Structure and Dynamics of the Breast Tissue Microbiomes Under Tumor Influences: An Approach With Neutral, Near-Neutral, and Niche-Neutral Hybrid Models.
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ABSTRACT:
SUBMITTER: Li L
PROVIDER: S-EPMC8326911 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Using 2,733 longitudinal vaginal microbiome samples (representing local microbial communities) from 79 individuals (representing meta-communities) in the states of healthy, BV (bacterial vaginosis) and pregnancy, we assess and interpret the relative importance of stochastic forces (e.g., stochastic drifts in bacteria demography, and stochastic dispersal) vs. deterministic selection (e.g., host genome, and host physiology) in shaping the dynamics of human vaginal microbiome (HVM) diversity by an integrated analysis with multi-site neutral (MSN) and niche-neutral hybrid (NNH) modeling. It was found that, when the traditional "default" P-value = 0.05 was specified, the neutral drifts were predominant (≥50% metacommunities indistinguishable from the MSN prediction), while the niche differentiations were moderate (<20% from the NNH prediction). The study also analyzed two challenging uncertainties in testing the neutral and/or niche-neutral hybrid models, i.e., lack of full model specificity - non-unique fittings of same datasets to multiple models with potentially different mechanistic assumptions - and lack of definite rules for setting the P-value thresholds (also noted as P t -value when referring to the threshold of P-value in this article) in testing null hypothesis (model). Indeed, the two uncertainties can be interdependent, which further complicates the statistical inferences. To deal with the uncertainties, the MSN/NNH test results under a series of P-values ranged from 0.05 to 0.95 were presented. Furthermore, the influence of P-value threshold-setting on the model specificity, and the effects of woman's health status on the neutrality level of HVM were examined. It was found that with the increase of P-value threshold from 0.05 to 0.95, the overlap (non-unique) fitting of MSN and NNH decreased from 29.1 to 1.3%, whereas the specificity (uniquely fitted to data) of MSN model was kept between 55.7 and 82.3%. Also with the rising P-value threshold, the difference between healthy and BV groups become significant. These findings suggested that traditional single P-value threshold (such as the de facto standard P-value = 0.05) might be insufficient for testing the neutral and/or niche neutral hybrid models.
| S-EPMC8417885 | biostudies-literature
Project description:The theoretical description of the forces that shape ecological communities focuses around two classes of models. In niche theory, deterministic interactions between species, individuals, and the environment are considered the dominant factor, whereas in neutral theory, stochastic forces, such as demographic noise, speciation, and immigration, are dominant. Species abundance distributions predicted by the two classes of theory are difficult to distinguish empirically, making it problematic to deduce ecological dynamics from typical measures of diversity and community structure. Here, we show that the fusion of species abundance data with genome-derived measures of evolutionary distance can provide a clear indication of ecological dynamics, capable of quantifying the relative roles played by niche and neutral forces. We apply this technique to six gastrointestinal microbiomes drawn from three different domesticated vertebrates, using high-resolution surveys of microbial species abundance obtained from carefully curated deep 16S rRNA hypervariable tag sequencing data. Although the species abundance patterns are seemingly well fit by the neutral theory of metacommunity assembly, we show that this theory cannot account for the evolutionary patterns in the genomic data; moreover, our analyses strongly suggest that these microbiomes have, in fact, been assembled through processes that involve a significant nonneutral (niche) contribution. Our results demonstrate that high-resolution genomics can remove the ambiguities of process inference inherent in classic ecological measures and permits quantification of the forces shaping complex microbial communities.
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Project description:The human microbiome consists of five major regional biomes distributed in or on our five body sites including skin, oral, lung, gut, and reproductive tract. Its biogeography (the spatial and temporal distribution of its biodiversity) has far-reaching implications to our health and diseases. Nevertheless, we currently have very limited understanding on the mechanisms shaping the biogeography, since it is often rather difficult to determine the relative importance of drift, dispersal, speciation, and selection, the four processes (mechanisms) determining the patterns of microbial biogeography and community dynamics according to a recent synthesis in community ecology and biogeography. To disentangle these mechanisms, I utilize multisite neutral (MSN) model and niche-neutral hybrid (NNH) model to analyze large number of truly multisite microbiome samples covering all five major human microbiome habitats, including 699 metacommunities and 5,420 local communities. Approximately 89% of metacommunities and 92% local communities exhibit patterns indistinguishable from neutral, and 20% indistinguishable from niche-neutral hybrid model, indicating the relative significance of stochastic neutral forces versus deterministic niche selection in shaping the biogeography of human microbiome. These findings cast supporting evidence to van der Gast's revision to classic Bass-Becking doctrine of microbial biogeography: "Some things are everywhere and some things are not. Sometimes the environment selects and sometimes it doesn't," offering the first educated guess for "some" and "sometimes" in the revised doctrine. Furthermore, the logistic/Cox regression models describing the relationships among community neutrality, niche differentiation, and key community/species characteristics (including community diversity, community/species dominance, speciation, and migration rates) were constructed to quantitatively describe the niche-neutral continuum and the influences of community/species properties on the continuum.
