Nausea and vomiting are among the most common symptoms of early pregnancy. Its most extreme form Hyperemesis gravidarum often requires hospitalization and has been linked as a risk factor of perinatal depression. The emetic reflex is to a large extent triggered in the intestinal epithelium by the enterochromaffin cells, however the interplay between gut microbiome and pregnancy nausea is yet unclear. The aim of this study is to investigate the variation in gut microbiota diversity on second-trimester pregnant women with different levels of nausea, and to ascertain potential key species involved in that variation. Using shotgun sequencing to capture bacterial diversity from 1078 fecal samples, we found a reduction on species richness on women with strong nausea. There are measurable differences in the gut microbiota community composition based on the strength of nausea although depression seemed to be even more relevant to explain those differences. Our results provide evidence for the association of nausea and perinatal depression, but further studies are needed to elucidate the mechanisms underpinning the gut-brain axis cross-talk role in nausea and perinatal depression. No evidence of variation in species evenness or differential abundance of species were found. Finally, random forests results point at Lactococcus lactis as potentially displaying a key role determining the intensity of the nausea, although better models are needed to infer clear assumptions.

Yes / Burkholderia spp. rely on N-acyl homoserine lactone as quorum-sensing signal molecules which coordinate their phenotype at the population level. In this work, we present the whole genome of Burkholderia sp. strain A9, which enables the discovery of its N-acyl homoserine lactone synthase gene. / UM High Impact Research Grants (UM-MOHE HIR grant UM C/625/1/HIR/MOHE/CHAN/01, H-50001-A000001 and UMMOHE HIR Grant UM C/625/1/HIR/MOHE/CHAN/14/1, H-50001- A000027)

Les bactéries magnétotactiques (MTB) appartiennent à différents phyla procaryotes et ont la capacité de synthétiser des magnetosomes (cristaux de magnétite entourés par une membrane). Durant la thèse, nous avons procédé à l’analyse génomique de 2 bactéries magnétotactiques: Magnetospira sp. QH-2 et Magnetococcus MO-1. La synthénie et la correlation génique des gènes impliqués dans la formation des magnétosomes montrent que l'insertion de cet îlot chez QH-2 a eu lieu après la divergence entre les Magnetospirillum sp et Magnetospira sp. L'analyse comparative a mis en évidence trois groupes distincts de MTB : Groupe I, comprenant les souches Magnetospirillum spp. et Magnetospira; Groupe II avec MO-1 et M. marinus MC-1 et le Groupe III, avec D. magneticus RS-1. QH-2 montre aussi une évolution adaptative distincte par comparaison aux souches marines ou d'eau douce. L'analyse comparative des réseaux métaboliques révèle une très grande similitude intra-Groupe et une importante variabilité inter-Groupe. Cela est probablement dû aux enzymes impliqués dans les voies métaboliques anoxiques, qui représentent ainsi la contrainte à une distribution taxonomique large des MTB. Ces enzymes permettent ainsi de prédire le phénotype métabolique nécessaire à la production des magnétosomes. Différentes analyses (des protéines ribosomales au genome entier) indiquent une composition taxonomique chimérique des gènes de MO-1 et MC-1, et peut représenter une nouvelle lignée taxonomique chez les Protéobactéries. J’ai aussi participé à l'analyse des génomes de deux bactéries piezophiles, d’une bactérie photosynthétique pourpre et l’analyse phylogénomique des tyrosine-Kinases bactériennes. / Magnetotactic bacteria (MTB) are a diverse group of aquatic prokaryotes, which synthesize membrane-Enclosed magnetic crystals known as magnetosomes. In this thesis, the genome sequences of two marine MTB strains, Magnetospira sp. QH-2 and magneto-Ovoid strain MO-1 were analyzed. The magnetosome gene cluster synteny and mam gene correlation indicate that the insertion of the magnetosome island into QH-2 chromosome occurred after divergence between freshwater and marine magnetospirilla. Comparative genomic analysis revealed three distinct groups of sequenced MTB strains: Group I with Magnetospirillum spp. strains and Magnetospira strain, Group II with MO-1 strain and M. marinus MC-1, and Group III including Desulfovibrio magneticus RS-1. In addition, it shows an adaptive evolution of two marine MTB strains to marine sediments in comparison with closely related freshwater species. Moreover, comparative metabolic network analysis reveals high level of intra-Group similarity and inter-Group variety in MTB. With anoxic network enzymes, potential “MTB” strains are predicted, and are consistent with recently isolated MTB strains. It suggested that the anoxic metabolic network might be one restricted constraint for MTB distribution in bacterial lineages. Interestingly, analyses from ribosomal proteins to the whole MTB genome strongly support a taxonomic chimeric nature of MO-1 and MC-1 genes, and may represent a novel Proteobacteria lineage. Additionally, I also participate to genome analyses of piezophilic Desulfovibrio and Phaeospirillum molischianum strains as well as genome-Wide analysis of bacterial tyrosine kinases.

