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Whole Genome Shotgun Sequencing-Based Insights into the Benzene and Xylene Degrading Potentials of Bacteria

FATIMA MUCCEE

FATIMA MUCCEE

School of Biochemistry and Biotechnology, University of PunjabLahore, Pakistan
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MUCCEE, FATIMA
, 
FARHAN MOHIUDDIN

FARHAN MOHIUDDIN

School of Biochemistry and Biotechnology, University of PunjabLahore, Pakistan
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MOHIUDDIN, FARHAN
, 
AANSA SHAHAB

AANSA SHAHAB

School of Biochemistry and Biotechnology, University of PunjabLahore, Pakistan
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SHAHAB, AANSA
, 
ALI ALMAJWAL

ALI ALMAJWAL

Department of Community Health Sciences, College of Applied Medical Sciences, King Saud UniversityRiyadh, Saudi Arabia
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ALMAJWAL, ALI
, 
TAYYABA AFSAR

TAYYABA AFSAR

Department of Community Health Sciences, College of Applied Medical Sciences, King Saud UniversityRiyadh, Saudi Arabia
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AFSAR, TAYYABA
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HOUDA AMOR

HOUDA AMOR

Department of Obstetrics and Gynaecology, Department of Endocrinology and Reproductive Medicine, University Clinic Freiburg, Freiburg im Breisgau, University of FreiburgFreiburg, Germany
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AMOR, HOUDA
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SUHAIL RAZAK

SUHAIL RAZAK

Department of Community Health Sciences, College of Applied Medical Sciences, King Saud UniversityRiyadh, Saudi Arabia
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RAZAK, SUHAIL
  
Jun 18, 2025
Whole Genome Shotgun Sequencing-Based Insights into the Benzene and Xylene Degrading Potentials of Bacteria's Cover Image
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Article Category: Original Paper
Published Online: Jun 18, 2025
Page range: 244 - 261
Received: Apr 07, 2025
Accepted: May 11, 2025
DOI: https://doi.org/10.33073/pjm-2025-020
Keywords
© 2025 FATIMA MUCCEE et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Fig. 1.

Total bases, GC and AT contents, and Q20 and Q30 ratios of total reads calculated during WGS analysis.
Total bases, GC and AT contents, and Q20 and Q30 ratios of total reads calculated during WGS analysis.

Fig. 2.

Krona image of taxonomic assignments to metagenomic contigs by Kraken.
Krona image of taxonomic assignments to metagenomic contigs by Kraken.

Fig. 3.

Pathways associated with aromatic compound metabolism, with their respective abundances, explored in a bacterial consortium using whole genome sequencing. BD – benzoate degradation, ABD – aminobenzoate degradation, FBD – fluorobenzoate degradation, CLAD – chloroalkane and chloroalkene degradation, CLHD – chlorocyclohexane and chlorobenzene degradation, TD – toluene degradation, XD – xylene degradation, SD – styrene degradation, AD – atrazine degradation, CD – caprolactam degradation, DD – dioxin degradation, ND – naphthalene degradation, PAHD – polycyclic aromatic hydrocarbon degradation, SD – steroid degradation, MP450 – metabolism of xenobiotics by cytochrome P450
Pathways associated with aromatic compound metabolism, with their respective abundances, explored in a bacterial consortium using whole genome sequencing. BD – benzoate degradation, ABD – aminobenzoate degradation, FBD – fluorobenzoate degradation, CLAD – chloroalkane and chloroalkene degradation, CLHD – chlorocyclohexane and chlorobenzene degradation, TD – toluene degradation, XD – xylene degradation, SD – styrene degradation, AD – atrazine degradation, CD – caprolactam degradation, DD – dioxin degradation, ND – naphthalene degradation, PAHD – polycyclic aromatic hydrocarbon degradation, SD – steroid degradation, MP450 – metabolism of xenobiotics by cytochrome P450

Fig. 4.

Reconstruction of ortho, meta and para-xylene degradation pathways based on whole genome shotgun functional annotation.
Reconstruction of ortho, meta and para-xylene degradation pathways based on whole genome shotgun functional annotation.

Fig. 5.

Reconstruction of benzene, 3-aminobenzene sulfonate, toluene and 2-, 3- and 4-fluorobenzoate degradation pathways based on whole genome shotgun functional annotation.
Reconstruction of benzene, 3-aminobenzene sulfonate, toluene and 2-, 3- and 4-fluorobenzoate degradation pathways based on whole genome shotgun functional annotation.

