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Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways

Journal article
Authors M. J. Pichler
C. Yamada
B. Shuoker
C. Alvarez-Silva
A. Gotoh
M. L. Leth
E. Schoof
T. Katoh
M. Sakanaka
T. Katayama
Chunsheng Jin
Niclas G. Karlsson
M. Arumugam
S. Fushinobu
M. Abou Hachem
Published in Nature Communications
Volume 11
Issue 1
ISSN 2041-1723
Publication year 2020
Published at Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology
Language en
Keywords human gut microbiome, blood-group-a, bacterial diversity, protein-sequence, breast-milk, gen. nov., bifidobacterium, health, purification, dynamics, Science & Technology - Other Topics
Subject categories Clinical Medicine


The early life human gut microbiota exerts life-long health effects on the host, but the mechanisms underpinning its assembly remain elusive. Particularly, the early colonization of Clostridiales from the Roseburia-Eubacterium group, associated with protection from colorectal cancer, immune- and metabolic disorders is enigmatic. Here, we describe catabolic pathways that support the growth of Roseburia and Eubacterium members on distinct human milk oligosaccharides (HMOs). The HMO pathways, which include enzymes with a previously unknown structural fold and specificity, were upregulated together with additional glycan-utilization loci during growth on selected HMOs and in co-cultures with Akkermansia muciniphila on mucin, suggesting an additional role in enabling cross-feeding and access to mucin O-glycans. Analyses of 4599 Roseburia genomes underscored the preponderance and diversity of the HMO utilization loci within the genus. The catabolism of HMOs by butyrate-producing Clostridiales may contribute to the competitiveness of this group during the weaning-triggered maturation of the microbiota. The assembly and maturation of the early life microbiome has life-long effects on human health. Here, the authors combine omics, functional assays and structural analyses to characterize the catabolic pathways that support the growth of butyrate producing Clostridiales members from the Roseburia and Eubacterium, on distinct human milk oligosaccharides.

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