, Fernanda Cristina & Morrison, Donald A. (2023). Markerless Genome Editing in Competent Streptococci, Oral Biology. Molecular Techniques and Applications. Springer. ISSN 9781071627792. p. 201–216. doi: 10.1007/978-1-0716-2780-8_13. Full text in Research Archive
• Dhariwal, Achal; Bråten, Lars Christian Haugli; Sturød, Kjersti; Silva, Gabriela Salvadori Da; Bargheet, Ahmed & Åmdal, Heidi Aarø [Show all 11 contributors for this article] (2023). Differential response to prolonged amoxicillin treatment: long-term resilience of the microbiome versus long-lasting perturbations in the gut resistome. Gut microbes. ISSN 1949-0976. 15(1). doi: 10.1080/19490976.2022.2157200. Full text in Research Archive Show summary

  The collateral impact of antibiotics on the microbiome has attained increasing attention. However, the ecological consequences of long-term antibiotic exposure on the gut microbiome, including anti- biotic resistance, are still limited. Here, we investigated long-term exposure effects to amoxicillin on the human gut microbiome and resistome. Fecal samples were collected from 20 patients receiving 3-months of amoxicillin or placebo treatment as part of a Norwegian multicenter clinical trial on chronic low back pain (AIM study). Samples were collected at baseline, last day of treatment, and 9 months after antibiotic cessation. The abundance and diversity of microbial and resistome composi- tion were characterized using whole shotgun and functional metagenomic sequencing data. While the microbiome profiles of placebo subjects were stable over time, discernible changes in diversity and overall microbiome composition were observed after amoxicillin treatment. In particular, health- associated short-chain fatty acid producing species significantly decreased in proportion. However, these changes were short-lived as the microbiome showed overall recovery 9 months post-treatment. On the other hand, exposure to long-term amoxicillin was associated with an increase in total antimicrobial resistance gene load and diversity of antimicrobial resistance genes, with persistent changes even at 9 months post-treatment. Additionally, beta-lactam resistance was the most affected antibiotic class, suggesting a targeted response to amoxicillin, although changes at the gene level varied across individuals. Overall, our results suggest that the impact of prolonged amoxicillin exposure was more explicit and long-lasting in the fecal resistome than in microbiome composition. Such information is relevant for designing rational administration guidelines for antibiotic therapies.

• Rajar, Polona; Dhariwal, Achal; Silva, Gabriela Salvadori Da; Junges, Roger; Åmdal, Heidi Aarø & Berild, Dag [Show all 12 contributors for this article] (2022). Microbial DNA extraction of high-host content and low biomass samples: Optimized protocol for nasopharynx metagenomic studies. Frontiers in Microbiology. 13, p. 1–15. doi: 10.3389/fmicb.2022.1038120. Full text in Research Archive Show summary

  Introduction Low microbial biomass and high human DNA content in nasopharyngeal aspirate samples hinder comprehensive characterization of microbiota and resistome. We obtained samples from premature infants, a group with increased risk of developing respiratory disorders and infections, and consequently frequent exposure to antibiotics. Our aim was to devise an optimal protocol for handling nasopharyngeal aspirate samples from premature infants, focusing on host DNA depletion and microbiome and resistome characterization. Methods Three depletion and three DNA extraction protocols were compared, using RT-PCR and whole metagenome sequencing to determine the efficiency of human DNA removal, taxonomic profiling and assignment of antibiotic resistance genes. Protocols were tested using mock communities, as well as pooled and individual patient samples. Results The only extraction protocol to retrieve the expected DNA yield from mock community samples was based on a lytic method to improve Gram positive recovery (MasterPure™). Host DNA content in non-depleted aliquots from pooled patient samples was 99%. Only samples depleted with MolYsis™ showed satisfactory, but varied reduction in host DNA content, in both pooled and individual patient samples, allowing for microbiome and resistome characterisation (host DNA content from 15% to 98%). Other depletion protocols either retrieved too low total DNA yields, preventing further analysis, or failed to reduce host DNA content. By using Mol_MasterPure protocol on aliquots from pooled patient samples, we increased the number of bacterial reads by 7.6 to 1,725.8-fold compared to non-depleted reference samples. PCR results were indicative of achieved microbial enrichment. Individual patient samples processed with Mol_MasterPure protocol varied greatly in total DNA yield, host DNA content (from 40% to 98%), species and antibiotic resistance gene richness. Discussion Despite high human DNA and low microbial biomass content in nasopharynx aspirates of preterm infants, we were able to reduce host DNA content to levels compatible with downstream shotgun metagenomic analysis, including bacterial species identification and coverage of antibiotic resistance genes. Whole metagenomic sequencing of microbes colonizing the nasopharynx may contribute to explaining the possible role of airway microbiota in respiratory conditions and reveal carriage of antibiotic resistance genes.

