Search

Microbial communities are complex and dynamic entities, and their structure arises from the interplay of a multitude of factors, including the interactions of microorganisms with each other and with the environment. Since each extant community has a unique eco-evolutionary history, it might appear that contingency rather than general rules govern their assembly. In spite of this, there is evidence that some general assembly principles exist, at least to a certain extent. In this work, we sought to identify those principles by performing a cross-study, cross-biome meta-analysis of microbial occurrence data in more than 5,000 samples from ten different environmental groups. We adopted a novel algorithm that allows the same taxa to aggregate with different partners in different habitats, capturing the complexity of interactions inherent to natural microbial communities. We tried to decouple function from phylogeny, the environment, and genome size, in order to provide an unbiased characterization of phylogenetic and functional redundancy in environmental microbial assemblages. We then examined the phylogenetic and functional composition of the resulting inferred communities, and searched for global patterns of assembly both at the community level and in individual metabolic pathways.Our analysis of the resulting microbial assemblages highlighted that environmental communities are more functionally redundant than expected by chance. This effect is greater for communities appearing in more than one environment, suggesting a link between functional redundancy and environmental adaptation. In spite of this, certain pathways are observed in fewer taxa than expected by chance, suggesting the presence of auxotrophy, and presumably cooperation among community members, which is supported by our analysis of amino acid biosynthesis pathways. Furthermore, this hypothetical cooperation may play a role in genome reduction, since we observed a negative relationship between the size of bacterial genomes and the number of taxa of the community they belong to.Overall, our results provide a global characterization of environmental microbial communities, and offer design principles for engineering robust bacterial communities.

Particulate organic matter (POM) in the ocean sustains diverse communities of bacteria that mediate the remineralization of organic complex matter. However, the variability of these particles and of the environmental conditions surrounding them present a challenge to the study of the ecological processes shaping particle-associated communities and their function. In this work, we utilize data from experiments in which coastal water communities are grown on synthetic particles to ask which are the most important ecological drivers of their assembly and associated traits. Combining 16S rRNA amplicon sequencing with shotgun metagenomics, together with an analysis of the full genomes of a subset of isolated strains, we were able to identify two-to-three distinct community classes, corresponding to early vs. late colonizers. We show that these classes are shaped by environmental selection (early colonizers) and facilitation (late colonizers) and find distinctive traits associated with each class. While early colonizers have a larger proportion of genes related to the uptake of nutrients, motility, and environmental sensing with few pathways enriched for metabolism, late colonizers devote a higher proportion of genes for metabolism, comprising a wide array of different pathways including the metabolism of carbohydrates, amino acids, and xenobiotics. Analysis of selected pathways suggests the existence of a trophic-chain topology connecting both classes for nitrogen metabolism, potential exchange of branched chain amino acids for late colonizers, and differences in bacterial doubling times throughout the succession. The interpretation of these traits suggests a distinction between early and late colonizers analogous to other classifications found in the literature, and we discuss connections with the classical distinction between r- and K-strategists., Frontiers in Microbiology, 13, ISSN:1664-302X

Particulate organic matter (POM) in the ocean sustains diverse communities of bacteria that mediate the remineralization of organic complex matter. However, the variability of these particles and of the environmental conditions surrounding them present a challenge to the study of the ecological processes shaping particle-associated communities and their function. In this work, we utilize data from experiments in which coastal water communities are grown on synthetic particles to ask which are the most important ecological drivers of their assembly and associated traits. Combining 16S rRNA amplicon sequencing with shotgun metagenomics, together with an analysis of the full genomes of a subset of isolated strains, we were able to identify two-to-three distinct community classes, corresponding to early vs. late colonizers. We show that these classes are shaped by environmental selection (early colonizers) and facilitation (late colonizers) and find distinctive traits associated with each class. While early colonizers have a larger proportion of genes related to the uptake of nutrients, motility, and environmental sensing with few pathways enriched for metabolism, late colonizers devote a higher proportion of genes for metabolism, comprising a wide array of different pathways including the metabolism of carbohydrates, amino acids, and xenobiotics. Analysis of selected pathways suggests the existence of a trophic-chain topology connecting both classes for nitrogen metabolism, potential exchange of branched chain amino acids for late colonizers, and differences in bacterial doubling times throughout the succession. The interpretation of these traits suggests a distinction between early and late colonizers analogous to other classifications found in the literature, and we discuss connections with the classical distinction between r- and K-strategists.

