Spatiotemporal metabolic modeling of microbial metabolism is a step closer to achieving higher dimensionalities in numerical studies (in silico) of biofilm maturation. Dynamic Flux Balance Analysis (DFBA) is an advanced modeling technique because this method incorporates Genome Scale Metabolic Modeling (GSMM) to compute the biomass growth rate and metabolite fluxes. Biofilm thickness is pertinent because this variable of biofilm maturation can be measured in a laboratory (in vitro). Pseudomonas aeruginosa (P. aeruginosa) is the model bacterium used in this computational model based on previous research conducted by Dr. Michael Henson, available GSMMs, and the societal significance of patients suffering from P. aeruginosa airway infections. Spatiotemporal Flux Balance Analysis (SFBA) will be the computational method used in this thesis to simulate biofilm growth. Another level of accuracy will be introduced to SFBA which is a dynamic finite difference grid that will vary relative to the biofilm’s velocity of expansion/contraction. This novel idea is governed by a differential equation that defines the biofilm’s velocity and updates the spatial dependency of the finite difference grid which has never been done while utilizing GSMM. Environmental conditions (bulk concentrations of metabolites) are altered to investigate how varying nutrients (glucose, oxygen, lactate, nitrate) affected biofilm maturation.

Diabetes mellitus ist ein entscheidender Risikofaktor in der Entstehung chronischer Wunden. Hyperglykämien, oxidativer Stress und Mikro- sowie Makroangiopathien führen zu einer pathologisch veränderten Wundheilung. Erhöhte Konzentrationen pro- inflammatorischer Zytokine, neutrophiler Granulozyten, Matrix-Metalloproteasen (MMPs) und geringere Expression von Wachstumsfaktoren resultieren in einem persistierenden Inflammationszustand mit Beeinträchtigung aller Phasen der Wundheilung. Eine offene Wunde begünstigt die bakterielle Besiedlung mit Entwicklung eines polymikrobiellen Biofilms und möglicher Entstehung einer chronischen Wunde. Das Ziel der vorliegenden Arbeit ist es, herauszufinden, ob die Lokaltherapie mit Polyvinylpyrrolidon-Iod (PVP-I) und liposomalem Polyvinylpyrrolidon-Iod-Hydrogel (PVP-ILH) zu einer Biofilmreduktion in diabetischen Wunden führt. Außerdem soll untersucht werden, welchen Einfluss beide Antiseptika auf die diabetische Wundheilung, insbesondere Gewichtsveränderung, Wundgröße, Neoangiogenese (CD31), Gewebeinflammation (CD45), Wundkontraktion (Smooth Muscle Actin α (α-SMA) und Remodeling (MMP-9) sowie durch Bestimmung von Interleukin-1α (IL-1α) im murinen Serum auf die systemische Inflammation haben. Dazu wurden Untersuchungen an einem Staphylococcus aureus – Biofilm im in – vivo – Rückenhautkammermodell der diabetischen Maus (BKS.Cg-Dock7m +/+ Leprdb (Db/Db)) nach lokaler Wundtherapie mit PVP-I oder PVP-ILH durchgeführt. PVP-I und PVP-ILH bewirkten keine signifikante Reduktion von Biofilmen. Jedoch war eine reduzierte bakterielle Aktivität in oberflächlicher und tiefere Muskelschicht nach PVP- ILH-Therapie zu beobachten, während nach PVP-I-Therapie weiterhin Biofilme in allen Schichten nachweisbar waren. PVP-ILH und PVP-I zeigten keinen signifikanten Einfluss auf die Wundgrößenreduktion. Jedoch wurden signifikant geringere Gewichtsverluste nach PVP- ILH-Therapie und eine nicht signifikante Reduktion von Gewichtsverlusten nach PVP-I- Therapie beobachtet. PVP-ILH und PVP-I zeigten keinen signifikanten Einfluss auf Gewebeinflammation oder Wundkontraktion. PVP-ILH demonstrierte