A conceptual framework for the phylogenetically constrained assembly of microbial communities

Microbial communities play essential and preponderant roles in all ecosystems. Understanding the rules that govern microbial community assembly will have a major impact on our ability to manage microbial ecosystems, positively impacting, for instance, human health and agriculture. Here, I present a phylogenetically constrained community assembly principle grounded on the well-supported facts that deterministic processes have a significant impact on microbial community assembly, that microbial communities show significant phylogenetic signal, and that microbial traits and ecological coherence are, to some extent, phylogenetically conserved. From these facts, I derive a few predictions which form the basis of the framework. Chief among them is the existence, within most microbial ecosystems, of phylogenetic core groups (PCGs), defined as discrete portions of the phylogeny of varying depth present in all instances of the given ecosystem, and related to specific niches whose occupancy requires a specific phylogenetically conserved set of traits. The predictions are supported by the recent literature, as well as by dedicated analyses. Integrating the effect of ecosystem patchiness, microbial social interactions, and scale sampling pitfalls takes us to a comprehensive community assembly model that recapitulates the characteristics most commonly observed in microbial communities. PCGs' identification is relatively straightforward using high-throughput 16S amplicon sequencing, and subsequent bioinformatic analysis of their phylogeny, estimated core pan-genome, and intra-group co-occurrence should provide valuable information on their ecophysiology and niche characteristics. Such a priori information for a significant portion of the community could be used to prime complementing analyses, boosting their usefulness. Thus, the use of the proposed framework could represent a leap forward in our understanding of microbial community assembly and functionThis work was funded by the Spanish Ministry of Science and Innovation grant BIO2016-80101-

A comprehensive human minimal gut metagenome extends the host’s metabolic potential

Accumulating evidence suggests that humans could be considered as holobionts in which the gut microbiota play essential functions. Initial metagenomic studies reported a pattern of shared genes in the gut microbiome of different individuals, leading to the definition of the minimal gut metagenome as the set of microbial genes necessary for homeostasis and present in all healthy individuals. This study analyses the minimal gut metagenome of the most comprehensive dataset available, including individuals from agriculturalist and industrialist societies, also embodying highly diverse ethnic and geographical backgrounds. The outcome, based on metagenomic predictions for community composition data, resulted in a minimal metagenome comprising 3412 genes, mapping to 1856 reactions and 128 metabolic pathways predicted to occur across all individuals. These results were substantiated by the analysis of two additional datasets describing the microbial community compositions of larger Western cohorts, as well as a substantial shotgun metagenomics dataset. Subsequent analyses showed the plausible metabolic complementarity provided by the minimal gut metagenome to the human genomeThis work was funded by the Spanish Ministry of Science and Innovation, grant numbers BIO2016-80101-R and PID2019-108797RB-I0

Considering external information to improve the phylogenetic comparison of microbial communities: A new approach based on constrained Double Principal Coordinates Analysis (cDPCoA)

© 2014 John Wiley & Sons Ltd. The use of next-generation sequencing technologies is revolutionizing microbial ecology by allowing a deep phylogenetic coverage of tens to thousands of samples simultaneously. Double Principal Coordinates Analysis (DPCoA) is a multivariate method, developed in community ecology, able to integrate a distance matrix describing differences among species (e.g. phylogenetic distances) in the analysis of a species abundance matrix. This ordination technique has been used recently to describe microbial communities taking into account phylogenetic relatedness. In this work, we extend DPCoA to integrate the information of external variables measured on communities. The constrained Double Principal Coordinates Analysis (cDPCoA) is able to enforce a priori classifications to retrieve subtle differences and (or) remove the effect of confounding factors. We describe the main principles of this new approach and demonstrate its usefulness by providing application examples based on published 16S rRNA gene data sets.Peer Reviewe

Composition and interactions among bacterial, microeukaryotic, and T4-like viral assemblages in lakes from both polar zones

In this study we assess global biogeography and correlation patterns among three components of microbial life: bacteria, microeukaryotes, and T4-like myoviruses. In addition to environmental and biogeographical considerations, we have focused our study on samples from high-latitude pristine lakes from both poles, since these simple island-like ecosystems represent ideal ecological models to probe the relationships among microbial components and with the environment. Bacterial assemblages were dominated by members of the same groups found to dominate freshwater ecosystems elsewhere, and microeukaryotic assemblages were dominated by photosynthetic microalgae. Despite inter-lake variations in community composition, the overall percentages of OTUs shared among sites was remarkable, indicating that many microeukaryotic, bacterial, and viral OTUs are globally-distributed. We observed an intriguing negative correlation between bacterial and microeukaryotic diversity values. Notably, our analyses show significant global correlations between bacterial and microeukaryotic community structures, and between the phylogenetic compositions of bacterial and T4-like virus assemblages. Overall, environmental filtering emerged as the main factor driving community structures

