Temporal shift of bacterial communities in poultry litter during the course of broiler chicken rearing: a 16S rRNA-based metagenomic study.

Abstract

Aim: To decipher the bacterial community transitions of poultry litter at various time frames over a 6-week rearing cycle in a commercial broiler chicken poultry farm in Marakanam, Tamil Nadu, India.

Methods and results: The bacterial consortia of poultry litter were elucidated using the 16S rRNA-based metagenomic Oxford nanopore sequencing method, followed by taxonomic assignment using the Kraken2 tool. Our findings unveiled the varied dominance patterns of bacteria in poultry litter (P1-P6) with Sphingobacterium sp. 21 (53%) in P1, Amphibacillus xylanus dominated in P2 (∼12%), Oceanimonas sp. GK1 in P3 (∼14%) and P6 (>50%), Anaerococcus prevotii in P4 (∼10%) and Marinobacter hydrocarbonoclasticus (∼15%) in P5. Importantly various bacteria involved in key biogeochemical cycles, including Nitrosomonas eutropha (nitrogen cycle), Bacillus subtilis (phosphorous cycle), and Acidithiobacillus caldus (sulphur cycle) were detected indicating a strong potential of utilizing the poultry litter as an effective biofertilizer. On the other hand, harmful human pathogens, including Mycobacterium tuberculosis, Escherichia coli, Salmonella enterica, and Streptococcus pneumoniae were also detected indicating significant public health concern associated with the application of poultry litter as fertilizer.

Conclusions: This study offers knowledge to both leverage the usefulness of poultry litter as biofertilizer and to mitigate transmission of harmful pathogens harboured by poultry litter.