Inflammatory bowel disease biomarkers revealed by the human gut microbiome network

Inflammatory bowel diseases (IBDs) are complex medical conditions in which the gut microbiota is attacked by the immune system of genetically predisposed subjects when exposed to yet unclear environmental factors. The complexity of this class of diseases makes them suitable to be represented and studied with network science. In this paper, the metagenomic data of control, Crohn’s disease, and ulcerative colitis subjects’ gut microbiota were investigated by representing this data as correlation networks and co-expression networks. We obtained correlation networks by calculating Pearson’s correlation between gene expression across subjects. A percolation-based procedure was used to threshold and binarize the adjacency matrices. In contrast, co-expression networks involved the construction of the bipartite subjects-genes networks and the monopartite genes-genes projection after binarization of the biadjacency matrix. Centrality measures and community detection were used on the so-built networks to mine data complexity and highlight possible biomarkers of the diseases. The main results were about the modules of Bacteroides, which were connected in the control subjects’ correlation network, Faecalibacterium prausnitzii, where co-enzyme A became central in IBD correlation networks and Escherichia coli, whose module has different patterns of integration within the whole network in the different diagnoses.


Superpathway of aromatic amino acid biosynthesis
The catabolism of fatty acids proceeds via several routes, which depend on the length of the acids, whether the number of carbons is odd or even, and whether they are saturated or unsaturated.This pathway represents the "core" cycle of β -oxidation, a mechanism that removes two carbon atoms with each turn of the cycle.

Fucose degradation
Escherichia Escherichia coli L-fucose can be used by some organisms as a total source of carbon and energy.

Dorea Dorea longicatena
Amino sugars can also be utilized as carbon and nitrogen sources.N-acetylglucosamine, -mannosamine and -neuraminic acid can all be transported into the cell and metabolized.

Blautia obeum
The pathway of L-isoleucine biosynthesis from Lthreonine is a five-step pathway that shares its last four steps with the pathway of L-valine biosynthesis.These entwined pathways are part of the superpathway of branched chain amino acid biosynthesis, that generates not only L-isoleucine and L-valine, but also L-leucine.

Bacteroides Bacteroides uniformis
This superpathway shows the various ways that bacteria like Escherichia coli can obtain pyridoxal 5'-phosphate, a coenzyme for many enzymes that participate in amino acid and glycogen metabolism.

PWY-1042 | ANAEROSTIPES_HADRUS Glycolysis IV (plant cytosol) Anaerostipes Anaerostipes hadrus
Glycolysis, which was first studied as a pathway for the utilization of glucose, is one of the major pathways of central metabolism, the other two being the pentose phosphate pathway and the TCA cycle.

Faecalibacterium prausnitzii
This pathway produces the polyamine putrescine.This metabolite like other polyamines is cationic and may be involved in interactions with proteins, DNA and RNA molecules.

Faecalibacterium prausnitzii
The enzymes of the Leloir pathway (here named Dgalactose degradation I (Leloir pathway)) catalyze the conversion of D-galactose to the more metabolically versatile D-glucopyranose 6-phosphate.This pathway is required since galactose itself cannot be used for glycolysis directly.

Bacteroides xylanisolvens
Peptidoglycan is best described as a fisherman's net, with each cell of the mesh defined by two segments of parallel, glycan threads, held together by two small elastic peptide crosslinks, which allow the net to expand or shrink.

Bacteroides Bacteroides uniformis
Peptidoglycan is best described as a fisherman's net, with each cell of the mesh defined by two segments of parallel, glycan threads, held together by two small elastic peptide crosslinks, which allow the net to expand or shrink.PWY-6527 | FAECALIBAC-TERIUM_PRAUSNITZII

Faecalibacterium prausnitzii
This pathway describes the degradation of stachyose and raffinose into α-D-galactopyranose.

Phocaeicola Phocaeicola vulgatus
The first purine nucleotide that is synthesized de novo is inosine-5'-phosphate (IMP).IMP is converted to xanthosine monophosphate (XMP) by the enzyme inosine 5'monophosphate dehydrogenase, and the latter is converted to the first guanosine nucleotide, GMP, by the action of GMP synthetase, an enzyme that can use either glutamine or ammonia as the nitrogen donor.

Bacteroides
Bacteroides fragilis The formation of the two heterocycles involved in the biosynthesis of thiamine diphosphate (vitamin B1), i.e. the thiazole and pyrimidine moiety.
UnclassifiedThe aromatic amino acids L-phenylalanine, L-tyrosine and L-tryptophan are biosynthesized from the principal common precursor chorismate.DTDPRHAMSYN-PWY | BACTEROIDES_OVATUS dTDP-L-rhamnose biosynthesis IBacteroidesBacteroides ovatus β -L-rhamnopyranose is a deoxysugar that functions as a building block of the glycan component of the lipopolysaccharide present in ECA, the enterobacterial common antigen, and of the O-antigens of many bacterial species.DTDPRHAMSYN It is part of the degradation of purines, which is found in many organisms-1-(5-phospho-β -D-ribosyl)imidazole (AIR) is a key intermediate in the biosynthesis of purine nucleotides and thiamine-1-(5-phospho-β -D-ribosyl)imidazole (AIR) is a key intermediate in the biosynthesis of purine nucleotides and thiamine PWY-6122 | FAECALIBAC-De novo biosynthesis of purines starts with the synthesis of inosine-5'-phosphate (IMP), which can be converted to all other purines.PWY-De novo biosynthesis of purines starts with the synthesis of inosine-5'-phosphate (IMP), which can be converted to all other purines.PWY-6151 | BAC-TEROIDES_UNIFORMIS S-adenosyl-L-methionine cycle I Bacteroides Bacteroides uniformis About 20% of the L-methionine pool is used as a building block of proteins.The rest is converted to S-adenosyl-Lmethionine (SAM), the major methyl donor in the cell.PWY-6151 | ROSE-BURIA_INTESTINALIS S-adenosyl-L-methionine cycle I Roseburia Roseburia intestinalis PWY-6151 | ROSE-BURIA_INULINIVORANS S-adenosyl-L-methionine cycle I -1-(5-phospho-β -D-ribosyl)imidazole (AIR) is a key intermediate in the biosynthesis of purine nucleotides and thiamine the degradation of purine nucleotides to purine nucleosides, purine bases, and urate.PWY-6385 | BAC-TEROIDES_XYLANISOLVENS Peptidoglycan biosynthesis III (mycobacteria) Six pathways are now recognized in bacteria, most algae, fungi and higher plants for the biosynthesis of lysine.They are divided into two groups -the diaminopimelate (DAP) pathways, and the L-2-aminoadipate pathways.
The first purine nucleotide that is synthesized de novo is inosine-5'-phosphate (IMP).IMP is converted to xanthosine monophosphate XMP by the enzyme inosine 5'monophosphate dehydrogenase, and the latter is converted to the first guanosine nucleotide, GMP, by the action of GMP synthetase, an enzyme that can use either glutamine or ammonia as substrate.PWY-7221 | PHOCAE-ICOLA_VULGATUS