Thèses sur le sujet « Commensalismo »

2007/2008
Nel mondo contemporaneo, i territori metropolitani presentano in larga misura fenomeni di instabilità urbana causati soprattutto da flussi migratori sempre crescenti, dovuti principalmente all’apertura delle frontiere e alla recessione economica. Questo fenomeno globale dovrebbe sollecitare la nostra disciplina a ricercare soluzioni abitative a costi ragionevoli e a tempo determinato. Nella realtà europea emerge un sistema-città che, nel suo insieme, non è definibile come entità data, certa, immutabile, sulla quale sovrapporre un nuovo disegno, è invece un sistema aperto in continua trasformazione, in perenne mutazione. Questo scritto parte dal presupposto che i modelli di intervento finora applicati per gestire il fabbisogno abitativo, o anche l’habitat minimo progettato per eventi calamitosi, possano ampliare i loro orizzonti verso nuove emergenze legate alle attuali esigenze sociali ed economiche di una sempre più considerevole porzione della popolazione. Lo spazio urbano è attraversato oggi da perenni flussi – di automobili, di persone, di informazioni – difficilmente gestibili con una pianificazione a lungo termine, ma solo limitatamente alla predisposizione di infrastrutture di collegamento dei sistemi urbani, la disciplina architettonica dovrebbe (potrebbe) assimilare la nozione di mutazione con la messa a punto di manufatti ad assetti variabili in grado di rispondere ad esigenze funzionali transitorie. La trattazione si sviluppa con l’intento di indagare quei fenomeni di modificazioni urbane temporanee che si collegano, non solo all’autogestione del territorio da parte del fruitore che costruisce, per necessità o spontaneamente, la propria casa, nonché di esaminare alcuni progetti teorici, in parte utopici e in parte futuribili degli ultimi cinquant’anni elaborati soprattutto da gruppi di avanguardia. Sono state indagate, pertanto, alcune micro realtà abitative connesse alla necessità di insediamento in contesti metropolitani in cui è difficile ritrovare il concetto di casa inteso come elemento di riconoscibilità geopolitica: fenomeni d’emergenza abitativa incontrollati, inseriti all’interno del tessuto urbano indifferentemente, innesti temporanei che compaiono e scompaiono velocemente, aggredendo qualsiasi porzione di spazio libero, dalle aree industriali dismesse, agli snodi infrastrutturali, ai centri storici fatiscenti. Ai limiti tra l’autocostruzione e la pratica dell’abusivismo, frequentemente, il tipo di rapporto che queste micro realtà instaurano con il tessuto urbano segue le regole parassitarie di vicendevole alleanza tra due insiemi biologici e garantisce la sopravvivenza di entrambi, ma su livelli diversi: quello legale, costituito da piani di sviluppo speculativi o in cui non esistono strumenti urbanistici efficaci e quello illegale, governato dall’esigenza di sopravvivere in condizioni metropolitane avverse. La richiesta di alloggi temporanei permette inoltre di considerare il costruito in maniera differente: scenario dove poter agganciare la casa, dove poter innestare l’habitat minimo in posizioni strategiche, innescando rapporti simbiotici tra l’esistente e l’innesto. Si tratta di fenomeni che, se analizzati criticamente, possono portare a conclusioni inedite. Proprio in Italia, paese nel quale poco si demolisce e molto si conserva, manipolazioni di questo tipo potrebbero rinnovare aree depresse o vaste zone industriali dismesse. Se si considera la residenza come efficace strumento di controllo sociale, i diversi gradi di simbiosi che si possono stabilire tra il costruito e gli innesti potrebbero generare risultati proficui sia sul piano economico ma soprattutto psicosociale degli utenti. L’architettura potrebbe scoprire una nuova espressività, una nuova scrittura, potrebbe nascere un’architettura virale che, come ci suggerisce Franco Purini, sia il risultato di una molteplicità di processi formali di tipo infettivo.
Nella prima parte si analizza una sezione della cultura architettonica europea che, nella seconda metà XX secolo, ha caratterizzato la ricerca disciplinare innescando un forte ripensamento sui mezzi e sulle finalità dell’architettura stessa, promuovendo modelli insediativi rivolti ad una società dotata di un alto grado di mobilità sociale. Fughe in avanti che sembrano sopite, ma dalle quali si possono ancora trarre utili insegnamenti – come dimostrano alcuni dei protagonisti dell’attuale dibattito architettonico globale – e ritrovare spunti di riflessione per gestire la complessità della metropoli contemporanea, concepita come modello dinamicamente e costantemente in evoluzione, in perenne accelerazione. Il pre-testo della ricerca affonda le radici nel saggio di Andrea Branzi Le profezie dell’architettura radicale, apparso nel volume Radicals a cura di Gianni Pettena del 1996. In esso Branzi definisce l’architettura radicale non tanto come «un movimento culturale preciso, piuttosto come un fenomeno energetico, un ‘territorio sperimentale’ che ha investito la cultura del progetto europeo tra gli anni Sessanta e gli anni Settanta». La ricerca tende ad individuare un filo rosso nel vasto dibattito sul tema dell’abitare radical attraverso la rilettura di alcuni frammenti che compongono le testimonianze del periodo, peraltro non ancora debitamente sistematizzate. Sono stati indagati avvenimenti e dibattiti del tempo, soprattutto in quei paesi in cui le lotte sociali hanno, senza alcun dubbio, condizionato le ricerche disciplinari. L’Italia, la Gran Bretagna, l’Austria e la Francia, tra il 1960 e il 1970, sono state considerate realtà rappresentative di condizioni in cui gli scontri ideologici legati all’esplosione della cultura di massa hanno prodotto sperimentazioni originali atte a rispondere alle trasformazioni sociali in atto, mettendo in discussione gli strumenti e le metodologie del progetto urbano e architettonico. I radicals, in ambito accademico prima e in quello professionale poi, hanno prodotto visioni di città future in cui l’uomo può liberamente muoversi in costruzioni dagli assetti variabili in grado di rispondere rapidamente alle richieste funzionali di un’utenza non più certa del proprio futuro ed in costante e continua evoluzione . Tra schizzi frettolosi, disegni ironici, fotomontaggi arditi prodotti nel periodo oggetto di indagine, sono stati selezionati alcuni studi sull’habitat minimo, fughe in avanti che tendevano a produrre oggetti, all’epoca, materialmente irrealizzabili ma divenuti oggi plausibili, in relazione alle opportunità fornite dallo sviluppo tecnologico, sia dal punto di vista costruttivo che funzionale.
Nella seconda parte, sono stati analizzati piccoli manufatti realizzati per aggiunta, per scavo, per manomissione del tessuto urbano contemporaneo, ponendo particolare attenzione a quelli di dimensioni abitative ridotte che, con la loro capacità di collaborare e/o di scontrarsi con pezzi di realtà costruita, si impastano con essa producendo inedite derive urbane. Operazioni di manipolazioni dell’esistente che coinvolgono principalmente due questioni: il limite da porre alla delirante espansione urbana e la riconversione ecologica dello stock edilizio contemporaneo prodotto, in particolar modo in Italia, durante il boom economico degli anni Cinquanta. Presa coscienza dell’impossibilità di operare con strategie edilizie che partano da un grado zero o che necessitino di modificare l’esistente in un ottica anti tabula rasa, sono stati privilegiati alcuni esempi campione che rielaborano e riarticolano il tessuto della città e dell’architettura, con scale d’intervento inattese, verosimilmente microscopiche. Nella contemporaneità si sono individuate due linee di ricerca che poggiano su presupposti simili e si sviluppano declinando scelte tecnologiche high o low tech. Da un lato, l’architettura rubata, fatta di micro inserimenti staminali innestabili sull’esistente, che producono soluzioni abitative legali, e dall’altro l’architettura dei rifiuti, fatta di oggetti di scarto, frutto della sovrabbondanza contemporanea di beni materiali, che vengono utilizzati per la costruzione di soluzioni abitative in territori illegalmente occupati. Entrambi gli approcci si legano a nuove o ritrovate esigenze d’uso dell’ambiente domestico e derivano sovente, dal parassitismo biologico, il concetto di mutazione. L’architettura della manipolazione o dell’innesto, può indicare alcune linee guida grazie alle quali operare in lembi urbani residuali tenendo conto della possibilità di variazione spontanea del costruito. Al di là degli evidenti aspetti di parassitismo connessi alle forme di sopravvivenza tipiche degli homeless, dei campi nomadi, delle conurbazioni improvvisate, delle favelas presenti in larga misura, ormai anche in Europa, ancor più interessante è rintracciare oggi metodologie costruttive parassitarie in tessuti urbani consolidati, legate a situazioni sociali connotate da preoccupanti fenomeni di precarietà economica. A conclusione della seconda parte sono state inserite, quasi a margine della trattazione generale, quindici schede sinottiche descrittive di progetti manifesto, di studi per piccole cellule, di esempi di habitat parassita, costruzioni inedite che, come sopra accennato, risultavano solo pochi lustri addietro carichi di componente utopica, sogni nei cassetti di giovani intellettuali vagheggianti mondi non sempre possibili. Queste microarchitetture risultano tuttavia oggi di grande attualità e addirittura fattibili con le tecnologie presenti sul campo. Ci sono apparsi pertanto come veri e propri riferimenti per altrettanti oggetti architettonici realizzati nella contemporaneità che, quasi provocatoriamente, sono stati accostati ai loro progenitori in questa piccola rassegna al fine di far meglio comprendere e cogliere criticamente il messaggio di un non lontano passato.
Nella terza parte sono documentati alcuni progetti, da me elaborati nel triennio, come strumenti di verifica degli assunti della ricerca: due concorsi internazionali sul tema dell’habitat minimo e gli esiti di un workshop didattico progettuale al quale ho partecipato in veste di tutor presso la Facoltà di Architettura di Trieste.
XXI Ciclo
1976

