ABSTRACT
Abstract: The Neotropics is one of the most diverse regions of the globe in terms of plants and animal species. Regarding the microbial world, however, little is known about the diversity and biogeography patterns of microorganisms in the Neotropics. The biogeography of several microbial taxonomic groups is still missing and/or incomplete, such as the protists. Despite the hard taxonomic identification of protists, the advance of molecular techniques (e.g., metabarcoding) have allowed to better explore the distribution of several protistan groups. Our goal here was to summarize the available information of Neotropical protists, focusing on metabarcoding studies, to explore what these data evidence on their ecology and biogeography. For this, we reviewed the findings from all articles that focused on or included the terrestrial protists using a metabarcoding approach and identified the gaps and future perspectives in this research field. We found that Neotropical protistan diversity patterns seem to be, at least in part, congruent with that of macro-organisms and, different than plants and bacteria, just weakly explained by environmental variables. We argue that studies with standardized protocols including different ecoregions are necessary, such as temperate forests, grasslands, and savannas from Southern of South America and Northern Atlantic Forest, to fully characterize the ecology and biogeography on Neotropical protists. Furthermore, dismembering evolutionary lineages and functional guilds of protists are important to better understand the relationship between diversity, dispersal abilities, and functionality of particular taxa of protists in their habitats.
Resumo: A região Neotropical é uma das mais diversas regiões do globo em termos de espécies vegetais e animais. Em relação ao mundo microbiano, entretanto, pouco se sabe sobre a diversidade e os padrões biogeográficos dos microrganismos no Neotrópico. Nesse contexto, a biogeografia de diversos grupos taxonômicos microbianos ainda é escasso e/ou incompleto como os protistas, devido à difícil identificação taxonômica de tais microscópicos organismos. Neste contexto, o avanço dos dados moleculares de amostras ambientais (por exemplo, metabarcoding) permitiu explorar a distribuição de vários grupos de protistas. Nosso objetivo aqui foi resumir as informações disponíveis dos protistas neotropicais, com foco em metabarcoding, para explorar o que esses dados evidenciam sobre sua ecologia e biogeografia. Para isso, revisamos os resultados de todos os artigos que enfocavam ou incluíam os protistas terrestres usando uma abordagem de metabarcoding e identificamos as lacunas e as perspectivas futuras neste campo de pesquisa. Os padrões de diversidade dos protistas Neotropicais parecem ser, pelo menos em parte, congruentes com os de macroorganismos e, diferentes das plantas e bactérias, sendo pouco explicados por variáveis ambientais. Estudos com protocolos padronizados incluindo diferentes Ecorregiões são necessários, como em florestas temperadas, campos nativos e savanas no sul da América do Sul e no norte da Mata Atlântica, para melhor caracterizar a ecologia e biogeografia de protistas Neotropicais. Além disso, é importante diferenciar linhagens evolutivas e guildas funcionais de protistas para entender melhor a relação entre diversidade, capacidade de dispersão e funcionalidade de determinados táxons de protistas em seus habitats.
ABSTRACT
Taxonomic profiling, using hyper-variable regions of 16S rRNA, is one of the important goals in metagenomics analysis.Operational taxonomic unit (OTU) clustering algorithms are the important tools to perform taxonomic profiling by grouping16S rRNA sequence reads into OTU clusters. Presently various OTU clustering algorithms are available within differentpipelines, even some pipelines have implemented more than one clustering algorithms, but there is less literature available forthe relative performance and features of these algorithms. This makes the choice of using these methods unclear. In this studyfive current state-of-the-art OTU clustering algorithms (CDHIT, Mothur’s Average Neighbour, SUMACLUST, Swarm, andUCLUST) have been comprehensively evaluated on the metagenomics sequencing data. It was found that in all the datasets,Mothur’s average neighbour and Swarm created more number of OTU clusters. Based on normalized mutual information(NMI) and normalized information difference (NID), Swarm and Mothur’s average neighbour showed better clusteringqualities than others. But in terms of time complexity the greedy algorithms (SUMACLUST, CDHIT, and UCLUST) performed well. So there is a trade-off between quality and time, and it is necessary while analysing large size of 16S rRNA genesequencing data.
ABSTRACT
Objective:To explore the effect of Chaihu Longgu Mulitang on intestinal microflora diversity of schizophrenic model rats, and further reveal its therapeutic characteristics and mechanisms based on the 16S rRNA technique. Method:Except the normal group, male SD rats were intraperitoneally injected dizocilpine maleate with daily dose of 0.1 mg·kg-1.After the success of the model, Chaihu Longgu Mulitang high, middle and low dose groups were converted into the human clinical upper limit daily, and the experimental rats were given Chaihu Longgu Mulitang with doses of 11.2, 5.6, 2.8 g·kg-1, respectively. And the positive drug group was treated with 0.4 mg·kg-1 of risperidone tablets.The normal group and model group was treated with water.The rats were continuous administrated 14 days with dosing volume of 10 mL·kg-1, the contents in caecum of rats were taken after anesthesia.Illumina MiSeq was used as the sequencing platform, the number of operational taxonomic units(OTUs), richness and diversity indexes, diversity of alpha and beta, differential phylum and genus of intestinal flora in V4 zone of 16S rRNA were comprehensively analyzed and evaluated. Result:Chaihu Longgu Mulitang could improve the number of OTUs, richness and diversity indexes of intestinal flora, imbalance of alpha and beta diversity of schizophrenic model rats.And this formula had a callback effect on 5 differential phyla of bacteria(Bacteroidetes, Acidobacteria, Proteobacteria, Firmicutes and TM7) and 20 genera of bacteria in schizophrenic model rats. Conclusion:Chaihu Longgu Mulitang plays an therapeutic effect on diversity of abnormal microflora in schizophrenic model rats, and this paper reveals the pathological mechanism of intestinal microflora in the state of schizophrenia by 16S rRNA technique.