Metagenomics – the key to the uncultured microbes

Streit, Wolfgang R.; Schmitz, Ruth A.

doi:10.1016/j.mib.2004.08.002

Cited by 430 publications

(258 citation statements)

References 51 publications

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“…Analyses of metagenomes, or composite genomes of microbial assemblages in particular habitats, (72,73) provide a new way at looking at in situ microbial communities and the relationships between genomes, organisms, populations and environments. (74,75,76,77,78,79,80) Although metagenomics is still at an early stage of constructing massive sequence inventories or gathering functional information, (81,82,83,84) the field could potentially lead to radical reappraisals of the nature of boundaries between biological entities and the organization of life itself. At the very least, it challenges highly individualistic assumptions of biological and molecular interaction.…”

Section: Applications To a Proposed Systemmentioning

confidence: 99%

Fundamental issues in systems biology

O’Malley¹,

Dupré²

2005

BioEssays

179

104

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FUNDAMENTAL ISSUES IN SYSTEMS BIOLOGY SummaryIn the context of scientists' reflections on genomics, we examine some fundamental issues in the emerging postgenomic discipline of systems biology.Systems biology is best understood as consisting of two streams. One, which we shall call 'pragmatic systems biology', emphasizes large-scale molecular interactions; the other, which we shall refer to as 'systems-theoretic biology', emphasizes system principles. Both are committed to mathematical modelling, and both lack a clear account of what biological systems are. We discuss the underlying issues in identifying systems and how causality operates at different levels of organization. We suggest that resolving such basic problems is a key task for successful systems biology, and that philosophers could contribute to its realization. We conclude with an argument for more sociologically informed collaboration between scientists and philosophers. KeywordsGenomics, systems biology, systems theory, philosophy of biology 3 FUNDAMENTAL ISSUES IN SYSTEMS BIOLOGYAs genomics matures from a data-collecting enterprise to an explanatory science, and as those scientific endeavours take on disciplinary contours, a range of underlying issues are being explicitly and implicitly addressed by the scientists involved. These reflections are an important part of the way a discipline constitutes itself as a field by setting out central problems and achievements alongside a history of conceptual and empirical precursors. One of the most widely discussed fields in emergent genomics is systems biology, and it raises several important questions that need to be resolved if the science is to advance.The issues that are most fundamental are how the systems that are the focus of systems biology are defined, and how those definitions affect the research agendas that arise from earlier scientific legacies. Preceding interpretations of genomicsThe early days of genomics began with fairly simple conceptualizations that emphasized the shift from identifying genes to sequencing and mapping entire genomes. (1) As the data poured in and the field achieved wide recognition, these definitions were expanded to give greater emphasis to functional analyses. (2,3) Although much of the discussion of the status of genomes has been conducted via evaluations of the evolving metaphors in genomic discourse -from the ineptness of the blueprint metaphor to analogies with jazz scores and Theseus's 4 ship - (4,5,6) there are also some excellent systematic discussions of genome conceptualizations. (7) Two issues concerning the status of knowledge in genomics are frequently discussed. The first is that early genomics shared the reductionist aspirations of genetics, which led to a preoccupation with sequence structure and deterministic accounts of function. (3, 8) Persistent (and prescient) demands for a more hierarchical and less simplistically deterministic understanding of molecular processes were voiced even in the early years of genomics. (9,10) These calls increased with ...

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Section: Applications To a Proposed Systemmentioning

confidence: 99%

Fundamental issues in systems biology

O’Malley¹,

Dupré²

2005

BioEssays

179

104

View full text Add to dashboard Cite

show abstract

“…Metagenomics implies a series of laboratory manipulations leading to the isolation of DNA originating from (ideally) the entire diversity of microorganisms found in a specific sample (soil, water, tissues and so on), bypassing the necessity of dealing with culturing techniques (Handelsman, 2004;Streit and Schmitz, 2004). Moreover, despite the enormous diversity of microorganisms that inhabit our planet, it is estimated that more than 99% of them are not growing in standard culture conditions (Amann et al, 1995;Rappe and Giovannoni, 2003), and thus await the development of new strategies that can disclose them, along with their wealth of resources (Riesenfeld et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Insights into bacterial cellulose biosynthesis by functional metagenomics on Antarctic soil samples

et al. 2009

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In this study, the mining of an Antarctic soil sample by functional metagenomics allowed the isolation of a cold-adapted protein (RBcel1) that hydrolyzes only carboxymethyl cellulose. The new enzyme is related to family 5 of the glycosyl hydrolase (GH5) protein from Pseudomonas stutzeri (Pst_2494) and does not possess a carbohydrate-binding domain. The protein was produced and purified to homogeneity. RBcel1 displayed an endoglucanase activity, producing cellobiose and cellotriose, using carboxymethyl cellulose as a substrate. Moreover, the study of pH and the thermal dependence of the hydrolytic activity shows that RBcel1 was active from pH 6 to pH 9 and remained significantly active when temperature decreased (18% of activity at 10 1C). It is interesting that RBcel1 was able to synthetize non-reticulated cellulose using cellobiose as a substrate. Moreover, by a combination of bioinformatics and enzyme analysis, the physiological relevance of the RBcel1 protein and its mesophilic homologous Pst_2494 protein from P. stutzeri, A1501, was established as the key enzymes involved in the production of cellulose by bacteria. In addition, RBcel1 and Pst_2494 are the two primary enzymes belonging to the GH5 family involved in this process.

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“…2012; Streit & Schmitz, 2004). Moreover, most biofilm cells exist in viable but non-culturable (VBNC) state (Li et al, 2014).…”

Section: Article Infomentioning

confidence: 99%

Bacterial Biofilm Cells Quantification Techniques: Where Is Consensus in Over Two Decades?

Olwal¹,

Ochiel²,

Onyango³

et al. 2017

J microb biotech food sci

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It is widely accepted that bacterial biofilms are overly resistant to antibiotics, host immunity and disinfectants. Biofilms develop on various food-processing surfaces hence pose major risks in food industries. Biofilms serve as protective niches for pathogens in food and water thus enhance transmission of food borne pathogens. Furthermore, biofilms are implicated in medical implant infections. The serious problems associated with bacterial biofilms in food, biomedical and environmental fields have stimulated active research on biofilms for over two decades. Biofilm cells quantification is important in many research applications especially in anti-biofilm efficacy studies and quality controls in many industries. However, to date there is no consensus on which technique is most suitable for quantifying bacterial biofilm cells. This apparent lack of a standard technique has hindered effective comparison of results from different bacterial biofilm studies since each technique has a unique readout. Furthermore, it appears that the choice of a biofilm cells quantification technique is largely a matter of convenience and availability of a technique. This may introduce biasness. Consequently, this review critically assesses the availability, suitability and limitations of different techniques for quantifying biofilm cells. This could inform better control and management of bacterial biofilms in environmental and clinical settings.

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Metagenomics – the key to the uncultured microbes

Cited by 430 publications

References 51 publications

Fundamental issues in systems biology

Fundamental issues in systems biology

Insights into bacterial cellulose biosynthesis by functional metagenomics on Antarctic soil samples

Bacterial Biofilm Cells Quantification Techniques: Where Is Consensus in Over Two Decades?

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