Microbial community mapping in intestinal tract of broiler chicken

Abstract

Domestic chickens are valuable sources of protein associated with producing meat and eggs for humans. The gastrointestinal tract (GIT) houses a large microbial community, and these microbiota play an important role in growth and health of chickens, contributing to the enhancement of nutrient absorption and improvement of the birds' immune systems. To improve our understanding of the chicken intestinal microbial composition, microbiota inhabiting 5 different intestinal locations (duodenum, jejunum, ileum, cecum, and colon) of 42-day-old broiler chickens were detected based on 16S rRNA gene sequence analysis. As a result, 1,502,554 sequences were clustered into 796 operational taxonomic units (OTUs) at the 97% sequence similarity value and identified into 15 phyla and 288 genera. Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Cyanobacteria were the major microbial groups and Firmicutes was the dominant phylum in duodenum, jejunum, ileum and colon accounting for > 60% of sequences, while Bacteroidetes was the dominant phylum in cecum (>50% of sequences), but little in the other four gut sections. At the genus level, the major microbial genera across all gut sections were Lactobacillus, Enterococcus, Bacteroides, and Corynebacterium. Lactobacillus was the predominant genus in duodenum, jejunum, and ileum (>35%), but was rarely present in cecum, and Bacteroides was the most dominant group in cecum (about 40%), but rarely present in the other 4 intestinal sections. Differences of microbial composition between the 5 intestinal locations might be a cause and consequence of gut functional differences and may also reflect host selection mediated by innate or adaptive immune responses. All these results could offer some information for the future study on the relationship between intestinal microbiota and broiler chicken growth performance as well as health.

Growth performance, carcass characteristics, meat and egg quality, and intestinal microbiota in Beijing-you chicken on diets with inclusion of fresh chicory forage

“…In agreement with our findings, plenty of studies indicated that the Firmicutes was the dominant phylum in duodenum and ileum of chickens, while caecum was inhabited mostly by the Bacteroidetes Xiao et al 2017;Zheng et al 2019). At the genus level, the Firmicutes and Bacteroidetes were primarily composed of the Lactobacillus and Bacteroides, respectively.…”

“…The results of PCoA suggested that microbial community in caecum formed a distinct cluster and separated from that in duodenum and ileum, confirming that microbial compositions in caecum were different from those in duodenum and ileum. Xiao et al (2017) suggested that variance in the microbiota among different GIT sections might be attributed to different GIT functions. As reported, the small intestine (duodenum, jejunum and ileum) is the important site for nutrient digestion and absorption, while intestinal microbiota in caecum carries many important roles such as fermentation and breaking undigested substrates (Shaufi et al 2015).…”

“…Previous studies suggested that dietary supplementation of forage had an impact on poultry performance by modifying the gut microbial structure to a bacterial community that is more conducive to host growth (Jiang et al 2014;Saeed et al 2017). Extensive studies have been conducted to disclose the most abundant microbial community in the chicken GIT by using culture-based approach, DNA fingerprinting method and polymerase chain reaction (PCR)-based sequencing (Xiao et al 2017). Although these studies have expanded our knowledge of the intestinal microbiota, they only identified a few of the most abundant operational taxonomic units (OTUs) present, because of their poor limits of detection (Zheng et al 2017).…”

Antibiotic Resistance Genes in Antibiotic-Free Chicken Farms

“…Analysis of the microbiota profile of the manure belt swabs showed a dominance of family Aeromonadaceae and genus Luteimonas, Jeotgalicoccus, Corynebacterium and Brachybacterium in the samples. The Corynebacterium genus was found abundant in chicken duodenum, jejunum, ileum, and colon [22]. However, other genera, such as Lactobacillus, Enterococcus, Bacteriodes and Ruminococcus, reported as abundant in the chicken gastrointestinal tract [22,23], were rarely detected in our results.…”

Effects of yeast cultures with different fermentation times on the growth performance, caecal microbial community and metabolite profile of broilers

“…A previous study has reported that these genera, which are present in most animals, can produce SCFA and promote intestinal health (Eckburg et al, 2005). We find that Faecalibacterium is richer in YC-treated groups than control group, revealing the function of caecum by the role of Faecalibacterium play in the chicken growth and health (Xiao et al, 2016). (Conlon & Bird, 2015;Cullen et al, 2015).…”