The impact of vitamin B12 deficiency on infant gut microbiota

  • Perran Boran
  • Hatice Ezgi BarisEmail author
  • Eda Kepenekli
  • Can Erzik
  • Ahmet Soysal
  • Duy M Dinh
Original Article


Although physiologic and neurologic consequences of micronutrient deficiencies have been addressed extensively, less is known about their impact on developing gut microbiota. Vitamin B12 deficiency is a common micronutrient deficiency in infants. We aimed to analyze the gut microbial composition of exclusively breastfed infants aged between 4 and 6 months with and without vitamin B12 deficiency by 16S rRNA gene sequencing. In a subgroup of infants with vitamin B12 deficiency, stool samples are recollected and reanalyzed after vitamin B12 supplementation. A total of 88 infants’ stool samples (median age 4 months [IQR 4–5], 50% males) were analyzed, of which 28 (31.8%) were vitamin B12 sufficient and 60 (68.2%) were vitamin B12 insufficient. Comparisons between vitamin B12-sufficient and vitamin B12-insufficient infants revealed no evidence of differences in the microbiota. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the most abundant phyla in all groups. There was no difference between the pre- and post-treatment composition of gut microbiota.

Conclusion: Vitamin B12-deficient infants have similar gut microbial composition as vitamin B12-sufficient infants. Since the samples were collected at an early period of life and the exposure to deficiency was relatively short, it may be possible that the effects were not fully established.

What is Known:

Vitamin B12 is an essential vitamin for humans and also a crucial compound for human gut microbiota.

Vitamin B12 deficiency is common in exclusively breastfed infants.

In contrast to the adult gut microbiota, infant gut microbiota has been shown to have decreased capacity for de novo synthesis of vitamin B12 and depend on dietary source of vitamin B12.

What is New:

There is no difference in the gut microbial composition of vitamin B12-deficient and vitamin B12-sufficient infants.


Infants Vitamin B12 Micronutrients Gut microbiota Breastfeeding 



False discovery rate


Operational taxonomic unit


Principal coordinate analysis


Authors’ contributions

P. Boran, E. Kepenekli, C. Erzik, and A. Soysal designed the study.

P. Boran and HE. Baris participated in recruitment of subjects and sample collection.

P. Boran, HE. Baris, C. Erzik, and DM. Dinh performed data analysis and interpretation.

DM. Dinh generated figures.

P. Boran and HE Baris wrote the first draft of the article.

P. Boran, HE Baris, E Kepenekli, C. Erzik, A. Soysal, and DM Dinh contributed to critical revision and approved the final manuscript.


This project was sponsored by Marmara University Scientific Research Commission, BAPKO, (SAG-A-091116-0488).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee (Marmara University, School of Medicine Ethics Committee, reference number: 09.2016.137) and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.

Informed consent

Informed consent was obtained from mothers of all individual participants included in the study.

Supplementary material

431_2019_3517_MOESM1_ESM.docx (1.9 mb)
ESM 1 (DOCX 1974 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Pediatrics, Division of Social PediatricsMarmara University School of MedicineIstanbulTurkey
  2. 2.Department of Pediatrics, Division of Pediatric Infectious DiseasesMarmara University School of MedicineIstanbulTurkey
  3. 3.Department of Medical BiologyMarmara University School of MedicineIstanbulTurkey
  4. 4.Pediatric Infectious DiseasesMemorial HospitalIstanbulTurkey
  5. 5.DiversigenHoustonUSA

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