More than 1 billion people live in informal settlements worldwide, where precarious living conditions pose unique challenges to managing a COVID-19 outbreak. Taking Northwest Syria as a case study, we simulated an outbreak in high-density informal Internally Displaced Persons (IDP) camps using a stochastic Susceptible-Exposed-Infectious-Recovered model. Expanding on previous studies, taking social conditions and population health/structure into account, we modelled several interventions feasible in these settings: moderate self-distancing, self-isolation of symptomatic cases and protection of the most vulnerable in 'safety zones'. We considered complementary measures to these interventions that can be implemented autonomously by these communities, such as buffer zones, health checks and carers for isolated individuals, quantifying their impact on the micro-dynamics of disease transmission. All interventions significantly reduce outbreak probability and some of them reduce mortality when an outbreak does occur. Self-distancing reduces mortality by up to 35% if contacts are reduced by 50%. A reduction in mortality by up to 18% can be achieved by providing one self-isolation tent per eight people. Protecting the most vulnerable in a safety zone reduces the outbreak probability in the vulnerable population and has synergistic effects with the other interventions. Our model predicts that a combination of all simulated interventions may reduce mortality by more than 90% and delay an outbreak's peak by almost 2 months. Our results highlight the potential for non-medical interventions to mitigate the effects of the pandemic. Similar measures may be applicable to controlling COVID-19 in other informal settlements, particularly IDP camps in conflict regions, around the world., BMJ Global Health, 6 (8)

Glycerol/diol dehydratases (GDH) are enzymes that catalyse the production of propionate from 1,2-propanediol, and acrolein from glycerol. Acrolein reacts with dietary carcinogenic heterocyclic amines (HCA), reducing HCA mutagenicity, but is itself also an antimicrobial agent and toxicant. Gut microbial GDH activity has been suggested as an endogenous acrolein source; however, there is limited information on the potential of the intestinal microbiota to have GDH activity, and what impact it can have on the intestinal ecosystem and host health. We hypothesized that GDH activity of gut microbiota is determined by the abundance and distribution of GDH-active taxa and can be enhanced by supplementation of the GDH active Anaerobutyricum hallii, and tested this hypothesis combining quantitative profiling of gdh, model batch fermentations, microbiota manipulation, and kinetic modelling of acrolein formation. Our results suggest that GDH activity is a common trait of intestinal microbiota shared by a few taxa, which was dependent on overall gdh abundance. Anaerobutyricum hallii was identified as a key taxon in GDH metabolism, and its supplementation increased the rate of GDH activity and acrolein release, which enhanced the transformation of HCA and reduced fermentation activity. The findings of this first systematic study on acrolein release by intestinal microbiota indicate that dietary and microbial modulation might impact GDH activity, which may influence host health.

Freshwater ecosystems are considered hotspots of biodiversity in Antarctic polar deserts. Anticipated warming is expected to change the hydrology of these systems due to increased meltwater and reduction of ice cover, with implications for environmental conditions and physical connectivity between habitats. Using 16S rRNA gene sequencing, we evaluated microbial mat and planktonic communities within a connected freshwater system in the McMurdo Wright Valley, Antarctica, to determine the roles of connectivity and habitat conditions in controlling microbial assemblage composition. We examined communities from glacial Lake Brownworth, the perennially ice-covered Lake Vanda and the Onyx River, which connects the two. In Lake Vanda, we found distinct microbial assemblages occupying sub-habitats at different lake depths, while the communities from Lake Brownworth and Onyx River were structurally similar. Despite the higher physical connectivity and dispersal opportunities between bacterial communities in the shallow parts of the system, environmental abiotic conditions dominated over dispersal in driving community structure. Functional metabolic pathway predictions suggested differences in the functional gene potential between the microbial mat communities located in shallower and deeper water depths. The findings suggest that increasing temperatures and meltwater due to future climate change will affect bacterial diversity and functioning in Antarctic freshwater ecosystems.

