The microbiome in pregnancy and early life-Highlights from the 11th Maria Delivoria-Papadopoulos Perinatal Symposium.

This review was based on a symposium that examined novel aspects of the microbiome during pregnancy and early life and explored papers published by the lecturers. For example, it showed that bacterial extracellular vesicles derived from the microbiome harboured in various maternal niches, carried bacterial deoxyribonucleic acid, were isolated from the placenta and may have confounded placental microbiome studies. Maternal diet was responsible for the composition and diversity of breast milk microbiota, and may have shaped the offspring's microbiome and influenced their immune components. Probiotics and antibiotics administered perinatally may have had beneficial but also long-lasting adverse effects on offspring.

SIR+ models: accounting for interaction-dependent disease susceptibility in the planning of public health interventions.

Avoiding physical contact is regarded as one of the safest and most advisable strategies to follow to reduce pathogen spread. The flip side of this approach is that a lack of social interactions may negatively affect other dimensions of health, like induction of immunosuppressive anxiety and depression or preventing interactions of importance with a diversity of microbes, which may be necessary to train our immune system or to maintain its normal levels of activity. These may in turn negatively affect a population's susceptibility to infection and the incidence of severe disease. We suggest that future pandemic modelling may benefit from relying on 'SIR+ models': epidemiological models extended to account for the benefits of social interactions that affect immune resilience. We develop an SIR+ model and discuss which specific interventions may be more effective in balancing the trade-off between minimizing pathogen spread and maximizing other interaction-dependent health benefits. Our SIR+ model reflects the idea that health is not just the mere absence of disease, but rather a state of physical, mental and social well-being that can also be dependent on the same social connections that allow pathogen spread, and the modelling of public health interventions for future pandemics should account for this multidimensionality.

Conspecific versus heterospecific transmission shapes host specialization of the phyllosphere microbiome.

In disease ecology, pathogen transmission among conspecific versus heterospecific hosts is known to shape pathogen specialization and virulence, but we do not yet know if similar effects occur at the microbiome level. We tested this idea by experimentally passaging leaf-associated microbiomes either within conspecific or across heterospecific plant hosts. Although conspecific transmission results in persistent host-filtering effects and more within-microbiome network connections, heterospecific transmission results in weaker host-filtering effects but higher levels of interconnectivity. When transplanted onto novel plants, heterospecific lines are less differentiated by host species than conspecific lines, suggesting a shift toward microbiome generalism. Finally, conspecific lines from tomato exhibit a competitive advantage on tomato hosts against those passaged on bean or pepper, suggesting microbiome-level host specialization. Overall, we find that transmission mode and previous host history shape microbiome diversity, with repeated conspecific transmission driving microbiome specialization and repeated heterospecific transmission promoting microbiome generalism.

Potential Pathogenic and Opportunistic Oral Bacteria in Early Life: The Role of Maternal Factors in a Portuguese Population.

In early life, maternal factors are of the utmost relevance for oral microbiome acquisition and maturation. Therefore, our study explored the impact of maternal factors, such as saliva and breastmilk colonization, cardiovascular risk factors (CRF), type of delivery, oral health, and caregiving habits on the prevalence of potential pathogenic and opportunistic oral bacteria in early life. A total of 26 healthy mothers, 23 mothers with CRF, and their 50 children were included and samples (child's oral swabs, mother's saliva, and breastmilk) were collected 4 to 12 weeks after delivery and inoculated in selective and differential media for detection of non-fastidious Gram-negative and Gram-positive bacteria to isolate potential pathogenic and opportunistic bacteria identified by MALDI-TOF MS (414 isolates). Within mother-child dyads, the same species were identified in 86% of the pairs and potential pathogenic microorganisms from the Staphylococcaceae and Enterobacteriaceae families were found to be statistically significantly concordant between mother-child samples, particularly in the healthy group. Staphylococcus saprophyticus and Stenotrophomonas maltophilia oral colonization in mother-child pairs were associated with the presence of CRF. Breastfeeding was related to the early life oral colonization of Staphylococcus epidermidis in children from healthy mothers and C-section was associated with higher diversity of pathogens, independent of cardiovascular status (p = 0.05). This study reveals the presence of potential oral opportunistic and pathogenic bacteria in early life and highlights the importance of maternal factors in its acquisition.

Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism.

