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京都大学 / 新制・課程博士 / 博士(農学) / 甲第23236号 / 農博第2443号 / 新制||農||1083(附属図書館) / 学位論文||R3||N5326(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 吉田 天士, 教授 澤山 茂樹, 准教授 神川 龍馬 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Resíduos produzidos em atividades industriais podem trazer danos significativos ao ambiente, principalmente quando estes não são degradáveis (ou são dificilmente degradáveis) por processos naturais. Polímeros sintéticos estão entre os principais resíduos descartados na natureza, permanecendo inertes por séculos e interferindo em processos ecológicos. Diante deste contexto, explorar o potencial biodegradável de plásticos e uma alternativa na substituição de embalagens descartáveis. Para a construção e otimização de materiais biodegradáveis, faz-se necessária a compreensão da ação da microbiota natural em processos de biodegradação natural. Neste trabalho, buscou-se compreender a dinâmica de microrganismos do filo Bacteroidetes no processo de biodegradação de blenda polimérica Poli (ɛ-caprolactona) / Amido/ Proteína Isolada de Soja (PCL/A/PIS), considerando solos e materiais plásticos distintos, como também a presença de genes notadamente associados a degradação biológica. Para tanto, partindo de amostras de DNA obtidas do solo ao longo do processo de biodegradação, foram utilizadas técnicas de PCR e PCR-DGGE (Reação de Polimerização em Cadeia - Eletroforese em Gel com Gradiente Desnaturante). Observou-se que: Bacteroidetes estão presentes em todos os momentos avaliados do processo de biodegradação da Blenda e do PCL; o solo Arenoso, onde a biodegradação e mais efetiva, apresenta comunidades com perfis bem delimitados, que se diferenciam na degradação da Blenda e do PCL; a dinâmica no solo Argiloso não exibe um padrão claro de influencia dos plásticos sobre a comunidade, apontando, porem para uma convergência de similaridade das comunidades sobre blenda e PCL no momento de maior atividade degradativa. Chitinophagaceae e uma família presente na biodegradação, sendo Chitinophaga pinensis uma das espécies presentes; genes exclusivos a esta espécie e outras da mesma família que codificam lipases e proteases, associados a degradação de polímeros pela literatura cientifica, estão presentes nas amostras de solo avaliadas, sendo possíveis atores na biodegradação dos plásticos. Bacteroidetes aparenta ser um filo importante em processos naturais de biodegradação de polímeros em solos, e explorar o potencial deste grupo e da família Chitinophagaceae pode oferecer subsídios para a construção de plásticos mais eficientes em sua biodegradação. / The human productive activity has brought significant damage to the environment, particularly by the disposal of non-degradable waste (or poorly degradable) by natural processes. Synthetic polymers are among the main materials discarded, remaining inert for centuries, causing damage to the natural wildlife or interfering with ecological processes. Given this context, the potential use of biodegradable plastics is an alternative, both for agriculture and for the replacement of disposable packaging. For the construction and optimization of biodegradable materials it is necessary to understand the action of natural microbial communities in the process. Microorganisms have predominant and diversified roles in the biodegradation process, with complex ecological relationships in their responses, either by their phylogenetic relationships or the enzymes used during the process. In this work, we sought to understand the dynamics of Bacteroidetes phylum in the biodegradation process of polymer blend poly (ɛ-caprolactone) / starch / Soy Protein Isolate (PCL/ A/ SPI), considering different soils and plastics, and also the presence of genes associated with biological degradation. Therefore, starting from DNA samples taken from the soil during the biodegradation process, PCR techniques and PCR-DGGE (Polymerization Chain Reaction - Denaturing Gradient Gel Electrophoresis) were used. It was observed that: the Phylum Bacteroidetes is present in all periods evaluated of the biodegradation process of Blend, PCL and even soils without the addition of plastics; the sandy soil, where the biodegradation is more effective, presents communities with well defined profiles that differ in the degradation of blends and PCL; the dynamics in clay soil does not show a clear pattern of plastics influence over the community, pointing to a convergence of communities similarity in blends and PCL over greater degradation activity. Chitinophagaceae is a family present in biodegradation, Chitinophaga pinensis being one of the species present; genes unique to this species and others of the same family encoding lipases and proteases, associated with the degradation of polymers reported in the scientific literature, are present in the evaluated soil samples, potentially acting on plastics biodegradation. Bacteroidetes appears to be an important phylum in natural processes of polymer biodegradation in soils, and to explore the potential of this taxon and of Chitinophagaceae family can shed light on the construction of more efficient biodegradable plastics.

