Evidence map›Paper›PMID 42173938›Full record

ArticleScientific reports2026

Metagenomic survey of pathogen prevalence in the infant gut.

Nienke van Beek, Ahmed Bargheet, Ching Jian, Hanna T Noordzij, Alise Ponsero, Veronika Kuchařová Pettersen, Katri E Korpela

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Nienke van BeekHuman Microbiome Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 63, 00014, Helsinki, Finland.
Ahmed BargheetHost-Microbe Interaction Research Group, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway.
Ching JianHuman Microbiome Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 63, 00014, Helsinki, Finland.
Hanna T NoordzijDepartment of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.
Alise PonseroHuman Microbiome Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 63, 00014, Helsinki, Finland.
Veronika Kuchařová PettersenHost-Microbe Interaction Research Group, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway.
Katri E KorpelaHuman Microbiome Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 63, 00014, Helsinki, Finland. katri.korpela@helsinki.fi.

Funding

ERC Starting Grant 101039583
6 · The paper itself

Abstract

The human microbiota impacts our health and well-being from infancy throughout our lives. Besides mutualistic and commensal strains, it also contains opportunistic pathogens. Infants may be especially vulnerable to opportunistic pathogen colonisation due to their immature immune systems and low microbial diversity.The study aims to examine associations between opportunistic pathogen prevalence and factors such as breastfeeding, antibiotic use, birth-mode, and the presence of other bacterial taxa. This study analysed 3981 publicly available shotgun metagenomes collected from 1275 infants and 415 mothers across ten countries to identify species that may be considered opportunistic pathogens in the infant gut. The prevalence of C. difficile was decreased in breastfed infants and in those carrying Faecalibacterium and Dorea spp. S. aureus carriage was negatively associated with antibiotic use and positively with skin contact and breastfeeding. K. pneumoniae was acquired later in life and was more prevalent in premature infants, and less commonplace in vaginal deliveries without antibiotics. Our findings indicate that opportunistic pathogen prevalence in the infant gut is influenced by medical and caregiving practices and may be modifiable through targeted interventions. Reducing the spread of these opportunistic pathogens could contribute to global efforts against early life infections.

Indexed as

BacteriaGastrointestinal MicrobiomeMetagenomeMetagenomicsOpportunistic InfectionsAnti-Bacterial AgentsBreast FeedingFemaleHumansInfantInfant, NewbornMalePrevalenceAnti-Bacterial AgentsAntimicrobial resistanceGut microbiotaInfant gutInfectious diseaseOpportunistic pathogen colonisation

Identifiers

PMID42173938
PMCPMC13408495

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.