We present a mathematical model that describes how cyanobacterial communities use natural light as a source of energy and water as a source of electrons to perform photosynthesis and therefore, grow and co-survive together with other bacterial species. We apply our model to a phototrophic population of bacteria, namely, cyanobacteria. Our model involves the use of light as a source of energy and inorganic carbon as a source of nutrients. First, we study a single species model involving only cyanobacteria, then we include heterotrophs in the two species model. The model consists of ordinary differential equations describing bacteria and chemicals evolution in time. Stability analysis results show that adding heterotrophs to a population of cyanobacteria increases the level of inorganic carbon in the medium, which in turns allows cyanobacteria to perform more photosynthesis. This increase of cyanobacterial biomass agrees with experimental data obtained by collaborators at the Center for Biofilm Engineering at Montana State University. / Mathematics

THE UNIVERSITY OF MANCHESTER ABSTRACT OF THESIS submitted by Raja Moftah Moman for the Degree of Doctor of Philosophy entitled Interactions of Oral Bacteria with Host Tissues and Allochthonous Microorganism. 15th June 2017. The oral microbiome is a taxonomically diverse microbial community situated principally upon the hard and soft tissue surfaces of the mouth. It represents a readily accessible biofilm community for the investigation of bacteria-bacteria and bacteria-host interactions, which are responsible for some of the main features of oral biofilms in health and disease (colonisation resistance, antimicrobial tolerance, metabolic cross feeding, and other cooperative phenomena). In the oral cavity these relate specifically to cariogenesis and interactions with soft tissue that are responsible for periodontal disease. This doctoral thesis presents a series of investigations that consider processes for which growth in the biofilm phenotype or bacterial-bacteria or bacteria-host cell interaction are responsible. Four distinct methods were used to assess the effect of the biofilm phenotype on susceptibility of eight distinct oral hygiene actives with various modes of action. Bisphenol microbicide triclosan and the bis-biguanide chlorhexidine were most effective. All were markedly more effective against bacteria grown planktonically than the same organisms grown as biofilms illustrating antimicrobial tolerance, an important biofilm characteristic. In studies of interactions between oral isolates, bacteria previously isolated from the saliva and different oral sites of the oral cavity were tested using a modified cross streak method, in all possible pair-wise combinations. The frequency and strength of physical interactions (coaggregation) between these isolates was also assessed. The incidence of positive interactions was higher than the incidence of negative interactions (15.21% vs. 1.04%) and the incidence of coaggregation in bacteria isolated from saliva was significantly lower than for bacteria isolated from oral biofilms. Together, these data suggest that bacterial cooperation plays a greater role in oral biofilm development and maintenance than competition. With respect to putatively beneficial interactions between bacteria and host, the potential of the candidate dental probiotics L. rhamnosus GG, L. reuteri and S. salivarius to protect host tissues from damage by three Gram negative periodontal pathogens were investigated using human oral cells culture and the (invertebrate) G. mellonella model system. All probiotics inhibited the growth of the test pathogens when applied simultaneously, and significantly decreased toxicity (p P. gingivalis > A. actinomycetemcomitans) in two distinct cell lines. Whilst all probiotics conferred protection against the periodontal pathogens, L. rhamnosus GG, had the greatest protective effect, regardless of probiotic or pathogen used, followed by L. reuteri. S. salivarius was the least effective. Prophylactic treatment with probiotics conferred greater protection than treatment concomitant with pathogen challenge. The data presented in this doctoral thesis demonstrate the functional significance of interactions between taxonomically distinct bacteria and between bacteria and host tissues. Such interactions may determine the outcome of exposure to antimicrobials and are, particularly significant in health and through further research, may be harnessed for prevention and treatment of oral disease.