Le microbiote a un impact majeur sur la physiologie de son hôte, cependant notre compréhension des mécanismes régulant la relation hôte/microbiote reste limitée. Nous utilisons un hôte modèle simple, la Drosophile, afin de répondre à ces questions. Durant mon doctorat, je me suis attaché à une étape particulière du cycle de vie de la Drosophile, sa phase larvaire. Celle-ci constitue sa phase de croissance et est influencée par le contexte nutritionnel. Le microbiote influence également cette étape: l’association avec la bactérie Lactobacillus plantarum tempère les effets de la carence alimentaire en soutenant un taux de croissance élevé et une maturation rapide, en modulant chez l’hôte l’activité de l’hormone Ecdysone et de l’insuline. En retour, L.plantarum bénéficie de l’association, les larvesassurant sa persistance dans la niche (la niche étant le substrat nutritif, les larves et les bactéries associées). Pour caractériser les mécanismes mis en jeu dans ce mutualisme nous avons décrit les réponses transcriptomiques et métaboliques de la larve et avons également étudié les perturbations métaboliques de la niche. Nos résultats mettent en avant l’optimisation de l’extraction des acides aminés du substrat comme facteur clef du mutualisme. L.plantarum active l’expression des protéases intestinales de l’hôte via la voie IMD/NF-κB, et bénéficierait en retour d’une quantité d’acides aminés plus importante assurant sa persistance. Ainsi, nos travaux contribuent à l’effort de compréhension desmécanismes régulant l’interaction hôte/microbiote et pourraient conduire à de nombreuses applications thérapeutiques, notamment dans le cadre de déséquilibres nutritionnels
Symbiotic bacterial populations (also called the “microbiota”) have a dramatic impact on their host’s physiology. However, our understanding of the mechanisms shaping host/microbes mutualism remains limited. We took advantage of Drosophila tractability to characterize the host’s and the microbial factors engaged in mutualism. During my PhD, I focused on the impact of the microbiota during the Drosophila larval phase, which constitutes its juvenile growth period. Drosophila larval phase is influenced by nutrition, but also by symbiotic microbes: specific association with the bacterium Lactobacillus plantarum buffers the deleterious effects of nutrient scarcity on the host’s juvenile growth, by sustaining greater growth rates and hastening maturation. L.plantarum mediate these effects by modulating the activity of the steroid hormone Ecdysone and the Insulin/Insulin-like Signaling pathway in its host. In return, L.plantarum benefits from Drosophila presence, as larvae ensure its long-term persistence in the niche (the niche being the nutritive substrate, the larvae and the bacteria dwelling on it). To characterize the mechanisms engaged in this mutualistic relationship, we described the host’s transcriptomic and metabolic responses to L.plantarum presence and characterized the metabolic perturbations occurring in the niche. Our results put forward the optimization of amino-acids extraction from the nutritive substrate as a cornerstone of mutualism. L.plantarum activates the expression of the host’s digestive proteases via IMD/NF-κB signaling and would benefit in return from an enhanced AA availability, which would help sustaining its long-term persistence. Altogether, our studies contribute to the understanding of the mechanisms regulating host/microbiota interaction and could lead to numerous therapeutic applications, notably aiming at counteracting the deleterious effects of nutritional imbalances

Dans la première partie de notre Thèse, nous avons revu la littérature de l’ensemble des espèces méthanogènes retrouvées dans les différents microbiotes de l’homme. Nous avons également fait un point sur les diverses méthodes utilisées en microbiologie clinique pour rechercher et identifier ces microorganismes. Dans une seconde partie de notre thèse, nous avons montré que le tractus digestif humain est colonisé par M. smithii dès le premier jour de la vie posant ainsi la question des sources potentielles d’acquisition de ce méthanogènes. Nous avons détecté et isolé M. smithii et M. oralis dans le colostrum et dans le lait maternel suggérant ainsi une contamination mère-enfant par allaitement. Concernant les prélèvements vaginaux, M. smithii est détecté dans 97 % des prélèvements collectés chez des patientes ayant une vaginose bactérienne. Par la suite, nous avons rapporté la détection de méthanogènes, M. oralis et M. smithii dans le fluide salivaire d'individus ne souffrant d'aucune maladie bucco-dentaire. Dans la troisième partie de notre thèse, nous avons montré pour la première fois que les méthanogènes font partie du microbiote urinaire dans lequel nous avons trouvé M. smithii avec une prévalence de 9 %. Enfin, nous avons optimisé les méthodes de recherche et d’isolement des méthanogènes. Nous avons développé une méthode chimique de production d’H2. L’expertise acquise et les résultats obtenus au cours de cette Thèse, nous invitent à poursuivre des travaux de recherche en microbiologie clinique des méthanogènes, en questionnant plus particulièrement leurs rôles en physiologie et en pathologie buccodentaire
In the first part of our thesis, we reviewed the literature of all the methanogenic species found in the different microbiota of humans. We also reviewed the various methods used in clinical microbiology to research and identify these microorganisms. In a second part of our thesis, we have shown that the human digestive tract is colonized by M. smithii from the first day of life thus posing the question of potential sources of acquisition of this methanogen. We detected and isolated M. smithii and M. oralis in colostrum and breast milk suggesting mother-to-child contamination by breastfeeding. For vaginal specimens, M. smithii is detected in 97% of the samples collected from patients with bacterial vaginosis. Subsequently, we reported the detection of methanogens, M. oralis and M. smithii in the salivary fluid of individuals with no oral disease. In the third part of our thesis, we have shown for the first time that methanogens are part of the urinary microbiota in which we found M. smithii with a prevalence of 9%. Finally, we have optimized the methods of research and isolation of methanogens. We have developed a chemical method for producing H2. The expertise acquired and the results obtained during this thesis, invite us to continue research work in clinical microbiology of methanogens, questioning more particularly their roles in physiology and oral pathology

Parce qu'ils sont constamment en contact avec toutes sortes de microorganismes présents dans leur environnement, les organismes pluricellulaires ont développé un système immunitaire qui leur permet de détecter leur présence et contrôler leur croissance. Les contacts se produisent naturellement au niveau des surfaces de l'animal qui sont exposés à l'environnement extérieur, comme la peau ou les muqueuses. Il existe au minimum deux types d'interactions : dans le premier cas, la présence de l'autre ne cause aucun problème pour chacun, et peut même éventuellement apporter un bénéfice. Dans le second, l'un des partenaires est aggressif envers l'autre, qui doit répondre à cette situation de stress en essayant de préserver son intégrité pour assurer sa survie. Du côté de l'hôte, cette réponse implique le système immunitaire et a généralement pour but de détruire le microorganisme. En utilisant l'insecte drosophila melanogaster comme organisme hôte modèle, j'ai étudié les interactions hôtes - microbes. Dans le cadre d'un premier projet, je me suis interessé aux cellules circulantes de la drosophiles, les plasmatocytes. Nous savions qu'elles sont capables de manifester certaines activités biologiques (sécrétion de cytokine et de facteurs coagulant, phagocytose), mais leur importance dans la résistance aux infections n'a jamais été évaluée. En générant des drosophiles dépourvues de plasmatocytes, j'ai pu montrer que ces cellules sont requises pour assurer la résistance à certaines infections bactériennes systémiques chez l'adulte, dont Staphylococcus aureus et Salmonella typhimurium, mais pas toutes
Because they are constantly exposed to contact with the various type of microorganisms present in their environment, multicellular organisms have evolved an immune system that allow them to sense their presence and control their growth. Close contact with these microbes naturally occurs in body parts that are exposed to the environment, like external body surfaces and internal mucosa, and at least two diffrerent kind of relations can be described. In the first case both the two parts do not harm the other, eventually allowing the relationship to go for a mutual benefit. In the second case, one part is agressive towards the other and lead it to induce a response to this stressful situation in order to preserve it's integrity and ultimately it's survival. From the host point of view, this response involves the immune system and most frequently aims at the eradication of the microbes. Using the fruitfly drosophila melanogaster as a model for the host side, i was interested in studying host-microbe interactions. A first project i worked on focused on drosophila circulating cells, the plasmatocytes, about which we knew some activities (secretion of cytokines, cloting factors, phagocytosis) but whose functional relevance to resist infection has never been tested. By generating plasmatocytes-depleted flies, I show that these cells are required for the survival of the adult upon some type of systemic bacterial infections, including Staphylococcus aureus and Salmonella typhimurium, but not all

Le commensalisme est une association biologique au sein de laquelle le commensal obtient un avantage, alors que son hôte n'obtient ni avantage, ni désavantage. Ce type d'association est théorisé durant la seconde moitié du dix-neuvième siècle, notamment par Pierre-Joseph Van Beneden (1809-1894). Zoologiste belge, professeur à l'université de Louvain, il propose dans son ouvrage de 1875 intitulé Les commensaux et les parasites dans le règne animal, 264 exemples d'associations qu'il classe parmi le commensalisme. Ses travaux ont un retentissement majeur dans l'univers des zoologistes de son époque. Le concept de commensalisme perdure alors jusqu'au vingt-et-unième siècle et interroge sur les notions d'individualité, d'individuation et d'association. Notre étude porte non seulement sur le développement de ce concept au cours du dix-neuvième siècle, que nous démontrons par de nombreux documents inédits issus des archives de Pierre-Joseph Van Beneden, mais aussi sur la pérennité du concept jusqu'à nos jours. Le commensalisme est interprété comme un " marqueur " de l'émergence de nouvelles sciences du vivant : la microbiologie et l'écologie. Plus qu'un concept scientifique, le commensalisme apparaît alors comme un concept illustrant la complexité du vivant

