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17 results for “wild gut microbiome”
Data from: Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population
<p>In humans, gut microbiome (GM) differences are often correlated with, and sometimes causally implicated in, ageing. However, it is unclear how these findings translate in wild animal populations. Studies that investigate how GM dynamics change within individuals, and with declines in physiological condition, are needed to fully understand links between chronological age, senescence, and the GM, but have rarely been done. Here, we use longitudinal data collected from a closed population of Seychelles warblers (<em>Acrocephalus sechellensis</em>) to investigate how bacterial GM alpha diversity, composition, and stability are associated with host senescence. We hypothesised that GM diversity and composition will differ, and become more variable, in older adults, particularly in the terminal year prior to death, as the GM becomes increasingly dysregulated due to senescence. However, GM alpha diversity and composition remained largely invariable with respect to adult age and did not differ in an individual's terminal year. Furthermore, there was no evidence that the GM became more heterogenous in senescent age groups (individuals older than 6 years), or in the terminal year. Instead, environmental variables such as season, territory quality, and time of day, were the strongest predictors of GM variation in adult Seychelles warblers. These results contrast with studies on humans, captive animal populations, and some (but not all) studies on non-human primates, suggesting that GM deterioration may not be a universal hallmark of senescence in wild animal species. Further work is needed to disentangle the factors driving variation in GM-senescence relationships across different host taxa.</p>
Data from: Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population
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Data from: Social and environmental predictors of gut microbiome age in wild baboons
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A time-lagged association between the gut microbiome, nestling weight and nestling survival in wild great tits
<ol> <li>Natal body mass is a key predictor of viability and fitness in many animals. While variation in body mass and therefore viability of juveniles may be explained by genetic and environmental factors, emerging evidence points to the gut microbiota as an important factor influencing host health. The gut microbiota is known to change during development, but it remains unclear whether the microbiome predicts fitness, and if it does, at which developmental stage it affects fitness traits.</li> <li>We collected data on two traits associated with fitness in wild nestling great tits (<i>Parus major</i>): weight and survival to fledging. We characterised the gut microbiome using 16S rRNA sequencing from nestling faeces and investigated temporal associations between the gut microbiome and fitness traits across development at day 8 (D8) and day 15 (D15) post-hatching. We also explored whether particular microbial taxa were 'indicator species' that reflected whether nestlings survived or not.</li> <li>There was no link between mass and microbial diversity on D8 or D15. However, we detected a time-lagged relationship whereby the microbial diversity at D8 was negatively associated with weight at D15, while controlling for weight at D8. Indicator species analysis revealed that while several taxa were unique to birds that either survived or did not survive, there were no universal taxa that were consistently found across all birds within either survival group. This suggests that the presence of particular bacterial taxa may be sufficient, but not necessary for determining future survival, perhaps owing to functional overlap in microbiota.</li> <li>We highlight that measuring microbiome-fitness relationships at just one time point may be misleading, especially early in life. Instead, microbial-host fitness effects should be investigated longitudinally as there may be critical development windows in which key microbiota are established and prime host traits associated with nestling weight. Pinpointing which features of the gut microbial community impact on host fitness, and when during development this occurs, will shed light on population level processes and has the potential to support conservation.</li> </ol>
Data from: Spatiotemporal variation in the gut microbiomes of co-occurring wild rodent species
<p>Mammalian gut microbiomes differ within and among individual hosts. Hosts that occupy a range of environmental conditions may exhibit greater spatiotemporal variation in their microbiome than those constrained as specialists to narrower subsets of resources or habitats. This can occur because widespread host species encounter a variety of ecological conditions that act to diversify their gut microbiomes and/or because generalized host species tend to form large populations that promote sharing and maintenance of diverse microbes. We studied spatiotemporal variation in the gut microbiomes of three co-occurring rodent species across an environmental gradient in a Kenyan savanna. We hypothesized: (<em>i</em>) the taxonomic, phylogenetic, and predicted functional composition of gut microbiomes differ significantly among host species, (<em>ii</em>) microbiome richness increases with population size for all host species, and (<em>iii</em>) host species exhibit different rates of seasonal change in their gut microbiomes, reflecting different sensitivities to environmental change. We evaluated changes in gut microbiome according to species identity, site, and host population density using three years of capture-mark-recapture data and 351 microbiome samples. Host species differed significantly in microbiome composition, though those with<em> </em>the more specialized diets and higher demographic sensitivities showed only slightly greater microbiome variability than those of a widespread dietary generalist. Total microbiome richness in populations of all species increased significantly with population size, but only one of the more specialized species also exhibited greater within-individual microbiome richness with population size. Across co-occurring rodent species with diverse diets and life histories, host population growth in response to rainfall was associated both with strong increases in population-level microbiome richness (sampling effects) and turnover in the relative abundance of bacterial taxa (environmental effects), but there was not consistent change in intra-individual richness (individual variation). Together, our results show that maintenance of large host populations contributes to the maintenance of gut microbiome diversity in wild mammals.</p>
Habitat shapes diversity of gut microbiomes in a wild population of blue tits Cyanistes caeruleus