The perinatal period represents a critical window for cognitive and immune system development, promoted by maternal and infant gut microbiomes and their metabolites. Here, we tracked the co-development of microbiomes and metabolomes from late pregnancy to 1 year of age using longitudinal multi-omics data from a cohort of 70 mother-infant dyads. We discovered large-scale mother-to-infant interspecies transfer of mobile genetic elements, frequently involving genes associated with diet-related adaptations. Infant gut metabolomes were less diverse than maternal but featured hundreds of unique metabolites and microbe-metabolite associations not detected in mothers. Metabolomes and serum cytokine signatures of infants who received regular-but not extensively hydrolyzed-formula were distinct from those of exclusively breastfed infants. Taken together, our integrative analysis expands the concept of vertical transmission of the gut microbiome and provides original insights into the development of maternal and infant microbiomes and metabolomes during late pregnancy and early life.

Transmission of the gut microbiome in cohousing goats and pigs.

Social interaction facilitates the horizontal transmission of the microbiota between different individuals. However, little is known about the level of microbiota transmission in different livestock animals and different digestive tracts. The Hainan black goat and Wuzhishan pig are typical tropical local breeds on Hainan Island in China. Thus, we sampled and analyzed the gut microbiome in Hainan black goats (cecum and rumen) and Wuzhishan pigs (cecum) to study horizontal transmission by rearing them in the same pen (six goats and six pigs) or separate pens (nine goats and nine pigs). De novo assembly and binning recovered 3,262 strain-level and 2,488 species-level metagenome-assembled genomes (MAGs) using ∼1.3 Tb sequencing data. Of these MAGs, 1,856 MAGs were identified as novel strain. Compared with goats living in separate pens, social interaction in the same pen promotes community homogeneity in the rumen microbiome (P < 0.05) and the cecum microbiome (P < 0.05), respectively. Notably, approximately 7.08% (231/3262) of the gut microbial population could transmit during cohousing, 12 strains only in inter-species transmission, versus 190 strains only in intra-species transmission, and 10 strains only in foregut and hindgut transmission. In addition, the social contact group has high transmitted strain abundance, which is correlated with community composition. This study provided a new insight into the influence of social interaction on the animal gut microbiota.

The road not taken: host genetics in shaping intergenerational microbiomes.

The early-life gut microbiome is linked to human phenotypes as an imbalanced microbiome of this period is implicated in diseases throughout life. Several determinants of early-life gut microbiome are explored, however, mechanisms of acquisition, colonization, and stability of early-life gut microbiome and their interindividual variability remain elusive. Host genetics play a vital role to shape the gut microbiome and interact with it to modulate individual phenotypes in human studies and animal models. Given the microbial linkage between host generations, we discuss the current state of roles of host genetics in forming intergenerational microbiomes associated with mothers, offspring, and those vertically transmitted, providing a basis for taking into account host genetics in future early-life microbiome research. We further expand our discussion to the bidirectional interactions between host gene expression and microbiome in human health.

Microbiome breeding: conceptual and practical issues.

Microbiome breeding is a new artificial selection technique that seeks to change the genetic composition of microbiomes in order to benefit plant or animal hosts. Recent experimental and theoretical analyses have shown that microbiome breeding is possible whenever microbiome-encoded genetic factors affect host traits (e.g., health) and microbiomes are transmissible between hosts with sufficient fidelity, such as during natural microbiome transmission between individuals of social animals, or during experimental microbiome transplanting between plants. To address misunderstandings that stymie microbiome-breeding programs, we (i) clarify and visualize the corresponding elements of microbiome selection and standard selection; (ii) elucidate the eco-evolutionary processes underlying microbiome selection within a quantitative genetic framework to summarize practical guidelines that optimize microbiome breeding; and (iii) characterize the kinds of host species most amenable to microbiome breeding.

Microbiomes of the Sydney Rock Oyster are acquired through both vertical and horizontal transmission.

BACKGROUND: The term holobiont is widely accepted to describe animal hosts and their associated microorganisms. The genomes of all that the holobiont encompasses, are termed the hologenome and it has been proposed as a unit of selection in evolution. To demonstrate that natural selection acts on the hologenome, a significant portion of the associated microbial genomes should be transferred between generations. Using the Sydney Rock Oyster (Saccostrea glomerata) as a model, we tested if the microbes of this broadcast spawning species could be passed down to the next generation by conducting single parent crosses and tracking the microbiome from parent to offspring and throughout early larval stages using 16S rRNA gene amplicon sequencing. From each cross, we sampled adult tissues (mantle, gill, stomach, gonad, eggs or sperm), larvae (D-veliger, umbo, eyed pediveliger, and spat), and the surrounding environment (water and algae feed) for microbial community analysis. RESULTS: We found that each larval stage has a distinct microbiome that is partially influenced by their parental microbiome, particularly the maternal egg microbiome. We also demonstrate the presence of core microbes that are consistent across all families, persist throughout early life stages (from eggs to spat), and are not detected in the microbiomes of the surrounding environment. In addition to the core microbiomes that span all life cycle stages, there is also evidence of environmentally acquired microbial communities, with earlier larval stages (D-veliger and umbo), more influenced by seawater microbiomes, and later larval stages (eyed pediveliger and spat) dominated by microbial members that are specific to oysters and not detected in the surrounding environment. CONCLUSION: Our study characterized the succession of oyster larvae microbiomes from gametes to spat and tracked selected members that persisted across multiple life stages. Overall our findings suggest that both horizontal and vertical transmission routes are possible for the complex microbial communities associated with a broadcast spawning marine invertebrate. We demonstrate that not all members of oyster-associated microbiomes are governed by the same ecological dynamics, which is critical for determining what constitutes a hologenome.