A handful of rat species are among the most pervasive mammal species across the globe, primarily because of their close relationship with humans. The processes involved in this relationship, commensalism, are described in detail. Two rat species, Rattus rattus and Rattus exulans, are the focus of this thesis and their biology and taxonomy are described and discussed. Their modern distributions are the direct result of some of the earliest and most extensive human migration events in human history. The archaeology of the Pacific and Indian Oceans is described and migration vectors and spheres of interaction are identified. These possible patterns of human migration and exchange networks provide testable hypotheses that can be investigated using the subject rat species as proxies for long distance human movement. Modern and archaeological tooth samples of R. exulans and modern samples of R. rattus are analysed using geometric morphometrics. The results reveal important aspects of human migration and differences between these species' biology. R. exulans was likely to have been transported out of Island Southeast Asia at a very early date. Human colonisation of the Pacific occurred in a series of complex pulses and pauses that are clearly reflected in the R. exulans data. For the first time it is possible to demonstrate, within one dataset, the multiple origins and directions of colonisation across the Pacific. The R. rattus data provides a striking comparison, showing very different results that allude to a different level of modern gene-­‐ flow and therefore a difference in behaviour and biology. The results provide a framework for comparison with future archaeological material. The results presented and hypotheses raised have immediate application to existing archaeological material and areas of interest. Further commensal species should be examined following similar lines of questioning as applied here.

Nous voulions déterminer les facteurs de l'anthropisation impliqués dans le commensalisme de la souris, selon une approche phylogéographique et historique.
La quantification de la variabilité actuelle des morphologies dentaires (analyses de Fourier) du genre Mus en Méditerranée a montré qu'il est possible de discriminer les espèces et sous-espèces du genre à partir du matériel fossile et qu'elle pouvait être un marqueur des flux géniques.
L'application archéozoologique nous a permis d'identifier l'émergence des pratiques de l'économie agricole néolithique (stockage des grains, champs cultivés...) au Proche-Orient comme le facteur déterminant dans l'adaptation de la souris à la niche commensale.
Enfin, nous avons montré que la souris domestique colonisa la Méditerranée occidentale lors de l'intensification conjointe des échanges et de l'urbanisation du premier millénaire av. J.-C., lui permettant de surmonter les barrières écologiques et génétiques qui, auparavant, empêchaient son invasion.

Nous voulions déterminer les facteurs de l'anthropisation impliqués dans le commensalisme de la souris, selon une approche phylogéographique et historique. La quantification de la variabilité actuelle des morphologies dentaires (analyses de Fourier) du genre Mus en Méditerranée a montré qu'il est possible de discriminer les espèces et sous-espèces du genre à partir du matériel fossile et qu'elle pouvait être un marqueur des flux géniques. L'application archéozoologique nous a permis d'identifier l'émergence des pratiques de l'économie agricole néolithique (stockage des grains, champs cultivés. . . ) au Proche-Orient comme le facteur déterminant dans l'adaptation de la souris à la niche commensale. Enfin, nous avons montré que la souris domestique colonisa la Méditerranée occidentale lors de l'intensification conjointe des échanges et de l'urbanisation du premier millénaire av. J. -C. , lui permettant de surmonter les barrières écologiques et génétiques qui, auparavant, empêchaient son invasion
We aimed to determine the factors of the anthropisation involved in the mouse commensalism, using both phylogeographical and historical approaches. The quantification of the variability in the molar shape (Fourier analyses) of Mediterranean mice species showed that it is possible to separate species and sub-species of the genus using dental morphology and that this variability might be a marker of genes flow. Zooarchaeological analyses allowed us to identify the emergence of Neolithic farming practices (seeds storage, cultivated fields. . . ) in the Near East as the determining factor for the adaptation of the mouse to the commensal niche. Finally, we showed that the house mouse colonized the western Mediterranean during the intensification of both exchanges and urbanization in the first millennium BC, allowing it to overcome the ecological and genetic barriers which, previously, prevented its invasion

Ce travail s'integre dans une problematique generale cherchant a determiner quels aspects de l'environnement de la souris domestique peuvent participer a l'etablissement d'une divergence chromosomique (par suite de fixation de fusions robertsoniennes) dans certaines de ses populations. La souris domestique occupe deux types d'habitat exterieur et commensal. Le phenomene robertsonien est correle avec l'habitat commensal. Ici le commensalisme est considere dans ses aspects sociaux resultant des fortes densites et de la reproduction continue dans ce type d'habitat. La sensibilite des individus de differentes populations a un stress psychogenique est mesuree a l'aide d'un indice physiologique: le taux de corticosterone plasmatique. Differents stress sont experimentes: la capture, l'exposition a un environnement nouveau et la rencontre d'un congenere inconnu. La corticosteronemie basale en periode diurne permet d'evaluer la reactivite quotidienne des individus. Ces differents indices permettent de differencier au sein de chaque population etudiee les femelles plus emotives que les males, et parmi les differentes populations de distinguer celles qui proviennent d'un habitat commensal de celles provenant de l'habitat exterieur. En habitat commensal les individus montrent une faible sensibilite vis-a-vis d'un stress psychogenique et une forte reactivite quotidienne, le contraire est observe chez les souris exterieures. Les resultats sont interpretes en terme d'adaptation. Les souris robertsoniennes semblent montrer une strategie mixte qui pourrait etre a l'origine d'un avantage adaptatif. Un nouveau modele sur la mise en place du phenomene est propose

L'habitat naturel du babouin hamadryas (papio hamadryas hamadryas) en Arabie saoudite a été profondément altère par le récent développement socio-économique du pays, et certaines populations de babouins sont devenues dépendantes de sources de nourriture d'origine humaine. Un recensement des populations commensales et des conflits hommes/babouins à travers le royaume a permis de mesurer l'ampleur de ce phénomène et d'identifier les causes de son développement singulièrement rapide. Différentes méthodes de lutte contre le commensalisme du babouin hamadryas ont par ailleurs été évaluées, et des solutions pratiques sont proposées pour la gestion des populations commensales et pour la conservation de l'espèce en Arabie saoudite. Afin de mieux comprendre les mécanismes de l'adaptation du babouin hamadryas au mode de vie commensal, l'étude socio-écologique d'une troupe de plus de 1,500 individus vivant sur le site de la décharge municipale de la ville de Taif été effectuée. Les résultats obtenus ont montré de fortes ressemblances entre la structure et l'organisation sociale de cette troupe et celles de troupes sauvages (société organisée en plusieurs niveaux dont l'unité de base est l'unité familiale, système de fission-fusion de la troupe lors des marches quotidiennes, utilisation d'un dortoir central). Mais d'importantes différences ont également été observées (existence de groupes de males célibataires, altération de l'exclusivité sexuelle au sein des unités familiales, etc. ). Ces disparités semblent pouvoir s'expliquer par une modification des stratégies socio-sexuelles individuelles, aussi bien des males que des femelles, sous l'effet de facteurs environnementaux liés au commensalisme (apport artificiel d'une nourriture riche et abondante et densité de population considérablement accrue). Le babouin hamadryas, considère au sein du genre papio comme le spécialiste des milieux semi-arides, semble donc capable d'une certaine flexibilité comportementale en réponse à des variations à court terme de son environnement écologique et social. Ceci suggère que son système social n'est pas aussi rigidement et irréversiblement spécialise qu'on a pu le croire jusqu'à présent.

Candida albicans colonizes the gastrointestinal tract of up to 75 % healthy individuals. It usually cohabits the gut as an innocuous commensal. But in critically ill patients whose gut barrier, immune system and normal gut microbiota are compromised, C. albicans often transmigrates the gut barrier, transforms into an invasive pathogen and causes fatal systemic infections. The genetic transitions that drive this transformation in C. albicans have been a major focus of research and have led to the identification of key transcription factors that regulate this commensal-to-pathogen transition. However, the current challenge lies in identifying the downstream pathways and effectors that bring this transition into effect. This thesis addressed this challenge by developing 11 new bioinformatics tools, including 6 comprehensive databases, 4 novel software packages and 1 analysis framework. These databases included a comprehensive topological map of the mammalian gut biogeography, a C. albicans microarray database comprising of 3,091 publically available microarray transcript profiles, C. albicans RNA-seq gene expression and small variant databases extracted from 1,177 publically available RNA-seq samples, a C. albicans gene alias database comprising of 113,297 gene aliases representing the 6,735 open reading frames of C. albicans, and a C. albicans gene ontology slim comprising of 1,194 C. albicans-specific gene ontology terms. These databases were accompanied by a robust analysis framework which brought together these resources for quality control, batch correction and weighted gene co-expression network analysis. All these tools were finally employed in a pilot exploration of the C. albicans gut commensal-to-pathogen transition, which demonstrated the effectiveness of these bioinformatics resources. The analysis unveiled known regulators, uncharacterized gene networks, pathways and effectors potentially crucial for the C. albicans gut commensal-topathogen transition. These resources are a step towards a better understanding of this transition and can also be utilized for examining various other aspects of C. albicans biology.

Recherche de l'effet algicide sur les especes commensales de chondrus. Etude de la reaction de chondrus crispus aux algicides retenus, de l'action de ces algicides sur certains aspects du metabolisme de c. C.

