Details of Microbe Species (MIC)

General Information of MIC (ID: MIC01263)
MIC Name Streptococcus pneumoniae (firmicutes)
MIC Synonyms Micrococcus pneumoniae
Body Site Nose
Lineage Kingdom: Bacteria
Phylum: Firmicutes
Class: Bacilli
Order: Lactobacillales
Family: Streptococcaceae
Genus: Streptococcus
Species: Streptococcus pneumoniae
Oxygen Sensitivity Facultative anaerobe
Microbial Metabolism Saccharolytic; Respiratory or Fermentative
Gram Positive
Host Relationship Pathogen
Genome Size (bp) 2188259
No. of Coding Genes 2080
No. of Non-Coding Genes 45
No. of Small Non-Coding Genes 45
No. of Gene Transcripts 2125
No. of Base Pairs 2188259
Description Streptococcus pneumoniae, or pneumococcus, is a facultative anaerobic, Gram-positive, alpha-hemolytic or beta-hemolytic member of the genus Streptococcus. They are usually found in pairs and do not form spores and are nonmotile. As a significant human pathogenic bacterium S. pneumoniae was recognized as a major cause of pneumonia.
External Links Taxonomy ID
1313
Genome Assembly ID
Spn.str2298_v1.0
GOLD Organism ID
Go0003791
Disease Relevance
          Chronic obstructive pulmonary disease  [ICD-11: CA22]
             Description Acute pulmonary infection by Streptococcus pneumoniae was characterized by high bacterial numbers in the lung. [1]
          Influenza  [ICD-11: 1E30]
             Description Much of the mortality attributed to influenza virus is due to secondary bacterial pneumonia, particularly from Streptococcus pneumoniae. [2]
          Otitis media  [ICD-11: AA80]
             Description Streptococcus pneumoniae was associated with chronic forms of otitis media. [3]
          Pneumonia  [ICD-11: CA40]
             Description The Gram-positive bacterium Streptococcus pneumoniae can cause pneumonia. [4]
          Pneumonia  [ICD-11: CA40]
             Description Streptococcus pneumoniae infection can lead to pneumococcal disease, a major cause of mortality in children under the age of five years. [5]
          Sepsis  [ICD-11: 1G41]
             Description Intracellular replication of Streptococcus pneumoniae inside splenic macrophages served as a reservoir for septicaemia. [6]
Host Genetic Factors (HGFs)
          DEFB103A
             HGF ID HGF2349 HGF Info       Class Copy Number Variation: Gene Deletion (CNV-GDe)
             Description The increased DEFB-CN has been significantly associated with the abundance of Streptococcus pneumoniae (p-value<0.05). [7]
          rs2275913
             HGF ID HGF1732 HGF Info       Class Single Nucleotide Polymorphism: Upstream variant (SNP-UV)
             Description The IL-17 SNP rs2275913 was connected with Streptococcus pneumoniae detection in the hypopharynx. [8]
Host Immune Factors (HIFs)
          Indoleamine 2,3-dioxygenase 1
             HIF ID HIFM0120 HIF Info       Class Checkpoint molecule (CM)
             Description The host tryptophan-catabolizing enzyme, indoleamine 2,3-dioxygenase 1(IDO1), is induced specifically in the lungs of mice infected with Streptococcus pneumoniae. [9]
          Programmed death-ligand 1
             HIF ID HIFM0189 HIF Info       Class Checkpoint molecule (CM)
             Description PD-L1 was important negative regulators of the adaptive immune response to the polysaccharide capsule of Streptococcus pneumoniae. [10]
          Programmed death-ligand 2
             HIF ID HIFM0190 HIF Info       Class Checkpoint molecule (CM)
             Description PD-L2 was important negative regulators of the adaptive immune response to the polysaccharide capsule of Streptococcus pneumoniae. [10]
          C-X-C motif chemokine 10
             HIF ID HIFM0074 HIF Info       Class Cytokine (Cyt)
             Description Streptococcus pneumoniae contributes to a faster and possibly higher level of CXCL10/IP-10 expression induced by RSV infection in human MDMs. [11]
          BATF3+ dendritic cells
             HIF ID HIFC0167 HIF Info       Class Dendritic cells (DCs)
             Description Batf3+ dendritic cells induced IgA responses which showed clearance of Streptococcus pneumoniae. [12]
