Skip to main content
SpringerLink
Log in

Metabolic and transcriptomic profiling of Streptococcus intermedius during aerobic and anaerobic growth

  • Original Article
  • Published:
Metabolomics Aims and scope Submit manuscript

Abstract

Streptococcus intermedius, S. constellatus, and S. anginosus comprise the Streptococcus Milleri/Anginosus group (SMG). They are facultative anaerobic bacteria that asymptomatically colonize the upper respiratory, gastrointestinal and urogenital tracts. They are also common pathogens in pyogenic invasive infections, as well as pulmonary and urinary tract infections. Most SMG infections are polymicrobial and associated with co-infecting obligate anaerobic bacteria. To better understand the effect of oxygen on the growth and physiology of these organisms, we compared the global metabolomic and transcriptomic profiles of S. intermedius strain B196 under aerobic and anaerobic conditions. The largest transcriptional changes were associated with induction of oxidative stress response genes under aerobic conditions. Modest changes in expression of genes associated with primary metabolism were observed under the two conditions. Intracellular and extracellular metabolites were measured using HILIC–LCMS. Differences in the abundance of specific metabolites were correlated with observed transcription changes in genes associated with their metabolism, implying that metabolism is primarily regulated at the transcriptional level. Rather than a large shift in primary metabolism under anaerobic conditions our results suggest a modest tuning of metabolism to support the accelerated growth rate of S. intermedius strain B196 in the absence of oxygen. For example, under anaerobic conditions, purine metabolism, pyrimidine de novo synthesis and pyrimidine salvage pathways were up-regulated at metabolic and transcriptional levels. This study provides a better understanding of differences between S. intermedius anaerobic and aerobic metabolism. The results reflect the organism’s predilection for anaerobic growth consistent with its pathogenic association with anaerobes in polymicrobial infections.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Ahn, S.-J., Ahn, S.-J., Browngardt, C. M., & Burne, R. A. (2009). Changes in biochemical and phenotypic properties of Streptococcus mutans during growth with aeration. Applied and Environment Microbiology, 75(8), 2517–2527.

    Article  CAS  Google Scholar 

  • Ahn, S.-J., Wen, Z. T., & Burne, R. A. (2007). Effects of oxygen on virulence traits of Streptococcus mutans. Journal of Bacteriology, 189(23), 8519–8527. doi:10.1128/JB.01180-07.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Asam, D., & Spellerberg, B. (2014). Molecular pathogenicity of Streptococcus anginosus. Mol Oral Microbiol, 29(4), 145–155.

    Article  CAS  PubMed  Google Scholar 

  • Bassit, N., Boquien, C.-Y., Picque, D., & Georges, C. (1993). Effect of initial oxygen concentration on diacetyl and acetoin production by Lactococcus lactis subsp. lactis biovar diacetylactis. Applied and Environment Microbiology, 59(6), 1893–1897.

    CAS  Google Scholar 

  • Brittan, J. L., Buckeridge, T. J., Finn, A., Kadioglu, A., & Jenkinson, H. F. (2012). Pneumococcal neuraminidase A: An essential upper airway colonization factor for Streptococcus pneumoniae. Molecular Oral Microbiology, 27(4), 270–283.

    Article  CAS  PubMed  Google Scholar 

  • Broadhurst, D. I., & Kell, D. B. (2006). Statistical strategies for avoiding false discoveries in metabolomics and related experiments. Metabolomics, 2(4), 171–196.

    Article  CAS  Google Scholar 

  • Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C. A., et al. (2014). The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Research, 42(D1), D459–D471.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Choi, K.-H., Heath, R. J., & Rock, C. O. (2000). β-Ketoacyl-acyl carrier protein synthase III (FabH) is a determining factor in branched-chain fatty acid biosynthesis. Journal of Bacteriology, 182(2), 365–370.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Coman, G., Pânzaru, C., Diculencu, D., Gotia, D., Cârlan, M., Dahorea, C., & Butnaru, F. (1995). Pyogenic infections with different locations caused by Streptococcus anginosus alone or in association with anaerobic bacteria. Revista Medico-Chirurgicala A Societatii de Medici si Naturalisti din Iasi, 99(3–4), 215–219.

