Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota

The recently isolated bacterium "Candidatus Uabimicrobium amorphum" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that "Ca. Uabimicrobium amorphum" represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in "Ca. Uabimicrobium amorphum", of which 66 families contained eukaryotic-like Serine/Threonine kinases with Pkinase domains. In total, we predicted 525 functional Serine/Threonine kinases in "Ca. Uabimicrobium amorphum", which represent 8% of the proteome and is the highest fraction of Serine/Threonine kinases in a bacterial proteome. The majority of Serine/Threonine kinases in this species are membrane proteins and 30% contain long, tandem arrays of WD40 or TPR domains. The pKinase domain was predicted to be located in the cytoplasm, while the WD40 and TPR domains were predicted to be located in the periplasm. Such domain combinations were also identified in the Serine/Threonine kinases of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the Serine/Threonine kinases in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the Serine/Threonine kinases in "Ca. Uabimicrobium amorphum". The results imply that expansions of eukaryotic-like signal transduction systems are not restricted to multicellular organisms, but have occurred in parallel in prokaryotes with predatory lifestyles and phagocytotic-like behaviors.

TADA: taxonomy-aware dataset aggregator

SUMMARY

The profusion of sequenced genomes across the bacterial and archeal domains offers unprecedented possibilities for phylogenetic and comparative genomic analyses. In general, phylogenetic reconstruction is improved by the use of more data. However, including all available data is (i) not computationally tractable, and (ii) prone to biases, as the abundance of genomes is very unequally distributed over the biological diversity. Thus, in most cases, subsampling taxa to build a phylogeny is necessary. Currently, though, there is no available software to perform that handily. Here we present TADA, a taxonomic-aware dataset selection workflow that allows sampling across user-defined portions of the prokaryotic diversity with variable granularity, while setting constraints on genome quality and balance between branches.

AVAILABILITY AND IMPLEMENTATION

TADA is implemented as a snakemake workflow and is freely available at https://github.com/emilhaegglund/TADA.

The evolution of intramitochondriality in Midichloria bacteria

Midichloria spp. are intracellular bacterial symbionts of ticks. Representatives of this genus colonise mitochondria in the cells of their hosts. To shed light on this unique interaction we evaluated the presence of an intramitochondrial localization for three Midichloria in the respective tick host species and generated eight high-quality draft genomes and one closed genome, showing that this trait is non-monophyletic, either due to losses or multiple acquisitions. Comparative genomics supports the first hypothesis, as the genomes of non-mitochondrial symbionts are reduced subsets of those capable of colonising the organelles. We detect genomic signatures of mitochondrial tropism, including the differential presence of type IV secretion system and flagellum, which could allow the secretion of unique effectors and/or direct interaction with mitochondria. Other genes, including adhesion molecules, proteins involved in actin polymerisation, cell wall and outer membrane proteins, are only present in mitochondrial symbionts. The bacteria could use these to manipulate host structures, including mitochondrial membranes, to fuse with the organelles or manipulate the mitochondrial network.

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.

Early divergence of translation initiation and elongation factors

Protein translation is a foundational attribute of all living cells. The translation function carried out by the ribosome critically depends on an assortment of protein interaction partners, collectively referred to as the translation machinery. Various studies suggest that the diversification of the translation machinery occurred prior to the last universal common ancestor, yet it is unclear whether the predecessors of the extant translation machinery factors were functionally distinct from their modern counterparts. Here we reconstructed the shared ancestral trajectory and subsequent evolution of essential translation factor GTPases, elongation factor EF-Tu (aEF-1A/eEF-1A), and initiation factor IF2 (aIF5B/eIF5B). Based upon their similar functions and structural homologies, it has been proposed that EF-Tu and IF2 emerged from an ancient common ancestor. We generated the phylogenetic tree of IF2 and EF-Tu proteins and reconstructed ancestral sequences corresponding to the deepest nodes in their shared evolutionary history, including the last common IF2 and EF-Tu ancestor. By identifying the residue and domain substitutions, as well as structural changes along the phylogenetic history, we developed an evolutionary scenario for the origins, divergence and functional refinement of EF-Tu and IF2 proteins. Our analyses suggest that the common ancestor of IF2 and EF-Tu was an IF2-like GTPase protein. Given the central importance of the translation machinery to all cellular life, its earliest evolutionary constraints and trajectories are key to characterizing the universal constraints and capabilities of cellular evolution.