Host Bias in Diet-Source Microbiome Transmission in Wild Cohabitating Herbivores: New Knowledge for the Evolution of Herbivory and Plant Defense.

It is commonly understood that dietary nutrition will influence the composition and function of the animal gut microbiome. However, the transmission of organisms from the diet-source microbiome to the animal gut microbiome in the natural environment remains poorly understood, and elucidating this process may help in understanding the evolution of herbivores and plant defenses. Here, we investigated diet-source microbiome transmission across a range of herbivores (insects and mammals) living in both captive and wild environments. We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. IMPORTANCE We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. This study shed new light on the coevolution of herbivory and plant defense.

Microbiome-Assisted Breeding to Understand Cultivar-Dependent Assembly in Cucurbita pepo.

Recently, it was shown that long-term plant breeding does not only shape plant characteristics but also impacts plant-associated microbiota substantially. This requires a microbiome-integrative breeding approach, which was not yet shown. Here we investigate this for the Styrian oil pumpkin (Cucurbita pepo L. subsp. pepo var. styriaca Greb.) by analyzing the microbiome of six genotypes (the complete pedigree of a three-way cross-hybrid, consisting of three inbred lines and one open pollinating cultivar) in the seed and rhizosphere as well as the progeny seeds. Using high-throughput amplicon sequencing targeting the 16S rRNA and the ITS1 genes, the bacterial and fungal microbiomes were accessed. Seeds were found to generally carry a significantly lower microbial diversity compared to the rhizosphere and soil as well as a different microbial composition, with an especially high fraction of Enterobacteriaceae (40-83%). Additionally, potential plant-beneficial bacterial taxa, including Bacillaceae, Burkholderiaceae, and Pseudomonadaceae, were found to be enriched in progeny seeds. Between genotypes, more substantial changes can be observed for seed microbiomes compared to the rhizosphere. Moreover, rhizosphere communities were assembled for the most part from soil. Interestingly, bacterial signatures are mainly linked from seed to seed, while fungal communities are shaped by the soil and rhizosphere. Our findings provide a deep look into the rhizosphere and seed microbiome assembly of pumpkin-associated communities and represent the first steps into microbiome-driven breeding for plant-beneficial microbes.

Social behavior of musk deer during the mating season potentially influences the diversity of their gut microbiome.

An increasing body of research has revealed that social behavior shapes the animal gut microbiome community and leads to the similarity among the same social group. However, some additional factors (e.g., diet and habitat within each social group) may also contribute to this similarity within the social group and dissimilarity between social groups. Here, we investigated the potential correlation between social behavior and the gut microbiome community in 179 musk deer from four breeding regions in the Maerkang Captive Center, Sichuan. The dominant gut microbiome phyla in the musk deer in this study were Firmicutes, Bacteroidetes, and Proteobacteria. We found significant effects on the alpha and beta diversity of the gut microbiome due to the breeding regions. The similarity within breeding regions was higher than that between the breeding regions. Due to their solitary lifestyle, captive musk deer are raised in single cages with no direct social contact most of the time. Deer in all of the breeding regions have the same diet and similar living conditions. However, during each mating season from November to January, in each region, one adult male and about six adult females will be put together into a large cage. Social behavior happens during cohabitation, including mating behavior, grooming within the same sex or between different sexes, and other social contact. Therefore, we speculated that high similarity within the breeding region might be associated with the social behavior during the mating season. This was a simple and straightforward example of the relationship between animal social behavior and the gut microbiome.

Vertical Transmission of Gut Microbiome and Antimicrobial Resistance Genes in Infants Exposed to Antibiotics at Birth.

