Biology subjects

Debray, R.

Publications and source records attributed to Debray, R..

10 recordsLinked to original sources

bioRxiv2026

Bacterial dispersal and host specificity shape microbiome strain sharing among great ape species in neighboring zoo exhibits

Animal microbiomes often exhibit host-species-specific structure, which could suggest a shared evolutionary history with their hosts. However, in wild populations this possibility has been difficult to disentangle from geographic or ecological barriers to microbial dispersal, particularly in taxa like non-human primates in which phylogeny and geography are closely related. To investigate microbiome transmission and adaptation in a common environment, the gut microbiomes of zoo-housed great apes were profiled longitudinally for four months. Even in a shared environment, phylogenetic structure emerged in both species- and strain-level microbiome composition. Longitudinal tracking of new strain acquisitions revealed that transmission across exhibits was possible, even between distantly related host species, suggesting that phylogenetic structure emerged in the longer term as different strains survived in different hosts. Comparison to metagenomes from humans and wild great apes revealed little evidence that human keepers, researchers, or zoo guests drive transmission between exhibits. Instead, across-exhibit transmission disproportionately involved spore-forming bacterial genera, possibly suggesting airborne spore transmission as a means of bacterial dispersal. By investigating microbiomes of different host species in a common geographic environment without direct inter-host interaction, this study identifies spatial constraints on transmission, bacterial dispersal ability, and differential survival of bacterial strains in different hosts as factors shaping the gut microbiomes of great apes.

evolutionary biology↗

bioRxiv2026

Social microbiome transmission predicts microbial specialization and host lifespan in a wild primate

Social interactions are proposed to provide reliable routes for microbial transmission between animals, facilitating animal-microbiome co-evolution. However, microbiome transmission remains challenging to measure in wild populations. Here we combine behavioral observations of wild baboons with repeated strain-resolved metagenomic profiling to identify individual gut microbial species that follow a dominant mode of social transmission. In an 18-year metagenomic time series from the same population, baboons with higher levels of socially transmitted species lived longer than those with lower levels of socially transmitted species. Socially transmitted species were also more stable and persistent within baboons, yet had narrower host ranges outside of baboons. Thus, social transmission is not only detectable in free-living primates, but may play a special role in both host and microbial fitness.

evolutionary biology↗

bioRxiv2025

Demographic, behavioral, and ecological data from a long-term field study of wild baboons in Amboseli, Kenya

Long-term data sets on individually recognized animals and their environments are critical to understanding animal behavior, evolution, and ecology. However, they are resource- and time-intensive and seldom made publicly available. The Amboseli Baboon Research Project (ABRP) is one of the longest-running studies of a wild mammal population in the world and has collected extensive data on the baboon population of the Amboseli ecosystem in Kenya since 1971. Here, we describe four ABRP data sets newly available to the evolutionary biology, behavioral ecology, and primatology communities: (1) the sizes and demographic compositions of 21 social groups from 1971-2023; (2) the activity budgets of adult females and immatures from 1984-2023; (3) behavioral data on diet for adult females and immatures from 1984-2023; and (4) weather data, including precipitation from 1976-2023 and temperature from 1976-2022. Data are aggregated annually and monthly to enable cross-data set analyses. These data offer a rare longitudinal perspective on behavioral and ecological change in a wild mammal population.

animal behavior and cognition↗

bioRxiv2023

Graduate student mentorship as a target for diversifying the biological sciences

Despite the importance of a diversity of backgrounds and perspectives in biological research, women, racial and ethnic minorities, and students from non-traditional academic backgrounds remain underrepresented in the composition of university faculty. Through a study on doctoral students at a research-intensive university, we pinpoint advising from faculty as a critical component of graduate student experiences and productivity. Graduate students from minority backgrounds reported lower levels of support from their advisors and research groups. However, working with an advisor from a similar demographic background substantially improved productivity and well-being of these students. Several other aspects of mentoring practices positively predicted student success and belonging, including frequent one-on-one meetings, empathetic and constructive feedback, and relationships with other peer or faculty mentors. Our study highlights the need to renovate graduate education with a focus on retention - not just recruitment - to best prepare students for success in scientific careers.

scientific communication and education↗

bioRxiv2023

Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics

1.The microbiome is increasingly receiving attention as an important modulator of host health and disease. However, while numerous mechanisms through which the microbiome influences its host have been identified, there is still a lack of approaches that allow to specifically modulate the abundance of individual microbes or microbial functions of interest. Moreover, current approaches for microbiome manipulation such as fecal transfers often entail a non-specific transfer of entire microbial communities with potentially unwanted side effects. To overcome this limitation, we here propose the concept of precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In a first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we present a metabolic modeling network framework that allows us to define precision prebiotics for a two-member C. elegans microbiome model community comprising the immune-protective Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71. Thus, we predicted compounds that specifically boost the abundance of the host-beneficial MYb11, four of which were experimentally validated in vitro (L-serine, L-threonine, D-mannitol, and {gamma}-aminobutyric acid). L-serine was further assessed in vivo, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that constraint-based metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.

systems biology↗

bioRxiv2022

Within-host adaptation alters priority effects within the phyllosphere microbiome