die höchste, jedoch nicht signifikante Neoangiogenese (CD31). Weder PVP-I noch PVP-ILH hatten einen Effekt auf das Remodeling (α-SMA) oder die lokale Inflammation (CD45). PVP-I bewirkte jedoch eine signifikante Reduktion der systemischen Inflammation (IL-1α). Die Daten lassen vermuten, dass PVP-I und PVP-ILH zu einer Bakterienreduktion in chronischen Wunden beitragen, obwohl sie in unserer Studie zu keiner signifikanten Biofilmeradikation führten. Die signifikant geringeren Gewichtsverluste in der mit PVP-ILH behandelten Gruppe sowie die signifikant geringere systemische Inflammation in der mit PVP-I behandelten Gruppe verdeutlichen positive Effekte beider Antiseptika in der Lokaltherapie Biofilm-besiedelter chronischer Wunden.:1 Abkürzungsverzeichnis 2 Einführung 2.1 Die Haut des Menschen 2.1.1 Aufbau der Haut 2.1.1.1 Epidermis 2.1.1.2 Dermis 2.1.1.3 Subkutis 2.2 Die Haut der Maus 2.2.1 Aufbau und Vergleich der Haut von Mensch und Maus 2.3 Grundlagen der humanen Wundheilung 2.3.1 Physiologische Wundheilung 2.3.1.1 Inflammationsphase 2.3.1.2 Proliferationsphase 2.3.1.3 Remodeling 2.3.2 Diabetische Wundheilung 2.3.2.1 Chronische Wunden 2.4 Biofilme 2.4.1 Entstehung eines Biofilms 2.4.2 Herausforderungen durch Biofilm-Besiedlung 2.5 Behandlung Biofilm-besiedelter, chronischer Wunden 2.5.1 Topische Antiseptika zur Behandlung Biofilm-besiedelter chronischer Wunden 2.5.1.1 Polyvinylpyrrolidon-Iod(PVP-Iod) 2.5.1.2 LiposomalesPolyvinylpyrrolidon-Iod-Hydrogel(PVP-ILH) 2.6 Überblick translationaler Mausmodelle der Wundheilung 2.6.1 Das Rückenhautkammermodell (RHK) 2.6.2 Leipziger Rückenhautkammer und Modifikation für diabetische Mäuse 2.6.3 Vorversuche mit dem Leipziger Rückenhautkammermodell 3 Aufgabenstellung 4 Materialien und Methoden 4.1 Materialien 4.1.1 Chemikalien 4.1.2 Medikamente 4.1.3 Antikörper für die Immunhistochemie 4.1.4 Verwendetes ELISA-Kit zur Serum-ELISA 4.1.5 Geräte und sonstige Materialien 4.1.6 Programme 4.1.7 Versuchstiere 4.2 Methoden 4.2.1 Studienaufbau 4.2.2 Implantation der Rückenhautkammer (RHK) 4.2.3 Intravital-Mikroskopie 4.2.4 Histologie 4.2.4.1 EinbettungundSchnittederGewebeproben 4.2.4.2 Hämatoxylin-Eisen-Färbung(HE-Färbung) 4.2.5 Immunhistochemie 4.2.6 Fluoreszenz-in-situ-Hybridisierung (FISH) 4.2.7 ELISA (Enzyme Linked Immunosorbent Assay) 4.2.8 Wundgrößenmessung 4.2.9 Auswertung der Immunhistochemie 4.2.10 Randomisierung der Versuchsgruppen mittels Random Group Generator 4.3 Statistische Auswertung 5 Ergebnisse 5.1 In – vivo - Ergebnisse 5.1.1 Gewichtsverlauf 5.1.2 Blutzuckerkontrollen 5.1.3 Wundgrößenmessungen 5.2 In – vitro - Ergebnisse 5.2.1 Histologie mit HE-Färbung 5.2.2 Immunhistochemie 5.2.3 FISH - Analyse 5.2.4 Serum-ELISA 6 Diskussion 6.1 Blutzuckerspiegel der Versuchstiere 6.2 Gewichtsverlust während des Versuchszeitraums 6.3 Einfluss von PVP-I und PVP-ILH auf die Wundgrößenreduktion 6.4 Einfluss von PVP-I und PVP- ILH auf die Gewebeinflammation (CD45) 6.5 Effekt von PVP-I und PVP- ILH auf die Neoangiogenese (CD31) 6.6 Einfluss von PVP-I und PVP-ILH auf den EZM- und Kollagenabbau (MMP-9) 6.7 Effekt von PVP-I- und PVP-ILH auf die Fibrogenese (α-SMA) 6.8 Einfluss der topischen PVP-I- und PVP-ILH-Behandlung auf die IL - 1α – Konzentration im murinen Serum 6.9 Effekt von PVP-I und PVP-ILH auf die Biofilmeradikation 6.10 Mögliche klinische Bedeutung der Ergebnisse für die diabetische Wundheilung 7 Zusammenfassung 8 Literatur 9 Anlagen 9.1 Abbildungsverzeichnis 9.2 Tabellenverzeichnis 9.3 Lebenslauf 9.4 Publikationen 9.5 Danksagung 10 Eigenständigkeitserklärung

