Human milk oligosaccharide metabolism and antibiotic resistance in early gut colonizers: insights from bifidobacteria and lactobacilli in the maternal-infant microbiome
Breast milk, rich in human milk oligosaccharides (HMOs), supports the early-life colonization of beneficial bacteria such as bifidobacteria and lactobacilli, potentially reducing early-life antibiotic resistance. However, antibiotic treatment may interfere with the beneficial functions of HMO-degrad...
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Taylor & Francis Group
2025-12-01
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| Series: | Gut Microbes |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/19490976.2025.2501192 |
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| author | Anna Samarra Simone Renwick Aleksandr A. Arzamasov Dmitry A. Rodionov Kennedy Spann Raul Cabrera-Rubio Antia Acuna-Gonzalez Cecilia Martínez-Costa Lindsay Hall Nicola Segata Andrei L. Osterman Lars Bode Maria Carmen Collado |
| author_facet | Anna Samarra Simone Renwick Aleksandr A. Arzamasov Dmitry A. Rodionov Kennedy Spann Raul Cabrera-Rubio Antia Acuna-Gonzalez Cecilia Martínez-Costa Lindsay Hall Nicola Segata Andrei L. Osterman Lars Bode Maria Carmen Collado |
| author_sort | Anna Samarra |
| collection | DOAJ |
| description | Breast milk, rich in human milk oligosaccharides (HMOs), supports the early-life colonization of beneficial bacteria such as bifidobacteria and lactobacilli, potentially reducing early-life antibiotic resistance. However, antibiotic treatment may interfere with the beneficial functions of HMO-degrading bacteria. This study investigated the metabolism of HMOs by bifidobacteria and lactobacilli isolated from human milk and mother-infant paired fecal samples, along with their antibiotic resistance profiles. Understanding these species- and sample-type-specific interactions will provide valuable insights into how bioactive components in human milk may shape the infant resistome during early life. A total of 39 Bifidobacterium and 14 Lactobacillaceae strains were isolated from paired mother-infant fecal and breast milk samples. Whole genome sequencing (WGS) allowed functional predictions on the HMO metabolism abilities and the resistance genotype of each strain. In vitro HMO utilization was assessed using growth kinetics assays combined with HMO glycoprofiling in culture supernatant. The minimum inhibitory concentration (MIC) was also determined for each strain. HMO metabolism by the bifidobacteria was species-specific. Bifidobacterium bifidum (B. bifidum) and Bifidobacterium longum subsp. infantis (B. infantis) exhibited the highest capacity for HMO degradation, consistent with genomic predictions. In contrast, lactobacilli were unable to degrade HMOs in vitro but were predicted to metabolize the by-products of HMO degradation. Phenotypic analysis revealed that B. bifidum strains had the lowest levels of antibiotic resistance, while Bifidobacterium animalis subsp. lactis (B. lactis) strains were resistant to most tested antibiotics. Overall, B. bifidum demonstrated the strongest HMO-degrading ability while remaining the most antibiotic-susceptible species. Early-life colonizing bifidobacterial species possess the essential machinery required to degrade HMOs and are highly susceptible to antibiotics. A better understanding of these dynamics could inform clinical strategies to protect and restore the infant gut microbiome, particularly in neonates exposed to antibiotics. |
| format | Article |
| id | doaj-art-34b8b32d44cc4333a0dfdbeb6a2b426f |
| institution | Kabale University |
| issn | 1949-0976 1949-0984 |
| language | English |
| publishDate | 2025-12-01 |
| publisher | Taylor & Francis Group |
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| series | Gut Microbes |
| spelling | doaj-art-34b8b32d44cc4333a0dfdbeb6a2b426f2025-08-20T03:27:47ZengTaylor & Francis GroupGut Microbes1949-09761949-09842025-12-0117110.1080/19490976.2025.2501192Human milk oligosaccharide metabolism and antibiotic resistance in early gut colonizers: insights from bifidobacteria and lactobacilli in the maternal-infant microbiomeAnna Samarra0Simone Renwick1Aleksandr A. Arzamasov2Dmitry A. Rodionov3Kennedy Spann4Raul Cabrera-Rubio5Antia Acuna-Gonzalez6Cecilia Martínez-Costa7Lindsay Hall8Nicola Segata9Andrei L. Osterman10Lars Bode11Maria Carmen Collado12Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Valencia, SpainDepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USAInfectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USAInfectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USADepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USADepartment of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Valencia, SpainFood, Microbiome