Biology subjects

Mengoni, A.

Publications and source records attributed to Mengoni, A..

At least 19 recordsLinked to original sources

bioRxiv2026

From code to natural language: MErlin - a multiomics toolkit for bacterial epigenomics delivered as Claude agent skill.

Interpreting a bacterial methylome is a multi-omics problem. It requires integrating modified-base calls with genome annotation, motif inventories, methyltransferase genotypes, transcript abundance, replichore position and, increasingly, chromosome conformation. These data types are commonly generated in incompatible formats, use inconsistent sequence and gene identifiers, and originate from different analytical workflows. The relevant algorithms are available, but assembling them into a coherent and statistically defensible analysis remains a substantial data-integration and interface problem. We present MErlin (Methylation-driven Expression & Regulation Linkage in Interacting Nuclear-domains), a multi-omics toolkit comprising seventeen composable modules, from basecalled modBAM files to ranked gene-level evidence and a self-contained HTML report. MErlin is distributed both as a conventional Python package and as an agent skill: a structured, version-controlled layer of procedural knowledge that enables a compatible large language model (LLM) assistant to select and operate the audited package without generating a new analysis implementation for each request. This design treats natural language as an interface to fixed analytical operations rather than as a substitute for tested scientific software. The skill encodes module-selection rules, mandatory preflight checks, questions that require human input, design-to-inference constraints, and interpretation guidance. We describe MErlin's architecture and statistics, validate it against a synthetic dataset with planted ground truth, and illustrate the conversational interface on a real methylome-transcriptome comparison in Pseudoalteromonas haloplanktis TAC125. MErlin is open source and available at https://github.com/IacopoPasseri/MErlin

bioinformatics↗

bioRxiv2026

Wild rice Oryza rufipogon outperforms cultivated rice in stimulating beneficial bacterial endophytes.

Beneficial interactions between plants and microorganisms strongly influence plant health and productivity, and root exudates play a central role in shaping these associations. This study analyzed the transcriptional responses of the bacterial endophytes Enterobacter asburiae RCA24 and Kosakonia sacchari RCA25 to root exudates from two commercial Italian rice accessions (Oryza sativa Baldo and Vialone Nano) and from an accession of the wild progenitor of tropical rice, Oryza rufipogon. Bacterial transcriptome analyses revealed that RCA24 responds differently to O. sativa varieties and that RCA25 was more stimulated by O. rufipogon. Changes in bacterial gene expression were mainly related to central metabolism, stress response, and signal transduction, highlighting a precise pattern of interaction. On the other hand, transcriptome analysis of inoculated rice revealed that RCA24 triggered broader transcriptional changes in plants than RCA25. Differentially expressed genes were related, especially in shoots, to defense responses, hormone-mediated signaling, and ribosome biogenesis, revealing that plants discriminate bacterial strains in a genotype-specific manner at the transcriptional level. Our findings suggest that traits beneficial to plant-soil microbiota interactions present in O. rufipogon and lost during domestication and diversification could be identified and reintroduced into modern rice varieties to improve sustainable field performance through beneficial microbial associations.

plant biology↗

bioRxiv2025

Bacterial community studies and novel Bradyrhizobium and Rhizobium strains from drought-tolerant legumes grown in Namibia

AimsAnalysis of the microbiota associated with root nodules of five species of drought-tolerant legumes grown in Namibia. These legumes were Lablab purpureus, Vigna radiata, Vigna unguiculata, Macrotyloma uniflorum, and Vigna aconitifolia. Methods16S rRNA gene amplicon sequencing analysis and isolation of rhizobial and non-rhizobial bacterial strains from root nodules was performed. Plant growth-promoting traits were assessed on some isolates and the genomes of four rhizobial strains were sequenced. ResultsThe microbiota analysis revealed Bradyrhizobium as the most prevalent genus in the root nodules, while most of the non-rhizobial community included members of Bacillus genus. In addition, a strain of Variovorax paradoxus was also isolated from V. unguiculata, representing the first documented isolation and characterization report in Namibia. In vitro phenotypic characterization of the non-rhizobial nodule endophytes indicated that they possessed several plant growth-promoting traits. The four rhizobial strains isolated were taxonomically affiliated to the genera Bradyrhizobium and Rhizobium. Genome sequencing revealed that these strains possibly belong to novel species since they share only a limited similarity (dDDH values<70%) to already known species. Impact StatementThis study demonstrated that drought-tolerant legume species harbour microbial diversity from Namibian soil, which allowed us to increase our knowledge on plant-associated bacteria and their possible use in sustainable farming systems, as potential bioinoculants for crop production and for soil revitalization. Utilizing locally isolated bacterial strains as microbial bioinoculants maximizes their compatibility with the local conditions increasing the potential for positive effects on plant health and ecosystem functioning.

