Abstract:
BACKGROUND:Wheat residues are a crucial determinant of the epidemiology of Septoria tritici blotch, as they support the sexual reproduction of the causal agent Zymoseptoria tritici. We aimed to characterize the effect of infection with this fungal pathogen on the microbial communities present on wheat residues and to identify microorganisms interacting with it. We used metabarcoding to characterize the microbiome associated with wheat residues placed outdoors, with and without preliminary Z. tritici inoculation, comparing the first set of residues in contact with the soil and a second set without contact with the soil, on four sampling dates in two consecutive years. RESULTS:The diversity of the tested conditions, leading to the establishment of different microbial communities according to the origins of the constitutive taxa (plant only, or plant and soil), highlighted the effect of Z. tritici on the wheat residue microbiome. Several microorganisms were affected by Z. tritici infection, even after the disappearance of the pathogen. Linear discriminant analyses and ecological network analyses were combined to describe the communities affected by the infection. The number of fungi and bacteria promoted or inhibited by inoculation with Z. tritici decreased over time and was smaller for residues in contact with the soil. The interactions between the pathogen and other microorganisms appeared to be mostly indirect, despite the strong position of the pathogen as a keystone taxon in networks. Direct interactions with other members of the communities mostly involved fungi, including other wheat pathogens. Our results provide essential information about the alterations to the microbial community in wheat residues induced by the mere presence of a fungal pathogen, and vice versa. Species already described as beneficial or biocontrol agents were found to be affected by pathogen inoculation. CONCLUSIONS:The strategy developed here can be viewed as a proof-of-concept focusing on crop residues as a particularly rich ecological compartment, with a high diversity of fungal and bacterial taxa originating from both the plant and soil compartments, and for Z. tritici-wheat as a model pathosystem. By revealing putative antagonistic interactions, this study paves the way for improving the biological control of residue-borne diseases.
journal_name
Microbiomejournal_title
Microbiomeauthors
Kerdraon L,Barret M,Laval V,Suffert Fdoi
10.1186/s40168-019-0736-0subject
Has Abstractpub_date
2019-08-30 00:00:00pages
125issue
1issn
2049-2618pii
10.1186/s40168-019-0736-0journal_volume
7pub_type
杂志文章相关文献
Microbiome文献大全abstract::Following publication of the original article [1], the authors reported an error in Fig. 2. The original Fig. 2 has been incorrectly replaced with the Supplementary Fig. 2. The correct Fig. 2 is presented here. ...
journal_title:Microbiome
pub_type: 杂志文章,已发布勘误
doi:10.1186/s40168-020-00829-6
更新日期:2020-04-06 00:00:00
abstract:BACKGROUND:The use of culture-independent nucleic acid techniques, such as ribosomal RNA gene cloning library analysis, has unveiled the tremendous microbial diversity that exists in natural environments. In sharp contrast to this great achievement is the current difficulty in cultivating the majority of bacterial spec...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/2049-2618-1-4
更新日期:2013-01-09 00:00:00
abstract:BACKGROUND:The role of the gut microbiome in arresting pathogen colonization and growth is important for protection against Clostridium difficile infection (CDI). Observational studies associate proton pump inhibitor (PPI) use and CDI incidence. We hypothesized that PPI use affected the distal gut microbiome over time,...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/2049-2618-2-42
更新日期:2014-11-25 00:00:00
abstract:BACKGROUND:Holobionts have a digestive microbiota with catabolic abilities allowing the degradation of complex dietary compounds for the host. In terrestrial herbivores, the digestive microbiota is known to degrade complex polysaccharides from land plants while in marine herbivores, the digestive microbiota is poorly c...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0430-7
更新日期:2018-03-27 00:00:00
abstract:BACKGROUND:The microbial populations of the human intestinal tract and their relationship to specific diseases have been extensively studied during the last decade. However, the characterization of the human bile microbiota as a whole has been hampered by difficulties in accessing biological samples and the lack of ade...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0712-8
更新日期:2019-07-04 00:00:00
abstract:BACKGROUND:Clostridium difficile infection (CDI) is the leading infectious cause of nosocomial diarrhea. Hospitalized patients are at increased risk of developing CDI because they are exposed to C. difficile spores through contact with the hospital environment and often receive antibiotics and other medications that ca...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0156-3
更新日期:2016-03-14 00:00:00
abstract:BACKGROUND:Archaea are one of the least-studied members of the gut-dwelling autochthonous microbiota. Few studies have reported the dominance of methanogens in the archaeal microbiome (archaeome) of the human gut, although limited information regarding the diversity and abundance of other archaeal phylotypes is availab...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00894-x
更新日期:2020-08-04 00:00:00
abstract:BACKGROUND:Lower respiratory tract infection (LRTI) is a major contributor to respiratory failure requiring intubation and mechanical ventilation. LRTI also occurs during mechanical ventilation, increasing the morbidity and mortality of intubated patients. We sought to understand the dynamics of respiratory tract micro...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0151-8
更新日期:2016-02-11 00:00:00
abstract:BACKGROUND:There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial microbiota associated with the addition of menthol, an additive that has been used by tobacco manufacture...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0235-0
更新日期:2017-02-15 00:00:00
abstract:BACKGROUND:Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulo...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0629-2
更新日期:2019-02-01 00:00:00
abstract:BACKGROUND:This proof-of-principle study examines whether postnatal, low-dose exposure to environmental chemicals modifies the composition of gut microbiome. Three chemicals that are widely used in personal care products-diethyl phthalate (DEP), methylparaben (MPB), triclosan (TCS)-and their mixture (MIX) were administ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0173-2
更新日期:2016-06-14 00:00:00
abstract:BACKGROUND:Alterations of gut microbiota are associated with colorectal cancer (CRC) in different populations and several bacterial species were found to contribute to the tumorigenesis. The potential use of gut microbes as markers for early diagnosis has also been reported. However, cohort specific noises may distort ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0451-2
更新日期:2018-04-11 00:00:00
abstract:BACKGROUND:Natural gas seeps contribute to global climate change by releasing substantial amounts of the potent greenhouse gas methane and other climate-active gases including ethane and propane to the atmosphere. However, methanotrophs, bacteria capable of utilising methane as the sole source of carbon and energy, pla...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0741-3
更新日期:2019-10-04 00:00:00
abstract:BACKGROUND:The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as "metaorganisms." The goal of the Collaborative Research Center "Origin and...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0743-1
更新日期:2019-09-14 00:00:00
abstract::Human genome-wide association studies (GWASs) have recurrently estimated lower heritability estimates than familial studies. Many explanations have been suggested to explain these lower estimates, including that a substantial proportion of genetic variation and gene-by-environment interactions are unmeasured in typica...