          Immunoglobulin M
             HIF ID HIFM0266 HIF Info       Class Immunoglobulin (Ig)
             Description IgM is effective during Streptococcus pneumoniae infection. [13]
          Immunoglobulin G2
             HIF ID HIFM0268 HIF Info       Class Immunoglobulin (Ig)
             Description IgG2 could response to Streptococcus pneumoniae. [14]
          Immunoglobulin G1
             HIF ID HIFM0269 HIF Info       Class Immunoglobulin (Ig)
             Description IgG1 could response to the choline-binding protein PspC of Streptococcus pneumoniae. [15]
          Immunoglobulin G
             HIF ID HIFM0270 HIF Info       Class Immunoglobulin (Ig)
             Description IgG could response to pneumococcal capsular polysaccharide (PCP). [16]
          Immunoglobulin A1
             HIF ID HIFM0275 HIF Info       Class Immunoglobulin (Ig)
             Description The activity of IgA1 proteases from Streptococcus pneumoniae could effect enzymolysis of human immunoglobulin A1(lgA1). [17]
          Immunoglobulin A2
             HIF ID HIFM0276 HIF Info       Class Immunoglobulin (Ig)
             Description Streptococcus pneumoniae surface antigen could have higher proportion of IgA2. [18]
          Immunoglobulin D
             HIF ID HIFM0277 HIF Info       Class Immunoglobulin (Ig)
             Description Elevated IgD levels is associated with Streptococcus pneumonia infection. [19]
          Immunoglobulin A
             HIF ID HIFM0272 HIF Info       Class Immunoglobulin (Ig)
             Description IgA immune responses was associated with Streptococcus pneumoniae. [20]
          Alveolar macrophages
             HIF ID HIFC0170 HIF Info       Class Macrophages (Mac)
             Description Induction of memory alveolar macrophages following viral exposure is associated with trained immunity against Streptococcus pneumoniae infection in the lung. [21]
          CD43++ monocytes
             HIF ID HIFC0212 HIF Info       Class Monocytes (Mono)
             Description CD43++ monocytes were preferentially reduced after intranasal infection with Streptococcus pneumoniae. [22]
          CD4+ regulatory T cells
             HIF ID HIFC0034 HIF Info       Class T cells (TCs)
             Description CD4+ T cells mediated humoral immune responses to type 3 capsular polysaccharide of Streptococcus pneumoniae. [23]
Environmental Factor(s)
             Disbiome ID
      122
             gutMDisorder ID
      gm0624
             aBiofilm Organism
      Streptococcus pneumoniae
References
1 Systemic disease during Streptococcus pneumoniae acute lung infection requires 12-lipoxygenase-dependent inflammation. J Immunol. 2013 Nov 15;191(10):5115-23. doi: 10.4049/jimmunol.1300522. Epub 2013 Oct 2.
2 Influenza promotes pneumococcal growth during coinfection by providing host sialylated substrates as a nutrient source. Cell Host Microbe. 2014 Jul 9;16(1):55-67. doi: 10.1016/j.chom.2014.06.005.
3 The outcome of H. influenzae and S. pneumoniae inter-species interactions depends on pH, nutrient availability and growth phase. Int J Med Microbiol. 2015 Dec;305(8):881-92. doi: 10.1016/j.ijmm.2015.09.003. Epub 2015 Sep 14.
4 Infection and metabolism - Streptococcus pneumoniae metabolism facing the host environment.Cytokine. 2018 Dec;112:75-86. doi: 10.1016/j.cyto.2018.07.021. Epub 2018 Aug 1.
5 Investigation of potential anti-pneumococcal effects of l-sulforaphane and metabolites: Insights from synchrotron-FTIR microspectroscopy and molecular docking studies. J Mol Graph Model. 2020 Jun;97:107568. doi: 10.1016/j.jmgm.2020.107568. Epub 2020 Feb 17.
6 Intracellular replication of Streptococcus pneumoniae inside splenic macrophages serves as a reservoir for septicaemia. Nat Microbiol. 2018 May;3(5):600-610. doi: 10.1038/s41564-018-0147-1. Epub 2018 Apr 16.
7 Copy number variation of the beta defensin gene cluster on chromosome 8p influences the bacterial microbiota within the nasopharynx of otitis-prone children.PLoS One. 2014 May 27;9(5):e98269. doi: 10.1371/journal.pone.0098269. eCollection 2014.
