Large-scale 16S gene assembly using metagenomics shotgun sequences.
BACKGROUND
Combining a 16S rRNA (16S) gene database with metagenomic shotgun sequences promises unbiased identification of known and novel microbes.


RESULTS
To achieve this, we herein report reference-based ribosome assembly (RAMBL), a computational pipeline, which integrates taxonomic tree search and Dirichlet process clustering to reconstruct full-length 16S gene sequences from metagenomic sequencing data with high accuracy. By benchmarking against the synthetic and real shotgun sequences, we demonstrated that full-length 16S gene assemblies of RAMBL were a good proxy for known and putative microbes, including Candidate Phyla Radiation. We found that 30-40% of bacteria genera in the terrestrial and intestinal biomes have no closely related genome sequences. We also observed that RAMBL was able to generate a more accurate determination of environmental microbial diversity and yield better disease classification, suggesting that full-length 16S gene assemblies are a powerful alternative to marker gene set and 16S short reads. RAMBL first realizes the access to full-length 16S gene sequences in the near-terabase-scale metagenomic shotgun sequences, which markedly improve metagenomic data analysis and interpretation.


METHODS
RAMBL is available at https://github.com/homopolymer/RAMBL for academic use.


BACKGROUND
zengfeng@xmu.edu.cn.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Automation, Xiamen University, Xiamen, Fujian, China.
Feng
F
Zeng
Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, China.
Zicheng
Z
Wang
Department of Automation, Xiamen University, Xiamen, Fujian, China.
Ying
Y
Wang
Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.|State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.|Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Jizhong
J
Zhou
Bioinformatics Division, TNLIST, and Department of Computer Science and Technology, Tsinghua University, Beijing, China.|Program in Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA, USA.
Ting
T
Chen
D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D016000:Cluster Analysis; D005798:Genes, Bacterial; D056186:Metagenomics / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D012336:RNA, Ribosomal, 16S