In an attempt to demonstrate the role of insects as possible carriers of pathogenic bacterial organisms this investigation has been concerned with the determination of the microbial population associated both internally and externally with the common house fly and three species of the cockroach.

Les relations entre le microbiote intestinal et la santé humaine ont été suggérées par les études métagénomiques. Microbial culturomics utilise de nombreuses conditions de culture avec une méthode d'identification rapide par MALDI-TOF, ou par séquençage de l'ARN 16S pour les colonies non identifiées. L'étude pionnière a permis d'identifier 340 bactéries différentes, dont 31 nouvelles espèces bactériennes et 174 espèces bactériennes décrite pour la première de l'intestin humain. Le séquençage du génome de chaque nouvelle espèce a permis de décrire le plus grand génome d'une bactérie isolée chez l'homme (Microvirga massiliensis, 9,3 Mo) et de générer environ 10 000 gènes précédemment inconnus (ORFans) facilitant les futures études métagénomiques. Le pyroséquençage sur les mêmes échantillons a révélé que seulement 51 espèces étaient détectées par les 2 techniques. Culturomics a démontré sa supériorité par rapport au pyroséquençage lors de l'étude d'une selle d'une patiente traitée pour une tuberculose ultra-résistante. Le pyroséquençage de 2 échantillons de selles de patients traités par antibiotiques a révélé 45 à 80% de séquences assignées au phylum des Verrucomicrobia. L'étude par culture de ces mêmes échantillons n'a pas permis d'isoler cette espèce.Grâce à l'étude de 14 échantillons de selles différents par culturomics, nous avons cultivé 520 espèces bactériennes différentes, dont 57 nouvelles espèces bactériennes et 260 espèces décrites pour la première fois à partir du microbiote digestif. Après cette phase de description, les études suivantes pourront tenter d'établir un lien entre les nouvelles espèces bactériennes et le statut clinique des patients étudiés. / Relationships between gut microbiota and human health have been already suggested thanks to metagenomics studies. Microbial culturomics is based on the use of a large number of culture conditions with a rapid identification method by MALDI-TOF or by 16SrRNA amplification and sequencing for the unidentified colonies. The seminal study allowed to identify 340 different bacteria including 31 new bacterial species, 174 bacterial species first described from the human gut. The genome sequencing of each new species allowed to describe the largest genome for a human bacteria (Microvirga massiliensis; 9,3 Mb) and to generate approximately 10,000 previously unknown genes (ORFans) facilitating the future metagenomics studies. In parallel, pyrosequencing performed on the 3 same samples revealed a dramatic low overlapping between the 2 methods with only 51 species detected. In addition, culturomics has demonstrated its superiority than pyrosequencing of a stool from a patient treated for a XDR-tuberculosis. Conversely, the pyrosequencing performed on 2 stool samples of patients treated by antibiotics revealed from 45 to 80% of sequences assigned to Verrucomicrobia although the culturomics study of these same samples did not allowed to culture this species.Currently, thanks to the study of 14 different stool samples by culturomics, we have cultured 520 different bacterial species including 57 new bacterial species and 260 species first described from human gut. After this comprehensive description phase, the following studies will attempt to make a link between new bacterial species and clinical status of the patients studied.

The use of a CO2 infrared (IR) laser and photocatalysis for water treatment microorganism disinfection purposes was investigated. During CO2 infrared (IR) laser treatment E. cloacae inactivation was comparable to inactivation via ultraviolet (UV) treatment; however no inactivation of the more resistant B. subtilis endospores occurred. Fourier Transform Infrared-Attenuated Total Reflectance (FTIR-ATR) spectroscopy of the bacterial cells displayed increased polysaccharide contents after IR treatment. FTIR and Raman spectroscopy of simple carbohydrates before and after IR laser treatment displayed no spectral changes, with the exception of N-acetyl-D-glucosamine (NAG), which was partially attributed to sampling techniques. E. cloacae inactivation during IR treatment was attributed to localised and overall temperature increases within the water. Due to the inability to inactivate B. subtilis endospores this technique is not suitable for water treatment purposes. Photocatalytic water treatment using novel TiO2 colloids prepared via a postsynthetic microwave-modification process (MW-treated) was also examined. These colloids were characterised using X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and Brunauer-Emmett-Teller (BET) analyses and compared to Degussa P25 and convection hydrothermally-treated (HT-treated) TiO2. Slurry suspensions displayed comparable E. coli inactivation rates, so the colloids were examined in immobilised form using both a model organic degradant, oxalic acid, and E. coli. Oxalic acid degradation studies showed that the MW-treated colloids displayed similar inactivation rates to the HT-treated TiO2, due to their pure anatase composition, while Degussa P25 displayed higher inactivation rates. Investigations into the effect of shortening UV wavelength were also performed. Degussa P25 was the only catalyst which displayed higher apparent quantum yields upon shortening the UV wavelength, which was attributed to its mixed-phase anatase-rutile composition. As E. coli inactivation was observed using distilled water, photocatalysis in natural river water was trailed. It was discovered that the pH had to be lowered from 7.5 to 5.0 and the initial cell concentration must be approximately 1 x 103 colony forming units (CFU) per cm3 or less for inactivation to be observed during a 5 hour treatment period. At a catalyst loading of 1.0 mg per cm2, Degussa P25 absorbed all the applied UVA irradiation; however the MW- and HT-treated TiO2 colloids did not due to their smaller particle size. Therefore sandwich experiments were devised to evaluate the effect of unabsorbed UV irradiation within the system. Small colony variants were identified after photocatalytic and UV treatment, which pose a potential threat to public health. Further investigation of the different TiO2 colloids was performed using in situ FTIR, both with and without an applied potential and compared to a thermally prepared TiO2 catalyst. The latter displayed potential dependent photocatalysis, while the mesoporous TiO2 catalysts displayed potential independent photocatalysis. All catalyst types displayed increased degradation rates upon the application of a positive bias, which was followed in situ via the production of CO2. Sodium oxalate and NAG was examined for photocatalytic degradation, both of which were degraded to CO2, with proposed break-down products identified when using NAG.