Master of Science / Division of Biology / Michael A. Herman / Stenotrophomonas maltophilia is an opportunistic bacterial pathogen found ubiquitously in the environment. Although S. maltophilia is an emerging pathogen associated with hospital-acquired infections in patients with respiratory diseases, particularly cystic fibrosis, very little is known about its mechanism of pathogenesis in any system. In addition, S. maltophilia isolates vary in pathogenicity to several hosts and are genetically diverse, including variation in virulence factors. In this thesis, I address the genetic basis of S. maltophilia pathogenesis from both host and bacterial perspectives. Our lab has previously developed Caenorhabditis elegans as a model for S. maltophilia infection. Stenotrophomonas is found in relatively high abundance in the microbiome of C. elegans, making it a suitable platform for studying S. maltophilia-host interactions. I performed a transcriptomic analysis to determine C. elegans responses to several S. maltophilia strains of varying pathogenicity. Treatments included K279a, an avirulent clinical isolate, JCMS, a virulent environmental strain isolated in association with nematodes near Manhattan, KS, and JV3, an even more virulent environmental isolate. Overall, I found that most genes (89%) that are differentially expressed in response to pathogenic S. maltophilia strains are upregulated, with many even further upregulated in response to the more virulent strain, JV3. Using information from a variety of transcriptomic datasets, I found that most of these genes are also commonly differentially expressed in C. elegans in response to other pathogens. Many more genes were differentially expressed specifically in response to JV3 when compared to all other strains (221 genes) than JCMS as compared to all other strains (14 genes), suggesting JV3 has unique virulence mechanisms that could explain its observed increased virulence. Candidate genes were chosen from the above differentially expressed gene sets (differentially expressed in response to both pathogenic S. maltophilia strains or in a strain-specific manner) for functional analysis. Mutational analysis of these candidate genes revealed that several mutants caused increased susceptibility of C. elegans to pathogenic S. maltophilia, regardless of the strain(s) that caused differential expression of that gene. Furthermore, many of these mutants also caused increased susceptibility to K279a, suggesting that K279a may also employ virulence mechanisms that wild-type C. elegans are able to defend against. To address the pathogen side of the interaction, we analyzed draft assemblies of the S. maltophilia strains, with the addition of another slightly pathogenic environmental strain, R551-3. We hypothesized that differences in observed pathogenicity and host responses to strains of S. maltophilia could be explained by differences in their genomes. When comparing draft assemblies to their respective reference genomes, few differences were observed. However, several genomic features were present in some strains and absent in others, including components of the CmeABC efflux pump and the Type IV secretion system, that might play a role in different virulence mechanisms. Genome-wide comparison of shared and unique genetic features across many S. maltophilia strains revealed that most S. maltophilia genes are strain-specific, suggesting that many potential virulence factors are unique and have yet to be functionally analyzed. Overall, variation in observed pathogenicity, differences in host transcriptional responses, and comparative genomics of S. maltophilia strains reveal that strain-specific mechanisms play important roles in S. maltophilia pathogenesis.

Carnobacterium maltaromaticum est une bactérie lactique atypique isolée de fromages à pâte molle. Les caractéristiques majeures de cette bactérie sont i) sa capacité à produire un arôme de type malté ou chocolaté, le 3-méthylbutanal à partir du catabolisme de la leucine ii) sa capacité à produire des bactériocines, peptides à activité antibactérienne vis-à-vis de flores pathogènes et/ou d'altération fréquemment rencontrées en industries alimentaire, telle que Listeria monocytogenes. Une caractérisation phénotypique et génotypique réalisée sur six souches de C. maltaromaticum isolées du même biotope a montré que celles-ci ne sont pas phylogénétiquement identiques. Même si ces souches n'ont pas la capacité à coaguler rapidement le lait, elles sont acidotolérantes. Elles n'influent pas sur la capacité ni la rapidité de coagulation des starters, Lactococcus lactis et Streptococcus thermophilus utilisés en industrie laitière. L'étude de l'impact de C. maltaromaticum sur la flore bactérienne du fromage a révélé que sa présence provoque la diminution de la concentration de Psychrobacter, germe pouvant être responsable d'une accélération du phénomène de vieillissement du fromage. Un plan d'expérience a été réalisé pour mettre en évidence ces inhibitions et les éventuelles interactions entre différents facteurs (concentration cellulaire initiale, concentration en NaCl, pH, durée d'incubation). Deux