The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome.

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 (geocaulosphere soil (GS), rhizosphere soil (RS), root-zone soil (ZS), and furrow soil (FS)) were analyzed for potato plants with naturally high (H) and low (L) scab severity levels. We aimed to determine the composition and putative function of the soil microbiome associated with potato CS. RESULTS:The copy numbers of the scab phytotoxin biosynthetic gene txtAB and the bacterial 16S rRNA gene as well as the diversity and composition of each of the four soil-root system compartments were examined; GS was the only compartment that exhibited significant differences between the H and L groups. Compared to the H group, the L group exhibited a lower txtAB gene copy number, lower bacterial 16S copy number, higher diversity, higher co-occurrence network complexity, and higher community function similarity within the GS microbiome. The community composition and function of the GS samples were further revealed by shotgun metagenomic sequencing. Variovorax, Stenotrophomonas, and Agrobacterium were the most abundant genera that were significantly and positively correlated with the scab severity level, estimated absolute abundance (EAA) of pathogenic Streptomyces, and txtAB gene copy number. In contrast, Geobacillus, Curtobacterium, and unclassified Geodermatophilaceae were significantly negatively correlated with these three parameters. Compared to the function profiles in the L group, several genes involved in "ABC transporters," the "bacterial secretion system," "quorum sensing (QS)," "nitrogen metabolism," and some metabolism by cytochrome P450 were enriched in the H group. In contrast, some antibiotic biosynthesis pathways were enriched in the L group. Based on the differences in community composition and function, a simple model was proposed to explain the putative relationships between the soil microbiome and CS occurrence. CONCLUSIONS:The GS microbiome was closely associated with CS severity in the soil-root system, and the occurrence of CS was accompanied by changes in community composition and function. The differential functions provide new clues to elucidate the mechanism underlying the interaction between CS occurrence and the soil microbiome, and varying community compositions provide novel insights into CS occurrence.

journal_name

Microbiome

journal_title

Microbiome

authors

Shi W,Li M,Wei G,Tian R,Li C,Wang B,Lin R,Shi C,Chi X,Zhou B,Gao Z

doi

10.1186/s40168-019-0629-2

subject

Has Abstract

pub_date

2019-02-01 00:00:00

pages

14

issue

1

issn

2049-2618

pii

10.1186/s40168-019-0629-2

journal_volume

7

pub_type

杂志文章
  • Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation.

    abstract:BACKGROUND:Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and i...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-016-0201-2

    authors: Kamke J,Kittelmann S,Soni P,Li Y,Tavendale M,Ganesh S,Janssen PH,Shi W,Froula J,Rubin EM,Attwood GT

    更新日期:2016-10-19 00:00:00

  • Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

    abstract:BACKGROUND:Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a ver...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0233-2

    authors: Huson DH,Tappu R,Bazinet AL,Xie C,Cummings MP,Nieselt K,Williams R

    更新日期:2017-01-25 00:00:00

  • Effect of postnatal low-dose exposure to environmental chemicals on the gut microbiome in a rodent model.

    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

    authors: Hu J,Raikhel V,Gopalakrishnan K,Fernandez-Hernandez H,Lambertini L,Manservisi F,Falcioni L,Bua L,Belpoggi F,L Teitelbaum S,Chen J

    更新日期:2016-06-14 00:00:00

  • Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children.

    abstract:BACKGROUND:The nasopharynx is a reservoir for pathogens associated with respiratory illnesses, such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome during health and disease. Most studies so far have surveyed the nasopharynx as a whole; however, less is known abou...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-016-0170-5

    authors: Pérez-Losada M,Crandall KA,Freishtat RJ

    更新日期:2016-06-16 00:00:00

  • The human gallbladder microbiome is related to the physiological state and the biliary metabolic profile.

    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

    authors: Molinero N,Ruiz L,Milani C,Gutiérrez-Díaz I,Sánchez B,Mangifesta M,Segura J,Cambero I,Campelo AB,García-Bernardo CM,Cabrera A,Rodríguez JI,González S,Rodríguez JM,Ventura M,Delgado S,Margolles A

    更新日期:2019-07-04 00:00:00

  • Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome.

    abstract:BACKGROUND:Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats; however, this hypothesis remains inconclusive so far. To understand the consequences of the introduction of exogenic antimicrobials into nat...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-020-00982-y

    authors: Wicaksono WA,Kusstatscher P,Erschen S,Reisenhofer-Graber T,Grube M,Cernava T,Berg G

    更新日期:2021-01-27 00:00:00

  • Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals.

    abstract:BACKGROUND:Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeot...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-016-0181-2

    authors: Ormerod KL,Wood DL,Lachner N,Gellatly SL,Daly JN,Parsons JD,Dal'Molin CG,Palfreyman RW,Nielsen LK,Cooper MA,Morrison M,Hansbro PM,Hugenholtz P

    更新日期:2016-07-07 00:00:00

  • MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches.

