Page 47 - Read Online

Kreuze et al. Microbiome Res Rep 2025;4:7 https://dx.doi.org/10.20517/mrr.2024.51 Page 5 of 14

Figure 3. Three types of MGEs and how they are transmitted vertically or horizontally between bacterial cells that are inherited from the
mother. The red color (left) represents conjugative elements (e.g., plasmids and ICEs), which can be maintained as extrachromosomal
elements or integrated into the host genome and be transferred horizontally between bacterial cells via conjugation. The magenta color
(center) represents P-Ps, which can be maintained as plasmids in host cells and transferred via viral lysis and potentially by conjugation.
The dark blue color (right) represents phages that can be maintained integrated in the host genome or transferred between bacterial
cells by viral lysis. MGEs: Mobile genetic elements; ICEs: integrative and conjugative elements; P-Ps: phage plasmids.

prophages that enter the gut with their hosts . There is increased prophage activity throughout infancy
[25]
that peaks at 1-8 months after birth, with some studies predicting that over 75% of the free phages in the
stool are temperate phages [41-45] . This induction spike may be an adaptation where phages attempt to
establish themselves after the colonization bottleneck by transferring onto more fit hosts, especially given
the high bacterial turnover during infancy. Supporting this, Vatanen et al. demonstrated that a maternal
prophage was found in a different bacterial genome in their infant’s gut . Importantly, such dynamics may
[19]
increase the rate of horizontal gene transfer in the infant gut, as they transfer potential fitness-enhancing
genes through processes such as lateral transduction .
[46]

Conjugative elements are well-studied MGEs composed of integrative and conjugative elements (ICEs, or
conjugative transposons) and conjugative plasmids, which both move horizontally between bacterial species
through conjugation [Figure 3]. This transfer mechanism does not depend on the lysis of their bacterial
hosts but requires close contact between bacterial cells. One key difference between ICEs and plasmids is
that the former are typically maintained as integrated into the host chromosome, while the latter are
maintained as extrachromosomal elements in the cytoplasm.

Plasmid and ICE compositions tend to be more similar between familial mother-infant pairs and differ
between vaginally and Cesarean section delivered infants [21,47,48] . For example, a highly prevalent plasmid
called pBI143 is frequently identical between mothers and their infants, suggestive of mother-to-infant
transmission . While studies on conjugation activity in the infant gut are lacking, plasmid groups that are
[49]
maintained for longer in the infant gut tend to encode conjugation-related genes . In addition to this,
[21]
some conjugative elements have been shown to increase conjugation rate in response to reactive oxygen
species and/or the SOS response [50-53] , signals that also trigger phage induction . The conjugation rate can
[54]