Thesis (PhD(Agric) Viticulture and Oenology. Wine Biotechnology))--University of Stellenbosch, 2009. / The main goal of this project was to elucidate the underlying genetic factors responsible for the different fermentation phenotypes and physiological adaptations of industrial wine yeast strains. To address this problem an ‘omic’ approach was pursued: Five industrial wine yeast strains, namely VIN13, EC1118, BM45, 285 and DV10, were subjected to transcriptional, proteomic and exometabolomic profiling during alcoholic fermentation in simulated wine-making conditions. The aim was to evaluate and integrate the various layers of data in order to obtain a clearer picture of the genetic regulation and metabolism of wine yeast strains under anaerobic fermentative conditions. The five strains were also characterized in terms of their adhesion/flocculation phenotypes, tolerance to various stresses and survival under conditions of nutrient starvation. Transcriptional profiles for the entire yeast genome were obtained for three crucial stages during fermentation, namely the exponential growth phase (day 2), early stationary phase (day 5) and late stationary phase (day 14). Analysis of changes in gene expression profiles during the course of fermentation provided valuable insights into the genetic changes that occur as the yeast adapt to changing conditions during fermentation. Comparison of differentially expressed transcripts between strains also enabled the identification of genetic factors responsible for differences in the metabolism of these strains, and paved the way for genetic engineering of strains with directed modifications in key areas. In particular, the integration of exo-metabolite profiles and gene expression data for the strains enabled the construction of statistical models with a strong predictive capability which was validated experimentally. Proteomic analysis enabled correlations to be made between relative transcript abundance and protein levels for approximately 450 gene and protein pairs per analysis. The alignment of transcriptome and proteome data was very accurate for interstrain comparisons. For intrastrain comparisons, there was almost no correlation between trends in protein and transcript levels, except in certain functional categories such as metabolism. The data also provide interesting insights into molecular evolutionary mechanisms that underlie the phenotypic diversity of wine yeast strains. Overall, the systems biology approach to the study of yeast metabolism during alcoholic fermentation opened up new avenues for hypothesis-driven research and targeted engineering strategies for the genetic enhancement/ modification of wine yeast for commercial applications.

La surface des vignobles mondiaux représente environ 7,9 millions ha, ce qui correspond à une production annuelle de 67 millions de tonnes de baies. La production mondiale annuelle de vins est de l’ordre de 300 millions hl/an. La surface du vignoble français est de 843 000 ha. La viticulture moderne doit affronter trois défis majeurs interdépendants : réduire l’utilisation des produits phytosanitaires, s'adapter au changement climatique, maîtriser la qualité et la typicité pour garder ou conquérir de nouveaux marchés.En 2007, la vigne est devenue la première espèce fruitière pérenne dont le génome a été séquencé. Cette avancée scientifique ouvre de nombreuses perspectives en termes de génomique fonctionnelle (ensemble de méthodes permettant de caractériser la fonction des gènes) et de biologie intégrative (ensemble de méthodes visant à appréhender le fonctionnement global de la plante et ses réponses à l’environnement). Ces perspectives dépendent pour une bonne part de la maîtrise de quantités importantes de données qu’il convient d’organiser et de corréler grâce à des outils informatiques adaptés.Des approches fonctionnelles concernant des gènes candidats et des approches transcriptomiques à haut débit ont permis d’identifier certains gènes ou certaines familles de gènes impliqués dans le développement et la maturation de la baie de raisin, mais au moment où cette thèse a débuté, aucun travail de biologie intégrative n’avait été entrepris.Le travail présenté ici, qui décrit l’obtention et l’analyse de métadonnées transcriptomiques et biochimiques portant sur la réponse de la baie à l’environnement radiatif, s’inscrit dans ce contexte. En procédant à un effeuillage partiel après la véraison, nous avons modulé l’exposition des baies au rayonnement solaire. Ceci a permis d’étudier l’influence du rayonnement (baie exposée, non exposée), de la position de la grappe (est, ouest) et de la position de la baie (à l’extérieur ou à l’intérieur de la grappe). Des baies ont été récoltées à 5 moments différents après l’effeuillage et utilisées pour des analyses métabolomiques et transcriptomiques. Leur contenu en sucres, acides organiques, acides aminés, anthocyanes et flavonols a été analysé par des dosages