microbiology↗

bioRxiv2025

Comparative Analysis of the Microbiota of Vaccinium myrtillus and Vaccinium uliginosum in the Central Italian Apennines

Vaccinium is a genus of shrubs known for their antioxidant and anti-inflammatory compounds. While the commercially cultivated blueberry (V. corymbosum) originates from North America, European species like myrtillus (bilberry) and V. uliginosum (bog bilberry) remain uncultivated due to poor adaptability to conventional growing media. At present, bilberries, which are more valued for fresh consumption, are exclusively harvested from wild populations, particularly in subalpine and mountain environments, where unique soil and climate conditions prevail. This study explores the bacterial and fungal communities associated with V. myrtillus and V. uliginosum in wild populations of the Central Italian Apennines, using 16S rRNA and ITS amplicon sequencing. Microbiota from plant and soil were analyzed, revealing distinct microbial community compositions based on species and plant compartments. Bacterial diversity was highest in bulk soil, while fungal diversity dominated plant tissues. Co-occurrence network analysis showed greater connectivity in V. uliginosum microbiota, suggesting higher resilience. Functional predictions indicated roles in nitrogen cycling, cellulose degradation, and plant-microbe interactions. These findings offer insights into the native microbiota of wild Vaccinium species and could inform conservation and cultivation efforts.

microbiology↗

bioRxiv2024

The acquisition of additional control over quorum sensing regulation buffers noise in microbial growth dynamics

Quorum sensing (QS) is a cell-to-cell communication system used by bacteria to act collectively. Often, bacteria possess more than one QS regulatory module that form complex regulatory networks. Presumably, these configurations have evolved through the integration of novel transcription factors into the native regulatory systems. The selective advantages provided by these alternative configurations on QS-related phenotypes is poorly predictable only based on their underlying network structure. Here we show that the acquisition of extra regulatory modules of QS has important consequences on the overall regulation of microbial growth dynamics by significantly reducing the variability in the final size of the population in Burkholderia. We mapped the distribution of horizontally transferred QS modules in extant bacterial genomes, finding that these tend to add up to already-present modules in the majority of cases, 63.32%. We then selected a strain harboring two intertwined QS modules and,using mathematical modelling, we predicted an intrinsic ability of the newly acquired module to buffer noise in growth dynamics. We experimentally validated this prediction choosing one strain possessing both systems, deleting one of the two and measuring key growth parameters and QS synthase expression. We extended such considerations on two other strains naturally implementing the two versions of the QS regulation studied herein. Finally, using transcriptomics, we show that the de-regulation of metabolism likely plays a key role in differentiating the two configurations. Our results shed light on the role of additional control over QS regulation and illuminate on the possible phenotypes that may arise after HGT events.

systems biology↗

bioRxiv2023

The pan-epigenome of the symbiotic nitrogen fixing bacterium Sinorhizobium meliloti unravels unexpected variability of DNA-methylation profiles in closely related strains