Host-adaptation in Legionellales is 1.9 Ga, coincident with eukaryogenesis

Bacteria adapting to living in a host cell caused the most salient events in the evolution of eukaryotes, namely the seminal fusion with an archaeon, and the emergence of both mitochondrion and chloroplast. A bacterial clade that may hold the key to understanding these events is the deep-branching gammaproteobacterial order Legionellales-containing among others Coxiella and Legionella-of which all known members grow inside eukaryotic cells. Here, by analyzing 35 novel Legionellales genomes mainly acquired through metagenomics, we show that this group is much more diverse than previously thought, and that key host-adaptation events took place very early in its evolution. Crucial virulence factors like the Type IVB secretion (Dot/Icm) system and two shared effector proteins were gained in the last Legionellales common ancestor (LLCA). Many metabolic gene families were lost in LLCA and its immediate descendants, including functions directly and indirectly related to molybdenum metabolism. On the other hand, genome sizes increased in the ancestors of the Legionella genus. We estimate that LLCA lived circa 1.89 Ga ago, probably predating the last eukaryotic common ancestor (LECA) by circa 0.4-1.0 Ga. These elements strongly indicate that host-adaptation arose only once in Legionellales, and that these bacteria were using advanced molecular machinery to exploit and manipulate host cells early in eukaryogenesis.

[Effectiveness of sacral neuromodulation in patients with Parkinson's disease]

INTRODUCTION

The urinary disorders of the patients with Parkinson's disease are complex and have a negative impact on their quality of life. None of therapy is considered effective ; whether drug or surgical. Sacral neuromodulation, recommended in other neurological pathologies such as multiple sclerosis, has never been studied in the patients with Parkinson's disease. The objective of our study is to assess the efficacy of sacral neuromodulation in the patients with Parkinson's disease.

MATERIAL AND METHOD

Multicentric retrospective cohort study, of 22 parkinsonian patients who underwent a sacral neuromodulation test. Epidemiological, clinical and urodynamic data were collected for each patient. A long-term effectiveness telephone survey was conducted.

RESULTS

Twenty two patients with Parkinson's disease had a sacral neuromodulation test. 17/22 (77%) had Idiopathic Parkinson's Disease and 5/22 (23%) had Systematized Multi Atrophy. Clinically, the indication for the sacral neuromodulation test was overactive bladder in 68% of the cases. Urodynamically, detrusor hyperactivity is found in 12 patients (8 MPI, 4 AMS). Sacral neuromodulation was effective in only 7 patients (6 MPI and 1 AMS). Rather, the profile of the patient in whom NMS is effective is female, mature, and with PID. The long-term effectiveness of NMS is disappointing. Only 2 permanently implanted patients retained urinary benefit.

CONCLUSION

NMS improves urinary symptoms in the patients with Parkinson's disease in 32% of cases. It fluctuates over time and loses its effectiveness in the long term.

LEVEL OF EVIDENCE

3.

Chromosomal Location Determines the Rate of Intrachromosomal Homologous Recombination in Salmonella

Homologous recombination is an important mechanism directly involved in the repair, organization, and evolution of prokaryotic and eukaryotic chromosomes. We developed a system, based on two genetic cassettes, that allows the measurement of recombinational repair rates between different locations on the chromosome. Using this system, we analyzed 81 different positional combinations throughout the chromosome to answer the question of how the position and orientation of sequences affect intrachromosomal homologous recombination. Our results show that recombination was possible between any two locations tested in this study and that recombinational repair rates varied by just above an order of magnitude. The observed differences in rate do not correlate with distance between the recombination cassettes or with distance from the origin of replication but could be explained if each location contributes individually to the recombination event. The relative levels of accessibility for recombination vary 5-fold between the various cassette locations, and we found that the nucleoid structure of the chromosome may be the major factor influencing the recombinational accessibility of each chromosomal site. Furthermore, we found that the orientation of the recombination cassettes had a significant impact on recombination. Recombinational repair rates for the cassettes inserted as direct repeats are, on average, 2.2-fold higher than those for the same sets inserted as inverted repeats. These results suggest that the bacterial chromosome is not homogenous with regard to homologous recombination, with regions that are more or less accessible, and that the orientation of genes affects recombination rates. IMPORTANCE Bacterial chromosomes frequently carry multiple copies of genes at separate chromosomal locations. In Salmonella, these include the 7 rrn operons and the duplicate tuf genes. Genes within these families coevolve by homologous recombination, but it is not obvious whether their rates of recombination reflect general rates of intrachromosomal recombination or are an evolved property particularly associated with these conserved genes and locations. Using a novel experimental system, we show that recombination is possible between all tested pairs of locations at rates that vary by just above 1 order of magnitude. Differences in rate do not correlate with distance between the sites or distance to the origin of replication but may be explained if each location contributes individually to the recombination event. Our results suggest the existence of bacterial chromosomal domains that are differentially available for recombination and that gene orientation affects recombination rates.

