Table 3.

The correlation between gut microbe and IBD in some research with various methods.

Methodology	Study subject	Major findings	References
Integrating taxonomic, metagenomic, metatranscriptomic, metaproteomic, and metabolic data	The Inflammatory Bowel Disease Multi'omics Database (IBDMDB) for 1,785 stool samples, 651 intestinal biopsies, and 529 quarterly blood samples	Demonstrate an increase in facultative anaerobes at the expense of obligate anaerobes, and molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum	(3, 10)
Healthy patient's biopsies	Five sites (cecum-ascending, transverse, descending, sigmoid, rectum) for healthy patient's biopsies	The composition of the microbiota in IBD patients differed from that of healthy controls. The high rate of bacterial DNA in the blood samples indicated translocation in inflammatory bowel disease	(148)
Whole-genome shotgun sequencing	Fecal DNA extracts from 13 healthy donors and 16 UC and 8 CD patients	Enterococcus faecium strains derived from UC patients displayed an inflammatory genotype that caused colitis	(149)
16S rRNA gene (RNA and DNA) pyrosequencing	Mucosal biopsies sampled from individuals of German, Lithuanian, and Indian origins	Faecalibacteria and Papillibacter belonged to Clostridium leptum subgroup had the respect to serving as reliable microbiomarkers	(150)
16S rRNA gene sequencing and Immunochip	Intestinal biopsies samples	Identified and confirmed a significant association between NOD2 risk allele count and increased relative abundance of Enterobacteriaceae, and 48 additional IBD-related SNPs had directionality of their associations with bacterial taxa	(151)
16S rRNA gene sequencing and microarray	Patients who had surgical management of UC and all patients had ileal pouch-anal anastomosis surgery at least 1 year prior to biopsy collection	Activation of host processes was inversely correlated with Sutterella, Akkermansia, Bifidobacteria, and Roseburia abundance and positively correlated with Escherichia abundance	(152)
16S rDNA sequencing and transcriptome analyses	Dextran sulfate sodium induced specific pathogen-free (SPF) and germ-free (GF) mice	Gut microbes were affected by diet and interfered with intestinal permeability and intestinal inflammation development	(153)
Metabolomics	The Human Metabolome Database (HMDB)	Established correlations between microbial composition and specific bacterial metabolic pathways; assessed the effects of small molecule products on IBD pathogenesis	(154)
Gut microorganisms	Two thousand three hundred and seventy-nine participants from two population-based cohorts (LLD and 500FG) and two disease cohorts (IBD and 300OB)	Identified several key species and pathways in IBD and obesity; provided evidence that altered microbial abundances in disease could influence their co-abundance relationship	(155)