Abstract Nutritional optimizations and rearing environment that meets welfare standards are prerequisite in the performance and health of laying hens. Rearing practices influence gastrointestinal development, microbiota, and immune function. However, little is known on the implications of rearing spacing allowance (SA) and feed ingredients on intestinal microbiota. We determined the abundance of selected cecal bacteria in pullets and hens in response to rearing SA and dietary omega-3 fatty acids (N-3 FA) and yeast bioactive (YB) from placement to 17 wk of age (woa). One-day old chicks (n = 2,632) were placed in cages in 2 SA of 24 cages each: High SA (HSA, 348 cm2/bird; ~50 birds/cage) and Low SA (LSA, 284 cm2/bird; ~68 birds/cage). Birds were fed corn and soybean-based diets (C), C + 3% co-extruded full fat flaxseed and pulse mixture (N-3 FA) and C + 0.05% YB processed with β-1,3-glucan hydrolase (YB). Birds were allocated to diets within SA according to 2 x 3 factorial design (n = 8 cage/treatment) and fed ad libitum. At 4 and 16 woa, 1 and 2 pullets/treatment respectively, were necropsied for ceca digesta from each cage and independently analyzed. At 18 woa, hens were placed in enriched cages based on rearing treatment identities in egg production facility and fed a commercial diet. At 35 woa, 18 hens per treatment were necropsied for ceca digesta samples and analyzed independently. Samples were analyzed for viable bacterial counts for E. coli, Enterococcus and Lactobacillus. Statistical analysis was performed by general linear mixed model procedures of SAS with diets, SA, sampling age and associated interactions as fixed factors, difference with P < 0.05 was considered significant. Comparison of log-transformed means (CFU/g) showed that diets and SA had no significant effect on cecal E. coli counts at 4, 8 and 35 woa (P > 0.05; Table 1). However, at 16 woa the least E. coli counts was found in LSA (P < 0.0001), with N-3-FA-fed and YB-fed pullets having fewer numbers (P = 0.007) than control-fed pullets. There was no interaction effects between diet and density for E. coli in all sampling wk (P >0.05). No significant effect of SA or diets were observed at any sampling week for Enterococcus counts, except LSA had a tendency at 8 woa (P = 0.078). At 8 woa, the cecal Lactobacillus counts (P = 0.009) were less in LSA relative to HSA pullets. In conclusion, feeding of N3-FA or YB during rearing influenced cecal microbiota. Supplementation of YB seemed to promote growth of beneficial Lactobacillus, which is associated with strengthened immunity.