Halle, Wittenberg, Universiẗat, Diss., 2004.

Thesis (M.S.)--Washington State University, December 2007. / Includes bibliographical references (p. 68-86).

Enterobacter cloacae strain ENHK is a Gram-negative endophyte belonging to the family Enterobacteriacae. Initially considered as an unknown bacterium, E. cloacae ENHK was first isolated from a diseased pepper (Capsicum annuum) plant infected by the bacterial plant pathogen Ralstonia solanacearum in Hong Kong in 2010. A pure isolate was obtained for whole genome sequencing. De novo shortgun and paired-end sequencing by 454 GS Junior platform were applied to obtain a draft genome sequence of E. cloacae ENHK containing 36 contigs in one scaffold. Gaps were closed by PCR and primer walking using Sanger sequencing to produce the first complete genome sequence of a plant-associated strain of E. cloacae. The genome size of E. cloacae ENHK consists of a single chromosome of 4,726,582kb, with a GC content of 55.1%. Gene annotation and analysis was performed using NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) and further annotation and comparative genome analysis was performed by the SEED-based automated annotation system provided by the RAST server. Comparative genome analysis indicated that E. cloacae ENHK shares major genomic features with Enterobacter sp.638 that is characterized for its plant-growth promoting and endophytic behaviors. Further genome analysis revealed antagonistic potentials of E. cloacae ENHK against other microbes by possessing antagonistic mechanisms which involve microbial competition, production of antimicrobial compounds and induction of plant defense response. Candidates of Chitinases and type VI secretion system associated rhs-related genetic element were identified and their potential antibacterial activity were investigated. E. cloacae ENHK was further demonstrated to suppress the growth of several plant pathogenic fungal species Alternaria sp., Choanephora infundibulifera, Colletotrichum capsici, Didymella bryoniae, Fusarium oxysporum, Sclerotinia sclerotiorum and Sclerotinia rolfsii and a plant pathogenic bacterial species Ralstonia solanacearum. Among the publicly available completed genome sequences of the Enterobacter species complex, E. cloacae ENHK is most closely related to E. cloacae subsp. cloacae ATCC13047, an opportunistic human pathogen. A comparative genome analysis showed that critical factors involving human pathogenesis in terms of virulence and specific adhesion were identified in the variable genomic regions in E. cloacae subsp. cloacae ATCC 13047 and are absent in E. cloacae ENHK. In addition, two microbial competition related type VI secretion systems (T6SS) were found conserved in both E. cloacae strains. Phylogenetic analysis revealed that the two systems were associated with other plant-associated and human/animal-associated species respectively in the Enterobacteriaceae. The results indicated that T6SSs may provide the E. cloacae strains fitness advantages for microbial competition in the microflora of a diverse environment. In short, comparative genome analysis suggested that the conserved chromosomal regions retain the general physiological and survival of the species, while variable genomic regions play a critical role in determining the functional differences of the pathogenic E. cloacae subsp. cloacae ATCC13047 and the endophytic E. cloacae ENHK. Finally, significant findings derived from the current thesis research are summarized and potential applications of E. cloacae ENHK in agricultural, medical and industrial areas, as well as future prospectus are discussed. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

