Comparative analysis of chicken cecal microbial diversity and taxonomic composition in response to dietary variation using 16S rRNA amplicon sequencing

Abstract

Antibiotic resistance poses a serious threat to human and animal health. As a consequence, their use in conventional poultry feed may be replaced by non-antibiotic additives (alternatives to antibiotics, ATAs). Phytogenic feed additives and organic acids have been gaining considerable attention that could abate the proliferation of pathogenic bacteria and strengthen gut function in broiler chickens. The aim of this study was to evaluate the effects of phytogenic feed additives and organic acids on cecal microbial diversity using 16S rRNA amplicon sequencing of the V3-V4 region. In this study, 240 chicks were divided into ve treatments comprising: a controlled basal diet (CON), antibiotic group (AB), phytogenic feed additives (PHY), organic acids (ORG) and a combination of PHY + ORG (COM). A distinctive microbial community structure was observed amongst different treatments with an increased microbial diversity in AB, ORG and COM (p < 0.05). The synergistic effects of PHY and ORG increased the population of bene cial bacteria that belonged to the phyla: Firmicutes, Bacteroides and Proteobacteria in the cecum. The presence of the species Akkermansia muciniphila (involved in mucin degradation) and Bacillus safensis (a probiotic bacterium) were noticed in COM and PHY, respectively. Clustering analysis revealed a higher relative abundance of similar microbial community composition between AB and ORG groups. In conclusion, treatments with PHY and ORG modi ed the relative abundance and presence/absence of speci c microbiota in the chicken cecum. Hence, cecal microbiota modulation through diet is a promising strategy to reduce cross-contamination of zoonotic poultry pathogens.

Grass Meal Acts as a Probiotic in Chicken

“…It is possible that the low protective effectiveness of the KS1 sample is due to the content of potential pathogens of chickens in it, representatives of the Saccharimonadia class (0.01% of the microbiome) or the genus Staphylococcus (0.16% of the microbiome); both of these groups were completely absent in the KS2 sample. There is evidence in the literature about the possibility of the presence of representatives of these groups in the human intestine and the association of their increased proportion in the microbiome with an unfavorable prognosis for diseases [44,45]. The TS2 sample exhibiting a high protective activity, along with the KS1 sample, contained few representatives of Bacilli sensu lato (0.3%, as shown by metagenomic analysis).…”

“…The effects of antibiotics and probiotics on the GIT microbiota in chickens were extensively studied by using metagenome sequencing (amplified libraries of 16S rDNA gene fragments were sequenced on the Illumina platform) [29,45]. It has been indicated that in the caeca of broilers, Clostridia are the predominant organisms [30], while the genus Lactobacillus is dominant in the ileum [46].…”

Effect of Dietary Supplementation of Enteric Avian-Origin Lactobacillus casei-Fermented Soybean Meal on the Growth Performance and Intestinal Health of Broiler Chickens

“…FSBM affected the intestinal flora, which was associated with intestinal health [48]. Healthy and economically efficient broilers can be produced by regulating the cecal microflora through diet [49][50][51]. Incorporating organic acids into feed had been shown to enhance broiler growth performance, while their synergistic combination with dietary fiber can further augment the humoral immune response [52].…”

Analysis of bacterial diversity associated with commercial broiler chicken in Lahore, Pakistan

“…Staphylococcus, Escherichia and Bacillus spp. are associated with the severe food poisoning and foodborne diseases due to the production of toxins produced by some bacteria e.g., B. cereus(Bhattacharyya and Das, 2022) Rashid et al (2021). confirmed microbial load variety on raw chicken meat including pathogens such as E. faecalis, Bordetella spp., Salmonella spp., E. aerogenes, S. aureus, K. pneumoniae, Micrococcus spp., Citrobacter spp., E. coli, S. epidermidis, Proteus spp., K. oxytoca, Providencia spp.…”