DOI: 10.5061/dryad.mgqnk99b4
title: Data from: Gut microbiota provide co-existing strategies for two species of symmetrically distributed rodents in competition for food

description: Gut microbiota provides an effective strategy for sympatric proximal
 species to coexist in interspecific competition. In the present
 study, 16SrDNA was used to investigate the gut microbial of the Cricetulus
 longicaudatus and Apodemus agrarius, which are two species
 distributed in the same domain, under natural ambient and varying
 dietary situations. Our data revealed that there were
 significant differences in gut microbial structure and diversity between
 the two species. Specifically, the voles demonstrated high alpha
 diversity and abundance of Lactobacillus, whereas the mice shown
 substantial enrichment of Verrucomicrobiota. Wild voles had a more complex
 co-occurrence network, with a low level of positive correlation rate,
 however, after being fed various diets, the network structure was
 simplified, and the positive correlation rate increased. On the contrary,
 wild mice had a simple co-occurrence network, with a high level of
 positive correlation rate, after exposure to different diets, the network
 structure became more complex, accompanied by a decrease in the positive
 correlation rate. Our results also revealed differences in
 dietary adaption between the two
 species. Voles exhibited a greater microbial
 adaptability under high-fat and high-fiber
 diet than mice, as indicating by a significant rise in
 the Firmicutes/Bacteroidetes ratio. While mice demonstrated
 reduced adaptation to dietary changes, and it had a stronger ability to
 adapt to high-fat diet than to high-fiber diet. Finally,
 our data revealed significant alterations in carbohydrate metabolism
 pathways between two species. This study provides new insights
 into how the gut microbiota of symmetrically distributed rodents provides
 effective survival strategies for species in the face of competition.
description: In this study, we conducted two experiments.
 Design of experiment one: First,
 we investigates the food adaptation strategies of two syntopic species in
 the wild by comparing the differences in gut microbiota of two types of
 mice under natural field conditions. The experimental design is outlined
 as follows: In the summer of 2024, six samples each of healthy adult male
 <em>C. longicaudatus</em> and
 <em>A. agrarius</em> were obtained using cage catches in
 Houyin Village, Xixian County, Shanxi Province (36.729°N, 110.839°E).
 Rectal fecal samples were promptly collected in the field and preserved at
 -80°C until the 16S rDNA sequencing was conducted.
 Design of experiment two: We tested the
 adaptive alterations in gut microbiota of two species using an indoor
 experiment including the feeding of animals with food from various
 nutritional layers under differing dietary circumstances. The experimental
 design is outlined as follows: Healthy adult
 male <em>C. longicaudatus</em> and
 <em>A. agrarius</em> were collected in Huyan Village, Xixian
 County, Shanxi Province (36.729°N, 110.839°E). Following a two-week
 adaptation stage in the laboratory, the experiment will commence. All
 animals are kept in individual cages under circumstances of 23±2℃
 temperature, 55±2% relative humidity, a natural light cycle, and a
 sufficient diet. <em>C. longicaudatus</em> and
 <em>A. agrarius</em> were respectively divided at random into
 three groups according to their body mass: Con (Control, standard rodent
 diet, n=6), HG (High-fiber diet, n=6), and HF (High-fat diet, n=6). Food
 composition are shown in Table 1. The animals continuous feeding for 28
 days, with free access to water and food during the period. After 28 days,
 rectal feces from all experimental samples were collected and preserved at
 -80°C until 16S rDNA sequencing was conducted in the indoor experimental
 group. The experimental procedure was rigorously executed in compliance
 with the "Regulations on the Administration of Experimental
 Animals" (2017 Revision) established by the Ministry of Science and
 Technology of the People's Republic of China.
 <strong>Bioinformatics analysis</strong>
 Following sequencing, the two brief Illumina reads were combined
 using PEAR software (version 0.9.8) based on their overlap, and the fastq
 files were processed to produce distinct FAST and QUAL files, which could
 subsequently be evaluated using standard methodologies. The effective tags
 were grouped into operational taxonomic units (OTUs) of ≥ 97% similarity
 using Usearch software (version 11.0.667). Chimeric sequences and
 singleton OTUs (containing only one read) were eliminated, following which
 the residual sequences were categorized into each sample according to the
 OTUs. The most abundant tag sequence was chosen as the typical sequence
 for each cluster. Bacterial and fungal OTU representative sequences were
 taxonomically identified by using BLAST searches against the RDP Database
 and the UNITE fungal ITS Database, respectively.