    CAS  PubMed  Google Scholar 

  • Cotter, P. D., & Hill, C. (2003). Surviving the acid test: Responses of gram-positive bacteria to low pH. Microbiology and Molecular Biology Reviews, 67(3), 429–453.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Creek, D. J., Dunn, W. B., Fiehn, O., Griffin, J. L., Hall, R. D., Lei, Z., et al. (2014). Metabolite identification: Are you sure? And how do your peers gauge your confidence? Metabolomics, 10(3), 350–353.

    Article  CAS  Google Scholar 

  • Crow, V. L., & Pritchard, G. G. (1977). Fructose 1,6-diphosphate-activated l-lactate dehydrogenase from Streptococcus lactis: Kinetic properties and factors affecting activation. Journal of Bacteriology, 131(1), 82–91.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cusumano, Z. T., & Caparon, M. G. (2015). Citrulline protects Streptococcus pyogenes from acid stress using the arginine deiminase pathway and the F1F0-ATPase. Journal of Bacteriology, 197(7), 1288–1296.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cusumano, Z. T., Watson, M. E., & Caparon, M. G. (2014). Streptococcus pyogenes arginine and citrulline catabolism promotes infection and modulates innate immunity. Infection and Immunity, 82(1), 233–242.

    Article  PubMed  PubMed Central  Google Scholar 

  • Derré-Bobillot, A., Cortes-Perez, N. G., Yamamoto, Y., Kharrat, P., Couvé, E., Da Cunha, V., et al. (2013). Nuclease A (Gbs0661), an extracellular nuclease of Streptococcus agalactiae, attacks the neutrophil extracellular traps and is needed for full virulence. Molecular Microbiology, 89(3), 518–531.

    Article  PubMed  Google Scholar 

  • Fei, F., Bowdish, D. M. E., & McCarry, B. E. (2014). Comprehensive and simultaneous coverage of lipid and polar metabolites for endogenous cellular metabolomics using HILIC-TOF-MS. Analytical and Bioanalytical Chemistry, 406(15), 3723–3733.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Filkins, L. M., Hampton, T. H., Gifford, A. H., Gross, M. J., Hogan, D. A., Sogin, M. L., et al. (2012). Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability. Journal of Bacteriology, 194(17), 4709–4717.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fozo, E. M., & Quivey, R. G. (2004). The fabM gene product of Streptococcus mutans is responsible for the synthesis of monounsaturated fatty acids and is necessary for survival at low pH. Journal of Bacteriology, 186(13), 4152–4158.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gossling, J. (1988). Occurrence and pathogenicity of the Streptococcus milleri group. Reviews of Infectious Diseases, 10(2), 257–285.

    Article  CAS  PubMed  Google Scholar 

  • Gruening, P., Fulde, M., Valentin-Weigand, P., & Goethe, R. (2006). Structure, regulation, and putative function of the arginine deiminase system of Streptococcus suis. Journal of Bacteriology, 188(2), 361–369.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gupta, R., Yang, J., Dong, Y., Swiatlo, E., Zhang, J.-R., Metzger, D. W., & Bai, G. (2013). Deletion of arcD in Streptococcus pneumoniae D39 impairs its capsule and attenuates virulence. Infection and Immunity, 81(10), 3903–3911.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Higuchi, M. (1984). The effect of oxygen on the growth and mannitol fermentation of Streptococcus mutans. Journal of General Microbiology, 130(7), 1819–1826.

    CAS  PubMed  Google Scholar 

  • Higuchi, M., Yamamoto, Y., & Kamio, Y. (2000). Molecular biology of oxygen tolerance in lactic acid bacteria: Functions of NADH oxidases and Dpr in oxidative stress. Journal of Bioscience and Bioengineering, 90(5), 484–493.

    Article  CAS  PubMed  Google Scholar 

  • Hirai, T., Kimura, S., & Mori, N. (2005). Head and neck infections caused by Streptococcus milleri group: An analysis of 17 cases. Auris, Nasus, Larynx, 32(1), 55–58.

