BACKGROUND:Metagenomics has a great potential to discover previously unattainable information about microbial communities. An important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. Most of prevalent homology-based approaches utilize solely the results of an alignment tool such as BLAST, limiting their estimation accuracy to high ranks of the taxonomy tree.RESULTS:We developed a new homology-based approach called Taxonomic Analysis by Elimination and Correction (TAEC), which utilizes the similarity in the genomic sequence in addition to the result of an alignment tool. The proposed method is comprehensively tested on various simulated benchmark datasets of diverse complexity of microbial structure. Compared with other available methods designed for estimating taxonomic composition at a relatively low taxonomic rank, TAEC demonstrates greater accuracy in quantification of genomes in a given microbial sample. We also applied TAEC on two real metagenomic datasets, oral cavity dataset and Crohn's disease dataset. Our results, while agreeing with previous findings at higher ranks of the taxonomy tree, provide accurate estimation of taxonomic compositions at the species/strain level, narrowing down which species/strains need more attention in the study of oral cavity and the Crohn's disease.CONCLUSIONS:By taking account of the similarity in the genomic sequence TAEC outperforms other available tools in estimating taxonomic composition at a very low rank, especially when closely related species/strains exist in a metagenomic sample.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-10-09T20:17:53Z No. of bitstreams: 1 ludemilamartinsdesouza.pdf: 1476036 bytes, checksum: 13c93142a0ac36c1cce3f43d89f846ca (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-10-10T12:20:05Z (GMT) No. of bitstreams: 1 ludemilamartinsdesouza.pdf: 1476036 bytes, checksum: 13c93142a0ac36c1cce3f43d89f846ca (MD5) / Made available in DSpace on 2017-10-10T12:20:05Z (GMT). No. of bitstreams: 1 ludemilamartinsdesouza.pdf: 1476036 bytes, checksum: 13c93142a0ac36c1cce3f43d89f846ca (MD5) Previous issue date: 2017-04-27 / Dados sobre a ecologia alimentar de duas aves de sub-bosque foram coletados na Reserva Biológica Municipal do Poço D’anta, Juiz de Fora – MG, sudeste do Brasil. Conopophaga lineata e Conopophaga melanops são encontradas ocorrendo em simpátria em algumas localidades da Região Sudeste. Estudos com espécies aparentadas e simpátricas podem ser úteis no sentido de avaliar a influência do nicho sobre co ocorrência e co-existência. Durante as amostragens utilizando redes ornitológicas obtivemos 29 capturas de 25 indivíduos de C. lineata, e 28 capturas de 21 indivíduos de C. melanops. Na triagem das amostras fecais de C. lineata e C. melanops foram encontrados, respectivamente, 310 e 276 itens. C. lineata consumiu predominantemente Formicidae (53,5%), Coleoptera (6,8%). Entretanto, o índice alimentar (IA) de Coleoptera (7,47) ficou abaixo de outros grupos como Formicidae (68,2) e Araneae (8,80). C. melanops consumiu altas proporções de Formicidae (23,2%), Coloptera (12,3%), Orthoptera (11,6%) e Isoptera (11,2%), embora em termos de IA o predomínio tenha sido de Formicidae (24,66) e Coleoptera (20,14). A sobreposição de nicho entre as espécies foi maior que o esperado (observado = 0.723). Apesar das diferenças nas proporções dos tipos de artrópodes consumidos não foram suficientes para revelar separação de seus nichos alimentares. Embora se encontrem na literatura que C. lineata seleciona tanto tipo de presas quanto artrópodes maiores que 5 mm em proporções acima do esperado pelo acaso, assim como foi observado para C. melanops predação preferencial sobre alguns táxons. Os resultados encontrados demonstram que, em alguns casos, os padrões ecológicos das respostas das aves aos recursos encontrados no ambiente podem ser diferentes daqueles encontrados em outras regiões. / Data on the food ecology of two understory birds were collected at the Municipal Reserva Biológica Municipal do Poço D’anta, Juiz de Fora – MG, Southeastern Brazil. Conopophaga lineata and Conopophaga melanops are found occurring in sympatry in some localities of the Southeast Region. Studies with related and sympatric species may be useful in assessing the influence of the niche on co-occurrence and co-existence. During the samplings using ontological networks were carried out 29 catches of 25 individuals of C. lineata, and 28 catches of 21 individuals of C. melanops. In the sorting of the fecal samples of C. lineata and C. melanops were found, respectively, 310 and 276 items. C. lineata consumed predominantly Formicidae (53.5%), Coleoptera (6.8%). However, Coleoptera dietary index (AI) (7.47) was below other groups such as Formicidae (68.2) and Araneae (8.80). C. melanops consumed high proportions of Formicidae (23.2%), Coloptera (12.3%), Orthoptera (11.6%) and Isoptera (11.2%), although in terms of AI the predominance was Formicidae (24.66) and Coleoptera (20.14). The niche overlap between species was higher than expected (observed = 0.723). Although differences in the proportions of the types of arthropods consumed were not sufficient to reveal separation of their food niches. Although it is found in the literature that C. lineata selects both prey and arthropod species larger than 5 mm in proportions above that expected by chance, just as it was observed for C. melanops preferential predation on some taxa. The results show that, in some cases, the ecological patterns of bird responses to the resources found in the environment may be different from those found in other regions.