Resíduos produzidos em atividades industriais podem trazer danos significativos ao ambiente, principalmente quando estes não são degradáveis (ou são dificilmente degradáveis) por processos naturais. Polímeros sintéticos estão entre os principais resíduos descartados na natureza, permanecendo inertes por séculos e interferindo em processos ecológicos. Diante deste contexto, explorar o potencial biodegradável de plásticos e uma alternativa na substituição de embalagens descartáveis. Para a construção e otimização de materiais biodegradáveis, faz-se necessária a compreensão da ação da microbiota natural em processos de biodegradação natural. Neste trabalho, buscou-se compreender a dinâmica de microrganismos do filo Bacteroidetes no processo de biodegradação de blenda polimérica Poli (ɛ-caprolactona) / Amido/ Proteína Isolada de Soja (PCL/A/PIS), considerando solos e materiais plásticos distintos, como também a presença de genes notadamente associados a degradação biológica. Para tanto, partindo de amostras de DNA obtidas do solo ao longo do processo de biodegradação, foram utilizadas técnicas de PCR e PCR-DGGE (Reação de Polimerização em Cadeia - Eletroforese em Gel com Gradiente Desnaturante). Observou-se que: Bacteroidetes estão presentes em todos os momentos avaliados do processo de biodegradação da Blenda e do PCL; o solo Arenoso, onde a biodegradação e mais efetiva, apresenta comunidades com perfis bem delimitados, que se diferenciam na degradação da Blenda e do PCL; a dinâmica no solo Argiloso não exibe um padrão claro de influencia dos plásticos sobre a comunidade, apontando, porem para uma convergência de similaridade das comunidades sobre blenda e PCL no momento de maior atividade degradativa. Chitinophagaceae e uma família presente na biodegradação, sendo Chitinophaga pinensis uma das espécies presentes; genes exclusivos a esta espécie e outras da mesma família que codificam lipases e proteases, associados a degradação de polímeros pela literatura cientifica, estão presentes nas amostras de solo avaliadas, sendo possíveis atores na biodegradação dos plásticos. Bacteroidetes aparenta ser um filo importante em processos naturais de biodegradação de polímeros em solos, e explorar o potencial deste grupo e da família Chitinophagaceae pode oferecer subsídios para a construção de plásticos mais eficientes em sua biodegradação. / The human productive activity has brought significant damage to the environment, particularly by the disposal of non-degradable waste (or poorly degradable) by natural processes. Synthetic polymers are among the main materials discarded, remaining inert for centuries, causing damage to the natural wildlife or interfering with ecological processes. Given this context, the potential use of biodegradable plastics is an alternative, both for agriculture and for the replacement of disposable packaging. For the construction and optimization of biodegradable materials it is necessary to understand the action of natural microbial communities in the process. Microorganisms have predominant and diversified roles in the biodegradation process, with complex ecological relationships in their responses, either by their phylogenetic relationships or the enzymes used during the process. In this work, we sought to understand the dynamics of Bacteroidetes phylum in the biodegradation process of polymer blend poly (ɛ-caprolactone) / starch / Soy Protein Isolate (PCL/ A/ SPI), considering different soils and plastics, and also the presence of genes associated with biological degradation. Therefore, starting from DNA samples taken from the soil during the biodegradation process, PCR techniques and PCR-DGGE (Polymerization Chain Reaction - Denaturing Gradient Gel Electrophoresis) were used. It was observed that: the Phylum Bacteroidetes is present in all periods evaluated of the biodegradation process of Blend, PCL and even soils without the addition of plastics; the sandy soil, where the biodegradation is more effective, presents communities with well defined profiles that differ in the degradation of blends and PCL; the dynamics in clay soil does not show a clear pattern of plastics influence over the community, pointing to a convergence of communities similarity in blends and PCL over greater degradation activity. Chitinophagaceae is a family present in biodegradation, Chitinophaga pinensis being one of the species present; genes unique to this species and others of the same family encoding lipases and proteases, associated with the degradation of polymers reported in the scientific literature, are present in the evaluated soil samples, potentially acting on plastics biodegradation. Bacteroidetes appears to be an important phylum in natural processes of polymer biodegradation in soils, and to explore the potential of this taxon and of Chitinophagaceae family can shed light on the construction of more efficient biodegradable plastics.

