The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant

Canaries' Microbiota: The Gut Bacterial Communities along One Female Reproductive Cycle

Investigations of bacterial communities are on the rise both in human and veterinary medicine. Their role in health maintenance and pathogenic mechanisms is in the limelight of infectious, metabolic, and cancer research. Among the most considered, gut bacterial communities take the cake. Their part in animals was assessed mainly to improve animal production, public health, and pet management. In this regard, canaries deserve attention, being a popular pet and source of economic income for bird-keepers, for whom breeding represents a pivotal point. Thus, the present work aimed to follow gut bacterial communities' evolution along on whole reproductive cycle of 12 healthy female canaries. Feces were collected during parental care, molting, and resting phase, and submitted for 16S rRNA sequencing. Data were analyzed and a substantial presence of Lactobacillus aviarius along all the phases, and a relevant shift of microbiota during molting and rest due to an abrupt decrease of the Vermiphilaceae family were detected. Although the meaning of such change is not clear, future research may highlight unforeseen scenarios. Moreover, Lactobacillus aviarius may be deemed for normal bacteria flora restoration in debilitated birds, perhaps improving their health and productivity.

Legionella pneumophila Rhizoferrin Promotes Bacterial Biofilm Formation and Growth within Amoebae and Macrophages

Previously, we showed that Legionella pneumophila secretes rhizoferrin, a polycarboxylate siderophore that promotes bacterial growth in iron-deplete media and the murine lung. Yet, past studies failed to identify a role for the rhizoferrin biosynthetic gene (lbtA) in L. pneumophila infection of host cells, suggesting the siderophore's importance was solely linked to extracellular survival. To test the possibility that rhizoferrin's relevance to intracellular infection was missed due to functional redundancy with the ferrous iron transport (FeoB) pathway, we characterized a new mutant lacking both lbtA and feoB. This mutant was highly impaired for growth on bacteriological media that were only modestly depleted of iron, confirming that rhizoferrin-mediated ferric iron uptake and FeoB-mediated ferrous iron uptake are critical for iron acquisition. The lbtA feoB mutant, but not its lbtA-containing complement, was also highly defective for biofilm formation on plastic surfaces, demonstrating a new role for the L. pneumophila siderophore in extracellular survival. Finally, the lbtA feoB mutant, but not its complement containing lbtA, proved to be greatly impaired for growth in Acanthamoeba castellanii, Vermamoeba vermiformis, and human U937 cell macrophages, revealing that rhizoferrin does promote intracellular infection by L. pneumophila. Moreover, the application of purified rhizoferrin triggered cytokine production from the U937 cells. Rhizoferrin-associated genes were fully conserved across the many sequenced strains of L. pneumophila examined but were variably present among strains from the other species of Legionella. Outside of Legionella, the closest match to the L. pneumophila rhizoferrin genes was in Aquicella siphonis, another facultative intracellular parasite of amoebae.

Sodium levels and grazing pressure shape natural communities of the intracellular pathogen Legionella

BACKGROUND

Legionella are parasites of freshwater protozoa, responsible for Legionellosis. Legionella can be found in a variety of aquatic environments, including rivers, lakes, and springs, as well as in engineered water systems where they can potentially lead to human disease outbarks. Legionella are considered to be predominantly freshwater organisms with a limited ability to proliferate in saline environments. Exposure of Legionella to high sodium concentrations inhibits growth and virulence of laboratory strains, particularly under elevated temperatures. Nonetheless, Legionella have been identified in some saline environments where they likely interact with various protozoan hosts. In this work, we examine how these selection pressures, sodium and grazing, help shape Legionella ecology within natural environments. Utilizing Legionella-specific primers targeting a variable region of the Legionella 16S rRNA gene, we characterized Legionella abundance, diversity, and community composition in natural spring clusters of varying sodium concentrations, focusing on high sodium concentrations and elevated temperatures.

