Abstract：
:Metagenomics is a novel field which deals with the sequencing and study of microbial organisms or viruses isolated directly from a particular environment. This has already provided a wealth of information and new insights for the inhabitants of various environmental niches. For a given sample, one would like to determine the phylogenetic provenance of the obtained fragments, the relative abundance of its different members, their metabolic capabilities, and the functional properties of the community as a whole. To this end, computational analyses are becoming increasingly indispensable tools. In this review, we focus on the problem of determining the phylogenetic identity of the sample fragments, a procedure known as 'binning'. This step is essential for the reconstruction of the metabolic capabilities of individual organisms or phylogenetic clades of a community, and the study of their interactions.
journal_name
Curr Opin Microbioljournal_title
Current opinion in microbiologyauthors
McHardy AC,Rigoutsos Idoi
10.1016/j.mib.2007.08.004subject
Has Abstractpub_date
2007-10-01 00:00:00pages
499-503issue
5eissn
1369-5274issn
1879-0364pii
S1369-5274(07)00118-Xjournal_volume
10pub_type
杂志文章,评审abstract：:Kinetoplastid parasites adapt to different environments with wide-reaching control of gene expression, but transcription of nuclear protein-coding genes is polycistronic: there is no individual control of transcription initiation. Mature mRNAs are made by co-transcriptional trans splicing and polyadenylation, and comp...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2016.04.018
更新日期：2016-08-01 00:00:00
abstract：:The family Arenaviridae consists of a unique genus (Arenavirus) that currently comprises 22 viral species, as recognized by the International Committee for Taxonomy of Viruses. Seven newly discovered represent putative new species. Here, our aims were to provide the most comprehensive phylogenetic analysis of members ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2008.06.001
更新日期：2008-08-01 00:00:00
abstract：:The acquisition of drug resistance by Plasmodium falciparum has severely curtailed global efforts to control malaria. Our ability to define resistance has been greatly enhanced by recent advances in Plasmodium genetics and genomics. Sequencing and microarray studies have identified thousands of polymorphisms in the P....
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2007.07.007
更新日期：2007-08-01 00:00:00
abstract：:During the past ten years, species-rich nations in the developing world have sought to capitalize on their 'biological patrimony' through a variety of business relationships with multinational corporations as a means of underwriting their conservation efforts. Initially lauded, these relationships have generated more ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/S1369-5274(99)80041-1
更新日期：1999-06-01 00:00:00
abstract：:We postulate that phenotypic resistance to antibiotics, persistence, is not an evolved (selected-for) character but rather like mutation, an inadvertent product of different kinds of errors and glitches. The rate of generation of these errors is augmented by exposure to these drugs. The genes that have been identified...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2014.06.016
更新日期：2014-10-01 00:00:00
abstract：:In two-component signaling systems, phosphorylated response regulators (RRs) are often dephosphorylated by their partner kinases in order to control the in vivo concentration of phospho-RR (RR approximately P). This activity is easily demonstrated in vitro, but these experiments have typically used very high concentra...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2010.01.013
更新日期：2010-04-01 00:00:00
abstract：:Phagocytic cells, including macrophages, neutrophils and dendritic cells, are critical components of the innate immune response to bacterial pathogens such as Salmonella typhimurium. These cells can have several roles during the early stage of an infection including controlling bacterial replication and producing cyto...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2003.12.008
更新日期：2004-02-01 00:00:00
abstract：:Dynamic properties of type IV pili are essential for their function in bacterial infection, twitching motility and gene transfer. Laser tweezers are versatile tools to study the molecular mechanism underlying pilus dynamics at the single molecule level. Recently, these optical tweezers have been used to monitor pilus ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2005.04.002
更新日期：2005-06-01 00:00:00
abstract：:Endolysins are phage-encoded enzymes that break down bacterial peptidoglycan at the terminal stage of the phage reproduction cycle. Their action is tightly regulated by holins, by membrane arrest, and by conversion from their inactive to active state. Recent research has not only revealed the unexpected diversity of t...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2005.06.002
更新日期：2005-08-01 00:00:00
abstract：:The epithelial cell layer of the major organs of the mammalian gastrointestinal (GI) tract is extensively invaginated into thousands of gland and crypt structures. These are lined by distinct sets of epithelial cells and may comprise discrete niches. The host maximizes the distance between the epithelial cell layer an...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2018.11.004
更新日期：2019-02-01 00:00:00
abstract：:The historical paradigm of the deep ocean as a biological 'desert' has shifted to one of a 'rainforest' owing to the isolation of many novel microbes and their associated bioactive compounds. Recently, there has been an explosion of information about novel bioactive compounds that have been isolated from marine microb...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2005.04.008
更新日期：2005-06-01 00:00:00
abstract：:Natural products are a rich source of bioactive compounds that have been used successfully in the areas of human health from infectious disease to cancer; however, traditional fermentation-based screening has provided diminishing returns over the last 20-30 years. Solutions to the unmet need of resistant bacterial inf...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2019.01.001
更新日期：2019-10-01 00:00:00
abstract：:The availability of genome information for microbial consortia, including unculturable species, from environmental samples has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. This provides a unique opportunity to characterize the molecular activi...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2012.04.008
更新日期：2012-06-01 00:00:00
abstract：:Successful execution of differentiation programs requires cells to assess multitudes of internal and external cues and respond with appropriate gene expression programs. Here, we review how Bacillus subtilis sporulation network deals with these tasks focusing on the lessons generalizable to other systems. With feedfor...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2016.07.011
更新日期：2016-12-01 00:00:00
abstract：:Biological nitrogen fixation is a much more important process in the nitrogen cycle of the oceans than previously thought. Further, nitrogen fixation may have an influence on the capacity of the oceans to sequester carbon. A greater diversity of marine nitrogen fixers has also been uncovered but their quantitative sig...