    Article  PubMed  Google Scholar 

  • Hocken, D. B., & Dussek, J. E. (1985). Streptococcus milleri as a cause of pleural empyema. Thorax, 40(8), 626–628.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hytönen, J., Haataja, S., & Finne, J. (2006). Use of flow cytometry for the adhesion analysis of Streptococcus pyogenes mutant strains to epithelial cells: Investigation of the possible role of surface pullulanase and cysteine protease, and the transcriptional regulator Rgg. BMC Microbiology, 6(1), 18.

    Article  PubMed  PubMed Central  Google Scholar 

  • Imlay, J. A. (2013). The molecular mechanisms and physiological consequences of oxidative stress: Lessons from a model bacterium. Nature Reviews Microbiology, 11(7), 443–454.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jakubovics, N. S., Smith, A. W., & Jenkinson, H. F. (2002). Oxidative stress tolerance is manganese (Mn(2+)) regulated in Streptococcus gordonii. Microbiology, 148(Pt10), 3255–3263.

    Article  CAS  PubMed  Google Scholar 

  • Kuhl, C., Tautenhahn, R., Böttcher, C., Larson, T.R., & Neumann, S. (2015). CAMERA: An integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84(1), 283–289.

    Article  Google Scholar 

  • Laupland, K. B., Ross, T., Church, D. L., & Gregson, D. B. (2006). Population-based surveillance of invasive pyogenic streptococcal infection in a large Canadian region. Clinical Microbiology & Infection, 12(3), 224–230.

    Article  CAS  Google Scholar 

  • Lee, E. Y., Khatwa, U., McAdam, A. J., Bastos, M. Almeida, Mahmood, S. A., Ervoes, J. P., & Boiselle, P. M. (2010). Streptococcus milleri group pleuropulmonary infection in children: Computed tomographic findings and clinical features. Journal of Computer Assisted Tomography, 34(6), 927–932.

    Article  PubMed  Google Scholar 

  • Marquis, R. E., Bender, G. R., Murray, D. R., & Wong, A. (1987). Arginine deiminase system and bacterial adaptation to acid environments. Applied and Environment Microbiology, 53(1), 198–200.

    CAS  Google Scholar 

  • Marraffini, L. A., & Sontheimer, E. J. (2010). CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nature Reviews Genetics, 11(3), 181–190.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marrakchi, H., Zhang, Y.-M., & Rock, C. O. (2002). Mechanistic diversity and regulation of Type II fatty acid synthesis. Biochemical Society Transactions, 30(part 6), 1050–1055.

    Article  CAS  PubMed  Google Scholar 

  • Midon, M., Schäfer, P., Pingoud, A., Ghosh, M., Moon, A. F., Cuneo, M. J., et al. (2011). Mutational and biochemical analysis of the DNA-entry nuclease EndA from Streptococcus pneumoniae. Nucleic Acids Research, 39(2), 623–634.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Olson, A. B., Kent, H., Sibley, C. D., Grinwis, M. E., Mabon, P., Ouellette, C., et al. (2013). Phylogenetic relationship and virulence inference of Streptococcus anginosus group : Curated annotation and whole-genome comparative analysis support distinct species designation. BMC Genomics, 14, 895.

    Article  PubMed  PubMed Central  Google Scholar 

  • Parkhomchuk, D., Borodina, T., Amstislavskiy, V., Banaru, M., Hallen, L., Krobitsch, S., et al. (2009). Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Research, 37(18), e123.

    Article  PubMed  PubMed Central  Google Scholar 

  • Parkins, M. D., Sibley, C. D., Surette, M. G., & Rabin, H. R. (2008). The Streptococcus milleri group—an unrecognized cause of disease in cystic fibrosis: A case series and literature review. Pediatric Pulmonology, 43(5), 490–497.

    Article  PubMed  Google Scholar 

  • Portela, C. A. F., Smart, K. F., Tumanov, S., Cook, G. M., & Villas-Bôas, S. G. (2014). Global metabolic response of Enterococcus faecalis to oxygen. Journal of Bacteriology, 196(11), 2012–2022.

