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. 2023 Feb 4;15(2):522. doi: 10.3390/pharmaceutics15020522

Table 1.

Proteomic data on extracellular vesicles produced by probiotics.

Bacterial Producer Methodology of Isolation/Determination Proteomic Data Reference
Total Number of Identified Proteins * Cellular Localization of Proteins The Most Abundant Representatives/
Proteins Highlighted by Authors
Escherichia coli
Nissle 1917		 Ultracentrifugation (vesicles)
Electrophoresis + LC-MS/MS (proteome)		 192 Outer membrane ~ 40%
Cytoplasm 40%
Periplasm 15%
Inner membrane < 5 %
  • -

    Fimbriae subunits: FocA, FocF, FocG, FocH

  • -

    Flagellins: FlgK, FlgE, FliD

  • -

    Murein hydrolase MltB

  • -

    Metabolic proteins: AnsB, CadA, FbaB, GapA, Icd, Mdh

 [52]
Ultracentrifugation + DGC (vesicles)
Electrophoresis + LC-MS/MS (proteome)		 189 Outer membrane 28%
Cytoplasm 36.5%
Periplasm 20%
Inner membrane 9.5%
Secretory 6%
  • -

    Fimbriae subunits: FocA, FocF, FocG, FocH

  • -

    Flagellins: FlgA, FlgE, FlgK

  • -

    Outer membrane proteins: OmpA, OmpC, OmpF

  • -

    Murein hydrolases: MltA, MltC

 [29]
Ultracentrifugation (vesicles)
Electrophoresis + LC-MS/MS (proteome)		 295 ND
  • -

    Peptidoglycan-associated lipoproteins: Pal, TolB

  • -

    Murein-interacting protein MipA

  • -

    Flagellin subunit FliC

  • -

    Outer membrane proteins: OmpA, OmpC, OmpF, NmpC

 [51]
Ultracentrifugation + DGC or SEC (vesicles)
Chemical precipitation + LC-MS/MS (proteome)		 189 Membrane ~ 60%
Cytoplasm ~ 40%
  • -

    Peptidoglycan-associated lipoproteins: Pal, Sat, LpoA, YbaY, SlyB

  • -

    Fimbrial protein Fim1C

  • -

    Flagellin FlgL

  • -

    Outer membrane proteins: OmpC, NmpC

 [72]
Lactiplantibacillus plantarum BGAN8 Ultracentrifugation (vesicles)
Electrophoresis + MALDI-TOF (proteome)		 1149 Membrane ~ 45%
Cytoplasm + ribosomes ~ 52%
Secretory < 1%
  • -

    Polysaccharide biosynthesis proteins: EpsN, MurJ

  • -

    Transporters of glycerol (GlpF), niacin (NiaP), oligopeptides (OppC), amino acids (SdaC, CycA)

  • -

    Translation proteins: 30S and 50S ribosomal subunits (55 different subunits)

 [54]
Lactiplantibacillus plantarum WCFS1 Chemical precipitation (vesicles)
Electrophoresis + LC-MS/MS (proteome)		 31 Membrane 42%
Cytoplasm 13%
Secretory 16%
  • -

    Cell wall remodeling proteins: Acm2, DltD, MreC, Lp_2847, Lp_3015, Lp_2162, Lp_3093, Lp_3421

  • -

    Metabolic proteins: TpiA, GapB, Pgi, Ldh1

 [32]
Lacticaseibacillus casei
ATCC 393		 Ultracentrifugation (vesicles)
Chemical precipitation + LC-MS/MS (proteome)		 43 Membrane ~ 20%
Cytoplasm 65%
Secretory 14%
  • -

    Putative family 15 glucoamylase LBCZ_2692

  • -

    Lysozyme-like proteins: LBCZ_0210, LCAUW4_1864

  • -

    N-acetylmuramoyl-L-alanine amidase LSEI_1536

  • -

    Putative cell wall-associated hydrolase LSEI_0281

 [38]
Lacticaseibacillus casei
BL23		 Ultracentrifugation (vesicles)
Electrophoresis + LC-MS/MS (proteome)		 103 Membrane + secretory 43%
Cytoplasm 57%
  • -

    Cell wall-associated hydrolases P40 and P75

  • -

    Metabolism proteins: GapA, Pgk, LdhL, Fba, AspB, Pyk

  • -

    Translation proteins: 30S ribosomal subunits (RpsJ, RpsL, RpsS, RpsT, RpsU) and 50S ribosomal subunits (11 different subunits)

 [36]
Limosilactobacillus reuteri ATCC 23272 Ultracentrifugation (vesicles)
Chemical precipitation + LC-MS/MS (proteome)		 17 Membrane 18%
Cytoplasm 82%
  • -

    Metabolic proteins: Lreu_0426, Lreu_1721, Lreu_1853

  • -

    NAD kinase NadK

 [38]
Limosilactobacillus reuteri
BBC3		 Ultracentrifugation + DGC (vesicles)
Chemical precipitation + LC-MS/MS (proteome)		 92 Membrane 27%
Cytoplasm 56.5%
Secretory 16%
  • -

    Metabolic proteins: GatB, ProS, SerS, IleS, LRI_0925, B5F04_03325, N134_06765

  • -

    Cell wall remodeling proteins: Lr1610, MreC

  • -

    Translation proteins: 30S ribosome subunit (RpsB) and 50S ribosome subunit (RplC)

 [34]
Ligilactobacillus animalis
ATCC 35046		 Ultracentrifugation + DGC (vesicles)
Chemical precipitation + nLC-MS/MS (proteome)		 340 From the top 74 proteins:
Membrane 25.7%
Cytoplasm 25.7%
Secretory 1.3%
Unknown 47.3%
  • -