modèles ont été choisis i) Psychrobacter sp. et ii) L. monocytogenes. La concentration cellulaire de C. maltaromatiucm est le facteur le plus important pour inhiber les bactéries testées. Cette espèce opportuniste pourrait être considérée comme un auxilliaire de fabrication intéressant et pourrait être retenue comme flore bactérienne d'affinage. Toutes les souches de C. maltaromaticum testées sont capables de produire du 3-méthylbutanal pouvant conférer une flaveur maltée au fromage. Les études menées sur la biosynthèse du 3-méthylbutanal ont montré la présence et la fonctionnalité de deux voies métaboliques; la voie directe impliquant l'alpha-cétoacide décarboxylase et la voie indirecte passant par l'alpha-cétoacide déshydrogénase. L'oxygénation du milieu de culture a un impact positif sur la formation du 3-méthylbutanal et du 3-méthylbutanol avec la stimulation des voies directes et indirectes / Carnobacterium maltaromaticum is a lactic acid bacterium isolated from atypical soft cheeses. The major characterstics of this bacterium are i) its ability to produce a malty or chocolate-like flavor 3-methylbutanal from leucine catabolism ii) its ability to produce bacteriocins against pathogenic and spoilage bacteria for instance, Listeria monocytogenes. Phenotypic and genotypic characterization of six strains of C. maltaromaticum isolated from the same habitat showed that they were not phylogenetically identical. Although these strains lacked the ability to coagulate the milk quickly, they were acid tolerant. They did not affect the milk coagulation capacity of startes, Lactococcus lactis and Streptococcus thermophilus used in dairy industry. The study on the impact of C. maltaromaticum on the bacterial flora of cheese showed that its presence resulted in the decrease of the concentration of Psychrobacter, which might be responsible for accelerating the aging phenomenon of cheese. An experimental plan was realized to highlight these inhibitions and possible interactions between factors (cell concentration, NaCl, pH, incubation time) by choosing two models i) Psychrobacter sp. and ii) L. monocytogenes. The cell concentration of C. maltaromatiucm was the factor more significant for the inhibitions of the tested bacteria. Being psychrotrophic, alkalinophilic, malty or chocolate flavor producing and biopreservative agent, this species could play a role as a ripening flora of cheese. All strains of C. maltaromaticum tested were able to produce 3-methylbutanal conferring any malt flavor to cheese. The results on the physiology involved in the biosynthesis of 3-methylbutanal showed the presence and functionality of both metabolic pathways; the direct by alpha-ketoacid dacarboxylase enzyme and indirect comprising alpha-keto acid dehydrogenase enzyme. The oxygenation of culture medium had a positif impact on the formation of 3-methylbutanal and 3-methylbutanol with the stimulation of both direct and indirect metabolic routes

O presente trabalho tem como objetivo estudar o perfil de acidificação e a inter-relação entre Streptococcus thermophilus TAO, Lactobacillus delbrueckii subsp. bulgaricus LB340, Lactobacillus acidophilus LAC, Lactobacillus rhamnosus LBA, Bifidobacterium lactis BL04 como culturas associadas em leite fermentado. Cinco leites fermentados foram preparados, sendo a composição das co-culturas a variável estudada. O perfil de acidificação foi monitorado e os parâmetros cinéticos, calculados. Os produtos foram submetidos às análises físico-químicas e microbiológicas durante o armazenamento a 4°C. As associações em cultura mista provocaram a redução do tempo de fermentação do leite. Durante os 21 dias de armazenamento o pH e a firmeza dos leites fermentados variaram. Streptococcus thermophilus TAO, Bifidobacterium lactis BL04 e Lactobacillus rhamnosus LBA forneceram contagens acima de 106 log UFC/mL, porém Lactobacillus acidophilus LAC e Lactobacillus bulgaricus LB340 foram inibidos em cultura mista, demonstrando dificuldades de crescimento quando associados às demais bactérias ácido-láticas. / The present study aimed to evaluate the acidification kinectic and inter-relation between Streptococcus thermophilus TAO, Lactobacillus delbrueckii subsp. bulgaricus LB340, Lactobacillus acidophilus LAC, Lactobacillus rhamnosus LBA, Bifidobacterium lactis BL04 like association cultures in fermented milk. Five fermented milks were prepared and studied variable analyzed was the co-cultures composition. Acidification was monitored and the kinectic parameters were calculated. The products were submitted to physical chemistry and microbiological analyses during the storage at 4°C. The associations in mixed cultures promoted the reduction of fermentation time of the milks. During 21 days of storage, pH and firmness of fermented milks varied. Streptococcus thermophilus TAO, Bifidobacterium lactis BL04 and Lactobacillus rhamnosus LBA presented counts above 106 log cfu/mL. However, Lactobacillus acidophilus LAC and Lactobacillus bulgaricus LB340 were inhibited in mixed cultures demonstrating that these strains had difficulty to grow when in associated cultures with lactic acid bacteria.