Enterobacter sakazakii é uma bactéria Gram-negativa, em forma de bastonete, pertencente a família Enterobacteriaceae e que não faz parte da microbiota normal do trato gastrointestinal humano ou animal. É reconhecida como um patógeno emergente de origem alimentar e já foi relacionada a diversos surtos e casos esporádicos de doenças envolvendo neonatos debilitados. A população de risco à infecção é composta por bebês prematuros ou bebês nascidos a termo até atingirem quatro a seis semanas de idade, bebês imunocomprometidos de qualquer idade e bebês que necessitem de cuidados especiais (UTI neonatal). Apesar do reservatório e do modo de transmissão de E. sakazakii não estarem claramente identificados, relatos mostraram que fórmulas infantis desidratadas, a base de leite, foram a fonte e o veículo de infecções para a população de risco. Os objetivos deste estudo foram avaliar a eficiência do meio cromogênico DFI na identificação do E. sakazakii; verificar a eficiência das metodologias ISO (TC 34/SC 5N) e FDA empregadas na enumeração de E. sakazakii e avaliar a população de Enterobacter sakazakii e de Enterobacteriaceae em fórmulas lácteas infantis, desidratadas, importadas ou nacionais, específicas para a faixa 0-6 meses de idade comercializadas na cidade de São Paulo, Brasil. Para tanto, foram examinadas 150 amostras de fórmulas lácteas infantis desidratadas, de diferentes lotes e marcas comerciais, adquiridas no comércio varejista da cidade de São Paulo. Para enumeração de E. sakazakii empregou-se o método preconizado pela ISO (TC 34/SC 5 N) com modificação. A enumeração de Enterobacteriaceae foi realizada empregando-se placas PetrifilmTM contagem de enterobactérias (3MTM). Todas as amostras examinadas, independente de marca comercial ou origem, apresentaram população de Enterobacter sakazakii < 0,03 NMP/100g e de Enterobacteriaceae < 5 UFC/g. O ágar DFI foi eficiente na identificação de colônias de E. sakazakii, mesmo na presença de Escherichia cloacae e Enterobacter aerogenes. E a metodologia ISO (TC 34/SC 5N) foi mais eficiente na enumeração de E. sakazakii que o método preconizado pelo FDA. / Enterobacter sakazakii is a Gram-negative rod from the Enterobacteriaceae family. This microorganism is not part of the normal microbiota of the human or animal gastrointestinal tract. It is recognized as an emergent pathogen of food origin and has already been related to outbreaks and sporadic cases of illnesses mainly involving weak in neonates. The population at risk of infection is composed by premature babies or newborn till they reach four to six weeks of age, immunocompromised babies of any age and babies in need of special care (neonatal ICU). Although the reservoir and the form of transmission of E. sakazakii is not clearly identified yet, studies have shown that milk-based dried-infant formula have been the source and the vehicle of infections for the at risk population. The objectives of this study were to evaluate the efficiency of DFI agar in the identification of E. sakazakii; to verify the efficiency of the methodologies proposed by ISO (TC 34/SC 5N) and FDA for the enumeration of E. sakazakii and to evaluate the population of Enterobacter sakazakii and Enterobacteriaceae in dehydrated infant milk formula, imported or domestic, specific for 0-6 months of age commercialized in the city of Sao Paulo, Brazil. 150 dehydrated milk infant formula samples from different commercial brands, acquired at retail level in the city of Sao Paulo, SP, Brazil were examined. For enumeration of E. sakazakii a modification of the method recommended by ISO (TC 34/SC 5N) was used. The enumeration of Enterobacteriaceae was carried out using PetrifilmTM Enterobacteriaceae count plate (3MTM). All the examined samples, independent of commercial brand or origin, presented population of Enterobacter sakazakii < 0,03 MPN/100g and < 5 CFU/g of Enterobacteriaceae. The DFI agar was efficient in the identification of colonies of E. sakazakii, even in the presence of Escherichia cloacae or Enterobacter aerogenes. The methodology ISO (TC 34/SC 5N) was more efficient for the enumeration of E. sakazakii that the one recomended by FDA.