Lors de la prospection de bactéries d’intérêt dans le milieu marin, nous avons isolé des colonies aux couleurs brillantes sous illumination directe, ressemblant à l’iridescence de certains papillons. L’iridescence est une couleur physique induite par des structures nanoscopiques périodiques. Ce phénomène est peu détaillé chez les procaryotes. Dans cette thèse nous avons souhaité caractériser le phénomène par des analyses physico-optiques,microbiologiques et écologiques. La souche fut identifiée comme appartenant à l’espèce Cellulophaga lytica.Les premières étapes ont permis d’illustrer le phénomène et de prouver une coloration structurale des colonies par microspectrophotométrie. Une comparaison de diverses souches a démontré l’iridescence singulière de C. lytica,dénommée iridescence « glitter-like ». Nous avons ainsi proposé la première classification des iridescences bactériennes. Certaines souches du même phylum Bacteroidetes exprimaient le phénomène. Un lien entre cette iridescence et la motilité « gliding » fut mis en évidence. De façon intéressante, l’iridescence était conservée en conditions mimant le biotope C. lytica. De plus, diverses souches marines iridescentes ont pu être ré-isolées. Elles étaient particulièrement abondantes sur les macro algues (rouges, brunes), mollusques, cnidaires et dans l’eau de mer. Nous supposons alors que ce phénomène pourrait avoir des rôles bio-écologiques. Grâce à la microscopie électronique à transmission et une modélisation, nous avons pour la première fois élucidé des structures reponsables d’une iridescence bactérienne : une organisation populationnelle de cellules alignées équidistantes.Les bases fondamentales et méthodologiques de l’iridescence bactérienne sont données dans cette thèse. Les applications correspondraient aux domaines des nanotechnologies et de la biomimétique. / During collections in the marine environment, colony with bright coloration under direct illumination was isolated. Colors were similar to butterly iridescence. Iridescence is a property of structural color where periodic nanoscopic structures are responsible of intense coloration. Bacterial iridescence is poorly described in the literature. In this work, we aimed to characterize the phenomenon by physico-optical, microbiological and ecological analysis. The marine bacterium was identified as Cellulophaga lytica.In the first experiment we illustrated and proved the physical color by micro spectrophotometry. Comparison with diverse bacteria permitted to demonstrate the uniqueness of C. lytica iridescence, named “glitter-like”. We proposed the first classification of iridescences within the prokaryotes. Others Bacteroidetes strains showed “glitterlike”iridescence effects. A link between iridescence and gliding motility was additionally identified. A biotic factors demonstrated conservation of the phenomenon under conditions that mimic C. lytica stressing biotope. Moreover,other iridescent marine strains were isolated. They were particularly associated to macroalgae (red, brown),mollusks, cnidarians and seawater. Biological and ecological functions of iridescence are then supposed. By using transmission electron microscopy and modeling, structures responsible for iridescence in the colony were first identified: alligned and equidistant cells at a population level.Bacterial iridescence’s fundamental and technical skills are described in this thesis. Applications could lead to biomimetic and nanotechnology of iridescent structures.

