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Chemical Components of Aqueous Extracts of Melia azedarach Fruits and Their Effects on The Transcriptome of Staphylococcus aureus

HONG PENG

HONG PENG

Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of SciencesGuangzhou, China
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PENG, HONG
, 
YING-SI WANG

YING-SI WANG

Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of SciencesGuangzhou, China
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WANG, YING-SI
, 
JIE WANG

JIE WANG

College of Food Science, South China Agricultural UniversityGuangzhou, China
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WANG, JIE
, 
SU-JUAN LI

SU-JUAN LI

Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of SciencesGuangzhou, China
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LI, SU-JUAN
, 
TING-LI SUN

TING-LI SUN

Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of SciencesGuangzhou, China
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SUN, TING-LI
, 
TONG LIU

TONG LIU

  • Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of SciencesGuangzhou, China
  • College of Food Science, South China Agricultural UniversityGuangzhou, China
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LIU, TONG
, 
QING-SHAN SHI

QING-SHAN SHI

  • Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of SciencesGuangzhou, China
  • College of Food Science, South China Agricultural UniversityGuangzhou, China
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SHI, QING-SHAN
, 
GANG ZHOU

GANG ZHOU

  • Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of SciencesGuangzhou, China
  • College of Food Science, South China Agricultural UniversityGuangzhou, China
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ZHOU, GANG
 and 
XIAO-BAO XIE

XIAO-BAO XIE

  • Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of SciencesGuangzhou, China
  • College of Food Science, South China Agricultural UniversityGuangzhou, China
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XIE, XIAO-BAO
  
Oct 29, 2021
Chemical Components of Aqueous Extracts of Melia azedarach Fruits and Their Effects on The Transcriptome of Staphylococcus aureus's Cover Image
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Article Category: original-paper
Published Online: Oct 29, 2021
Page range: 447 - 459
Received: Jun 20, 2021
Accepted: Sep 15, 2021
DOI: https://doi.org/10.33073/pjm-2021-041
Keywords
© 2021 Hong Peng et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
The planktonic growth (A) and biofilm formation (B) of Staphylococcus aureus can be inhibited by aqueous extracts of Melia azedarach fruits in a dose-dependent manner
The planktonic growth (A) and biofilm formation (B) of Staphylococcus aureus can be inhibited by aqueous extracts of Melia azedarach fruits in a dose-dependent manner

Fig. 1.

Effect of aqueous extracts of Melia azedarach fruits on planktonic growth (A) and biofilm formation (B) of Staphylococcus aureus ATCC 6538. S. aureus ATCC 6538 was cultured on LB media supplemented with different concentrations of aqueous extracts of chinaberry fruits at 37°C for 48 h. The S. aureus planktonic cells and biofilms stained with crystal violet were measured at OD600 and OD590, respectively, using a Multiskan GO plate reader.
Effect of aqueous extracts of Melia azedarach fruits on planktonic growth (A) and biofilm formation (B) of Staphylococcus aureus ATCC 6538. S. aureus ATCC 6538 was cultured on LB media supplemented with different concentrations of aqueous extracts of chinaberry fruits at 37°C for 48 h. The S. aureus planktonic cells and biofilms stained with crystal violet were measured at OD600 and OD590, respectively, using a Multiskan GO plate reader.

Fig. 2.

Representative CLSM images of Staphylococcus aureus ATCC 6538 biofilms grown in the presence of different concentrations of aqueous extracts of Melia azedarach fruits and stained with SYTO9. The biofilms were cultivated on the surface of glass coverslips for 48 h at 37°C. The constructed biofilms were stained with the fluorescent dye SYTO9 and then observed under a Zeiss LSM 710 CLSM. Scale bar = 50 μm. CLSM, confocal laser scanning microscopy.
Representative CLSM images of Staphylococcus aureus ATCC 6538 biofilms grown in the presence of different concentrations of aqueous extracts of Melia azedarach fruits and stained with SYTO9. The biofilms were cultivated on the surface of glass coverslips for 48 h at 37°C. The constructed biofilms were stained with the fluorescent dye SYTO9 and then observed under a Zeiss LSM 710 CLSM. Scale bar = 50 μm. CLSM, confocal laser scanning microscopy.

