Abstract：
:Organisms do not exist isolated from each other, but constantly interact. Cells can sense the presence of interaction partners by a range of receptors and, via complex regulatory networks, specifically react by changing the expression of many of their genes. Technological advances in next-generation sequencing over the recent years now allow us to apply RNA sequencing to two species at the same time (dual RNA-seq), and thus to directly study the gene expression of two interacting species without the need to physically separate cells or RNA. In this review, we give an overview over the latest studies in interspecies interactions made possible by dual RNA-seq, ranging from pathogenic to symbiotic relationships. We summarize state-of-the-art experimental techniques, bioinformatic data analysis and data interpretation, while also highlighting potential problems and pitfalls starting from the selection of meaningful time points and number of reads to matters of rRNA depletion. A short outlook on new trends in the field of dual RNA-seq concludes this review, looking at sequencing of non-coding RNAs during host-pathogen interactions and the prediction of molecular interspecies interactions networks.
journal_name
Curr Opin Microbioljournal_title
Current opinion in microbiologyauthors
Wolf T,Kämmer P,Brunke S,Linde Jdoi
10.1016/j.mib.2017.09.001subject
Has Abstractpub_date
2018-04-01 00:00:00pages
7-12eissn
1369-5274issn
1879-0364pii
S1369-5274(17)30132-7journal_volume
42pub_type
杂志文章,评审abstract：:Since 2003, dozens of giant viruses that infect amoebas (GVA), including mimiviruses and marseilleviruses, have been discovered. These giants appear to be common in our biosphere. From the onset, their presence and possible pathogenic role in humans have been serendipitously observed or investigated using a broad rang...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2016.04.012
更新日期：2016-06-01 00:00:00
abstract：:Selective autophagy is an important effector mechanism of cell autonomous immunity, in particular against invasive bacterial species. Anti-bacterial autophagy is activated by rupture of bacteria-containing vacuoles and exposure of bacteria to the cytosol. The autophagy cargo receptors p62, NDP52 and Optineurin detect ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2013.03.010
更新日期：2013-06-01 00:00:00
abstract：:We have now complete genome sequences of several pairs of closely related prokaryotes (conspecific strains or congeneric species). Surprisingly, even strains of the same species can differ by as much as 20% in gene content. Conceptual and methodological approaches for dealing with such diversity are now being develope...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(00)00204-6
更新日期：2001-06-01 00:00:00
abstract：:In contrast to obligate pathogens opportunistic pathogens such as Aspergillus fumigatus do not need a specific host to propagate or survive. However several characteristics of the saprophytic life-style and the selective pressure encountered in the primary ecological niche contribute to the virulence of A. fumigatus. ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2017.11.015
更新日期：2017-12-01 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：:Candida albicans is a regular member of the intestinal microbiota in the majority of the human population. This underscores C. albicans' adaptation to life in the intestine without inducing competitive interactions with other microbes, or immune responses detrimental to its survival. However, specific conditions such ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2020.05.006
更新日期：2020-08-01 00:00:00
abstract：:In Myxococcus xanthus morphogenetic cell movements constitute the basis for the formation of spreading vegetative colonies and fruiting bodies in starving cells. M. xanthus cells move by gliding and gliding motility depends on two polarly localized engines, type IV pili pull cells forward, and slime extruding nozzle-l...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2004.10.004
更新日期：2004-12-01 00:00:00
abstract：:The protozoan parasite Trypanosoma brucei is the causative agent of African sleeping sickness and the wasting disease, nagana, in cattle. The parasite is transmitted to the mammalian host by the bite of a tsetse fly. These parasites lack transcriptional regulation, and their gene expression is mainly regulated post-tr...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2014.06.006
更新日期：2014-08-01 00:00:00
abstract：:Microbial growth can be characterized by a limited set of macroscopic parameters such as growth rate, biomass yield and substrate affinity. Different culturing protocols for laboratory evolution have been developed to select mutant strains that have one specific macroscopic growth parameter improved. Some of those mut...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2016.03.007
更新日期：2016-06-01 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：:In the process of yeast budding, an aged and deteriorated mother cell gives rise to a youthful and pristine daughter cell. This remarkable event offers a tractable model system for identifying factors affecting life expectancy and it has been established that multiple aging factors operate in parallel. Herein, we will...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2014.02.003
更新日期：2014-04-01 00:00:00
abstract：:Type III secretion is a mechanism of protein export in bacteria, by which proteins (termed effectors) are exported from the bacteria to the external environment. One topic that has escaped much attention is the potential link between the secretion of effectors and transcriptional regulation of genes encoding the effec...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(02)00303-x
更新日期：2002-04-01 00:00:00
abstract：:Quorum sensing is an important mechanism for the regulation of genes in many Gram-negative and Gram-positive bacteria. In the opportunistic pathogen Pseudomonas aeruginosa, the absence of one or more components of the quorum-sensing system results in a significant reduction in virulence. Recent advances in the past ye...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(03)00008-0