journal_title:Microbiome
pub_type: 信件
doi:10.1186/s40168-020-00839-4
更新日期:2020-06-08 00:00:00
abstract:BACKGROUND:The interconnectivities of built and natural environments can serve as conduits for the proliferation and dissemination of antibiotic resistance genes (ARGs). Several studies have compared the broad spectrum of ARGs (i.e., "resistomes") in various environmental compartments, but there is a need to identify u...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0735-1
更新日期:2019-08-29 00:00:00
abstract:BACKGROUND:The study of the microbial communities in the built environment is of critical importance as humans spend the majority of their time indoors. While the microorganisms in living spaces, especially those in the air, can impact health and well-being, little is known of their identity and the processes that dete...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-015-0128-z
更新日期:2015-12-10 00:00:00
abstract:BACKGROUND:Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed community state types (CSTs). This approach is advantageous because collapsing a hyper-dimensional taxonomic profile into a single categorical variable enables efforts such as data exploration, epide...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00934-6
更新日期:2020-11-23 00:00:00
abstract:BACKGROUND:Plants have developed defense strategies for phytopathogen and herbivore protection via coordinated metabolic mechanisms. Low-molecular weight metabolites produced within plant tissues, such as salicylic acid, represent one such mechanism which likely mediates plant - microbe interactions above and below gro...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0668-8
更新日期:2019-05-18 00:00:00
abstract::Human microbiome reference datasets provide epidemiological context for researchers, enabling them to uncover new insights into their own data through meta-analyses. In addition, large and comprehensive reference sets offer a means to develop or test hypotheses and can pave the way for addressing practical study desig...
journal_title:Microbiome
pub_type: 杂志文章,评审
doi:10.1186/s40168-015-0117-2
更新日期:2015-11-04 00:00:00
abstract::Immigration is a process that can influence the assembly of microbial communities in natural and engineered environments. However, it remains challenging to quantitatively evaluate the contribution of this process to the microbial diversity and function in the receiving ecosystems. Currently used methods, i.e., counti...
journal_title:Microbiome
pub_type: 杂志文章,评审
doi:10.1186/s40168-019-0760-0
更新日期:2019-11-06 00:00:00
abstract:BACKGROUND:Bacteriophage-prokaryote dynamics and interaction are believed to be important in governing microbiome composition and ecosystem functions, yet our limited knowledge of the spatial and temporal variation in phage and prokaryotic community compositions precludes accurate assessment of their roles and impacts....
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0272-8
更新日期:2017-05-31 00:00:00
abstract:BACKGROUND:Early disruption of the microbial community may influence life-long health. Environmental toxicants can contaminate breast milk and the developing infant gut microbiome is directly exposed. We investigated whether environmental toxicants in breastmilk affect the composition and function of the infant gut mic...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0645-2
更新日期:2019-02-27 00:00:00
abstract:BACKGROUND:Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets or require reference genomes. Here, we present MetaCHIP, a pipeline for reference-independent HGT ide...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0649-y
更新日期:2019-03-04 00:00:00
abstract:BACKGROUND:Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Br...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00902-0
更新日期:2020-08-31 00:00:00
abstract::An amendment to this paper has been published and can be accessed via the original article. ...
journal_title:Microbiome
pub_type: 已发布勘误
doi:10.1186/s40168-020-00905-x
更新日期:2020-08-20 00:00:00
abstract:BACKGROUND:Otitis media (OM) imposes a great burden of disease in indigenous populations around the world, despite a variety of treatment and prevention programs. Improved understanding of the pathogenesis of OM in indigenous populations is required to advance treatment and reduce prevalence. We conducted a systematic ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0577-2
更新日期:2018-11-05 00:00:00
abstract:BACKGROUND:Recent evidence supports that the maternal gut microbiota impacts the initial infant gut microbiota. Since the gut microbiota may play a causal role in the development of obesity, it is important to understand how pre-pregnancy weight and gestational weight gain (GWG) impact the gut microbiota of mothers at ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0332-0
更新日期:2017-09-04 00:00:00
abstract:BACKGROUND:Metallo-β-lactamases are bacterial enzymes that provide resistance to carbapenems, the most potent class of antibiotics. These enzymes are commonly encoded on mobile genetic elements, which, together with their broad substrate spectrum and lack of clinically useful inhibitors, make them a particularly proble...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0353-8
更新日期:2017-10-12 00:00:00
abstract:BACKGROUND:Aphids are known to live in symbiosis with specific bacteria, called endosymbionts which can be classified as obligate or accessory. Buchnera aphidicola is generally the only obligatory symbiont present in aphids, supplying essential nutrients that are missing in the plants phloem to its host. Pentalonia nig...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-015-0130-5
更新日期:2015-12-15 00:00:00