Fig. 6.

Reactions of benzene and xylene metabolism catalyzed by bacterial enzymes identified in the current study using whole genome shotgun functional annotation.
Reactions of benzene and xylene metabolism catalyzed by bacterial enzymes identified in the current study using whole genome shotgun functional annotation.

Statistics of contigs produced by the metaSPAdes program_

No. Quast quality parameters Statistics (bp)
1 Contigs > 10,000 bp 4,992
2 Contigs ≥ 5,000 bp 940
3 Contigs ≥ 10,000 bp 431
4 Contigs ≥ 25,000 bp 169
5 Contigs ≥ 50,000 bp 76
6 Largest contig 469,435
7 Total length 30,570,959
8 Total length ≥ 1,000 bp 27,559,880
9 Total length ≥ 5,000 bp 19,294,370
10 Total length ≥ 10,000 bp 15,759,083
11 Total length ≥ 25,000 bp 11,859,173
12 Total length ≥ 50,000 bp 8,511,336
13 N50 10,938

Stoichiometry of reactions involved in benzene, xylene and toluene degradation identified in the current study bacteria based on WGS_

No. of reaction Stoichiometry of reactions
Reactants Products
Benzene degradation pathway
I C6H6 + H2 + CO2 benzene C7H8O + [O-]benzyl alcohol
II C7H8O C7H6O + H2benzaldehyde
III C7H6O + [O-] C7H6O2benzoate
IV C7H6O2 + [O-] + H2O C7H8O4cis-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate
V C7H8O4 C6H6O2catechol
VI C6H6O2 + 2 [H+] C6H5O4- + 3 [H+]cis, cis-muconate
VII C6H5O4- C6H6O4muconolactone
VIII C6H6O4 C6H5O4+ [H+]3-oxoadipate enol lactone
IX C6H5O4 C6H5O52-3-oxoadipate
X C6H5O52- + [H+] + C21H36N7O16P3S C27H42N7O20P3S + [O]3-oxoadipyl-CoA
XI C27H42N7O20P3S + 5H2O C23H38N7O17P3S + 4CO2+ 7H2Oacetyl-CoA
p-Xylene degradation pathway
I C8H10 + [O-] p-xylene C8H10O4-methylbenzyl alcohol
II C8H10O + CO2 C9H10O2 + [O-]p-methylbenzoate
III C9H10O2 + 2O2 C8H9O4 + CO2 + [H+]cis-1-2-dihydroxy-4-methylcyclohexa-3,5-diene-1-carboxylate
IV C8H9O4 C7H8O2 + CO2 + [H+]4-methylcatechol
V C7H8O2 + O2 C7H8O42-hydroxyl-5-methyl-cis, cis-muconic semialdehyde
VI C7H8O4 + [O] C7H8O52-hydroxyl-5-methyl-cis, cis-muconate
VII C7H8O5 C7H8O52-oxo-5-methyl-cis-muconate
VIII C7H8O5 C6H8O3 + CO22-hydroxyl-cis-hexa-2,4-dienoate
IX C6H8O3 + H2O C6H10O44-hydroxyl-2-oxohexanoate
X C6H10O4 + 2O2 + H2O 3CO2+ C3H3O3- + H2Opyruvate
m-Xylene degradation pathway
I C8H10+ [O] m-xylene C8H10O3-methylbenzyl alcohol
II C8H10O C8H8O + H23-methylbenzaldehyde
III C8H8O + CO2+ H2 C9H10O2 + H2Om-methylbenzoate
IV C9H10O2 + CO2 C8H8O4 + H21,2-dihydroxy-3-methylcyclohexa-3,5-dienecarboxylate
o-Xylene degradation pathway
I C8H10 + [O-] o-xylene C8H10O2-methylbenzyl alcohol
II C8H10O C8H8O + H22-methylbenzaldehyde
III C8H8O + CO2 + H2 C9H10O2 + [O]o-methylbenzoate
IV C9H10O + CO2 C8H10O41,2-dihydroxy-6-methylcyclohexa-3,5-dienecarboxylate
V C8H10O4 C7H8O2 + CO2 + H23-methylcatechol
VI C7H8O2 + O2 C7H8O4cis, cis-2-hydroxyl-6-oxohept-2,4-dienoate
VII C7H8O4 + [O-] C5H6O3 + 2CO2 + H2cis-2-hydroxy penta-2,4-dienoate
VIII C5H6O3 + H2O C5H7O4- + [H+]4-hydroxyl-2-oxopentanoate
IX C5H7O4- + [O-] C3H3O3- + 2CO2 + 2H2 pyruvate
Toluene degradation pathway
I C6H5CH3 + [O] toluene C6H5CH2OHbenzyl alcohol
II C6H5CH2OH benzyl alcohol C6H5CHO + H2benzaldehyde
III C6H5CHO + [O] benzaldehyde C7H5O2 + [H]benzoate