enzymatiques et par chromatographie liquide à haute performance). L’expression des gènes a été étudiée avec des microarrays représentatifs de l’ensemble du génome de la vigne (29600 gènes) pour les conditions présentant les différences métaboliques les plus marquées (baies exposées, situées à l’ouest et à l’extérieur de la grappe vs baies non exposées, situées à l’est et à l’intérieur de la grappe). Des analyses statistiques et corrélatives ont été conduites pour (a) déterminer les métabolites qui répondent au traitement et les facteurs qui les influencent (b) déterminer les gènes qui répondent aux traitements et ceux qui semblent co-régulés (c) préciser les réseaux de gènes et de métabolites qui semblent reliés. L’effeuillage n’affecte pas la teneur en sucres ou en acide tartrique des baies, il affecte peu les acides aminés, mais il augmente la teneur en flavonols et diminue la teneur en acide malique. Il affecte plus particulièrement les gènes associés au stress abiotique, au métabolisme secondaire, au transport et au métabolisme hormonal. Des expériences complémentaires ont permis d’identifier divers gènes spécifiquement associés à la composante thermique de l’exposition au soleil, parmi lequels des gènes codant pour des HSP, des transporteurs ABC, et des enzymes du métabolisme flavonoïdique. Des réseaux reliant des gènes et des métabolites ont pu être construits, qui associent des métabolites secondaires à des gènes de fonctions connues, ou à de nouveaux gènes candidats dont il conviendra d’étudier la fonction précise. / The total surface of vineyards worldwide is about 7.9 millions ha, which corresponds to an annual production of 67 millions tons berries. The annual world production of wines is about 300 millions hl/year. The French wineyard occupies 843 000 ha, among which 481 000 ha are dedicated to high quality wines (VQPRD) and 362 000 ha to table wines. Modern viticulture must deal with three major and related challenges : reduce the use of organic and inorganic phytochemicals, adapt the vineyard to climatic change and control the quality and the typicity in order to keep or gain new markets.In 2007, the grapevine became the first perennial fruit species whose genome was sequenced. This scientific breakthrough opens new pespectives in terms of functional genomics (set of methods allowing to characterize the function of genes) and integrative biology (set of methods allowing to study the global functioning of the plant and its response to the environment). These perspectives mainly depend on our ability to analyze large sets of data with adequate informatic tools.Functional approaches on candidate genes, and high throughput transcriptomic approaches have allowed to identify some genes or some gene families involved in the development and ripening of the grape berry, but when this Ph. D work started, no paper based on integrative biology was published on grapevine. The present work, which describes the collection and analysis of transcriptomic and metabolomic metadata related to the response of the berry to sun exposure. The exposure of the berries to the sun was controlled through a partial defoliation after veraison. This allowed to study the effects of sun exposure (exposed or shaded berries), of the position of the cluster (east, west) and of the anatomical position of the berry (outside or inside the berry). Berries were collected at 5 different time points after defoliation and used for metabolomic and transcriptomic analysis. Their content in sugars, amino acids, organic acids, anthocyanins and flavonols was analyzed by enzymatic assays and high performance liquid chromatography. For the berries whose metabolic content differed the most (exposed, west and outside berries vs shaded, east and inside berries), gene expression was studied with microarrays bearing a set of probes covering the whole genome of grapevine (29600 genes). Correlative and statistical analysis were conducted in order to (a) determine the metabolites that are the most responsive to the treatment, and the most important factors that control them (b) determine the genes that respond to the treatment and seem to be co-regulated (c) to precise the networks of genes and metabolites which seem related. Defoliation does not affect the sugar and tartaric acid contents, hardly affects amino acids, but it increases flavonol content and decreases malic acid content. It affects more specifically genes associated with abiotic stress, secondary metabolism, transport and hormonal metabolism. Additional experiments allowed us to identify genes that are specifically associated with the thermal component of sun exposure, among which genes encoding HSP, ABC transporters, and enzymes of flavonoid metabolism. Networks relating genes and metabolites could be constructed. These networks associate secondary metabolites with genes of known function and new candidate genes for which the function will have to be precised.