In prokaryotes, DNA methylation has been found to be involved in several mechanisms, such as DNA repair, DNA-protein interactions, gene expression, cell cycle progression and self-DNA recognition (the Restriction-Modification systems). Studies on representatives from the same bacterial species have found that genome-wide DNA methylation patterns can be highly variable and may affect phenotypic variation and gene transfer among closely related strains. However, broader evolutionary studies on such epigenomic variation in bacteria are still scarce. Here, we addressed this point by performing an epigenomic analysis on 21 strains of the facultative plant symbiotic nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti. Strains of these species are characterized by a divided (multipartite) genome structure, including a chromosome, a chromid and a (more recently acquired) megaplasmid. Since these strains display extensive genomic and phenotypic variation, they are good models to test evolutionary hypotheses on the relationships among epigenomic signatures, genome structure evolution and phenotypic switches. Results showed the presence of a wide pan-epigenome with 16 DNA methylated motifs, including both 4mC and 6mA palindromic and nonpalindromic motifs. While 9 motifs have been found methylated by all strains, the remaining had differential methylation between S. meliloti strains, constituting a dispensable epigenome. Differences in frequency of methylation were found among replicons, with the megaplasmid and the additional plasmids displaying several motifs with different methylation frequency with respect to the chromosome and the chromid. Moreover, differences between coding, upstream and intergenic regions, were found, suggesting that DNA methylation at specific motifs may play a role in gene regulation and consequently in phenotypic variability among strains. Altogether, our data indicate the presence of a large epigenomic diversity in S. meliloti, with epigenome signatures differing between replicons, reflecting their timing of evolutionary acquisition in S. meliloti genomes and suggesting a role of DNA methylation in the variability of gene expression among strains.

genomics↗

bioRxiv2022

Extraction and analysis of methylation features from Pacific Biosciences SMRT reads using MeStudio

MotivationDNA methylation is the most relevant epigenetic information, present in eukaryotes and prokaryotes, and is related to several biological phenomena, from cellular differentiation to control of gene flow, pathogenesis and virulence. The widespread use of third-generation sequencing technologies allows direct and easy detection of genome-wide methylation profiles, offering increasing opportunities to understand and exploit the epigenomics landscape. ResultsWe introduce MeStudio, a pipeline which allows to analyse and combine genome-wide methylation profiles with genomic features. Outputs report the presence of DNA methylation in coding sequences, noncoding sequences, intergenic sequences, and sequences upstream to CDS. We show the usage and performances of MeStudio on a set of single-molecule real time sequencing outputs from the bacterial species Sinorhizobium meliloti. Availability and ImplementationMeStudio is written in Python, Bash and C and is freely available under an open source GPLv3 license at https://github.com/combogenomics/MeStudio Supplementary informationSupplementary data are available at Bioinformatics online. Contactcombo.unifi@gmail.com

bioinformatics↗

bioRxiv2021

Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation

The alphaproteobacterial family Rhizobiaceae is highly diverse, with 168 species with validly published names classified into 17 genera with validly published names. Most named genera in this family are delineated based on genomic relatedness and phylogenetic relationships, but some historically named genera show inconsistent distribution and phylogenetic breadth. Most problematic is Rhizobium, which is notorious for being highly paraphyletic, as most newly described species in the family being assigned to this genus without consideration for their proximity to existing genera, or the need to create novel genera. In addition, many Rhizobiaceae genera lack synapomorphic traits that would give them biological and ecological significance. We propose a common framework for genus delimitation within the family Rhizobiaceae. We propose that genera in this family should be defined as monophyletic groups in a core-genome gene phylogeny, that are separated from related species using a pairwise core-proteome average amino acid identity (cpAAI) threshold of approximately 86%. We further propose that the presence of additional genomic or phenotypic evidence can justify the division of species into separate genera even if they all share greater than 86% cpAAI. Applying this framework, we propose to reclassify Rhizobium rhizosphaerae and Rhizobium oryzae into the new genus Xaviernesmea gen. nov. Data is also provided to support the recently proposed genus "Peteryoungia", and the reclassifications of Rhizobium yantingense as Endobacterium yantingense comb. nov., Rhizobium petrolearium as Neorhizobium petrolearium comb. nov., Rhizobium arenae as Pararhizobium arenae comb. nov., Rhizobium tarimense as Pseudorhizobium tarimense comb. nov., and Rhizobium azooxidefex as Mycoplana azooxidifex comb. nov. Lastly, we present arguments that the unification of the genera Ensifer and Sinorhizobium in Opinion 84 of the Judicial Commission is no longer justified by current genomic and phenotypic data. We thus argue that the genus Sinorhizobium is not illegitimate and now encompasses 17 species.