Le tractus digestif des mammifères est composé d’une microflore dont la complexité limite l'analyse interactive. Les modèles animaux mono-associés permettent l'étude de l’interaction entre une bactérie et son hôte et non celle entre bactéries. Celle-ci est essentielle pour comprendre les processus de persistance et de coopération/compétition dans l’intestin. Le travail présenté dans ce mémoire correspond à l'identification de facteurs régissant la colonisation et les interactions de trois bactéries commensales : Escherichia coli, Lactobacillus johnsonii et Bifidobacterium longum. Après la détermination de la distribution anatomique de ces micro-organismes dans le tube digestif, ce microcosme a été volontairement perturbé par l’introduction de trois autres souches d’ Escherichia, Lactobacillus ou Bifidobacterium. Les transcriptomes de Bifidobacterium longum et de Lactobacillus johnsonii isolés de différents segments intestinaux ont été comparés et les résultats de cette analyse confirment la théorie des niches nutritionnelles. Pour persister dans le tractus gastro-intestinal, une bactérie doit développer un taux de réplication et des activités métaboliques en conséquence. Cependant, l’importance environnementale de certains gènes ne peut être observée qu' in vivo. La combinaison de l'analyse génomique comparative et de la mutagenèse spécifique associée à un système expérimental animal a été nécessaire pour mieux définir les performances écologiques des souches étudiées. Ainsi, une approche génomique et transcriptomique a été appliquée à deux isolats de Lactobacillus johnsonii caractérisés par des temps de persistance différents dans le tube digestif de la souris. Cette approche mixte a permis d’identifier trois groupes de gènes impliqués dans la persistance. Ces résultats ont été confirmés en comparant, par compétition in vivo, la persistance de la souche sauvage et celle de mutants isogéniques présentant une délétion des gènes impliqués. Nous avons observé que la délétion de gènes, codant pour le transport d’un sucre et pour une protéase d’IgA, diminue le temps de résidence dans l'intestin, à l'inverse, un mutant obtenu par délétion des gènes impliqués dans la synthèse des exopolysaccharides s’est avéré capable de résider plus longtemps
The microbiota complexity in mammal gut seriously hampers the analysis of microbe-microbe and microbe-host interactions in situ. Microbes compete for colonization sites on the gut surface and for the use of food resources. At the same time, they cooperate in the digestion of complex food substrates, where the waste of one bacterium becomes the food of another bacterium. Currently, the relative contribution of competition and cooperation at the microbe/microbe interface is not well understood. The aim of this work was to explore the interaction of three common gut commensals, namely Escherichia coli, Lactobacillus and Bifidobacterium, which were jointly introduced into axenic mice. After determination of their anatomical distribution, the system was disturbed by the introduction of three other strains of Escherichia, Lactobacillus and Bifidobacterium. To obtain an idea about their physiological activity, we performed expression profiling analysis of B. Longum and Lb. Johnsonii along the different gut segments, and the results of this analys supported the nutrient niche theory. Moreover, an important task is to associate the in vivo phenotype, displayed by a bacterium in its ecological niche, with its genotype. Thus, genes affecting the intestinal residence time between two Lb. Johnsonii strains were targeted for analysis. We hypothesized that the underlying genes are specific for the long-persisting strain and are expressed during gut passage of the bacterium. Fusion of datasets from comparative genomic and in vivo expression profiling analysis identified three gene loci that were expressed in vivo and specific to the gut ecotype. Knock-out mutants were constructed for all three loci to investigate their involvement in the gut residence phenotype. The experiments revealed that the deletion of genes annotated as a sugar transporter and an IgA protease decreased the residence time, while a mutant with a deleted exopolysaccharide cluster showed an increased persistence time

Mestrado Vinifera Euromaster - Viticulture and Enology - Instituto Superior de Agronomia
This research work addresses the under explored interaction between malolactic bacteria and non-Saccharomyces yeast, specifically commercial strains of Metschnikowia Pulcherrima and Oenococcus oeni. Chemically defined media and two chardonnay juices were used to evaluate sequential and co-inoculated malolactic fermentation strategies, investigating the effect of M. Pulcherrima on O. oeni viability and malolactic fermentation kinetics. L-malic acid consumption, and bacteria viability were tracked during fermentation, along with sampling for organic acid analysis. Our findings showed the addition of M. pulcherrima significantly influenced malolactic fermentation kinetics and increased O. oeni bacteria viability in chemically defined media, and select Chardonnay treatments. Further work is investigating the source of commensalism between M. pulcherrima and O. oeni. Exploring alternative strain pairs and understanding non- Saccharomyces and bacteria interactions will help increase winemakers control when implementing co-inoculation strategies for malolactic fermentation. This has a promising application in the industrial production of sparkling base wine, increasing malolactic fermentation efficiency and closing the gap for potential spoilage associated with conducting malolactic after alcoholic fermentation
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Pour epurer et valoriser le lactoserum doux brut (non deproteine, non pasteurise), un procede de production de proteines de levure par culture de candida kefir ly496 avait ete mis au point. L'application de ce procede aux trois principales categories de lactoserums (lactoserum doux, lactoserum acide et permeat) bruts, a ete etudiee. Les interactions eventuelles (effet killer, nutritionnelles) entre la souche utilisee (c. Kefir ly496) et les levures autochtones presentes dans ces substrats et prealablement identifiees, ont ete recherchees. Seules les souches de l'espece candida valida ont ete retrouvees associees a candida kefir ly496. Une interaction de type commensal entre les deux especes, ayant pour mediateur l'ethanol a ete envisage et optimise. Cette culture mixte a permis, en batch (fermenteur 6 litres), un gain de productivite de 20%. En culture continue, a un taux de dilution de 0,20 h-l a 35#oc et ph 3,5 les performances se sont revelees stables, le lactose est alors totalement consomme et il ne substite pas d'ethanol dosable dans le milieu. La productivite est comprise entre 3,8+/ 0,4 kg. M-3 selon les substrats. Les rapports de population entre les deux especes c. Kefir et c. Valida sont stables; ils se situent respectivement a 60-40% sur lactoserum doux et permeat et a 40-60% sur lactoserum acide. La recuperation de la biomasse (ultrafiltration tangentille), sa composition (elementaire, teneurs en proteines et acides nucleiques, aninogramme) ainsi que son innocuite ont ete etudiees. Cette culture mixte du fait de ses caracteristiques biologiques et biochimiques, presente un interet majeur pour la production de proteines levures a partir des lactoserums bruts et des permeats laitiers

Escherichia coli est le commensal aérobie le plus fréquent du tube digestif de l’homme et des animaux à sang chaud et le bacille à Gram négatif pathogène opportuniste le plus souvent impliqué dans les infections intestinales et extra intestinales de l’homme. C’est une espèce clonale chez laquelle 4 groupes phylogénétiques principaux, A, B1, B2 et D ont été décrits. L’objectif de cette thèse est d’étudier l’adaptation de E. coli et les rapports de cette adaptation avec la structure génétique de l’espèce caractérisée par les 4 groupes phylogénétiques dans deux circonstances : le commensalisme intestinal de l’homme et de plusieurs espèces animales sauvages et domestiques, herbivores et omnivores d’une part et la virulence extra-intestinale mesurée par l’expression des gènes codants pour un sidérophore, la yersiniabactine, dont les gènes sont situés au sein de l’ilot de pathogénicité HPI (PAI IV). La répartition dans les 4 groupes phylogénétiques des souches commensales du tube digestif de 100 hommes et de 137 animaux a été étudiée par une technique de PCR en temps réel originale. Trois principaux entérocolitypes, correspondant à des associations préférentielles de phylogroupes ont été ainsi décrits comme plus fréquents en fonction de la nature des hôtes.Chez l’homme, les souches du groupe B2 ont été retrouvés exclusives chez 15 % des individus et ont été clairement distinctes des souches B2 des animaux sauvages par la plus grande fréquence de leurs facteurs de virulences (sfa/foc et pks). L’effet du fond génétique des sous groupes II, III et IX du groupe B2 sur l’expression de la virulence liée au HPI a été étudié dans un modèle murin de virulence extra-intestinale et dans un modèle d’amibe sociale Dictyostelium discoideum, pouvant être assimilé à un macrophage. Le HPI chez E. coli interagît avec la clonalité de l’espèce qui s’exprime par l’existence des sous-groupes de B2. Dans les modèles de virulence que nous avons développés, les mêmes gènes ont, en fonction du fond génétique des différents isolats naturels, des effets différents
Escherichia coli is the most abundant aerobic bacteria of the human microbiota, and a major opportunistic pathogen in humans. It is the clonal species for wich main phylogenetic groups have been described. The aim of this thesis is to study E. coli adaptation through the genetic structure of the specis in two circumstances : the intestinal comensalism, and the extra-intestinal virulence estimated via expression of genes encoding for yersiniabactin, a major siderophore, located on a high patogenicity island (HPI). The repartition of the 4 phylogroups has been studied in faecal microbiota of 100 humans and 137 animals thanks to an original quantitative PCR assay. Three main enterocolitypes, corresponding to associations of phylogroups, have been described. In humans, B2 phylogroup strains were exclusive in 15% of individuals and were shown to be clearly distinct from animal B2 strains on the base of the presence of two virulence factors (sfa/foc and pks). The impact of the genetic background of the B2 sub-groups II, III an IX on the virulence based on HPI was studied in a mice model and in an amoeba model Dictyostelium discoideum. The HPI interacts with the clonality of the species represented by the existence of the B2 subgroups

Bacteria of the Neisseria are predominately commensal, though N. gonorrhoeae and N. meningitidis are capable of causing disease. Both of these species often asymptomatically colonize humans, a trait reminiscent of their commensal cousins. The factors that shift the balance between asymptomatic carriage and disease are unknown. Pathogenic Neisseria use retractile surface structures called Type IV pili to coordinate community behavior and to initiate and sustain infection. Previously, the contributions of pilus retraction have been studied by deleting the pilus retraction motor, PilT. Recent findings suggest the speed and force exerted by pilus retraction is responsive to environmental cues. By examining several PilT mutants that maintain the ability to retract pili, I show retraction, per se, is not required for N. gonorrhoeae social interactions with bacteria or with human cells. Furthermore, Type IV pilus retraction by the commensal N. elongata affects the host cell differently than retraction by N. gonorrhoeae. These observations collectively suggest pilus retraction properties shape the host cell response to Neisseria colonization and could tip the balance of asymptomatic colonization to symptomatic disease.