    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

    authors: Song W,Wemheuer B,Zhang S,Steensen K,Thomas T

    更新日期:2019-03-04 00:00:00

  • Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore.

    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

    authors: Gobet A,Mest L,Perennou M,Dittami SM,Caralp C,Coulombet C,Huchette S,Roussel S,Michel G,Leblanc C

    更新日期:2018-03-27 00:00:00

  • Hybridization capture reveals microbial diversity missed using current profiling methods.

    abstract:BACKGROUND:Microorganisms comprise the majority of living organisms on our planet. For many years, exploration of the composition of microbial communities has been performed through the PCR-based study of the small subunit rRNA gene due to its high conservation across the domains of life. The application of this method...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0442-3

    authors: Gasc C,Peyret P

    更新日期:2018-03-27 00:00:00

  • Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment.

    abstract:BACKGROUND:Determining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 t...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-020-00960-4

    authors: Minich JJ,Ali F,Marotz C,Belda-Ferre P,Chiang L,Shaffer JP,Carpenter CS,McDonald D,Gilbert J,Allard SM,Allen EE,Knight R,Sweeney DA,Swafford AD

    更新日期:2021-01-22 00:00:00

  • Correction to: Microbiome definition re-visited: old concepts and new challenges.

    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

    authors: Berg G,Rybakova D,Fischer D,Cernava T,Vergès MC,Charles T,Chen X,Cocolin L,Eversole K,Corral GH,Kazou M,Kinkel L,Lange L,Lima N,Loy A,Macklin JA,Maguin E,Mauchline T,McClure R,Mitter B,Ryan M,Sarand I,Smidt H

    更新日期:2020-08-20 00:00:00

  • Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation.

    abstract:BACKGROUND:Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional capacity of mature plaque is gradually shaped during several stages of community assembly via processe...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0591-4

    authors: Edlund A,Yang Y,Yooseph S,He X,Shi W,McLean JS

    更新日期:2018-12-06 00:00:00

  • Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments.

    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

    authors: Mu DS,Wang S,Liang QY,Du ZZ,Tian R,Ouyang Y,Wang XP,Zhou A,Gong Y,Chen GJ,Van Nostrand J,Yang Y,Zhou J,Du ZJ

    更新日期:2020-08-31 00:00:00

  • Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.

    abstract:BACKGROUND:The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of primary bile acids and their subsequent deconjugation and transformation by the gut microbiome. To understand these system-level host-microbe inter...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0689-3

    authors: Heinken A,Ravcheev DA,Baldini F,Heirendt L,Fleming RMT,Thiele I

    更新日期:2019-05-15 00:00:00

  • Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month.

    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

    authors: Iszatt N,Janssen S,Lenters V,Dahl C,Stigum H,Knight R,Mandal S,Peddada S,González A,Midtvedt T,Eggesbø M

    更新日期:2019-02-27 00:00:00

  • Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model.

    abstract:BACKGROUND:The development of the rumen is an important physiological challenge for young ruminants. Previous studies have shown that starter feeding can effectively facilitate the growth and development of the rumen in ruminants. However, the mechanism through which starter feeding stimulates the development of the ru...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0701-y

    authors: Lin L,Xie F,Sun D,Liu J,Zhu W,Mao S

    更新日期:2019-06-03 00:00:00

  • Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation.

    abstract:BACKGROUND:Increasing evidence reveals the importance of the microbiome in health and disease and inseparable host-microbial dependencies. Host-microbe interactions are highly relevant in patients receiving allogeneic hematopoietic stem cell transplantation (HSCT), i.e., a replacement of the cellular components of the ...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0745-z

    authors: Ingham AC,Kielsen K,Cilieborg MS,Lund O,Holmes S,Aarestrup FM,Müller KG,Pamp SJ

    更新日期:2019-09-13 00:00:00

  • Niche differentiation rather than biogeography shapes the diversity and composition of microbiome of Cycas panzhihuaensis.

    abstract:BACKGROUND:Given their adaptation to nutrient-poor and drought environments, cycads are vital models for plant-microbiome interaction research because they are likely to host an important reservoir of beneficial microbes that may support cycad survival. However, a comprehensive understanding of the diversity and commun...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0770-y

    authors: Zheng Y,Gong X

    更新日期:2019-12-02 00:00:00

  • Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission.