A obesidade é considerada uma doença multifatorial e pode envolver, em sua gênese, aspectos genéticos, metabólicos, ambientais, psicológicos e socioeconômicos. O crescimento expressivo da incidência mundial da obesidade desencadeia o surgimento contínuo de novas pesquisas em relação a esse tema e, nesse contexto, estudos recentes sugerem que a microbiota intestinal é um fator que pode contribuir com o desenvolvimento desta doença. Assim, existe a premissa que a alteração da composição da microbiota intestinal pode ser influenciada pelo estado nutricional (obesidade x eutrofia) e pela qualidade da alimentação. O presente estudo teve como objetivos: i. comparar a proporção dos filos predominantes da microbiota intestinal Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia e a razão Firmicutes/Bacteroidetes entre mulheres com obesidade grau III e mulheres eutróficas, e ii. investigar o impacto de uma dieta hipocalórica para perda de peso na composição da microbiota intestinal. Estudo prospectivo longitudinal, no qual foram selecionadas 20 mulheres com média de idade 33±3,1 anos, as quais foram divididas em dois grupos: Grupo Intervenção (GI): 10 mulheres com obesidade grau III (Índice de Massa Corporal (IMC) >40 kg/m2) que foram submetidas à intervenção nutricional (dieta hipocalórica) durante 8 semanas e Grupo Controle (GC):10 mulheres eutróficas (IMC entre 18,5 a 24,9 kg/m2). No GI, as coletas foram realizadas antes e após oito semanas da intervenção (GI) e, no GC em um único momento. Em cada momento, foram aferidos o peso e estatura; realizado o cálculo do IMC, análise composição corporal, taxa metabólica de repouso, consumo alimentar, glicemia e lipidograma, e coleta de amostra fecal. A análise da composição da microbiota intestinal em relação à abundância relativa dos Filos foi realizada por reação em cadeia da polimerase em tempo real (qPCR). Após oito semanas de dieta hipocalórica, houve redução do peso (119,5±10,3 para 114,9±10,2 kg), IMC (43,6±2,4 para 41,9±2,6 kg/m2), massa corporal gorda (MG) (62,4±7,5 para 58,9±7,7 kg), triglicérides (TG) (143,2±60,9 para 117,94±48,3 mg/dL). Evidenciou-se que mulheres com obesidade apresentam menor abundância dos filos pesquisados em relação às eutróficas. Ainda, a dieta hipocalórica promoveu diminuição da abundância relativa do filo Proteobacteria, o qual apresentou correlações positivas com a ingestão de lipídio total (%), ômega 6 (g). Conclui-se que a intervenção com dieta hipocalórica foi eficaz na redução de peso, IMC, MG e TG e na modulação da microbiota intestinal, com a diminuição do filo Proteobacteria / Obesity is considered a multifactorial disease and it may involve, in its genesis, genetic, metabolic, environmental, psychological and socioeconomic aspects. The expressive growth of a worldwide incidence of obesity triggers the continual emergence of new researches on this subject and, in this context, recent studies have suggested that the intestinal microbiota is a factor that may contribute to the development of this disease. Thus, there is the premise that the changes in the composition of the intestinal microbiota can be influenced by the nutritional status (obesity x eutrophy) and by the diet quality.The present study aimed at: i. comparing the proportion of the predominant phyla of the intestinal microbiota Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia and ratio Firmicutes/Bacteroidetes among degree III obese women and eutrophic women, and ii. investigating the impact of a low-calorie diet for weight loss on the intestinal microbiota composition. This was a longitudinal prospective study in which 20 women at the average age of 33 ± 3.1 years old were selected and divided into two groups: Intervention Group (IG): 10 women with grade III obesity (Body Mass Index (BMI) > 40 kg / m2) who were submitted to a nutritional intervention (a low-calorie diet) for 8 weeks, and the Control