SRA

The persistence of Campylobacter jejuni in the natural environment, despite its microaerophilic nature, continues to be a subject of active investigation. Its survival and persistence likely stem from a combination of factors, including interactions with amoebae. C. jejuni transiently interacts with Acanthamoebae and this is thought to provide protection against unfavourable conditions and prime the bacteria for interactions with warm-blooded hosts. Acanthamoebae play vital roles in ecosystems by preying on microorganisms and establishing ecological niches with various bacterial species, some of which are clinically important pathogens. To gain a better understanding on the role of Acanthamoebae in the persistence of C. jejuni in the natural environment, we examined their interactions at the molecular level. Overall design: RNA was extracted using Qiagen RNA extraction kit after treatment with RNA protect. Samples were subjected to quality control and quantification using Agilent Bioanayzer before being sent for processing and sequencing by Azenta (Genewiz). The paired-end reads were trimmed and filtered using Conda; Kallisto was used to map the reads against the reference sequence, Genome assembly Acastellanii.strNEFF v1 GCA_000313135.1. Kallisto was also used to convert annotations from GFF to GTF format. Library was sequenced by Genewiz (Azenta)- Performer using NovaSeq 6000 system.The paired-end reads were trimmed and filtered using Conda; Kallisto was used to map the reads against the reference sequence, Genome assembly Acastellanii.strNEFF v1 GCA_000313135.1. Kallisto was also used to convert annotations from GFF to GTF format. Statistical analysis was performed in R using the combined data generated from the bioinformatics as well as metadata associated with the study (multifactorial design). Adjusted p-value significance cut-off of <0.05, and log fold change cut-off of >2, was used for multiple comparison.