• Shekhar, Sudhanshu; Åmdal, Heidi Aarø & Petersen, Fernanda Cristina (2021). Vaccination With the Commensal Streptococcus mitis Expressing Pneumococcal Serotype 5 Capsule Elicits IgG/IgA and Th17 Responses Against Streptococcus pneumoniae. Frontiers in Immunology. doi: 10.3389/fimmu.2021.676488. Full text in Research Archive Show summary

  Recent studies have identified a clinical isolate of the commensal Streptococcus mitis that expresses Streptococcus pneumoniae serotype 5 capsule (S. mitis serotype 5) and shows serospecificity toward pneumococcal serotype 5. However, it remains unknown whether S. mitis serotype 5 induces protective immunity against pneumococcal serotype 5. In this study, we evaluated the ability of S. mitis serotype 5 to generate protective immunity in a mouse model of lung infection with pneumococcal serotype 5. Upon challenge infection with S. pneumoniae serotype 5, mice intranasally immunized with S. mitis serotype 5 exhibited reduced pneumococcal loads in the lungs, nasal wash, and bronchoalveolar lavage fluid compared with those receiving PBS (control). The immunized mice displayed significantly higher levels of IgG and IgA antibodies reactive to S. mitis serotype 5, S. pneumoniae serotype 5 or S. pneumoniae serotype 4 than the antibody levels in control mice. In vaccinated mice, the IgG/IgA antibody levels reactive to S. mitis serotype 5 or S. pneumoniae serotype 5 were higher than the levels reactive to S. pneumoniae serotype 4. Furthermore, in-vitro restimulation of the lung-draining mediastinal lymph node cells and splenocytes from immunized mice with killed S. mitis serotype 5, S. pneumoniae serotype 5 or S. pneumoniae serotype 4 showed enhanced Th17, but not Th1 and Th2, responses. Overall, our findings show that mucosal immunization with S. mitis serotype 5 protects against S. pneumoniae serotype 5 infection and induces Th17 and predominant serotype-specific IgG/IgA antibody responses against pneumococcal infection.

• Junges, Roger; Sturød, Kjersti; Salvadori, Gabriela; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina (2019). Characterization of a Signaling System in Streptococcus mitis That Mediates Interspecies Communication with Streptococcus pneumoniae. Applied and Environmental Microbiology. ISSN 0099-2240. 85(2). doi: 10.1128/AEM.02297-18. Full text in Research Archive
• Filho, Antonio Pedro Ricomini; Khan, Rabia; Åmdal, Heidi Aarø & Petersen, Fernanda Cristina (2019). Conserved Pheromone Production, Response and Degradation by Streptococcus mutans. Frontiers in Microbiology. 10. doi: 10.3389/fmicb.2019.02140. Full text in Research Archive Show summary