Group (CG): 10 eutrophic women (BMI from 18.5 to 24.9 kg / m2) who were not submitted to any intervention. In the IG, sampling was carried out before and after the eight-week intervention (IG) and in the CG it was carried out only in a single moment. At each sampling, weight and height were checked; BMI was calculated, body composition was analyzed, resting metabolic rate, food intake, fasting blood glucose, and lipidogram tests were performed, and fecal sample collected. The analysis of the intestinal microbiota composition in relation to a relative abundance of every phila was performed by real-time polymerase chain reaction (qPCR). After eight weeks of a low-calorie diet, some of the observed results were weight reduction (119.5 ± 10.3 to 114.9 ± 10.2 kg), BMI (43.6 ± 2.4 to 41.9 ± 2.6 kg / m2), fat body mass (FM) (62.4 ± 7.5 to 58.9 ± 7.7 kg), triglycerides (TG) (143.2 ± 60.9 to 117.94 ± 48.3 mg / dL). It was evidenced that obese women present a lower abundance of the studied phyla in relation to the eutrophic ones. Moreover, the lowcalorie diet promoted a decrease in the relative abundance of Proteobacteria phylum, which presented positive correlations with the intake of total lipid (%) and omega 6 (g). It was concluded that the intervention with a low-calorie diet was effective in reducing BMI, FM and TG and in modulating the intestinal microbiota, by reducing Proteobacteria phylum

Dans le contexte de la bioéconomie, la découverte et la caractérisation des enzymes capables de dégrader la paroi végétale est particulièrement intéressante pour l’utilisation de la biomasse lignocellulosique dans l’industrie. A cet égard, la métagénomique fonctionnelle est un outil puissantpour découvrir de nouvelles enzymes à partir d’écosystèmes microbiens variés, comme l’illustrent les travaux sur le tube digestif du termite Pseudacanthotermes militaris. Cette étude a fourni une mine d’informations et identifié un hypothétique locus d’utilisation du xylane (XUS), codant pour cinq glycosides hydrolases (GH) et une carbohydrate esterase (CE) de Bacteroidales.Le XUS du métagénome de Pseudacanthotermes militaris contient une xylanase de la famille GH10 qui possède une organisation modulaire complexe dans laquelle la séquence du domaine GH10 est interrompue par une insertion de deux carbohydrate binding modules (CBM). Des travaux préliminaires ont montré que cette enzyme modulaire, désignée Pm25, est active sur xylane. Par conséquent, un des objectifs de cette étude a été la caractérisation détaillée des propriétés biochimiques et catalytiques de Pm25. Le rôle des CBM a également été examiné en quantifiant les interactions protéines-sucres et permettant ainsi une meilleure compréhension du rôle spécifique de ces modules, les résultats obtenus permettent de cerner l’impact de la modularité de Pm25 sur ses propriétés fonctionnelles.Dans une deuxième partie de l’étude, nous avons entrepris d’étudier la fonction de Pm25 dans le contexte du cluster XUS. Pour ce faire, nous avons étudié les enzymes adjacentes à Pm25 sur le locus,une autre GH10, une GH11, une GH115 et une GH43. La comparaison des paramètres cinétiques et une étude détaillée des produits d’hydrolyse ont été analysés par spectrométrie de masse et ont révélé que la GH10 et la GH11 étaient les enzymes clefs de la dépolymérisation en étant 20 fois plus efficaces que Pm25. En parallèle, nous avons développé un protocole pour l’utilisation de la micro-thermophorèse (MST) pour quantifier les interactions CBM-sucres, une approche intéressante qui nécessite peut d’échantillon et de ligand contrairement à d’autres méthodes biophysiques. Dans l’ensemble, cette étude a révélé le rôle important de Pm25 et ses homologues dans les locus d’utilisation des xylanes chez les Bacteroidetes et a permis d’identifié le sens de cette architecture particulière. / In the context of bioeconomy, the discovery and study of plant-cell wall