Characterisation of caecum and crop microbiota of Indian indigenous chicken targeting multiple hypervariable regions within 16S rRNA gene

Abstract

A comparative analysis of caecum and crop microbiota of chick, grower and adult stages of Indian indigenous chickens was conducted to investigate the role of the microbiota of the gastrointestinal tract, which play an important role in host performance, health and immunity. High-throughput Illumina sequencing was performed for V3, V4 and V4-V6 hypervariable regions of the 16S rRNA gene. M5RNA and M5NR databases under MG-RAST were used for metagenomic datasets annotation. In the crop, Firmicutes (~78%) and Proteobacteria (~16%) were the predominant phyla whereas in the caecum, Firmicutes (~50%), Bacteroidetes (~29%) and Actinobacteria (~10%) were predominant. The Shannon-Wiener diversity index suggested that sample richness and diversity increased as the chicken aged. For the first time, the presence of Lactobacillus species such as L. frumenti, L. antri, L. mucosae in the chicken crop along with Kineococcus radiotolerans, Desulfohalobium retbaense and L. jensenii in the caecum are reported. Many of these bacterial species have been found to be involved in immune response modulation and disease prevention in pigs and humans. The gut microbiome of the indigenous chicken was enriched with microbes having probiotic potential which might be essential for their adaptability.

Dietary synbiotic incorporation as an alternative to antibiotic improves growth performance, intestinal morphology, immunity and antioxidant capacity of broilers

“…The consequence of synbiotic supplementation on cecal microflora composition of broilers including the present study is usually determined by the simple culture medium measurement . The 16S rRNA‐based analysis of gut microbiota has received increasing attention in poultry and swine, and further studies should employ the 16S rRNA‐based analysis to better reveal the relationship between synbiotic administration and gut bacterial communities in broiler chickens.…”

Novel Isolates of Lactobacilli from Crop of Algerian Poultry as Potential Probiotic for Food Industry

“…This diversity could be linked to environmental conditions. Count of total bacteria is between 7.5×10 6 to 9.0×10 6 .…”

“…The community structure and the diversity of the microflora of the GI tract are continuously affected by factors associated with the host health and nutrition and the outside environment [2][3]. The crop as a part of the GI tract contains considerable amount of bacterial species which might play an important role in host performance, for example to assist the digestion of food, to produce micronutrients and to modulate the immune system… [4][5][6].…”

“…The presence of Lactobacillus species in the chicken crop is reported. Many of these bacterial species contribute to maintaining the ecological balance of the GI tract ecosystem [6]. Several works reported the properties of lactic acid bacteria (LAB) isolated from animals such as antimicrobial activity against pathogens [7] and their possible use as probiotic in animal feed [8].…”

Cecal microbiota affects chicken growth performance by regulating fat metabolism

“…The chicken gastrointestinal tract harbors very complex microbial communities, with the highest bacterial diversity in the cecum [9][10][11][12][13]. Increasingly, studies in chickens have established the importance of the gut microbiota, especially the cecal microbiome, in improving feed digestion, nutrient absorption and growth performance [14][15][16].…”