Xanthomonas oryzae pv. oryae (Xoo) est l'agent causal de la bactériose vasculaire du riz (BLB), maladie entraînant des pertes de rendement importantes dans la plupart des régions rizicoles, notamment en Afrique. La virulence des souches Asiatiques de Xoo dépend des effecteurs de la famille AvrBs3/PthA ou TAL (pour Transcription Activator-Like). Des études appro fondies sur le mode d'action des effecteurs TAL ont montré que l'activité de virulence ou d'avirulence que les TAL confèrent à la bactérie dépend essentiellement de leur interaction avec les gènes de sensibilité et/ou de résistance correspondants chez le riz. Les souches de Xoo originaires d'Afrique isolées récemment ne présentent que huit effecteurs de type TAL dans leur génome et leur rôle dans la virulence est jusqu'à présent inconnu. Les travaux de cette thèse ont porté sur la caractérisation des effecteurs de type TAL dans la souche africaine de Xoo BAI3. Une mutagenèse systématique par recombinaison homologue sur l'ensemble des huit gènes tal de la souche BAI3 a été effectuée et a conduit à l'identification et à la caractérisation du gène talC. TalC se caractérise par 21.5 répétitions et est phylogénétiquement proche des TAL de Xanthomonas oryzae pv. oryzicola (Xoc). Le mutant BAI3ΔtalC est incapable de développer les symptômes de la maladie sur plante sensible. Toutefois, les bactéries se multiplient très bien au niveau de l'apex foliaire proche du site d'inoculation, laissant supposer que TalC est requis pour la colonisation du système vasculaire. Parmi les cibles directes potentielles identifiées via l'analyse du transcriptome de feuilles de riz sensible (BAI3 versus BAI3ΔtalC), Os11N3 code une protéine de la famille des noduline-3 MtN3 et est fortement induit durant l'infection par la souche sauvage BAI3. Nous avons identifié dans la région promotrice de Os11N3 une séquence nucléotidique ciblée par TalC et démontré qu'elle était fonctionnelle via des expériences d'expression en trans dans N. benthamiana. Les travaux de cette thèse montrent pour la première fois que les effecteurs de type TAL contribuent de manière importante à la virulence de la souche africaine Xoo BAI3. Ces travaux contribueront à l'amélioration génétique des lignées de riz pour la résistance à la bactériose vasculaire du riz en Afrique. / Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of Bacterial Leaf Blight (BLB) on rice, a serious disease causing important yield losses in the main rice growing regions including Africa. The virulence of Asian Xoo strains mainly depends on the type III effectors of avrBs3/pthA gene family, namely TAL (for Transcription Activator Like) effectors. In depth studies on the function of TAL effectors revealed that the virulence and/or the avirulence activities conferred by these effectors requires the binding and the induction of the corresponding S and/or R genes. African Xoo strains was shown to harbor 8 TAL effectors in their genomes. However, the contribution of these TAL effectors to Xoo virulence is still unknown. This work reports on the identification and characterization of TAL effectors in the African Xoo strain BAI3R. A random mutagenesis based on homologous recombination in the genes encoding TAL effector was conducted in Xoo str ain BAI3R and led to the identification of talC. TalC harbors 21.5 repeats in its central domain and is phylogenetically more related to TAL effectors of Xanthomonas oryzae pv. oryzicola (Xoc). The BAI3RΔtalC mutant is seriously impaired in its virulence on susceptible rice varieties. Interestingly, bacteria are still able to grow at wild-type levels in the apex of the leaf, suggesting a requirement of talc for vascular colonization. Potential direct host targets were identified by conducting a transcriptomic analysis of rice leaves challenged with Xoo strain BAI3R vs. BAI3RΔtalC. Among the identified targets, the rice gene Os11N3 was found to be highly induced upon infection by the wild type strain but not the mutant one. A DNA target box for TalC was located in the Os11N3 upstream region and proved to be functional using GUS assays. We also show that the Os11N3 341-bp upstream region is transcriptionnally activated by TalC. Our results demonstrated for the first time that TAL effectors play an important role in the virulence of Xoo strain BAI3R. Our work will contribute to better improve rice for resistance to bacterial leaf blight.

No description available.