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Project description:pH is an important factor that shapes the structure of bacterial communities. However, we have very limited information about the patterns and processes by which overall bacterioplankton communities assemble across wide pH gradients in natural freshwater lakes. Here, we used pyrosequencing to analyze the bacterioplankton communities in 25 discrete freshwater lakes in Denmark with pH levels ranging from 3.8 to 8.8. We found that pH was the key factor impacting lacustrine bacterioplankton community assembly. More acidic lakes imposed stronger environmental filtering, which decreased the richness and evenness of bacterioplankton operational taxonomic units (OTUs) and largely shifted community composition. Although environmental filtering was determined to be the most important determinant of bacterioplankton community assembly, the importance of neutral assembly processes must also be considered, notably in acidic lakes, where the species (OTU) diversity was low. We observed that the strong effect of environmental filtering in more acidic lakes was weakened by the enhanced relative importance of neutral community assembly, and bacterioplankton communities tended to be less phylogenetically clustered in more acidic lakes. In summary, we propose that pH is a major environmental determinant in freshwater lakes, regulating the relative importance and interplay between niche-related and neutral processes and shaping the patterns of freshwater lake bacterioplankton biodiversity.
| S-EPMC4393436 | biostudies-literature
Project description:Two major sources of stochasticity in the dynamics of neutral alleles result from resampling of finite populations (genetic drift) and the random genetic background of nearby selected alleles on which the neutral alleles are found (linked selection). There is now good evidence that linked selection plays an important role in shaping polymorphism levels in a number of species. One of the best-investigated models of linked selection is the recurrent full-sweep model, in which newly arisen selected alleles fix rapidly. However, the bulk of selected alleles that sweep into the population may not be destined for rapid fixation. Here we develop a general model of recurrent selective sweeps in a coalescent framework, one that generalizes the recurrent full-sweep model to the case where selected alleles do not sweep to fixation. We show that in a large population, only the initial rapid increase of a selected allele affects the genealogy at partially linked sites, which under fairly general assumptions are unaffected by the subsequent fate of the selected allele. We also apply the theory to a simple model to investigate the impact of recurrent partial sweeps on levels of neutral diversity and find that for a given reduction in diversity, the impact of recurrent partial sweeps on the frequency spectrum at neutral sites is determined primarily by the frequencies rapidly achieved by the selected alleles. Consequently, recurrent sweeps of selected alleles to low frequencies can have a profound effect on levels of diversity but can leave the frequency spectrum relatively unperturbed. In fact, the limiting coalescent model under a high rate of sweeps to low frequency is identical to the standard neutral model. The general model of selective sweeps we describe goes some way toward providing a more flexible framework to describe genomic patterns of diversity than is currently available.
| S-EPMC3430537 | biostudies-literature
Project description:In this work we propose an index to estimate the gut microbiota biodiversity using a modeling approach with the aim of describing its relationship with health and aging. The gut microbiota, a complex ecosystem that links nutrition and metabolism, has a pervasive effect on all body organs and systems, undergoes profound changes with age and life-style, and substantially contributes to the pathogenesis of age-related diseases. For these reasons, the gut microbiota is a suitable candidate for assessing and quantifying healthy aging, i.e. the capability of individuals to reach an advanced age, avoiding or postponing major age-related diseases. The importance of the gut microbiota in health and aging has been proven to be related not only to its taxonomic composition, but also to its ecological properties, namely its biodiversity. Following an ecological approach, here we intended to characterize the relationship between the gut microbiota biodiversity and healthy aging through the development a parsimonious model of gut microbiota from which biodiversity can be estimated. We analysed publicly available metagenomic data relative to subjects of different ages, countries, nutritional habits and health status and we showed that a hybrid niche-neutral model well describes the observed patterns of bacterial relative abundance. Moreover, starting from such ecological modeling, we derived an estimate of the gut microbiota biodiversity that is consistent with classical indices, while having a higher statistical power. This allowed us to unveil an increase of the gut microbiota biodiversity during aging and to provide a good predictor of health status in old age, dependent on life-style and aging disorders.
| S-EPMC7599046 | biostudies-literature
Project description:That both stochastic neutral and deterministic niche forces are in effect in shaping the community assembly and diversity maintenance is becoming an increasingly important consensus. However, assessing the effects of disease on the balance between the two forces in the human microbiome has not been explored to the best of our knowledge. In this article, we applied a hybrid model to address this issue by analyzing the potential effect of HIV infection on the human gut microbiome and adopted a further step of multimodality testing to improve the interpretation of their model. Our study revealed that although niche process is the dominant force in shaping human gut microbial communities, niche process- and neutral process-driven taxa could coexist in the same microbiome, confirming the notion of their joint responsibility. However, we failed to detect the effect of HIV infection in changing the balance. This suggests that the rule governing community assembly and diversity maintenance may be changed by the disturbance from HIV infection-caused dysbiosis. Although we admit that the general question of disease effect on community assembly and diversity maintenance may still be an open question, our study presents the first piece of evidence to reject the significant influence of diseases.