8 The polymorphism of IL-17 G-152A was associated with childhood asthma and bacterial colonization of the hypopharynx in bronchiolitis.J Clin Immunol. 2010 Jul;30(4):539-45. doi: 10.1007/s10875-010-9391-8. Epub 2010 May 2.
9 Indoleamine 2,3-dioxygenase 1 is a lung-specific innate immune defense mechanism that inhibits growth of Francisella tularensis tryptophan auxotrophs.Infect Immun. 2010 Jun;78(6):2723-33. doi: 10.1128/IAI.00008-10. Epub 2010 Apr 12.
10 PD-L2 Regulates B-1 Cell Antibody Production against Phosphorylcholine through an IL-5-Dependent Mechanism.J Immunol. 2017 Sep 15;199(6):2020-2029. doi: 10.4049/jimmunol.1700555. Epub 2017 Aug 2.
11 RSV Infection in Human Macrophages Promotes CXCL10/IP-10 Expression during Bacterial Co-Infection.Int J Mol Sci. 2017 Dec 7;18(12):2654. doi: 10.3390/ijms18122654.
12 Microbiota regulate the ability of lung dendritic cells to induce IgA class-switch recombination and generate protective gastrointestinal immune responses.J Exp Med. 2016 Jan 11;213(1):53-73. doi: 10.1084/jem.20150567. Epub 2015 Dec 28.
13 IgM in microbial infections: taken for granted. Immunol Lett. 2009 Aug 15;125(2):79-85. doi: 10.1016/j.imlet.2009.06.003. Epub 2009 Jun 17.
14 Measurement of the IgG2 response to Pneumococcal capsular polysaccharides may identify an antibody deficiency in individuals referred for immunological investigation.J Immunoassay Immunochem. 2017;38(5):514-522. doi: 10.1080/15321819.2017.1340897. Epub 2017 Jun 14.
15 Genome-wide association study of IgG1 responses to the choline-binding protein PspC of Streptococcus pneumoniae.Genes Immun. 2015 Jul-Aug;16(5):289-96. doi: 10.1038/gene.2015.12. Epub 2015 Apr 30.
16 Purification and characterisation of anti-pneumococcal capsular polysaccharide IgG immunoglobulins.Clin Biochem. 2017 Jan;50(1-2):80-83. doi: 10.1016/j.clinbiochem.2016.08.009. Epub 2016 Aug 17.
17 Effect of mutations in the human immunoglobulin A1 (IgA1) hinge on its susceptibility to cleavage by diverse bacterial IgA1 proteases.Infect Immun. 2005 Mar;73(3):1515-22. doi: 10.1128/IAI.73.3.1515-1522.2005.
18 Subclass distribution of natural salivary IgA antibodies against pneumococcal capsular polysaccharide of type 14 and pneumococcal surface adhesin A (PsaA) in children.Clin Exp Immunol. 2006 Mar;143(3):543-9. doi: 10.1111/j.1365-2249.2006.03009.x.
19 Evidence for altered levels of IgD in the nasal airway mucosa of patients with chronic rhinosinusitis.J Allergy Clin Immunol. 2017 Dec;140(6):1562-1571.e5. doi: 10.1016/j.jaci.2017.05.032. Epub 2017 Jun 16.
20 Assignment of Serotype-Specific IgG1, IgG2, and IgA Weight-Based Antibody Units to the Human Pneumococcal Standard Reference Serum, 007sp.mSphere. 2019 Jun 19;4(3):e00400-19. doi: 10.1128/mSphere.00400-19.
21 Induction of Autonomous Memory Alveolar Macrophages Requires T Cell Help and Is Critical to Trained Immunity.Cell. 2018 Nov 29;175(6):1634-1650.e17. doi: 10.1016/j.cell.2018.09.042. Epub 2018 Oct 25.
22 Increased TNF expression in CD43++ murine blood monocytes.Immunol Lett. 2008 Jun 30;118(2):142-7. doi: 10.1016/j.imlet.2008.03.012. Epub 2008 Apr 22.
23 T Cell-Mediated Humoral Immune Responses to Type 3 Capsular Polysaccharide of Streptococcus pneumoniae. J Immunol. 2017 Jul 15;199(2):598-603. doi: 10.4049/jimmunol.1700026. Epub 2017 May 31.

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