and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UKDepartment of Pediatrics, School of Medicine, University of Valencia, Valencia, SpainFood, Microbiome and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UKDepartment CIBIO, University of Trento, Trento, ItalyInfectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USADepartment of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USADepartment of Biotechnology, Institute of Agrochemistry and Food Technology- National Spanish Research Council (IATA-CSIC), Valencia, SpainBreast milk, rich in human milk oligosaccharides (HMOs), supports the early-life colonization of beneficial bacteria such as bifidobacteria and lactobacilli, potentially reducing early-life antibiotic resistance. However, antibiotic treatment may interfere with the beneficial functions of HMO-degrading bacteria. This study investigated the metabolism of HMOs by bifidobacteria and lactobacilli isolated from human milk and mother-infant paired fecal samples, along with their antibiotic resistance profiles. Understanding these species- and sample-type-specific interactions will provide valuable insights into how bioactive components in human milk may shape the infant resistome during early life. A total of 39 Bifidobacterium and 14 Lactobacillaceae strains were isolated from paired mother-infant fecal and breast milk samples. Whole genome sequencing (WGS) allowed functional predictions on the HMO metabolism abilities and the resistance genotype of each strain. In vitro HMO utilization was assessed using growth kinetics assays combined with HMO glycoprofiling in culture supernatant. The minimum inhibitory concentration (MIC) was also determined for each strain. HMO metabolism by the bifidobacteria was species-specific. Bifidobacterium bifidum (B. bifidum) and Bifidobacterium longum subsp. infantis (B. infantis) exhibited the highest capacity for HMO degradation, consistent with genomic predictions. In contrast, lactobacilli were unable to degrade HMOs in vitro but were predicted to metabolize the by-products of HMO degradation. Phenotypic analysis revealed that B. bifidum strains had the lowest levels of antibiotic resistance, while Bifidobacterium animalis subsp. lactis (B. lactis) strains were resistant to most tested antibiotics. Overall, B. bifidum demonstrated the strongest HMO-degrading ability while remaining the most antibiotic-susceptible species. Early-life colonizing bifidobacterial species possess the essential machinery required to degrade HMOs and are highly susceptible to antibiotics. A better understanding of these dynamics could inform clinical strategies to protect and restore the infant gut microbiome, particularly in neonates exposed to antibiotics.https://www.tandfonline.com/doi/10.1080/19490976.2025.2501192Human milkoligosaccharidesantibiotic resistancebifidobacteriainfantmother |
| spellingShingle | Anna Samarra Simone Renwick Aleksandr A. Arzamasov Dmitry A. Rodionov Kennedy Spann Raul Cabrera-Rubio Antia Acuna-Gonzalez Cecilia Martínez-Costa Lindsay Hall Nicola Segata Andrei L. Osterman Lars Bode Maria Carmen Collado Human milk oligosaccharide metabolism and antibiotic resistance in early gut colonizers: insights from bifidobacteria and lactobacilli in the maternal-infant microbiome Gut Microbes Human milk oligosaccharides antibiotic resistance bifidobacteria infant mother |
| title | Human milk oligosaccharide metabolism and antibiotic resistance in early gut colonizers: insights from bifidobacteria and lactobacilli in the maternal-infant microbiome |
| title_full | Human milk oligosaccharide metabolism and antibiotic resistance in early gut colonizers: insights from bifidobacteria and lactobacilli in the maternal-infant microbiome |
| title_fullStr | Human milk oligosaccharide metabolism and antibiotic resistance in early gut colonizers: insights from bifidobacteria and lactobacilli in the maternal-infant microbiome |
| title_full_unstemmed | Human milk oligosaccharide metabolism and antibiotic resistance in early gut colonizers: insights from bifidobacteria and lactobacilli in the maternal-infant microbiome |
| title_short | Human milk oligosaccharide metabolism and antibiotic resistance in early gut colonizers: insights from bifidobacteria and lactobacilli in the maternal-infant microbiome |
| title_sort | human milk oligosaccharide metabolism and antibiotic resistance in early gut colonizers insights from bifidobacteria and lactobacilli in the maternal infant microbiome |
| topic | Human milk oligosaccharides antibiotic resistance bifidobacteria infant mother |
| url | https://www.tandfonline.com/doi/10.1080/19490976.2025.2501192 |
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