    Sortase SrtA

  • -

    Transporters of phosphate (PstS), glutamine (GlnP), nitrate/sulfonate/bicarbonate (Lani381_1252)

  • -

    Metabolism protein Pgi

  • -

    Antioxidative protein Dsp

 [76]
Lactobacillus acidophilus
ATCC 53544		 Ultracentrifugation (vesicles)
Chemical precipitation + LC-MS/MS (proteome)		 26 Membrane ~ 30%
Cytoplasm 62%
Secretory 12%
  • -

    Surface proteins: FmtB, SlpX

  • -

    Mucus binding protein Mub

  • -

    Transporters of maltose (LBA1864) and glutamine (GlnP)

  • -

    Bacteriocin LBA1805

 [38]
Lactobacillus gasseri
BC12		 Ultracentrifugation (vesicles)
Electrophoresis + LC-ESI-MS/MS (proteome)		 15 Membrane ~ 44%
Cytoplasm ~ 44%
Secretory ~ 11%
  • -

    Foldase protein PrsA

  • -

    Enolase 1 (Eno1) and 2 (Eno2)

  • -

    Translation proteins: elongation factor (EF-Tu) and 30S ribosomal subunit (RpsD)

  • -

    Metabolism proteins: AtpA, AtpD, AtpF, AtpH, Pyk, TpiA

  • -

    Phosphonates transporter PhnC

 [74]
Lactobacillus crispatus
BC5		 Ultracentrifugation (vesicles)
Electrophoresis + LC-ESI-MS/MS (proteome)		 11 Membrane ~ 45%
Cytoplasm ~ 45%
Secretory ~ 9%
  • -

    Enolase Eno1

  • -

    Translation proteins: 30S ribosomal subunit (RpsD) and 50S ribosomal subunits (RplB, RplU)

  • -

    Metabolism proteins: AtpA, AtpD, AtpF

  • -

    Phosphonates transporter PhnC

 [74]
Lactobacillus johnsonii
N6.2		 Ultracentrifugation (vesicles)
Electrophoresis + LC-MS/MS (proteome)		 366 Cytoplasm + ribosomes 86%
Secretory 14%
  • -

    Foldase protein PrsA

  • -

    Aggregation promoting factors: Apf1, Apf2

  • -

    Translation proteins: 30S ribosome subunits (RpsB, RpsC, RpsE) and 50S ribosome subunit (RplA)

  • -

    Metabolic proteins: PtsP, GalE, InuJ, RfbB, PfkA

 [33]
Bifidobacterium longum
NCC 2705		 Ultracentrifugation (vesicles)
Electrophoresis + LC-MS/MS (proteome)		 24 Membrane 21%
Cytoplasm 75%
  • -

    Iron transporter BL1134_04745

  • -

    Metabolism proteins: GltX, Pyk, GatA, GapA, SerS, Ppa

  • -

    Translation proteins: elongation factor (EF-Tu), 30S ribosomal subunits (RpsC, RpsI), 50S ribosomal subunit (RplY)

 [64]
Propionibacterium freudenreichii CIRM-BIA 129 SEC (vesicles)
Electrophoresis + LC-ESI-MS/MS (proteome)		 319 Membrane 16%
Cytoplasm 75%
Secretory 9%
  • -

    Enolase Eno1

  • -

    Aconitase Acn

  • -

    Surface-layer proteins: SlpB, SplE, BopA, InlA

  • -

    Antioxidative proteins: SodA, AhpC

  • -

    Metabolic proteins: GlnA1, Gpi, Tpi1

 [78]
SEC (vesicles)
Electrophoresis + LC-MS/MS (proteome)		 391
(medium-dependent; 358 common for all)		 Membrane 16.5%
Cytoplasm 74%
Secretory 9.5%
  • -

    Surface proteins: SlpB, SlpD, BopA, InlA

  • -

    Metabolism proteins: LacZ, IolC, IolE1, AroH, NirA2

  • -

    Translation proteins: 30S ribosomal subunit (RpsG) and 50S ribosomal subunits (RplB, RplC, RplT, RplV)

  • -

    Antioxidative protein AhpC

 [79]
Lactococcus lactis
FM-YL11		 Ultracentrifugation (vesicles)
Magnetic precipitation + LC-MS/MS (proteome)		 1283 From the top 320 proteins:
Membrane 16.5%
Cytoplasm 74%
Secretory 9.5%
  • -

    Translation proteins: elongation factor (EF-Tu), 30S ribosomal subunits (RpsA, RpsB, RpsC, RpsD, RpsE, RpsG, RpsK, RpsM), 50S ribosomal subunits (RplB, RplC, RplD, RplE, RplS, RplT, RplU)

  • -

    Metabolic proteins: LacB, PyrG, LLT1_01140

 [62]
Pediococcus pentosaceus ** Ultracentrifugation (vesicles)
Electrophoresis + LC-MS/MS (proteome)		 103 Membrane 9%
Cytoplasm + ribosomes ~ 83%
Secretory 5.5%
  • -

    Foldase protein PrsA

  • -

    Enolase Eno1

  • -

    Translation proteins: elongation factors (EF-Tu, EF-G) and 50S ribosome subunits (RplD, RplO, RplQ)

  • -

    Metabolic proteins: TpiA, ldhL

 [42]

Abbreviations: ND, no data; DGC, density gradient centrifugation; LC-MS/MS, liquid chromatography with tandem mass spectrometry; nLC-MS/MS, nano-scale liquid chromatographic tandem mass spectrometry; LC-ESI-MS/MS, liquid chromatography electrospray ionization with tandem mass spectrometric; MALDI-TOF, matrix-assisted laser desorption/ionization-time of flight; SEC, size exclusion chromatography. * Total number of whole-length gene products, ** bacterial strain was not reported.