Gut microbiota sequences of the long-tailed dwarf hamster (Cricetulus longicaudatus) using 16S rDNA

In the summer of 2022, natural populations of Cricetulus longicaudatus were captured using cage trapping from Wutai County (WT), Lishi District (LS), Yuci District (YC), Xi County (XX) and Zuoquan County (ZQ) in Shanxi, China. Based on 16S rDNA high-throughput sequencing combined with bioinformatics analysis was used to investigate the succession process of the gut microbiota and effects of different nutrients on the composition and function of the gut microbiota., Fastp 0.19.6 software was used for quality control and raw data filtering. Paired-end sequences based on overlapping regions were merged in Flash 1.2.11 software. Filtering the obtained merged sequences, we retained sequences with length > 200 bp, without ambiguous bases, and with an average sequence quality score≥ 20. Detected chimeric sequences were removed using Uchime 11.0 to obtain high-quality, valid data. The valid data for clustering analysis using the Uparse algorithm were divided into Operational Taxonomic Units (OTUs) based on a similarity threshold of≥ 97%. The standardized process was executed by single_rarefaction.py, followed by OTU clustering analysis after distinguishing sequences by sample. The representative sequences of OTUs were classified using RDP classifier 2.11, and the composition of each sample’s community was tallied., , The experiment was divided into two phases. First, the animals were grouped by geographical location: WT group (n=5), LS group (n=5), YC group (n=5), XX group (n=5), and ZQ group (n=5). Fresh feces were collected in the wild, denoted as day 0 sample, and fresh faeces collected on day 7, day 14, day 21, day 28, and day 35 were recorded as samples on day 7, day 14, day 21, day 28 and day 35, respectively. For example, “WT-14 d-1” represents the fecal sample sequences of individual 1 in WT group on day 14.

In the second phase, 25 individuals were re-randomized according to diet: WH group (n=5), WA group (n=5), WP group (n=5), WM group (n=5), and MIX group (n=5). Fecal samples after re-randomization were recorded as day 0 samples, and fresh faeces collected on day 7, day 14, day 21, day 28, and day 35 were recorded as samples on day 7, day 14, day 21, day 28 and day 35, respectively. For example, “WH-28 d-2” represents the fecal sample sequences of individual 2 in WH group on day 28.

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