Freshwater ecosystems are considered hotspots of biodiversity in Antarctic polar deserts. Anticipated warming is expected to change the hydrology of these systems due to increased meltwater and reduction of ice cover, with implications for environmental conditions and physical connectivity between habitats. Using 16S rRNA sequencing, we evaluated the structure of microbial mat and planktonic communities within a connected watershed in the McMurdo Wright Valley, Antarctica to determine the roles of connectivity and habitat conditions in controlling microbial assemblage composition. We examined benthic and planktonic samples from glacial Lake Brownworth, the perennially ice-covered Lake Vanda, and the Onyx River, which connects the two. In Lake Vanda, we found distinct microbial assemblages occupying sub-habitats at different lake depths, while the communities from Lake Brownworth and Onyx River were structurally similar between them. Despite the higher connectivity between bacterial communities in the shallow parts of the system, environmental filtering dominated over dispersal in driving bacterial community structure. Functional metagenomics predictions identified genes related to degradation of halogenated aromatic compounds in surface microbial mats exposed to changes in water regimes, which progressively disappeared with increasing depth. Shifting environmental conditions due to increasing connectivity, rather than dispersal, may become the dominant drivers of bacterial diversity and functioning in Antarctic freshwater ecosystems.

Recent theory and experiments have reported a reproducible tendency for the coexistence of microbial species under controlled environmental conditions. This observation has been explained in the context of competition for resources and metabolic complementarity given that, in microbial communities (MCs), many excreted by-products of metabolism may also be resources. MCs therefore play a key role in promoting their own stability and in shaping the niches of the constituent taxa. We suggest that an intermediate level of organization between the species and the community level may be pervasive, where tightly knit metabolic interactions create discrete consortia that are stably maintained. We call these units Metabolically Cohesive Consortia (MeCoCos) and we discuss the environmental context in which we expect their formation, and the ecological and evolutionary consequences of their existence. We argue that the ability to identify MeCoCos would open new avenues to link the species-, community- and ecosystem-level properties, with consequences for our understanding of microbial ecology and evolution, and an improved ability to predict ecosystem functioning in the wild. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

A central goal in microbial ecology is to simplify the extraordinary biodiversity that inhabits natural environments into ecologically coherent units. We profiled (16S rRNA sequencing) > 700 semi-aquatic bacterial communities while measuring their functional capacity when grown in laboratory conditions. This approach allowed us to investigate the relationship between composition and function excluding confounding environmental factors. Simulated data allowed us to reject the hypothesis that stochastic processes were responsible for community assembly, suggesting that niche effects prevailed. Consistent with this idea we identified six distinct community classes that contained samples collected from distant locations. Structural equation models showed there was a functional signature associated with each community class. We obtained a more mechanistic understanding of the classes using metagenomic predictions (PiCRUST). This approach allowed us to show that the classes contained distinct genetic repertoires reflecting community-level ecological strategies. The ecological strategies resemble the classical distinction between r- and K-strategists, suggesting that bacterial community assembly may be explained by simple ecological mechanisms., Nature Communications, 11 (1), ISSN:2041-1723

Recent theory and experiments have reported a reproducible tendency for the coexistence of microbial species under controlled environmental conditions. This observation has been explained in the context of competition for resources and metabolic complementarity given that, in microbial communities, many excreted by-products of metabolism may also be resources. Microbial communities therefore play a key role in promoting their own stability and in shaping the niches of the constituent taxa. We suggest that an intermediate level of organisation between the species and the community level may be pervasive, where tightly-knit metabolic interactions create discrete consortia that are stably maintained. We call these units Metabolically Cohesive Consortia (MeCoCos) and we discuss the environmental context in which we expect their formation, and the ecological and evolutionary consequences of their existence. We argue that the ability to identify MeCoCos would open new avenues to link the species-, community-, and ecosystem-level properties, with consequences for our understanding of microbial ecology and evolution, and an improved ability to predict ecosystem functioning in the wild.

