Intestinal GCN2 controls Drosophila systemic growth in response to Lactiplantibacillus plantarum symbiotic cues encoded by r/tRNA operons.

Symbiotic bacteria interact with their host through symbiotic cues. Here, we took advantage of the mutualism between Drosophila and Lactiplantibacillus plantarum (Lp) to investigate a novel mechanism of host-symbiont interaction. Using chemically defined diets, we found that association with Lp improves the growth of larvae-fed amino acid-imbalanced diets, even though Lp cannot produce the limiting amino acid. We show that in this context Lp supports its host's growth through a molecular dialogue that requires functional operons encoding ribosomal and transfer RNAs (r/tRNAs) in Lp and the general control nonderepressible 2 (GCN2) kinase in Drosophila's enterocytes. Our data indicate that Lp's r/tRNAs are packaged in extracellular vesicles and activate GCN2 in a subset of larval enterocytes, a mechanism necessary to remodel the intestinal transcriptome and ultimately to support anabolic growth. Based on our findings, we propose a novel beneficial molecular dialogue between host and microbes, which relies on a non-canonical role of GCN2 as a mediator of non-nutritional symbiotic cues encoded by r/tRNA operons.

Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria.

Insertion sequences (IS) are ubiquitous bacterial mobile genetic elements, and the mutations they cause can be deleterious, neutral, or beneficial. The long-term dynamics of IS elements and their effects on bacteria are poorly understood, including whether they are primarily genomic parasites or important drivers of adaptation by natural selection. Here, we investigate the dynamics of IS elements and their contribution to genomic evolution and fitness during a long-term experiment with Escherichia coli. IS elements account for ~35% of the mutations that reached high frequency through 50,000 generations in those populations that retained the ancestral point-mutation rate. In mutator populations, IS-mediated mutations are only half as frequent in absolute numbers. In one population, an exceptionally high ~8-fold increase in IS150 copy number is associated with the beneficial effects of early insertion mutations; however, this expansion later slowed down owing to reduced IS150 activity. This population also achieves the lowest fitness, suggesting that some avenues for further adaptation are precluded by the IS150-mediated mutations. More generally, across all populations, we find that higher IS activity becomes detrimental to adaptation over evolutionary time. Therefore, IS-mediated mutations can both promote and constrain evolvability.

Metabolic Cooperation among Commensal Bacteria Supports Drosophila Juvenile Growth under Nutritional Stress.

The gut microbiota shapes animal growth trajectory in stressful nutritional environments, but the molecular mechanisms behind such physiological benefits remain poorly understood. The gut microbiota is mostly composed of bacteria, which construct metabolic networks among themselves and with the host. Until now, how the metabolic activities of the microbiota contribute to host juvenile growth remains unknown. Here, using Drosophila as a host model, we report that two of its major bacterial partners, Lactobacillus plantarum and Acetobacter pomorum, engage in a beneficial metabolic dialogue that boosts host juvenile growth despite nutritional stress. We pinpoint that lactate, produced by L. plantarum, is utilized by A. pomorum as an additional carbon source, and A. pomorum provides essential amino acids and vitamins to L. plantarum. Such bacterial cross-feeding provisions a set of anabolic metabolites to the host, which may foster host systemic growth despite poor nutrition.

Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth.

The interplay between nutrition and the microbial communities colonizing the gastrointestinal tract (i.e., gut microbiota) determines juvenile growth trajectory. Nutritional deficiencies trigger developmental delays, and an immature gut microbiota is a hallmark of pathologies related to childhood undernutrition. However, how host-associated bacteria modulate the impact of nutrition on juvenile growth remains elusive. Here, using gnotobiotic Drosophila melanogaster larvae independently associated with Acetobacter pomorumWJL (ApWJL) and Lactobacillus plantarumNC8 (LpNC8), 2 model Drosophila-associated bacteria, we performed a large-scale, systematic nutritional screen based on larval growth in 40 different and precisely controlled nutritional environments. We combined these results with genome-based metabolic network reconstruction to define the biosynthetic capacities of Drosophila germ-free (GF) larvae and its 2 bacterial partners. We first established that ApWJL and LpNC8 differentially fulfill the nutritional requirements of the ex-GF larvae and parsed such difference down to individual amino acids, vitamins, other micronutrients, and trace metals. We found that Drosophila-associated bacteria not only fortify the host's diet with essential nutrients but, in specific instances, functionally compensate for host auxotrophies by either providing a metabolic intermediate or nutrient derivative to the host or by uptaking, concentrating, and delivering contaminant traces of micronutrients. Our systematic work reveals that beyond the molecular dialogue engaged between the host and its bacterial partners, Drosophila and its associated bacteria establish an integrated nutritional network relying on nutrient provision and utilization.

