Abstract:
:Microbial and plant specialized metabolites, also known as natural products, are key mediators of microbe-microbe and host-microbe interactions and constitute a rich resource for drug development. In the past decade, genome mining has emerged as a prominent strategy for natural product discovery. Initially, such mining was performed on the basis of individual microbial genome sequences. Now, these efforts are being scaled up to fully genome-sequenced strain collections, pangenomes of bacterial genera, and large sets of metagenome-assembled genomes from microbial communities. The Medema research group aims to play a leading role in these developments by developing and applying computational approaches to identify, classify, and prioritize specialized metabolite biosynthetic gene clusters and pathways and to connect them to specific molecules and microbiome-associated phenotypes. Moreover, we are extending the scope of genome mining from microbes to plants, which will allow more comprehensive interpretation of the chemical language between hosts and microbes in a microbiome setting.
journal_name
mSystemsjournal_title
mSystemsauthors
Medema MHdoi
10.1128/mSystems.00182-17subject
Has Abstractpub_date
2018-03-06 00:00:00issue
2issn
2379-5077pii
mSystems00182-17journal_volume
3pub_type
杂志文章相关文献
mSystems文献大全abstract::Globally, dental caries is the most prevalent chronic oral disease and affects roughly half of all children. The aim of this report was to use metagenomic analyses to investigate the relationship between the oral microbiome and caries in preschool children. A total of 25 preschoolers, aged 3 to 5 years old with severe...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00450-19
更新日期:2019-11-05 00:00:00
abstract::GapMind is a Web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl.gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 s. To avoid error-prone transitive annotations, GapMind relies primarily on a dat...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00291-20
更新日期:2020-06-23 00:00:00
abstract::In pregnant and lactating sows, metabolism and immunity undergo drastic changes, which can lead to constipation, abortion, and intrauterine growth restriction (IUGR) and reduce production performance. Dietary fiber can regulate animal gut microbiota, alleviate inflammatory responses, and improve performance. Here, 48 ...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00591-20
更新日期:2021-01-26 00:00:00
abstract::Sulfur is an essential nutrient that contributes to cellular redox homeostasis, transcriptional regulation, and translation initiation when incorporated into different biomolecules. Transport and reduction of extracellular sulfate followed by cysteine biosynthesis is a major pathway of bacterial sulfur assimilation. F...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00285-19
更新日期:2019-08-06 00:00:00
abstract::The human gut microbiome plays a vital role in both health and disease states and as a mediator of cognitive and physical performance. Despite major advances in our understanding of the role of gut microbes in host physiology, mechanisms underlying human-microbiome dynamics have yet to be fully elucidated. This knowle...
journal_title:mSystems
pub_type: 杂志文章,评审
doi:10.1128/mSystems.00487-20
更新日期:2020-10-27 00:00:00
abstract::Apoptosis is generally considered the first line of defense against viral infection. However, the role of apoptosis in the interactions between plant viruses and their insect vectors has rarely been investigated. By studying plant DNA viruses of the genus Begomovirus within the family Geminiviridae, which are transmit...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00433-20
更新日期:2020-09-22 00:00:00
abstract::The gut microbiota has been implicated in immunoglobin A nephropathy (IgAN) because the intestinal immune response is assumed to be one of the disease triggers. Since the microbial composition is heritable, we hypothesize that genetic variants controlling gut microbiota composition may be associated with susceptibilit...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00819-20
更新日期:2021-01-12 00:00:00
abstract::Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from t...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00162-16
更新日期:2017-01-17 00:00:00
abstract::ABSRTACTKlebsiella pneumoniae is a common cause of human-pneumonia-derived sepsis with high morbidity and mortality. The microbiota promotes and maintains host immune homeostasis. The mechanisms by which the gut microbiota affects the host defenses in the respiratory system systematically, however, remain poorly under...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00587-20
更新日期:2020-11-03 00:00:00
abstract::High-nucleic-acid (HNA) and low-nucleic-acid (LNA) bacteria are two operational groups identified by flow cytometry (FCM) in aquatic systems. A number of reports have shown that HNA cell density correlates strongly with heterotrophic production, while LNA cell density does not. However, which taxa are specifically ass...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00093-19
更新日期:2019-09-10 00:00:00
abstract::The identification of ancestral traits is essential to understanding the evolution of any group. In the case of parasitic groups, this helps us understand the adaptation to this lifestyle and a particular host. Most diplomonads are parasites, but there are free-living members of the group nested among the host-associa...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00774-20
更新日期:2020-12-22 00:00:00
abstract::Methylobacter species, members of the Methylococcales, have recently emerged as some of the globally widespread, cosmopolitan species that play a key role in the environmental consumption of methane across gradients of dioxygen tensions. In this work, we approached the question of how Methylobacter copes with hypoxia,...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00770-19
更新日期:2020-01-21 00:00:00
abstract::Although a few studies have investigated the intestinal microbiota of women with polycystic ovary syndrome (PCOS), the functional and metabolic mechanisms of the microbes associated with PCOS, as well as potential microbial biomarkers, have not yet been identified. To address this gap, we designed a two-phase experime...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00017-19
更新日期:2019-04-16 00:00:00