Complex networks have been useful to link experimental data with mechanistic models, and have become widely used across many scientific disciplines. Recently, the increasing amount and complexity of data, particularly in biology, has prompted the development of multidimensional networks, where dimensions reflect the multiple qualitative properties of nodes, links, or both. As a consequence, traditional quantities computed in single dimensional networks should be adapted to incorporate this new information. A particularly important problem is the detection of communities, namely sets of nodes sharing certain properties, which reduces the complexity of the networks, hence facilitating its interpretation.In this work, we propose an operative definition of “function” for the nodes in multidimensional networks, and we exploit this definition to show that it is possible to detect two types of communities: i) modules, which are communities more densely connected within their members than with nodes belonging to other communities, and ii) guilds, which are sets of nodes connected with the same neighbours, even if they are not connected themselves. We provide two quantities to optimally detect both types of communities, whose relative values reflect their importance in the network.The flexibility of the method allowed us to analyze different ecological examples encompassing mutualistic, trophic and microbial networks. We showed that by considering both metrics we were able to obtain deeper ecological insights about how these different ecological communities were structured. The method mapped pools of species with properties that were known in advance, such as plants and pollinators. Other types of communities found, when contrasted with external data, turned out to be ecologically meaningful, allowing us to identify species with important functional roles or the influence of environmental variables. Furthermore, we found the method was sensitive to community-level topological properties like the nestedness.In ecology there is often a need to identify groupings including trophic levels, guilds, functional groups, or ecotypes.The method is therefore important in providing an objective means of distinguishing modules and guilds. The method we developed, functionInk (functional linkage), is computationally efficient at handling large multidimensional networks since it does not require optimization procedures or tests of robustness. The method is available at: HTTPS://GITHUB.COM/APASCUALGARCIA/FUNCTIONINK.

Understanding the principles that govern the assembly of microbial communities across earth's biomes is a major challenge in modern microbial ecology. This pursuit is complicated by the difficulties of mapping functional roles and interactions onto communities with immense taxonomic diversity and of identifying the scale at which microbes interact [1]. To address this challenge, here, we focused on the bacterial communities that colonize and degrade particulate organic matter in the ocean [2–4]. We show that the assembly of these communities can be simplified as a linear combination of functional modules. Using synthetic polysaccharide particles immersed in natural bacterioplankton assemblages [1, 5], we showed that successional particle colonization dynamics are driven by the interaction of two types of modules: a first type made of narrowly specialized primary degraders, whose dynamics are controlled by particle polysaccharide composition, and a second type containing substrate-independent taxa whose dynamics are controlled by interspecific interactions—in particular, cross-feeding via organic acids, amino acids, and other metabolic byproducts. We show that, as a consequence of this trophic structure, communities can assemble modularly—i.e., by a simple sum of substrate-specific primary degrader modules, one for each complex polysaccharide in the particle, connected to a single broad-niche range consumer module. Consistent with this model, a linear combination of the communities on single-polysaccharide particles accurately predicts community composition on mixed-polysaccharide particles. Our results suggest that the assembly of heterotrophic communities that degrade complex organic materials follows simple design principles that could be exploited to engineer heterotrophic microbiomes. Enke et al. show that particle-attached marine microbial communities assemble by recruiting functional groups of taxa in an additive manner. Specialist groups degrade specific polysaccharides, whereas generalist byproduct utilizers invade independently of particle substrate. This simple organization allows prediction of community structure., Simons Foundation. Simons Early Career Award (410104), Alfred P. Sloan Foundation. Fellowship (FG-20166236), National Science Foundation (U.S.) (Grant OCE-1658451), Simons Collaboration: Principles of Microbial Ecosystems (PriME) (Award 542395)