Le système immunitaire muqueux, et plus particulièrement les réponses intestinales IgA sont essentielles non seulement à la défense contre les agents pathogènes, mais aussi au façonnement de la flore intestinale commensale. Dans les modèles murins de déficit en IgA, on observe une dysbiose intestinale majeure associée à une inflammation muqueuse, réversibles après restauration des IgA. Le but de ce travail est de décrire l'impact de l'absence d'IgA chez l'homme sur la composition du microbiote intestinal ainsi que ses conséquences locales et systémiques. L'étude comparative par analyse métagénomique des selles de 17 sujets déficitaires en IgA et de 34 donneurs sains retrouve l'absence de différence majeure en termes de répartition des phyla dominants, de diversité et de richesse génique bactériennes entre les deux groupes. En revanche, en analysant à l'échelon des espèces, on observe dans le déficit en IgA une surreprésentation d'espèces pro-inflammatoires et une sous-représentation d'espèces anti-inflammatoires. En outre, en l'absence d'IgA, nous observons la présence de réponses IgM qui opsonisent partiellement les genres ciblés par l'IgA, mais semblent maintenir la diversité au sein des Actinobactéries. Les patients présentent un biais phénotypique lymphocytaire T circulant (TH17) associé à des stigmates de translocation bactérienne. Enfin, l'absence d'IgA s'associe à une perturbation du réseau bactérien minimal "obligatoire". Ces résultats suggèrent que le déficit en IgA humain s'accompagne d'une dysbiose modérée associée à une altération de l'architecture du réseau bactérien induisant une hyperactivation du système immunitaire, malgré la présence de réponses IgM
IgA responses play a key role in gut mucosa, defending host against pathogens but also shaping the commensal flora. In order to get insights into the specific contributions of IgA to host/microbial symbiosis in humans, we explored patients that lack only IgA, using gut microbial metagenomics and systems immunology. Microbiota composition was compared between 34 healthy controls and 17 selective IgA deficiency (sIgAd) patients. Contrary to what was observed in murine models of IgA deficiency, we show that human sIgAd is not associated with massive perturbations of gut microbial ecology, regarding phyla distribution, bacterial diversity and gene richness. A clear gut microbial signature is however associated to sIgAd: we found 19 over-represented MGS mainly described to be pro-inflammatory, but also 14 under-represented MGS, mainly known to be beneficial. We also explored local consequences of IgA deficiency, particularly whether IgM could replace IgA at host/bacterial interface. Using a combination of bacterial flow sorting and DNA sequencing, we therefore analysed the composition of IgM-coated microbiomes observed in sIgAd. We show that IgM only partially supply IgA deficiency, as not all typical IgA targets can also be opsonized by IgM, but nevertheless contribute to maintain Actinobacteria diversity. IgA deficiency is associated with a skewed circulating CD4+ T cell profile towards TH17, as well as markers of bacterial translocation. Finally, sIgAd is associated with a perturbation of the minimal bacterial network. Altogether our results suggest that human IgA deficiency is associated with a mild dysbiosis associated to systemic inflammation despite the presence of IgM

ABSTRACTThis thesis situates the Harry Potter books into the greater body of food studies and into the extant children's literary tradition through an examination of how food can be used to understand cultural identity. Food is a biological need, but because we have created social rules and rituals around food consumption and sharing, there is more to eating than simple nutritional value. The Harry Potter series is as much about overcoming childhood adversity, and good versus evil, as it is about magic, and food in the Harry Potter series is both abundant and relevant to the narrative, context, and themes of the books. Sweets such as candy, puddings, and cakes, help construct both wizard and Muggle identity in addition to serving as a bridge between readers and characters. How the characters use sweets to create and reinforce friendships or exclude those who do not belong is important, especially since children usually lack other cultural capital and, in their worlds, food is reward, treat, and punishment. Examples of this are shown in the scene where Harry first travels on the Hogwarts Express, in the ways the Dursleys deny Harry birthday celebrations, and in how holidays are celebrated by the witches and wizards in the series.The sharing of food in the novels builds tensions, creates bonds, and codes different characters as "acceptable" or "unacceptable" based on their willingness, or refusal, to share food. Teatime and feasting are examples of how food is shared by analogous and disparate groups of people in the series. Tea is served most often by those in subordinate positions of power, but is one way in which the characters can socialize and create community. Feasts at the beginning and end of the school term bookmark the year by immersing students and faculty into a shared world at first, and then by sending them back to their families, aware of their own triumphs and accomplishments. When feasts are used to unite outside groups, such as before the Triwizard Tournament, the ways that different foods are embraced or rejected serve to reinforce identity and inclusion.Using cultural studies methods in conjunction with food studies and Reader-Response critical theory, this thesis argues that food in the Harry Potter series represents the socially constructed identities of the characters within the texts, and also serves to bridge the gap between the readers and the characters.

Precise descriptions and comprehensive taxonomies of species and their ecology are essential in monitoring changes in marine biodiversity at multiple spatial scales. A currently undescribed species of commensal amphipod in the genus Leucothoe is reported from New Zealand, collected from the endemic tunicate Cnemidocarpa bicornuta. This species differs from others in the genus in having a one-articulate first maxilla palp and an apically produced tuberculate lobe on the inner margin of the outer plate of the maxilliped. Previous taxonomic surveys in New Zealand waters did not document this species, indicating that it may be a recent arrival. This research highlights the importance of biodiversity monitoring and taxonomic surveys to record occurrences of undescribed or recently-arrived taxa.

This study investigated commensal feeding interactions between the European harvestman (P. opilio L.) and the predatory mites Balaustium spp. and Anystis baccarum L. It also investigated the feeding behaviour of P. opilio. Experiments were conducted in the laboratory using standardised temperature, humidity, photoperiod and experimental arenas, with eggs of the brown blowfly (Calliphora stygia F.) as prey facsimiles. Due to initial difficulties in obtaining enough predatory mites, mite feeding was manually simulated piercing blowfly eggs with a minuten pin. P. opilio consumed significantly more freeze-killed than live blowfly eggs, indicating that freezing induced chemical and/or physical changes to blowfly eggs that are detected by P. opilio. Significantly more manually pierced eggs were consumed by P. opilio compared with unpierced ones, demonstrating that piercing caused a chemical and/or physical to the egg and increased the feeding rates of P. opilio. Different densities of eggs had no effect on the numbers eaten by P. opilio and placing single pierced eggs next to groups of unpierced eggs also had no effect on the numbers of unpierced eggs eaten. These results suggest that P. opilio does not exhibit klinokinesis or orthokinesis to intensify its search for prey around the area where previous prey were located. P. opilio ate significantly more brown blowfly eggs that had previously been fed on by mites, demonstrating that a short term commensal interaction existed. However, further work is required to demonstrate if the relationship is commensal in the longer term. A comparison between hand-pierced and mite-pierced eggs showed that P. opilio ate significantly more of the former indicating that mite and hand piercing were quantitatively different. The potential for, and importance of, other commensal or mutual relationships between predators in agroecosystems is discussed. The lack of klinokinesis and orthokinesis in P. opilio is compared with other predators and parasitoids that do exhibit these behaviours. The means by which prey are detected by P. opilio are discussed in relation to interpreting behaviours such as prey inspection. Concerns about the effect of pre-treatment and handling of sentinel prey and the problems of using prey facsimiles are raised.

The primary objectives of this research were to demonstrate that: 1.) antibiotic resistant bacteria can promote the survival of antibiotic sensitive organisms when grown simultaneously as biofilms in antibiotics, 2.) community-level multiple antibiotic resistance of polymicrobial consortia can lead to biofilm formation despite the presence of multiple antibiotics, and 3.) biofilms may benefit plasmid retention and heterologous protein production in the absence of selective pressure. Quantitative analyses of confocal data showed that ampicillin resistant organisms supported populations of ampicillin sensitive organisms in steady state ampicillin concentrations 13 times greater than that which would inhibit sensitive cells inoculated alone. The rate of reaction of the resistance mechanism influenced the degree of protection. Spectinomycin resistant organisms did not support their sensitive counterparts, although flow cytometry indicated that GFP production by the sensitive strain was improved. When both organisms were grown in both antibiotics, larger numbers of substratum-attached pairs at 2 hours resulted in greater biofilm formation at 48 hours. For biofilms grown in both antibiotics, a benefit to spectinomycin resistant organism’s population size was detectable, but the only benefit to ampicillin resistant organisms was in terms of GFP production. Additionally, an initial attachment ratio of 5 spectinomycin resistant organisms to 1 ampicillin resistant organism resulted in optimal biofilm formation at 48 hours. Biofilms also enhanced the stability of high-copy number plasmids and heterologous protein production. In the absence of antibiotic selective pressure, plasmid DNA was not detected after 48 hours in chemostats, where the faster growth rate of plasmid-free cells contributed to the washout of plasmid retaining cells. The plasmid copy number per cell in biofilms grown without antibiotic selective pressure steadily increased over a six day period. Flow cytometric monitoring of bacteria grown in biofilms indicated that 95 percent of the population was producing GFP at 48 hours. This research supports the idea that ecological interactions between bacteria contribute to biofilm development in the presence of antibiotics, and demonstrates that community-level multiple antibiotic resistance is a factor in biofilm recalcitrance against antibiotics. Additionally, biofilms may provide an additional tool for stabilizing high copy number plasmids used for heterologous protein production.