abstract::Improvements in growth performance and health are key goals in broiler chicken production. Inclusion of prebiotic galacto-oligosaccharides (GOS) in broiler feed enhanced the growth rate and feed conversion of chickens relative to those obtained with a calorie-matched control diet. Comparison of the cecal microbiota id...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00827-19
更新日期:2020-01-14 00:00:00
abstract::Fecal microbiota transplantation (FMT) is a proposedly useful strategy for the treatment of gastrointestinal (GI) disorders through remediation of the patient gut microbiota. However, its therapeutic success has been variable, necessitating research to uncover mechanisms that improve patient response. Antibiotic pretr...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00404-19
更新日期:2020-01-28 00:00:00
abstract::Biological sulfur cycling in polar, low-temperature ecosystems is an understudied phenomenon in part due to difficulty of access and the dynamic nature of glacial environments. One such environment where sulfur cycling is known to play an important role in microbial metabolisms is located at Borup Fiord Pass (BFP) in ...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00504-20
更新日期:2020-08-04 00:00:00
abstract::Microbiology, like many areas of life science research, is increasingly data-intensive. As such, bioinformatics and data science skills have become essential to leverage microbiome sequencing data for discovery. Short intensive courses have sprung up as formal computational training opportunities at individual institu...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00467-19
更新日期:2019-08-20 00:00:00
abstract::Persister cells are genetically identical variants in a bacterial population that have phenotypically modified their physiology to survive environmental stress. In bacterial pathogens, persisters are able to survive antibiotic treatment and reinfect patients in a frustrating cycle of chronic infection. To better defin...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00609-19
更新日期:2020-02-11 00:00:00
abstract::As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored "differential coverage binning" method on 22-Gb metagenomic sequences, we re...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00184-16
更新日期:2017-03-21 00:00:00
abstract::The intestinal microbiota and the expanded endocannabinoid (eCB) system, or endocannabinoidome (eCBome), have both been implicated in diet-induced obesity and dysmetabolism. These systems were recently suggested to interact during the development of obesity. We aimed at identifying the potential interactions between g...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00407-19
更新日期:2019-12-17 00:00:00
abstract::Bacterial motility is thought to play an important role in virulence. We have previously shown that proficient bacterial swimming and swarming in vitro is correlated with the persistent intramammary infection phenotype observed in cattle. However, little is known about the gene regulation differences important for dif...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00064-16
更新日期:2016-08-09 00:00:00
abstract::Marine oil spills can impact both coastal and offshore marine environments, but little information is available on how the microbial response to oil and dispersants might differ between these biomes. Here, we describe the compositional and functional response of microbial communities to different concentrations of oil...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00668-20
更新日期:2020-08-25 00:00:00
abstract::Tripartite symbioses between bacteriophages, the epithelial cell layers of the human gut, and bacterial symbionts may play an important and unrecognized role in the function of the gut microbiome. Traditionally, phages residing within the gut were considered to interact only with their bacterial hosts and thereby to f...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00105-19
更新日期:2019-05-07 00:00:00
abstract::Pullorum disease is one of the most common diarrhea-related diseases caused by Salmonella enterica subspecies enterica serovar Gallinarum biovar Pullorum (S Pullorum); it negatively affects the poultry industry. However, limited studies have explored the association between the gut microbiota and S Pullorum infection ...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.01192-20
更新日期:2021-01-05 00:00:00
abstract::Dimorphic plant and human mycopathogens require a switch from the usual yeast growth to filamentous growth for host tissue penetration, and the switch is controlled by multiple signaling systems other than the central developmental pathway. Unlike these fungi, dimorphic insect mycopathogens usually grow by hyphal exte...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00140-19
更新日期:2019-07-09 00:00:00
abstract::Nutrient acquisition from the host environment is crucial for the survival of intracellular pathogens, but conceptual and technical challenges limit our knowledge of pathogen diets. To overcome some of these technical roadblocks, we exploited an experimentally accessible model for early infection of human macrophages ...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00057-17
更新日期:2017-08-22 00:00:00
abstract::It is important to expedite our understanding of antibiotic resistance to address the increasing numbers of fatalities and environmental pollution due to the emergence of antibiotic resistance and multidrug-resistant strains. Here, we combined the CRISPR-enabled trackable genome engineering (CREATE) technology and tra...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00232-20
更新日期:2020-04-21 00:00:00
abstract::Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets ...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00288-19
更新日期:2019-08-13 00:00:00
abstract::Studying perturbations in the gut ecosystem using animal models of disease continues to provide valuable insights into the role of the microbiome in various pathological conditions. However, understanding whether these changes are consistent across animal models of different genetic backgrounds, and hence potentially ...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00058-19
更新日期:2019-04-30 00:00:00
abstract::Health-associated oral Streptococcus species are promising probiotic candidates to protect against dental caries. Ammonia production through the arginine deiminase system (ADS), which can increase the pH of oral biofilms, and direct antagonism of caries-associated bacterial species are desirable properties for oral pr...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00158-18
更新日期:2018-12-18 00:00:00