  Streptococcus mutans, a bacterium with high cariogenic potential, coordinates competence for natural transformation and bacteriocin production via the XIP and CSP pheromones. CSP is effective in inducing bacteriocin responses but not competence in chemically defined media (CDM). This is in contrast to XIP, which is a strong inducer of competence in CDM but can also stimulate bacteriocin genes as a late response. Interconnections between the pathways activated by the two pheromones have been characterized in certain detail in S. mutans UA159, but it is mostly unknown whether such findings are representative for the species. In this study, we used bioassays based on luciferase reporters for the bacteriocin gene cipB and the alternative sigma factor sigX to investigate various S. mutans isolates for production and response to CSP and XIP pheromones in CDM. Similar to S. mutans UA159, endogenous CSP was undetectable in the culture supernatants of all tested strains. During optimization of the bioassay using the cipB reporter, we discovered that the activity of exogenous CSP used as a standard was reduced over time during S. mutans growth. Using a FRET-CSP reporter peptide, we found that S. mutans UA159 was able to degrade CSP, and that such activity was not significantly different in isogenic mutants with deletion of the protease gene htrA or the competence genes sigX, oppD, and comR. CSP cleavage was also detected in all the wild type strains, indicating that this is a conserved feature in S. mutans. For the XIP pheromone, endogenous production was observed in the supernatants of all 34 tested strains at peak concentrations in culture supernatants that varied between 200 and 26000 nM. Transformation in the presence of exogenous XIP was detected in all but one of the isolates. The efficiency of transformation varied, however, among the different strains, and for those with the highest transformation rates, endogenous XIP peak concentrations in the supernatants were above 2000 nM XIP. We conclude that XIP production and inducing effect on transformation, as well as the ability to degrade CSP, are conserved functions among different S. mutans isolates. Understanding the functionality and conservation of pheromone systems in S. mutans may lead to novel strategies to prevent or treat unbalances in oral microbiomes that may favor diseases.

• Salvadori, Gabriela; Junges, Roger; Åmdal, Heidi Aarø; Chen, T.; Morrison, D.A. & Petersen, Fernanda Cristina (2018). High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes. BMC Genomics. 19(1). doi: 10.1186/s12864-018-4802-y. Full text in Research Archive Show summary

  Background In streptococci of the mitis group, competence for natural transformation is a transient physiological state triggered by competence stimulating peptides (CSPs). Although low transformation yields and the absence of a widespread functional competence system have been reported for Streptococcus mitis, recent studies revealed that, at least for some strains, high efficiencies can be achieved following optimization protocols. To gain a deeper insight into competence in this species, we used RNA-seq, to map the global CSP response of two transformable strains: the type strain NCTC12261T and SK321. Results All known genes induced by ComE in Streptococcus pneumoniae, including sigX, were upregulated in the two strains. Likewise, all sets of streptococcal SigX core genes involved in extracellular DNA uptake, recombination, and fratricide were upregulated. No significant differences in the set of induced genes were observed when the type strain was grown in rich or semi-defined media. Five upregulated operons unique to S. mitis with a SigX-box in the promoter region were identified, including two specific to SK321, and one specific to NCTC12261T. Two of the strain-specific operons coded for different bacteriocins. Deletion of the unique S. mitis sigX regulated genes had no effect on transformation. Conclusions Overall, comparison of the global transcriptome in response to CSP shows the conservation of the ComE and SigX-core regulons in competent S. mitis isolates, as well as species and strain-specific genes. Although some S. mitis exhibit truncations in key competence genes, this study shows that in transformable strains, competence seems to depend on the same core genes previously identified in S. pneumoniae.

• Junges, Roger; Salvadori, Gabriela; Shekhar, Sudhanshu; Åmdal, Heidi Aarø; Periselneris, Jimstan & Chen, Tsute [Show all 8 contributors for this article] (2017). A quorum-sensing system that regulates Streptococcus pneumoniae biofilm formation and surface polysaccharide production. mSphere. 2(5), p. 1–18. doi: 10.1128/mSphere.00324-17. Full text in Research Archive Show summary