We investigate the stability of Lotka-Volterra (LV) models constituted by two groups of species such as plants and animals in terms of the intragroup effective competition matrix, which allows separating the equilibrium equations of the two groups. In matrix analysis, the effective competition matrix represents the Schur complement of the species interaction matrix. It has been previously shown that the main eigenvalue of this effective competition matrix strongly influences the structural stability of the model ecosystem. Here, we show that the spectral properties of the effective competition matrix also strongly influence the dynamical stability of the model ecosystem. In particular, a necessary condition for diagonal stability of the full system, which guarantees global stability, is that the effective competition matrix is diagonally stable, which means that intergroup interactions must be weaker than intra-group competition in appropriate units. For mutualistic or competitive interactions, diagonal stability of the effective competition is a sufficient condition for global stability if the inter-group interactions are suitably correlated, in the sense that the biomass that each species provides to (removes from) the other group must be proportional to the biomass that it receives from (is removed by) it. For a non-LV mutualistic system with saturating interactions, we show that the diagonal stability of the corresponding LV system close to the fixed point is a sufficient condition for global stability.

During the past years, an increasing number of research funders and governments have been supporting Open Access (OA) publishing. In the USA, the Fair Access to Science and Technology Research Act and the Public Access to Public Science Act require that results from research supported with public funding are made freely accessible [1]. The EU has also decided that all publications funded by Horizon 2020 should be freely available [2]. Most authors who publish their work as OA—whether mandated or not—usually choose Gold OA, in which the cost of publishing is covered by the authors (Fig 1). Figure 1. The current conflicts of interest could be alleviated through a new publishing system Simplified schematic representation of conflicts of interest in Gold OA publishing (left) and how they can be alleviated (right). Accessibility to services and scientific outcomes is illustrated with locks and may be free (open) or subjected to fees (closed). However, Gold OA has some drawbacks. Most importantly, it creates a conflict of interest: in a situation where the number of scientists is larger than the number of available positions, both journals and scientists benefit from publishing as many articles as possible [3]. This is a fertile ground for cheaters on both sides, and helps to explain the emergence of predatory journals [4] and the increasing number of cases of scientific misconduct [5]. An alternative to Gold OA is Green OA, by which authors self‐archive their articles in online repositories [6]. However, the fact that Green OA lacks peer review discourages many scientists from self‐archiving their papers. In addition, journals offer …

The molecular clock hypothesis, which states that substitutions accumulate in protein sequences at a constant rate, plays a fundamental role in molecular evolution but it is violated when selective or mutational processes vary with time. Such violations of the molecular clock have been widely investigated for protein sequences, but not yet for protein structures. Here, we introduce a novel statistical test (Significant Clock Violations) and perform a large scale assessment of the molecular clock in the evolution of both protein sequences and structures in three large superfamilies. After validating our method with computer simulations, we find that clock violations are generally consistent in sequence and structure evolution, but they tend to be larger and more significant in structure evolution. Moreover, changes of function assessed through Gene Ontology and InterPro terms are associated with large and significant clock violations in structure evolution. We found that almost one third of significant clock violations are significant in structure evolution but not in sequence evolution, highlighting the advantage to use structure information for assessing accelerated evolution and gathering hints of positive selection. Clock violations between closely related pairs are frequently significant in sequence evolution, consistent with the observed time dependence of the substitution rate attributed to segregation of neutral and slightly deleterious polymorphisms, but not in structure evolution, suggesting that these substitutions do not affect protein structure although they may affect stability. These results are consistent with the view that natural selection, both negative and positive, constrains more strongly protein structures than protein sequences. Our code for computing clock violations is freely available at https://github.com/ugobas/Molecular_clock.

