Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations

Abstract

Microbiomes are transmitted between generations by a variety of different vertical and/or horizontal modes, including vegetative reproduction (vertical), via female germ cells (vertical), coprophagy and regurgitation (vertical and horizontal), physical contact starting at birth (vertical and horizontal), breast-feeding (vertical), and via the environment (horizontal). Analyses of vertical transmission can result in false negatives (failure to detect rare microbes) and false positives (strain variants). In humans, offspring receive most of their initial gut microbiota vertically from mothers during birth, via breast-feeding and close contact. Horizontal transmission is common in marine organisms and involves selectivity in determining which environmental microbes can colonize the organism’s microbiome. The following arguments are put forth concerning accurate microbial transmission: First, the transmission may be of functions, not necessarily of species; second, horizontal transmission may be as accurate as vertical transmission; third, detection techniques may fail to detect rare microbes; lastly, microbiomes develop and reach maturity with their hosts. In spite of the great variation in means of transmission discussed in this paper, microbiomes and their functions are transferred from one generation of holobionts to the next with fidelity. This provides a strong basis for each holobiont to be considered a unique biological entity and a level of selection in evolution, largely maintaining the uniqueness of the entity and conserving the species from one generation to the next.

Roles for non-human primate-associated phage diversity in improving medicine and public health

“…The study of phages within a single primate species, baboons, revealed that neighboring social groups harbored evolutionarily and compositionally distinct phageomes that were structured by their superhost’s social behavior; close grooming partners had more similar phage communities, even after controlling for relatedness or diet of the superhosts [ 16 ]. This study joined a growing body of literature suggesting that maintenance of microbial communities within groups through social behavior serves to create a pan-microbiome that can act to maintain microbial diversity across evolutionary time scales and contributing to the evolution of host species-specific gut microbial communities [ 18 , 19 ].…”

Microbial transmission, colonisation and succession: from pregnancy to infancy

“…Bacteria such as Parabacteroides distasonis, Alistipes onderdonkii, Bacteroides faecis, Bacteroides caccae and Bacteroides salyersiae from the maternal oral cavity and skin are frequently transferred to infants through kissing, touching and hugging. [208][209][210] One study focused on early microbial seeding and suggested that fathers also play an essential role in the establishment of the neonatal microbiome. 8 Distinct from maternal seeding at the start of birth, fathers mainly provide novel strains that colonise infants later in life.…”

Eco-evolutionary implications of helminth microbiomes

“…The extensive range of variability in the bacteriome of helminths leads to questioning the microbial sources of individual helminths in a population (Rosenberg & Zilber-Rosenberg, 2021): helminths may horizontally acquire bacteria, from their habitat, be it the external environment when they are in the infectious larval stages, or their surroundings within their host, and their diet, whatever they feed on (host tissue, or even other co-infecting parasites) (Jorge et al, 2020(Jorge et al, , 2022b. Helminths may also vertically acquire bacteria, which means bacteria are transmitted among parasite generations (Jorge et al, 2020(Jorge et al, , 2022b.…”