Les macroalgues hébergent de nombreux micro-organismes, collectivement désignés sous le terme de microbiote algal, qui ont un rôle essentiel dans le développement et l’état de santé de leur hôte. Dans ce travail, nous avons exploré le microbiote fongique et bactérien d’algues brunes, ainsi que l’impact des interactions bactérie-champignon sur la médiation chimique et, en particulier, sur le quorum sensing bactérien. Par des approches de metabarcoding ciblant l’ADNr 16S et l’ITS2, nous avons montré que les communautés fongiques et bactériennes associées à la macroalgue brune Saccharina latissima étaient très riches, principalement composées de quelques OTUs dominants, et d’une grande abondance d’OTUs « rares ». De manière intéressante, les communautés fongiques comme bactériennes différaient de celles de l’eau de mer environnante et paraissaient spécifiques des tissus algaux. Cependant, de grandes variations intra et interindividuelles de composition ont été observées au sein des échantillons de tissus d’algue. Ainsi, ce qui définit la spécificité des communautés microbiennes reste à préciser. En parallèle, nous avons exploré la médiation chimique au sein de l’endomicrobiote de quatre algues brunes : Saccharina latissima, Laminaria digitata, Pelvetia canaliculata et Ascophylum nodosum, et révélé que de nombreux endophytes fongiques et bactériens isolés synthétisaient des métabolites interférant avec les systèmes de quorum sensing bactériens, en les induisant ou les inhibant. De plus, les bioessais basés sur les biosenseurs, couplés à une approche métabolomique, effectués sur les co-cultures, ont mis en évidence en quoi les interactions bactéries-champignons au sein de l’endomicrobiote d’algues brunes pouvaient affecter la production de médiateurs chimiques, et notamment de molécules interférant avec le quorum sensing bactérien. Ensemble, ces résultats suggèrent que le quorum sensing pourrait jouer un rôle clé dans le réseau complexe d’interactions au sein du microbiote algal, et ainsi dans l’équilibre hôte-microbiote. / Macroalgae host various microorganisms, collectively referred as the algal microbiota, which play an essential role in the development and health status of their host. In this work, we explored the bacterial and fungal microbiota of brown algae, as well as the impact of bacterial fungal interactions on the chemical mediation and, in particular, on the bacterial quorum sensing. Using 16S rDNA-based and ITS2-based metabarcoding approaches we showed that the fungal and bacterial communities associated with the brown macroalgae Saccharina latissima were very rich, mainly composed of few dominant OTUs, and a large abundance of “rare” OTUs. Interestingly, both fungal and bacterial communities differed from the ones of the surrounding seawater and appeared specific to the algal tissues. However, high intra and interindividual variations of composition were observed among the algal tissue samples. Thus what define the specificity of the microbial communities remains to be clarified. In parallel, we explored the chemical mediation within the cultivable endomicrobiota of four brown algae: Saccharina latissima, Laminaria digitata, Pelvetia canaliculata and Ascophylum nodosum, and pointed out that many of the isolated bacterial and fungal endophytes could synthetize metabolites interfering with bacterial quorum sensing systems, either inducing or inhibiting them. Additionally, biosensor-based bioassays coupled with metabolomics approaches performed on co-culture experiments, highlighted how bacterial-fungal interactions within the endomicrobiota of brown algae could affect the production of chemical mediators, including those interfering with bacterial quorum sensing. Altogether, the results suggest that the quorum sensing could play a key role in the complex network of interactions within the algal microbiota, and thus in the host-microbiota equilibrium.

O presente trabalho tem como objetivo estudar o perfil de acidificação e a inter-relação entre Streptococcus thermophilus TAO, Lactobacillus delbrueckii subsp. bulgaricus LB340, Lactobacillus acidophilus LAC, Lactobacillus rhamnosus LBA, Bifidobacterium lactis BL04 como culturas associadas em leite fermentado. Cinco leites fermentados foram preparados, sendo a composição das co-culturas a variável estudada. O perfil de acidificação foi monitorado e os parâmetros cinéticos, calculados. Os produtos foram submetidos às análises físico-químicas e microbiológicas durante o armazenamento a 4°C. As associações em cultura mista provocaram a redução do tempo de fermentação do leite. Durante os 21 dias de armazenamento o pH e a firmeza dos leites fermentados variaram. Streptococcus thermophilus TAO, Bifidobacterium lactis BL04 e Lactobacillus rhamnosus LBA forneceram contagens acima de 106 log UFC/mL, porém Lactobacillus acidophilus LAC e Lactobacillus bulgaricus LB340 foram inibidos em cultura mista, demonstrando dificuldades de crescimento quando associados às demais bactérias ácido-láticas. / The present study aimed to evaluate the acidification kinectic and inter-relation between Streptococcus thermophilus TAO, Lactobacillus delbrueckii subsp. bulgaricus LB340, Lactobacillus acidophilus LAC, Lactobacillus rhamnosus LBA, Bifidobacterium lactis BL04 like association cultures in fermented milk. Five fermented milks were prepared and studied variable analyzed was the co-cultures composition. Acidification was monitored and the kinectic parameters were calculated. The products were submitted to physical chemistry and microbiological analyses during the storage at 4°C. The associations in mixed cultures promoted the reduction of fermentation time of the milks. During 21 days of storage, pH and firmness of fermented milks varied. Streptococcus thermophilus TAO, Bifidobacterium lactis BL04 and Lactobacillus rhamnosus LBA presented counts above 106 log cfu/mL. However, Lactobacillus acidophilus LAC and Lactobacillus bulgaricus LB340 were inhibited in mixed cultures demonstrating that these strains had difficulty to grow when in associated cultures with lactic acid bacteria.