RESULTS

We observed the highest abundance of Legionella in spring clusters of high salinity, particularly in combination with elevated temperatures. Legionella abundance was strongly related to sodium concentrations. The Legionella community structure in saline environments was characterized by relatively low diversity, compared to spring clusters of lower salinity. The community composition in high salinity was characterized by few dominant Legionella genotypes, not related to previously described species. Protozoan microbial community structure and composition patterns resembled those of Legionella, suggesting a common response to similar selection pressures. We examined Legionella co-occurrence with potential protozoan hosts and found associations with Ciliophora and Amoebozoa representatives.

CONCLUSIONS

Our results indicate that selection forces in saline environments favor a small yet dominant group of Legionella species that are not closely related to known species. These novel environmental genotypes interact with various protozoan hosts, under environmental conditions of high salinity. Our findings suggest that alternative survival mechanisms are utilized by these species, representing mechanisms distinct from those of well-studied laboratory strains. Our study demonstrate how salinity can shape communities of opportunistic pathogens and their hosts, in natural environments, shedding light on evolutionary forces acting within these complex environments. Video Abstract.

Rapid adaptations of Legionella pneumophila to the human host

Legionella pneumophila are host-adapted bacteria that infect and reproduce primarily in amoeboid protists. Using similar infection mechanisms, they infect human macrophages, and cause Legionnaires' disease, an atypical pneumonia, and the milder Pontiac fever. We hypothesized that, despite the similarities in infection mechanisms, the hosts are different enough that there exist high-selective value mutations that would dramatically increase the fitness of Legionella inside the human host. By comparing a large number of isolates from independent infections, we identified two genes, mutated in three unrelated patients, despite the short duration of the incubation period (2-14 days). One is a gene coding for an outer membrane protein (OMP) belonging to the OmpP1/FadL family. The other is a gene coding for an EAL-domain-containing protein involved in cyclic-di-GMP regulation, which in turn modulates flagellar activity. The clinical strain, carrying the mutated EAL-domain-containing homologue, grows faster in macrophages than the wild-type strain, and thus appears to be better adapted to the human host. As human-to-human transmission is very rare, fixation of these mutations into the population and spread into the environment is unlikely. Therefore, parallel evolution - here mutations in the same genes observed in independent human infections - could point to adaptations to the accidental human host. These results suggest that despite the ability of L. pneumophila to infect, replicate in and exit from macrophages, its human-specific adaptations are unlikely to be fixed in the population.

Protein sociology of ProA, Mip and other secreted virulence factors at the Legionella pneumophila surface

The pathogenicity of L. pneumophila, the causative agent of Legionnaires' disease, depends on an arsenal of interacting proteins. Here we describe how surface-associated and secreted virulence factors of this pathogen interact with each other or target extra- and intracellular host proteins resulting in host cell manipulation and tissue colonization. Since progress of computational methods like AlphaFold, molecular dynamics simulation, and docking allows to predict, analyze and evaluate experimental proteomic and interactomic data, we describe how the combination of these approaches generated new insights into the multifaceted "protein sociology" of the zinc metalloprotease ProA and the peptidyl-prolyl cis/trans isomerase Mip (macrophage infectivity potentiator). Both virulence factors of L. pneumophila interact with numerous proteins including bacterial flagellin (FlaA) and host collagen, and play important roles in virulence regulation, host tissue degradation and immune evasion. The recent progress in protein-ligand analyses of virulence factors suggests that machine learning will also have a beneficial impact in early stages of drug discovery.

Microbiome network in the pelagic and benthic offshore systems of the northern Adriatic Sea (Mediterranean Sea)

Because of their recognized global importance, there is now the urgent need to map diversity and distribution patterns of marine microbial communities. Even if available studies provided some advances in the understanding the biogeographical patterns of marine microbiomes at the global scale, their degree of plasticity at the local scale it is still underexplored, and functional implications still need to be dissected. In this scenario here we provide a synoptical study on the microbiomes of the water column and surface sediments from 19 sites in a 130 km2 area located 13.5 km afar from the coast in the North-Western Adriatic Sea (Italy), providing the finest-scale mapping of marine microbiomes in the Mediterranean Sea. Pelagic and benthic microbiomes in the study area showed sector specific-patterns and distinct assemblage structures, corresponding to specific variations in the microbiome network structure. While maintaining a balanced structure in terms of potential ecosystem services (e.g., hydrocarbon degradation and nutrient cycling), sector-specific patterns of over-abundant modules—and taxa—were defined, with the South sector (the closest to the coast) characterized by microbial groups of terrestrial origins, both in the pelagic and the benthic realms. By the granular assessment of the marine microbiome changes at the local scale, we have been able to describe, to our knowledge at the first time, the integration of terrestrial microorganisms in the marine microbiome networks, as a possible natural process characterizing eutrophic coastal area. This raises the question about the biological threshold for terrestrial microorganisms to be admitted in the marine microbiome networks, without altering the ecological balance.

