Data from: Gut microflora may facilitate adaptation to anthropic habitat: a comparative study in Rattus

• Main Authors: Varudkar, Amruta, Ramakrishnan, Uma
• Format: Dataset
• Language: unknown
• Published: 2019
• Subjects: physiological plasticity; intestinal microflora; Rattus rattus; 16S metagenomics; anthropo-dependent; Rattus satarae
• Online Access: https://zenodo.org/record/5001296; https://doi.org/10.5061/dryad.5gj7056

Anthropophilic species ('commensal' species) that are completely dependent upon anthropic habitats experience different selective pressures particularly in terms of food than their non-commensal counterparts. Using a next-generation-sequencing approach, we characterized and compared the gut microflora community of 53 commensal Rattus rattus and 59 non-commensal Rattus satarae captured in 10 locations in the Western Ghats, India. We observed that while species identity was important in characterizing the microflora communities of the two Rattus hosts, environmental factors also had a significant effect. While there was significant geographic variation in the microflora of the non-commensal R. satarae, there was no effect of geographic distance on gut microflora of the commensal R. rattus. Interestingly, host genetic distance did not significantly influence the community in either Rattus hosts. Collectively, these results indicate that a shift in habitat is likely to result in a change in the gut microflora community and imply that the gut microflora is a complex trait, influenced by various parameters in different habitats. Final OTU tableTable of Operational Taxonomic Units (OTUs) created using the uclust algorithm at a 97% similarity threshold and filtering unclassifiable and unalignable reads as well as singletons.otu_table_biomv1.biomMapping fileMapping file with sample descriptions and metadata.mapping_assembly_corrected.txtFasta file containing aligned representative sequencesFor each OTU, longest read was chosen as the representative sequence. All representative sequences were aligned using the PyNAST algorithm and filtered the alignment using a lane mask file.filtered_nochim_rep_set.fastaPhylogenetic treePhylogenetic tree was constructed for the representative sequences using FastTree.tree_filtered.tre