Molecular Characterization of Multidrug-Resistant Yersinia enterocolitica From Foodborne Outbreaks in Sweden

The foodborne pathogen Yersinia enterocolitica causes gastrointestinal infections worldwide. In the spring of 2019, the Swedish Public Health Agency and Statens Serum Institut in Denmark independently identified an outbreak caused by Yersinia enterocolitica 4/O:3 that after sequence comparison turned out to be a cross-border outbreak. A trace-back investigation suggested shipments of fresh prewashed spinach from Italy as a common source for the outbreak. Here, we determined the genome sequences of five Y. enterocolitica clinical isolates during the Swedish outbreak using a combination of Illumina HiSeq short-read and Nanopore Technologies’ MinION long-read whole-genome sequencing. WGS results showed that all clinical strains have a fully assembled chromosome of approximately 4.6 Mbp in size and a 72-kbp virulence plasmid; one of the strains was carrying an additional 5.7-kbp plasmid, pYE-tet. All strains showed a high pathogen probability score (87.5%) with associated genes for virulence, all of which are closely related to an earlier clinical strain Y11 from Germany. In addition, we identified a chromosomally encoded multidrug-resistance cassette carrying resistance genes against chloramphenicol (catA1), streptomycin (aadA1), sulfonamides (sul1), and a mercury resistance module. This chromosomally encoded Tn2670 transposon has previously been reported associated with IncFII plasmids in Enterobacteriaceae: a Shigella flexneri clinical isolate from Japan in 1950s, a Klebsiella pneumoniae outbreak from Australia in 1997, and Salmonella enterica serovar Typhimurium. Interestingly, we identified an additional 5.7-kbp plasmid with tetB (encoding an ABC transporter), Rep, and its own ORI and ORIt sites, sharing high homology with small tetB-Rep plasmids from Pasteurellaceae. This is the first time that Tn2670 and Pasteurellaceae plasmids have been reported in Y. enterocolitica. Taken together, our study showed that the Swedish Y. enterocolitica outbreak strains acquired multi-antibiotic and metal-resistance genes through horizontal gene transfer, suggesting a potential reservoir of intraspecies dissemination of multidrug-resistance genes among foodborne pathogens. This study also highlights the concern of food-chain contamination of prewashed vegetables as a perpetual hazard against public health.

Expression of the qepA1 gene is induced under antibiotic exposure

Background

The qepA1 gene encodes an efflux pump that reduces susceptibility to ciprofloxacin. Little is known about the regulation of qepA1 expression.

Objectives

To assess the potential role of ciprofloxacin and other antibiotics in the regulation of qepA1 gene expression. To identify the promoter that drives qepA1 expression and other factors involved in expression regulation. To assess whether the identified features are universal among qepA alleles.

Methods

A translational qepA1-yfp fusion under the control of the qepA1 upstream region was cloned into the Escherichia coli chromosome. Expression of the fusion protein was measured in the presence of various antibiotics. Deletions within the upstream region were introduced to identify regions involved in gene expression and regulation. The qepA1 coding sequence and upstream region were compared with all available qepA sequences.

Results

Cellular stress caused by the presence of various antibiotics can induce qepA1 expression. The qepA1 gene is fused to a class I integron and gene expression is driven by the Pc promoter within the integrase gene. A segment within the integron belonging to a truncated dfrB4 gene is essential for the regulation of qepA1 expression. This genetic context is universal among all sequenced qepA alleles.

Conclusions

The fusion of the qepA1 gene to a class I integron has created a novel regulatory unit that enables qepA1 expression to be under the control of antibiotic exposure. This setup mitigates potential negative effects of QepA1 production on bacterial fitness by restricting high-level expression to environmental conditions in which QepA1 is beneficial.

[Penile prosthesis for erectile dysfunction in the neurological patient, indication, complications and satisfaction: Retrospective study on 27 patients]

INTRODUCTION

Penile prosthesis for erectile dysfunction in patients with spinal cord injury or multiple sclerosis is sometimes discussed after failure of drug or instrumental treatments (vacuum). The objective of this study was to evaluate the complications, evolution and patient satisfaction after the implantation of a penile prosthesis in the neurological patient.