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil

Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages.IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.

Ten-Year Retrospective Analysis of Legionella Diffusion in Hospital Water Systems and Its Serogroup Seasonal Variation

INTRODUCTION

Legionella spp. are ubiquitous aquatic organisms found to be associated with community-acquired pneumoniae (CAP) as well as hospital-acquired pneumonia (HAP). Direct inhalation of aerosols from environmental colonisation is typically the source of infection. The aim of this study was to determine the level of colonisation in hospital water supply systems in order to assess the criticality of the water distribution network and strengthen preventive measures.

METHODS

From 2009 to 2018, 769 water samples were collected and then analysed according to the standard methods indicated in ISO11731-2:2004 and ISO11731:2017 for Legionella detection.

RESULTS

The samples were positive in 37.1% cases (n. 285) and negative in 62.9% cases (n. 484). The threshold of 10,000 CFU/L was exceeded in 15.1% cases and led to decolonisation as indicated by Italian and European ECDC guidelines. In the autumn-winter period SG1 showed a positivity of 41.2% (n. 40) with a decrease in the spring-summer period with 9.6% (n. 18) of positivity. In contrast, SG2-15 showed a positivity of 30.9% (n. 30) in autumn-winter, which tends to increase to 56.9% (n. 112) in spring-summer (p < 0.001).

CONCLUSION

Surprisingly, besides showing a seasonal trend already described previously in the literature, the positivity of our sample was not balanced even for serogroups in the two periods. This could be due to genetic differences and ecological niches to be further investigated that could also have links with the greater pathogenicity of SG1. Environmental microbiological surveillance and risk assessment should be performed more frequently and disinfection must be carried out, especially in health facilities where people are more susceptible to infections.

DVC-FISH to identify potentially pathogenic Legionella inside free-living amoebae from water sources

Despite all safety efforts, drinking and wastewater can still be contaminated by Legionella and free-living amoebae (FLA) since these microorganisms are capable of resisting disinfection treatments. An amoebae cyst harboring pathogenic Legionella spp. can be a transporter of this organism, protecting it and enhancing its infection abilities. Therefore, the aim of this work is to identify by DVC-FISH viable Legionella spp and Legionella pneumophila cells inside FLA from water sources in a specific and rapid way with the aim of assessing the real risk of these waters. A total of 55 water samples were processed, 30 reclaimed wastewater and 25 drinking water. FLA presence was detected in 52.7% of the total processed water samples. When DVC-FISH technique was applied, the presence of viable internalized Legionella spp. cells was identified in 69.0% of the total FLA-positive samples, concretely in 70.0% and 66.7% of wastewater and drinking water samples, respectively. L. pneumophila was simultaneously identified in 48.3% of the total FLA-positive samples, specifically in 50.0% and 44.4% of wastewater and drinking water samples, respectively. By culture, potentially pathogenic Legionella cells were recovered in 27.6% of the total FLA-positive bacteria, particularly in 35.0% and 11.1% of wastewater and drinking water samples, respectively. These findings demonstrate that FLA may promote resistance of bacteria to the performed disinfection treatments for drinking as well as for wastewater. So, in addition to the risk for the presence of pathogenic FLA in water it is necessary to take into account that these can be transporters of the pathogenic bacteria Legionella, which are able to survive inside them. The DVC-FISH method described here has been proved to be a rapid and specific tool to identify pathogenic Legionella spp. and L. penumophila viable cells harboured by FLA in these water sources, posing particular public health concern.