    abstract:BACKGROUND:The correct establishment of the human gut microbiota represents a crucial development that commences at birth. Different hypotheses propose that the infant gut microbiota is derived from, among other sources, the mother's fecal/vaginal microbiota and human milk. RESULTS:The composition of bifidobacterial c...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0282-6

    authors: Duranti S,Lugli GA,Mancabelli L,Armanini F,Turroni F,James K,Ferretti P,Gorfer V,Ferrario C,Milani C,Mangifesta M,Anzalone R,Zolfo M,Viappiani A,Pasolli E,Bariletti I,Canto R,Clementi R,Cologna M,Crifò T,Cusumano

    更新日期:2017-06-26 00:00:00

  • An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community.

    abstract:BACKGROUND:Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communiti...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0634-5

    authors: Yu K,Yi S,Li B,Guo F,Peng X,Wang Z,Wu Y,Alvarez-Cohen L,Zhang T

    更新日期:2019-02-06 00:00:00

  • Gut-dependent microbial translocation induces inflammation and cardiovascular events after ST-elevation myocardial infarction.

    abstract:BACKGROUND:Post-infarction cardiovascular remodeling and heart failure are the leading cause of myocardial infarction (MI)-driven death during the past decades. Experimental observations have involved intestinal microbiota in the susceptibility to MI in mice; however, in humans, identifying whether translocation of gut...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0441-4

    authors: Zhou X,Li J,Guo J,Geng B,Ji W,Zhao Q,Li J,Liu X,Liu J,Guo Z,Cai W,Ma Y,Ren D,Miao J,Chen S,Zhang Z,Chen J,Zhong J,Liu W,Zou M,Li Y,Cai J

    更新日期:2018-04-03 00:00:00

  • Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China.

    abstract:BACKGROUND:The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulatin...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0572-7

    authors: Liu YR,Delgado-Baquerizo M,Bi L,Zhu J,He JZ

    更新日期:2018-10-18 00:00:00

  • Metabolic capability and in situ activity of microorganisms in an oil reservoir.

    abstract:BACKGROUND:Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microb...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0392-1

    authors: Liu YF,Galzerani DD,Mbadinga SM,Zaramela LS,Gu JD,Mu BZ,Zengler K

    更新日期:2018-01-05 00:00:00

  • Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis.

    abstract:BACKGROUND:Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the ge...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-016-0197-7

    authors: Hammond M,Homa F,Andersson-Svahn H,Ettema TJ,Joensson HN

    更新日期:2016-10-06 00:00:00

  • Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens.

    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

    authors: Chopyk J,Chattopadhyay S,Kulkarni P,Claye E,Babik KR,Reid MC,Smyth EM,Hittle LE,Paulson JN,Cruz-Cano R,Pop M,Buehler SS,Clark PI,Sapkota AR,Mongodin EF

    更新日期:2017-02-15 00:00:00

  • Encrustations on ureteral stents from patients without urinary tract infection reveal distinct urotypes and a low bacterial load.

    abstract:BACKGROUND:Current knowledge of the urinary tract microbiome is limited to urine analysis and analysis of biofilms formed on Foley catheters. Bacterial biofilms on ureteral stents have rarely been investigated, and no cultivation-independent data are available on the microbiome of the encrustations on the stents. RESU...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0674-x

    authors: Buhmann MT,Abt D,Nolte O,Neu TR,Strempel S,Albrich WC,Betschart P,Zumstein V,Neels A,Maniura-Weber K,Ren Q

    更新日期:2019-04-13 00:00:00

  • Host genetic variation in mucosal immunity pathways influences the upper airway microbiome.

    abstract:BACKGROUND:The degree to which host genetic variation can modulate microbial communities in humans remains an open question. Here, we performed a genetic mapping study of the microbiome in two accessible upper airway sites, the nasopharynx and the nasal vestibule, during two seasons in 144 adult members of a founder po...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-016-0227-5

    authors: Igartua C,Davenport ER,Gilad Y,Nicolae DL,Pinto J,Ober C

    更新日期:2017-02-01 00:00:00

  • Humans as holobionts: implications for prevention and therapy.

    abstract::The human gut microbiota is increasingly recognized for its important or even decisive role in health. As it becomes clear that microbiota and host mutually affect and depend on each other in an intimate relationship, a holistic view of the gut microbiota-host association imposes itself. Ideally, a stable state of equ...

    journal_title:Microbiome

    pub_type: 杂志文章,评审

    doi:10.1186/s40168-018-0466-8

    authors: van de Guchte M,Blottière HM,Doré J

    更新日期:2018-05-01 00:00:00

  • 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice.

    abstract:BACKGROUND:Characterisation of the bacterial composition of the gut microbiota is increasingly carried out with a view to establish the role of different bacterial species in causation or prevention of disease. It is thus essential that the methods used to determine the microbial composition are robust. Here, several w...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-015-0087-4

    authors: Walker AW,Martin JC,Scott P,Parkhill J,Flint HJ,Scott KP

    更新日期:2015-06-22 00:00:00