Vertical transmission of maternal microbes is a major route for establishing the gut microbiome in newborns. The impact of perinatal antibiotics on vertical transmission of microbes and antimicrobial resistance is not well understood. Using a metagenomic approach, we analyzed the fecal samples from mothers and vaginally delivered infants from a control group (10 pairs) and a treatment group (10 pairs) receiving perinatal antibiotics. Antibiotic-usage had a significant impact on the main source of inoculum in the gut microbiome of newborns. The control group had significantly more species transmitted from mothers to infants (P = .03) than the antibiotic-treated group. Approximately 72% of the gut microbial population of infants at 3-7 days after birth in the control group was transmitted from their mothers, versus only 25% in the antibiotic-treated group. In conclusion, perinatal antibiotics markedly disturbed vertical transmission and changed the source of gut colonization towards horizontal transfer from the environment to the infants.

Microbiome Transmission During Sexual Intercourse Appears Stochastic and Supports the Red Queen Hypothesis.

Microbes inhabit virtually everywhere on and/or in our bodies, including the seminal and vaginal fluids. They have significant importance in maintaining reproductive health and protecting hosts from diseases. The exchange of microbes during sexual intercourse is one of the most direct and significant microbial transmissions between men and women. Nevertheless, the mechanism of this microbial transmission was little known. Is the transmission mode stochastic, passive diffusion similar to the random walk of particles, or driven by some deterministic forces? What is the microbial transmission probability? What are the possible evolutionary implications, particularly from the perspective of sexual reproduction (selection)? We tackle these intriguing questions by leveraging the power of Hubbell's unified neutral theory of biodiversity, specifically implemented as the HDP-MSN (hierarchical Dirichlet process approximated multi-site neutral model), which allows for constructing truly multi-site metacommunity models, simultaneously including vaginal and semen microbiomes. By reanalyzing the microbiome datasets of seminal and vaginal fluids from 23 couples both before and after sexual intercourses originally reported by Mändar and colleagues, we found that the microbial transmission between seminal and vaginal fluids is a stochastic, passive diffusion similar to the random walk of particles in physics, rather than driven by deterministic forces. The transmission probability through sexual intercourse seems to be approximately 0.05. Inspired by the results from the HDP-MSN model, we further conjecture that the stochastic drifts of microbiome transmissions during sexual intercourses can be responsible for the homogeneity between semen and vaginal microbiomes first identified in a previous study, which should be helpful for sexual reproduction by facilitating the sperm movement/survival and/or egg fertilization. This inference seems to be consistent with the classic Red Queen hypothesis, which, when extended to the co-evolutionary interactions between humans and their symbiotic microbiomes, would predict that the reproductive system microbiomes should support sexual reproduction.

The study of host-microbiome (co)evolution across levels of selection.

Microorganismal diversity can be explained in large part by selection imposed from both the abiotic and biotic environments, including-in the case of host-associated microbiomes-interactions with eukaryotes. As such, the diversity of host-associated microbiomes can be usefully studied across a variety of scales: within a single host over time, among host genotypes within a population, between populations and among host species. A plethora of recent studies across these scales and across diverse systems are: (i) exemplifying the importance of the host genetics in shaping microbiome composition; (ii) uncovering the role of the microbiome in shaping key host phenotypes; and (iii) highlighting the dynamic nature of the microbiome. They have also raised a critical question: do these complex associations fit within our existing understanding of evolution and coevolution, or do these often intimate and seemingly cross-generational interactions follow novel evolutionary rules from those previously identified? Herein, we describe the known importance of (co)evolution in host-microbiome systems, placing the existing data within extant frameworks that have been developed over decades of study, and ask whether there are unique properties of host-microbiome systems that require a paradigm shift. By examining when and how selection can act on the host and its microbiome as a unit (termed, the holobiont), we find that the existing conceptual framework, which focuses on individuals, as well as interactions among individuals and groups, is generally well suited for understanding (co)evolutionary change in these intimate assemblages. This article is part of the theme issue 'The role of the microbiome in host evolution'.

Sex Bias in Gut Microbiome Transmission in Newly Paired Marmosets (Callithrix jacchus).