microbiology↗

bioRxiv2021

Organ-specific microbiota enhances the terrestrial lifestyle of a brachyuran crab

Brachyuran crabs originated in the oceans and evolved specific morphological and physiological adaptations to live in freshwater, intertidal and even terrestrial habitats but the role of a selection mechanism involving symbiotic microorganisms long these colonization processes are not known. In this work we investigated the associated microbiota of three populations of a terrestrial brachyuran crab, Chiromantes haematocheir, to find evidence of a conserved crab-specific microbiome unrelated to the population of origin and dissimilar from environmental microbial assemblages. Bacterial 16S rRNA gene and fungal ITS sequences were obtained from selected crab organs and environmental matrices to profile microbial communities. In spite of the presence of truly marine larval stages and no gregarious behaviour, favouring microbiota exchanges, we found common, organ-specific microbiota, associated to the gut and the gills of the crabs (with more than 15% of the genera detected specifically enriched only in one organ). Our results suggest an early establishment of a new common, stable microbiota in the transition from water to land.

zoology↗

bioRxiv2021

DNA methylation patterns in bacteria of the genus Ensifer during free living growth and during nitrogen-fixing symbiosis with Medicago spp.

Methylation of specific DNA sequences is ubiquitous in bacteria and has known roles in immunity and regulation of cellular processes, such as the cell cycle. Using single-molecule real-time sequencing, six genome-wide methylated motifs were identified across four Ensifer strains, five of which were strain-specific. Only the GANTC motif, recognized by the cell cycle-regulated CcrM methyltransferase, was methylated in all strains. In actively dividing cells, methylation of GANTC motifs increased progressively from the ori to ter regions in each replicon, in agreement with a cell cycle-dependent regulation of CcrM. In contrast, there was near full genome-wide GANTC methylation in the early stage of symbiotic differentiation. This was followed by a moderate decrease in the overall extent methylation and a progressive decrease in chromosomal GANTC methylation from the ori to ter regions in later stages of differentiation. We interpret these observations as evidence of dysregulated and constitutive CcrM activity during terminal differentiation, and we hypothesize that it is a driving factor for endoreduplication of terminally differentiated bacteroids.

microbiology↗

bioRxiv2020

Competitiveness prediction for nodule colonization in Sinorhizobium meliloti through combined in vitro tagged strain characterization and genome-wide association analysis

Associations between leguminous plants and symbiotic nitrogen fixing bacteria (rhizobia) are a classical example of mutualism between a eukaryotic host and a specific group of prokaryotic microbes. Though being in part species-specific, different strains may colonize the same plant symbiotic structure (nodule). It is known that some rhizobial strains are better competitor than others, but detailed analyses aimed to predict from the rhizobial genome its competitive abilities are still scarce. Here we performed a bacterial genome wide association (GWAS) analysis to define the genomic determinants related to the competitive capabilities in the model rhizobial species Sinorhizobium meliloti. Thirteen tester strains were GFP-tagged and assayed against three reference competitor strains RFP-tagged (Rm1021, AK83 and BL225C) in a Medicago sativa nodule occupancy test. Competition data in combination with strains genomic sequences were used to build-up a model for GWAS based on k-mers. The model was then trained and applied for competition capabilities prediction. The model was able to well predict the competition abilities against two partners, BL225C, Rm1021 with coefficient of determination of 0.96 and 0.84, respectively. Four strains showing the highest competition phenotypes (> 60% single strain nodule occupancy; GR4, KH35c, KH46 and SM11) versus BL225C were used to identify k-mers associated with competition. The k-mers with highest scores mapped on the symbiosis-related megaplasmid pSymA and on genes coding for transporters, proteins involved in the biosynthesis of cofactors and proteins related to metabolism (i.e. glycerol, fatty acids) suggesting that competition abilities reside in multiple genetic determinants comprising several cellular components. IMPORTANCEDecoding the competitive pattern that occurs in the rhizosphere is challenging in the study of bacterial social interaction strategies. To date, single-gene approach has been mainly used to uncover the bases of nodulation, but there is still a gap about the main features that a priori turn out rhizobial strains able to outcompete indigenous rhizobia. Therefore, tracking down which traits make different rhizobial strains able to win the competition for plant infection over other indigenous rhizobia will allow ameliorating strain selection and consequently plant yield in sustainable agricultural production systems. We have proven that a k-mer based GWAS approach can effectively predict the competition abilities of a panel of strains, which were analyzed for their plant tissue occupancy by using double fluorescent labeling. The reported strategy could be used for detailed studies on the genomic aspects of the evolution of bacterial symbiosis and for an extensive evaluation of rhizobial inoculants.