This study turns to what is for many an everyday item – yogurt – as a critical zone observatory, a synergistic, place-based laboratory which aims to integrate heterogenous representations of planetary phenomena as they are registered at a common surface. Yogurt has an impressive cultural endurance largely derived from its prominence in various paradigms of health. The product has culturally endured in another sense: as a common cultural medium where humans and microbes have met for generations. This study begins with a profile of yogurt as most encounter it today to consider how normative notions of health interface with the temporal and spatial imaginaries entailed in commodity geographies. Commoditized yogurt is characterized by a low and limited microbial biodiversity compared to yogurts produced outside of the commodity context. Yogurt is therefore presented as a micro case study to consider modes by which we sense and valuate ecological phenomena beyond the perceptible surface, how such sens-abilities intersect models of health, and to what effect. To trace a history of yogurt along these contours, I introduce it as a particular kind of artefact: a global object. As an object of environmental history, I define a global object as a global commodity with a high potential to be re-localized, and therefore with a high potential to re-shape commodity geographies. However, this trajectory is contingent upon framing yogurt as a critical zone observatory – a site where global phenomena like human-microbial interaction may become familiar and intimate. Guided by new materialist theory, I weave together historical and ethnographic case studies from the following consortium: resident yogurt bacteria, artisanal yogurt producers and home fermenters, a mystical immunologist, and an 11th century linguistic scholar. Through these perspectives, I both sketch and apply a framework for de-centered, interspecies histories of cultural (re)production through an extended metaphor of biofilm: the coagulative bacterial structure giving yogurt its characteristic texture. In so doing I provide a re-articulation of “the probiotic” as an integrative case of human and more-than-human health. The study concludes by directing these implications towards a consideration of aesthetic engagement by displaying how fermentation practice may enliven matters of re-diversification and re-localization.

The study explored the prevalence of biofilm formers and its association with multidrug resistance in Klebsiella Pneumonia, a gram-negative bacterium that has high propensity to form antibiotic resistant strains and forms biofilms. Biofilms are complex microbial community with attributes that vary from planktonic cells. Antibiotic resistance is a property that has shown evidence to be higher in biofilms as compared to planktonic cells. Multi-drug resistance, a higher form of antibiotic resistance, is defined as resistance to at least one agent in three or more antibiotic categories. A single-armed and a two-armed meta-analysis was done to assess prevalence of biofilm formers and to find association between biofilm formation capacity and multi drug resistance. The one-armed meta-analysis revealed 74% (95% CI: 64%-83%) prevalence of biofilm formers among clinical isolates of Klebsiella Pneumonia. The prevalence rate is comparable with that of prevalence rate attained by other bacterium by similar meta-analysis studies. This high prevalence of biofilm formers warrants for a paradigm shift in treatment strategies for treatment of infections. The two-armed meta-analysis showed that there was identical risk of multi drug resistance among the biofilm formers and non-biofilm formers. The result challenges the intrinsic capacity of planktonic cells to resist against antibiotics to achieve multi drug resistance. Further research to update the biofilm formation profiles and to understand the resistance mechanism in commonly occurring bacterial infections in of utmost importance.

