Abstract：
:Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology. Function-driven single-cell genomics provides a solution by using a function-based screen to subsample complex microbial communities in a targeted manner for the isolation and genome sequencing of single cells. This enables single-cell sequencing to be focused on cells with specific phenotypic or metabolic characteristics of interest. Recovered genomes are conclusively implicated for both encoding and exhibiting the feature of interest, improving downstream annotation and revealing activity levels within that environment. This emerging approach has already improved our understanding of microbial community functioning and facilitated the experimental analysis of uncharacterized gene product space. Here we provide a comprehensive review of strategies that have been applied for function-driven single-cell genomics and the future directions we envision.
journal_name
FEMS Microbiol Revjournal_title
FEMS microbiology reviewsauthors
Doud DFR,Woyke Tdoi
10.1093/femsre/fux009subject
Has Abstractpub_date
2017-07-01 00:00:00pages
538-548issue
4eissn
0168-6445issn
1574-6976pii
3861942journal_volume
41pub_type
杂志文章abstract：:Meningococcal disease is a serious and rapidly progressing illness. It is therefore very important to monitor changes in the level of antibiotic susceptibility among clinical isolates. Different aspects such as interpretation of laboratory results, determination of breakpoints predicting treatment failure as well as d...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2006.00049.x
更新日期：2007-01-01 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：:The production of the fusion protein staphylococcal protein A/E. coli beta-galactosidase in Escherichia coli was studied in batch and fed batch cultivations. Batch cultivation of a recombinant E. coli strain yielded a final cell dry weight of 16.4 g l-1 with a final intracellular product concentration of recombinant p...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章
doi：10.1111/j.1574-6976.1994.tb00072.x
更新日期：1994-05-01 00:00:00
abstract：:The initiation of transcription is the most important step for gene regulation in eubacteria. To initiate transcription, RNA polymerase has to associate with a small protein, known as a sigma-factor. The sigma-factor directs RNA polymerase to a specific class of promoter sequences. Most bacterial species synthesize se...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.1998.tb00364.x
更新日期：1998-09-01 00:00:00
abstract：:Antibiotics are the most common type of medication prescribed to children, including infants, in the Western world. While use of antibiotics has transformed previously lethal infections into relatively minor diseases, antibiotic treatments can have adverse effects as well. It has been shown in children, adults and ani...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1093/femsre/fuy018
更新日期：2018-07-01 00:00:00
abstract：:A high frequency of human cytomegalovirus (HCMV) genome and antigens in tumor samples of patients with different malignancies is now well documented, although the causative role for HCMV in the development of the neoplasias remains to be established. HCMV infection can modulate multiple cellular regulatory and signall...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1016/j.femsre.2003.07.005
更新日期：2004-02-01 00:00:00
abstract：:Natural genetic transformation is widely distributed in bacteria. It is a genetically programmed process that is inherent to the species. Transformation requires a specialized membrane-associated machinery for uptake of exogenous double-stranded DNA. It also requires dedicated cytosolic proteins, some of which have be...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2009.00164.x
更新日期：2009-05-01 00:00:00
abstract：:The genus Corynebacterium belongs to the taxonomic class Actinobacteria representing the high G+C branch of gram-positive bacteria. Among the most prominent members of this genus is Corynebacterium glutamicum, which is used by the biotechnological industry for the fermentative production of l-amino acids. Because of i...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2010.00228.x
更新日期：2010-09-01 00:00:00
abstract：:Water is one of the most important bacterial habitats on Earth. As such, water represents also a major way of dissemination of bacteria between different environmental compartments. Human activities led to the creation of the so-called urban water cycle, comprising different sectors (waste, surface, drinking water), a...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/1574-6976.12062
更新日期：2014-07-01 00:00:00
abstract：:Quinolone-resistant Salmonella enterica usually contain a mutation in gyrA within the region encoding the quinolone resistance determining region of the A subunit of DNA gyrase. These mutations confer substitutions analogous to Escherichia coli Ser83-->Phe and Asp87-->Gly or Tyr, or a novel mutation resulting in Ala11...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章
doi：10.1111/j.1574-6976.2002.tb00596.x
更新日期：2002-03-01 00:00:00
abstract：:It has become increasingly and widely recognised that bacteria do not exist as solitary cells, but are colonial organisms that exploit elaborate systems of intercellular communication to facilitate their adaptation to changing environmental conditions. The languages by which bacteria communicate take the form of chemi...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2001.tb00583.x
更新日期：2001-08-01 00:00:00
abstract：:Arsenic compounds have been abundant at near toxic levels in the environment since the origin of life. In response, microbes have evolved mechanisms for arsenic resistance and enzymes that oxidize As(III) to As(V) or reduce As(V) to As(III). Formation and degradation of organoarsenicals, for example methylarsenic comp...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2002.tb00617.x
更新日期：2002-08-01 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：:The bacterium Chlamydia trachomatis is the etiological agent of the most common sexually transmitted infection in North America and Europe. Medical complications resulting from genital C. trachomatis infections arise predominantly in women where the initial infections often remain asymptomatic and thus unrecognized. U...
