The gut microbiota of poultry has evolved to its current form incorporating many different microorganisms from the environment, animals, and humans with which they come into contact. This means that the phylogenetic composition of the gut microbiota of birds largely overlaps with the microbiota of humans and other farm animals.

Currently, recent research on the gut microbiota of chickens has suggested that the industrialization of chicken production has transformed its gut microbiota to such an extent that it probably has a very different composition than would be found in its wild precursors, due to unnatural incubation practices and unnatural environments such as hatcheries.

Commercial poultry production practices expose newborn chicks to microbes from the hatchery environment, human handlers, shipping crates and transport vehicles, prior to their arrival on the farm. This process usually takes place in the first days of life, during the period when there is a rapid increase in bacterial diversity and load in the intestine. These environmental sources of bacteria appear to have a significant influence on the establishment of the gut microbiota, as the most significant colonization in chickens occurs within the first few days after hatching.

Until recently, it was believed that chicks were sterile in ovo and that colonization began after hatching. The application of recent technological advances has suggested that, at least in some circumstances, there may be very low level in ovo bacterial colonization. Bacterial colonization of the gut is likely to be a competitive process in which initial bacterial colonizers inhibit or promote the establishment of subsequent bacterial invaders by modifying the environment and/or cross-feeding metabolites that support or retard the growth of other bacteria.

The formation of the microbial community in chickens is very fast with 10⁸ and 10¹⁰ bacteria per gram of content in the ileum and cecum respectively, one day after hatching. The numbers increase to 10⁹ and 10¹¹ respectively by the third day and remain high as they continually adapt and respond to environmental changes and stressors. This indicates that the first few days after hatching are critical for controlled and restricted microbial exposure to pathogens.

Gut microbiota in broilers

The gastrointestinal compartments of chickens are densely populated by complex microbial communities (bacteria, fungi, archaea, protozoa, and viruses) dominated by bacteria that play important roles in bird nutrition, physiology, and gut development. The intestinal microbiota can form a protective barrier by adhering to the epithelial walls of the enterocyte and thus reducing the opportunity for pathogenic bacteria to colonize. These bacteria produce vitamins, short-chain fatty acids, organic acids, antimicrobial compounds, and induce non-pathogenic immune responses, which provide nutrition and protection to the animal. On the other hand, the digestive microbiome can also be a source of bacterial pathogens such as Salmonella and Campylobacter that can spread to humans or act as a source of resistance and transmission to antibiotics and thus can be a public health hazard.

The main benefits provided by the commensal microbiota are the competitive exclusion of pathogens or foreign microbes, immune stimulation and programming, and contributions to host nutrition. The commensal microbiota can stimulate the development of the immune system, including the mucosal layer, the epithelial monolayer, intestinal immune cells, and the lamina propria. Likewise, the microbiota also produces energy and nutrients such as vitamins, amino acids, and short-chain fatty acids (SCFAs) from the undigested food, which ultimately become available to the host. These SCFA have bacteriostatic properties that are capable of killing foodborne pathogens such as Salmonella spp. SCFAs are also a source of energy for animals and can further stimulate intestinal epithelial cell proliferation, thus increasing the gastrointestinal absorptive surface. It has also been established that SCFA production lowers the pH of the colon, which inhibits the conversion of bile-to-bile by-products. In addition, some of the nitrogen in the diet is incorporated into bacterial cell protein, and therefore the bacteria themselves can be a source of protein/amino acids.

The digestive tract of chickens harbors a very complex microbiota, with more than 600 different bacterial species from more than 100 bacterial genera. In general, the most abundant phylum in the chicken gut microbiota is Firmicutes, followed by two minor phylum, Proteobacteria and Bacteroidetes. In addition, members of the phylum Actinobacteria, Tenericutes Cyanobacteria and Fusobacteria can be found in a low proportion. Bacterial communities vary considerably by location along the GI tract of chickens. The crop, gizzard and duodenum share a similar microbiota, dominated by the genus Lactobacillus, up to 99% in some poultry. The greatest diversity of Lactobacillus was demonstrated in the crop. The jejunum is also dominated by Lactobacillus species, primarily L. salivarius and L. aviarius. The microbial composition of the ileum is more diverse and less stable compared to the duodenum and jejunum. The ileum is dominated by Lactobacillus, Candidatus Arthromitus, Enterococcus, Escherichia coli, Shigella, and Clostridium XI. The cecum is by far the most densely colonized and studied microbial habitat of chickens and its bacterial diversity is much greater than that of the upper digestive tract. The cecum is a key region for bacterial fermentation of indigestible carbohydrates and an important site for colonization by pathogens. It has been reported that the cecum is occupied mainly by the genus Clostridia followed by the genus Lactobacillus and Ruminococcus. Most of the clostridia detected in the cecum belong mainly to three main families, Clostridiaceae, Lachnospiraceae and Ruminococcaceae. The cecum is also rich in unknown and unclassified resident bacteria. At the species level, Bacteroides fragilis, L. crispatus, L. johnsonii, L. salivarius, and L. reuteri comprise more than 40% of the cecal microbiota.