MATERIALS AND METHODS

Multi-center retrospective study of 27 consecutive patients including 18 spinal cord injured patients and 9 patients with multiple sclerosis benefiting from the implantation of a penile prosthesis for erectile dysfunction purposes in two French centers between 2009 and 2019. Post-implantation complications, evolution of the use of the prosthesis and global patient satisfaction were evaluated using the standardized questionnaire Erectile Dysfunction Inventory of Treatment Satisfaction (EDITS) during a telephone call between March and May 2020.

RESULTS

The average age of implantation was 46.4 years (±12.74). The length of follow-up to date of call was 6.05 years (±2.86). 8/27 patients (29.6 %) had at least one complication of any Clavien-Dindo grade included 2 infection. 2/27 (7,4 %) patients had a mechanical prosthesis injury during follow-up. The patient's dexterity with inflation of the prosthesis was perfect in 85 % of cases, and 75 % for deflation. The satisfaction rate for prosthesis use at the time of the call was 75.36/100pts for the patient and 66.88/100pts for the partner.

CONCLUSION

This study found an increased rate of prothesis infection compared to the general population in the neurologic patient, but patient and partner satisfaction remain sustainable after more than 5 years of implantation. Dexterity was maintained over the long term, demonstrating a good selection of indications. These data invite to favorably consider the installation of a penile prosthesis in neurological patients who have failed first-line treatments.

LEVEL OF EVIDENCE

4.

[Cystocele repair by a light tension-free vaginal mesh: results after 6 years of follow-up]

INTRODUCTION

The objective of this study was to evaluate the long-term anatomical and functional efficacy, but also the safety of tension-free vaginal mesh in cystocele repair.

METHODS

This retrospective and monocentric study included 90 women who underwent a prolapse repair between June 2006 and November 2008. A light-weight polypropylene vaginal mesh (22g/m2, Novasilk COLOPLAST®) was used without any fixation. Females were followed at 1 month, 1 year, 3 years and 6 years. Only long-term results are presented in this study. The anatomical result was assessed by the POP-Q classification and the functional results by standardized symptoms (PFDI-20), sexuality (PISQ-12) and quality of life (PFIQ-7) questionnaires.

RESULTS

6 years after surgery, the follow-up rate was 74%. Anatomically, the prolapse recurrence rate (Ba≥0) was 17% (n=8). Functionally, the overall patient satisfaction rate was 89%. Quality of life and symptoms scores (4,11±8.45 vs. 17.5±14.4 and 35.8±15.9 vs 94±23.4 respectively) were significantly improved (p<0.001). Concerning the prevalence of the complication, the retraction and exposition rate was 1.7% (n=1) and a re-intervention rate was 6.7% (n=4). The rate of de novo dyspareunia was 1.7% (n=1).

CONCLUSION

In this short retrospective series of vaginal mesh interposition for cystocele repair, the prevalence of medium-term patient satisfaction was high.

Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures

Bacteria of the phylum Planctomycetes have a unique cell plan with an elaborate intracellular membrane system, thereby resembling eukaryotic cells. The origin and evolution of these remarkable features is debated. To study the evolutionary genomics of bacteria with complex cell architectures, we have resequenced the 9.2-Mb genome of the model organism Gemmata obscuriglobus and sequenced the 10-Mb genome of G. massiliana Soil9, the 7.9-Mb genome of CJuql4, and the 6.7-Mb genome of Tuwongella immobilis, all of which belong to the family Gemmataceae. A gene flux analysis of the Planctomycetes revealed a massive emergence of novel protein families at multiple nodes within the Gemmataceae. The expanded protein families have unique multidomain architectures composed of domains that are characteristic of prokaryotes, such as the sigma factor domain of extracytoplasmic sigma factors, and domains that have proliferated in eukaryotes, such as the WD40, leucine-rich repeat, tetratricopeptide repeat and Ser/Thr kinase domains. Proteins with identifiable domains in the Gemmataceae have longer lengths and linkers than proteins in most other bacteria, and the analyses suggest that these traits were ancestrally present in the Planctomycetales. A broad comparison of protein length distribution profiles revealed an overlap between the longest proteins in prokaryotes and the shortest proteins in eukaryotes. We conclude that the many similarities between proteins in the Planctomycetales and the eukaryotes are due to convergent evolution and that there is no strict boundary between prokaryotes and eukaryotes with regard to features such as gene paralogy, protein length, and protein domain composition patterns.

miComplete: weighted quality evaluation of assembled microbial genomes

SUMMARY

Metagenomics and single-cell genomics have revolutionized the study of microorganisms, increasing our knowledge of microbial genomic diversity by orders of magnitude. A major issue pertaining to metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) is to estimate their completeness and redundancy. Most approaches rely on counting conserved gene markers. In miComplete, we introduce a weighting strategy, where we normalize the presence/absence of markers by their median distance to the next marker in a set of complete reference genomes. This approach alleviates biases introduced by the presence/absence of shorter DNA pieces containing many markers, e.g. ribosomal protein operons.

