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 Jan 18;614(7946):125–135. doi: 10.1038/s41586-022-05620-1

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Extended Data Fig. 4 — A) Phylogeny of Bifidobacterium animalis (SGB17278) produced with StrainPhlAn (Methods) including strains reconstructed from human gut metagenomes, from mice samples (grey dots) and MAGs reconstructed from fermented food 32 (yellow dots). Differently from strains found in mice, 94% of human-derived strains are at ≤0.0015 single nucleotide variation (SNV) rate to MAGs obtained from fermented food (Methods), suggesting that the presence of this species in humans is associated with consumption of commercial dietary products, and were consequently excluded from further analyses (horizontal grey bars). B) Phylogeny of Streptococcus thermophilus-salivarius-vestibularis (SGB8002) produced with StrainPhlAn (Methods) including strains reconstructed from human gut metagenomes together with MAGs reconstructed from fermented food 32 (yellow dots), suggesting only a subset of strains found in the human gut is associated with fermented food intake. Only the leaves in the enlarged subtree (“Fermented food subtree”) were at ≤0.0015 single nucleotide variation (SNV) rate to MAGs obtained from fermented food (Methods) and were consequently excluded from further analyses.