 <strong>Data analysis</strong> The
 α-diversity indices (including Chao1, Simpson, and Shannon indices) were
 quantified in terms of OTU richness. To assess sample adequacy,
 rarefaction curves of the observed numbers of OTUs were constructed, all
 α-diversity indices were calculated with Mothur software (version 3.8.31).
 The OTU rarefaction curve and rank abundance curves were plotted in R
 (version 3.6.0). To estimate the diversity of the microbial community of
 the sample, we calculated the within-sample (alpha) diversity by T-test
 for two groups and multiple group comparisons were made using ANOVA test.
 Beta diversity evaluates differences in the microbiome among samples and
 is normally combined with dimensional reduction methods such as principal
 coordinate analysis (PCoA) to obtain visual representations. These
 analyses were visualized using Rvegan package (version 2.5-6), and finally
 the inter-sample distances were presented as scatterplots. Venn diagrams
 were drawn using R 3.2.6 (Venn Diagram package) to describe common and gap
 flora between groups. Difference comparison is used to identify features
 with significantly different abundances between groups using LefSe
 (version 1.1.0 ). The data were further examined and network analysis was
 produced using R 3.2.6 and Gephi v.0.9.2 software. Functional prediction
 analysis of bacteria and archaea using PICRUSt (v1.1.4) software, by
 comparing existing 16S rDNA gene sequencing data with a microbial
 reference genome database of known metabolic functions, enables the
 prediction of bacterial and archaeal metabolic functions. The experimental
 results were expressed as mean ± standard deviation (mean ± SD). SPSS 26.0
 software was used to calculate samples among groups by one-way ANOVA
 analysis. Statistical differences between treatments were considered
 significant at <em>P</em> &lt; 0.05,
 <em>P</em> &lt; 0.01, and <em>P</em> &lt;
 0.001.
description: # Data from: Gut microbiota provide co-existing strategies for two species
 of symmetrically distributed rodents in competition for food Dataset DOI:
 [10.5061/dryad.mgqnk99b4](https://doi.org/10.5061/dryad.mgqnk99b4) ##
 Description of the data and file structure ### Files and variables ####
 File: CWCS-Con-1.raw.fastq \**Description: *Cricetulus longicaudatus*
 control sample #### File: CWCS-Con-3.raw.fastq
 **Description:** *Cricetulus longicaudatus* control sample #### File:
 CWCS-Con-2.raw.fastq **Description:** *Cricetulus longicaudatus* control
 sample #### File: CWCS-Con-4.raw.fastq **Description:** *Cricetulus
 longicaudatus* control sample #### File: CWCS-Con-5.raw.fastq
 **Description:** *Cricetulus longicaudatus* control sample #### File:
 CWCS-Con-6.raw.fastq **Description:** *Cricetulus longicaudatus* control
 sample #### File: CWCS-HF-1.raw.fastq **Description:** *Cricetulus
 longicaudatus* sample of the HF group #### File: CWCS-HF-2.raw.fastq
 **Description:** *Cricetulus longicaudatus* sample of the HF group ####
 File: CWCS-XIX-1.raw.fastq **Description:** Wild samples of the
 *Cricetulus longicaudatus* #### File: CWCS-HF-3.raw.fastq
 **Description:** *Cricetulus longicaudatus* sample of the HF group ####
 File: CWCS-HF-4.raw.fastq **Description:** *Cricetulus longicaudatus*
 sample of the HF group #### File: HXJS-Con-1.raw.fastq
