Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions

Fountain‐Jones, Nicholas M.; Giraud, Tatiana; Zinger, Lucie; Bik, Holly; Creer, Simon; Videvall, Elin

doi:10.1111/mec.17223

Cited by 3 publications

(1 citation statement)

References 144 publications

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“…Our simulations provide continuous data across all generations of the modelled microbiota (Fig. 1 ), something which is rarely available when collecting data empirically (Jones et al 2023 , Fountain-Jones et al 2024 ). Nevertheless, repeated measures of the same individual can provide invaluable insights into drivers of microbial community assembly (e.g.…”

Section: The Importance Of Repeated Samplingmentioning

confidence: 99%

Long-distance movement dynamics shape host microbiome richness and turnover

Pearman,

Duffy,

Gemmell

et al. 2024

FEMS Microbiology Ecology

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Host-associated microbial communities are shaped by host migratory movements. These movements can have contrasting impacts on microbiota, and understanding such patterns can provide insight into the ecological processes that contribute to community diversity. Furthermore, long-distance movements to new environments are anticipated to occur with increasing frequency due to host distribution shifts resulting from climate change. Understanding how hosts transport their microbiota with them could be of importance when examining biological invasions. Although microbial community shifts are well-documented, the underlying mechanisms that lead to the restructuring of these communities remain relatively unexplored. Using literature and ecological simulations, we develop a framework to elucidate the major factors that lead to community change. We group host movements into two types—regular (repeated/cyclical migratory movements, as found in many birds and mammals) and irregular (stochastic/infrequent movements that do not occur on a cyclical basis, as found in many insects and plants). Ecological simulations and prior research suggest that movement type and frequency, alongside environmental exposure (e.g. internal/external microbiota) are key considerations for understanding movement-associated community changes. From our framework, we derive a series of testable hypotheses, and suggest means to test them, to facilitate future research into host movement and microbial community dynamics.

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Section: The Importance Of Repeated Samplingmentioning

confidence: 99%

Long-distance movement dynamics shape host microbiome richness and turnover

Pearman,

Duffy,

Gemmell

et al. 2024

FEMS Microbiology Ecology

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Subtle diurnal microbial rhythms in a large mammalian carnivore

Melville,

Rojas,

Risely

et al. 2024

Journal of Mammalogy

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Mounting evidence suggests that the cyclic interaction between host cells and the gut microbiota orchestrates metabolic and immunological homeostasis throughout the day. Yet, examples of gut microbial rhythms in natural populations are scarce, limiting our understanding of their downstream consequences for host health, particularly in mammals that demonstrate strong co-evolutionary links with their microbiota. Furthermore, disregarding diurnal microbial variation restricts our ability to account and control for them in future studies. Here, we re-analyzed gut microbiota data from a 23-year longitudinal field study of 12 wild adult female spotted hyenas (Crocuta crocuta) in the Masai Mara National Reserve in Kenya to examine whether time of day was correlated with variation in gut microbial composition in this crepuscular–nocturnal carnivore. Overall, we found that gut microbial composition and structure, but not alpha diversity, slightly changed over the course of the day. Differences in microbiota composition between morning and afternoon became particularly apparent when restricting the analysis to the core microbiota (i.e., bacterial genera present in more than 85% of samples). Among the core microbiota, 11 genera—composed largely of the bacterial class Clostridia—varied in abundance with time of day, making this the second study to document gut microbial rhythms in a longitudinally sampled wildlife population. In contrast with the diurnal gut microbial oscillations of wild meerkats, those of hyenas are subtle, yet both species exhibit shifts specifically in the bacterial class Clostridia. This pattern implies that diurnal fluctuations are likely a characteristic of specific, common host-associated bacteria and their amplitude may be a product of host ecology. While our study detected diurnal trends, we encourage studies to employ a temporally denser sampling scheme. In this way, one can overlay short-term oscillations of the microbiome with information on host ecology and clarify consequences for the circadian phenotype of the host.

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The gut microbiota-immune-brain axis in a wild vertebrate: dynamic interactions and health impacts

Pereira,

Hoffamn,

Krüger

et al. 2024

Preprint

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The gut microbiota-immune-brain axis is a feedback network which influences diverse physiological processes and plays a pivotal role in overall health and well-being. Although research in humans and laboratory mice has shed light into the associations and mechanisms governing this communication network, evidence of such interactions in wild, especially in young animals, is lacking. We therefore investigated these interactions during early development in a population of common buzzards (Buteo buteo) and their effects on individual condition. In a longitudinal study, we used a multi-marker approach to establish potential links between the bacterial and eukaryotic gut microbiota, a panel of immune assays and feather corticosterone measurements as a proxy for long-term stress. Using Bayesian structural equation modelling, we found no support for feedback between gut microbial diversity and immune or stress parameters. However, we did find strong relationships in the feedback network. Immunity was negatively correlated with corticosterone levels, and microbial diversity was positively associated with nestling body condition. Furthermore, corticosterone levels and eukaryotic microbiota diversity decreased with age while immune activity increased. The absence of conclusive support for the microbiota-immune-brain axis in common buzzard nestlings, coupled with the evidence for stress mediated immunosuppression, suggests a dominating role of stress-dominated maturation of the immune system during early development. Confounding factors inherent to wild systems and developing animals might override associations known from adult laboratory model subjects. The positive association between microbial diversity and body condition indicates the potential health benefits of possessing a diverse and stable microbiota.

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Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions

Cited by 3 publications

References 144 publications

Long-distance movement dynamics shape host microbiome richness and turnover

Long-distance movement dynamics shape host microbiome richness and turnover

Subtle diurnal microbial rhythms in a large mammalian carnivore

The gut microbiota-immune-brain axis in a wild vertebrate: dynamic interactions and health impacts

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