Functional annotation of genes associated with aromatic compound degradation via the KEGG database_

No. Associated biochemical pathway Genes identified
1 Xylene degradation pathway toluene methyl-monooxygenase [EC:1.14.15.26],aryl-alcohol dehydrogenase [EC:1.1.1.90],benzaldehyde dehydrogenase (NAD) [EC:1.2.1.28],benzoate/toluate 1,2-dioxygenase subunit α [EC:1.14.12.-],dihydroxycyclohexadiene carboxylate dehydrogenase [EC:1.3.1.-, 1.3.1.67, 1.3.1.68],catechol 2,3-dioxygenase [EC:1.13.11.2],2-hydroxymuconate-semialdehyde hydrolase [EC:3.7.1.9],2-oxopent-4-enoate/cis-2-oxohex-4-enoate hydratase [EC:4.2.1.80, 4.2.1.132],4-hydroxy-2-oxovalerate/4-hydroxy-2-oxohexanoate aldolase [EC:4.1.3.39 4.1.3.43],acetaldehyde/propanal dehydrogenase [EC:1.2.1.10, 1.2.1.87],aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehydedehydrogenase [EC:1.2.1.32 1.2.1.85],4-oxalocrotonate tautomerase [EC:5.3.2.6],2-oxo-3-hexenedioate decarboxylase [EC:4.1.1.77],2-keto-4-pentenoate hydratase [EC:4.2.1.80],4-hydroxy 2-oxovalerate aldolase [EC:4.1.3.39],acetaldehyde dehydrogenase [EC:1.2.1.10]
2 Toluene degradation pathway toluene methyl-monooxygenase [EC:1.14.15.26],aryl-alcohol dehydrogenase [EC:1.1.1.90],benzaldehyde dehydrogenase (NAD) [EC:1.2.1.28]
3 Benzene benzoate/toluate 1,2-dioxygenase subunit alpha [EC:1.14.12.10], dihydroxycyclohexadiene carboxylate dehydrogenase [EC:1.3.1.25],catechol 1,2-dioxygenase [EC:1.13.11.1],muconate cycloisomerase [EC:5.5.1.1],muconolactone D-isomerase [EC:5.3.3.4],3-oxoadipate enol-lactonase [EC:3.1.1.24],3-oxoadipate CoA-transferase, alpha subunit [EC:2.8.3.6],acetyl-CoA acyltransferase [EC:2.3.1.16],3-oxoadipyl-CoA thiolase [EC:2.3.1.174],catechol 2,3-dioxygenase [EC:1.13.11.2],2-hydroxymuconate-semialdehyde hydrolase [EC:3.7.1.9],2-keto-4-pentenoate hydratase [EC:4.2.1.80],4-hydroxy 2-oxovalerate aldolase [EC:4.1.3.39],acetaldehyde dehydrogenase [EC:1.2.1.10],protocatechuate 3,4-dioxygenase, alpha subunit [EC:1.13.11.3],3-carboxy-cis, cis-muconate cycloisomerase [EC:5.5.1.2],4-carboxymuconolactone decarboxylase [EC:4.1.1.44],3-hydroxybenzoate 6-monooxygenase [EC:1.14.13.24]
3 Aminobenzoate degradation pathway benzaldehyde dehydrogenase (NAD) [EC:1.2.1.28],amidase [EC:3.5.1.4],4-hydroxybenzoate decarboxylase subunit C [EC:4.1.1.61]
4 Fluorobenzoate degradation pathway benzoate/toluate 1,2-dioxygenase subunit alpha [EC:1.14.12.10],dihydroxycyclohexadiene carboxylate dehydrogenase [EC:1.3.1.25],catechol 1,2-dioxygenase [EC:1.13.11.1],muconate cycloisomerase [EC:5.5.1.1]
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