Genetic Basis of Exploiting Ecological Opportunity During the Long-Term Diversification of a Bacterial Population.

Adaptive diversification is an essential evolutionary process, one that produces phenotypic innovations including the colonization of available ecological niches. Bacteria can diverge in sympatry when ecological opportunities allow, but the underlying genetic mechanisms are often unknown. Perhaps, the longest-lasting adaptive diversification seen in the laboratory occurred during the long-term evolution experiment, in which 12 populations of Escherichia coli have been evolving independently for more than 65,000 generations from a common ancestor. In one population, two lineages, S and L, emerged at ~6500 generations and have dynamically coexisted ever since by negative frequency-dependent interactions mediated, in part, by acetate secretion by L. Mutations in spoT, arcA, and gntR promoted the emergence of the S lineage, although they reproduced only partially its phenotypic traits. Here, we characterize the evolved mechanism of acetate consumption by the S lineage that enabled invasion and coexistence with the L lineage. We identified an additional mutation in acs that, together with the arcA mutation, drove an early restructuring of the transcriptional control of central metabolism in S, leading to improved acetate consumption. Pervasive epistatic interactions within the S genome contributed to the exploitation of this new ecological opportunity. The emergence and maintenance of this long-term polymorphism is a complex multi-step process.

Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification.

Metabolic cross-feeding interactions between microbial strains are common in nature, and emerge during evolution experiments in the laboratory, even in homogeneous environments providing a single carbon source. In sympatry, when the environment is well-mixed, the reasons why emerging cross-feeding interactions may sometimes become stable and lead to monophyletic genotypic clusters occupying specific niches, named ecotypes, remain unclear. As an alternative to evolution experiments in the laboratory, we developed Evo2Sim, a multi-scale model of in silico experimental evolution, equipped with the whole tool case of experimental setups, competition assays, phylogenetic analysis, and, most importantly, allowing for evolvable ecological interactions. Digital organisms with an evolvable genome structure encoding an evolvable metabolic network evolved for tens of thousands of generations in environments mimicking the dynamics of real controlled environments, including chemostat or batch culture providing a single limiting resource. We show here that the evolution of stable cross-feeding interactions requires seasonal batch conditions. In this case, adaptive diversification events result in two stably co-existing ecotypes, with one feeding on the primary resource and the other on by-products. We show that the regularity of serial transfers is essential for the maintenance of the polymorphism, as it allows for at least two stable seasons and thus two temporal niches. A first season is externally generated by the transfer into fresh medium, while a second one is internally generated by niche construction as the provided nutrient is replaced by secreted by-products derived from bacterial growth. In chemostat conditions, even if cross-feeding interactions emerge, they are not stable on the long-term because fitter mutants eventually invade the whole population. We also show that the long-term evolution of the two stable ecotypes leads to character displacement, at the level of the metabolic network but also of the genome structure. This difference of genome structure between both ecotypes impacts the stability of the cross-feeding interaction, when the population is propagated in chemostat conditions. This study shows the crucial role played by seasonality in temporal niche partitioning and in promoting cross-feeding subgroups into stable ecotypes, a premise to sympatric speciation.

Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment.

BACKGROUND: Predicting adaptive trajectories is a major goal of evolutionary biology and useful for practical applications. Systems biology has enabled the development of genome-scale metabolic models. However, analysing these models via flux balance analysis (FBA) cannot predict many evolutionary outcomes including adaptive diversification, whereby an ancestral lineage diverges to fill multiple niches. Here we combine in silico evolution with FBA and apply this modelling framework, evoFBA, to a long-term evolution experiment with Escherichia coli. RESULTS: Simulations predicted the adaptive diversification that occurred in one experimental population and generated hypotheses about the mechanisms that promoted coexistence of the diverged lineages. We experimentally tested and, on balance, verified these mechanisms, showing that diversification involved niche construction and character displacement through differential nutrient uptake and altered metabolic regulation. CONCLUSION: The evoFBA framework represents a promising new way to model biochemical evolution, one that can generate testable predictions about evolutionary and ecosystem-level outcomes.

