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Longitudinal culture-enriched metagenomics reveals persistence and sharing of culturable infant gut and breast milk microbiota

Wang, Shaopu ; Grimaud, Ghjuvan LU orcid ; S. Morais, Emilene ; Warda, Alicja ; Boyaval, Patrick ; Ryan, C. Anthony ; Forssten, Sofia D. ; Kailanto, Henna-Maria ; Dempsey, Eugene M. and Stanton, Catherine , et al. (2026) In npj Biofilms and Microbiomes
Abstract
The importance of gut microbiota in early life and the contribution of
breast milk to human health and disease prevention has attracted
extensive attention as studied by culture-independent metagenomic
technologies. However, the fraction and assembled dynamics of culturable
early gut and breast milk microbiota remain unexplored. In this study,
longitudinal culture-enriched metagenomic sequencing was applied to
examine the proportion, assembly, persistence and sharing of culturable
microbiota from the infant gut and breast milk in the first six months
of life. Compared to culture-independent sequencing of infant fecal
samples, an average of 54% at species level, 69% at subspecies level,
and... (More)
The importance of gut microbiota in early life and the contribution of
breast milk to human health and disease prevention has attracted
extensive attention as studied by culture-independent metagenomic
technologies. However, the fraction and assembled dynamics of culturable
early gut and breast milk microbiota remain unexplored. In this study,
longitudinal culture-enriched metagenomic sequencing was applied to
examine the proportion, assembly, persistence and sharing of culturable
microbiota from the infant gut and breast milk in the first six months
of life. Compared to culture-independent sequencing of infant fecal
samples, an average of 54% at species level, 69% at subspecies level,
and 82% at strain-level resolution of gut microbiota were cultured with
14 different culture media or a representative subset of media,
representing 93% of the relative abundance at species level. No
difference was observed in the capacity of media used to recover gut
microorganisms from infants born vaginally or by cesarean section
(C-section). Depletion of culturable Bacteroides and Bifidobacterium and an enrichment of culturable Citrobacter, Klebsiella, and Veillonella
were observed in infants born via C-section. The metagenomic assembled
genomes from infant fecal samples and breast milk were significantly
improved with culture enrichment, particularly for breast milk. By
integrating newly assembled and existing genomes from gut microbiota, 31
and 26 culturable strains were persistent (presence in at least two
time points) in infants born vaginally or by C-section, respectively,
with the former distributed more diversely at phylum level. Twenty
culturable strains were shared between breast milk and infant gut
samples. Collectively, these results provide the first evidence for the
culturable microbiota from infant gut and breast milk regarding their
assembly, persistence and sharing status, with potential implications
for probiotic development and infant health. (Less)
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organization
publishing date
type
Contribution to journal
publication status
epub
subject
in
npj Biofilms and Microbiomes
pages
16 pages
publisher
Nature Publishing Group
ISSN
2055-5008
DOI
10.1038/s41522-026-01111-7
language
English
LU publication?
yes
id
886c9e81-35a4-44f6-aaf7-be95a7a9f0e3
date added to LUP
2026-08-26 10:57:33
date last changed
2026-09-08 03:36:06
@article{886c9e81-35a4-44f6-aaf7-be95a7a9f0e3,
  abstract     = {{The importance of gut microbiota in early life and the contribution of <br>
breast milk to human health and disease prevention has attracted <br>
extensive attention as studied by culture-independent metagenomic <br>
technologies. However, the fraction and assembled dynamics of culturable<br>
 early gut and breast milk microbiota remain unexplored. In this study, <br>
longitudinal culture-enriched metagenomic sequencing was applied to <br>
examine the proportion, assembly, persistence and sharing of culturable <br>
microbiota from the infant gut and breast milk in the first six months <br>
of life. Compared to culture-independent sequencing of infant fecal <br>
samples, an average of 54% at species level, 69% at subspecies level, <br>
and 82% at strain-level resolution of gut microbiota were cultured with <br>
14 different culture media or a representative subset of media, <br>
representing 93% of the relative abundance at species level. No <br>
difference was observed in the capacity of media used to recover gut <br>
microorganisms from infants born vaginally or by cesarean section <br>
(C-section). Depletion of culturable <i>Bacteroides</i> and <i>Bifidobacterium</i> and an enrichment of culturable <i>Citrobacter</i>, <i>Klebsiella</i>, and <i>Veillonella</i><br>
 were observed in infants born via C-section. The metagenomic assembled <br>
genomes from infant fecal samples and breast milk were significantly <br>
improved with culture enrichment, particularly for breast milk. By <br>
integrating newly assembled and existing genomes from gut microbiota, 31<br>
 and 26 culturable strains were persistent (presence in at least two <br>
time points) in infants born vaginally or by C-section, respectively, <br>
with the former distributed more diversely at phylum level. Twenty <br>
culturable strains were shared between breast milk and infant gut <br>
samples. Collectively, these results provide the first evidence for the <br>
culturable microbiota from infant gut and breast milk regarding their <br>
assembly, persistence and sharing status, with potential implications <br>
for probiotic development and infant health.}},
  author       = {{Wang, Shaopu and Grimaud, Ghjuvan and S. Morais, Emilene and Warda, Alicja and Boyaval, Patrick and Ryan, C. Anthony and Forssten, Sofia D. and Kailanto, Henna-Maria and Dempsey, Eugene M. and Stanton, Catherine and Ross, R. Paul}},
  issn         = {{2055-5008}},
  language     = {{eng}},
  publisher    = {{Nature Publishing Group}},
  series       = {{npj Biofilms and Microbiomes}},
  title        = {{Longitudinal culture-enriched metagenomics reveals persistence and sharing of culturable infant gut and breast milk microbiota}},
  url          = {{http://dx.doi.org/10.1038/s41522-026-01111-7}},
  doi          = {{10.1038/s41522-026-01111-7}},
  year         = {{2026}},
}