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
abstract：:Lipopeptides constitute a structurally diverse group of metabolites produced by various bacterial and fungal genera. In the past decades, research on lipopeptides has been fueled by their antimicrobial, antitumour, immunosuppressant and surfactant activities. However, the natural functions of lipopeptides in the lifes...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2010.00221.x
更新日期：2010-11-01 00:00:00
abstract：:Human protein kinase C (PKC) isoforms have been implicated in diseases such as Alzheimer's, diabetes and cancers. In contrast to mammals, which have at least nine genes, fungi have only one or two. The yeast Saccharomyces cerevisiae produces only a single Pkc1 and is employed in the study of specific human isozymes, i...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1093/femsre/fux051
更新日期：2018-01-01 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：:First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and chara...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1093/femsre/fux027
更新日期：2017-08-01 00:00:00
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：:Gram-positive bacteria have developed elaborate mechanisms to control ammonium assimilation, at the levels of both transcription and enzyme activity. In this review, the common and specific mechanisms of nitrogen assimilation and regulation in Gram-positive bacteria are summarized and compared for the genera Bacillus,...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2010.00216.x
更新日期：2010-07-01 00:00:00
abstract：:Since the 1960s, several new attempts have been made to improve the management of single prokaryotic cells using micromanipulator techniques. In order to facilitate the isolation of pure cultures we have recently developed an improved micromanipulation method for routine work. With the aid of this method single prokar...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2000.tb00558.x
更新日期：2000-12-01 00:00:00
abstract：:Ribonuclease P is the endonuclease required for generating the mature tRNA 5'-end. The ribonucleoprotein character of this enzyme has now been proven in most organisms and organelles. Exceptions, however, are still the chloroplasts, plant nuclei and animal mitochondria where no associated RNAs have been detected to da...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.1999.tb00406.x
更新日期：1999-06-01 00:00:00
abstract：:In recent years, there has been accumulating evidence that antibiotics, besides their antimicrobial action, potentially have a number of undesired side effects that can, at least in some cases, promote genetic variability of bacteria. In addition to resistant variants, antibiotics have also been shown to select mutato...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1111/j.1574-6976.2009.00165.x
更新日期：2009-05-01 00:00:00
abstract：:The initial step of methanogenesis from CO2 is the formation of formyl-methanofuran (formyl-MFR) from methanofuran (MFR), CO2 and H2. The enzymology of this novel type of CO2 fixation reaction has been difficult to study because formyl-MFR synthesis is subject to a complex activation. Recently, however, a number of ad...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1016/0378-1097(90)90473-4
更新日期：1990-12-01 00:00:00
abstract：:DNA microarrays are a powerful and promising approach to gain a detailed understanding of the bacterial response and the molecular cross-talk that can occur as a consequence of host-pathogen interactions. However, published studies mainly describe the host response to infection. Analysis of bacterial gene regulation i...
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
abstract：:The wealth of information existing on the general principle of S-layers has revealed a broad application potential. The most relevant features exploited in applied S-layer research are: (i) pores passing through S-layers show identical size and morphology and are in the range of ultrafiltration membranes; (ii) functio...
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：:Gene conversion is defined as the non-reciprocal transfer of information between homologous sequences. Despite methodological problems to establish non-reciprocity, gene conversion has been demonstrated in a wide variety of bacteria. Besides examples of high-frequency reversion of mutations in repeated genes, gene con...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1016/j.femsre.2004.10.004
更新日期：2005-04-01 00:00:00
abstract：:Type II (proteic) toxin-antitoxin (TA) operons are widely spread in bacteria and archaea. They are organized as operons in which, usually, the antitoxin gene precedes the cognate toxin gene. The antitoxin generally acts as a transcriptional self-repressor, whereas the toxin acts as a co-repressor, both proteins consti...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1093/femsre/fuv002
更新日期：2015-07-01 00:00:00
abstract：:Respiratory syncytial virus is the major respiratory pathogen of infants and children worldwide, with no effective treatment or vaccine available. Steady progress has been made in understanding the respiratory syncytial virus life cycle and the consequences of infection, but many areas of respiratory syncytial virus b...
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
abstract：:The natural light environment is important to many prokaryotes. Most obviously, phototrophic prokaryotes need to acclimate their photosynthetic apparatus to the prevailing light conditions, and such acclimation is frequently complemented by motility to enable cells to relocate in search of more favorable illumination ...
journal_title：FEMS microbiology reviews
pub_type： 杂志文章,评审
doi：10.1093/femsre/fux045
更新日期：2017-11-01 00:00:00