<p>Microbiome constitutes and important axis of individual variation that, together with genes and the environment, influences an individual's physiology and fitness. Microbiomes are dependent not only on an individual's body condition but also on external factors, such as diet or stress levels, and as such can be involved into feedbacks between the external ecological factors and internal physiology. In our study we used a wild population of blue tits (Cyanistes caeruleus) to investigate the impact of external habitat composition on the microbiome of adult birds. We hypothesized, that – through differences in plant composition, potentially affecting diet complexity – habitat type may impact the diversity and structure of the gut microbiome. Blue tits breeding in dense deciduous forests tended to have more diverse microbiomes, and significantly different in terms of microbiome composition from birds breeding in open, sparsely forested hay meadows. Distinct study plots also tended to differ in a number of parameters describing microbiome diversity. We observed no microbiome differentiation according to individual characteristics such as sex or age. The study emphasizes, that external environment is one of the important modulators of microbiome diversity and calls for more such studies in wild animal populations.</p>
The gut microbiome of wild American marten in the Upper Peninsula of Michigan
<p>Directory Information for The gut microbiome of wild American marten in the Upper Peninsula of Michigan<br> #######</p> <p>"R Code" contains:</p> <p>--- "marten_phyobj.rds" is the phyloseq object that can be directly imported for statistical analysis if the user prefers not to go entire QIIME2 pipeline. The phyloseq object was created from QIIME2 artifacts from the "QIIMEpipe.html" pipeline: the cleaned rooted tree, the cleaned taxonomy table and the cleaned ASV table. <strong>This requires the command "readRDS()" to import. <em>The "load()" command will not work.</em></strong></p> <p><br> --- "Stat.Rmd" Markdown file for "Stat.html"</p> <p>--- "Stat.html" knitted statistical analysis file to view the studies outputs quickly</p> <p>--- "Stat.R" R code if user prefers over Rmarkdown</p> <p>#######</p> <p>"QIIME" contains:<br> --- "martendemux.qza" demultiplexed QIIME2 artifact</p> <p>--- "martendemux.qzv" visualization output of demultiplexed sequence that can be viewed at qiimeview.org</p> <p>--- "MartenMeta.tsv" metadata file for QIIME2 pipeline and statistical analysis</p> <p>--- "QIIMepipe.html" code for bioinformatic pipeline for downstream analysis</p> <p>- "Sequences" folder:<br> --- "R1_demultiplxed_pairedend_marten.fastq.gz" forward reads of demultiplexed, EMP paired end sequences (Illumina Miseq) if the user prefers to use another bioinformatic platform besides QIIME2.</p> <p>--- "R2_demultiplxed_pairedend_marten.fastq.gz" reverse reads of demultiplexed, EMP paired end sequences (Illumina Miseq) if the user prefers to use another bioinformatic platform besides QIIME2.<br> </p>
Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes
<p>Primates acquire gut microbiota from conspecifics through direct social contact and shared environmental exposures. Host behavior is a prominent force in structuring gut microbial communities, yet the extent to which group or individual-level forces shape the long-term dynamics of gut microbiota is poorly understood. We investigated the effects of three aspects of host sociality (social groupings, dyadic interactions, and individual dispersal between groups) on gut microbiome composition and plasticity in 58 wild Verreaux's sifaka (<i>Propithecus verreauxi</i>) from six social groups. Over the course of three dry seasons in a five-year period, the six social groups maintained distinct gut microbial signatures, with the taxonomic composition of individual communities changing in tandem among co-residing group members. Samples collected from group members during each season were more similar than samples collected from single individuals across different years. In addition, new immigrants and individuals with less stable social ties exhibited elevated rates of microbiome turnover across seasons. Our results suggest that permanent social groupings shape the changing composition of commensal and mutualistic gut microbial communities and thus may be important drivers of health and resilience in wild primate populations.</p>
A time-lagged association between the gut microbiome, nestling weight and nestling survival in wild great tits
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Habitat shapes diversity of gut microbiomes in a wild population of blue tits Cyanistes caeruleus
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Data from: Group living and male dispersal predict the core gut microbiome in wild baboons
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Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes
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Data from: Spatiotemporal variation in the gut microbiomes of co-occurring wild rodent species
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Data from: Social networks predict gut microbiome composition in wild baboons
Social relationships have profound effects on health in humans and other primates, but the mechanisms that explain this relationship are not well understood. Using shotgun metagenomic data from wild baboons, we found that social group membership and social network relationships predicted both the taxonomic structure of the gut microbiome and the structure of genes encoded by gut microbial species. Rates of interaction directly explained variation in the gut microbiome, even after controlling for diet, kinship, and shared environments. They therefore strongly implicate direct physical contact among social partners in the transmission of gut microbial species. We identified 51 socially structured taxa, which were significantly enriched for anaerobic and non-spore-forming lifestyles. Our results argue that social interactions are an important determinant of gut microbiome composition in natural animal populations—a relationship with important ramifications for understanding how social relationships influence health, as well as the evolution of group living.
Data from: Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology
The metabolic activities of gut microbes significantly influence host physiology; thus, characterizing the forces that modulate this micro-ecosystem is key to understanding mammalian biology and fitness. To investigate the gut microbiome of wild primates and determine how these microbial communities respond to the host's external environment, we characterized faecal bacterial communities and, for the first time, gut metabolomes of four wild lowland gorilla groups in the Dzanga-Sangha Protected Areas, Central African Republic. Results show that geographical range may be an important modulator of the gut microbiomes and metabolomes of these gorilla groups. Distinctions seemed to relate to feeding behaviour, implying energy harvest through increased fruit consumption or fermentation of highly fibrous foods. These observations were supported by differential abundance of metabolites and bacterial taxa associated with the metabolism of cellulose, phenolics, organic acids, simple sugars, lipids and sterols between gorillas occupying different geographical ranges. Additionally, the gut microbiomes of a gorilla group under increased anthropogenic pressure could always be distinguished from that of all other groups. By characterizing the interplay between environment, behaviour, diet and symbiotic gut microbes, we present an alternative perspective on primate ecology and on the forces that shape the gut microbiomes of wild primates from an evolutionary context.
Data from: Social networks predict gut microbiome composition in wild baboons
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Data from: Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.