To predict microbiome composition and function over time, it is essential to understand how evolution alters priority effects between resident and invading species. In an experimental evolution study on tomato plants, an early-colonizing bacterial species rapidly evolved to invade a new niche, altering its ecological interactions with other members of the plant microbiome, as well as its effect on the host. Prevailing models have assumed that adaptation primarily improves the efficiency of resident species within their existing niches, yet we conclude that host habitats can offer alternative evolutionary opportunities, complicating the application of existing theory to the community ecology of microbiomes.

ecology↗

bioRxiv2022

Early phyllosphere microbial associations impact plant reproductive success

O_LIThe above-ground plant microbiome (the phyllosphere) is increasingly recognized as an important component of plant health. We hypothesized that phyllosphere interactions may be disrupted in a greenhouse setting, where microbial dispersal is limited, and that adding a microbial amendment might yield important benefits to the host plant. C_LIO_LIUsing a newly developed synthetic phyllosphere microbiome for Tomato, we tested this hypothesis across multiple trials by manipulating microbial colonization of leaves and measuring subsequent plant growth and reproductive success, comparing results from plants grown in both greenhouse and field settings. C_LIO_LIWe confirmed that greenhouse-grown plants have a depauperate phyllosphere microbiome and that the addition of the synthetic microbial community was responsible for a clear and repeatable increase in fruit production in this setting. We further show that this effect is synergistic with the addition of micronutrient-based soil amendments, with important implications for agriculture. C_LIO_LIThese results suggest that greenhouse environments have poor phyllosphere microbiome establishment, with negative impacts on the plant. The results also implicate the phyllosphere microbiome as a key component of plant fitness, emphasizing that these communities have a clear role to play in the ecology and evolution of plant communities. C_LI

plant biology↗

bioRxiv2022

Historical contingency drives compensatory evolution and rare reversal of phage resistance

Bacteria and lytic viruses (phages) engage in highly dynamic coevolutionary interactions over time, yet we have little idea of how transient selection by phages might shape the future evolutionary trajectories of their host populations. To explore this question, we generated genetically diverse phage-resistant mutants of the bacterium Pseudomonas syringae. We subjected the panel of mutants to prolonged experimental evolution in the absence of phages. Some populations re-evolved phage sensitivity, while others acquired compensatory mutations that reduced the costs of resistance without altering resistance levels. To ask whether these outcomes were driven by the initial genetic mechanisms of resistance, we next evolved independent replicates of each mutant lineage in the absence of phages. We found a strong signature of historical contingency: some mutations were highly reversible across replicate populations, while others were highly entrenched. Through whole-genome sequencing of bacteria over time, we also found that populations with resistance mutations in the same gene acquired more parallel sets of mutations than populations with resistance mutations in different genes, suggesting that compensatory adaptation is also contingent on how resistance initially evolved. Our study identifies an evolutionary ratchet in bacteria-phage coevolution, and may explain previous observations that resistance persists over time in some bacterial populations but is lost in others. We add to a growing body of work describing the key role of phages in the ecological and evolutionary dynamics of their host communities. Beyond this specific trait, our study provides new insight into the genetic architecture of historical contingency, a crucial component of interpreting and predicting evolution.

evolutionary biology↗

bioRxiv2021

Water Stress and Disruption of Mycorrhizae Induce Parallel Shifts in Phyllosphere Microbiome Composition

Water and nutrient limitation are key stressors that affect plant health and ecosystem function. These environmental factors impact both soil- and root-associated microbial communities, and systemically alter plant physiology, but it is less clear how they affect aboveground plant-microbe interactions. Through experimental manipulations in the field and growth chamber, we examined the interacting effects of irrigation, soil fertility, and root mycorrhizal associations on bacterial and fungal communities of the tomato phyllosphere (Solanum lycopersicum). Both water stress and mycorrhizal disruption reduced bacterial richness within plants, homogenized bacterial community diversity among plants, and reduced the relative abundance of dominant fungal taxa. We observed striking parallelism in the individual microbial taxa affected by irrigation and mycorrhizal associations. Given the increasingly understood role of the phyllosphere in shaping plant health and pathogen susceptibility, these results offer an additional mechanism by which belowground conditions shape plant fitness.

ecology↗

bioRxiv2018

Social integration predicts mitochondrial DNA copy number in rhesus macaques

In many social mammals, social adversity predicts compromised health and reduced fitness. These effects are thought to be driven in part by chronic social stress, but their molecular underpinnings are not well understood. Recent work suggests that chronic stress can affect mitochondrial copy number, heteroplasmy rates, and function. Here, we tested the first two possibilities, for the first time in nonhuman primates. We manipulated dominance rank in captive female rhesus macaques (n=45), where low rank induces chronic social stress, and measured mitochondrial DNA copy number and heteroplasmy in five peripheral blood mononuclear cell types from each study subject. We found no effect of dominance rank on either mtDNA copy number or heteroplasmy rates. However, grooming rates, a measure of affiliative social behavior predicted by high social status, was positively associated with mtDNA copy number in B cells, cytotoxic T cells, and monocytes. Our results suggest that social interactions can influence mtDNA regulation in immune cells. Further, they indicate the importance of considering both affiliative and competitive interactions in investigating this relationship.

animal behavior and cognition↗