degrading enzymes is particularly relevant for the use of lignocellulosic biomass for industrial purposes. In this respect, functional metagenomics has proven to be a powerful tool to discover new enzymes from a variety of microbial ecosystems, as exemplified by work performed on the gut of the termite Pseudacanthotermes militaris. This study provided a wealth of information and identified an interesting hypothetical xylan utilization system, encoding five glycoside hydrolases (GH) and one carbohydrate esterase (CE) annotated from bacteroidales. The Pseudacanthotermes militaris-derived putative XUS cluster contains a GH10 xylanase that displays a quite complex modular arrangement wherein the GH10 catalytic module contains two insertional carbohydrate binding modules (CBM). During the preliminary work, this modular enzyme, designated Pm25, was shown to be active on xylan, thus in the present research we set out to more thoroughly characterize its biochemical and catalytic properties.The role of the CBM was also investigated, quantifying protein-carbohydrate interactions and thus providing better insight into the specific role of the modules. Taken together, the results obtained provide insight into how Pm25 modularity translates into functional properties. In second part of our study, we set out investigate the function of Pm25 in the context of the XUS cluster. To achieve this we studied a xylan utilization system, which is constituted by another GH10, GH11, GH115 and GH43. The comparison of kinetic parameters and a detailed end product analysis by mass spectrometry showed that GH10 and GH11 outweigh over 20 fold Pm25 catalytic efficiency. In parallel, we developed the use of MicroScale Thermophoresis (MST) to quantify CBM-carbohydrates interactions, an interesting approach requiring smaller concentration of proteinsand ligands compared to other biophysical methods. Overall this study highlighted the important role of Pm25 homologs in the xylan utilization system in Bacteroidetes, and pinpointed the meaning of its unusual architecture.

Lors de la prospection de bactéries d'intérêt dans le milieu marin, nous avons isolé des colonies aux couleurs brillantes sous illumination directe, ressemblant à l'iridescence de certains papillons. L'iridescence est une couleur physique induite par des structures nanoscopiques périodiques. Ce phénomène est peu détaillé chez les procaryotes. Dans cette thèse nous avons souhaité caractériser le phénomène par des analyses physico-optiques,microbiologiques et écologiques. La souche fut identifiée comme appartenant à l'espèce Cellulophaga lytica.Les premières étapes ont permis d'illustrer le phénomène et de prouver une coloration structurale des colonies par microspectrophotométrie. Une comparaison de diverses souches a démontré l'iridescence singulière de C. lytica,dénommée iridescence " glitter-like ". Nous avons ainsi proposé la première classification des iridescences bactériennes. Certaines souches du même phylum Bacteroidetes exprimaient le phénomène. Un lien entre cette iridescence et la motilité " gliding " fut mis en évidence. De façon intéressante, l'iridescence était conservée en conditions mimant le biotope C. lytica. De plus, diverses souches marines iridescentes ont pu être ré-isolées. Elles étaient particulièrement abondantes sur les macro algues (rouges, brunes), mollusques, cnidaires et dans l'eau de mer. Nous supposons alors que ce phénomène pourrait avoir des rôles bio-écologiques. Grâce à la microscopie électronique à transmission et une modélisation, nous avons pour la première fois élucidé des structures reponsables d'une iridescence bactérienne : une organisation populationnelle de cellules alignées équidistantes.Les bases fondamentales et méthodologiques de l'iridescence bactérienne sont données dans cette thèse. Les applications correspondraient aux domaines des nanotechnologies et de la biomimétique.

