The role of Bifidobacterium genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Samarra A, Cabrera-Rubio R, Martínez-Costa C, Collado MC
Journal
Gut microbes
Year
2024
Keywords:
Bifidobacterium, antibiotic, gut, infant, microbiota, resistance
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.
Experiment 1
Needs review
Subjects
- Location of subjects
- Spain
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low-Bifidobacterium group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-Bifidobacterium group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High-Bifidobacterium group in the seven (7) day-old infants.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 57
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- LEfSe
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- antibiotic exposure, feeding practices, mode of birth
Signature 1
Needs review
Source: Figure 2
Description: Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.
Abundance in Group 1: increased abundance in High-Bifidobacterium group
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Corynebacterium | ||
| Streptococcus |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 2
Description: Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.
Abundance in Group 1: decreased abundance in High-Bifidobacterium group
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus | ||
| Enterococcus | ||
| Klebsiella | ||
| Clostridium |
Revision editor(s): Aleru Divine
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High-Bifidobacterium group in the one (1) month-old infants.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 58
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
Statistical Analysis
Signature 1
Needs review
Source: Figure 2 and 3
Description: Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.
Abundance in Group 1: increased abundance in High-Bifidobacterium group
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Bifidobacterium | ||
| Enterococcus | ||
| Rothia | ||
| Streptococcus | ||
| Bifidobacterium sp. |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 2 and 3
Description: Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.
Abundance in Group 1: decreased abundance in High-Bifidobacterium group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Bifidobacterium dentium | ||
| Clostridium | ||
| Finegoldia | ||
| Gemella | ||
| Klebsiella | ||
| Parabacteroides sp. |
Revision editor(s): Aleru Divine
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