Fig. 3.

Histogram depiction of enriched Gene Ontology classification of the DEGs of Staphylococcus aureus ATCC 6538 treated with 0.25 g/ml aqueous extracts of Melia azedarach fruits. The results were categorized into three main categories of biological process, molecular function, and cellular component. The x-axis indicates the gene numbers in each subcategory. The top 10 subcategories in each main category are shown here.
Histogram depiction of enriched Gene Ontology classification of the DEGs of Staphylococcus aureus ATCC 6538 treated with 0.25 g/ml aqueous extracts of Melia azedarach fruits. The results were categorized into three main categories of biological process, molecular function, and cellular component. The x-axis indicates the gene numbers in each subcategory. The top 10 subcategories in each main category are shown here.

Fig. 4.

Functional analysis of DEGs of Staphylococcus aureus ATCC 6538 treated with 0.25 g/ml aqueous extracts of Melia azedarach fruits based on the KEGG pathway. Among the top 20 pathways, the first two pathways, the ribosome (pae03010) and valine, leucine, and isoleucine biosynthesis (pae00290), were significantly enriched (padj < 0.05). The right y-axis represents the KEGG pathway. The x-axis exhibits the enrichment factor, which denotes the ratio of the DEG numbers to the annotated gene numbers enriched in a specific pathway. DEG, differentially expressed genes; KEGG, Kyoto Encyclopedia of Genes and Genomes.
Functional analysis of DEGs of Staphylococcus aureus ATCC 6538 treated with 0.25 g/ml aqueous extracts of Melia azedarach fruits based on the KEGG pathway. Among the top 20 pathways, the first two pathways, the ribosome (pae03010) and valine, leucine, and isoleucine biosynthesis (pae00290), were significantly enriched (padj < 0.05). The right y-axis represents the KEGG pathway. The x-axis exhibits the enrichment factor, which denotes the ratio of the DEG numbers to the annotated gene numbers enriched in a specific pathway. DEG, differentially expressed genes; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Fig. 5.

HMDB classification annotation of the components of aqueous extracts of Melia azedarach fruits in both positive and negative ion modes. The x-axis represents metabolite numbers, and the y-axis represents annotated HMDB entries.
HMDB classification annotation of the components of aqueous extracts of Melia azedarach fruits in both positive and negative ion modes. The x-axis represents metabolite numbers, and the y-axis represents annotated HMDB entries.

Fig. 6.

Lipidmaps classification annotation of components of aqueous extracts of Melia azedarach fruits in both positive and negative ion modes. The x-axis represents metabolite numbers, and the y-axis represents annotated Lipidmaps entries.
Lipidmaps classification annotation of components of aqueous extracts of Melia azedarach fruits in both positive and negative ion modes. The x-axis represents metabolite numbers, and the y-axis represents annotated Lipidmaps entries.

Fig. 7.

KEGG enrichment chart of the components of aqueous extraction of Melia azedarach fruits in both positive and negative ion modes. The x-axis represents metabolite numbers, and the y-axis represents enriched KEGG pathways. KEGG, Kyoto Encyclopedia of Genes and Genomes.
KEGG enrichment chart of the components of aqueous extraction of Melia azedarach fruits in both positive and negative ion modes. The x-axis represents metabolite numbers, and the y-axis represents enriched KEGG pathways. KEGG, Kyoto Encyclopedia of Genes and Genomes.

Identification results of the top 25 metabolites from aqueous extracts of Melia azedarach fruits in a positive mode_