microbiology↗

bioRxiv2020

Dissecting transcriptomic signatures of genotype x genotype interactions during the initiation of plant-rhizobium symbiosis

Rhizobia are ecologically important, facultative plant symbiotic microbes. In nature there exists large variability in the association of rhizobial strains and host plant of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of host plant. RNA-sequencing of the model rhizobium Sinorhizobium meliloti exposed to root exudates or luteolin was performed in a combination of three S. meliloti strains and three Medicago sativa varieties. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, expression of 35% were influenced by strain genotype, 16% by the plant genotype, and 29% by strain x host plant genotype interactions. We also examined the response of a hybrid S. meliloti strain, in which the symbiotic megaplasmid (~ 20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes resulted up-regulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes is influenced by the genotypes of both symbiotic partners, and their interaction, suggesting a wide genetic spectrum of partner choice selection in plant-rhizobium symbiosis.

microbiology↗

bioRxiv2020

Significant and conflicting correlation of IL-9 with Prevotella and Bacteroides in human colorectal cancer

BackgroundColorectal cancer (CRC) is a widespread disease that represents an example of chronic inflammation-associated tumor. In fact, the immune system, besides protecting the host from developing tumors, can support the CRC progression. In this scenario, the gut microbiota (GM) is essential to modulate immune responses and a dysbiotic condition can favor chronic/abnormal immune activation that support the tumor growth. GM can elicit the production of cytokines, influencing the immunostimulatory or immunosuppressive reactions, such as the tendency to mount Th1, Th17, Tregs or Th9 responses that play different roles towards colon cancer. Paradigmatic is the role of IL-9 that can both promote tumor progression in hematological malignancies and inhibit tumorigenesis in solid cancers. Therefore, to investigate the microbiota-immunity axis in CRC patients is crucial to well understand the cancer development with positive relapses in prevention and treatment. AimThe cellular and molecular characterization of the immune response and the evaluation of GM composition in healthy and tumor mucosa, focusing on the correlation between cytokines profile and GM signature. MethodsWe collected tumoral (CRC) and healthy (CRC-S) mucosa samples of 45 CRC patients. For each sample, we characterized the Tissue Infiltrating Lymphocytes (TIL)s subset profile and the GM composition. In addition, in 14 CRC patients, we evaluated the CRC and CRC-S molecular inflammatory response (26 cytokines/chemokines) and we correlated this profile with GM composition using the Dirichlet Multinomial Regression. ResultsThe analysis of T cells subsets distribution showed that CRC samples displayed higher percentages of Th17, Th2, Tregs, Tc17, Tc1/Tc17, and Tcreg, compared to CRC-S. Notably, also the number of Th9 was higher, even if not significantly, in CRC tissue compared to healthy one. In addition, we found that MIP-1, IL-1{beta}, IL-2, IP-10, IL-6, IL-8, IL-17A, IFN-{gamma}, TNF-, MCP-1, IL-1, P-selectin and IL-9 were significantly increased in CRC compared to CRC-S. Moreover, the GM analysis revealed that CRC samples had significantly higher levels of Fusobacteria, Proteobacteria, Fusobacterium, Ruminococcus2 (Lachnospiraceae family) and Ruminococcus (Ruminococcaceae family) than CRC-S. Finally, we found that the abundance of Prevotella spp in CRC samples was negatively correlated with IL-17A and positively with IL-9. In addition, the abundance of Bacteroides and Escherichia/Shigella species in CRC samples showed a negative association with IL-9 and IP-10 respectively. ConclusionsOur data show a clear dissimilarity of inflammatory profile and GM composition between the tumor and the adjacent healthy tissue, displaying the generation of a peculiar CRC microenvironment. Interestingly, relating the tissue cytokine profile with the GM composition, we confirmed the presence of a bidirectional crosstalk between the immune response and the hosts commensal microorganisms; in detail, we documented for the first time that Prevotella spp. and Bacteroides spp. are correlated (positively and negatively, respectively) with the IL-9, whose role in CRC development is still debated.