Candida albicans est une levure commensale du tube digestif de l’Homme mais également un pathogène opportuniste responsable d’infections dont la gravité est fonction des défenses immunitaires de l’hôte. Au cours de l’interaction avec l’hôte, cette levure est confrontée à de nombreux stress environnementaux et immunitaires imposant des capacités d’adaptation rapides pour survivre. Le travail de thèse présenté dans ce manuscrit est consacré à l'étude de la diversité génomique de C. albicans chez l’individu sain mais également au cours de l’interaction pathologique de longue durée chez l’Homme. Dans une première partie nous montrons qu’il existe un niveau élevé d’hétérogénéité génomique essentiellement dus à des évènements de perte d’hétérozygoties, entre les isolats de C. albicans issus de prélèvements buccaux de porteurs sains et démontrons que celle-ci n’est pas le reflet de problèmes inhérents à la technique et à l’analyse des données de séquençage à haut débit. Puis, nous avons évalué dans quelle mesure le génome de C. albicans était capable d’évoluer, dans un contexte pathologique de longue durée grâce à l’étude de souches chronologiques provenant de patients atteints de candidose cutanéo-muqueuse chronique. Nous montrons qu’il existe une importante dynamique dans l’apparition et l’élimination de variants phénotypiques et génotypique au cours de l’interaction pathologique chez l’hôte pouvant être la conséquence de l'adaptation des souches à l’interaction pathologique chronique. Un phénotype d’importance est la survenue de résistance de ces souches aux antifongiques. Une étude approfondie des gènes impliqués dans la résistance aux antifongiques a permis de décrire de nouvelles mutations dans les gènes ERG11 et TAC1 impliquées dans la résistance aux antifongiques azolés
Candida albicans is a common component of the human digestive tract and is considered the major opportunistic fungal pathogen. During interaction with the host, this yeast is confronted with numerous environmental and immune stresses imposing rapid adaptation capacities to survive. This manuscript aimed to study the genomic diversity of C. albicans, in healthy individuals and during long-term pathological interaction. In the first part of this work, we showed that there is a high level of genomic heterogeneity, especially linked to loss-of-heterozygosity, between isolates of C. albicans in oral samples from healthy carriers. Furthermore, we demonstrated that the heterogeneity observed is not reflective of technical problems nor associated to the high throughput sequencing data analysis. Then, we evaluated to which extent the C. albicans genome was able to evolve in a long-term pathological context, thanks to the study of chronological strains isolated from patients suffering from chronic mucocutaneous candidiasis. We have shown that there is an important dynamic in the appearance and the elimination of phenotypic and genotypic variants during the pathological interaction with the host. This may be the consequence of the adaptation of the strains to the chronic pathological interaction with its host. One of the interesting phenotype is the appearance of resistance to antifungal agents in these strains. An in-depth study of the genes involved in resistance to antifungal agents has enabled the detection and the description of new mutations in the ERG11 and TAC1 genes, involved in resistance to azole antifungals

L'objectif de cette thèse est d’étudier la production de phénotypes différents chez des populations sauvages d’un rongeur de la sous famille des Murinae, endémique au continent africain, le genre Mastomys. Nous avons identifier des patrons de variation de la structure crânienne et déterminer l’importance respective de diverses contraintes sur l’évolution morphologique (contrainte génétique, contrainte environnementale liée au type d’habitat ou à une infection virale par l’arénavirus Lassa). La confrontation des données issues des études morphométriques, génétiques et épidémiologiques a permis de montrer que l’évolution de la variation phénotypique chez Mastomys avait deux origines différentes : la modification de la sensibilité du phénotype cible aux conditions environnementales (canalisation environnementale) et génétiques (canalisation génétique). De plus, nos résultats ont révélé une instabilité développementale chez les individus infectés par le virus Lassa, survenue probablement au cours de la gestation lors de la transmission verticale du virus.

Les bactéries et microalgues marines sont acteurs clés du fonctionnement des écosystèmes océaniques et leur contribution dans les cycles biogéochimiques majeurs est largement reconnue. Dans ce contexte, il apparaît essentiel de mieux comprendre les interactions existant entre bactéries et microalgues. Dans l’environnement marin, les interactions spécifiques entre microorganismes nécessitent une forte proximité qui n’est souvent rendue possible que par un attachement cellulaire. La première partie de ce travail de thèse a consisté à sélectionner les microalgues qui présentaient des bactéries physiquement attachées. Deux diatomées appartenant aux genres Thalassiosira et Chaeoceros ont été retenues afin d’étudier leur microflore épibionte issue d’associations à long terme (culture de microalgues établies depuis plusieurs années) et à court terme (microalgues prélevées directement dans l’environnement). Ces travaux ont permis de mettre en évidence une forte ressemblance des communautés épibiontes dans les associations à long terme, qui s’opposait à la forte différence des épibiontes issus des associations à court terme. Les communautés d’épibiontes bactériens étaient majoritairement composées d’alpha- et gammaprotéobactéries, mais aussi de Bacteroidetes et d’actinobactéries. Cette étude a également permis de mettre en évidence que la surface des microalgues représentait un écosystème particulier puisque près de la moitié des épibiontes isolés correspondaient à de nouveaux taxons (genres et espèces). Une de ces souches qui constitue un nouveau genre a été complètement caractérisée, contribuant à l’enrichissement de la diversité bactérienne décrite. Enfin, la nature des interactions entre les deux diatomées et leurs bactéries épibiontes a été analysée par l’intermédiaire de co-cultures, afin d’identifier une interaction forte, qui pourra être examinée par transcriptomique. De très nombreuses interactions commensalismes ont été mises en évidence, reflet de la reminéralisation de la matière organique par les bactéries. Cependant, un faible impact des bactéries sur la croissance des microalgues a été observé. Les conditions expérimentales qui excluent au maximum les stress abiotiques et biotiques, masquent peut-être les interactions qui pourraient se produire dans un environnement naturel plus fluctuant. Ces résultats témoignent de la complexité des interactions biotiques, fournissent des méthodes et des organismes modèles permettant de les étudier et soulèvent de nombreuses hypothèses exaltantes pour les travaux futurs
Marine microalgal and bacterial contribution to the global biogeochemical cycles is largely recognized and lead to define them as key actors of oceanic ecosystems. In this context, it is essential to better understand the interactions occurring between bacteria and microalgae. In the marine environment, specific interactions between microorganisms require tight physical association that is made possible by cellular attachment. In this work, we first selected microalgae with physically attached bacteria. Two diatoms belonging to the genus Thalassiosira and Chaetoceros were selected to study the epibiotic microflora from long-term (microalgae in culture) and short-term (microalgae directly collected from natural communities) associations. This work highlighted strong similarities between epibiotic assemblages from long-term associations and a higher difference for epibiotic communities from short-term associations. The bacterial epibiotic assemblages were mainly composed of Alpha- and Gammaproteobacteria but also Bacteroidetes and Actinobacteria. This study also highlighted that the surface of microalgae represented a peculiar ecosystem where nearly half isolates constituted new taxa (genera and species). One of them representing a new genus has been completely characterized, contributing to the enrichment of the described bacterial diversity. Finally, the nature of interactions between diatoms and their epibiotic bacteria was analyzed by co-culturing to identify strong interactions, to be further examined by transcriptomics. Numerous commensal interactions have been identified, corresponding to the bacterial remineralization of organic matter. However, only small effects of bacteria on microalgal growth were observed. The experimental conditions that exclude a maximum of abiotic and biotic stresses may mask potential interactions that could occur in an unstable natural environment. These results reflect the complexity of biotic interactions, provide methods and model organisms to study them, and raise many exciting hypotheses for future work

This study investigated commensal feeding interactions between the European harvestman (P. opilio L.) and the predatory mites Balaustium spp. and Anystis baccarum L. It also investigated the feeding behaviour of P. opilio. Experiments were conducted in the laboratory using standardised temperature, humidity, photoperiod and experimental arenas, with eggs of the brown blowfly (Calliphora stygia F.) as prey facsimiles. Due to initial difficulties in obtaining enough predatory mites, mite feeding was manually simulated piercing blowfly eggs with a minuten pin. P. opilio consumed significantly more freeze-killed than live blowfly eggs, indicating that freezing induced chemical and/or physical changes to blowfly eggs that are detected by P. opilio. Significantly more manually pierced eggs were consumed by P. opilio compared with unpierced ones, demonstrating that piercing caused a chemical and/or physical to the egg and increased the feeding rates of P. opilio. Different densities of eggs had no effect on the numbers eaten by P. opilio and placing single pierced eggs next to groups of unpierced eggs also had no effect on the numbers of unpierced eggs eaten. These results suggest that P. opilio does not exhibit klinokinesis or orthokinesis to intensify its search for prey around the area where previous prey were located. P. opilio ate significantly more brown blowfly eggs that had previously been fed on by mites, demonstrating that a short term commensal interaction existed. However, further work is required to demonstrate if the relationship is commensal in the longer term. A comparison between hand-pierced and mite-pierced eggs showed that P. opilio ate significantly more of the former indicating that mite and hand piercing were quantitatively different. The potential for, and importance of, other commensal or mutual relationships between predators in agroecosystems is discussed. The lack of klinokinesis and orthokinesis in P. opilio is compared with other predators and parasitoids that do exhibit these behaviours. The means by which prey are detected by P. opilio are discussed in relation to interpreting behaviours such as prey inspection. Concerns about the effect of pre-treatment and handling of sentinel prey and the problems of using prey facsimiles are raised.