Due to the adverse effects of ammonia on the environment, many governments, including Canada, have imposed new regulations to reduce the discharge of ammonia wastewater effluent into natural receiving waters, which has resulted in the upgrade of ammonia removal at water resource recovery facilities (WRRFs) across the world. There is therefore a need to investigate present urban/peri-urban and rural challenges associated with municipal total ammonia (TAN) removal. In particular, there is a need to further advance and optimize technologies such as the moving bed biofilm reactor (MBBR) to meet these critical challenges. The first objective of this thesis is to validate an elevated loaded strategy for partial nitritation (PN) MBBR as an application for mainstream urban and peri-urban municipal wastewater treatment and to elucidate the mechanism of nitrite-oxidation suppression of this system. The second objective is to identify practical storage strategies for nitrifying MBBR units as rural municipal wastewater upgrade systems (lagoon systems), optimizing the TAN removal performance during seasonal discharge periods. In the context of the present climate change crisis and sustainable development requirements, there is an increased need for efficient TAN removal from urban and peri-urban municipal wastewaters. The application of the energy and cost-efficient partial nitritation/anammox (PN/A) technology to mainstream urban and peri-urban municipal wastewater can prove challenging because of limited ability to achieve the stable PN. Hence, there is a need for the validation of the present strategies for achieving effective and stable PN in the mainstream portion of conventional urban and peri urban WRRFs. The 45 days operation of a laboratory-scale, elevated loaded PN MBBR with average surface area loading rate (SALR) of 5.2 ± 0.1 g TAN/m²·d and a hydraulic retention time of 2h showed a successful and stable nitrite accumulation. The average surface area removal rate (SARR) of 2.3 ± 0.2 g TAN/m²·d (theoretical performance objective of 2.7 g TAN/m²·d), TAN removal efficiency of 43.1 ± 3.4% (theoretical performance objective of 53%) and NO₂- / (NO₂- + NO₃-) ratio of 82.4 ± 4.8% (theoretical performance objective of 100%) meets the necessary requirement to support subsequent cost-efficient anammox process. Biofilm analyses of the laboratory-scale, elevated loaded PN MBBR indicated that the attached biofilm was thick and dense, stable biofilm that did not show and biofilm loss or washout. Biofilm cell viability analyses was indicative of an active biofilm. The ratio of AmoA gene targets of the ammonia oxidizing bacteria (AOB) in the MBBR biofilm to the targeted gene region of the Nitrospira nitrite oxidizing bacteria (NOB) population demonstrates that NOB activity suppression of this technology was the dominant mechanism of nitrite-oxidation in the elevated loaded PN MBBR system. In North America, the TAN removal performance of waste stabilization ponds (also termed wastewater treatment lagoon systems), which are widely applied as rural WRRFs, is often not stable due to seasonal temperature variations. Nitrifying MBBR as an upgrade TAN removal unit has been successfully applied to improve TAN removal during winter. However, re-seeding the nitrifying MBBR biofilm during each seasonal operation period is not sustainable. There is therefore an urgent need for optimizing storage strategies of nitrifying MBBR carriers when used as TAN removal upgrade systems of rural WRRFs. The study of storage strategies for nitrifying MBBR as lagoon upgrading systems indicated the batch storage of the nitrifying MBBR biofilms with intermittent aeration could be an effective storage strategy for short-term (12 weeks) storage. Carriers stored in continuous flow aerated condition was shown to be the second most suitable storage method for nitrifying MBBR carriers for systems exposed to less than 12 weeks of storage. Carriers stored in dry condition, batch aerated conditions without flow, and continuous flow aerated condition for long-term (over 18 weeks) failed to achieve full nitrification following 18 days of operation conditions. Carriers stored in dry condition did not successfully achieve full nitrification for short-term and long-term storage and may not be applied to store full nitrification MBBR carriers. The study suggested that, compared to re-seeding start up strategy of the lagoon upgrading nitrifying MBBR biofilm, the use of the appropriate storage strategies, such as batch aerated conditions without flow, has the potential to shorten the start-up time and save energy during the non-discharge periods.

Tiefe sternale Wundheilungsstörungen nach medianer Sternotomie treten mit einer Inzidenz 0,4 – 5 % selten auf. Dennoch stellen sie mit einer Mortalität von 10 – 47 % ernst zu nehmende Komplikationen in einem multimorbiden Patientengut dar. Mikrobiologisch dominieren vorwiegend Erreger des grampositiven Spektrums. Mischinfektionen und multiresistente Erreger verstärken zudem die mikrobiologische Komplexität. Auf Grundlage dessen sind tiefe sternale Wundinfektionen im klinischen Alltag nur schwer kontrollierbar und stellen damit eine große Herausforderung dar. In dem Zeitraum von Mai 2012 bis Mai 2013 wurden 52 Patienten mit tiefen sternalen Wundheilungsstörungen im Universitätsklinikum Leipzig und im Herzzentrum Leipzig behandelt. Die sternalen Wundinfektionen traten hierbei als postoperative Komplikationen nach herzchirurgischen Eingriffen auf. Das einheitliche Behandlungskonzept bestand aus einem radikalen chirurgischen Wunddébridement und einer lappenplastischen Brustwandrekonstruktion unter simultaner resistogrammgerechter Antibiotikatherapie. Im Rahmen des Wunddébridements wurden drei mikrobiologische Abstriche nach standardisiertem Schema entnommen (präoperativ, intraoperativ vor Débridement, intraoperativ nach Débridement). Die Datenauswertung erfolgte retrospektiv anhand der Patientenakten und klinikinternen Datenbanken. Von besonderem Interesse waren patientenspezifische Parameter wie Alter, Geschlecht und das Vorhandensein von Komorbiditäten. Ebenso waren die mikrobiologischen Abstriche, die Methode der plastischen Rekonstruktion sowie Komplikationen im stationären Verlauf von großer Relevanz. Ziel dieser retrospektiven Arbeit war es, das vorherrschende bakteriologische Keimspektrum zu analysieren und das Patientenkollektiv im Hinblick auf Risikofaktoren für sternale Wundheilungsstörungen zu untersuchen. Ebenso wurde die Effektivität des angewandten Therapiekonzeptes unserer Klinik im Patientenkollektiv geprüft. Wir konnten nachweisen, dass Staphylokokkus epidermidis in 64,5 % der Fälle der dominierende Erreger im intraoperativen Abstrich war. Infektionen bedingt durch multiresistente Erreger kamen nur bei 12,9 % der Patienten vor. Intraoperative Wundbesiedelungen mit MRSA waren in der vorliegenden Arbeit nicht nachweisbar. Zudem konnten wir die ernst zu nehmende Pathogenität des Staphylokokkus epidermidis belegen. Im Vergleich zur Kontrollgruppe entwickelten Patienten mit Nachweis von Staphylokokkus epidermidis deutlich schneller sternale Wundheilungsstörungen nach der kardiochirurgischen Operation (47,4 Tage vs. 71,5 Tage). Ebenso resultierten mehr Revisionseingriffe (55,5 % vs. 27,3 %) und hierdurch längere Hospitalisierungszeiten (65,6 T age vs. 37,4 T age). Die antibiotische Behandlung des Staphylokokkus epidermidis ist daher bei diesem Patientengut im Therapiealgorithmus neben einem radikalen Débridement essentiell. Nur in der Kombination kann das Infektionsgeschehen effektiv beherrscht und der Patient aus dieser lebensbedrohlichen Situation geführt werden.