  Despite vaccines, Streptococcus pneumoniae kills more than a million people yearly. Thus, understanding how pneumococci transition from commensals to pathogens is particularly relevant. Quorum sensing regulates collective behaviors and thus represents a potential driver of commensal-to-pathogen transitions. Rgg/small hydrophobic peptide (SHP) quorum-sensing systems are widespread in streptococci, yet they remain largely uncharacterized in S. pneumoniae. Using directional transcriptome sequencing, we show that the S. pneumoniae D39 Rgg0939/SHP system induces the transcription of a single gene cluster including shp and capsule gene homologs. Capsule size measurements determined by fluorescein isothiocyanate-dextran exclusion allowed assignment of the system to the regulation of surface polysaccharide expression. We found that the SHP pheromone induced exopolysaccharide expression in R36A, an unencapsulated derivative of D39. In the encapsulated parent strain, overexpression of the Rgg system resulted in a mutant with increased capsule size. In line with previous studies showing that capsule expression is inversely associated with biofilm formation, we found that biofilm formed on lung epithelial cells was decreased in the overexpression strain and increased in an rgg deletion mutant. Although no significant differences were observed between D39 and the rgg deletion mutant in a mouse model of lung infection, in competitive assays, overexpression reduced fitness. This is the first study to reveal a quorum-sensing system in streptococci that regulates exopolysaccharide synthesis from a site distinct from the original capsule locus.

• Khan, Rabia; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute; Morrison, Donald A & Petersen, Fernanda Cristina (2017). A positive feedback loop mediated by Sigma X enhances expression of the streptococcal regulator ComR. Scientific Reports. 7(1). doi: 10.1038/s41598-017-04768-5. Full text in Research Archive Show summary

  Natural transformation is used by bacteria to take up DNA from their surroundings and incorporate it into their genomes. Streptococci do so during a transient period of competence, triggered by pheromones that they produce, secrete and sense under conditions influenced by the environment. In Streptococcus mutans, Streptococcus suis, and species of the bovis, salivarius and pyogenic groups of streptococci, the pheromone XIP is sensed by the intra-cellular regulator ComR, that in turn activates the transcription of comS, encoding the XIP precursor, and of sigX, encoding the only known alternative sigma factor in streptococci. Although induction of comR during competence has been known for more than fifteen years, the mechanism regulating its expression remains unidentified. By a combination of directional RNA-sequencing, optimal competence conditions, stepwise deletions and marker-less genome editing, we found that SigX is the missing link in overproduction of ComR. In the absence of comR induction, both sigX expression and transformation were significantly reduced. Placing comR and comS transcripts under the control of different regulators so as to form two interlocked positive feedback circuits may enable S. mutans to fine-tune the kinetics and magnitude of the competence response according to their need.

• Salvadori, Gabriela; Junges, Roger; Khan, Rabia; Åmdal, Heidi Aarø; Morrison, Donald A. & Petersen, Fernanda Cristina (2017). Natural transformation of oral streptococci by use of synthetic pheromones. Methods in molecular biology. ISSN 1064-3745. p. 219–232. doi: 10.1007/978-1-4939-6685-1_13. Full text in Research Archive Show summary

  The discovery that Streptococcus pneumoniae uses a competence-stimulating peptide (CSP) to induce competence for natural transformation, and that other species of the mitis and the anginosus streptococcal groups use a similar system, has expanded the tools to explore gene function and regulatory pathways in streptococci. Two other classes of pheromones have been discovered since then, comprising the bacteriocin-inducing peptide class found in Streptococcus mutans (also named CSP, although different from the former) and the SigX-inducing peptides (XIP), in the mutans, salivarius, bovis, and pyogenes groups of streptococci. The three classes of peptide pheromones can be ordered from peptide synthesis services at affordable prices, and used in transformation assays to obtain competent cultures consistently at levels usually higher than those achieved during spontaneous competence. In this chapter, we present protocols for natural transformation of oral streptococci that are based on the use of synthetic pheromones, with examples of conditions optimized for transformation of S. mutans and Streptococcus mitis. This is a post-peer-review, pre-copyedit version of an article published in Oral Biology. © Springer Science+Business Media LLC 2017.