Wydział Biologiczno – Chemiczny. Instytut Biologii
Każdy żywy organizm podlega interakcjom z innymi żywymi organizmami. Interakcje te odgrywają podstawową rolę w ewolucji biologicznej i pełnią główną rolę w funkcjonowaniu współczesnego świata. Przykładem związku jaki obserwujemy w przyrodzie, są zgrupowania drobnych organizmów zwierzęcych związane z powierzchnią ciała innego zwierzęcia. Zespół takich bezkręgowców, spędzających na gospodarzu część lub całe swoje życie, nazywamy epizoonem. Do organizmów epizoicznych należą także wrotki. Niewiele wiemy o epizoizmie wśród wrotków, a zależności między Rotifera i Bivalvia, nie były dotychczas przedmiotem zainteresowania rotiferologów. Badania nad epizoicznymi zespołami Rotifera zasiedlającymi powierzchnię muszli żywych małży mają wiec charakter pionierski. O ile bowiem doniesienia poświęcone występowaniu wrotków na jakichkolwiek żywych gospodarzach są nieliczne, to brak w literaturze informacji o epizoicznej faunie wrotków zasiedlającej małże. Celem prowadzonych badań było poznanie struktury gatunkowej oraz ekologii zespołów Rotifera związanych w swym występowaniu z powierzchnią muszli małży słodkowodnych. Ze względu na pionierski charakter badań należało stwierdzić czy małże są zasiedlane przez zespoły wrotków epizoicznych. Potwierdzenie istnienia takich zespołów umożliwiło sformułowanie kilku następujących hipotez badawczych: 1) Bivalvia posiadają specyficzne dla nich zespoły epizoicznych Rotifera, 2) gatunek gospodarza decyduje o strukturze zasiedlającego go zespołu epizoicznych wrotków, 3) charakter siedliska (limniczne versus lotyczne) ma wpływ na bogactwo gatunkowe i obfitość Rotifera bytujących na słodkowodnych małżach, 4) głębokość występowania gospodarzy ma znaczenie przy zasiedlaniu ich przez różne gatunki Rotifera, 5) w epizoonie małży występują gatunki wrotków nie spotykane lub rzadko spotykane w innych mikrosiedliskach. Zespoły epizoicznych Rotifera pobrano z dwóch rodzajów środowisk - lotycznego i limnicznego. Wytypowano osiem stanowisk na rzece Krutyni (Pojezierze Mazurskie), która charakteryzuje się naturalnym korytem i mało przekształconą zlewnią. Analizy siedlisk limnicznych dokonano w przybrzeżnej strefie jedenastu jezior północno - wschodniej Polski: Bartąg, Bartężek, Isąg, Kiełpińskie, Lekarty, Leleskie, Majcz Wielki, Rumian, Sarąg, Szymbarskie oraz Gorczyckie. O wyborze jezior decydowały: obecność małży z rodziny Unionidae, stopień izolacji geograficznej gospodarzy oraz brak połączenia między zlewniami jezior. Epizoon pobierany był z pięciu gatunków żywych małży należących do rodziny Unionidae (rząd Unionoida): Anodonta anatina (LINNAEUS, 1758), A. cygnea (LINNAEUS, 1758), Unio crassus PHILIPSSON, 1788, U. pictorum (LINNAEUS, 1758) i U. tumidus PHILIPSSON, 1788. Powierzchnia muszli oczyszczana była miękką szczoteczką a cały uzyskany osad po utrwaleniu analizowany był pod mikroskopem świetlnym. W zespołach epizoicznych wrotków obecnych na słodkowodnych małżach znaleziono 147 gatunków Rotifera z podgromady Monogononta oraz licznych przedstawicieli podgromady Bdelloidea. Najliczniej reprezentowanymi rodzajami były Lecane, Cephalodella i Trichocerca. Stwierdzono, że Bivalvia, jako duże bezkręgowce posiadają swoiste zoobionty, którymi są dwa gatunki wrotków - Lecane pumila i Wulfertia sp. - nie notowane dotąd w Polsce a znalezione na powierzchni muszli małży słodkowodnych, zarówno w środowisku lotycznym, jak i w limnicznym. Piętnaście gatunków wrotków: Cephalodella forficula, Collotheca balatonica, Colurella colurus, Lecane arcula, L. bifurca, L. flexilis, L lunaris, L. tenuiseta, Proalinopsis squamipes, Ptygura furcillata, P. melicerta, P. pilula, Testudinella truncata, Trichocerca taurocephala i T. weberi, wyraźnie preferowało przebywanie na powierzchni muszli, tworząc grupę gatunków zoofilnych. Gatunek gospodarza nie decydował o strukturze gatunkowej zasiedlającego go zespołu epizoicznych wrotków, choć została wyodrębniona grupa tzw. gatunków wyłącznych, charakterystycznych tylko dla jednego gospodarza i występujących na nim w jednym lub obu środowiskach. W środowisku limnicznym zanotowano niemal dwukrotnie więcej gatunków wrotków należących do gromady Monogononta, niż w środowisku lotycznym. W przypadku Monogononta, w obu typach środowiska zanotowano odmienną strukturę gatunkową występujących na powierzchni muszli zespołów. Każde ze środowisk charakteryzowało się odmiennym zestawem dominantów i gatunków osiągających wysoką frekwencję w zespołach epizoicznych. Badania nad wpływem głębokości występowania gospodarza na epizoiczne wrotki, wykazały brak zależności między głębokością i liczbą gatunków wrotków oraz ich zagęszczeniem. Zarówno liczba gatunków obecnych na powierzchni muszli małży, jak i podobieństwo faunistyczne między zespołami wrotków z obu badanych grup gospodarzy było zbliżone. Fauna wrotków na odmiennych głębokościach nie była ani zbyt oryginalna ani charakterystyczna wyłącznie dla płytkiego lub głębokiego litoralu. Na powierzchni muszli małży wystąpiły także gatunki wrotków uznawanych w Polsce za rzadkie, o mniejszej walencji ekologicznej. W obu typach środowiska znaleziono łącznie 32 takie gatunki. Trzech hipotez badawczych nie można było odrzucić. Pierwszej mówiącej o tym, że Bivalvia posiadają specyficzne dla nich zespoły epizoicznych Rotifera, gdyż wyodrębniono epizoiczne gatunki wrotków. Nie odrzucono też hipotezy mówiącej że charakter siedliska (limniczne versus lotyczne) ma wpływ na bogactwo gatunkowe i obfitość Rotifera bytujących na słodkowodnych małżach, gdyż w środowisku limnicznym zanotowano niemal dwukrotnie więcej gatunków wrotków należących do gromady Monogononta, niż w środowisku lotycznym. Trzecią hipotezą, której nie można było odrzucić jest ta, mówiąca o tym, że w epizoonie małży występują gatunki wrotków nie spotykane lub rzadko spotykane w innych mikrosiedliskach. Małże posiadają swoiste zoobionty, którymi są dwa gatunki wrotków -Lecane pumila i Wulfertia sp. - nie notowane dotąd w Polsce a znalezione na powierzchni muszli małży słodkowodnych, zarówno w środowisku lotycznym, jak i w limnicznym. Pozostałe dwie hipotezy należało odrzucić, gdyż ani gatunek gospodarza, ani głębokość nie miały wpływu na skład gatunkowy epizoicznych Rotifera.
Every living organism is subject to interactions with other living organisms. These interactions play a fundamental role in biological evolution and play a central role in the modern world. An example of a compound as observed in nature, small clusters are associated with the other animal body surface. Organisms that spend on the surface of another animal part or all of their lives are called epizoic. Epizoic organisms are also rotifers. Little is known about epizoism of rotifers and the relationship between Rotifera and bivalves have not been the subject of scientists interest. Research on epizoic Rotifera colonizing the surface of the shells of live bivalves are so pioneering. While the reports devoted to the occurrence of rotifers to any living hosts are scarce, in the literature is the lack of information about epizoic rotifer fauna inhabiting the mussels of freshwater bivalves. The aim of this study was to investigate the structure of the species and ecology Rotifera related to its occurrence on surface of freshwater bivalve. Due to the pioneering nature of the research should determine if the bivalve are populated by community of epizoic rotifers. Confirmation of the existence of such communities has enabled the formulation of several of the following hypotheses: (1) bivalves have their specific epizoic communities of Rotifera, (2) the species of the host determines the structure inhabit it epizoic rotifers, (3) the nature of the habitat ( limnic versus lotic ) has an impact on species richness and abundance of Rotifera on freshwater bivalves, (4) the depth of occurrence of the host is important in colonization them by various species of Rotifera, (5) epizoic species of rotifers on bivalves are not common or rare in other microhabitats. Epizoic communities of Rotifera were collected from two types of environments - lotic and limnic. On the Krutynia River (Masurian Lake District) which is characterized by a natural streambed and little transformed basin, were selected eight sampling sites. Analysis of limnic habitat was made in the coastal zone of the eleven lakes in the north - eastern Poland: Bartąg, Bartężek, Isąg, Kiełpińskie, Lekarty, Leleskie, Majcz Wielki, Rumian, Sarąg, Szymbarskie and Gorczyckie. The choice of lakes was determined by the presence of bivalves from the family Unionidae, the geographic isolation and lack of connections between the basins of lakes. Epizoon was collected from five species of bivalve belonging to the family Unionidae (category Unionoida): Anodonta anatina (Linnaeus, 1758), A. cygnea (Linnaeus, 1758), Unio crassus Philipsson, 1788, U. pictorum (Linnaeus, 1758) and U. tumidus Philipsson 1788. Shell surface was cleaned with a soft brush and the resultant precipitate was analyzed after fixation under a light microscope. The epizoic rotifers communities present on freshwater bivalves found 147 species of Rotifera of the subdivision Monogononta and many in subdivision Bdelloidea. Most well-represented types were Lecane, Cephalodella and Trichocerca. It was found that bivalves, as large invertebrates have specific zoobionts, which are two species of rotifers - Lecane pumila and Wulfertia sp - not traded so far in Poland and found on the surface of the freshwater bivalves in both the lotic as well as limnic habitat. Fifteen species of rotifers: Cephalodella forficula, Collotheca balatonica, Colurella colurus, Lecane arcula, L. bifurca, L. flexilis, L. lunaris, L. tenuiseta, Proalinopsis squamipes, Ptygura furcillata, P. melicerta, P. pilula, Testudinella truncata, Trichocerca taurocephala and T. weberi clearly have preferred staying on the surface of the shell, forming a zoophilic species. Host species not determined the structure of their epizoic rotifers community, although was spun exclusive group of species characteristic for only one host and found in one or both types of habitat. In limnic habitat recorded almost twice as many species of rotifers belonging to the Monogononta than lotic habitat. For Monogononta, in both types of habitat different species structure was observed on the surface of the shell. Each of the habitat characterized by a different set of dominant species and achieving high turnout in epizoic community. Studies on the influence of the depth of occurrence of the host of epizoic rotifers showed no relationship between depth and number of species of rotifers and their density. Both the number of species present on the surface of the shells of bivalves as well as faunal similarity between the rotifers communities of both groups was similar. Rotifers at different depths was neither very original nor a characteristic only for shallow or deep littoral. On the surface of bivalves observed species of rotifers also recognized in Poland as rare, with less ecological valence. In both types of habitat found a total of 32 such species. Three hypotheses could not be rejected. First speaks that bivalves have their specific epizoic rotifer community. The second not rejected hypothesis was that the nature of the habitat (limnic versus lotic) has an impact on species richness and abundance of Rotifera on freshwater bivalve as in the limnic habitat recorded almost twice as many species of rotifers belonging to the Monogononta than lotic habitat. The third hypothesis, which could not be rejected is the one talking about the fact that in epizoic species of rotifers are not common but rare in other microhabitat. Bivalve have a specific zoobiont, which are two species of rotifers - Lecane pumila and Wulfertia sp - not listed so far in Poland and found on the surface of the freshwater bivalves, in both the lotic as well as limnic habitat. The other two hypotheses had to be rejected because neither host species, nor depth had no effect on the epizoic Rotifera species composition.

