Table 1 Parts of the poultry GIT, their functions and associated microbiota

Crop

Actinobacteria, Firmicutes, Bacteroides, Proteobacteria.

Feed storage and pre-treatment

Na

[72, 84]

Gizzard

Firmicutes (Lactobacillus, Enterococcus), coliforms

Feed grinding, low pH acts as a microbial barrier

Na

[13]

Duodenum

Clostridia, Streptococci, Enterobacteria and Lactobacilli

Reception of digestive enzymes from the pancreatic and bile ducts, dilution of digesta by secreted bile

Na

[85]

Ileum

Proteobacteria, Firmicutes, Cytophaga, Flexibacter, Bacteroides, Actinobacteria and Cyanobacteria

Passage of small amounts of digesta to the caecum

Na

[78, 84]

Caecum

Firmicutes, Actinobacteria, Bacteroides, Proteobacteria, Clostridiales and Anaerobic microbes, plus Campylobacter, Helicobacter and Megamonas; Fusobacteria (Fusobacterium sp.), Elusimicrobia (Elusimicrobium sp.), Synergistetes (Cloacibacillus sp.), Spirochaetes (Treponema sp.) or Verrucomicrobia (Akkermansia sp.).

Nutrients fermentation; Polysaccharides to short chain volatile fatty acids (SCFA) using enzymes (carbohydrate esterase, polysaccharide lyase, and glycoside hydrolase);

Host performance and health

20%

[35, 72, 74, 86,87,88]

Protein and amino acids metabolism, Effective nitrogen metabolism

9%

1%

[13, 75]

Fatty acid and lipid metabolism

1%–2%

[75]

Methanogenic Archaea

Na

Na

[42, 71, 75, 86]

Large intestine

Firmicutes (Lactobacillus), Proteobacteria (E. coli)

Retention of little or no digesta

Na

[25]