Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum

Abstract

Traditional sampling methods for the study of poultry gut microbiota preclude longitudinal studies as they require euthanasia of birds for the collection of caecal and ileal contents. Some recent research has investigated alternative sampling methods to overcome this issue. The main goal of this study was to assess to what extent the microbial composition of non-invasive samples (excreta, litter and poultry dust) are representative of invasive samples (caecal and ileal contents). The microbiota of excreta, dust, litter, caecal and ileal contents (n = 110) was assessed using 16S ribosomal RNA gene amplicon sequencing. Of the operational taxonomic units (OTUs) detected in caecal contents, 99.7% were also detected in dust, 98.6% in litter and 100% in excreta. Of the OTUs detected in ileal contents, 99.8% were detected in dust, 99.3% in litter and 95.3% in excreta. Although the majority of the OTUs found in invasive samples were detected in non-invasive samples, the relative abundance of members of the microbial communities of these groups were different, as shown by beta diversity measures. Under the conditions of this study, correlation analysis showed that dust could be used as a proxy for ileal and caecal contents to detect the abundance of the phylum Firmicutes, and excreta as a proxy of caecal contents for the detection of Tenericutes. Similarly, litter could be used as a proxy for caecal contents to detect the abundance of Firmicutes and Tenericutes. However, none of the non-invasive samples could be used to infer the overall abundance of OTUs observed in invasive samples. In conclusion, non-invasive samples could be used to detect the presence and absence of the majority of the OTUs found in invasive samples, but could not accurately reflect the microbial community structure of invasive samples.

Dynamics and Diversity of Microbial Contamination in Poultry Bedding Materials Containing Parts of Medicinal Plants

“…Staphylococcus sp. widely occurs in the litter and comes from the birds excreta [35]. Therefore, its significantly lower presence observed in the P5 material after 14 days of bedding exploitation in both experimental cycles is an important finding.…”

“…Since Escherichia sp. develops in the gastrointestinal tract of birds, it is widely present in birds' excreta [35]. Infection with these gram-negative bacteria is the main cause of diarrhea.…”

“…Even though the microbiological contamination of various used poultry bedding materials has been a subject of several prior studies [25][26][27][28][29][30][31][32][33][34][35], still little is known about the effects of using parts of different medicinal plants on the microbial contamination in bedding materials containing such parts. Given this background, the objective of our study is to investigate the total count of mesophilic aerobic bacteria, the total count of yeasts and moulds, and the presumptive count of Staphylococcus sp., Escherichia sp., Listeria sp., Salmonella sp., and Candida sp.…”

Feed Composition and Isolate of Histomonas meleagridis Alter Horizontal Transmission of Histomonosis in Turkeys. Proof of Concept

“…In other intestinal protozoa affecting human beings, such as Entamoeba histolytica and Trichomonas vaginalis, the bacteria can affect the virulence and adhesion of the protozoa (25,26). In the case of H. meleagridis, the protozoa are probably influenced by the intestinal microbiota and the litter microbiota (22)(23)(24)27). There is a direct correlation between gut and litter microbiota, and both are the reflection of the interaction between feed, ventilation, air quality, water quality, gender, among others (22)(23)(24)27).…”

Probiotics: Symbiotic Relationship with the Animal Host

“…Moreover, the gastrointestinal transit is shorter than that of mammals and is highly colonized by microorganisms that interact directly with the host [148,149]. Fermentation takes place in the ceca of poultry [150] because a complex microbiome is housed in this part of the GIT, which is densely populated with beneficial bacteria [151]. Hence, manipulating the microbiota by orally administering nutrients/supplements directly affects the intestinal morphology, nutrient digestibility and metabolic processes [152].…”