TABLE 3.

Studies using defined communities in nonrodents to study host-microbe interactions in vivo (n = 6)^a

Consortium (no. of speciesb)	Division of phylae	Strain source	Host species (strain)	Part of the gut studiedf	No. of animals/group	Chow	Sex	Age (collection time[s]c)	Study outcomesd	Reference
Bristol (3 and 4 species), modified ASF (6 and 7 species)  3 species: Lactobacillus amylovorus DSM 16698T, Clostridium glycolicum, and Parabacteroides sp. (ASF519)  4 species: 3 species + R. intestinalis  6 species: Clostridium sp. (ASF356), Lactobacillus sp. (ASF360), Lactobacillus animalis (ASF361), E. plexicaudatum (ASF492), Parabacteroides sp. (ASF519), and Propionibacterium sp.  7 species: 6 species + Staphylococcus sp. or Bacillus sp.	3 species: 4 species: 6 species: 7 species:	Pig	Pig (commercial hybrid and Babraham)		2–6	Evaporated milk	NR	0–17 days (14–21 days after 1st inoculation)	Presence of bacteria and mean total bacterial content in proximal and distal jejunum, terminal ileum, cecum, and colon; serum immunoglobulin concn	52
Bristol (3 species)		Pig	Pig ([Great York × Pie] × ‘Dalland’ cross)		6	Pasteurized sow colostrum (first hours), ad libitum milk replacer diet (days 0–4), moist diet (remaining)	NR	Neonates (26–37 days)	Relative OR51E1 expression in jejunum	59
Bristol (3 species)		Pig	Pig ([Great York × Pietrain] × ‘Dalland’ cross)		6	Sow serum or pasteurized sow colostrum, followed by ad libitum milk replacer diet (days 0–4), followed by a control diet or medium-chain-fatty-acid diet	NR	1 day (2–3 wk)	Oxyntic mucosa transcriptome	60
DMF (7 and 8 species)  7 species: Bifidobacterium adolescentis, B. longum, B. thetaiotaomicron, E. faecalis, L. brevis, Streptococcus bovis, and C. clostridioforme  8 species: DMF + E. coli Nissle	7 species: 8 species:	Pig	Pig (Landrace × Yorkshire × Duroc cross-bred)		3–6	NR	NR	7 days (35 days)	Fecal virus shedding; mean duration of diarrhea; diarrhea severity and % of diarrhea; gene expression levels of ChgA, Muc2, PCNA, SOX9, and villin in jejunal intestinal epithelial cells	62
		Pig	Pig (NR)		3–5	NR	NR	5 days (14–35 days)	Bacterial content in rectum, duodenum, jejunum, ileum, colon, and feces/rectal swabs; diarrhea and virus shedding after virulent human rotavirus challenge	63

^aNR, not reported; ChgA, chromogranin A.

^bTwo different strains tested are counted as one species. Strains were not always reported. Pathogenic species, in the case of an infection model, are not included.

^cThe colonization time includes the time from colonization (time zero in the case of transfer of microbiota to offspring) until and including the time of sacrifice or the end of experimental (e.g., dietary) manipulations, in cases where this is clearly stated in the paper. If age is given and animals are colonized at birth, the age is included in the colonization time.

^dStudy outcomes are reported only for the animals colonized with the defined community of interest.

^e , Firmicutes; , Bacteroidetes; , Actinobacteria; , Proteobacteria; , Verrucomicrobia; , other.

^fThe color codes from left to right in the illustration are as follows: , stomach; , duodenum; , jejunum; , ileum; , cecum; , colon; , rectum; , feces.