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, 11 (6), e0158498
eCollection

Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota

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Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota

Rocio Martin et al. PLoS One.

Abstract

Colonization of the infant gut is believed to be critically important for a healthy growth as it influences gut maturation, metabolic, immune and brain development in early life. Understanding factors that influence this process is important, since an altered colonization has been associated with a higher risk of diseases later in life. Fecal samples were collected from 108 healthy neonates in the first half year of life. The composition and functionality of the microbiota was characterized by measuring 33 different bacterial taxa by qPCR/RT qPCR, and 8 bacterial metabolites. Information regarding gender, place and mode of birth, presence of siblings or pets; feeding pattern and antibiotic use was collected by using questionnaires. Regression analysis techniques were used to study associations between microbiota parameters and confounding factors over time. Bacterial DNA was detected in most meconium samples, suggesting bacterial exposure occurs in utero. After birth, colonization by species of Bifidobacterium, Lactobacillus and Bacteroides was influenced by mode of delivery, type of feeding and presence of siblings, with differences found at species level and over time. Interestingly, infant-type bifidobacterial species such as B. breve or B. longum subsp infantis were confirmed as early colonizers apparently independent of the factors studied here, while B. animalis subsp. lactis presence was found to be dependent solely on the type of feeding, indicating that it might not be a common infant gut inhabitant. One interesting and rather unexpected confounding factor was gender. This study contributes to our understanding of the composition of the microbiota in early life and the succession process and the evolution of the microbial community as a function of time and events occurring during the first 6 months of life. Our results provide new insights that could be taken into consideration when selecting nutritional supplementation strategies to support the developing infant gut microbiome.

Conflict of interest statement

Competing Interests: Nutricia Research and Yakult funded the study. RM, KBA, MR, SS, ACY, JK are paid by Nutricia Research, whereas HM, HK, TS, EI, KO, AK are paid by Yakult. This does not alter the authors' adherence to all PLOS ONE policies on sharing data and materials.

Figures

Fig 1
Fig 1. Effect of mode of delivery on the colonization by Bacteroides species.
Prevalence of different Bacteroides species in fecal samples of infants born by caesarean section (red) or vaginal delivery (blue) at birth, 2, 7, 30, 90 and 180 days of life, using the original data.
Fig 2
Fig 2. Effect of mode of delivery on the colonization by Bifidobacterium.
Bifidobacterium count (in log10 cell/g of feces) in infants born by caesarean section (red) compared to those born by vaginal delivery (blue) over time as calculated by the statistical model (A) or as represented from original data (B). (C) Prevalence of B. longum in infants born by CS (red) or vaginal delivery (blue) at birth, 2, 7, 30, 90 and 180 days of life. The graph is generated using the raw data.
Fig 3
Fig 3. Effect of mode of delivery on the probability to detect different bacteria.
(A) Probability to detect Atopobium cluster, B. fragilis group and B. catenulatum group in infants born by VD (blue) compared to those born by CS (red) over time as calculated by the statistical model. (B) Prevalence of Atopobium cluster, B. fragilis group and B. catenulatum group in in infants born by VD (blue) compared to those born by CS (red) over time as represented by the original data.
Fig 4
Fig 4. Effect of mode of delivery on the colonization by Enterococcus and Clostridium perfringens.
Prevalence of Enterococcus and Clostridium perfringens in fecal samples of infants born by caesarean section (red) or vaginal delivery (blue) at birth, 2, 7, 30, 90 and 180 days of life, using the original data.
Fig 5
Fig 5. Effect of mode of delivery on the organic acid profile.
Probability to detect organic acids (acetic, lactic and succinic acid) in infants born by caesarean section (red) compared to those born by vaginal delivery (blue) over time as calculated by the statistical model.
Fig 6
Fig 6. Influence of type of feeding on the colonization by Bifidobacterium during the first 3 months of life.
Bifidobacterium count (in log10 cell/g of feces) in exclusively breastfed infants (green) compared to those receiving mix-feeding (black) over time as calculated by the statistical model (A) or as represented from the original data (B).
Fig 7
Fig 7. Influence of type of feeding on the presence of B. animalis subsp. lactis during the first 3 months of life.
(A) Probability to detect B. animalis in exclusively breastfed infants (green) compared to those receiving mix-feeding (black) as calculated by the statistical model. (B) Prevalence of B. animalis in infants receiving mix-feeding (black) or exclusively breast fed (green) at birth, 2, 7, 30 and 90 days of life as represented by the original data.
Fig 8
Fig 8. Effect of type of feeding on the colonization pattern of different bacteria during the first 3 months of life.
(A) Probability to detect C. leptum group, C. perfringens, and L. casei subgroup in infants receiving exclusive breastfeeding (green) compared to those receiving mix-feeding (black) over time as calculated by the statistical model. (B) Prevalence of C. leptum group, C. perfringens, and L. casei subgroup in infants receiving mix-feeding (black) or exclusive breast feeding (green) over time as represented by the original data.
Fig 9
Fig 9. Bacterial groups or species influenced by the presence/absence of older siblings (I).
(A) Probability to detect Atopobium cluster, B. fragilis group and B. bifidum in firstborn infants (orange) compared to those having older siblings (grey) during the first 3 months of life as calculated by the statistical model. (B) Prevalence of Atopobium cluster, B. fragilis group and B. bifidum in firstborn infants (orange) compared to those having older siblings (grey) during the first 3 months of life as represented by the original data.
Fig 10
Fig 10. Bacterial groups or species influenced by the presence/absence of older siblings (II).
(A) Probability to detect B. adolescentis and C. perfringens in firstborn infants (orange) compared to those having older siblings (grey) during the first 3 months of life as calculated by the statistical model. (B) Prevalence of B. adolescentis and C. perfringens in firstborn infants (orange) compared to those having older siblings (grey) during the first 3 months of life as represented by the original data.

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Grant support

The study was funded by Yakult and Nutricia Research. The following authors are paid by Nutricia Research: RM, KBA, MR, SS, ACY, JK, whereas HM, HK, TS, EI, KO, AK are paid by Yakult. The specific roles of these authors are articulated in the ‘author contributions’ section.
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