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Ladeira et al. Microbiome Res Rep 2023;2:9 Microbiome Research
DOI: 10.20517/mrr.2023.01
Reports

Original Article Open Access

Exploring Bifidobacterium species community and
functional variations with human gut microbiome

structure and health beyond infancy

Ruben Ladeira 1 , Julien Tap 1,2,* , Muriel Derrien 1,*
1
Advanced Health & Science, Danone Global Research & Innovation Center, Gif-sur-Yvette 91190, France.
2
Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas 78350, France.
* Correspondence to: Dr. Julien Tap, Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Domaine de Vilvert, Jouy-
en-Josas 78350, France. E-mail: julien.tap@inrae.fr; Dr. Muriel Derrien, Advanced Health & Science, Danone Global Research &
Innovation Center, RD128 Zac du Moulon, Gif-sur-Yvette 91190, France. E-mail: muriel.derrien@danone.com
How to cite this article: Ladeira R, Tap J, Derrien M. Exploring Bifidobacterium species community and functional variations with
human gut microbiome structure and health beyond infancy. Microbiome Res Rep 2023;2:9.
https://dx.doi.org/10.20517/mrr.2023.01

Received: 2 Jan 2023 First Decision: 20 Feb 2023 Revised: 15 Mar 2023 Accepted: 20 Mar 2023 Published: 31 Mar 2023

Academic Editor: Christian Milani Copy Editor: Ke-Cui Yang Production Editor: Ke-Cui Yang

Abstract
Aim: The human gut Bifidobacterium community has been studied in detail in infants and following dietary
interventions in adults. However, the variability of the distribution of Bifidobacterium species and intra-species
functions have been little studied, particularly beyond infancy. Here, we explore the ecology of Bifidobacterium
communities in a large public dataset of human gut metagenomes, mostly corresponding to adults.

Methods: We selected 9.515 unique gut metagenomes from curatedMetagenomicData. Samples were partitioned
by applying Dirichlet’s multinomial mixture to Bifidobacterium species. A functional analysis was performed on >
2.000 human-associated Bifidobacterium metagenome-assembled genomes (MAGs) paired with participant gut
microbiome and health features.

Results: We identified several Bifidobacterium-based partitions in the human gut microbiome differing in terms of
the presence and abundance of Bifidobacterium species. The partitions enriched in both B. longum and B. adolescentis
were associated with gut microbiome diversity and a higher abundance of butyrate producers and were more
prevalent in healthy individuals. B. bifidum MAGs harboring a set of genes potentially related to phages were more
prevalent in partitions associated with a lower gut microbiome diversity and were genetically more closely related.

© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0
International License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, sharing,
adaptation, distribution and reproduction in any medium or format, for any purpose, even commercially, 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.

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