AVAILABILITY AND IMPLEMENTATION

miComplete is written in Python 3 and released under GPLv3. Source code and documentation are available at https://bitbucket.org/evolegiolab/micomplete.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

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

Legionellales is an order of the Gammaproteobacteria, only composed of host-adapted, intracellular bacteria, including the accidental human pathogens Legionella pneumophila and Coxiella burnetii. Although the diversity in terms of lifestyle is large across the order, only a few genera have been sequenced, owing to the difficulty to grow intracellular bacteria in pure culture. In particular, we know little about their global distribution and abundance.

Here, we analyze 16/18S rDNA amplicons both from tens of thousands of published studies and from two separate sampling campaigns in and around ponds and in a silver mine. We demonstrate that the diversity of the order is much larger than previously thought, with over 450 uncultured genera. We show that Legionellales are found in about half of the samples from freshwater, soil and marine environments and quasi-ubiquitous in man-made environments. Their abundance is low, typically 0.1%, with few samples up to 1%. Most Legionellales OTUs are globally distributed, while many do not belong to a previously identified species.

This study sheds a new light on the ubiquity and diversity of one major group of host-adapted bacteria. It also emphasizes the need to use metagenomics to better understand the role of host-adapted bacteria in all environments.

Origin and Evolution of the Bartonella Gene Transfer Agent

Gene transfer agents (GTAs) are domesticated bacteriophages that have evolved into molecular machines for the transfer of bacterial DNA. Despite their widespread nature and their biological implications, the mechanisms and selective forces that drive the emergence of GTAs are still poorly understood. Two GTAs have been identified in the Alphaproteobacteria: the RcGTA, which is widely distributed in a broad range of species; and the BaGTA, which has a restricted host range that includes vector-borne intracellular bacteria of the genus Bartonella. The RcGTA packages chromosomal DNA randomly, whereas the BaGTA particles contain a relatively higher fraction of genes for host interaction factors that are amplified from a nearby phage-derived origin of replication. In this study, we compare the BaGTA genes with homologous bacteriophage genes identified in the genomes of Bartonella species and close relatives. Unlike the BaGTA, the prophage genes are neither present in all species, nor inserted into homologous genomic sites. Phylogenetic inferences and substitution frequency analyses confirm codivergence of the BaGTA with the host genome, as opposed to multiple integration and recombination events in the prophages. Furthermore, the organization of segments flanking the BaGTA differs from that of the prophages by a few rearrangement events, which have abolished the normal coordination between phage genome replication and phage gene expression. Based on the results of our comparative analysis, we propose a model for how a prophage may be transformed into a GTA that transfers amplified bacterial DNA segments.

Legionella pneumophila recurrently isolated in a Spanish hospital: Two years of antimicrobial resistance surveillance

OBJECTIVES

The aim of this study was to monitor the spread, persistence and antibiotic resistance patterns of Legionella spp. strains found in a hospital water distribution system. These environmental studies are intended to help detect the presence of antibiotic resistant strains before they infect patients.

METHODS

Antimicrobial surveillance tests were performed at 27 different sampling points of the water network of a large Spanish hospital over two years. Water samples were screened for Legionella according to ISO 11731:2007. Legionella spp. isolates were identified by serotyping and by mass spectrometry (MALDI-ToF). Epidemiological molecular typing was done by Pulse-Field Gel Electrophoresis (PFGE) and by Sequence-Based Typing (SBT). Antibiotic susceptibility tests were performed using disk diffusion and ETEST®.

RESULTS

Legionella spp. were recurrently isolated for 2 years. All isolates belonged the same group, L. pneumophila serogroups 2-14. Isolates were all attributed by SBT to sequence type (ST) ST328, although PFGE revealed 5 different patterns. No significant change in antibiotic susceptibility could be observed for this study period, irrespectively of the method used.

CONCLUSION

Colonization of water systems by Legionella spp. is still occurring, although all the prevention rules were strictly followed. Antibiotic resistance monitoring may help us to find resistance in bacteria with environmental reservoirs but difficult to isolate from patients. The knowledge of the antibiotic susceptibility in environmental strains may help us to predict changes in clinical strains. This study might also help reconsidering Legionnaires' disease (LD) diagnostic methods. L. pneumophila serogroups 2-14 present all along the time of the investigation in the water distribution system can cause LD. However, they may not be detected by routine urine tests run on patients, thereby missing an ongoing LD infection.