    Article  PubMed  PubMed Central  Google Scholar 

  • Prüb, B. M., Nelms, J. M., Park, C., & Wolfe, A. J. (1994). Mutations in NADH: Ubiquinone oxidoreductase. Journal of Bacteriology, 176(8), 2143–2150.

    Google Scholar 

  • Ripley, R. T., Cothren, C. C., Moore, E. E., Long, J., Johnson, J. L., & Haenel, J. B. (2006). Streptococcus milleri infections of the pleural space: Operative management predominates. American Journal of Surgery, 192(6), 817–821.

    Article  PubMed  Google Scholar 

  • Rogers, A. H., Zilm, P. S., & Gully, N. J. (1987). Influence of arginine on the coexistence of Streptococcus mutans and S. milleri in glucose-limited mixed continuous culture. Microbial Ecology, 14(3), 193–202.

    Article  CAS  PubMed  Google Scholar 

  • Ruoff, K. L. (1988). Streptococcus anginosus (“Streptococcus milleri”): the unrecognized pathogen. Clinical Microbiology Reviews, 1(1), 102–108.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sapranauskas, R., Gasiunas, G., Fremaux, C., Barrangou, R., Horvath, P., & Siksnys, V. (2011). The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Research, 39(21), 9275–9282.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Serbanescu, M. A., Cordova, M., Krastel, K., Flick, R., Beloglazova, N., Latos, A., et al. (2015). Role of the Streptococcus mutans CRISPR-Cas systems in immunity and cell physiology. Journal of Bacteriology, 197(4), 749–761.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sezonov, G., Joseleau-Petit, D., & D’Ari, R. (2007). Escherichia coli physiology in Luria-Bertani broth. Journal of Bacteriology, 189(23), 8746–8749.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shinzato, T., & Saito, A. (1994). A mechanism of pathogenicity of “Streptococcus milleri group” in pulmonary infection: Synergy with an anaerobe. Journal of Medical Microbiology, 40, 118–123.

    Article  CAS  PubMed  Google Scholar 

  • Shinzato, T., & Saito, A. (1995). The Streptococcus milleri group as a cause of pulmonary infections. Clinical Infectious Diseases, 21(Supplement 3), S238–S243.

    Article  PubMed  Google Scholar 

  • Sibley, C. D., Church, D. L., Surette, M. G., Dowd, S. E., & Parkins, M. D. (2012). Pyrosequencing reveals the complex polymicrobial nature of invasive pyogenic infections: Microbial constituents of empyema, liver abscess, and intracerebral abscess. European Journal of Clinical Microbiology and Infectious Diseases, 31(10), 2679–2691.

    Article  CAS  PubMed  Google Scholar 

  • Sibley, C. D., Parkins, M. D., Rabin, H. R., Duan, K., Norgaard, J. C., & Surette, M. G. (2008). A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients. Proceedings of the National Academy of Sciences of the United States of America, 105(39), 15070–15075.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Siegman-Igra, Y., Azmon, Y., & Schwartz, D. (2012). Milleri group streptococcus—a stepchild in the viridans family. European Journal of Clinical Microbiology and Infectious Diseases, 31(9), 2453–2459.

    Article  CAS  PubMed  Google Scholar 

  • Smith, C. A., Want, E. J., O’Maille, G., Abagyan, R., & Siuzdak, G. (2006). XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Analytical Chemistry, 78(3), 779–787.

    Article  CAS  PubMed  Google Scholar 

  • Stadelmann, B., Hanevik, K., Andersson, M. K., Bruserud, O., & Svärd, S. G. (2013). The role of arginine and arginine-metabolizing enzymes during Giardia—host cell interactions in vitro. BMC Microbiology, 13, 256.

    Article  PubMed  PubMed Central  Google Scholar 

  • Sumner, L. W., Amberg, A., Barrett, D., Beale, M. H., Beger, R., Daykin, C. A., et al. (2007). Proposed minimum reporting standards for chemical analysis chemical analysis working group (CAWG) metabolomics standards initiative (MSI). Metabolomics, 3(3), 211–221.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D. R., et al. (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 7(3), 562–578.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trotter, E. W., Rolfe, M. D., Hounslow, A. M., Craven, C. J., Williamson, M. P., Sanguinetti, G., et al. (2011). Reprogramming of Escherichia coli K-12 metabolism during the initial phase of transition from an anaerobic to a micro-aerobic environment. PLoS One, 6(9), e25501.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van der Auwera, P. (1985). Clinical significance of Streptococcus milleri. European Journal of Clinical Microbiology, 4(4), 386–390.

