Abstract
The gut is inhabited by a densely populated ecosystem, the gut microbiota, that is established at birth. However, the succession by which different bacteria are incorporated into the gut microbiota is still relatively unknown. Here, we analyze the microbiota from 471 Swedish children followed from birth to 5 years of age, collecting samples after 4 and 12months and at 3 and 5 years of age as well as from their mothers at birth using 16S rRNA gene profiling. We also compare their microbiota to an adult Swedish population. Genera follow 4 different colonization patterns during establishment where Methanobrevibacter and Christensenellaceae colonize late and do not reached adult levels at 5 years. These late colonizers correlate with increased alpha diversity in both children and adults. By following the children through age-specific community types, we observe that children have individual dynamics in the gut microbiota development trajectory.
Highlights
The newborn infant is considered sterile in utero during normal pregnancy (de Goffau et al, 2019), but acquires bacteria through transmission from the mother and the environment at delivery (Ferretti et al, 2018)
Community richness and composition of the gut microbiota in children up to five years Here, we expand on our previous study (Ba€ckhed et al, 2015) by increasing the number of children (n = 471) and follow them for the first 5 years of their lives to investigate the establishment of the gut microbiota
The fecal microbiota was profiled by sequencing the V4 region of the 16S rRNA gene during the first week of life, at 4 months (4M; n = 411), 12 months (12M; n = 397), 3 years (3Y; n = 336), and 5 years (5Y; n = 288) (Table 1)
Summary
The newborn infant is considered sterile in utero during normal pregnancy (de Goffau et al, 2019), but acquires bacteria through transmission from the mother and the environment at delivery (Ferretti et al, 2018). The ecological succession within the gut microbiota is a dynamic process during infancy (Ba€ckhed et al, 2015; Eggesbø et al, 2011; Palmer et al, 2007), but stabilizes during childhood (Hollister et al, 2015; Stewart et al, 2018; Yatsunenko et al, 2012). The mode of birth, diet (breast or formula feeding), and antibiotic use (Bokulich et al, 2016; Dominguez-Bello et al, 2010; Eggesbø et al, 2011; Koenig et al., 2011; La Rosa et al, 2014), as well as host factors (Donaldson et al, 2018) are major contributing factors to the initial seeding and development of the gut microbiota and have been associated with health outcomes later in life (Tamburini et al, 2016; Tun et al, 2018). It is unclear to what extent these factors contribute to the development of an adult gut microbiota (Derrien et al, 2019). It has been suggested that priority effects, the order by which species appear in the gut microbiota during succession, may have long-lasting effects on the community structure and function (Sprockett et al, 2018).
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