更新日期：2003-02-01 00:00:00
abstract：:In Gram-negative bacteria such as Escherichia coli the peptidoglycan sacculus resides in the periplasm, a compartment that experiences changes in pH value, osmolality, ion strength and other parameters depending on the cell's environment. Hence, the cell needs robust peptidoglycan growth mechanisms to grow and divide ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2017.01.006
更新日期：2017-04-01 00:00:00
abstract：:All organisms must secure essential trace nutrients, including iron, zinc, manganese and copper for survival and proliferation. However, these very nutrients are also highly toxic if present at elevated levels. Mammalian immunity has harnessed both the essentiality and toxicity of micronutrients to defend against micr...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2016.05.013
更新日期：2016-08-01 00:00:00
abstract：:Legionella pneumophila is a water-borne opportunistic pathogen causing a life-threatening pneumonia called 'Legionnaires' disease'. The Legionella quorum sensing (Lqs) system produces and responds to the α-hydroxyketone signaling molecule 3-hydroxypentadecane-4-one (Legionella autoinducer-1, LAI-1). The Lqs system con...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2017.11.010
更新日期：2018-02-01 00:00:00
abstract：:Recently, a number of endophytic fungi have been discovered that produce volatile organic compounds (VOCs) whilst growing on agricultural waste substrates, whose chemistry is best defined as hydrocarbon and hydrocarbon-like. These compounds have potential use as both 'green chemicals' and fuels. This report discusses ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章
doi：10.1016/j.mib.2014.06.003
更新日期：2014-06-01 00:00:00
abstract：:Intracellular protozoans co-evolved with their mammalian host cells a range of strategies to cope with the composite and dynamic cell surface features they encounter during migration and infection. Therefore, these single-celled eukaryotic parasites represent a fascinating source of living probes for precisely capturi...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2019.06.007
更新日期：2019-12-01 00:00:00
abstract：:The existence of bacterial clones was evident in early phenotypic studies that recognised high levels of similarity in geographically and temporally separated isolates. Multilocus sequence typing (MLST) has become the most common method for genetically characterizing clones of several bacterial pathogens, allowing the...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2004.04.002
更新日期：2004-06-01 00:00:00
abstract：:Associations between marine invertebrates and their cooperative bacterial symbionts offer access to an understanding of the roots of host-microbe interaction; for example, several symbioses like the squid-vibrio light organ association serve as models for investigating how each partner affects the developmental biolog...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(00)00147-8
更新日期：2000-12-01 00:00:00
abstract：:Antibiotic lethality is a complex physiological process, sensitive to external cues. Recent advances using systems approaches have revealed how events downstream of primary target inhibition actively participate in antibiotic death processes. In particular, altered metabolism, translational stress and DNA damage each ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2017.09.002
更新日期：2017-10-01 00:00:00
abstract：:Secretion systems play a central role in infectious diseases by enabling pathogenic bacteria to deliver virulence factors into target cells. The type VI secretion system (T6SS) mediates bacterial antagonism in various environments including eukaryotic niches, such as the gut. This molecular machine injects lethal toxi...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2015.11.006
更新日期：2016-02-01 00:00:00
abstract：:Bacterial biofilms are generally described as surface-associated bacterial communities comprising exopolysaccharide-surrounded microcolonies. Interspersed between these microcolonies are water-filled channels that may serve as primitive circulatory systems. Over the past few years, much progress has been made in our u...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(99)00028-4
更新日期：1999-12-01 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：:The environment is suffused with nearly countless types of fungi, and our immune systems must be tuned to cope with constant exposure to them. In addition, it is becoming increasingly clear that many surfaces of our bodies are colonized with complex populations of fungi (the mycobiome) in the same way that they are co...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2013.05.004
更新日期：2013-06-01 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 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：:Gene clusters contributing to processes such as cell growth and pathogenicity are often controlled by two-component signal transduction systems (TCSs). Specific inhibitors against TCS systems work differently from conventional antibiotics, and developing them into new drugs that are effective against various drug-resi...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2010.01.008
更新日期：2010-04-01 00:00:00
abstract：:Helminths parasites undergo developmental changes and migration within their definitive host, in addition to establishing chronic infection. Essential to this is the evasion of host immune responses; the canonical Th2 response is effective at removing parasites resident in the intestine. Conversely, helminths also pro...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2018.09.002
更新日期：2018-12-01 00:00:00
abstract：:Infections caused by the apicomplexan parasites Plasmodium and Toxoplasma are wide-spread, life-threatening and therapeutically challenging. These pathogens are obligate intracellular microorganisms that invade mammalian cells by forming a self-made niche, the parasitophorous vacuole that is impervious to host lysosom...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2017.10.009
更新日期：2017-12-01 00:00:00