 **Description:** *Apodemus agrarius* control sample #### File:
 CWCS-XIX-2.raw.fastq **Description:** Wild samples of the *Cricetulus
 longicaudatus* #### File: CWCS-HF-5.raw.fastq **Description:** *Cricetulus
 longicaudatus* sample of the HF group #### File: CWCS-HF-6.raw.fastq
 **Description:** *Cricetulus longicaudatus* sample of the HF group ####
 File: CWCS-HG-1.raw.fastq **Description:** *Cricetulus longicaudatus*
 sample of the HG group #### File: HXJS-Con-2.raw.fastq
 **Description:** *Apodemus agrarius* control sample #### File:
 CWCS-XIX-3.raw.fastq **Description:** Wild samples of the *Cricetulus
 longicaudatus* #### File: HXJS-HF-1.raw.fastq **Description:** *Apodemus
 agrarius* sample of the HF group #### File: CWCS-HG-2.raw.fastq
 **Description:**  *Cricetulus longicaudatus* sample of the HG group ####
 File: CWCS-XIX-4.raw.fastq **Description:** Wild samples of the
 *Cricetulus longicaudatus* #### File: HXJS-XIX-1.raw.fastq
 **Description:** Wild samples of the *Apodemus agrarius* #### File:
 CWCS-HG-3.raw.fastq **Description:**  *Cricetulus longicaudatus* sample of
 the HG group #### File: CWCS-HG-4.raw.fastq **Description:**  *Cricetulus
 longicaudatus* sample of the HG group #### File: HXJS-Con-3.raw.fastq
 **Description:** *Apodemus agrarius* control sample #### File:
 CWCS-HG-5.raw.fastq **Description:**  *Cricetulus longicaudatus* sample of
 the HG group #### File: HXJS-Con-4.raw.fastq **Description:** *Apodemus
 agrarius* control sample #### File: HXJS-HF-2.raw.fastq
 **Description:** *Apodemus agrarius* sample of the HF group #### File:
 HXJS-Con-5.raw.fastq **Description:** *Apodemus agrarius* control sample
 #### File: CWCS-XIX-5.raw.fastq **Description:** Wild samples of the
 *Cricetulus longicaudatus* #### File: CWCS-HG-6.raw.fastq
 **Description:** *Cricetulus longicaudatus* sample of the HG group ####
 File: CWCS-XIX-6.raw.fastq **Description:** Wild samples of the
 *Cricetulus longicaudatus* #### File: HXJS-XIX-2.raw.fastq
 **Description:** Wild samples of the *Apodemus agrarius* #### File:
 HXJS-Con-6.raw.fastq **Description:** *Apodemus agrarius* control sample
 #### File: HXJS-HF-3.raw.fastq **Description:** *Apodemus agrarius* sample
 of the HF group #### File: HXJS-HF-4.raw.fastq **Description:** *Apodemus
 agrarius* sample of the HF group #### File: HXJS-HF-5.raw.fastq
 **Description:** *Apodemus agrarius* sample of the HF group #### File:
 HXJS-XIX-3.raw.fastq **Description:** Wild samples of the *Apodemus
 agrarius* #### File: HXJS-XIX-5.raw.fastq **Description:** Wild samples of
 the *Apodemus agrarius* #### File: HXJS-XIX-4.raw.fastq
 **Description:** Wild samples of the *Apodemus agrarius* #### File:
 HXJS-HF-6.raw.fastq **Description:** *Apodemus agrarius* sample of the HF
 group #### File: HXJS-HG-1.raw.fastq **Description:** *Apodemus agrarius*
 sample of the HG group #### File: HXJS-HG-2.raw.fastq
 **Description:** *Apodemus agrarius* sample of the HG group #### File:
 HXJS-HG-3.raw.fastq **Description:** *Apodemus agrarius* sample of the HG
 group #### File: HXJS-XIX-6.raw.fastq **Description:** Wild samples of the
 *Apodemus agrarius* #### File: HXJS-HG-4.raw.fastq
 **Description:** *Apodemus agrarius* sample of the HG group #### File:
 HXJS-HG-5.raw.fastq **Description:** *Apodemus agrarius* sample of the HG
 group #### File: HXJS-HG-6.raw.fastq **Description:** *Apodemus agrarius*
 sample of the HG group ## Code/software n/a