Social behavior can alter the microbiome composition via transmission among social partners, but there have been few controlled experimental studies of gut microbiome transmission among social partners in primates. We collected longitudinal fecal samples from eight unrelated male-female pairs of marmoset monkeys prior to pairing and for 8 weeks following pairing. We then sequenced 16S rRNA to characterize the changes in the gut microbiome that resulted from the pairing. Marmoset pairs had a higher similarity in gut microbiome communities after pairing than before pairing. We discovered sex differences in the degrees of change in gut microbiome communities following pairing. Specifically, the gut microbiome communities in males exhibited greater dissimilarity from the prepairing stage (baseline) than the gut microbiome communities in females. Conversely, females showed a gradual stabilization in the rate of the gut microbiome community turnover. Importantly, we found that the male fecal samples harbored more female-source gut microbes after pairing, especially early in pairing (paired test, P < 0.05), possibly linked to sex bias in the frequencies of social behavior. From this controlled study, we report for the first time that pair-living primates undergo significant changes in gut microbiome during pairing and that females transmit more microbes to their partners than males do. The potential biases influencing which microbes are transmitted on the basis of sex and whether they are due to sex biases in other behavioral or physiological features need to be widely investigated in other nonhuman primates and humans in the future.IMPORTANCE In this controlled study, we collected longitudinal fecal samples from 16 male and female marmoset monkeys for 2 weeks prior to and for 8 weeks after pairing in male-female dyads. We report for the first time that marmoset monkeys undergo significant changes to the gut microbiome following pairing and that these changes are sex-biased; i.e., females transmit more microbes to their social partners than males do. Marmosets exhibit pair bonding behavior such as spatial proximity, physical contact, and grooming, and sex biases in these behavioral patterns may contribute to the observed sex bias in social transmission of gut microbiomes.

Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan.

The transgenerational maintenance of symbiotic microbes that benefit host nutrition and health is evolutionarily advantageous. In some vertebrate lineages, coprophagy is used as a strategy for effectively transmitting microbes across generations. However, this strategy has still not been studied in birds. Accordingly, the aim of the present study was to evaluate the role of maternal cecal feces consumption by Japanese rock ptarmigan (Lagopus muta japonica) chicks as a strategy for acquiring essential gut microbes. Both the duration of coprophagy behavior by the chicks and the development process of the chick cecal microbiome (n=20 one- to three-week-old chicks, from three broods) were investigated. In all three broods, coprophagy behavior was only observed from 3 to 18 days of age. Furthermore, there was no significant difference in the number of bacterial operational taxonomic units (OTUs) in 1-week-old chicks (n=651) and adults (n=609), and most of the main OTUs observed in the adults were already present in the 1-week-old chicks. These results indicate that, in this precocial bird species, coprophagy may contribute to the early establishment of cecal bacteria that are essential for food digestion and, thus, chick survival. In fact, Japanese rock ptarmigan chicks consume the same food as their hens from the time of hatching. This behavior may have applications to ex-situ conservation.

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.

The acquisition and development of the infant microbiome are key to establishing a healthy host-microbiome symbiosis. The maternal microbial reservoir is thought to play a crucial role in this process. However, the source and transmission routes of the infant pioneering microbes are poorly understood. To address this, we longitudinally sampled the microbiome of 25 mother-infant pairs across multiple body sites from birth up to 4 months postpartum. Strain-level metagenomic profiling showed a rapid influx of microbes at birth followed by strong selection during the first few days of life. Maternal skin and vaginal strains colonize only transiently, and the infant continues to acquire microbes from distinct maternal sources after birth. Maternal gut strains proved more persistent in the infant gut and ecologically better adapted than those acquired from other sources. Together, these data describe the mother-to-infant microbiome transmission routes that are integral in the development of the infant microbiome.

The Value of a Comparative Approach to Understand the Complex Interplay between Microbiota and Host Immunity.

The eukaryote immune system evolved and continues to evolve within a microbial world, and as such is critically shaped by-and in some cases even reliant upon-the presence of host-associated microbial species. There are clear examples of adaptations that allow the host to simultaneously tolerate and/or promote growth of symbiotic microbiota while protecting itself against pathogens, but the relationship between immunity and the microbiome reaches far beyond simple recognition and includes complex cross talk between host and microbe as well as direct microbiome-mediated protection against pathogens. Here, we present a broad but brief overview of how the microbiome is controlled by and interacts with diverse immune systems, with the goal of identifying questions that can be better addressed by taking a comparative approach across plants and animals and different types of immunity. As two key examples of such an approach, we focus on data examining the importance of early exposure on microbiome tolerance and immune system development and function, and the importance of transmission among hosts in shaping the potential coevolution between, and long-term stability of, host-microbiome associations. Then, by comparing existing evidence across short-lived plants, mouse model systems and humans, and insects, we highlight areas of microbiome research that are strong in some systems and absent in others with the hope of guiding future research that will allow for broad-scale comparisons moving forward. We argue that such an approach will not only help with identification of generalities in host-microbiome-immune interactions but also improve our understanding of the role of the microbiome in host health.