Enterobacter sakazakii é uma bactéria Gram-negativa, em forma de bastonete, pertencente a família Enterobacteriaceae e que não faz parte da microbiota normal do trato gastrointestinal humano ou animal. É reconhecida como um patógeno emergente de origem alimentar e já foi relacionada a diversos surtos e casos esporádicos de doenças envolvendo neonatos debilitados. A população de risco à infecção é composta por bebês prematuros ou bebês nascidos a termo até atingirem quatro a seis semanas de idade, bebês imunocomprometidos de qualquer idade e bebês que necessitem de cuidados especiais (UTI neonatal). Apesar do reservatório e do modo de transmissão de E. sakazakii não estarem claramente identificados, relatos mostraram que fórmulas infantis desidratadas, a base de leite, foram a fonte e o veículo de infecções para a população de risco. Os objetivos deste estudo foram avaliar a eficiência do meio cromogênico DFI na identificação do E. sakazakii; verificar a eficiência das metodologias ISO (TC 34/SC 5N) e FDA empregadas na enumeração de E. sakazakii e avaliar a população de Enterobacter sakazakii e de Enterobacteriaceae em fórmulas lácteas infantis, desidratadas, importadas ou nacionais, específicas para a faixa 0-6 meses de idade comercializadas na cidade de São Paulo, Brasil. Para tanto, foram examinadas 150 amostras de fórmulas lácteas infantis desidratadas, de diferentes lotes e marcas comerciais, adquiridas no comércio varejista da cidade de São Paulo. Para enumeração de E. sakazakii empregou-se o método preconizado pela ISO (TC 34/SC 5 N) com modificação. A enumeração de Enterobacteriaceae foi realizada empregando-se placas PetrifilmTM contagem de enterobactérias (3MTM). Todas as amostras examinadas, independente de marca comercial ou origem, apresentaram população de Enterobacter sakazakii < 0,03 NMP/100g e de Enterobacteriaceae < 5 UFC/g. O ágar DFI foi eficiente na identificação de colônias de E. sakazakii, mesmo na presença de Escherichia cloacae e Enterobacter aerogenes. E a metodologia ISO (TC 34/SC 5N) foi mais eficiente na enumeração de E. sakazakii que o método preconizado pelo FDA. / Enterobacter sakazakii is a Gram-negative rod from the Enterobacteriaceae family. This microorganism is not part of the normal microbiota of the human or animal gastrointestinal tract. It is recognized as an emergent pathogen of food origin and has already been related to outbreaks and sporadic cases of illnesses mainly involving weak in neonates. The population at risk of infection is composed by premature babies or newborn till they reach four to six weeks of age, immunocompromised babies of any age and babies in need of special care (neonatal ICU). Although the reservoir and the form of transmission of E. sakazakii is not clearly identified yet, studies have shown that milk-based dried-infant formula have been the source and the vehicle of infections for the at risk population. The objectives of this study were to evaluate the efficiency of DFI agar in the identification of E. sakazakii; to verify the efficiency of the methodologies proposed by ISO (TC 34/SC 5N) and FDA for the enumeration of E. sakazakii and to evaluate the population of Enterobacter sakazakii and Enterobacteriaceae in dehydrated infant milk formula, imported or domestic, specific for 0-6 months of age commercialized in the city of Sao Paulo, Brazil. 150 dehydrated milk infant formula samples from different commercial brands, acquired at retail level in the city of Sao Paulo, SP, Brazil were examined. For enumeration of E. sakazakii a modification of the method recommended by ISO (TC 34/SC 5N) was used. The enumeration of Enterobacteriaceae was carried out using PetrifilmTM Enterobacteriaceae count plate (3MTM). All the examined samples, independent of commercial brand or origin, presented population of Enterobacter sakazakii < 0,03 MPN/100g and < 5 CFU/g of Enterobacteriaceae. The DFI agar was efficient in the identification of colonies of E. sakazakii, even in the presence of Escherichia cloacae or Enterobacter aerogenes. The methodology ISO (TC 34/SC 5N) was more efficient for the enumeration of E. sakazakii that the one recomended by FDA.

Submitted in complete fulfillment for the Degree of Master of Applied Sciences in Biotechnology, Durban University of Technology, Durban, South Africa, 2016. / A bacterial strain producing an extracellular phytase was identified as Enterobacter sp. ACSS. Optimization of process parameters using statistical methods such as Plackett-Burman design (PBD), the steepest ascent method, and response surface methodology (RSM) significantly improved phytase production by 4.6–fold in shake-flasks. In addition, an overall 1.9-fold increase in phytase production was attained in fed-batch fermentations in a 5 l laboratory fermenter, respectively. The purified 62 kDa phytase from Enterobacter sp. ACSS was active between 40 to 80°C and an acidic pH range of 2.0 to 6.0 with half-life of 693 and 577.5 min at 60°C and pH 2.0, respectively. Additionally, the enzyme is fairly stable with proteolytic enzymes under physiological conditions. It was activated by Ca+2, Mg+2 and Mn+2 while inhibition was caused by Zn+2, Cu+2, Fe+2, Pb+2, Co+2, Ba+2 and surfactants. The Km, Vmax and Kcat observed were 0.21 mM, 131.58 nmol mg-1s-1 and 1.64 × 103 s-1, respectively. The enzyme released inorganic phosphate from animal feed (4.0-6.62 mg/g of diet) and insoluble metal-phytates (45-219 µg/ml) and was effective in improving the characteristics of brown bread. Overall, this study shows that Enterobacter sp. ACSS has the potential to produce significant titres of a thermo- and acid-stable phytase and can be applied in dephytinizing animal feeds, and the baking industry. / M

Thesis (M.S. in food science)--Washington State University, December 2009. / Title from PDF title page (viewed on Jan. 20, 2010). "School of Food Science." Includes bibliographical references (p. 55-59).

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

Thesis (M.S.)--West Virginia University, 2008. / Title from document title page. Document formatted into pages; contains ix, 111 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references (p. 104-110).

Thesis (M.Sc.)--University of Adelaide, 1956. / Typewr. copy.