Withdrawn as Duplicate: The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant

Legionellales is an order of the Gammaproteobacteria, only composed of host-adapted, intracellular bacteria, including the accidental human pathogens Legionella pneumophila and Coxiella burnetii. Although the diversity in terms of lifestyle is large across the order, only a few genera have been sequenced, owing to the difficulty to grow intracellular bacteria in pure culture. In particular, we know little about their global distribution and abundance.Here, we analyze 16/18S rDNA amplicons both from tens of thousands of published studies and from two separate sampling campaigns in and around ponds and in a silver mine. We demonstrate that the diversity of the order is much larger than previously thought, with over 450 uncultured genera. We show that Legionellales are found in about half of the samples from freshwater, soil and marine environments, and quasi-ubiquitous in man-made environments. Their abundance is low, typically 0.1%, with few samples up to 1%. Most Legionellales OTUs are globally distributed, while many do not belong to a previously identified species.This study sheds a new light on the ubiquity and diversity of one major group of host-adapted bacteria. It also emphasizes the need to use metagenomics to better understand the role of host-adapted bacteria in all environments.

Experimental Determination and Prediction of the Fitness Effects of Random Point Mutations in the Biosynthetic Enzyme HisA

The distribution of fitness effects of mutations is a factor of fundamental importance in evolutionary biology. We determined the distribution of fitness effects of 510 mutants that each carried between 1 and 10 mutations (synonymous and nonsynonymous) in the hisA gene, encoding an essential enzyme in the l-histidine biosynthesis pathway of Salmonella enterica. For the full set of mutants, the distribution was bimodal with many apparently neutral mutations and many lethal mutations. For a subset of 81 single, nonsynonymous mutants most mutations appeared neutral at high expression levels, whereas at low expression levels only a few mutations were neutral. Furthermore, we examined how the magnitude of the observed fitness effects was correlated to several measures of biophysical properties and phylogenetic conservation.We conclude that for HisA: (i) The effect of mutations can be masked by high expression levels, such that mutations that are deleterious to the function of the protein can still be neutral with regard to organism fitness if the protein is expressed at a sufficiently high level; (ii) the shape of the fitness distribution is dependent on the extent to which the protein is rate-limiting for growth; (iii) negative epistatic interactions, on an average, amplified the combined effect of nonsynonymous mutations; and (iv) no single sequence-based predictor could confidently predict the fitness effects of mutations in HisA, but a combination of multiple predictors could predict the effect with a SD of 0.04 resulting in 80% of the mutations predicted within 12% of their observed selection coefficients.

Resurrecting ancestral genes in bacteria to interpret ancient biosignatures

Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behaviour of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can downselect to a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can one use modern life to reconstruct ancestral behaviours? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the laboratory to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and then to link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first step beyond single-molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the beta-carbonic anhydrase protein. We assess how carbonic anhydrase proteins meet our selection criteria for reconstructing ancient biosignatures in the laboratory, which we term palaeophenotype reconstruction.This article is part of the themed issue 'Reconceptualizing the origins of life'.

[Results of conservative surgical management of ureteral injuries]

INTRODUCTION

The ureter is a retroperitoneal organ. Ureteral injuries are rare, with a prevalence of 0.083% of surgical interventions over 10 years. The objective of this study was to evaluate the surgical management of ureteric injuries according to the time of discovery, their size and their location. We also evaluated the results of this management on the renal repercussion as well as the predictive factors of the severity of the ureteric injuries.

MATERIAL AND METHODS

This was a monocentric retrospective study carried out on the basis of a systematic review of the CHU surgery files.

RESULTS

The average follow-up was 30 months. The average hospital stay was 8 days. Thirty-four patients (73.9%) underwent initial endoscopic management by attempting a double J probe. Only 20 patients received this double J probe and only 11 patients (55%) did not recidivate the ureteral injury with a median duration of maintenance of the double J probe of 90 days (28-240). Thirty-five patients received open surgical management (76.1%). We found 57% ureterovesical reimplantations (n=20), corresponding to pelvic ureteral injuries (n=32). We also found 20% of nephrectomies. No patient had recurrence of the ureteral injury. Eight patients had secondary dilatation of the pyelocalicious cavities (28.57%). The success of surgical treatment was therefore 57%.

CONCLUSION

The management of surgically treated ureter injuries provides good results but remains relatively diversified due to the different lesion levels. It was effective in 57% of cases including nephrectomies as failure of treatment.