We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding. In our experience, developed at a Master’s course at the Universidad Autónoma de Madrid (Spain), the concreteness of this example helps to overcome difficulties caused by the interdisciplinary nature of this field and its high level of abstraction, in particular for students coming from traditional disciplines. The puzzle will allow us discussing a simple algorithm for finding folded solutions, through which we will introduce the concept of the configuration space and the contact matrix representation. This is a central tool for comparing protein structures, for studying simple models of protein energetics, and even for a qualitative discussion of folding kinetics, through the concept of the Contact Order. It also allows a simple representation of misfolded conformations and their free energy. These concepts will motivate evolutionary questions, which we will address by simulating a structurally constrained model of protein evolution, again modelled on the snake puzzle. In this way, we can discuss the analogy between evolutionary concepts and statistical mechanics that facilitates the understanding of both concepts. The proposed examples and literature are accessible, and we provide supplementary material (see ‘Data Availability’) to reproduce the numerical experiments. We also suggest possible directions to expand the unit. We hope that this work will further stimulate the adoption of games in teaching practice.

Here we present a project aiming to provide specialized educational bibliography on Bioinformatics for Spanish speakers. The idea of writing a book in Spanish language covering the most important topics in the field of Bioinformatics was born in the XIth Spanish Symposium on Bioinformatics in Barcelona two years ago. Different scientists have been involved in the project, from senior scientists to PhD students from different countries. The book intends to be the beginning of an open project, where all the chapters are susceptible of being updated and new topics can be incorporated in future versions. Current book version can be accessed online at http://goo.gl/UYG0o7.

Here we study the properties and the evolution of proteins that constitute the Centrosome, the complex molecular assembly that regulates the division and differentiation of animal cells. We found that centrosomal proteins are predicted to be significantly enriched in disordered and coiled-coil regions, more phosphorylated and longer than control proteins of the same organism. Interestingly, the ratio of these properties in centrosomal and control proteins tends to increase with the number of cell-types. We reconstructed indels evolution, finding that indels significantly increase disorder in both centrosomal and control proteins, at a rate that is typically larger along branches associated with a large growth in cell-types number, and larger for centrosomal than for control proteins. Substitutions show a similar trend for coiled-coil, but they contribute less to the evolution of disorder. Our results suggest that the increase in cell-types number in animal evolution is correlated with the gain of disordered and coiled-coil regions in centrosomal proteins, establishing a connection between organism and molecular complexity. We argue that the structural plasticity conferred to the Centrosome by disordered regions and phosphorylation plays an important role in its mechanical properties and its regulation in space and time., This work was supported from the Spanish Science and Innovation Ministry through the Consolider grant CSD2006-00023, the grant BIO2008-04384, the Ramo´n y Cajal program (UB) and the FPI grant BES- 2009-013072 to APG. Research at the CBMSO is facilitated by the Fundacio´n Ramon Areces.

The molecular clock hypothesis, stating that protein sequences diverge in evolution by accumulating amino acid substitutions at an almost constant rate, played a major role in the development of molecular evolution and boosted quantitative theories of evolutionary change. These studies were extended to protein structures by the seminal paper by Chothia and Lesk, which established the approximate proportionality between structure and sequence divergence. Here we analyse how function influences the relationship between sequence and structure divergence, studying four large superfamilies of evolutionarily related proteins: globins, aldolases, P-loop and NADP-binding. We introduce the contact divergence, which is more consistent with sequence divergence than previously used structure divergence measures. Our main findings are: (1) Small structure and sequence divergences are proportional, consistent with the molecular clock. Approximate validity of the clock is also supported by the analysis of the clustering coefficient of structure similarity networks. (2) Functional constraints strongly limit the structure divergence of proteins performing the same function and may allow to identify incomplete or wrong functional annotations. (3) The rate of structure versus sequence divergence is larger for proteins performing different functions than for proteins performing the same function. We conjecture that this acceleration is due to positive selection for new functions. Accelerations in structure divergence are also suggested by the analysis of the clustering coefficient. (4) For low sequence identity, structural diversity explodes. We conjecture that this explosion is related to functional diversification. (5) Large indels are almost always associated with function changes., Ramón y Cajal (BIO2008-04384); Spanish Ministery of Science and Innovation (CSD200623)

The main theories of biodiversity either neglect species interactions or assume that species interact randomly with each other. However, recent empirical work has revealed that ecological networks are highly structured, and the lack of a theory that takes into account the structure of interactions precludes further assessment of the implications of such network patterns for biodiversity. Here we use a combination of analytical and empirical approaches to quantify the influence of network architecture on the number of coexisting species. As a case study we consider mutualistic networks between plants and their animal pollinators or seed dispersers. These networks have been found to be highly nested, with the more specialist species interacting only with proper subsets of the species that interact with the more generalist. We show that nestedness reduces effective interspecific competition and enhances the number of coexisting species. Furthermore, we show that a nested network will naturally emerge if new species are more likely to enter the community where they have minimal competitive load. Nested networks seem to occur in many biological and social contexts, suggesting that our results are relevant in a wide range of fields.

