Abstract：
:Microbial networks are an increasingly popular tool to investigate microbial community structure, as they integrate multiple types of information and may represent systems-level behaviour. Interpreting these networks is not straightforward, and the biological implications of network properties are unclear. Analysis of microbial networks allows researchers to predict hub species and species interactions. Additionally, such analyses can help identify alternative community states and niches. Here, we review factors that can result in spurious predictions and address emergent properties that may be meaningful in the context of the microbiome. We also give an overview of studies that analyse microbial networks to identify new hypotheses. Moreover, we show in a simulation how network properties are affected by tool choice and environmental factors. For example, hub species are not consistent across tools, and environmental heterogeneity induces modularity. We highlight the need for robust microbial network inference and suggest strategies to infer networks more reliably.
journal_name
FEMS Microbiol Revjournal_title
FEMS microbiology reviewsauthors
Röttjers L,Faust Kdoi
10.1093/femsre/fuy030subject
Has Abstractpub_date
2018-11-01 00:00:00pages
761-780issue
6eissn
0168-6445issn
1574-6976pii
5061627journal_volume
42pub_type
杂志文章,评审abstract：:Perhaps the biggest single task facing a bacterial cell is to divide into daughter cells that contain the normal complement of chromosomes. Recent technical and conceptual breakthroughs in bacterial cell biology, combined with the flood of genome sequence information and the excellent genetic tools in several model sy...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2000.tb00554.x
更新日期：2000-10-01 00:00:00
abstract：:Antibiotic resistance can be acquired by mutation or horizontal transfer of a resistance gene, and generally an acquired mechanism results in a predictable increase in phenotypic resistance. However, recent findings suggest that the environment and/or the genetic context can modify the phenotypic expression of specifi...
journal_title：FEMS microbiology reviews
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1016/0168-6445(89)90035-1
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journal_title：FEMS microbiology reviews
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doi：10.1093/femsre/fux003
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journal_title：FEMS microbiology reviews
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doi：10.1093/femsre/fuv014
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
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更新日期：2006-01-01 00:00:00
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
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更新日期：2001-08-01 00:00:00
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
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更新日期：1995-08-01 00:00:00
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2008.00103.x
更新日期：2008-05-01 00:00:00
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
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更新日期：2001-01-01 00:00:00
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2012.00325.x
更新日期：2012-09-01 00:00:00
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2001.tb00590.x
更新日期：2001-12-01 00:00:00
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.1997.tb00306.x
更新日期：1997-06-01 00:00:00
abstract：:Cyanobacteria of the genera Synechococcus and Prochlorococcus dominate the prokaryotic component of the picophytoplankton in the oceans. It is still less than 10 years since the discovery of phages that infect marine Synechococcus and the beginning of the characterisation of these phages and assessment of their ecolog...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1016/S0168-6445(03)00016-0
更新日期：2003-04-01 00:00:00
abstract：:Fungal mycelial by-products from fermentation industries present a considerable affinity for soluble metal ions (e.g. Zn, Cd, Ni, Pb, Cr, Ag) and could be used in biosorption processes for purification of contaminated effluents. In this work the influence of pH on sorption parameters is characterized by measuring the ...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章
doi：10.1111/j.1574-6976.1994.tb00106.x
更新日期：1994-08-01 00:00:00
abstract：:Small regulatory RNAs have been identified in a wide range of organisms, where they modify mRNA stability, translation or protein function. Small RNA regulators (sRNAs) either pair with mRNA targets or modify protein activities. Here we discuss current knowledge of the various proteins that interact with RNA regulator...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2007.00079.x
更新日期：2007-09-01 00:00:00
abstract：:Understanding the structure, functionalities and biology of functional amyloids is an issue of emerging interest. Inclusion bodies, namely protein clusters formed in recombinant bacteria during protein production processes, have emerged as unanticipated, highly tunable models for the scrutiny of the physiology and arc...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1093/femsre/fuy038
更新日期：2019-01-01 00:00:00
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2008.00119.x
更新日期：2008-07-01 00:00:00
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1093/femsre/fuw027
更新日期：2016-11-01 00:00:00
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2006.00025.x
更新日期：2006-09-01 00:00:00
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
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更新日期：2010-11-01 00:00:00
abstract：:The successful genetic manipulation of Clostridium acetobutylicum for the increased production of solvents will depend on an understanding of gene structure and regulation in the bacterium. The glutamine synthetase (glnA) gene is regulated by antisense RNA, transcribed from a downstream promoter, in the opposite direc...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.1995.tb00213.x
更新日期：1995-10-01 00:00:00
abstract：:Many fungi produce exocellular beta-glucan-degrading enzymes, the beta-glucanases including the noncellulolytic beta-(1,3)- and beta-(1,6)-glucanases, degrading beta-(1,3)- and beta-(1,6)-glucans. An ability to purify several exocellular beta-glucanases attacking the same linkage type from a single fungus is common, a...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章
doi：10.1111/j.1574-6976.2006.00055.x
更新日期：2007-03-01 00:00:00
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journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.1996.tb00239.x
更新日期：1996-05-01 00:00:00
abstract：:The yeast Saccharomyces cerevisiae has been a favorite organism for pioneering studies on nutrient-sensing and signaling mechanisms. Many specific nutrient responses have been elucidated in great detail. This has led to important new concepts and insight into nutrient-controlled cellular regulation. Major highlights i...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/1574-6976.12065
更新日期：2014-03-01 00:00:00
abstract：:The gram-negative bacterium Proteus mirabilis can exist in either of two cell types, a vegetative cell characterized as a short rod and a highly elongated and hyperflagellated swarmer cell. This differentiation is triggered by growth on solid surfaces and multiple inputs are sensed by the cell to initiate the differen...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2010.00229.x
更新日期：2010-09-01 00:00:00
abstract：:Purine salvage is an essential function for all obligate parasitic protozoa studied to date and most are also capable of efficient uptake of preformed pyrimidines. Much progress has been made in the identification and characterisation of protozoan purine and pyrimidine transporters. While the genes encoding protozoan ...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1016/j.femsre.2005.03.004
更新日期：2005-11-01 00:00:00
abstract：:Metals are required cofactors for numerous fundamental processes that are essential to both pathogen and host. They are coordinated in enzymes responsible for DNA replication and transcription, relief from oxidative stress, and cellular respiration. However, excess transition metals can be toxic due to their ability t...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/1574-6976.12087
更新日期：2014-11-01 00:00:00
abstract：:Pseudomonas putida is a gram-negative rod-shaped gammaproteobacterium that is found throughout various environments. Members of the species P. putida show a diverse spectrum of metabolic activities, which is indicative of their adaptation to various niches, which includes the ability to live in soils and sediments con...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2010.00249.x
更新日期：2011-03-01 00:00:00