LEVEL OF EVIDENCE

4.

phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics

Summary

With the wealth of available genome sequences, a difficult and tedious part of inferring phylogenomic trees is now to select genomes with an appropriate taxon density in the different parts of the tree. The package described here offers tools to easily select the most representative organisms, following a set of simple rules based on taxonomy and assembly quality, to retrieve the genomes from public databases (NCBI, JGI), to annotate them if necessary, to identify given markers in these, and to prepare files for multiple sequence alignment.

Availability and Implementation

phyloSkeleton is a Perl module and is freely available under GPLv3 at https://bitbucket.org/lionelguy/phyloskeleton/ .

Contact

lionel.guy@imbim.uu.se.

The genome of Rhizobiales bacteria in predatory ants reveals urease gene functions but no genes for nitrogen fixation

Gut-associated microbiota of ants include Rhizobiales bacteria with affiliation to the genus Bartonella. These bacteria may enable the ants to fix atmospheric nitrogen, but no genomes have been sequenced yet to test the hypothesis. Sequence reads from a member of the Rhizobiales were identified in the data collected in a genome project of the ant Harpegnathos saltator. We present an analysis of the closed 1.86 Mb genome of the ant-associated bacterium, for which we suggest the species name Candidatus Tokpelaia hoelldoblerii. A phylogenetic analysis reveals a relationship to Bartonella and Brucella, which infect mammals. Novel gene acquisitions include a gene for a putative extracellular protein of more than 6,000 amino acids secreted by the type I secretion system, which may be involved in attachment to the gut epithelium. No genes for nitrogen fixation could be identified, but genes for a multi-subunit urease protein complex are present in the genome. The urease genes are also present in Brucella, which has a fecal-oral transmission pathway, but not in Bartonella, which use blood-borne transmission pathways. We hypothesize that the gain and loss of the urease function is related to transmission strategies and lifestyle changes in the host-associated members of the Rhizobiales.

Coetzeea brasiliensis gen. nov., sp. nov. isolated from larvae of Anopheles darlingi

A Gram-stain-negative, rod-shaped strain, Braz8T, isolated from larvae of Anopheles darlingi was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Braz8T was related most closely to species of the genus Thorsellia, with 95.6, 96.5 and 96.6 % similarity to the type strains of Thorsellia anophelis, Thorsellia kandunguensis and Thorsellia kenyensis, respectively, and formed a separate branch in the phylogenetic tree next to the monophyletic cluster of the genus Thorsellia. Chemotaxonomic data supported the allocation of the strain to the family Thorselliaceae. The major fatty acids were C18 : 1ω7c, C16 : 0 and C14 : 0. The quinone system was composed of ubiquinones Q-8 and Q-7 (1 : 0.3), the predominant polar lipids were diphosphatidylglycerol and phosphatidylglycerol, and the polyamine pattern showed the major compound putrescine. However, qualitative and quantitative differences in the major polyamine, polar lipid profile and fatty acid patterns distinguished strain Braz8T from species of the genus Thorsellia. Phylogenetic analysis based on 16S rRNA gene sequences, average nucleotide identity, DNA-DNA hybridization, multilocus sequence analysis as well as physiological and biochemical tests distinguished strain Braz8T both genotypically and phenotypically from the three Thorsellia species but also showed its placement in the family Thorselliaceae. Thus, strain Braz8T is considered to represent a novel species of a new genus most closely related to the genus Thorsellia, for which the name Coetzeea brasiliensis gen. nov., sp. nov. is proposed. The type strain of Coetzeea brasiliensis is Braz8T (=LMG 29552T=CIP 111088T).

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteobacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal ‘dark matter’, is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. The maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.

[Endoscopic management of postoperative ureteral wound. Retrospective unicentric study from October 2003 to June 2014]

BACKGROUND

Ureteral wounds are rare with an incidence of 0.5 to 1% of pelvic surgeries. Their supports and their prognosis remain dependant of the period of support and the level of ureteral lesion. The importance of early treatment reduces morbidity and improves patient prognosis.

METHODS

A retrospective study from October 2003 to June 2014 was performed in a university hospital using a systematic chart review of patients' urology, digestive surgery, vascular surgery and gynecology.

RESULTS

Forty-six wounds were found in 43 patients. The majority of the ureteral wound was found at the pelvic ureter, i.e. 69.6% of the study population (n=32). The main cause was gynecological surgery (n=25). In the simple wound group, endoscopic treatment was effective in nearly 90% of cases (n=6). In the other two groups, the efficacy was only 30% and imposed a surgical treatment as second-line.