journal_title：Current opinion in microbiology
pub_type： 杂志文章
doi：10.1016/s1369-5274(00)00215-0
更新日期：2001-06-01 00:00:00
abstract：:The obligatory intracellular bacterial pathogens Anaplasma and Ehrlichia infect leukocytes by hijacking host-cell components and processes. The type IV secretion system is up-regulated during infection. Among type IV secretion candidate substrates, an ankyrin repeat protein of Anaplasma phagocytophilum, AnkA, is deliv...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2009.12.008
更新日期：2010-02-01 00:00:00
abstract：:Members of the YidC/Oxa1/Alb3 membrane protein family are multifunctional mediators of membrane protein integration, folding and assembly into large complexes. Their evolutionary conserved and physiologically important role appears to relate to the assembly of major energy-transducing membrane protein complexes. ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2005.02.004
更新日期：2005-04-01 00:00:00
abstract：:Dectin-1 is an innate immune pattern recognition receptor (PRR) that, through its ability to bind β-glucans, is involved in the recognition of several pathogenic fungi. Dectin-1 can stimulate a variety of cellular responses via the Syk/CARD9 signalling pathway, including phagocytosis, cytokine production and the respi...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2011.07.001
更新日期：2011-08-01 00:00:00
abstract：:The review highlights the dual role that the conserved master regulator FoxO has in aging by coordinating both stem cell proliferation and antimicrobial peptides, effector molecules of the innate immune system. As observed in non-senescent Hydra, continuously high activity of the transcription factor FoxO contributes ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2017.06.009
更新日期：2017-08-01 00:00:00
abstract：:In this paper, we discuss recent advances in our knowledge of the dengue virus life cycle based on new structural data of the virus and its proteins. Specifically, we focus on the structure of the pre-membrane protein, prM and its role in virus assembly, the first full-length structure of a multi-domain dengue virus r...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2008.06.004
更新日期：2008-08-01 00:00:00
abstract：:Recent developments have increased our understanding of the evolution of mutualistic associations between Epichloë endophytes and their grass hosts. Most of the asexual species appear to be interspecific hybrids. Although endophytes form compatible associations with their natural hosts, transfers to other hosts elicit...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(00)00224-1
更新日期：2001-08-01 00:00:00
abstract：:The recently decoded genomes of the major clostridial toxin-producing pathogens Clostridium perfringens, Clostridium tetani, Clostridium botulinum and Clostridium difficile have provided a huge amount of new sequence data. Recent studies have focused on the identification and investigation of pathogenic determinants a...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2005.08.006
更新日期：2005-10-01 00:00:00
abstract：:Motile bacteria seek optimal living habitats by following gradients of attractant and repellent chemicals in their environment. The signaling machinery for these chemotactic behaviors, although assembled from just a few protein components, has extraordinary information-processing capabilities. Escherichia coli, the be...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2005.02.008
更新日期：2005-04-01 00:00:00
abstract：:The quest for the discovery of novel natural products has entered a new chapter with the enormous wealth of genetic data that is now available. This information has been exploited by using whole-genome sequence mining to uncover cryptic pathways, or biosynthetic pathways for previously undetected metabolites. Alternat...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2006.04.002
更新日期：2006-06-01 00:00:00
abstract：:While natural microbial communities are composed of a mix of microbes with often unknown functions, the construction of synthetic microbial communities allows for the generation of defined systems with reduced complexity. Used in a top-down approach, synthetic communities serve as model systems to ask questions about ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2014.02.002
更新日期：2014-04-01 00:00:00
abstract：:Chemical communication between cells ensures coordination of behavior. In prokaryotes, this chemical communication is usually referred to as quorum sensing, while eukaryotic cells signal through hormones. In the past years, a growing number of reports have shown that bacterial quorum sensing signals, called autoinduce...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2009.01.006
更新日期：2009-04-01 00:00:00
abstract：:The human pathogenic Yersinia species cause diseases that represent a significant source of morbidity and mortality. Despite this, specific mechanisms underlying Yersinia pathogenesis and protective host responses remain poorly understood. Recent studies have shown that Yersinia disrupt cell death pathways, perturb in...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2015.11.001
更新日期：2016-02-01 00:00:00
abstract：:Bacteria furnish tractable models for complex biological processes, and morphogenesis is now taking its turn. We can already explain in general terms how such elementary forms as rods and cocci are produced, and the shapes of several individual organisms are coming into focus. In most bacteria shape is maintained by t...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2007.07.003
更新日期：2007-12-01 00:00:00
abstract：:Mast cells (MCs) have been implicated in orchestrating the host's early innate immune and adaptive immune responses in several models of acute bacterial infections. Most of this activity results in early clearance of the bacteria and timely resolution of infection. However, during chronic infections because of the pro...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2011.10.007
更新日期：2012-02-01 00:00:00
abstract：:The three dimensional ultrastructure of cells and tissues comes to light with tomography. There is an inherent tension between representing molecular detail at the highest possible resolution, on one hand, and visualizing spatial relations between large organelles or even neighboring cells in large volumes, on the oth...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2018.01.001
更新日期：2018-06-01 00:00:00