The coexistence of humans and rodents lasts from the beginnings of the history of agriculture. Many rodent populations accepted to synanthropic way of life and as commensals accompany human societies until today. In the first study we wanted to find out, how the evolution of non-commensal rodent species, a Cypriot mouse (Mus cypriacus), was influenced by people. This endemic island species evolved on the Cyprus Island without presence of any mammalian competitors or predators. In last 10.000 years humans arrived on the island, bringing several mammalian species, which affected the environment markedly. A black rat (Rattus rattus) is now dominant species there and presumably it is an important competitor for the Cypriot mouse. We supposed that the mice should avoid its odour. Nevertheless the rats odour was preferred by the mouse, probably as an odour of phylogenetically related species. On the contraty, the odour of domestic cat (species, which is also widespread on the island), was avoided. In conclusion, the long-term isolation from mammalian predators did not affect the antipredatory reactions of the Cypriot mouse. Our next study was focuse on changes in behavioural strategies of different populations of mice: the main question was how the commensal way of life affects their exploratory...

The objective of this work was to investigate whether there are differences between commensal and non-commensal populations of spiny mice (Acomys spp.). There is a good evidence that some populations of Acomys cahirinus have been commensal since the time of ancient Egypt, that is for at least 3,500 years. Therefore, it could be expected that some adaptation for a commensal way of life have evolved. To find out, I tested twelve populations of spiny mice in two types of open field test - a vertical test and a hole board test. In the vertical test, a wire mesh was added and offered to spiny mice to climb on. Since human settlements represent an environment with a new predation pressure as well as new hiding opportunities like those in heights above the ground, I hypothesized that commensal populations of A. cahirinus would (1) explore less on the ground and (2) prefer to spend more time on the wire mesh than the non-commensal populations. Results supported the first hypothesis as in both tests commensal spiny mice spent less time exploring on the ground than other populations. The second hypothesis, however, was not supported - all populations showed approximately equal interest in the wire mesh and commensal spiny mice did not spend more time on it compared to the others. Nevertheless, an overall...

Symbiosis is the close and protracted interaction between organisms. The molecular interactions that occur during symbiosis are complex with multiple barriers that must be overcome. Many Gram-negative, host-associated bacteria use a type III secretion system to mediate associations with their eukaryotic hosts. This secretion system is a specialized apparatus for the injection of type III effector proteins directly into host cells, which in the case of plant pathogens, are collectively necessary to modulate host defense. The type III secretion system is not a mechanism exclusive to pathogens, however, as many strains of commensal Pseudomonas fluorescens and mutualistic rhizobia demonstrably require a type III secretion system to interact with their host plants. The work presented in this thesis describes genome-enabled approaches for characterizing type III effector genes across the range of plant symbiosis. Using high-throughput sequencing technology, draft genome sequences were generated for the plant pathogen, Xanthomonas hortorum pv. carotae M081, the plant commensal, Pseudomonas fluorescens WH6, and six strains from the plant mutualists Sinorhizobium fredii and Bradyrhizobium japonicum. Analyses of the draft genome sequences and publicly available finished sequences contributed insights into mechanisms of host-association and to increasing the inventory of type III effector sequences as well as developing methods directly applicable for agriculture. Finally, characterization of the genetic diversity of type III effectors from rhizobia shows that collections of type III effectors of mutualists are static, with little diversity in content and sequence variation. This represents the first comprehensive cataloging of type III effector from species of mutualistic bacteria and the first to provide evidence for purifying selection of this important class of genes.
Graduation date: 2012

Streptococcus pneumoniae, pneumococcus, is a frequent asymptomatic colonizer of the human upper respiratory tract. Although infrequently, pneumococci can reach other body sites and cause diseases. These are associated with high morbidity and mortality worldwide. Co-colonization by more than one pneumococcal strain occurs and interactions can be established between strains. These interactions may be important to shape the pneumococcal population and how it evolves. Although the mechanisms underlying these interactions are poorly studied, they are important to understand vaccine impact and colonization dynamics. A previous study from the group identified interactions occurring between pneumococcal strains grown in an in vitro biofilm model. Two strong interactions were identified: i) an amensalism interaction in which strain 1990-19F inhibited strain 7031-NT’s growth; and ii) a commensalism interaction in which strain 5435-NT benefited when in co-culture with strain 7632-15A. The aim of this thesis was to identify the molecular mechanisms underlying these specific interactions. Experiments were conducted using variants of each strain labelled with green or red fluorescent protein (GFP or RFP, respectively) which enabled cell counts and strain discrimination by flow cytometry in experiments using mixed cultures. The amensalism interaction was also detectable in planktonic cultures. The interaction was shown to be mediated by a secreted protein and possibly other factors. Competence-induced fratricide (a competitive mechanism mediated by protein effectors), medium acidification and differences in the growth patterns of strains did not seem to play a determinant role in the interaction. The commensalism interaction was inconsistent in planktonic growth and, in a transwell experiment, this interaction was shown to be cell contact dependent. The 15A capsule itself was suggested to be important for the beneficial effect observed on the NT strain. In conclusion, this work provided new insights into the factors that may mediate amensalism and commensalism interactions between pneumococcal strains.
Streptococcus pneumoniae (pneumococo) coloniza assintomaticamente o trato respiratório superior humano. Em algumas circunstâncias o pneumococo causa infeções que estão associadas a uma elevada morbilidade e mortalidade a nível mundial. A colonização simultânea por mais de uma estirpe de pneumococos é frequente, criando oportunidade para estas interagirem. Estas interações parecem ser importantes para a evolução da população pneumocócica. Assim, o estudo das interações que ocorrem é importante para compreender a dinâmica de colonização e avaliar o impacto das vacinas. Um estudo realizado previamente pelo grupo, identificou interações entre estirpes de pneumococos num modelo in vitro de biofilme. Nesse estudo identificaram-se duas interações fortes: i) uma interação de amensalismo em que a estirpe 1990-19F inibiu a estirpe 7031-NT; e ii) uma interação de comensalismo em que a estirpe 5435-NT beneficiou ao crescer com a estirpe 7632-15A. Esta tese teve como objetivo identificar os mecanismos moleculares que modelam as interações acima descritas. Nas experiências realizadas utilizaram-se variantes das estirpes marcadas com GFP ou RFP (green ou red fluorescente protein, respetivamente) que permitiram a contagem de células e a distinção entre estirpes por citometria de fluxo em experiências com co-culturas. A interação de amensalismo foi também detetada em culturas planctónicas. Identificou-se que a interação deverá ser mediada por uma proteína secretada, possivelmente em conjunto com outros fatores. Observou-se que o fratricídio induzido por competência (mediado por efetores proteicos), alterações de pH ou diferenças nos padrões de crescimento das duas estirpes não são determinantes para a interação. A interação de comensalismo não foi consistente em crescimento planctónico. Através de um ensaio transwell, identificou-se que esta deverá ser dependente de contacto celular. Observou-se que a cápsula 15A poderá ser importante para a interação. Em conclusão, este trabalho permitiu identificar potenciais mecanismos mediadores de interações de amensalismo e comensalismo entre estirpes de pneumococos.