CONCLUSION

The management is based primarily on early detection or intraoperative, and on a correct initial knowledge of the location and size of the lesion. Endoscopic treatment can in most cases treated with a simple and minimally invasive operation an ureteral wound with nearly 90% success rate. In more complex wounds, endoscopy remains a step in the management with about 30% success rate in our study.

LEVEL OF EVIDENCE

5.

Complex archaea that bridge the gap between prokaryotes and eukaryotes

The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.

Proposal of Thorsellia kenyensis sp. nov. and Thorsellia kandunguensis sp. nov., isolated from larvae of Anopheles arabiensis, as members of the family Thorselliaceae fam. nov

Two Gram-negative, rod-shaped strains, T2.1(T) and W5.1.1(T), isolated from larvae of the mosquito Anopheles arabiensis, were investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity studies, strains T2.1(T) and W5.1.1(T) were shown to belong to the genus Thorsellia, both showing 97.8 % similarity to the type strain of Thorsellia anophelis, with 98.1 % similarity to each other. Chemotaxonomic data supported the allocation of the strains to the genus Thorsellia: their major fatty acids were C18 : 1ω7c, C16 : 0 and C14 : 0 and they harboured a ubiquinone Q-8 quinone system and a polyamine pattern with the major compound 1,3-diaminopropane. Qualitative and quantitative differences in their polar lipid profiles distinguished strains T2.1(T) and W5.1.1(T) from each other and from T. anophelis. Average nucleotide identity (ANI), DNA-DNA hybridization, multilocus sequence analysis (MLSA) as well as physiological and biochemical tests allowed T2.1(T) and W5.1.1(T) to be distinguished both genotypically and phenotypically from each other and from the type strain of T. anophelis. Thus, we propose that these isolates represent two novel species of the genus Thorsellia, named Thorsellia kenyensis sp. nov. (type strain T2.1(T) = CCM 8545(T) = LMG 28483(T) = CIP 110829(T)) and Thorsellia kandunguensis sp. nov. (type strain W5.1.1(T) = LMG 28213(T) = CIP 110794(T)). Furthermore, phylogenetic analysis based on nearly full-length 16S rRNA gene sequences showed that the genus Thorsellia forms a separate branch, distinct from the families Enterobacteriaceae, Pasteurellaceae and Orbaceae. As a consequence, a new family Thorselliaceae fam. nov. is proposed. An emended description of Thorsellia anophelis is also provided.

[Pain evaluation during extracorporeal lithotropsy]

OBJECTIVE

The aim of this study was to demonstrate the feasibility of extracorporeal lithotripsy using lithotripter Sortz MODULITH SLK(®) without analgesics.

MATERIALS AND METHODS

An anonymous self-administered questionnaire was sent to 854 patients post-shock wave lithotripsy for urinary lithiasis. No patient had pain medication. The questionnaire included seven questions to assess the pain symptoms due to treatment. After 15 days, a reminder letter was sent.

RESULTS

The response rate was 69% (591/854). The extracorporeal lithotripsy without analgesic treatment was generally well tolerated. About 70% of patients felt just a few or no pain and average pain assessment was 3.6/10 on VAS. The pain was often considered to be multifactorial, related to the treatment itself, the duration of the session and the position on the table. Anxiety seemed to play an equally important role in pain relief with an average VAS 4.5 against 2.9 for non-anxious patients. If a new session of extracorporeal lithotripsy was necessary, 53% of patients would require no pain medication.

CONCLUSIONS

The extracorporeal lithotripsy could easily be done without systematic analgesics allowing for outpatient care. In contrast, anxiety seemed to be an important predictor of poor tolerance of sessions so the idea of a prophylactic anxiolytic treatment based on psychological profile of the patient should allow less aggressive and less costly management of urolithiasis.

The archaeal legacy of eukaryotes: a phylogenomic perspective

The origin of the eukaryotic cell can be regarded as one of the hallmarks in the history of life on our planet. The apparent genomic chimerism in eukaryotic genomes is currently best explained by invoking a cellular fusion at the root of the eukaryotes that involves one archaeal and one or more bacterial components. Here, we use a phylogenomics approach to reevaluate the evolutionary affiliation between Archaea and eukaryotes, and provide further support for scenarios in which the nuclear lineage in eukaryotes emerged from within the archaeal radiation, displaying a strong phylogenetic affiliation with, or even within, the archaeal TACK superphylum. Further taxonomic sampling of archaeal genomes in this superphylum will certainly provide a better resolution in the events that have been instrumental for the emergence of the eukaryotic lineage.