Different storage conditions affect microbial profiles in samples of chicken caecal chyme and lung

This study has evaluated the effect of storage temperature on microbial composition to provide a suitable preparation method for clinical samples. In this study, fresh chicken pulmonary and caecal samples were harvested and set as the control, after which they were stored at different temperatures: −20℃, −80℃, or −196℃ for 7 days. The total ribosomal deoxyribonucleic acid content of the samples was extracted and sequenced to compare differences in microbial composition. At the phylum level, the abundances of Campilobacteria stored at −80°C and −196℃ were lower than in the control and at −20℃. The richness of Proteobacteria in the samples at −20℃ and −80℃ was increased than those in the control. At the genus level, Bacteroides , Rikenellaceas _ RC9 , Clostrida _ vadinBB60 , norank_f_norank _o_ rhodospirllales , and norank_ f_ Barnesiellaceae accounted for the largest proportion. The abundances of Bacteroides , Helicobacter and Clostridia _ vadinBB60 were reduced at −20℃ and −80℃ compared with the control. For the caecal samples, the number of OTUs in control was higher than those stored at −196℃, whereas no difference was observed between the fresh samples and those stored at −20℃ and −80℃. At the phylum level, the abundance of Proteobacteria and unclassified_k_norank_d_ bacteria increased in the treated samples compared to the control, whereas the diversity of Firmicute and Bacteroidota was reduced compared with that in the control. Especially, the Cyanobacteria , Campilobacterota , and Synergistota phyla at −80℃ and −196℃ were further reduced than those of the control and at −20℃. At the genus level, Bacteroides , Lactobacillus , Megasphaera , norank_f_ ruminococcaceae , Helicobacter , and norank_f_ norank_o_ Gastranaerophilales were more abundant in the control samples than in the treated samples. However, the richness of unclassified_k_norank_d_ bacteria , Sphingomonas and norank_f_ norank_o_ SJA－15 were higher in all of the treated samples than in the control. The pulmonary and caecal samples stored at −80℃ and −196℃ had reduced the bacterial diversities compared with those in the control and at −20℃ as suggested by the linear discriminant analysis. In conclusion, samples of the lung and caecal chyme stored at −20℃ for 7 days can promote the colonisation of microbiota, leading to inaccurate sequencing data. Samples stored at −80℃ and −196℃can decrease the abundance of the microbial composition. • Samples of lung and cecal chyme stored in −20 °C can improve the microbial composition. • Different microbial composition and diversity with fresh samples led to inaccurate in interpreting data. • In −80 °C and −196 °C storage can decline the microbial diversity compared with fresh samples.