• Junges, Roger; Khan, Rabia; Tovpeko, Yanina; Åmdal, Heidi Aarø; Petersen, Fernanda Cristina & Morrison, Donald (2017). Markerless genome editing in competent streptococci. Methods in molecular biology. ISSN 1064-3745. 1537, p. 233–247. doi: 10.1007/978-1-4939-6685-1_14. Full text in Research Archive Show summary

  Selective markers employed in classical mutagenesis methods using natural genetic transformation can affect gene expression, risk phenotypic effects, and accumulate as unwanted genes during successive mutagenesis cycles. In this chapter, we present a protocol for markerless genome editing in Streptococcus mutans and Streptococcus pneumoniae achieved with an efficient method for natural transformation. High yields of transformants are obtained by combining the unimodal state of competence developed after treatment of S. mutans with sigX-inducing peptide pheromone (XIP) in a chemically defined medium (CDM) or of S. pneumoniae with the competence-stimulating peptide (CSP) together with use of a donor amplicon carrying extensive flanking homology. This combination ensures efficient and precise integration of a new allele by the recombination machinery present in competent cells. This is a post-peer-review, pre-copyedit version of an article published in Oral Biology. © Springer Science+Business Media LLC 2017

• Khan, Rabia; Rukke, Håkon Valen; Høvik, Hedda; Åmdal, Heidi Aarø; Chen, T. & Morrison, Donald A. [Show all 7 contributors for this article] (2016). Comprehensive Transcriptome Profiles of Streptococcus mutans UA159 Map Core Streptococcal Competence Genes. mSystems. 1(2). doi: 10.1128/mSystems.00038-15. Full text in Research Archive Show summary

  In Streptococcus mutans, an oral colonizer associated with dental caries, development of competence for natural genetic transformation is triggered by either of two types of peptide pheromones, competence-stimulating peptides (CSPs) (18 amino acids [aa]) or SigX-inducing peptides (XIPs) (7 aa). Competence induced by CSP is a late response to the pheromone that requires the response regulator ComE and the XIP-encoding gene comS. XIP binds to ComR to allow expression of the alternative sigma factor SigX and the effector genes it controls. While these regulatory links are established, the precise set of effectors controlled by each regulator is poorly defined. To improve the definition of all three regulons, we used a high-resolution tiling array to map global changes in gene expression in the early and late phases of the CSP response. The early phase of the CSP response was limited to increased gene expression at four loci associated with bacteriocin production and immunity. In the late phase, upregulated regions expanded to a total of 29 loci, including comS and genes required for DNA uptake and recombination. The results indicate that the entire late response to CSP depends on the expression of comS and that the immediate transcriptional response to CSP, mediated by ComE, is restricted to just four bacteriocin-related loci. Comparison of the new data with published transcriptome data permitted the identification of all of the operons in each regulon: 4 for ComE, 2 for ComR, and 21 for SigX. Finally, a core set of 27 panstreptococcal competence genes was identified within the SigX regulon by comparison of transcriptome data from diverse streptococcal species.

• Morrison, D.A.; Khan, Rabia; Junges, Roger; Åmdal, Heidi Aarø & Petersen, Fernanda Cristina (2015). Genome editing by natural genetic transformation in Streptococcus mutans. Journal of Microbiological Methods. ISSN 0167-7012. 119, p. 134–141. doi: 10.1016/j.mimet.2015.09.023. Full text in Research Archive

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• Dhariwal, Achal; Salvadori, Gabriela; Åmdal, Heidi Aarø; Dutta, Anirban; Mande, Sharmila & Nangia, Sushma [Show all 7 contributors for this article] (2026). Exploring Resistomes in Low-Microbial-Biomass Airway Microbiomes Using Functional Metagenomics. Full text in Research Archive
• Brar, Navdeep Kaur; Dhariwal, Achal; Åmdal, Heidi Aarø; Junges, Roger; Salvadori, Gabriela & Petersen, Fernanda Cristina (2022). The Impact of Ampicillin on the Oral Microbiome and Resistome. Full text in Research Archive
• Rajar, Polona; Dhariwal, Achal; Salvadori, Gabriela; Junges, Roger; Åmdal, Heidi Aarø & Berild, Dag [Show all 12 contributors for this article] (2022). Microbial DNA extraction of high-host content and low biomass samples: optimized protocol for nasopharynx metagenomic studies. Full text in Research Archive Show summary