As repetições ricas em leucina (LRR) são domínios presentes em diversas famílias de proteínas com diferentes funções, sendo responsáveis pela formação de uma estrutura capaz de estabelecer interações protéicas. Em decorrência do projeto de caracterização de um segmento do cromossomo 17 de L. amazonensis, identificamos um gene que codifica uma proteína de 72 kDa, contendo em sua região central, seis motivos LRR. Genes ortólogos estão presentes nos genomas de L. major e L. braziliensis. Observamos que o gene LRR17 é regulado de forma distinta ao longo dos ciclos biológicos de L. braziliensis e L. amazonensis. A proteína LRR17 de L. braziliensis e secretada tanto nos estágios promastigota como amastigota. Identificamos também a secreção da proteína LRR17 em promastigotas de L. amazonensis. Obtivemos mutantes hiperexpressores da proteína LRR17 em L. braziliensis e L. amazonensis. As linhagens mutantes foram mais infectivas em infecções de macrófagos in vitro quando comparadas com a linhagem selvagem. A proteína LRR17 parece estar envolvida no processo de invasão do parasita em infecções in vitro e no estabelecimento da infecção da forma amastigota de Leishmania. / Leucine-rich repeats (LRRs) are versatile binding motifs found in a variety of proteins involved in protein-protein interactions. The LaLRR17 gene, identified initially in the L. amazonensis genome, encodes a protein with 6 LRR in its central region, that is secreted to the cytoplasm of L. amazonensis-infected macrophages. An orthologue to LaLRR17 was identified in L. braziliensis chromosome 17. LRR17 gene expression is regulated differentially during the life cycle of L. braziliensis and L. amazonensis. The LbLRR17 protein is secreted in L. braziliensis promastigotes and amastigotes. To characterize the function of the LRR17 protein we obtained transgenic parasite lines of L. amazonensis overexpressing the LaLRR17 gene and of L. braziliensis overexpressing the LbLRR17 gene. The mutants were more infective to macrophages in vitro when compared with the wild type strains, indicating that the LRR17 protein may interact with macrophage molecules, modulating the cellular response to increase parasite survival.

No description available.

As repetições ricas em leucina (LRR) são domínios presentes em diversas famílias de proteínas com diferentes funções, sendo responsáveis pela formação de uma estrutura capaz de estabelecer interações protéicas. Em decorrência do projeto de caracterização de um segmento do cromossomo 17 de L. amazonensis, identificamos um gene que codifica uma proteína de 72 kDa, contendo em sua região central, seis motivos LRR. Genes ortólogos estão presentes nos genomas de L. major e L. braziliensis. Observamos que o gene LRR17 é regulado de forma distinta ao longo dos ciclos biológicos de L. braziliensis e L. amazonensis. A proteína LRR17 de L. braziliensis e secretada tanto nos estágios promastigota como amastigota. Identificamos também a secreção da proteína LRR17 em promastigotas de L. amazonensis. Obtivemos mutantes hiperexpressores da proteína LRR17 em L. braziliensis e L. amazonensis. As linhagens mutantes foram mais infectivas em infecções de macrófagos in vitro quando comparadas com a linhagem selvagem. A proteína LRR17 parece estar envolvida no processo de invasão do parasita em infecções in vitro e no estabelecimento da infecção da forma amastigota de Leishmania. / Leucine-rich repeats (LRRs) are versatile binding motifs found in a variety of proteins involved in protein-protein interactions. The LaLRR17 gene, identified initially in the L. amazonensis genome, encodes a protein with 6 LRR in its central region, that is secreted to the cytoplasm of L. amazonensis-infected macrophages. An orthologue to LaLRR17 was identified in L. braziliensis chromosome 17. LRR17 gene expression is regulated differentially during the life cycle of L. braziliensis and L. amazonensis. The LbLRR17 protein is secreted in L. braziliensis promastigotes and amastigotes. To characterize the function of the LRR17 protein we obtained transgenic parasite lines of L. amazonensis overexpressing the LaLRR17 gene and of L. braziliensis overexpressing the LbLRR17 gene. The mutants were more infective to macrophages in vitro when compared with the wild type strains, indicating that the LRR17 protein may interact with macrophage molecules, modulating the cellular response to increase parasite survival.

