The role of Bifidobacterium genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life

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Reviewed Marked as Reviewed by Svetlana up on 2024-7-19
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


Reviewed Marked as Reviewed by Svetlana up on 2024-7-19

Curated date: 2024/06/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine, Victoria, Scholastica

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).
log transformation
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

Reviewed Marked as Reviewed by Svetlana up on 2024-7-19

Curated date: 2024/06/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bifidobacterium
Corynebacterium
Streptococcus

Revision editor(s): Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-19

Curated date: 2024/06/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Staphylococcus
Enterococcus
Klebsiella
Clostridium

Revision editor(s): Aleru Divine

Experiment 2


Reviewed Marked as Reviewed by Svetlana up on 2024-7-19

Curated date: 2024/06/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine, Victoria, Scholastica

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

Reviewed Marked as Reviewed by Svetlana up on 2024-7-19

Curated date: 2024/06/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Actinomyces
Bifidobacterium
Enterococcus
Rothia
Streptococcus
Bifidobacterium sp.

Revision editor(s): Aleru Divine

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-19

Curated date: 2024/06/09

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bacteroides
Bifidobacterium dentium
Clostridium
Finegoldia
Gemella
Klebsiella
Parabacteroides sp.

Revision editor(s): Aleru Divine