Vaccines have had a profound influence on human health with no other health intervention rivalling their impact on the morbidity and mortality associated with infectious disease. However, the magnitude and persistence of vaccine immunity varies considerably between individuals, a phenomenon that is not well understood. Recent studies have used contemporary technologies to correlate variations in the genome and transcriptome to complex phenotypic traits, and these approaches have started to provide fresh insight into the intrinsic factors determining the generation and persistence of vaccine-induced immunity. This thesis aimed to describe the relationship between genomic and transcriptomic variations, and the immunogenicity of childhood immunisations. Candidate gene and genome-wide genotyping was conducted to evaluate the influence of genetic variants on vaccine-induced immunity following childhood immunisation. Furthermore, contemporary methodologies were used to assess non-coding and coding gene transcript profiles following vaccination, to further dissect the molecular systems involved in vaccine responses. Key findings from this thesis include the description of the first genome-wide association studies into the persistence of immunity to three routine childhood immunisations: capsular group C meningococcal (MenC) conjugate vaccine, Haemophilus influenzae type b (Hib) conjugate vaccine and tetanus toxoid (TT) vaccine. Genome-wide genotyping was completed on over 2000 participants, with an additional 1000 participants genotyped at selected genetic markers. Genome-wide significant associations (p<5×10⁻⁸) were described between single- nucleotide polymorphisms (SNPs) in two genes, CNTN6 and ENKUR, and the persistence of serological immunity to MenC following immunisation of children 6-15 years of age. In addition, genome-wide significant associations were described between SNPs within an intergenic region of chromosome 10 and the persistence of TT-specific IgG concentrations following childhood immunisations. Furthermore, a number of variants in loci with putative involvement in the immune system such as FOXP1, the human leukocyte antigen locus and the lambda light chain immunoglobulin locus, were shown to have suggestive associations (p<1×10⁻⁵) with the persistence of vaccine-induced serological immunity. The fundamental challenge will be to describe functional mechanisms associated with these findings, and to translate these into innovative and pragmatic strategies to develop new and more effective vaccines.

L'ingénierie écologique a permis l'émergence de nouvelles technologies telles que la phytoremédiation, une approche de dépollution des sols basée sur l'utilisation des plantes. Cependant, jusqu'à présent, les mécanismes physiologiques et moléculaires qui contrôlent la dégradation des polluants organiques, en particulier les HAPs, restent très mal documentés chez les plantes supérieures. Dans ce travail, une approche intégrative et un profilage trancriptomique à l'échelle du génome entier ont permis d'étudier les premiers événements moléculaires impliqués dans la réponse, chez les plantes, à un stress provoqué par le phénanthrène. Un réseau de gènes susceptibles d'intervenir dans la perception, la dégradation et/ou la transformation des HAPs en molécules moins dangereuses a ainsi été identifié. D'autre part, nous avons pu montrer que le saccharose induit une tolérance à ce polluant, qui se traduit (i) par une activité transcriptionnelle très rapide, ce qui suggère un effet signalétique, (ii) une reconfiguration importante à l'échelle transcriptionnelle du génome exprimé, qui conduit à une mise en place des voies métaboliques de production d'énergie, de détoxification et de réparation cellulaire. Parallèlement, un site pilote de dépollution a été conçu et mis en œuvre, en exploitant les données obtenues au laboratoire. Cette expérimentation, sur deux ans, nous a permis de comparer l'efficacité de plusieurs espèces végétales mais aussi de tester l'effet protecteur du saccharose in-situ. Malgré l'obtention de résultats contrastés, cette étude confirme l'incidence de la nature des espèces végétales et des pratiques culturales sur l'efficacité de cette méthode de dépollution. Elle souligne également le rôle important de l'interaction plante-microorganismes du sol. / Ecological engineering strategies allowed the emergence of new technologies such as phytoremediation to clean up environmental pollution. Polycyclic Aromatic Hydrocarbons (PAHs) are ubiquitous and hazardous molecules for natural ecosystems and human health. However, molecular mechanisms involved in PAHs detoxification in plant remain largely unknown. This work allowed to decipher the early plant response of phenanthrene induced stress through an integrative investigation using wide genome transcriptomic and targeted metabolomic approaches. Hence, a gene network was identified to be involved in the early perception and signalization of PAHs and putative degradation and/or transformation to harmless molecules. Additionally, we showed that sucrose mitigate phenanthrene induced stress, while Arabidopsis development was arrested and seedlings were unable to accumulate chlorophyll in the presence of high phenanthrene concentration, sucrose allowed growth and chlorophyll accumulation. These phenotypical changes were associated with (i) very early transcriptional regulation, suggesting a sucrose signaling effect (ii) reconfiguration of wide genome transcriptional changes, as metabolic, detoxification and cell repair pathways were induced. In parallel, based on previous results accumulated in controlled conditions. Field investigation allowed the evaluation of the ability of different plant species to clean up PAHs polluted soil. We also evaluate the impact of sucrose supply on natural phytoremediation efficiency. Despite contrasted results, this study confirms the incidence of the plant species and the cultural practices on the efficiency of this method. It also underlines the role of soil microorganisms and plant interactions.