In spite of its major impact on life-long health, the process of microbial succession in the gut of infants remains poorly understood. Here, we analyze the patterns of taxonomic and functional change in the gut microbiota during the first year of life for a birth cohort of 13 infants. We detect that individual instances of gut colonization vary in the temporal dynamics of microbiota richness, diversity, and composition at both functional and taxonomic levels. Nevertheless, trends discernible in a majority of infants indicate that gut colonization occurs in two distinct phases of succession, separated by the introduction of solid foods to the diet. This change in resource availability causes a sharp decrease in the taxonomic richness of the microbiota due to the loss of rare taxa (p = 2.06e-9), although the number of core genera shared by all infants increases substantially. Moreover, although the gut microbial succession is not strictly deterministic, we detect an overarching directionality of change through time towards the taxonomic and functional composition of the maternal microbiota. Succession is however not complete by the one year mark, as significant differences remain between one-year-olds and their mothers in terms of taxonomic (p = 0.009) and functional (p = 0.004) microbiota composition, and in taxonomic richness (p = 2.76e-37) and diversity (p = 0.016). Our results also indicate that the taxonomic composition of the microbiota shapes its functional capacities. Therefore, the observed inter-individual variability in taxonomic composition during succession is not fully compensated by functional equivalence among bacterial genera and may have important physiological consequences. Finally, network analyses suggest that positive interactions among core genera during community assembly contribute to ensure their permanence within the gut, and highlight an expansion of complexity in the interactions network as the core of taxa shared by all infants grows following the introduction of solid foods. © 2014 Vallès et al., This work has been supported by the Spanish MICINN (project SAF2009-13032-C02-02 and project CSD2009-00006 of the CONSOLIDER program). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