No.Compound_IDNameFormulaMolecular WeightRetention Time (min)
1Com_2_posD-Pyrrolidine-2-Carboxylic acidC5H9NO2115.06341.382
2Com_3_posDL-ArginineC6H14N4O2174.11151.425
3Com_6_posCholineC5H13NO103.09991.275
4Com_49_posL-Glutamic acidC5H9NO4147.05291.434
5Com_28_posNicotinic acidC6H5NO2123.03211.773
6Com_44_posPerillartineC10H15NO165.11527.342
7Com_30_pos6-Hydroxynicotinic acidC6H5NO3139.02681.988
8Com_59_posMaltolC6H6O3126.03185.271
9Com_21_posIsoamylamineC5H13N87.105174.875
10Com_75_pos5-oxoprolineC5H7NO3129.04261.45
11Com_71_posEthyl 4-amino-2-(methylsulfanyl)-1,3-thiazole-5-carboxylateC7H10N2O2S2218.0191.265
12Com_77_posDL-TryptophanC11H12N2O2204.08976.801
13Com_98_posEcgonine methyl esterC10H17NO3199.12068.349
14Com_103_posScopoletinC10H8O4192.04218.708
15Com_105_posGamma-Aminobutyric acidC4H9NO2103.06371.292
16Com_85_posKinetinC10H9N5O237.06352.048
17Com_104_posN-Acetyl-DL-serineC5H9NO4147.05291.284
18Com_116_posPipecolinic acidC6H11NO2129.0791.734
19Com_119_pos2-Methylenesuccinic acidC5H6O4130.02631.284
20Com_168_pos2-Picolinic acidC6H5NO2123.03211.523
21Com_165_pos6-O-(2-Methylbutanoyl)-α-D-glucopyranosyl α-D-glucopyranosideC17H30O12443.19978.133
22Com_135_pos(+/-)12(13)-DiHOMEC18H34O4296.234514.142
23Com_171_posCorylifol AC25H26O4390.182310.9
24Com_78_posOleoyl ethylamideC20H39NO309.302515.542
25Com_114_posCytidineC9H13N3O5243.08938.013

Quantification of biofilm topologies in the presence of different concentrations of aqueous extracts of Melia azedarach fruits_

ParametersControl0.25 g/ml0.33 g/ml0.50 g/ml1.00 g/ml
Maximum thickness (μm)  10 ± 0.00a  10 ± 0.00a  10 ± 0.00a  10 ± 0.00a  10 ± 0.00a
Average thickness (μm)7.75 ± 0.10a6.68 ± 0.36b3.37 ± 0.17c2.11 ± 0.19d1.11 ± 0.03e
Total biomass (μm3/μm2)9.81 ± 1.78a6.97 ± 0.08b2.98 ± 0.25c1.40 ± 0.24cd0.22 ± 0.02d

Identification results of the top 25 metabolites from aqueous extracts of Melia azedarach fruits in a negative mode_

No.Compound_IDNameFormulaMolecular WeightRetention Time (min)
1Com_2_negD-Saccharic acidC6H10O8210.03721.174
2Com_6_negPalmitic acidC16H32O2256.239714.6
3Com_4_negCitric acidC6H8O7192.02671.214
4Com_11_negN-Acetylneuraminic acidC11H19NO9309.10551.296
5Com_17_negElaidic acidC18H34O2282.255314.704
6Com_15_negSucroseC12H22O11402.1371.39
7Com_22_negD-(–)-LyxoseC5H10O5150.05261.268
8Com_21_negGluconic acidC6H12O7196.0581.256
9Com_29_negDL-Malic acidC4H6O5134.02141.186
10Com_23_neg4-OxoprolineC5H7NO383.037091.293
11Com_31_negPyruvic acidC3H4O388.015951.186
12Com_25_negD-(–)-FructoseC6H12O6180.06321.307
13Com_48_negGlutaconic acidC5H6O4130.02651.172
14Com_56_neg2-Furoic acidC5H4O3112.0161.155
15Com_47_negToosendaninC30H38O11574.241411.083
16Com_57_negα-Eleostearic acidC18H30O2278.224114.157
17Com_50_negα-LactoseC12H22O11388.12131.373
18Com_71_negNomilinC28H34O9514.219310.413
19Com_54_neg4-Acetamidobutanoic acidC6H11NO3145.07391.439
20Com_59_negD-(+)-GlucoseC6H12O6180.06321.484
21Com_70_neg6-SialyllactoseC23H39NO19633.21271.319
22Com_78_negPurineC5H4N4120.04221.274
23Com_77_neg2-C-methyl D-erythritol 4-phosphateC5H13O7P216.03991.27
24Com_72_negAzelaic acidC9H16O4188.10475.304
25Com_81_neg16-Hydroxyhexadecanoic acidC16H32O3254.224214.26
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