Traditional water monitoring encounter limitations due to the large number of contaminants present in our waters possible giving raise to mixture effects. This thesis aimed to investigate how the emerging omics approaches (transcriptomics, proteomics and metabolomics) can be used as an effect-based monitoring approach to assess and predict adverse effects in the freshwater environment. Moreover, this thesis analysed challenges and barrier with omics. A systematic literature search was conducted using Scopus and Web of Science to find case-studies using omics in field studies and reviews regarding challenges and barriers. The results in this thesis suggest that the use of fish species (either collected in the wild or in situ set-ups), transcriptomics and investigations of WWTP recipient was the most common way to apply omics. In order to interpret omics-data multiple studies conducted chemical monitoring in conjunction, investigated additional traditional biomarkers and/or used omics to identify altered biological or functional pathways that possible could lead to adverse effects at higher levels. According to the challenges and barriers identified in this thesis, the future of omics in environmental monitoring rely on the possibility to characterise and quantify natural variability, define appropriate critical effect sizes (i.e. thresholds of critical effects) and define baseline data. Moreover, it is necessary to develop frameworks and standardisations for omics-approaches (e.g. study-designs) to promote the interpretation of the results. Future research is also needed to develop and increase the understanding of how the proteomics and metabolomics can be applied. By improving the use of omics a more holistic water monitoring can be achieved including screenings for biological responses and the ability to detect early warnings which will enhance the prioritisation and site management of polluted water bodies, including those with limited prior knowledge regarding potential contaminants.

No description available.

Le genre Mucor appartient au phylum des Mucoromycota, un groupe issu de l’une des lignées ayant divergé très tôt dans l'évolution des espèces fongiques (early diverging lineages). Ces groupes restent encore très peu connus par rapport aux Ascomycètes et Basidiomycètes. Le genre Mucor est un genre d'espèces saprophytes, avec cependant une certaine diversité au niveau du mode de vie. Il existe en effet au sein du genre, des endophytes de plantes (comme M. endophyticus) ou encore des pathogènes opportunistes d'animaux (comme les espèces thermophiles M. circinelloides ou M. indicus). Le genre est ubiquiste mais il existe des associations à certains habitats qui semblent dénoter une certaine spécialisation. L’objectif de cette thèse était de mieux connaître les potentialités génétiques du genre Mucor lui permettant ce mode de vie ubiquiste, son potentiel d'adaptation mais également de mieux comprendre l'existence au sein du genre d'espèces semblant s'être spécialisées en colonisant préférentiellement ou exclusivement certains habitats comme le fromage. Afin d'atteindre cet objectif des études transcriptomiques et génomiques comparées ont été menées dans le cadre de cette thèse, afin de déterminer les principales caractéristiques des génomes de Mucor aussi bien structurelles que fonctionnelles, identifier les similitudes au niveau des espèces étudiées et aussi leur spécificités et en fonction des modes de vie/habitats et déterminer s'il existe chez les espèces fréquemment rencontrées dans les fromages (et notamment pour celles considérées comme technologiques) des traces d'adaptation voire de domestication. / The genus Mucor belongs to the phylum Mucoromycota; a group that derived from the lineages that diverged early in the evolution of fungal species (early diverging lineages). These groups have been less well studied and are less well understood in comparison to Ascomycetes and Basidiomycetes. The genus Mucor is composed of saprophytic species, but also encompasses species with diverse lifestyles.For example, it includes plant endophytes (such as M. endophyticus) or opportunistic animal pathogens (such as the thermophilic species M. circinelloides or M. indicus). The genus is ubiquitous but there are some associations with specific habitats which seem to indicate specialisation. The aim of this thesis is to better understand the genetic potential of the genus Mucor in particular, to decipher how it maintains this ubiquitous lifestyle, its capacity to adapt to diverses habitats and to better understand the existence within the genus of species that may have undergone specialization allowing them to preferentially or exclusively colonise certain habitats, such as cheese. In order to achieve this, we have performed comparative transcriptomic and genomic studies in order to determine the main structural and functional characteristics of the Mucor genomes, identify similarities among the species studied and also assess whether there exist specific genetic associations with lifestyle/habitat and determine whether the species frequently found in cheese (in particular those species considered as technological) harbour imprints of adaptation or even domestication.