[Background] Since the landmark Santa Rosalia paper by Hutchinson, niche theory addresses the determinants of biodiversity in terms of both environmental and biological aspects. Disentangling the role of habitat filtering and interactions with other species is critical for understanding microbial ecology. Macroscopic biogeography explores hypothetical ecological interactions through the analysis of species associations. These methods have started to be incorporated into microbial ecology relatively recently, due to the inherent experimental difficulties and the coarse grained nature of the data., [Results] Here we investigate the influence of environmental preferences and ecological interactions in the tendency of bacterial taxa to either aggregate or segregate, using a comprehensive dataset of bacterial taxa observed in a wide variety of environments. We assess significance of taxa associations through a null model that takes into account habitat preferences and the global distribution of taxa across samples. The analysis of these associations reveals a surprisingly large number of significant aggregations between taxa, with a marked community structure and a strong propensity to aggregate for cosmopolitan taxa. Due to the coarse grained nature of our data we cannot conclusively reject the hypothesis that many of these aggregations are due to environmental preferences that the null model fails to reproduce. Nevertheless, some observations are better explained by ecological interactions than by habitat filtering. In particular, most pairs of aggregating taxa co-occur in very different environments, which makes it unlikely that these associations are due to habitat preferences, and many are formed by cosmopolitan taxa without well defined habitat preferences. Moreover, known cooperative interactions are retrieved as aggregating pairs of taxa. As observed in similar studies, we also found that phylogenetically related taxa are much more prone to aggregate than to segregate, an observation that may play a role in bacterial speciation., [Conclusions] We hope that these results stimulate experimental verification of the putative cooperative interactions between cosmopolitan bacteria, and we suggest several groups of aggregated cosmopolitan bacteria that are interesting candidates for such an investigation., This work was supported by the Spanish Ministry of Economy and Competitiveness (FPI grant BES-2009-013072 to APG and grants BFU2011-24595 and BFU2012-40020 to UB) and by the Comunidad de Madrid (Amarauto program to UB). Research at the CBMSO is facilitated by the Fundación Ramón Areces. We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 17-04-2015, In this thesis we analyse emergent patterns in complex biological systems. We say that these patterns emerge, given that they result from behaviours of the system that are di cult to explain starting from a microscopic description. These behaviours are strongly dependent on the interactions between elements, and thus our research focuses on the identi cation and evaluation of interaction networks. In particular, we have analysed interactions that may re ect the response of the system to long term conditions, whose analysis may be compatible with an evolutionary interpretation. The methodological and conceptual framework needed for the development of our research is complex. This is the reason why the rst part of the thesis is devoted to clarify the epistemological approximation we have followed. In subsequent chapters, we present our research results, which have been developed around three systems with notable di erences among them. The rst system considers a representative subset of all the protein structures known up to date. We develop a method that objectively demonstrates the existence of structural protein classes known as folds, de ning conserved interaction patterns between amino-acids. We go deeper into the evolutionary interpretation of this result investigating the role of protein function in the structural conservation and divergence. Second, we analyse high-throughput sequencing experiments collecting the presence of bacterial taxa in di erent environments. From this data we infer aggregation and segregation patterns suggesting that bacterial mutualistic interactions are very relevant, and whose functional role is explored in more detail analysing the bacterial assembly process in a group of infants during their development. Last, we have considered mutualistic communities of plants and pollinators. We predict the structural stability of this system de ning two magnitudes: the e ective interspeci c competition and the propagation of perturbations. These magnitudes rationalize the relative e ect of competition versus mutualism and, in particular, of the di erent mutualistic networks in the structural stability, which we show has a main role for sustaining biodiversity, En esta tesis analizamos patrones emergentes en sistemas biológicos complejos. Estos patrones los cali camos como emergentes porque son el resultado de comportamientos del sistema difíciles de caracterizar partiendo de una descripción microscópica. Dichos comportamientos son fuertemente dependientes de las interacciones entre elementos, por lo que nos centramos en la identi cación y evaluación de redes de interacción. En particular, hemos analizado interacciones que esperamos que re ejen la respuesta del sistema a condiciones relevantes en escalas de tiempo largas, cuyo análisis puede ser compatible con una interpretación evolutiva. El marco metodológico y conceptual necesario para el desarrollo de nuestra investigación es complejo. Por ello, la primera parte de la tesis está orientada a clari car la aproximación epistemológica que hemos seguido. En los siguientes capítulos presentamos el resultado de nuestra investigación, desarrollada alrededor de tres sistemas con notables diferencias entre ellos. El primer sistema considera un conjunto representativo de todas las estructuras de proteínas conocidas hasta la fecha. Desarrollamos un método que demuestra objetivamente la existencia de clases estructurales de proteí- nas conocidas como folds, que de nen patrones de interacción entre aminoácidos. Profundizamos en la interpretación evolutiva del resultado investigando el rol de la función de proteínas en la conservación o divergencia estructural. En segunda lugar analizamos experimentos de secuenciación masiva que recogen la presencia de taxones bacterianos en distintos ambientes. De estos datos inferimos patrones de agregación y segregación que sugieren que las interacciones mutualistas entre bacterias son muy relevantes, y cuyo rol funcional es explorado en más detalle analizando el proceso de ensamblaje bacteriano en un grupo de bebés durante su desarrollo. Por último, hemos considerado comunidades mutualistas de plantas y polinizadores. Predecimos la estabilidad estructural de este sistema de niendo dos magnitudes: la competición efectiva interespecí ca y la propagación de las perturbaciones. Estas magnitudes permiten racionalizar el efecto relativo de la competición versus el mutualismo y, en particular, de las distintas redes mutualistas en la estabilidad estructural, cuyo papel mostramos que es esencial en el sostenimiento de la biodiversidad