Use of 16S rRNA Gene Based Clone Libraries to Assess Microbial Communities Potentially Involved in Anaerobic Methane Oxidation in a Mediterranean Cold Seep

This study provides data on the diversities of bacterial and archaeal communities in an active methane seep at the Kazan mud volcano in the deep Eastern Mediterranean sea. Layers of varying depths in the Kazan sediments were investigated in terms of (1) chemical parameters and (2) DNA-based microbial population structures. The latter was accomplished by analyzing the sequences of directly amplified 16S rRNA genes, resulting in the phylogenetic analysis of the prokaryotic communities. Sequences of organisms potentially associated with processes such as anaerobic methane oxidation and sulfate reduction were thus identified. Overall, the sediment layers revealed the presence of sequences of quite diverse bacterial and archaeal communities, which varied considerably with depth. Dominant types revealed in these communities are known as key organisms involved in the following processes: (1) anaerobic methane oxidation and sulfate reduction, (2) sulfide oxidation, and (3) a range of (aerobic) heterotrophic processes. In the communities in the lowest sediment layer sampled (22–34 cm), sulfate-reducing bacteria and archaea of the ANME-2 cluster (likely involved in anaerobic methane oxidation) were prevalent, whereas heterotrophic organisms abounded in the top sediment layer (0–6 cm). Communities in the middle layer (6–22 cm) contained organisms that could be linked to either of the aforementioned processes. We discuss how these phylogeny (sequence)-based findings can support the ongoing molecular work aimed at unraveling both the functioning and the functional diversities of the communities under study

The gut microbiome: scourge, sentinel or spectator?

The gut microbiota consists of trillions of prokaryotes that reside in the intestinal mucosa. This long-established commensalism indicates that these microbes are an integral part of the eukaryotic host. Recent research findings have implicated the dynamics of microbial function in setting thresholds for many physiological parameters. Conversely, it has been convincingly argued that dysbiosis, representing microbial imbalance, may be an important underlying factor that contributes to a variety of diseases, inside and outside the gut. This review discusses the latest findings, including enterotype classification, changes brought on by dysbiosis, gut inflammation, and metabolic mediators in an attempt to underscore the importance of the gut microbiota for human health. A cautiously optimistic idea is taking hold, invoking the gut microbiota as a medium to track, target and treat a plethora of diseases

Consensos sobre o papel do gestor estadual na regionalização da assistência à saúde no Sistema Único de Saúde (SUS) Consensus regarding the role of the State manager in the regionalization of health care in Brazilian National Health System (SUS)

OBJETIVOS: identificar os consensos acerca do papel do gestor estadual na regionalização da assistência à saúde no SUS. MÉTODOS: foram elaborados um modelo teórico-lógico e uma matriz de avaliação acerca das atribuições do gestor estadual na condução da regionalização. Essa matriz foi submetida à apreciação de especialistas que julgaram a importância dos indicadores de análise definidos, estabelecendo-se o consenso ou o dissenso a partir de pontos de corte previamente definidos, utilizando-se como técnica a Conferência de Consenso. RESULTADOS: a matriz de avaliação resultante do consenso apresenta três níveis de análise (governo, gestão e assistência), que estão desmembrados em seis dimensões compostas de 14 critérios e 82 indicadores de avaliação que exploram as responsabilidades do gestor estadual do SUS frente à regionalização da saúde. Do total de indicadores, apenas quatro não apresentaram consenso, o que indica que a matriz se mostra um instrumento eficiente para avaliação da regionalização da assistência no SUS, abordando as diferentes dimensões dessa intervenção em saúde. CONCLUSÕES: apesar de provisório, o consenso ora estabelecido pode constituir um referencial de elevada utilidade para a realização de pesquisas, podendo servir de base para a realização de investigações avaliativas sobre a implantação dos processos de regionalização, de forma a permitir maior comparabilidade entre os estudos.<br>OBJECTIVES: to identify points of agreement regarding the role of the State manager in the regionalization of health care in Brazilian National Health System (SUS). METHODS: a theoretical framework and evaluation grid were drawn up to evaluate the role of the State manager in regionalization. These were ratified by specialists, who confirmed the importance of the indicators chosen to establish the existence of consensus or the lack of it, on the basis of previously established cut-off points, using the Consensus Conference technique. RESULTS: the evaluation grid resulting from the consensus achieved involves three levels of analysis (government, management and care), which are broken down into six categories comprising 14 criteria and 82 indicators exploring the responsibility of the State manager of the SUS vis-à-vis the regionalization of health care. There was not a consensus regarding only four of these indicators, suggesting that the grid adopted is an efficient instrument for the evaluation of the regionalization of health care in SUS care and covers the various levels of this healt care intervention. CONCLUSIONS: the consensus now established, however provisional, may be taken as an extremely useful point of reference for further research and could serve as the basis for future evaluations of the implementation of regionalization, in such a way as to allow for comparative studies to be carried out

Who eats what, where and when? Isotope-labelling experiments are coming of age

Isotope-labelling experiments have changed the way microbial ecologists investigate the ecophysiology of microbial populations and cells in the environment. Insight into the 'uncultivated majority' accompanies methodology that involves the incorporation of stable isotopes or radioisotopes into sub-populations of environmental samples. Subsequent analysis of labelled biomarkers of sub-populations with stable-isotope probing (DNA-SIP, RNA-SIP, phospholipid-derived fatty acid-SIP) or individual cells with a combination of fluorescence in situ hybridization and microautoradiography reveals linked phylogenetic and functional information about the organisms that assimilated these compounds. Here, we review some of the most recent literature, with an emphasis on methodological improvements to the sensitivity and utility of these methods. We also highlight related isotope techniques that are in continued development and hold promise to transform the way we link phylogeny and function in complex microbial communities

Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation

Identifying the roles played by individual heterotrophic bacteria in the degradation of high molecular weight (HMW) substrates is critical to understanding the constraints on carbon cycling in the ocean. At five sites in the Atlantic Ocean, we investigated the processing of organic matter by tracking changes in microbial community composition as HMW polysaccharides were enzymatically hydrolysed over time. During this investigation, we discovered that a considerable fraction of heterotrophic bacteria uses a newly-identified ‘selfish’ mode of substrate processing. We therefore additionally examined the balance of individual substrate utilisation mechanisms at different locations by linking individual microorganisms to distinct substrate utilisation mechanisms. Through FISH and uptake of fluorescently-labelled polysaccharides, ‘selfish’ organisms were identified as belonging to the Bacteroidetes, Planctomycetes and Gammaproteobacteria. ‘Sharing’ (extracellular enzyme producing) and ‘scavenging’ (non-enzyme producing) organisms predominantly belonged to the Alteromonadaceae and SAR11 clades, respectively. The extent to which individual mechanisms prevail depended on the initial population structure of the bacterial community at a given location and time, as well as the growth rate of specific bacteria. Furthermore, the same substrate was processed in different ways by different members of a pelagic microbial community, pointing to significant follow-on effects for carbon cycling