Haemophilus influenzae (Hi) é uma bactéria Gram-negativa comensal da nasofaringe e um patógeno oportunista cujo único hospedeiro natural conhecido é o ser humano. As cepas de Hi que possuem cápsula de polissacarídeo estão associadas a doenças invasivas mais graves, sendo as de sorotipo b (Hib) as principais causadoras da meningite bacteriana em populações não vacinadas. Para produzir a vacina contra Hib, o polissacarídeo purificado desta bactéria é conjugado quimicamente ao toxóide tetânico. Industrialmente, a produção do polissacarídeo é realizada cultivando esse micro-organismo em biorreatores, entretanto o rendimento em polissacarídeo é baixo, mesmo com fornecimento de nutrientes, controle de pH e outros ajustes das condições no decorrer do cultivo. O estudo dos diferentes perfis fisiológicos da população bacteriana de Hib no decorrer do cultivo através da transcritômica traz a possibilidade de aprofundar o conhecimento sobre o metabolismo desse micro- organismo. As taxas de transcrição dos genes expressos em diferentes momentos considerados como pontos metabolicamente significativos do cultivo de Hib linhagem GB 3291 em batelada alimentada conduzido em Biorreator de 10 L, com aeração submersa e controles de pH (7,0) e temperatura (30° C) foram obtidas através de sequenciamento de RNA paralelo massivo (RNA-seq). A análise de co-expressão dos genes foi realizada com WGCNA, em que oito módulos de genes co-expressos foram identificados, quatro dos quais apresentaram correlação alta com dados fenotípicos dos cultivos, inclusive produtividade de acetato e de polissacarídeo. Análise de enriquecimento funcional identificou vias metabólicas associadas a ribossomo, síntese de parede celular, transportadores e consumo de carbono. A análise de expressão diferencial permitiu observar o comportamento desta bactéria durante o cultivo. Através da análise das taxas de transcrição dos genes foi possível identificar as principais vias de síntese de acetato e de polissacarídeo capsular, sendo esta última feita principalmente através da via de pentose fosfato, em detrimento da via de interconversão pentose-glucuronato. Nossos dados mostram que as diferentes etapas do cultivo de Hib leva à ação conjunta de vários grupos de genes, com destaque àqueles ligados às funções celulares básicas, como a síntese de proteínas e de parede celular, o transporte e a síntese de aminoácidos. Esses resultados contribuem para o entendimento dos processos bioquímicos e celulares que ocorrem durante o processo de cultivo de Hib, possibilitando que sejam feitas sugestões de modificações genéticas em Hib e alteração no processo de cultivo com propósito de diminuir produção de acetato e aumentar produção do polissacarídeo. / Haemophilus influenzae (Hi) is a nasopharynx commensal Gram-negative bacterium and an opportunistic pathogen whose only known natural host is human being. Hi strains with polysaccharide capsule are related to more severe invasive diseases, wherein type b capsule (Hib) strains are the main cause of bacterial meningitis in unvaccinated population. To produce Hib vaccine, purified polysaccharide of this bacterium is chemically conjugated to tetanus toxoid protein. Industrially, polysaccharide production is performed by cultivating this micro-organism in bioreactors; however, the yield of polysaccharide is low, even with supply of nutrients, pH control and further adjustments of the fermentation conditions during cultivation. The study of different physiological profiles of Hib bacterial population during cultivation by transcriptomics brings the possibility to deepen the knowledge about the metabolism of this micro-organism. Transcription of genes expressed at different times considered metabolically significant points of Hib strain GB 3291 grown in fed-batch conducted in a 10 L bioreactor with submerged aeration and pH (7.0) and temperature (30 ° C) control rates were obtained through massive parallel RNA sequencing (RNA-seq). Gene co-expression analysis was performed with WGCNA, in which eight modules of co-expressed genes were identified, four of which showed high correlation with cultivation data traits, including acetate and polysaccharide productivity. Enrichment analysis identified pathways related to ribosome, cell wall synthesis, transports and carbon consumption. Differential expression analysis allowed to observe this bacteria behaviour during cultivation. Through transcription rate analysis, it was possible to identify the main pathways for acetate and polysaccharide synthesis, which is through pentose phosphate pathway instead of glucoronate-pentose pathway. Our data show that different stages in Hib cultivation leads to joint action of several gene groups, highlighting genes related to basic cellular roles, like protein and cell wall synthesis, transport and aminoacid synthesis. These results contribute to the understanding of biochemical and cellular processes that ocurr during Hib cultivation process, allowing suggestions to be made to modify Hib gene circuitry and to change cultivation process in order to decrease acetate production and to decrease acetate production and increase polysaccharide production.