Les G-quadruplexes sont des structures non-canoniques fascinantes de l’ADN et/ou de l’ARN qui surviennent dans les régions riches en Guanines. La surreprésentation de ces structures dans des régions spécifiques comme les promoteurs des oncogènes et les télomères, suggère leur intervention dans les processus cellulaires clés comme la transcription, la réplication ou bien la maturation de l’ARN. De nouveaux outils in silico, in vitro et in cellulo pour la prédiction des G-quadruplexes ont été proposés, reflétant la pertinence croissante de ces structures. Des cibles potentielles de G-quadruplexes ont été décrites dans le génome humain, chez la levure, des bactéries, virus et bien d’autres. Cependant, un des problèmes dans l’étude des G4s dans le génome humain est le grand nombre de séquences susceptibles de former des structures G4s (370,000 PQS selon Quadparser et plus d’un million en utilisant un seuil de 1.5 selon G4Hunter). Il est alors presque impossible de déconvoluer les effets biologiques reliés aux G-quadruplexes dans les cellules humaines. Pour cela, nous avons choisi Dictyostelium discoideum – dont le génome est pauvre en G4s - comme modèle eucaryote pour compléter les études sur le génome humain. Avec une analyse in silico du génome de dicty en utilisant G4Hunter, un algorithme développé dans notre laboratoire, nous avons pu détecter entre 249 (seuil=2) et 1055 (seuil=1.5) séquences pouvant adopter une structure G4. D’une façon intéressante, bien que les promoteurs soient plus pauvres encore en GC que le reste du génome de dicty, la densité des G4s dans ces régions est significativement plus haute. En utilisant une combinaison de différentes méthodes biophysiques et biochimiques, nous avons démontré que parmi les séquences prédites, 14 séquences qui sont présentes dans des gènes susceptibles de jouer des rôles importants dans dicty forment des structures G4 stables. En plus, cinq gènes de dicty contenant des séquences G4s dans leurs promoteurs ont été étudiés pour l’effet d’un nouveau ligand G4 dérivé de Porphyrine sur leur expression. Nous avons démontré que ce nouveau ligand inhibe l’expression de ces gènes significativement. Globalement, nos résultats constituent le premier pas dans le but d’adopter Dictyostelium discoideum comme un nouveau modèle pour l’étude des G-quadruplexes. / G-quadruplexes (G4) are fascinating non-canonical DNA/RNA secondary structures that occur in genomic Guanine-rich regions. The over-representation of such structures in specific regions such as promoters of oncogenes and telomeres, suggests their involvement in key processes such as transcription, replication or RNA maturation. The development of in silico, in vitro and in cellulo tools for G4 prediction is emerging, reflecting the increasing relevance of these structures. Putative G4 forming sequences (PQS) have been reported in Homo sapiens, yeast, bacteria, viruses and many others. However, one of the problems in studying G4 structures in the human genome is indeed the high number of putative G4 forming sequences (370,000 PQS according to Quadparser and over 1 million when using a threshold of 1.5 with G4Hunter). It is therefore difficult to deconvolute G4-related biological effects in human cells. For this, we chose Dictyostelium discoideum - a G4 poor genome - as a eukaryotic model to complement the human studies. By an in silico analysis of dicty genome with G4Hunter a home-made algorithm, we detected 249 (threshold=2) to 1055 (threshold=1.5) G4-prone motifs. Interestingly, despite an even lower GC content in comparison to the whole dicty genome, the density of G4 motifs in dicty promoters is significantly higher than in the rest of the genome. By using a combination of different biophysical and biochemical methods, we demonstrated that 14 dicty sequences located in key genes fold into stable G4 structures. In addition, five dicty genes containing G4-prone motifs in their promoters were studied for the effect of a new Porphyrin derivative on their expression. Our results demonstrated that the new ligand decreased the expression of the several dicty genes significantly. Overall, our results constitute the first step to adopt Dictyostelium discoideum as a model for G4 studies.

