Table 1.

Studies on the effects of urbanization-associated factors on the gut microbiome in relation to host health.

UrbanisaUrbanization-associated factors	Host	Alteration in the gut microbiome		Effects on host immunity/metabolism	NCDs potentially caused by the altered gut microbiome	Ref.
		Increase taxon	Decrease taxon
Environmental factors
PM 2.5	Mouse	f_Lachnospiraceae f_Rikenellaceae g_Marvinbryanatia s_Alistipes finegoldii	Bacterial richness c_Epsilonproteobacteria o_Campylobacterales f_Helicobacteraceae f_Peptostreptococcaceae f_Clostriiaceae g_Romboutsia g_Papillibacter g_Allobaculum g_Turicibacter	Glucose intolerance Insulin resistance	Diabetes	20
PM 10	Mouse	p_Firmicutes p_Verrucomicrobia	p_Bacteroidota	TNF-α, CXCL-1, IL-1β, IL-12, IL-13, IL-17, IL-10 ↑ IFN-γ and IL-2 ↓ Isovalerate and isobutyrate ↑ Butyrate and valerate ↓	Acute and chronic intestinal inflammatory	21
PM2.5 and PM1	Human	-	α diversity p_Firmicutes p_Proteobacteria p_Verrucomicrobia	Impaired fasting glucose	T2DM	5
Nitrogen oxides	Human	f_Coriobacteriaceae	f_Bacteroidaceae	Impaired fasting glucose	T2DM and obesity	22
Hygiene factors
Lipids and lipid-like molecules from cleaning products and detergents	Human	g_Candida g_Aspergillus	α diversity g_Debaryomyces g_Saccharomyces g_Trichosporon g_Fusarium	-	-	23
Dietary factors
Western diet	Human	β diversity g_Alistipes g_Bilophila g_Bacteroides	g_Roseburia s_Eubacterium rectale s_Ruminococcus bromii	Colonic deoxycholic concentrations ↑ Colonic H2S ↑	CRC and IBD	24
		g_Prevotella	g_Bacteroides	Fecal tryptophan ↓	Obesity	25
		-	s_Eubacterium rectale s_Clostridium symbiosum s_Oscillospira guillermondii s_Roseburia intestinalis	Secondary bile acids ↑ Colonic butyrate ↓ TMAO ↑	CRC and CVD	26
	Mouse	c_Erysipelotrichi c_Bacilli s_Clostridium innocuum s_Eubacterium dolichum, s_Catenibacterium mitsuokai	p_Bacteroidota	-	Obesity	27
Choline and carnitine in red meats and processed meats	Human	f_Peptostreptococcaceae f_Clostridiaceae g_Prevotella g_Clostridium	g_Lachnospira	TMA ↑ TMAO ↑	CVD	28
Heme in red meats	Mouse	p_Bacteroidota p_Proteobacteria p_Verrucomicrobia s_Akkermansia muciniphila	-	Colonic mucus barrier integrity ↓ Fecal trisulfide ↑	CRC	29
Dietary emulsifiers (carboxymethylcellulose and polysorbate-80)	Mouse	p_Proteobacteria p_Verrucomicrobia s_Ruminococcus gnavus s_Akkermansia muciniphila	o_Bacteroidales	Colonic mucus barrier integrity ↓ Fasting glucose ↑ Fecal level of butyrate ↓	Obesity Metabolic syndrome Colitis	30
Artificial sweeteners	Human	s_Prevotella copri s_Bacteroides xylanisolvens s_Bacteroides coprophilus s_Parabacteroides goldsteinii s_Lachnospira spp.	-	Serum level of serine, N-acetyl alanine, aspartate, quinolinate, cystine, lysine, and glycyl-L-valine ↑	Glucose intolerance	31
	Mouse	g_Anaeroplasma g_Parabacteroides s_Bacteroides acidifaciens	o_Clostridiales g_Clostridium s_Lactobacillus reuteri	Fecal level of propionate and acetate ↑	Glucose intolerance	32
Urban lifestyles
Sedentary lifestyle	Human	f_Enterobacteriaceae o_Enterobacteriales	f_Paraprevotellaceae f_Lachnospiraceae g_Lachnospira	SCFA ↓	Obesity	33
Prevalent antibiotic use
Vancomycin	Human	p_Proteobacteria g_Haemophilus g_Serratia s_Escherichia coli	α diversity p_Firmicutes Clostridium cluster IV/XIVa s_Lactobacillus plantarum s_Faecalibacterium prausnitzii s_Eubacterium hallii	Primary bile acids ↑ Secondary bile acids ↓	Insulin sensitivity ↓ T2DM	6
Ampicillin, bacitracin, meropenem, neomycin, vancomycin	Mouse	-	Eradication of most of commensal bacteria	Acetate, Butyrate, Propionate ↓ TMA ↓ Adenine ↓ Uracil ↓ Brain-derived neurotrophic factor ↓ N-methyl-d-aspartate receptor subunit 2B ↑ Serotonin transporter ↑ Neuropeptide ↑	Cognitive deficit	34
Tylosin, amoxicillin	Mouse	f_Prevotellaceae f_Enterobacteriaceae s_Clostridium citroniae	Microbial richness and evenness	Treg ↓ TNF-α ↑ IL-22 ↓ Muc2 ↓	IBD	35
Early life exposure
Cesarean section	Human	-	g_Bifidobacterium g_Bacteroides g_Lactobacillus g_Enterobacter g_Haemophilus g_Staphylococcus g_Streptococcus	Treg ↓	Asthma	36,37
Milk formula	Human	s_Clostridium difficile s_Granulicatella adiacens s_Citrobacter spp. s_Enterobacter cloacae s_Bilophila wadsworthia	s_Lactobacillus johnsonii s_Lactobacillus gasseri s_Lactobacillus paracasei s_Lactobacillus casei s_Bifidobacterium longum	-	-	38

Abbreviation: PM, particulate matters; TNF, tumor necrosis factor; CXCL, the chemokine (C-X-C motif) ligand; IL, interleukin; IFN, interferon; H₂S, hydrogen sulfide; CRC, colorectal cancer; IBD, inflammatory bowel disease; TMAO, trimethylamine N-oxide; CVD, cardiovascular diseases; TMA, trimethylamine; SCFA, short-chain fatty acid; Treg, regulatory T cell.