  Low microbial biomass and high human DNA content in nasopharyngeal aspirate samples hinder comprehensive characterization of microbiota and resistome. We obtained samples from premature infants, a group with increased risk of developing respiratory disorders and infections, and consequently frequent exposure to antibiotics. Our aim was to devise an optimal protocol for handling nasopharyngeal aspirates from premature infants, focusing on host DNA depletion and microbiome and resistome characterization. Three depletion and three DNA extraction protocols were compared, using RT-PCR and whole metagenome sequencing to determine the efficiency of human DNA removal, taxonomic profiling and assignment of antibiotic resistance genes. Protocols were tested using mock communities, as well as pooled and individual patient samples. The only extraction protocol to retrieve the expected DNA yield from mock community samples was based on a lytic method to improve Gram positive recovery (MasterPure™). Only samples depleted with MolYsis™ showed satisfactory, but varied reduction in host DNA content, in both pooled and individual patient samples, allowing for microbiome and resistome characterisation (host DNA content from 15% to 98%). PCR results were indicative of achieved microbial enrichment. Despite high human DNA and low microbial biomass content in nasopharynx aspirates of preterm infants, we were able to reduce host DNA content to levels compatible with downstream shotgun metagenomic analysis, including bacterial species identification and coverage of antibiotic resistance genes. Whole metagenomic sequencing of microbes colonizing the nasopharynx may contribute to explaining the possible role of airway microbiota in respiratory conditions and reveal carriage of antibiotic resistance genes.

• Shekhar, Sudhanshu; Åmdal, Heidi Aarø & Petersen, Fernanda Cristina (2021). Vaccination with the commensal Streptococcus mitis expressing pneumococcal serotype 5 capsule elicits IgG/IgA and Th17 responses against Streptococcus pneumoniae. Full text in Research Archive
• Petersen, Fernanda Cristina; Dhariwal, Achal; Bråten, Lars Christian Haugli; Sturød, Kjersti; Junges, Roger & Salvadori, Gabriela [Show all 10 contributors for this article] (2021). Off-target impact of long-term amoxicillin treatment. Full text in Research Archive
• Salvadori, Gabriela; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute; Morrison, Donald A & Petersen, Fernanda Cristina (2018). Molecular Characterization of Genetic Competence in Streptococcus mitis. Full text in Research Archive
• Salvadori, Gabriela; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute; Morrison, Donald A & Petersen, Fernanda Cristina (2018). Insights into regulatory pathways of competence development in Streptococcus mitis type strain and SK321. Full text in Research Archive
• Junges, Roger; Sturød, Kjersti; Salvadori, Gabriela; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina (2018). Interspecies activation of a virulent pathway by an oral commensal. Full text in Research Archive
• Petersen, Fernanda Cristina; Khan, Rabia; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Morrison, Donald A. (2015). A new link between the Streptococcus mutans XIP and CSP pheromone pathways revealed by directional RNA-sequencing. Full text in Research Archive
• Junges, Roger; Khan, Rabia; Åmdal, Heidi Aarø; Morrison, Donald A. & Petersen, Fernanda Cristina (2015). Transcriptome response of Streptoccocus mutans to the sigX-inducing peptide (XIP). Full text in Research Archive
• Salvadori, Gabriela; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina (2015). Transcriptome response of Streptococcus mitis to the competence pheromone. Full text in Research Archive
• Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina (2015). A New Pheromone in Streptococcus mitis Enhances Biofilm Formation. Full text in Research Archive
• Junges, Roger; Khan, Rabia; Åmdal, Heidi Aarø; Morrison, Donald A. & Petersen, Fernanda Cristina (2015). A new link between two Streptococcus mutans pheromones. Full text in Research Archive
• Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina (2015). Characterization of an Rgg/SHP system in Streptococcus mitis that allows communication with Streptococcus pneumoniae. Full text in Research Archive
• Salvadori, Gabriela; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina (2015). Identification of Streptococcus mitis competence pheromone responsive genes by transcriptome analysis. Full text in Research Archive
• Silva, Gabriela Salvadori; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina (2015). Streptococcus mitis response to the competence pheromone. Full text in Research Archive
• Silva, Gabriela Salvadori; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina (2015). Transcriptome analysis of Streptococcus mitis response to the competence pheromone. Full text in Research Archive

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