immunology↗

bioRxiv2020

Symbiotic and non-symbiotic members of the genus Ensifer (syn. Sinorhizobium) are separated into two clades based on comparative genomics and high-throughput phenotyping

Rhizobium - legume symbioses serve as a paradigmatic example for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and inter-kingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF emerged several times within the genus Ensifer, likely through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the "symbiotic" and "non-symbiotic" clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the non-symbiotic clade. Characterizing a subset of ten Ensifer strains identified several phenotypic differences between the clades. Strains of the non-symbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.

microbiology↗

bioRxiv2020

Defining the resilience of the human salivary microbiota by a 520 days longitudinal study in confined environment: the Mars500 mission

The human microbiota plays several roles in health and disease but is often difficult to determine which part is in intimate relationships with the host vs. the occasional presence. During the Mars500 mission, six crewmembers lived completely isolated from the outer world for 520 days following standardized diet regimes. The mission constitutes the first spaceflight simulation to Mars and was a unique experiment to determine, in a longitudinal study design, the composition and importance of the resident vs. a more variable microbiota--the fraction of the human microbiota that changes in time and according to environmental conditions--in humans. Here we report the characterization of the salivary microbiota from 88 samples taken during and after the mission for a total of 720 days. Amplicon sequencing of the V3-V4 region of 16S rRNA gene was performed and results were analyzed monitoring the diversity of the microbiota while evaluating the effect of the three main variables present in the experimental system: time, diet, and individuality of each subject. Results, though showing statistically significant effects of all three variables, highlighted a main contribution of salivary microbiota personalized features, that is an individual-based resilience of the microbiota. Such findings open the way to consider salivary microbiota under the light of a pronounced personalization even after sharing the same physical space for more than a year.

microbiology↗

bioRxiv2019

A Virtual Nodule Environment (ViNE) for modelling the inter-kingdom metabolic integration during symbiotic nitrogen fixation

Biological associations are often premised upon metabolic cross-talk between the organisms, with the N2-fixing endosymbiotic relationship between rhizobia and leguminous plants being a prime example. Here, we report the in silico reconstruction of a metabolic network of a Medicago truncatula plant nodulated by the bacterium Sinorhizobium meliloti. The nodule tissue of the model contains five spatially distinct developmental zones and encompasses the metabolism of both the plant and the bacterium. Flux balance analysis (FBA) suggested that the majority of the metabolic costs associated with symbiotic nitrogen fixation are directly related to supporting nitrogenase activity, while a minority is related to the formation and maintenance of nodule and bacteroid tissue. Interestingly, FBA simulations suggested there was a non-linear relationship between the rate of N2-fixation per gram of nodule and the rate of plant growth; increasing the N2-fixation efficiency was associated with diminishing returns in terms of plant growth. Evaluating the metabolic exchange between the symbiotic partners provided support for: i) differentiating bacteroids having access to sugars (e.g., sucrose) as a major carbon source, ii) ammonium being the major nitrogen export product of N2-fixing bacteria, and iii) N2-fixation being dependent on the transfer of protons from the plant cytoplasm to the bacteria through acidification of the peribacteroid space. Our simulations further suggested that the use of C4-dicarboxylates by N2-fixing bacteroids may be, in part, a consequence of the low concentration of free oxygen in the nodule limiting the activity of the plant mitochondria. These results demonstrate the power of this integrated model to advance our understanding of the functioning of legume nodules, and its potential for hypothesis generation to guide experimental studies and engineering of symbiotic nitrogen fixation.

