DOI: 10.5061/dryad.tx95x6b51
title: Gut microbiota sequences of the long-tailed dwarf hamster (Cricetulus longicaudatus) using 16S rDNA

description: 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.
description: 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 &gt; 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.
description: 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. **[Sample
 title：](https://doi.org/10.5061/dryad.tx95x6b51)**[Group - Sampling time -
 *Cricetulus longicaudatus*
 number](https://doi.org/10.5061/dryad.tx95x6b51) **[First
 phase：](https://doi.org/10.5061/dryad.tx95x6b51)** [WT-0 d-1，  WT-7 d-1
 ，WT-14 d-1 ，WT-21 d-1 ，WT-28 d-1， WT-35
 d-1](https://doi.org/10.5061/dryad.tx95x6b51) [WT-0 d-2 ，WT-7 d-2 ，WT-14
 d-2 ，WT-21 d-2 ，WT-28 d-2 ，WT-35
 d-2](https://doi.org/10.5061/dryad.tx95x6b51) [WT-0 d-3，WT-7 d-3 ，WT-14
 d-3 ，WT-21 d-3 ，WT-28 d-3 ，WT-35
 d-3](https://doi.org/10.5061/dryad.tx95x6b51) [WT-0 d-4 ，WT-7 d-4 ，WT-14
 d-4 ，WT-21 d-4 ，WT-28 d-4 ，WT-35
 d-4](https://doi.org/10.5061/dryad.tx95x6b51) [WT-0 d-5 ，WT-7 d-5 ，WT-14
 d-5 ，WT-21 d-5 ，WT-28 d-5 ，WT-35
 d-5](https://doi.org/10.5061/dryad.tx95x6b51) [LS-0 d-1 ，LS-7 d-1 ，LS-14
 d-1 ，LS-21 d-1 ，LS-28 d-1 ，LS-35
 d-1](https://doi.org/10.5061/dryad.tx95x6b51) [LS-0 d-2 ，LS-7 d-2 ，LS-14
 d-2 ，LS-21 d-2 ，LS-28 d-2 ，LS-35
 d-2](https://doi.org/10.5061/dryad.tx95x6b51) [LS-0 d-3 ，LS-7 d-3 ，LS-14
 d-3 ，LS-21 d-3 ，LS-28 d-3 ，LS-35
 d-3](https://doi.org/10.5061/dryad.tx95x6b51) [LS-0 d-4 ，LS-7 d-4 ，LS-14
 d-4 ，LS-21 d-4 ，LS-28 d-4 ，LS-35
 d-4](https://doi.org/10.5061/dryad.tx95x6b51) [LS-0 d-5 ，LS-7 d-5 ，LS-14
 d-5 ，LS-21 d-5 ，LS-28 d-5 ，LS-35
 d-5](https://doi.org/10.5061/dryad.tx95x6b51) [YC-0 d-1 ，YC-7 d-1 ，YC-14
 d-1 ，YC-21 d-1 ，YC-28 d-1 ，YC-35
 d-1](https://doi.org/10.5061/dryad.tx95x6b51) [YC-0 d-2 ，YC-7 d-2 ，YC-14
 d-2 ，YC-21 d-2 ，YC-28 d-2 ，YC-35
 d-2](https://doi.org/10.5061/dryad.tx95x6b51) [YC-0 d-3 ，YC-7 d-3 ，YC-14
 d-3 ，YC-21 d-3 ，YC-28 d-3 ，YC-35
 d-3](https://doi.org/10.5061/dryad.tx95x6b51) [YC-0 d-4 ，YC-7 d-4 ，YC-14
 d-4 ，YC-21 d-4 ，YC-28 d-4 ，YC-35
 d-4](https://doi.org/10.5061/dryad.tx95x6b51) [YC-0 d-5 ，YC-7 d-5 ，YC-14
 d-5 ，YC-21 d-5 ，YC-28 d-5 ，YC-35
 d-5](https://doi.org/10.5061/dryad.tx95x6b51) [XX-0 d-1 ，XX-7 d-1 ，XX-14
 d-1 ，XX-21 d-1 ，XX-28 d-1 ，XX-35
 d-1](https://doi.org/10.5061/dryad.tx95x6b51) [XX-0 d-2 ，XX-7 d-2 XX-14
 d-2 XX-21 d-2 XX-28 d-2 XX-35
 d-2](https://doi.org/10.5061/dryad.tx95x6b51) [XX-0 d-3 ，XX-7 d-3 ，XX-14
 d-3 ，XX-21 d-3 ，XX-28 d-3 ，XX-35
 d-3](https://doi.org/10.5061/dryad.tx95x6b51) [XX-0 d-4 ，XX-7 d-4 ，XX-14
 d-4 ，XX-21 d-4 ，XX-28 d-4 ，XX-35
 d-4](https://doi.org/10.5061/dryad.tx95x6b51) [XX-0 d-5 ，XX-7 d-5 ，XX-14
 d-5 ，XX-21 d-5 ，XX-28 d-5 ，XX-35
 d-5](https://doi.org/10.5061/dryad.tx95x6b51) [ZQ-0 d-1 ，ZQ-7 d-1 ，ZQ-14
 d-1 ，ZQ-21 d-1 ，ZQ-28 d-1 ，ZQ-35
 d-1](https://doi.org/10.5061/dryad.tx95x6b51) [ZQ-0 d-2 ，ZQ-7 d-2 ，ZQ-14
