16S rRNA Gene Amplicon Profiling of Baby and Adult Captive Elephants in Thailand.

Sangam Kandel,Thidathip Wongsurawat,Piroon Jenjaroenpun,Supaphen Sripiboon,David W Ussery,Michael S Robeson,Intawat Nookaew,Julia A Maresca

doi:10.1128/mra.00248-20

Abstract

Here, we present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of baby and adult elephants from four different geographical locations in Thailand. The dominant phyla among baby and adult elephants were Bacteroidetes, Firmicutes, Proteobacteria, Kiritimatiellaeota, Euryarchaeota, and Tenericutes.

Highlights

We present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of baby and adult elephants from four different geographical locations in Thailand
Raw sequencing reads were first imported in QIIME 2 using the q2-import plugin and were demultiplexed using the q2-demux plugin
Microbial taxonomy was assigned to the amplicon sequence variants (ASVs) using a naive Bayes classifier trained on the Silva

Summary

Introduction

The 16S rRNA gene was amplified and subsequently sequenced using a MiSeq sequencing platform (Illumina, Inc., USA) by generating paired-end reads from libraries with 250-bp inserts following the Illumina Earth Microbiome Protocol [4]. The 16S rRNA V4 region was amplified using the barcoded primer set 515FB (5=-GTGYCAGCMGCCG CGGTAA-3=) and 806RB (5=GGACTACNVGGGTWTCTAAT-3=) [5]. Microbiome analysis was done using QIIME 2 version 2018.11 [6].

Results

Conclusion