Microbiological effects of periodontal therapy plus azithromycin in patients with diabetes: results from a randomized clinical trial.

Current evidence suggests that periodontal infection may aggravate diabetes control. The aim of this study was to determine the changes in the frequency with which Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola and Aggregatibacter actinomycetemcomitans were detected in patients with diabetes with the use of non-surgical therapy plus azithromycin in a randomized clinical trial. One hundred and five (105) patients with diabetes and chronic periodontitis were randomly assigned to three treatment groups: subgingival mechanical therapy with azithromycin, subgingival mechanical therapy with placebo and supragingival prophylaxis with azithromycin. Complete periodontal clinical examinations and detection of periodontal pathogens using polymerase chain reaction were carried out at baseline, 3, 6 and 9 months after periodontal therapy. The frequency with which Porphyromonas gingivalis, Treponemadenticola and Aggregatibacter actinomycetemcomitans were detected decreased at 3 months in all groups. Tannerella forsythia increased after3 months in all groups. All organisms had similar frequencies at 9 months in all groups. Subgingival mechanical therapy with adjunctive azithromycin had no additional effect on the frequency with which the periodontal pathogens investigated were detected in patients with diabetes.

Microbiological effects of periodontal therapy plus azithromycin in patients with diabetes: results from a randomized clinical trial

Evidencia actual sugiere que la infección periodontal puede agravar el control de la diabetes. El objetivo de este estudiofue determinar los cambios en la frecuencia de detección de porphyromonas gingivalis, Tannerella forsythia, Treponema denticola y Aggregatibacter actinomycetemcomitans en pacientes con diabetes con el uso de terapia mecánica no quirúrgica mas azitromicina en un estudio clínico controlado aleatorizado.Ciento cinco pacientes (105) con diabetes y perio -dontitis fueron asignados aleatoriamente en tres grupos: terapiamecánica mas azitromicina, terapia mecánica mas placebo y profilaxis supragingival mas azitromicina. Un análisis periodontal completo y detección de patógenos perio dontales por medio de reacción en cadena de la polimerasa (PCR) se realizaron al inicio, 3, 6 y 9 meses después de la terapia pe -riodontal. La frecuencia de detección de Porphyromonas gingivalis, Treponema denticola y Aggregatibacter actinomycetemcomitans disminuyó a los 3 meses en todos los grupos. La frecuencia de detección de Tannerella forsythia se incrementó a los 3 meses en todos los grupos. Todos los patógenosperiodontales mostraron una frecuencia de detección similar a los 9 meses en todos los grupos. La terapia periodontal mas azitromicina no tuvo efectos adicionales sobre la frecuencia dedetección de los patógenos periodontales investigados en pacientes diabéticos...

Structural and thermodynamic characterization of doxycycline/ß-cyclodextrin supramolecular complex and its bacterial membrane interactions.

Doxycycline is a semi-synthetic antibiotic commonly used for the treatment of many aerobic and anaerobic bacteria. It inhibits the activity of matrix metalloproteinases (MMPs) and affects cell proliferation. In this study, the structural and thermodynamic parameters of free DOX and a DOX/ßCD complex were investigated, as well as their interactions and effects on Staphylococcus aureus cells and cellular cytotoxicity. Complexation of DOX and ßCD was confirmed to be an enthalpy- and entropy-driven process, and a low equilibrium constant was obtained. Treatment of S. aureus with higher concentrations of DOX or DOX/ßCD resulted in an exponential decrease in S. aureus cell size, as well as a gradual neutralization of zeta potential. These thermodynamic profiles suggest that ion-pairing and hydrogen bonding interactions occur between DOX and the membrane of S. aureus. In addition, the adhesion of ßCD to the cell membrane via hydrogen bonding is hypothesized to mediate a synergistic effect which accounts for the higher activity of DOX/ßCD against S. aureus compared to pure DOX. Lower cytotoxicity and induction of osteoblast proliferation was also associated with DOX/ßCD compared with free DOX. These promising findings demonstrate the potential for DOX/ßCD to mediate antimicrobial activity at lower concentrations, and provides a strategy for the development of other antimicrobial formulations.