Parmi les plus grandes menaces de la santé publique dans le monde entier, la résistance aux antibiotiques est à la pointe. Ceci en partie est dû à l'augmentation des infections causées par des bactéries pathogènes résistantes aux antibiotiques ainsi que la diminution du nombre actuel de nouveaux antibiotiques. Dans le souci de remédier à cette situation malheureuse, il y a eu récemment la ré-surfaçage des antibiotiques anciens et abandonnés comme les polymyxines. Colistine, un membre des antibiotiques de polymyxine, est maintenant considéré comme un antibiotique de «dernier recours» pour le traitement des infections bactériennes à Gram-négatives graves en raison de son action puissante contre ces agents pathogènes. Cependant, la résistance à la colistine parmi ces agents pathogènes a émergé dans plusieurs pays et est actuellement en augmentation. En raison de la nouvelle réintroduction relative de cet antibiotique, il ya un manque d'information complètes sur ses propriétés pharmacologiques ainsi que des mécanismes par lequel les bactéries développent une résistance contre celle-ci.Afin de combler ce manque d'information en ce qui concerne le mécanisme de résistance, nous avons donc entrepris ce projet. Tout d'abord, pour procéder à une surveillance épidémiologique des bactéries résistantes à la colistine chez les humains et les animaux domestiques et d'autre part, de décrypter les mécanismes moléculaires de résistance à la colistine parmi les bactéries résistantes isolées. / Among one of the greatest threats facing public health worldwide, antibiotic resistance is at the forefront. This is partly due to increase in infections caused by antibiotic-resistant pathogenic bacterial as well as the current dwindling number of new antibiotics. In a way to address this unfortunate situation, there have been recent resuscitation of old and abandoned antibiotics such as polymyxins. Colistin, a member of polymyxin antibiotics, is now regarded as a 'last-resort' antibiotic for the treatment of severe Gram-negative bacterial infections owing to its potent action against these pathogens. However, resistance to colistin among these pathogens has emerged in several countries and is currently on increase. Due to the relatively new reintroduction of this antibiotic, there is a lack of comprehensive information on its pharmacological properties as well as mechanisms by which bacteria develop resistance against it.In order to bridge this information gap in relation to the mechanism of resistance, we therefore undertook this project. First, to carry out an epidemiological surveillance of colistin-resistant bacteria in humans and domesticated animals and secondly, to decipher the molecular mechanisms mediating colistin resistance among the isolated resistant bacteria.

Understanding others is a deeply human urge basic in our existential quest. It requires knowing where someone has come from and where they sit amongst peers. Phylogenetic analysis and genome wide association studies seek to tell us where we’ve come from and where we are relative to one another through evolutionary history and genetic makeup. Current methods do not address the computational complexity caused by new forms of genomic data, namely long-read DNA sequencing and increased abundances of assembled genomes, that are becoming evermore abundant. To address this, we explore specialized data structures for storing and comparing genomic information. This work resulted in the creation of novel data structures for storing multiple genomes that can be used for identifying structural variations and other types of polymorphisms. Using these methods we illuminate the genetic history of organisms in our efforts to understand the world around us.

Acidophilic iron oxidizing bacteria of the betaproteobacterial genus “Ferrovum” are ubiquitously distributed in acid mine drainage (AMD) habitats worldwide. Since their isolation and maintenance in the laboratory has proved to be extremely difficult, members of this genus are not accessible to a “classical” microbiological characterization with exception of the designated type strain “Ferrovum myxofaciens” P3G. The present study reports the characterization of “Ferrovum” strains at genome and transcriptome level. “Ferrovum” sp. JA12, “Ferrovum” sp. PN-J185 and “F. myxofaciens” Z-31 represent the iron oxidizers of the mixed cultures JA12, PN-J185 and Z-31. The mixed cultures were derived from the mine water treatment plant Tzschelln close to the lignite mining site in Nochten (Lusatia, Germany). The mixed cultures also contain a heterotrophic strain of the genus Acidiphilium. The genome analysis of Acidiphilium sp. JA12-A1, the heterotrophic contamination of the mixed culture JA12, indicates an interspecies carbon and phosphate transfer between Acidiphilium and “Ferrovum” in the mixed culture, and possibly also in their natural habitat. The comparison of the inferred metabolic potentials of four “Ferrovum” strains and the analysis of their phylogenetic relationships suggest the existence of two subgroups within the genus “Ferrovum” (i.e. the operational taxonomic units OTU-1 and OUT-2) harboring characteristic metabolic profiles. OTU-1 includes the “F. myxofaciens” strains P3G and Z-31, which are predicted to be motile and diazotrophic, and to have a higher acid tolerance than OTU-2. The latter includes two closely related proposed species represented by the strains JA12 and PN-J185, which appear to lack the abilities of motility, chemotaxis and molecular nitrogen fixation. Instead, both OTU-2 strains harbor the potential to use urea as alternative nitrogen source to ammonium, and even nitrate in case of the JA12-like species. The analysis of the genome architectures of the four “Ferrovum” strains suggests that horizontal gene transfer and loss of metabolic genes, accompanied by genome reduction, have contributed to the evolution of the OTUs. A trial transcriptome study of “Ferrovum” sp. JA12 supports the ferrous iron oxidation model inferred from its genome sequence, and reveals the potential relevance of several hypothetical proteins in ferrous iron oxidation. Although the inferred models in “Ferrovum” spp. share common features with the acidophilic iron oxidizers of the Acidithiobacillia, it appears to be more similar to the neutrophilic iron oxidizers Mariprofundus ferrooxydans (“Zetaproteobacteria”) and Sideroxydans lithotrophicus (Betaproteobacteria). These findings suggest a common origin of ferrous iron oxidation in the Beta- and “Zetaproteobacteria”, while the acidophilic lifestyle of “Ferrovum” spp. may have been acquired later, allowing them to also colonize acid mine drainage habitats.