The role of Bifidobacterium genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life
Open accessAbstract
Resistance to antibiotics in newborns is a huge concern as their immune system is still developing, and infections and resistance acquisition in early life have short- and long-term consequences for their health. Bifidobacterium species are important commensals capable of dominating the infant gut microbiome and are known to be less prone to possess antimicrobial resistance genes than other taxa that may colonize infants. We aimed to study the association between Bifidobacterium-dominated infant gut microbiota and the antibiotic resistant gene load in neonates, and to ascertain the perinatal factors that may contribute to the antibiotic resistance acquisition. Two hundred infant fecal samples at 7 days and 1 month of age from the MAMI birth cohort were included in the study and for whom maternal-neonatal clinical records were available. Microbiota profiling was carried out by 16S rRNA amplicon sequencing, and targeted antibiotic resistance genes (ARGs) including tetM, tetW, tetO, blaTEM, blaSHV and ermB were quantified by qPCR. Infant microbiota clustered into two distinct groups according to their Bifidobacterium genus abundance: high and low. The main separation of groups or clusters at each time point was performed with an unsupervised non-linear algorithm of k-means partitioning to cluster data by time points based on Bifidobacterium genus relative abundance. Microbiota composition differed significantly between both groups, and specific bifidobacterial species were enriched in each cluster. Lower abundance of Bifidobacterium in the infant gut was associated with a higher load of antibiotic resistance genes. Our results highlight the relevance of Bifidobacterium genus in the early acquisition and establishment of antibiotic resistance in the gut. Further studies are needed to develop strategies to promote a healthy early colonization and fight against the spread of antibiotic resistances.
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Bifidobacterium supplementation has been associated with lower ARG abundance in the infant gut microbiome, likely due to the competitive exclusion of ARG-rich pathobionts.
“Bifidobacterium, and Bifidobacterium supplementation has been associated with lower ARG abundance in the infant gut microbiome, likely due to the competitive exclusion of ARG-rich pathobionts56–59.”
From Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants. (2025) · cites this paper as [57]
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Self-citation
- Authors
- Samarra, A., Cabrera-Rubio, R., Martínez-Costa, C., & Collado, M. C.
- Affiliations
- Consejo Superior de Investigaciones Científicas (ES)
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Paterna, Valencia, Spain
- Department of Pediatrics, School of Medicine, University of Valencia, Valencia, Spain
- Venue
- Gut Microbes
- Publisher
- Informa UK Limited
- Published
- 2024-05-26
- Volume
- 16
- Issue
- 1
- Pages
- 2357176-2357176
- ISSN
- 1949-0976 (ISSN-L)
- 1949-0984
- PMC
- PMC11135851
- OpenAlex
- W4399034506
- Cited by
- 25
- References
- 72
- Citations by year
- 2026: 9 · 2025: 10 · 2024: 6
- FWCI
- 3.81
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Gut Microbes (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Repository of Digital Objects for Teaching Research and Culture (University of Valencia) (submittedVersion, cc-by-nc)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- PROMETEO/Generalitat Valenciana (NeoHealth, ref. 2020/012)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Keywords
- Bifidobacterium, infant gut microbiota, antibiotic resistance genes, tetM, tetW, tetO, blaTEM, blaSHV, ermB, perinatal factors, early life colonization, fecal microbiota
- MeSH terms
- Gastrointestinal Microbiome, Anti-Bacterial Agents, Bifidobacterium, Feces, Female, Humans, Infant, Infant, Newborn, Male, RNA, Ribosomal, 16S, Drug Resistance, Bacterial
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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