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Project description:A fundamental challenge in ecology is to understand the mechanisms that govern patterns of relative species abundance. Previous numerical simulations have suggested that complex niche-structured models produce species abundance distributions (SADs) that are qualitatively similar to those of very simple neutral models that ignore differences between species. However, in the absence of an analytical treatment of niche models, one cannot tell whether the two classes of model produce the same patterns via similar or different mechanisms. We present an analytical proof that, in the limit as diversity becomes large, a strong niche model give rises to exactly the same asymptotic form of SAD as the neutral model, and we verify the analytical predictions for a Panamanian tropical forest data set. Our results strongly suggest that neutral processes drive patterns of relative species abundance in high-diversity ecological communities, even when strong niche structure exists. However, neutral theory cannot explain what generates high diversity in the first place, and it may not be valid in low-diversity communities. Our results also confirm that neutral theory cannot be used to infer an absence of niche structure or to explain ecosystem function.
| S-EPMC2936647 | biostudies-literature
Project description:It is estimated that human body is inhabited by approximately 380 trillions of viruses, which exist in the form of viral communities and are collectively termed as human virome. How virome is assembled and what kind of forces maintain the composition and diversity of viral communities is still an open question. The question is of obvious importance because of its implications to human health and diseases. Here we address the question by harnessing the power of Hubbell's unified neutral theory of biodiversity (UNTB) in terms of three neutral models including standard Hubbell's neutral model (HNM), Sloan's near-neutral model (SNM) and Harris et al. (2017) multi-site neutral model (MSN), further augmented by Ning et al. (2019) normalized stochasticity ratio (NSR) and Hammal et al. (2015) power analysis for the neutral test (PNT). With the five models applied to 179 virome samples, we aim to obtain robust findings given both Type-I and Type-II errors are addressed and possible alternative, non-neutral processes are detected. It was found that stochastic neutral drifts seem prevalent: approximately 65-92% at metacommunity/landscape scales and 67-80% at virus species scale. The non-neutral selection is approximately 26-28% at community scale and 23% at species scale. The false negative rate is about 2-3%, which suggested rather limited confounding effects of non-neutral process on neutrality tests. We postulate that prevalence of neutrality in human virome is likely due to extremely simple structure of viruses (stands of DNA/RNA) and their inter-species homogeneities, forming the foundation of species equivalence-the hallmark of neutral theory.
| S-EPMC9065738 | biostudies-literature
Project description:This study investigated the origins and maintenance of biodiversity by integrating ecological and evolutionary mechanisms into a spatially-explicit synthesis between niche-based processes and neutral dynamics (ND). An individual-based model on a two-dimensional grid with periodic boundary conditions was used to compare a niche-neutral continuum induced in contrasting spatial and environmental settings while characterizing the operational scaling of deterministic-stochastic processes. The spatially-explicit simulations revealed three major findings. First, the number of guilds in a system approaches a stationary state and the species composition in a system converges to a dynamic equilibrium of ecologically-equivalent species generated by the speciation-extinction balance. This convergence of species composition can be argued under a point mutation mode of speciation and niche conservatism due to the duality of ND. Second, the dispersal modes of biota may affect how the influence of environmental filtering changes across ecological-evolutionary scales. This influence is greatest in compactly-packed areas within biogeographic units for large-bodied active dispersers, such as fish. Third, the species are filtered along the environmental gradient and the coexistence of ecologically-different species in each local community in a homogeneous environment is allowed by dispersals in a set of local communities. Therefore, the ND among the single-guild species, extinction-colonization trade-off among species of similar environmental optima and different levels of specialization, and mass effect, such as weak species-environment associations, operate simultaneously in patchy habitats. In spatially-explicit synthesis, characterizing where a metacommunity falls along a niche-neutral continuum is too superficial and involves an abstraction that any biological process is probabilistic; therefore, they are dynamic-stochastic processes. The general patterns observed in the simulations allowed a theoretical synthesis of a metacommunity and explained the complex patterns observed in the real world.
| S-EPMC9943931 | biostudies-literature