Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2023 Nov 20;42(9):1394–1403. doi: 10.1038/s41587-023-01988-1

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Fig. 2 — a, Bacterial reference of the mouse gut microbiome. Phylogenetic tree of SPF colonic content, representing the 65 species colored to highlight taxonomic families and genera. b, Enhanced annotation performance of the deep learning model. Average Pearson correlation coefficient (y axis) between true and predicted taxonomic labels from spatial spots (Methods) on five taxonomic levels (x axis) when using Kraken2 (orange) or Kraken2 together with the deep learning model (blue) (y axis) (n = 3). Error bars: 95% confidence intervals. c, Highly specific mapping of bacterial reads. Overall bacterial alignment rates to reference genomes (y axis, %) for GF (left, n = 3), ASF (middle, n = 3) and SPF (right, n = 3) tissue sections using spatial 16S sequencing. d, High reproducibility of bacterial abundances in SPF mouse colons by SHM-seq. Percentage (y axis) of the top 10 most abundant bacteria genera in each of three independent samples of SPF mouse colons (x axis). e, SHM-seq compares well to 16S rRNA sequencing. Pseudo-bulk abundances of bacterial genera (dot) from SHM-seq (x axis, SPF mice, n = 3) and bulk 16S rRNA sequencing⁶² (y axis, SPF mice, n = 3). Top left: Pearson r. f, Enzymatic (SHM-seq) extraction of bacterial content agrees with established mechanic extraction. Pseudo-bulk abundances of each bacterial genera (dot) from SHM-seq (x axis, SPF mice, n = 3) and mechanical extraction (y axis, SPF mice, n = 3). g–i, SHM-seq agreement with FISH probes targeting ASF502. g, Distribution (box plot, normalized signals per region) and individual measurements (scatter plot, mean signal per region and sample, n = 6) of ASF502 counts by FISH (y axis) and SHM-seq (x axis). Shaded areas: 95% confidence interval. c,g, Box plots: center black line, median; color-coded box, interquartile range; error bars, 1.5× interquartile range; black dots; outliers. h, Cross-section of an ASF mouse colon (scale bar, 180 μm) with four regions (red rectangles) and their zoom-ins (i) (scale bar, 25 μm). Colors: tissue (blue), fibers (gray) and ASF502 (red). e,f, Line: linear regression model fit. Shaded areas: 95% confidence interval. norm, normalized; DL, deep learning.