Ecosystem function decays by fungal outbreaks in Antarctic microbial mats

Antarctica harbours a remarkably diverse range of freshwater bodies and terrestrial ecosystems, where microbial mats are considered the most important systems in terms of biomass and metabolic capabilities. We describe the presence of lysis plaque-like macroscopic blighted patches within the predominant microbial mats on Livingston Island (Antarctic Peninsula). Those blighting circles are associated with decay in physiological traits as well as nitrogen depletion and changes in the spatial microstructure; these alterations were likely related to disruption of the biogeochemical gradients within the microbial ecosystem caused by an unusually high fungal abundance and consequent physical alterations. This phenomenon has been evidenced at a time of unprecedented rates of local warming in the Antarctic Peninsula area, and decay of these ecosystems is potentially stimulated by warmer temperaturesWe thank the LIMNOPOLAR team members for their assistance in collecting samples and the UTM and Las Palmas Navy crew for logistical support. We are grateful to Warwick F. Vincent for comments that improved the final manuscript. This study was supported by grants CGL2005–06549-CO2-1, POL2006–06635 and CTM2011– 28736 to A.Q. CTM2008–05134-E/ANT and CTM2009–08644-E to A.A., and CTM2012–38222-C02–02 to A.dR. D.V. was supported by the Spanish Ministry of Science and Innovation grant BES-2006–14027, A.LB. by the Ramón y Cajal contract RYC-2010–06300, and D.AdC. by the Marie Curie IIF grant PIIF-GA-2012-328287. In memoriam: We are grateful to Fernando Pinto for technical assistance with LTSE

Estudio de los efectos causados por la introducción de sistemas de rizorremediación en las poblaciones bacterianas nativas de un suelo contaminado por PCBs

Los diferentes análisis llevados a cabo en este estudio sostienen que la comunidad bacteriana de la rizosfera, que evolucionó de la población nativa de un suelo con un historial de contaminación por bifenilos policlorados, durante el desarrollo de las raíces de Salix vimminalis, fue diferente de la comunidad parental tanto a niveles funcionales como estructurales. La rizosfera estuvo enriquecida en especies de Proteobacteria, y en genes de ISP altamente relacionados con el grupo de las bacterias Gram negativas. La rizosfera seleccionó y sustentó ciertas bacterias poseedoras de genes ISP (posibles degradadoras de PCBs), posiblemente por su competencia en la colonización de la rizosfera, hecho que podría ser empleado en futuras estrategias rizorremediadoras. Además, el descubrimiento de un clúster nuevo de secuencias ISP que contiene un alto grado de variación de secuencia, abre el camino para la detección de enzimas novedosos y de gran utilidad, al haber sido seleccionados bajo las condiciones ambientales existentes en el suelo contaminado estudiado. El impacto causado por la introducción de dos sistemas integrados sauce-microorganismo modificado genéticamente (diseñados para rizorremediación) en la estructura y función de las poblaciones bacterianas nativas de un suelo con un historial de contaminación por bifenilos policlorados, resultó imperceptible en comparación con la utilización de la cepa salvaje. Por el contrario, dicho impacto fue perceptible en las poblaciones rizosféricas desarrolladas, siendo, además, variable en función del grupo bacteriano estudiado.N

The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units

Abstract The complex community of microbes living in the human gut plays an important role in host wellbeing. However, defining a ‘healthy’ gut microbiome in terms of composition has remained an elusive task, despite its anticipated medical and scientific importance. In this regard, a central question has been if there is a ‘core’ microbiome consisting of bacterial groups common to all healthy humans. Recent studies have been able to define a compositional core in human gut microbiome datasets in terms of taxonomic assignments. However, the description of the core microbiome in terms of taxonomic assignments may not be adequate when considering subsequent analyses and applications. Through the implementation of a dynamic clustering approach in the meta-analyisis of comprehensive 16S rRNA marker gene datasets, this study found that the human gut pan-microbiome presents a preeminent compositional core comprised of discrete units of varying phylogenetic depth present in all individuals studied. Since both microbial traits and ecological coherence show signs of phylogenetic conservation, this outcome provides a new conceptual framework in the study of the ecosystem, as well as important practical considerations which should be taken into account in future research

Estudio de los efectos causados por la introducción en las poblaciones baterianas nativas de un suelo contaminado por PCBs

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología. Fecha de lectura 13-01-200

Evaluation of viral genome assembly and diversity estimation in deep metagenomes

[Background] Viruses have unique properties, small genome and regions of high similarity, whose effects on metagenomic assemblies have not been characterized so far. This study uses diverse in silico simulated viromes to evaluate how extensively genomes can be assembled using different sequencing platforms and assemblers. Further, it investigates the suitability of different methods to estimate viral diversity in metagenomes.[Results] We created in silico metagenomes mimicking various platforms at different sequencing depths. The CLC assembler revealed subpar compared to IDBA_UD and CAMERA, which are metagenomic-specific. Up to a saturation point, Illumina platforms proved more capable of reconstructing large portions of viral genomes compared to 454. Read length was an important factor for limiting chimericity, while scaffolding marginally improved contig length and accuracy. The genome length of the various viruses in the metagenomes did not significantly affect genome reconstruction, but the co-existence of highly similar genomes was detrimental. When evaluating diversity estimation tools, we found that PHACCS results were more accurate than those from CatchAll and clustering, which were both orders of magnitude above expected.[Conclusions] Assemblers designed specifically for the analysis of metagenomes should be used to facilitate the creation of high-quality long contigs. Despite the high coverage possible, scientists should not expect to always obtain complete genomes, because their reconstruction may be hindered by co-existing species bearing highly similar genomic regions. Further development of metagenomics-oriented assemblers may help bypass these limitations in future studies. Meanwhile, the lack of fully reconstructed communities keeps methods to estimate viral diversity relevant. While none of the three methods tested had absolute precision, only PHACCS was deemed suitable for comparative studies. © 2015 Aguirre de Cárcer et al.. licensee BioMed Central Ltd.This work was funded in part by the Spanish Ministry of Science and Innovation grant CTM2011-15091-E/ANT. Daniel Aguirre de Cárcer was supported by the Marie Curie International Incoming Fellow grant PIIF-GA- 2012-328287. Florent Angly was supported by the Australian Research Council’s Discovery Early Career Research Award DE120101213We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI)Peer Reviewe