Lors de la prospection de bactéries d'intérêt dans le milieu marin, nous avons isolé des colonies aux couleurs brillantes sous illumination directe, ressemblant à l'iridescence de certains papillons. L'iridescence est une couleur physique induite par des structures nanoscopiques périodiques. Ce phénomène est peu détaillé chez les procaryotes. Dans cette thèse nous avons souhaité caractériser le phénomène par des analyses physico-optiques,microbiologiques et écologiques. La souche fut identifiée comme appartenant à l'espèce Cellulophaga lytica.Les premières étapes ont permis d'illustrer le phénomène et de prouver une coloration structurale des colonies par microspectrophotométrie. Une comparaison de diverses souches a démontré l'iridescence singulière de C. lytica,dénommée iridescence " glitter-like ". Nous avons ainsi proposé la première classification des iridescences bactériennes. Certaines souches du même phylum Bacteroidetes exprimaient le phénomène. Un lien entre cette iridescence et la motilité " gliding " fut mis en évidence. De façon intéressante, l'iridescence était conservée en conditions mimant le biotope C. lytica. De plus, diverses souches marines iridescentes ont pu être ré-isolées. Elles étaient particulièrement abondantes sur les macro algues (rouges, brunes), mollusques, cnidaires et dans l'eau de mer. Nous supposons alors que ce phénomène pourrait avoir des rôles bio-écologiques. Grâce à la microscopie électronique à transmission et une modélisation, nous avons pour la première fois élucidé des structures reponsables d'une iridescence bactérienne : une organisation populationnelle de cellules alignées équidistantes.Les bases fondamentales et méthodologiques de l'iridescence bactérienne sont données dans cette thèse. Les applications correspondraient aux domaines des nanotechnologies et de la biomimétique.

Cytoplasmic incompatibility (CI) is an intriguing, widespread, symbiont-induced reproductive failure that decreases offspring production of arthropods through crossing incompatibility of infected males with uninfected females or with females infected with a distinct symbiont genotype. For years, the molecular mechanism of CI remained unknown. Recent genomic, proteomic, biochemical, and cell biological studies have contributed to understanding of CI in the alphaproteobacterium Wolbachia and implicate genes associated with the WO prophage. Besides a recently discovered additional lineage of alphaproteobacterial symbionts only moderately related to Wolbachia, Cardinium (Bacteroidetes) is the only other symbiont known to cause CI, and genomic evidence suggests that it has very little homology with Wolbachia and evolved this phenotype independently. Here, we present the first transcriptomic study of the CI Cardinium strain cEper1, in its natural host, Encarsia suzannae, to detect important CI candidates and genes involved in the insect-Cardinium symbiosis. Highly expressed transcripts included genes involved in manipulating ubiquitination, apoptosis, and host DNA. Female-biased genes encoding ribosomal proteins suggest an increase in general translational activity of Cardinium in female wasps. The results confirm previous genomic analyses that indicated that Wolbachia and Cardinium utilize different genes to induce CI, and transcriptome patterns further highlight expression of some common pathways that these bacteria use to interact with the host and potentially cause this enigmatic and fundamental manipulation of host reproduction. IMPORTANCE The majority of insects carry maternally inherited intracellular bacteria that are important in their hosts' biology, ecology, and evolution. Some of these bacterial symbionts cause a reproductive failure known as cytoplasmic incompatibility (CI). In CI, the mating of symbiont-infected males and uninfected females produces few or no daughters. The CI symbiont then spreads and can have a significant impact on the insect host population. Cardinium, a bacterial endosymbiont of the parasitoid wasp Encarsia in the Bacteroidetes, is the only bacterial lineage known to cause CI outside the Alphaproteobacteria, where Wolbachia and another recently discovered CI symbiont reside. Here, we sought insight into the gene expression of a CI-inducing Cardinium strain in its natural host, Encarsia suzannae. Our study provides the first insights into the Cardinium transcriptome and provides support for the hypothesis that Wolbachia and Cardinium target similar host pathways with distinct and largely unrelated sets of genes.