Gut microbiota in laying hens

The composition of the gut microbiota in laying hens varies between the different functional segments of the gastrointestinal tract, reflecting their different physicochemical microenvironments. The pH, growth substrates, antibacterial secretions, and metabolites from the host and microbiota all influence the colonization efficiency of microbes in intestinal segments. The proximal segments of the intestine are characterized by a low pH, which strongly selects for acid-tolerant bacteria and limits the growth of most pathogens.

The crop is dominated by Blautia, Lactobacillus, Bacillus, Pseudomonas, Enterococcus and Staphylococcus, while in the cecum, in addition to the above, other bacteria such as Faecalibacterium, Bifidobacterium, Clostridium and Ruminococcus also abound. In the caecum of mature laying hens, representative microbial communities at the phylum level are Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Deferribacteres, Fusobacteria, Verrucomicrobia, Synergistetes, and Lentisphaerae.

Rearing conditions and host-related factors such as production system, sex, age, breed, and diet can have profound effects on gut microbiota development and composition. Correlations have been observed between gender, genotype, age and body composition, and the abundance of various microbial genus. For example, the gut microbiota develops rapidly from day 1 to 3, and by day 7, most of the organisms found in the mature microbiota are already present. After 2 weeks of hatching, Ruminococcus and Oscillospira increase substantially while Enterococcus decreases. At week 30 Firmicutes and Bacteroidetes become more abundant in the intestine. Proteobacteria, Firmicutes, and Bacteroidetes form the vast majority of the microbiota at all ages, demonstrating that Gram-negative bacteria dominate the gut at an early age, while Firmicutes become more prominent in adulthood in hens.

Gut microbiota in turkey and duck

In all turkey intestinal regions, the largest number of organisms identified belonged to the Firmicutes phylum, ranging from 76% in the proximal tract to 85% in the distal tract. Lactobacillaceae (30.73%) and Peptostreptococcaceae (15.39%) were the most common families found in the jejunum, but rarely present in the cecum (1.52% and 1.97%, respectively). There the dominant microorganisms belonged to the families Lachnospiraceae (32.50 %) and Ruminococcaceae (18.44 %). Bacteria belonging to the families Clostridia UCG-014 (8.59 %) and vadinBB60 (6.07 %), as well as Oscillospiraceae (8.43 %), were more abundant in the distal tract than in the proximal, where there were more Erysipelotrichaceae (4.12%), Aerococcaceae (2.43%) and Staphylococcaceae (2.38%). In the jejunum, Bacteroidaceae (1.93%) was the most abundant, while Rikenellaceae (8.88%) predominated in the cecum. The Enterobacteriaceae family constituted 5.6% of the total microbiota in the proximal intestinal tract compared to 2.33% in the distal intestinal tract.

In Peking ducks, the microbial population was determined to be strongly correlated with duck age, showing a clear transition in dominant taxa as the ducks matured. The cecal content of the ducklings showed high levels of proteobacteria that decreased with age. The taxonomic transition led to a dominance of Firmicutes for the remainder of the penned ducks’ lives. Day 1 ducks were dominated by the phylum Proteobacteria, which ranged from 77 to 99% of an individual’s microbial population. By day 8, the population had passed into the domain of the Firmicutes phylum, which ranged from 81 to 98% of the population in an individual. Firmicutes dominance extended through the remainder of the fattening period, constituting an average of 96% of the microbial population. Rather, the transition led to two major phyla, Firmicutes and Bacteroidetes, in farm-raised ducks.

Lung microbiota in broilers. The respiratory microbiota in broilers is dominated by the phylum Firmicutes and has immune, antimicrobial, and respiratory tissue protective functions. However, these beneficial effects can be diminished by pathogens or environmental conditions such as ammonia.

Fungal microbiota in poultry

Regarding the origin of the fungal intestinal mycobiota, its origin is almost exclusively food and environmental. Typically, at least 20 fungal species are reported in the digestive tract of birds, and Candida is frequently described as the most abundant genus in the gastrointestinal tract of chickens and turkeys, although the dominant Candida species vary according to reports existing. Regarding the beak and crop, the two most dominant fungi are F. pseudonygamai and C. albicans. In proventriculus and gizzard, Penicillium, Aspergillus and Fusarium fungi predominate with seasonal oscillations due to the seasonality of cereals. In the intestinal tract, from the duodenum to the ileocecal region, filamentous molds of the genus Mucor predominate, followed by Rhizopus. While the ceca are mainly colonized by the genus Candida.

Like happens with the bacteria of the microbiota, some of these fungi can become pathogenic, in case of dysbiosis, but others have a bacterial control effect (Penicillium) or produce enzymes that help digest food (Aspergillus). For this reason, penicilliosis and aspergillosis primary digestive are rare.