systems biology↗

bioRxiv2019

The personalized temporal dynamics of microbiome in the airways of cystic fibrosis patients

Although the cystic fibrosis (CF) lung microbiome has been characterized in several studies, little is still known about the functions harboured by those bacteria, and how they change with disease status and antibiotic treatment. The aim of this study was to investigate the taxonomic and functional temporal dynamics of airways microbiome in a cohort of CF patients. Multiple sputum samples were collected over 15 months from 22 patients with chronic P. aeruginosa infection, for a total of 79 samples. DNA extracted from samples was subjected to shotgun metagenomic sequencing allowing either strain-level taxonomic profiling and assessment of the functional metagenomic repertoire. High inter-patient taxonomic heterogeneity was found with short-term compositional changes during exacerbations and following antibiotic treatment. Each patient exhibited distinct sputum microbial communities at the taxonomic level, and strain-specific colonization of traditional CF pathogens, including P. aeruginosa, and emerging pathogens. Sputum microbiome was found to be extraordinarily resilient following antibiotic treatment, with rapid recovery of taxa and metagenome-associated gene functions. In particular, a large core set of genes, including antibiotic resistance genes, were shared across patients despite observed differences in clinical status or antibiotic treatment, and constantly detected in the lung microbiome of all subjects independently from known antibiotic exposure, suggesting an overall microbiome-associated functions stability despite taxonomic fluctuations of the communities. IMPORTANCEWhile the dynamics of CF sputum microbial composition were highly patient-specific, the overall sputum metagenome composition was stable, showing a high resilience along time and antibiotic exposure. The high degree of redundancy in the CF lung microbiome could testifies ecological aspects connected to the disease that were never considered so far, as the large core-set of genes shared between patients despite observed differences in clinical status or antibiotic treatment. Investigations on the actual functionality (e.g. by metatranscriptomics) of the identified core-set of genes could provide clues on genetic function of the microbiome to be targeted in future therapeutic treatments.

microbiology↗

bioRxiv2018

Emergence and features of the multipartite genome structure of the family Burkholderiaceae revealed through comparative and evolutionary genomics

The multipartite genome structure is found in a diverse group of important symbiotic and pathogenic bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished {beta}-proteobacterial genomes to study the role and emergence of multipartite genomes. Nearly all essential secondary replicons (chromids) of the {beta}-proteobacteria are found in the family Burkholderiaceae. These replicons arose from just two plasmid acquisition events, and they were likely stabilized early in their evolution by the presence of core genes, at least some of which were likely acquired through an inter-replicon translocation event. On average, Burkholderiaceae genera with multipartite genomes had a larger total genome size, but smaller chromosome, than genera without secondary replicons. Pangenome-level functional enrichment analyses suggested that inter-replicon functional biases are partially driven by the enrichment of secondary replicons in the accessory pangenome fraction. Nevertheless, the small overlap in orthologous groups present in each replicons pangenome indicates a clear functional separation of the replicons. Chromids appeared biased to environmental adaptation, as the functional categories enriched on chromids were also over-represented on the chromosomes of the environmental genera (Paraburkholderia, Cupriavidus) compared to the pathogenic genera (Burkholderia, Ralstonia). Using ancestral state reconstruction, it was predicted that the rate of accumulation of modern-day genes by chromids was more rapid than the rate of gene accumulation by the chromosomes. Overall, the data are consistent with a model where the primary advantage of secondary replicons is in facilitating increased rates of gene acquisition through horizontal gene transfer, consequently resulting in a replicon enriched in genes associated with adaptation to novel environments.

genomics↗