Exploring prokaryotic diversity in the genomic era

Our understanding of prokaryote biology from study of pure cultures and genome sequencing has been limited by a pronounced sampling bias towards four bacterial phyla - Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes - out of 35 bacterial and 18 archaeal phylum-level lineages. This bias is beginning to be rectified by the use of phylogenetically directed isolation strategies and by directly accessing microbial genomes from environmental samples

Building on basic metagenomics with complementary technologies

Supplementing metagenomic approaches to studying natural microbial communities with metatranscriptomics and metaproteomics should reap big dividend

Evolutionary conservation of sequence and secondary structures in CRISPR repeats

The categorisation and structural analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) sequences from 195 microbial genomes show that repeats from diverse organisms can be grouped based on sequence similarity, and that some groups have pronounced secondary structures with compensatory base changes

The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide

The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates information on over 1500 sequencing projects, of which 294 have been completed and the data deposited in the public databases. GOLD v.2 has been expanded to provide information related to organism properties such as phenotype, ecotype and disease. Furthermore, project relevance and availability information is now included. GOLD is available at . It is also mirrored at the Institute of Molecular Biology and Biotechnology, Crete, Greece a

On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria

The origin of oxygenic photosynthesis in Cyanobacteria led to the rise of oxygen on Earth ~2.3 billion years ago, profoundly altering the course of evolution by facilitating the development of aerobic respiration and complex multicellular life. Here we report the genomes of 41 uncultured organisms related to the photosynthetic Cyanobacteria (class Oxyphotobacteria), including members of the class Melainabacteria and a new class of Cyanobacteria (class Sericytochromatia) that is basal to the Melainabacteria and Oxyphotobacteria. All members of the Melainabacteria and Sericytochromatia lack photosynthetic machinery, indicating that phototrophy was not an ancestral feature of the Cyanobacteria and that Oxyphotobacteria acquired the genes for photosynthesis relatively late in cyanobacterial evolution. We show that all three classes independently acquired aerobic respiratory complexes, supporting the hypothesis that aerobic respiration evolved after oxygenic photosynthesis

Co-evolution is the primary force shaping termite gut microbial communities

Tese de Mestrado em Robótica apresentada à Faculdade de Ciências e Tecnologia da Universidade de CoimbraThis work is integrated in a project of development of a novel measurement device, the BMG-4 sensor, and its application in the calibration of industrial robots. The aim of the work is to define procedures and strategies that enable, through the BMG-4, to identify both geometric and compliance errors that are present in 6-axes serial industrial robots. The importance of accuracy and robot calibration as well as the problem of the suitability of most measurement systems to industrial environments is highlighted. Consequently, the BMG-4 is introduced as a solution that meets the demands of those conditions. A geometrical methodology is defined to determine the direction of a robot’s axis and to assess its accuracy. A protocol that allows to identify the real angular geometric parameters of the robot, as well as the offsets of some axes is presented. Then, a strategy is developed in order to be able to identify the compliances of the last five axes of the robot. All the tests are performed in an ABB IRB 6600 industrial robot. For axes 2 and 3, the maximum values obtained for inaccuracy are 0,062° and 0,229°, respectively. Also, the robot presents several considerable joints’ offsets errors. For axes 4 and 5 those values are −0,99° and 0,83°. The combined offset of axes 2 and 3 is −0,28°. The stiffness of axis 2 is determined, having an estimated value of 2,4 × 106 N.m/rad. Finally, a standard robot convention is proposed in order to correct the identified errors with a generalized compensation algorithm.Este trabalho está integrado num projeto de desenvolvimento de um novo dispositivo de medição, o sensor BMG-4, e da sua aplicação na calibração de robôs industriais. O objetivo do trabalho é a definição de procedimentos e estratégias que permitem, através do BMG-4, identificar erros provenientes tanto da geometria como da flexibilidade das articulações do robô que estão presentes em robôs industriais de 6-eixos. A importância da precisão e da calibração robótica, bem como o problema da adequação da maioria dos sistemas de medição em ambientes industriais são destacados. Consequentemente, o BMG-4 é introduzido como uma solução que satisfaz essas condições. Uma metodologia geométrica é definida para determinar a direção do eixo de um robô e para avaliar a sua precisão. Um protocolo que permite identificar os parâmetros geométricos angulares reais do robô, bem como os offsets de alguns eixos, é apresentado. Em seguida, uma estratégia é desenvolvida de maneira a identificar os valores de rigidez dos últimos cinco eixos do robô. Todos os testes são realizados no robô industrial ABB IRB 6600. Para os eixos 2 e 3, os valores máximos obtidos para a análise da imprecisão são 0,062° e 0,229°, respectivamente. Além disso, o robô apresenta erros de offset consideráveis. Para os eixos 4 e 5 esses valores são −0,99° e 0,83°. O valor combinado dos eixos 2 e 3 é −0,28°. A rigidez do eixo 2 é determinada, tendo um valor estimado de 2,4 × 106 N.m/rad. Finalmente, uma convenção standard de robôs é proposta e cuja finalidade é corrigir os erros previamente identificados através de um algoritmo de compensação global e independente do fabricante do robô considerado

Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool

<p>Abstract</p> <p>Background</p> <p>Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence database. Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies.</p> <p>Results</p> <p>We have developed an automated iterative procedure for delineating stable (monophyletic) hierarchical groups to large (or small) trees and naming those groups according to a set of sequentially applied rules. In addition, we have created an associated ungrouping tool for removing existing groups that do not meet user-defined criteria (such as monophyly). The procedure is implemented in a program called GRUNT (GRouping, Ungrouping, Naming Tool) and has been applied to the current release of the Greengenes (Hugenholtz) 16S rRNA gene taxonomy comprising more than 130,000 taxa.</p> <p>Conclusion</p> <p>GRUNT will facilitate researchers requiring comprehensive hierarchical grouping of large tree topologies in, for example, database curation, microarray design and pangenome assignments. The application is available at the greengenes website <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>.</p

Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates

Massively parallel pyrosequencing of the small subunit (16S) ribosomal RNA gene has revealed that the extent of rare microbial populations in several environments, the 'rare biosphere', is orders of magnitude higher than previously thought. One important caveat with this method is that sequencing error could artificially inflate diversity estimates. Although the per-base error of 16S rDNA amplicon pyrosequencing has been shown to be as good as or lower than Sanger sequencing, no direct assessments of pyrosequencing errors on diversity estimates have been reported. Using only Escherichia coli MG1655 as a reference template, we find that 16S rDNA diversity is grossly overestimated unless relatively stringent read quality filtering and low clustering thresholds are applied. In particular, the common practice of removing reads with unresolved bases and anomalous read lengths is insufficient to ensure accurate estimates of microbial diversity. Furthermore, common and reproducible homopolymer length errors can result in relatively abundant spurious phylotypes further confounding data interpretation. We suggest that stringent quality-based trimming of 16S pyrotags and clustering thresholds no greater than 97% identity should be used to avoid overestimates of the rare biosphere