Broiler chicken trial the objective of which was to evaluate the effect of addition to feed probiotic Bacillus subtilis strains on broiler chicken performance, intestinal health and microbiota under necrotic enteritis challenged conditions was carried out. Chicken digesta samples were analyzed using %G+C microbial profiling and sequencing of 16S rRNA gene amplified from obtained %G+C fractions.

It was hypothesized that dietary inclusion of Bacillus subtilis DSM 32315 could inhibit Clostridium perfringens induced Necrotic Enteritis (NE), thereby improving performance of broilers. Male, day-old chicks were randomly assigned 14 birds/pen, 11 pens/treatment in 3 treatments; a basal diet control (Control), an antibiotic fed control (Narasin), and a group receiving the direct fed microbial B. subtilis DSM 32315 (DFM). NE was induced in all birds by oral inoculation of Eimeria maxima oocysts on d 12 and a field strain of C. perfringens on day 16. Mortality was reduced in DFM and Narasin compared to Control. The DFM reduced FCR compared to Control. Furthermore, DFM and Narasin reduced footpad lesions compared to Control. The DFM was shown to increase Bacillus and decrease C. perfringens in the ileum and cecum at several time points. To investigate microbiome changes in the cecum, digesta samples were analyzed with %G+C microbial profiling which fractionates bacterial chromosomes based on the % guanine and cytosine in DNA. The method revealed significant treatment profile differences in low (27.0-34.5%), mid (40.5-54.0%) and high (59.0-68.0%) %G+C fractions. 16S rRNA gene amplification and next generation sequencing was conducted on each of these fractions in order to elucidate specific bacterial population differences. In the low and mid %G+C fractions DFM had greater abundance of Lactobacillacea family members (P = 0.03 and P = 0.01, respectively) and Lactobacillus salivarus (P = 0.04 and P = 0.01, respectively) than Control or Narasin. Lactobacillus johnsonii was also greater in the low %G+C fraction compared to Control and Narasin (P = 0.01). Lachnospiraceae (P = 0.04) and Ruminococcaceae (P < 0.01) in the mid %G+C fraction were reduced in the DFM compared to Control. Positive alterations to the microbial populations in the gut of broilers may at least be a partial mechanism by which B. subtilis DSM 32315 reduced pathology and improved performance of broilers in the NE challenge.