| RRC ID |
75571
|
| Author |
Jin J, Yamamoto R, Takeuchi T, Cui G, Miyauchi E, Hojo N, Ikuta K, Ohno H, Shiroguchi K.
|
| Title |
High-throughput identification and quantification of single bacterial cells in the microbiota.
|
| Journal |
Nat Commun
|
| Abstract |
The bacterial microbiota works as a community that consists of many individual organisms, i.e., cells. To fully understand the function of bacterial microbiota, individual cells must be identified; however, it is difficult with current techniques. Here, we develop a method, Barcoding Bacteria for Identification and Quantification (BarBIQ), which classifies single bacterial cells into taxa-named herein cell-based operational taxonomy units (cOTUs)-based on cellularly barcoded 16S rRNA sequences with single-base accuracy, and quantifies the cell number for each cOTU in the microbiota in a high-throughput manner. We apply BarBIQ to murine cecal microbiotas and quantify in total 3.4 × 105 bacterial cells containing 810 cOTUs. Interestingly, we find location-dependent global differences in the cecal microbiota depending on the dietary vitamin A deficiency, and more differentially abundant cOTUs at the proximal location than the distal location. Importantly, these location differences are not clearly shown by conventional 16S rRNA gene-amplicon sequencing methods, which quantify the 16S rRNA genes, not the cells. Thus, BarBIQ enables microbiota characterization with the identification and quantification of individual constituent bacteria, which is a cornerstone for microbiota studies.
|
| Volume |
13(1)
|
| Pages |
863
|
| Published |
2022-2-22
|
| DOI |
10.1038/s41467-022-28426-1
|
| PII |
10.1038/s41467-022-28426-1
|
| PMID |
35194029
|
| PMC |
PMC8863893
|
| MeSH |
Animals
Bacteria / genetics
DNA, Bacterial / genetics
High-Throughput Nucleotide Sequencing* / methods
Mice
Microbiota* / genetics
RNA, Ribosomal, 16S / genetics
Sequence Analysis, DNA
|
| Resource |
| General Microbes |
JCM 1297
JCM 5824
JCM 5827
JCM 9498
JCM 10188
JCM 14656
JCM 17463 |
