RT Journal
A1 Lyu, Lin
A1 Li, Xue
A1 Feng, Ru
A1 Zhou, Xin
A1 Guha, Tuhin K.
A1 Yu, Xiaofei
A1 Chen, Guo Qiang
A1 Yao, Yufeng
A1 Su, Bing
A1 Zou, Duowu
A1 Snyder, Michael P.
A1 Chen, Lei
T1 Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing
JF Genome Research 
JO Genome Research 
YR 2023 
FD March 01 
VO 33 
IS 3 
SP 401 
OP 411 
DO 10.1101/gr.277178.122 
UL http://genome.cshlp.org/content/33/3/401.abstract 
AB We developed an analysis pipeline that can extract microbial sequences from spatial transcriptomic (ST) data and assign taxonomic labels, generating a spatial microbial abundance matrix in addition to the default host expression matrix, enabling simultaneous analysis of host expression and microbial distribution. We called the pipeline spatial metatranscriptome (SMT) and applied it on both human and murine intestinal sections and validated the spatial microbial abundance information with alternative assays. Biological insights were gained from these novel data that showed host–microbe interaction at various spatial scales. Finally, we tested experimental modification that can increase microbial capture while preserving host spatial expression quality and, by use of positive controls, quantitatively showed the capture efficiency and recall of our methods. This proof-of-concept work shows the feasibility of SMT analysis and paves the way for further experimental optimization and application.