Microbiological effects of periodontal therapy plus azithromycin in patients with diabetes: results from a randomized clinical trial. / Microbiological effects of periodontal therapy plus azithromycin in patients with diabetes: results from a randomized clinical trial.

Current evidence suggests that periodontal infection may aggravate diabetes control. The aim of this study was to determine the changes in the frequency with which Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola and Aggregatibacter actinomycetemcomitans were detected in patients with diabetes with the use of non-surgical therapy plus azithromycin in a randomized clinical trial. One hundred and five (105) patients with diabetes and chronic periodontitis were randomly assigned to three treatment groups: subgingival mechanical therapy with azithromycin, subgingival mechanical therapy with placebo and supragingival prophylaxis with azithromycin. Complete periodontal clinical examinations and detection of periodontal pathogens using polymerase chain reaction were carried out at baseline, 3, 6 and 9 months after periodontal therapy. The frequency with which Porphyromonas gingivalis, Treponemadenticola and Aggregatibacter actinomycetemcomitans were detected decreased at 3 months in all groups. Tannerella forsythia increased after3 months in all groups. All organisms had similar frequencies at 9 months in all groups. Subgingival mechanical therapy with adjunctive azithromycin had no additional effect on the frequency with which the periodontal pathogens investigated were detected in patients with diabetes.

Peptides: ß-cyclodextrin inclusion compounds as highly effective antimicrobial and anti-epithelial proliferation agents.

BACKGROUND: The use of antimicrobial peptides (AMPs) as therapeutic agents for periodontal infections has great advantages, such as broad spectrum of action, low toxicity, and limited bacterial resistance. However, their practical use is limited because of the large amount of peptide required to exercise the microbicidal function. METHODS: LyeTxI, LL37f, and KR12 cationic peptides were prepared with ß-cyclodextrin (ßCD) at 1:1 molar ratios. The susceptibility of Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Fusobacterium nucleatum were assessed in anaerobic conditions. Cytotoxicity assays were performed using osteoblast and Caco-2 epithelial cells, and hemolytic activity was assessed on rabbit erythrocytes at an absorbance of 414 nm. Parameters of surface roughness and electrical charge were established by atomic force microscopy and zeta (ζ) potential, respectively. RESULTS: AMP/ßCDs drastically decreased the peptide concentration required for activity against the bacteria tested. Moreover, AMPs associated with ßCD were able to modify cell-surface parameters, such as roughness and ζ potential. On the other hand, AMP/ßCD did not alter the degree of hemolysis induced by the pure AMPs. The effective concentration at half-maximum values of the peptides and compounds on osteoblasts were greater than the concentrations required to achieve inhibition of bacterial growth in all the species tested. AMP/ßCDs inhibited the proliferation of Caco-2 epithelial cells in a more efficient manner than AMPs alone. CONCLUSION: AMP/ßCD compounds more effectively inhibit periodontopathogenic bacteria than AMPs alone, with the additional ability of inhibiting the proliferation of epithelial cells at concentrations that are non-cytotoxic for osteoblasts and erythrocytes.

[Enteric Gram negative rods and unfermented of glucose bacteria in patients with peri-implant disease]. / Bacilos Gram negativos entéricos y no fermentadores de la glucosa en pacientes con enfermedad periimplante.

INTRODUCTION: Implants can be colonized by microorganisms from oral biofilms and may affect peri-implant tissues health. Among these bacteria, pathogens typically associated with periodontitis can be found, such as Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis, as well as Gram negative enteric bacilli not typically associated with periodontal diseases. OBJECTIVE: Superinfecting bacteria were characterized from peri-implant lesions in patients with history of periodontitis. MATERIALS AND METHODS: Sixty-eight implants were studied in 55 patients; the average patient age was 56 years. Forty-nine implants had peri-implant lesions and 19 were considered stable. Subgingival samples were obtained in affected and stable implants. The samples were streaked on Mac-Conkey agar and incubated at 37°C for 24 hours. The colonies were identified with the kit-BD BBL Crystal E/NF®. RESULTS: Superinfecting organisms were detected in 20 patients--they were seen more frequently at diseased implants (n=15) than at healthy implants (n=5). The prevalence of superinfecting bacteria on the selected implants was 33.8% (n=23/68). These bacteria were more prevalent among affected implants (n=17 or 25%) than those with stable implants n=6 (8.8%). Klebsiella pneumoniae was the most frequent Gram negative rod detected (n=12). CONCLUSIONS: One-third of the implants had superinfecting organisms. Implants with a peri-implant lesion had a higher frequency of superinfecting bacteria. Klebsiella pneumoniae was the most common superinfecting organism isolated. A multiple infection caused by superinfecting bacteria was present only at diseased implants. These microbial agents potentially affect implant stability.