    Article  PubMed  Google Scholar 

  • Whiley, R. A. A., Beighton, D., Winstanley, T. G. G., Fraser, H. Y. Y., & Hardie, J. M. M. (1992). Streptococcus intermedius, Streptococcus constellatus, and Streptococcus anginosus (the Streptococcus milleri group): association with different body sites and clinical infections. Journal of Clinical Microbiology, 30(1), 243–244.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wong, C. A., Donald, F., & Macfarlane, J. T. (1995). Streptococcus milleri pulmonary disease: A review and clinical description of 25 patients. Thorax, 50(10), 1093–1096.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia, J., Sinelnikov, I. V., Han, B., & Wishart, D. S. (2015). MetaboAnalyst 3.0–making metabolomics more meaningful. Nucleic Acids Research, 43(W1), W251–W257.

    Article  PubMed  PubMed Central  Google Scholar 

  • Zheng, L., T’Kind, R., Decuypere, S., von Freyend, S. J., Coombs, G. H., & Watson, D. G. (2010). Profiling of lipids in Leishmania donovani using hydrophilic interaction chromatography in combination with Fourier transform mass spectrometry. Rapid Communications in Mass Spectrometry, 24, 2074–2082.

    Article  CAS  PubMed  Google Scholar 

  • Zúñiga, M., Pérez, G., & González-Candelas, F. (2002). Evolution of arginine deiminase (ADI) pathway genes. Molecular Phylogenetics and Evolution, 25(3), 429–444.

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This work is dedicated to the late Prof. Brian McCarry (1946–2013). FF was supported by an Ontario Graduate Scholarship. MGS and DMEB are supported by the CIHR and hold Canada Research Chairs. Work in the Bowdish laboratory is supported by the McMaster Immunology Research Centre (MIRC) and work in the Bowdish and Surette labs are supported by the M.G. DeGroote Institute for Infectious Disease Research (IIDR). The authors would like to thank the Center for Microbial Chemical Biology (CMCB) at McMaster for access to the LC–MS. This study was funded by a grant from the Canadian Institutes of Health Research to DMEB and MGS (Grant # 108032).

Author information

Author notes

    Authors and Affiliations

    1. Department of Chemistry and Chemical Biology, McMaster University, Hamilton, L8S4M1, Canada

      Fan Fei & Brian E. McCarry

    2. Department of Pathology and Molecular Medicine, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, L8N3Z5, Canada

      Fan Fei & Dawn M. E. Bowdish

    3. Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8S4K1, Canada

      Michelle L. Mendonca & Michael G. Surette

    4. Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, L8S4K1, Canada

      Michael G. Surette

    Authors
    1. Fan Fei
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Michelle L. Mendonca
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Brian E. McCarry
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. Dawn M. E. Bowdish
      View author publications

      You can also search for this author in PubMed Google Scholar

    5. Michael G. Surette
      View author publications

      You can also search for this author in PubMed Google Scholar

    Corresponding author

    Correspondence to Michael G. Surette.

    Ethics declarations

    Conflict of interest

    All authors declared no conflict of interest.

    Human and animal informed consent

    This article does not contain any studies with human participants or animals performed by any of the author.

    Additional information

    Fan Fei, and Michelle L. Mendonca have contributed equally to this work.

    Electronic supplementary material

    Rights and permissions

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Fei, F., Mendonca, M.L., McCarry, B.E. et al. Metabolic and transcriptomic profiling of Streptococcus intermedius during aerobic and anaerobic growth. Metabolomics 12, 46 (2016). https://doi.org/10.1007/s11306-016-0966-0

    Download citation

    • Received:

    • Accepted:

    • Published:

    • DOI: https://doi.org/10.1007/s11306-016-0966-0

    Keywords

    Search

    Navigation