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.

Three experiments with a 2 × 2 × 2 factorial arrangement were conducted to evaluate maize-based diets for broilers containing different lipid sources [soybean oil (S) or beef tallow (T)] supplemented with or without lysophospholipids and organic acids on nutrient balance (Experiment I, evaluation period of 10–14 d), on liver concentration of fat-soluble vitamins, on jejunal microbiota (Experiment II, sampling at d 14) and on performance (Experiment III, accumulated periods of 1–14, 1–21 and 1–42 d).

A total of 1344 male chicks were used. In each experiment, the birds were allotted in a completely randomised design with 8 replications. The lysophospholipids were mainly composed of lysolecithins and the organic acids blend was constituted by lactic (40%), acetic (7%) and butyric acids (1%).

An interaction between lipid sources and lysophospholipids was observed on faecal apparent digestibility of lipid (ADL), which improved with lysophospholipids addition in T diets. Broilers fed on S had higher ADL and faecal apparent digestibility of nitrogen-corrected gross energy (ADGE_N).

It was not possible to demonstrate a significant treatment effect on the liver concentration of vitamins A and E, even with the differences in fatty acid profile between S and T.

Enterobacteria values were below the detection threshold. Lysophospholipid supplementation reduced gram-positive cocci in T-fed birds. S diets promoted lower total anaerobe counts compared with T diets, independent of additives.

S diets increased BW gain and feed:gain ratio in all evaluation periods. Lysophospholipids and organic acids improved feed:gain ratio at 1–21 d in T diets. Furthermore, main effects were observed for lysophospholipids and organic acids at 1–42 d, which increased BW gain and improved feed:gain ratio, respectively.

No positive interactions between additives were found.