Bacilos Gram negativos entéricos y no fermentadores de la glucosa en pacientes con enfermedad periimplante / Enteric Gram negative rods and unfermented of glucose bacteria in patients with peri-implant disease

Introducción. Los implantes pueden ser colonizados por microorganismos de la biopelícula oral y así afectarse su salud. Entre los patógenos encontrados están los típicamente relacionados con periodontitis, como Aggregatibacter actinomycetemcomitans y Porphyromonas gingivalis, así como bacilos Gram negativos entéricos, los cuales no son clásicos de la enfermedad periodontal. Objetivo. Determinar el perfil de las bacterias sobreinfecciosas en lesiones periimplante (mucositis o periimplantitis), en pacientes con historia de periodontitis. Materiales y métodos. Se estudiaron 68 implantes en 55 pacientes; 49 implantes tuvieron lesión periimplante19 se consideraron estables. Se obtuvieron muestras subgingivales de implantes afectados y estables; éstas fueron sembradas en Agar MacConkey e incubadas a 37 °C por 24 horas. Las colonias aisladas fueron identificadas con el estuche BD BBL-Cristal E/NF®. Resultados. En 20 de los pacientes estudiados se detectaron bacterias sobreinfecciosas, pero, con mayor frecuencia en pacientes con implantes afectados (n=15) que en portadores de implantes sanos (n=5). La prevalencia de bacterias sobreinfecciosas en todos los implantes fue de 33,8 % (n=23/68), y también fue más frecuente su aislamiento en implantes afectados (n=17) (25%), que en estables (n=6) (8,8%). Klebsiella pneumoniae fue el microorganismo que se aisló con mayor frecuencia en todos los implantes (n=12). Conclusiones. Un tercio de los implantes estudiados presentaron organismos sobreinfecciosos. Los implantes con lesiones periimplante presentan una mayor frecuencia de bacterias sobreinfecciosas. K. pneumoniae es la especie sobreinfecciosa más frecuente en los implantes estudiados. Se presentó infección múltiple con dichas bacterias en los implantes afectados. Estos microorganismos pueden afectar la estabilidad de los implantes.

Introduction. Implants can be colonized by microorganisms from oral biofilms and may affect peri-implant tissues health. Among these bacteria, pathogens typically associated with periodontitis can be found, such as Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis, as well as Gram negative enteric bacilli not typically associated with periodontal diseases. Objective. Superinfecting bacteria were characterized from peri-implant lesions in patients with history of periodontitis. Materials and methods. Sixty-eight implants were studied in 55 patients; the average patient age was 56 years. Forty-nine implants had peri-implant lesions and 19 were considered stable. Subgingival samples were obtained in affected and stable implants. The samples were streaked on Mac-Conkey agar and incubated at 37°C for 24 hours. The colonies were identified with the kit-BD BBL Crystal E/NF®. Results. Superinfecting organisms were detected in 20 patients--they were seen more frequently at diseased implants (n=15) than at healthy implants (n=5). The prevalence of superinfecting bacteria on the selected implants was 33.8% (n=23/68). These bacteria were more prevalent among affected implants (n=17 or 25%) than those with stable implants n=6 (8.8%). Klebsiella pneumoniae was the most frequent Gram negative rod detected (n=12). Conclusions. One-third of the implants had superinfecting organisms. Implants with a peri-implant lesion had a higher frequency of superinfecting bacteria. Klebsiella pneumoniae was the most common superinfecting organism isolated. A multiple infection caused by superinfecting bacteria was present only at diseased implants. These microbial agents potentially affect implant stability.