The Trinity River is an urbanized, effluent-dominated river, and is heavily relied upon for drinking water. The benthic macroinvertebrate community has been monitored for over 20 years, with the focus of this dissertation on three studies (1987-88, 2005, and 2011). Water quality improvement following dechlorination resulted in increased benthic metrics. Overall habitat quality, in-stream cover, surface water total organic carbon, sediment total organic carbon, near-field urban land-use, near-field forested land-use, surface water surfactant toxic units, and depositional sediment biofilm fatty acids all have statistically significant relationships with benthic macroinvertebrate metrics. These relationships are better defined with increased taxonomic resolution at the genus/species level for all benthic taxa, including Chironomidae and Oligochaeta. It is recommend that benthic identifications for state and city water quality assessments be done at the genus/species level. A novel method for quantifying depositional sediment biofilm fatty acids has been produced and tested in this dissertation. Benthic metrics are directly related to fatty acid profiles, with several essential fatty acids found only at upstream sites.

No description available.

Archaeological dental calculus represents a depositional environment that entraps oral microbes, and debris of dietary, environmental, and cultural material that entered the mouth throughout the host’s life. Hence, they represent valuable archives of information about the host’s lifestyle, health, and environment. The aim of this study was to identify if the farming transition and its’ associated change in diet composition, may have influenced species composition in the oral cavity. To shed some light into the evolution of ancient oral microbiomes from Africa, 3 novel Iron Age dental calculus metagenomes together with a comparative dataset of 18 archaeological dental calculus metagenomes from North African Upper Palaeolithic, Later Stone Age, Iron Age, and 18th-19th century populations where analysed. Shotgun sequencing data was used to reconstruct 21 oral metagenomes from the past 15,000 years. This study found an oral microbiome that has been maintained from the Upper Palaeolithic (North Africa) to the 19th Century. However, closer examination to the relative abundance of three keystone species of the subgingival plaque, portray a chronological evolution that reflects that of its host during the major dietary and cultural transition that occurred during the farming revolution in the Iron Age.

The presence of nutrients, such as nitrogenous compounds, in wastewater can pose serious environmental concerns to water systems leading to reduced water quality and potential risks to the public health. Nutrient removal in conventional wastewater treatment systems is becoming increasingly more costly due to the extensive energy requirements and high aeration costs. Anaerobic ammonium oxidation (Anammox) is an alternative method for nutrient removal which can reduce overall treatment costs due to less aeration requirements and less sludge production. Anammox process can be implemented with other innovative technologies, such as membrane aerated biofilm reactors (MABR) to achieve effective and sustainable nutrient removal. A major challenge associated with Anammox process is effective control of nitrite oxidizing bacteria (NOB). High temperature in wastewater treatment systems can promote Anammox bacterial growth and inhibit NOB activity. This research aims to investigate the feasibility of integrating Anammox processes with MABR technologies and to examine the effects of high temperature aeration supplied to MABR systems on Anammox bacterial growth and NOB suppression. The nitrogen removal by Anammox bacteria in a lab-scaled MABR is examined to determine the impact of aeration temperature on inhibition of NOB. / Thesis / Master of Applied Science (MASc)