Caracterização fenotípica e genômica de bactérias da família Mycobacteriaceae e avaliação de degradação de pectina, amido e carboximetilcelulose
Data
2021-10-27
Autores
Romagnoli, Camila Lopes 
Orientadores
Viana-Niero, Cristina
Tipo
Tese de doutorado
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Resumo
A família Mycobacteriaceae é composta majoritariamente por bactérias saprofíticas e potencialmente patogênicas, encontradas em diversos ambientes naturais e artificiais, como sistemas de tratamento e distribuição de água. São capazes de sobreviver e multiplicar-se sob variáveis condições de temperatura, pH, oxigênio, o que atribui a essas bactérias a característica de serem ubíquas. Nosso grupo de pesquisa tem estudado a diversidade destas bactérias e seu potencial de biodegradar substratos de interesse industrial. O objetivo geral deste trabalho foi estudar uma coleção de isolados bacterianos pertencentes aos gêneros Mycobacterium, Mycolicibacter, Mycobacteroides e Mycolicibacterium para posicioná-los filogeneticamente, verificar a existência de novas espécies e avaliar o potencial de degradação de pectina, amido e carboximetilcelulose (CMC). Sequências de três genes (hsp65, rpoB V e 16S rRNA) foram utilizadas para realizar uma análise filogenética concatenada para 198 isolados com identificação inconclusiva, e os resultados apontaram para a existência de novas espécies. Assim, os genomas de cinco isolados (MYC017, MYC098, MYC101, MYC123 e MYC340) foram sequenciados e analisados. Os resultados das análises genômicas e filogenéticas confirmaram a existência de quatro novas espécies do gênero Mycolicibacter, para as quais foram realizados testes fenotípicos, bioquímicos e de susceptibilidade a antimicrobianos para caracterização e proposição de novas espécies. Adicionalmente, todos os isolados da coleção foram analisados por testes de triagem fenotípica qualitativa para avaliar a habilidade de degradação de pectina, amido e carboximetilcelulose. Os resultados revelaram a presença de bactérias com capacidade de degradar os substratos analisados, sendo que cinco isolados identificados como Mycolicibacterium austroafricanum (MYC038, MYC040, MYC211, MYC221 e MYC223) foram selecionados para avaliação de crescimento na presença de cada substrato como fonte única de carbono e para ter os genomas sequenciados para a busca de genes potencialmente envolvidos nas vias catabólicas de interesse. Foi possível encontrar dois genes potencialmente envolvidos na degradação de pectina (pel1 e kdgA), cinco de amido (malL, malQ, amyL, glgX2 e treX) e três de celulose (cel6, blgB e CBD2). Os resultados aqui apresentados contribuem para a taxonomia da família Mycobacteriaceae, em especial para o gênero Mycolicibacter, bem como para o conhecimento relacionado ao metabolismo de substratos de interesse industrial por parte de isolados de M. austroafricanum.
The Mycobacteriaceae family is most composed by potencially pathogenic and saprophytic bacteria, which are found in several types of ecosystems, like water treatment plants and distribution systems. They are capable of surviving and grow under several temperature, pH and oxygen conditions, which give to them the characteristic of being ubiquitous. Our research team has been studying Mycobacteriaceae diversity and their potential biodegradation of substrates of industrial interest. The general aim of this work was to study an Mycolicibacterium isolates collection, belonging to the Mycobacterium, Mycolicibacter, Mycobacteroides and Mycolicibacterium genera, in order to provide a phylogenetic position to them, verify the existence of new species and evaluate the potential to degrade pectin, starch and carboxymethyl cellulose (CMC). Sequences of three genes (hsp65, rpoB V e 16S rRNA) were concateneted to execute a phylogeny for 198 isolates with inconclusive identification, and the results indicated for new species existence. Of these, five isolates genomes (MYC017, MYC098, MYC101, MYC123 e MYC340) were sequenced and analyzed. The results of genomic sequencing and phylogeny analyzes confirmed the existence of four new species of Mycolicibacter genera, for which phenotypic, biochemical and antimicrobial susceptibility tests were performed to characterize and propose new species. Adicionally, all collection isolates were screened by phenotypical tests for pectin, starch and CMC degradation. The results revealed presence of bacteria capable of degrading all substrates, of which five isolates of Mycolicibacterium austroafricanum species (MYC038, MYC040, MYC211, MYC221 e MYC223) were selected to evaluate the growth capacity in each substrate as the single carbon source and to have their genomes sequenced, in order to search for genes potencially involved in catabolic pathways. It was possible to find two genes potentially involved in pectin biodegradation (pel1 e kdgA), five in starch (malL, malQ, amyL, glgX2 e treX) and three in carboxymetyl celulose (cel6, blgB e CBD2). The results showed here contibute to Mycobacteriaceae taxonomy, specially Mycolicibacter genera, and also contribute to the knowledge about the metabolism of substrates of industrial interest.
The Mycobacteriaceae family is most composed by potencially pathogenic and saprophytic bacteria, which are found in several types of ecosystems, like water treatment plants and distribution systems. They are capable of surviving and grow under several temperature, pH and oxygen conditions, which give to them the characteristic of being ubiquitous. Our research team has been studying Mycobacteriaceae diversity and their potential biodegradation of substrates of industrial interest. The general aim of this work was to study an Mycolicibacterium isolates collection, belonging to the Mycobacterium, Mycolicibacter, Mycobacteroides and Mycolicibacterium genera, in order to provide a phylogenetic position to them, verify the existence of new species and evaluate the potential to degrade pectin, starch and carboxymethyl cellulose (CMC). Sequences of three genes (hsp65, rpoB V e 16S rRNA) were concateneted to execute a phylogeny for 198 isolates with inconclusive identification, and the results indicated for new species existence. Of these, five isolates genomes (MYC017, MYC098, MYC101, MYC123 e MYC340) were sequenced and analyzed. The results of genomic sequencing and phylogeny analyzes confirmed the existence of four new species of Mycolicibacter genera, for which phenotypic, biochemical and antimicrobial susceptibility tests were performed to characterize and propose new species. Adicionally, all collection isolates were screened by phenotypical tests for pectin, starch and CMC degradation. The results revealed presence of bacteria capable of degrading all substrates, of which five isolates of Mycolicibacterium austroafricanum species (MYC038, MYC040, MYC211, MYC221 e MYC223) were selected to evaluate the growth capacity in each substrate as the single carbon source and to have their genomes sequenced, in order to search for genes potencially involved in catabolic pathways. It was possible to find two genes potentially involved in pectin biodegradation (pel1 e kdgA), five in starch (malL, malQ, amyL, glgX2 e treX) and three in carboxymetyl celulose (cel6, blgB e CBD2). The results showed here contibute to Mycobacteriaceae taxonomy, specially Mycolicibacter genera, and also contribute to the knowledge about the metabolism of substrates of industrial interest.
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Citação
Romagnoli, C.L. Caracterização fenotípica e genômica de bactérias da família Mycobacteriaceae e avaliação de degradação de pectina, amido e carboximetilcelulose. Tese (doutorado em CIências) - Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo. São Paulo, p. 142. 2021.