 d-2 ，ZQ-21 d-2 ，ZQ-28 d-2 ，ZQ-35
 d-2](https://doi.org/10.5061/dryad.tx95x6b51) [ZQ-0 d-3 ，ZQ-7 d-3 ，ZQ-14
 d-3 ，ZQ-21 d-3 ，ZQ-28 d-3 ，ZQ-35
 d-3](https://doi.org/10.5061/dryad.tx95x6b51) [ZQ-0 d-4 ，ZQ-7 d-4 ，ZQ-14
 d-4 ，ZQ-21 d-4 ，ZQ-28 d-4 ，ZQ-35
 d-4](https://doi.org/10.5061/dryad.tx95x6b51) [ZQ-0 d-5 ，ZQ-7 d-5 ，ZQ-14
 d-5 ，ZQ-21 d-5 ，ZQ-28 d-5 ，ZQ-35
 d-5](https://doi.org/10.5061/dryad.tx95x6b51) **[Second
 phase：](https://doi.org/10.5061/dryad.tx95x6b51)** [WH-7 d-1 ，WH-14 d-1
 ，WH-21 d-1 ，WH-28 d-1 ，WH-35 d-1](https://doi.org/10.5061/dryad.tx95x6b51)
 [WH-7 d-2 ，WH-14 d-2 ，WH-21 d-2 ，WH-28 d-2 ，WH-35
 d-2](https://doi.org/10.5061/dryad.tx95x6b51) [WH-7 d-3 ，WH-14 d-3 ，WH-21
 d-3 ，WH-28 d-3 ，WH-35 d-3](https://doi.org/10.5061/dryad.tx95x6b51) [WH-7
 d-4 ，WH-14 d-4 ，WH-21 d-4 ，WH-28 d-4 ，WH-35
 d-4](https://doi.org/10.5061/dryad.tx95x6b51) [WH-7 d-5 ，WH-14 d-5 ，WH-21
 d-5 ，WH-28 d-5 ，WH-35 d-5](https://doi.org/10.5061/dryad.tx95x6b51) [WA-7
 d-1 ，WA-14 d-1 ，WA-21 d-1 ，WA-28 d-1 ，WA-35
 d-1](https://doi.org/10.5061/dryad.tx95x6b51) [WA-7 d-2 ，WA-14 d-2 ，WA-21
 d-2 ，WA-28 d-2 ，WA-35 d-2](https://doi.org/10.5061/dryad.tx95x6b51) [WA-7
 d-3 ，WA-14 d-3 ，WA-21 d-3 ，WA-28 d-3 ，WA-35
 d-3](https://doi.org/10.5061/dryad.tx95x6b51) [WA-7 d-4 ，WA-14 d-4 ，WA-21
 d-4 ，WA-28 d-4 ，WA-35 d-4](https://doi.org/10.5061/dryad.tx95x6b51) [WA-7
 d-5 ，WA-14 d-5 ，WA-21 d-5 ，WA-28 d-5 ，WA-35
 d-5](https://doi.org/10.5061/dryad.tx95x6b51) [WP-7 d-1 ，WP-14 d-1 ，WP-21
 d-1 ，WP-28 d-1 ，WP-35 d-1](https://doi.org/10.5061/dryad.tx95x6b51) [WP-7
 d-2 ，WP-14 d-2 ，WP-21 d-2 ，WP-28 d-2 ，WP-35
 d-2](https://doi.org/10.5061/dryad.tx95x6b51) [WP-7 d-3 ，WP-14 d-3 ，WP-21
 d-3 ，WP-28 d-3 ，WP-35 d-3](https://doi.org/10.5061/dryad.tx95x6b51) [WP-7
 d-4 ，WP-14 d-4 ，WP-21 d-4 ，WP-28 d-4 ，WP-35
 d-4](https://doi.org/10.5061/dryad.tx95x6b51) [WP-7 d-5 ，WP-14 d-5 ，WP-21
 d-5 ，WP-28 d-5 ，WP-35 d-5](https://doi.org/10.5061/dryad.tx95x6b51) [WM-7
 d-1 ，WM-14 d-1 ，WM-21 d-1 ，WM-28 d-1 ，WM-35
 d-1](https://doi.org/10.5061/dryad.tx95x6b51) [WM-7 d-2 ，WM-14 d-2 ，WM-21
 d-2 ，WM-28 d-2 ，WM-35 d-2](https://doi.org/10.5061/dryad.tx95x6b51) [WM-7
 d-3 ，WM-14 d-3 ，WM-21 d-3 ，WM-28 d-3 ，WM-35
 d-3](https://doi.org/10.5061/dryad.tx95x6b51) [WM-7 d-4 ，WM-14 d-4 ，WM-21
 d-4 ，WM-28 d-4 ，WM-35 d-4](https://doi.org/10.5061/dryad.tx95x6b51) [WM-7
 d-5 ，WM-14 d-5 ，WM-21 d-5 ，WM-28 d-5 ，WM-35
 d-5](https://doi.org/10.5061/dryad.tx95x6b51) [MIX-7 d-1 ，MIX-14 d-1
 ，MIX-21 d-1 ，MIX-28 d-1 ，MIX-35
 d-1](https://doi.org/10.5061/dryad.tx95x6b51) [MIX-7 d-2 ，MIX-14 d-2
 ，MIX-21 d-2 ，MIX-28 d-2 ，MIX-35
 d-2](https://doi.org/10.5061/dryad.tx95x6b51) [MIX-7 d-3 ，MIX-14 d-3
 ，MIX-21 d-3 ，MIX-28 d-3 ，MIX-35
 d-3](https://doi.org/10.5061/dryad.tx95x6b51) [MIX-7 d-4 ，MIX-14 d-4
 ，MIX-21 d-4 ，MIX-28 d-4 ，MIX-35
 d-4](https://doi.org/10.5061/dryad.tx95x6b51) [MIX-7 d-5 ，MIX-14 d-5
 ，MIX-21 d-5 ，MIX-28 d-5 ，MIX-35
 d-5](https://doi.org/10.5061/dryad.tx95x6b51)