Table 3.

Mouse knock-out studies demonstrating altered microbiome composition

Gene	Chromosome	Phenotype	Reference
Tlr5	1	The gut microbiotica shows enrichment or reduction of 116 bacterial phylotypes relative to wild-type controls and transplanting gut microbiota from homozygotes to germ-free control hosts confers many aspects of the metabolic disease phenotype	(Chassaing et al. 2014); (Vijay-Kumar et al. 2010)
Card9	2	The LEfSe analysis revealed differences including decreases in Adlercreutzia (genus), Actinobacteria (phylum), and Lactobacillus reuter in the Card9 − / − mouse microbiota. Mice fail to metabolize tryptophan into metabolites that act as aryl hydrocarbon receptor (AHR) ligands	(Lamas et al. 2016)
Pglyrp3	3	Have reduced Lactobacillus/Lactococcus, Enterobacteriaceae, and Eubacterium rectale/Clostridium coccoides, and Clostridium perfringen groups	(Saha et al. 2010)
Pglyrp4	3	Have reduced Lactobacillus/Lactococcus and segmented filamentous bacteria groups increased Bacteroides group	(Saha et al. 2010)
Tlr2	3	Display a threefold increase in Firmicutes and a slight increase in Bacteroidetes compared with controls	(Caricilli et al. 2011)
Lepr	4	Have a significant higher abundance of Firmicutes, Proteobacteria, and Fibrobacteres phyla in db/db mice compared to lean mice	(Geurts et al. 2011)
Ptpn11	5	Have an increase in Enterobacteriaceae and a decrease in Firmicutes were observed in the colon of these mice	(Coulombe et al. 2016)
Aicda	6	Mice exhibit an increase in bacteria, especially anaerobic bacteria, in the small intestine compared with wild-type mice. Some mice exhibit an expansion of unclassified Lachnospiraceae of the order Clostridiales while others exhibit increased Bacteroidales or Lactobacillus compared with wild-type mice	(Wei et al. 2011)
Reg3g	6	Mice exhibit a higher mucosal bacterial loads (gram-positive Firmicutes phylum [Lactobacillus, Eubacterium rectale, and segmented filamentous bacteria (SFB) groups]) compared with wild-type mice; however, luminal bacterial loads are normal	(Vaishnava et al. 2011)
Lep	6	ob/ob animals have a 50% reduction in the abundance of Bacteroidetes and a proportional increase in Firmicutes	(Ley et al. 2005)
Nlrp2	7	Dysbiosis marked by increased obesity-associated Erysipelotrichaceae but reduced Lachnospiraceae family and the associated enzymes r	(Truax et al. 2018)
Nlrp6	7	Mice and co-housed wild-type mice exhibit expanded bacterial phylotypes compared with wild-type mice	(Elinav et al. 2011)
Pglyrp1	7	Have reduced segmented filamentous bacteria	(Saha et al. 2010)
Fut2	7	Salmonella typhimurium susceptibility	(Goto et al. 2014)
Nod2	8	Relative abundances of several clostridial genera were associated with disease phenotype, NOD2 composite genotype, and/or ATG16L1genotype	(Frank et al. 2011; Rehman et al. 2011)
Myd88	9	Increased abundances of Lactobacillaceae, Rikenellaceae, and Porphyromonadaceae phylotype	(Wen et al. 2008)
Apoa1	9	12% variation of a Partial Least-Square Discriminate Analysis of microbiota structure accounted for by genotype	(Zhang et al. 2010)
Mmp7	9	Increased sensitivity to Salmonella typhimurium. KO mice also have increase Firmicutes (specifically Clostridia) an decreased Bacteroidete) compared to wild type	(Wilson et al. 1999), (Salzman et al. 2010)
Atg5	10	Have a dramatically altered composition of the gut microbiota and reduced alpha diversity. “Candidatus Arthromitus” and the Pasteurellaceae family were increased in KO mice, whereas Akkermansia muciniphila and the Lachnospiraceae family were reduced	(Yang et al. 2018)
Ikzf1	11	The intestinal flora contains more numbers and more diverse groups of bacteria than in controls	(Georgopoulos et al 1994)
Nlrp3	11	Mice fed a Western diet show a greater gut microbiota dysbiosis than controls on the same diet	(Pierantonelli et al 2017)
Pik3cg	12	Between WT and KO 11 taxa were found to increase significantly and five taxa decreased significantly in KO mice compared to WT mice	(Li et al. 2020)
Igha	12	Mice deficient in IgA harbor an increased abundance of SFB	(Suzuki et al. 2004)
Ccl28	13	The abundance of Class Bacilli bacteria is increased in the intestine	(Matsuo et al. 2018)
Sugct	13	Mice show differences in the proportion of and type of bacteria species in stool, with an increase of firmicutes relative to Bacteroidetes (strongest in Blautia genus containing the families Ruminococcaceae and Lachnospiraceae, then Adlercreutzia genus, Bilophilia genus, and AF12 genus and a decrease in Bifidobacterium genus); microbiome changes resemble those seen in microbiome disbalance in metabolic diseases like diabetes	(Niska-Blakie et al. 2020)
Olfm4	14	Following oral challenge, mice exhibit reduced colonization by Helicobacter pylori and increased infiltration of inflammatory cells in the gastric mucosa compared with wild-type mice	(Liu et al. 2010)
Vdr	15	Lactobacillus was depleted in the fecal stool, whereas Clostridium and Bacteroides were enriched. Bacterial taxa along the Sphingobacteria-to-Sphingobacteriaceae lineage were enriched	(Jin et al. 2015)
Retnlb	16	Fifteen Bacteriodetes lineages, and 1 lineage of Proteobacteria, changed in abundance between genotypes, whereas 15 Firmicutes lineages changed in abundance	(Hildebrandt et al. 2009)
Percc1	17	Display an altered intestinal and fecal microbiome composition	(Oz-Levi et al. 2019)
Pglyrp2	17	Have reduced Lactobacillus/Lactococcus, segmented filamentous bacteria, Clostridium perfringens, and Bacteroides groups	(Saha et al. 2010)
Npc1	18	The gut microbiota composition shifted and increased microbial richness and diversity Specifically, Staphylococcus spp. and unclassified Mogibacteriaceae spp. Mice showed significantly higher levels in relative abundance in the KO mice compared to WT mice, whereas the abundance of Allobaculum spp. was significantly lower. Relevantly, the unclassified Mogibacteriaceae spp	(Houben et al. 2019)
HLA-DRB1*0401	Tg	Clostridium-like bacterium abundance altered	(Gomez et al. 2012)
DEFA5	Tg	Mice have a decreased proportion of bacteria from the Firmicutes, and decreased SFB	(Salzman et al. 2010)