The gastro-intestinal tract of poultry is mostly sterile at the time of hatch and it develops rapidly during the initial stages of chick’s growth. The colonisation of the infant gastro-intestinal tract by microbes is an essential process in the life cycle of the chick. There exists a natural balance between beneficial and harmful bacteria in a healthy chicken, which is known as Eubiosis. Intensive system of rearing inflicts considerable stress and significant impact on bird health which affects the natural balance of microbiota.
Metagenomics (‘’Meta’’- beyond oneself) is the study of the metagenome. Metagenome is the collective genome of microorganisms from an environment. Genomics is the study of the genome of an organism.

At the beginning of the large intestine, there are two blind patches known as caeca. Caeca has lower passage rate of intestinal contents and is an ideal habitat for diverse microbiome. The caecal microbiota density is around 100 times more than that of ileum. The undigested nutrients reach caeca and the microbiota inside the caeca ferments it. The process of fermentation releases energy precursors like VFAs (Volatile fatty acids). Energy substrates released in the caecum includes Acetic acid (65%), Butyric acid (16%), Propionic acid (12%) and other short chain fatty acids. These substrates help the bird to better utilise the energy, around 5-10% from the diet. They also help in inhibiting the pathogenic bacteria in the gut.

The taxonomy of gut microbiota:

Taxonomy is the practice and science of classification especially of organisms into Kingdom, Phylum, Class, Order, Family, Genus and Species. Under the Kingdom Monera (prokaryotae) which includes bacteria found in the poultry caeca, there are some predominant Phyla, like Firmicutes, Bacteroidetes, Proteobacteria etc.

Literature review on caecal microbiota suggests, Firmicutes are energy harvesting microbes.

Literature review on caecal microbiota suggests, Firmicutes are energy harvesting microbes. Firmicutes play an important role in the fermentation of dietary compounds, transporting many substrates across their cellular membranes. It has been surmised that Firmicutes-dominant phenotypes have been related to an increased ability to harvest energy from the diet, with carbohydrate metabolism being an important factor. Firmicutes are known to ferment host nutrients to generate VFA ( Corrigan 2015).
Bacteroidetes are common bacteria in the gut of birds, involved in many important metabolic activities, including the fermentation of carbohydrates, the utilization of nitrogenous substances, the biotransformation of bile acids and the prevention of pathogen colonization (Corrigan et al , 2015).

Proteobacteria is generally represented by certain pathogenic forms like E.coli, Salmonella etc.

Significance of F/B ratio (Firmicutes: Bacteroidetes ratio)
Higher F/B ratios are often associated with better FCR and body weight in broilers. There is a wealth of evidence in top research journals to support improvement in performance of poultry when the Firmicute percentage in the caeca goes up. Greater F/B ratio have been associated with bacterial profiles with higher capacity of energy harvesting (Costa CM et al PlosOne 2017). It is also interesting to note that many growth promoters improve F/B ratio (Salaheen et al 2017)

Design of experiment

  • Experimental model: Magnesium chloride induced diarrhoea model
  • Trial done in broilers: Cobb 430 birds
  • Trial groups:
    • Normal control (no Magnesium chloride given)
    • Negative Control (Magnesium chloride given)
    • Stodi (Magnesium chloride + Stodi)
  • Metagenomics:
    • Caeca harvested on 42nd day in special tubes for DNA storage form 10 birds per group
    • Pooling of DNA plan: 10 samples from each group were made into 5 pools (2 birds /pool)

The Phylum level outcome suggests a significant increase in Firmicutes level and decrease in Bacteroidetes level in the Stodi treated group. This suggests an increase in F/B ratio. The Proteobacteria levels are also decreased in the Stodi treated group.

Firmicutes: Bacteroidetes ratio has been found be highest in Stodi group when compared to Normal diet and Negative trial.

Performance data has also been found to be better in Stodi group when compared to Negative trial in terms of body weight at 42 days of age and FCR.
Similar outcome was observed in Class level, Family level and Species level also where beneficial bacterial strains were found to have favourable growth in Stodi treated group.

Oscillospira sp: involved in the fermentation of various mono- and oligo-saccharides, producing SCFAs which could contribute around 10% of energy (J´ozefiak et al., 2004), in addition to their health promoting effects (Mookiah et al., 2014)

Megamonas sp: Is involved in polysaccharide degradation with sugar transport and utilization in Megamonas, a gene cluster encoding secreted endo-glucanases, a cellobiose phosphotransferase system and a 6-phospho-beta-glucocidase, which together form an extracellular complex capable of degrading NSPs to cellobiose, which is then imported and cleaved to give D-glucose. (Sergeant MJ et al, 2014. PlosOne)

Faecalibacterium prauntzii: were recently shown to contribute to the caecal microbiota of chickens. These bacteria produce SCFA such as formic and butyric acid, which have important function in performance and defence against pathogens. (Torok VA et al 2011)

Impact on pathogenic flora

The family level bar plot reveals reduction in the count of Campylobacteriaceae and Enterobacteriaceae, which indicates impact of Stodi on pathogenic microflora.

Principal Coordinate Analysis Plot (PCA) for Beta Diversity

STODI treatment distinctly shifts the micro-flora in the caeca as revealed by PCA plot


  1. Stodi treatment had a definite impact on caecal microflora
  2. Stodi treatment augmented the Firmicute abundance percentage significantly. Firmicutes are known to harvest energy from poultry diet and provide it to host.
  3. Stodi treatment improved the F/B ratio significantly. F/B ratio improvement is correlated with improved performance of birds.
  4. The observed improvement in body weight and FCR by Stodi could be due to improvement of microflora which are known to harvest energy from the diet
  5. Specifically, bacteria belonging to Lachnospirarceae, Ruminococcaceae were upregulated by Stodi treatment