Influence of Different Litter Regimens on Ceca Microbiota Profiles in <i>Salmonella</i>-Challenged Broiler Chicks

A 14-day study was conducted to evaluate the effect of litter type (dirty litter, DL; fresh litter, FL) and <i>Salmonella</i> Enteritidis SE challenge (no challenge, NC; challenge, SE) on the growth performance and cecal microbial composition of neonate chicks. Day-old chicks (<i>n</i> = 240, Ross 708 male) were allocated to a 2 × 2 factorial design consisting of four treatments: chicks raised on dirty litter (CONDL), chicks raised on fresh litter (CONFL); and chicks raised on litter types similar to CONDL and CONFL but inoculated with 7.46 × 108 CFU SE/mL at d 1 (CONDLSE and CONFLSE). The performance indices measured included body weight (BW), body weight gain (BWG), feed intake (FI), mortality, and feed conversion ratio (FCR). Cecal SE concentration was assessed on d 3 and 14, and ceca were collected from chicks on day 14 for DNA extraction. The Illumina Miseq platform was used for microbiome analysis of the V3–V4 region of the 16S rRNA gene. The interaction of litter type and SE influenced FCR and FI. CONDL recorded the poorest FCR (1.832). FI was highest and similar in CONFLSE, CONDL, and CONDLSE (0.655, 0.692, and 0.677, respectively). Cecal SE concentration was significantly reduced in CONDLSE at d 3 and 14. Alpha diversity was higher (<i>p</i> < 0.05) in the DL compared to that in NC. Beta diversity showed a separation (<i>p</i> < 0.05) between the DL and the FL. Comparative tree analysis revealed 21 differential significant genera, with 14 prevalent in the DL and 7 in the FL, specifically, bacteria genera such as <i>Lactobacillus</i>, <i>Clostridia_vadinBB60_group</i>, <i>Lachnospira</i>, <i>Oscillospiraceae UCG_005</i>, and <i>Marvinbryantia</i>, which play significant roles relating to improved growth performance, metabolic homeostasis within the gut, energy metabolism, and short-chain fatty acid (SCFA) utilization. Our results concluded that litter management regimen differentially alters the microbiome of chicks, which accounts for the improved performance and exclusion of pathogens in the study.