Diversity and temporal dynamics of primate milk microbiomes

Abstract

Milk is inhabited by a community of bacteria and is one of the first postnatal sources of microbial exposure for mammalian young. Bacteria in breast milk may enhance immune development, improve intestinal health, and stimulate the gut-brain axis for infants. Variation in milk microbiome structure (e.g., operational taxonomic unit[OTU] diversity, community composition) may lead to different infant developmental outcomes. Milk microbiome structure may depend on evolutionary processes acting at the host species level and ecological processes occurring over lactation time, among others. We quantified milk microbiomes using 16S rRNA high-throughput sequencing for nine primate species and for six primate mothers sampled over lactation. Our data set included humans (Homo sapiens, Philippines and USA) and eight nonhuman primate species living in captivity (bonobo [Pan paniscus], chimpanzee [Pan troglodytes], western lowland gorilla [Gorilla gorilla gorilla], Bornean orangutan [Pongo pygmaeus], Sumatran orangutan [Pongo abelii], rhesus macaque [Macaca mulatta], owl monkey [Aotus nancymaae]) and in the wild (mantled howler monkey [Alouatta palliata]). For a subset of the data, we paired microbiome data with nutrient and hormone assay results to quantify the effect of milk chemistry on milk microbiomes.We detected a core primate milk microbiome of seven bacterial OTUs indicating a robust relationship between these bacteria and primate species. Milk microbiomes differed among primate species with rhesus macaques, humans and mantled howler monkeys having notably distinct milk microbiomes. Gross energy in milk from protein and fat explained some of the variations in microbiome composition among species.Microbiome composition changed in a predictable manner for three primate mothers over lactation time, suggesting that different bacterial communities may be selected for as the infant ages. Our results contribute to understanding ecological and evolutionary relationships between bacteria and primate hosts, which can have applied benefits for humans and endangered primates in our care. K E Y W O R D Sbacteria, breast milk, infant, lactation, mammals, microbiota, symbiosis

Gut Microbiomes Differ Among Dietary Types and Stool Consistency in the Captive Red Wolf (Canis rufus)

“…All statistical analyses were conducted in R version 3.5.0 (R Core Team, 2018 ) and significance was determined as p < 0.05. We used analysis framework based on previous research ( Muletz-Wolz et al, 2019a , b ) to examine microbiome structure in red wolves. We addressed two main questions through statistical analyses: (1) how do red wolf gut microbiomes differ between loose stool consistency and normal stool consistency and (2) how does dietary type relate to stool consistency and red wolf gut microbiomes?…”

Neonatal Immune System Ontogeny: The Role of Maternal Microbiota and Associated Factors. How Might the Non-Human Primate Model Enlighten the Path?

“…The qualitative and quantitative composition of breast milk changes among women but also during the lactation period (between colostrum, transition, and mature milk for example) [89]. The composition and evolution of the milk is similar in various primate species and partly depends on the relative amount of fat and protein in the milk [139]. It is also different for women who give birth at term or preterm [140].…”

Testing the “(Neo-)Darwinian” Principles against Reticulate Evolution: How Variation, Adaptation, Heredity and Fitness, Constraints and Affordances, Speciation, and Extinction Surpass Organisms and Species

“…Even the human placenta appears to house a specific microbiome [147] that helps fetal development [148]. In the context of infective heredity, during lactation of offspring, numerous beneficial microbes as well as antibodies against pathogens are passed on that strengthen the offspring's immunity and that enables offspring to survive successfully and to adapt to their environmental surroundings (a process first described by Ehrlich [149], but see also [150,151]). Endogenous retroviruses have moreover had a significant impact on vertebrate reproduction by playing a physiological role in the formation of the mammalian placenta, including the human placenta [152,153].…”