High-throughput identification and quantification of single bacterial cells in the microbiota

• Published in: Nature communications Vol. 13; no. 1; p. 863
• Main Authors: Jin, Jianshi, Yamamoto, Reiko, Takeuchi, Tadashi, Cui, Guangwei, Miyauchi, Eiji, Hojo, Nozomi, Ikuta, Koichi, Ohno, Hiroshi, Shiroguchi, Katsuyuki
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22.02.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 13/62; 45/23; 45/47; 45/77; 631/1647/2234; 631/326/2565/2134; 631/326/41/2537; 631/61/212/2142; 631/61/514/2254; 64/60; Animals; Bacteria; Bacteria - genetics; Cecum; Cell number; Diet; DNA barcoding; DNA, Bacterial - genetics; Gene sequencing; High-Throughput Nucleotide Sequencing - methods; Humanities and Social Sciences; Mice; Microbiomes; Microbiota; Microbiota - genetics; multidisciplinary; Nutrient deficiency; RNA, Ribosomal, 16S - genetics; rRNA 16S; Science; Science (multidisciplinary); Sequence Analysis, DNA; Taxonomy; Vitamin A
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-28426-1

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 × 10 5 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. Here, Jin et al ., develop a method called Barcoding Bacteria for Identification and Quantification (BarBIQ), which allows to both characterize the global microbiome and to identify and quantify single-cell bacterial members in a high-throughput manner.