当前位置： SCI文献检索 > Microbiome期刊下所有文献 > MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics.

MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics.

Abstract：

BACKGROUND:Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in most microbial communities as chief predators, decomposers, phototrophs, bacterial hosts, symbionts, and parasites to plants and animals. Investigating their roles is therefore of great interest to ecology, biotechnology, human health, and evolution. However, the generally lower sequencing coverage, their more complex gene and genome architectures, and a lack of eukaryote-specific experimental and computational procedures have kept them on the sidelines of metagenomics. RESULTS:MetaEuk is a toolkit for high-throughput, reference-based discovery, and annotation of protein-coding genes in eukaryotic metagenomic contigs. It performs fast searches with 6-frame-translated fragments covering all possible exons and optimally combines matches into multi-exon proteins. We used a benchmark of seven diverse, annotated genomes to show that MetaEuk is highly sensitive even under conditions of low sequence similarity to the reference database. To demonstrate MetaEuk's power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project. MetaEuk predicted >12,000,000 protein-coding genes in 8 days on ten 16-core servers. Most of the discovered proteins are highly diverged from known proteins and originate from very sparsely sampled eukaryotic supergroups. CONCLUSION:The open-source (GPLv3) MetaEuk software (https://github.com/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation. Video abstract.

journal_name

Microbiome

journal_title

Microbiome

authors

Levy Karin E,Mirdita M,Söding J

doi

10.1186/s40168-020-00808-x

subject

Has Abstract

pub_date

2020-04-03 00:00:00

pages

48

issue

1

issn

2049-2618

pii

10.1186/s40168-020-00808-x

journal_volume

8

pub_type

杂志文章

相关文献

Microbiome文献大全
  • Facultative methanotrophs are abundant at terrestrial natural gas seeps.

    abstract：BACKGROUND:Natural gas contains methane and the gaseous alkanes ethane, propane and butane, which collectively influence atmospheric chemistry and cause global warming. Methane-oxidising bacteria, methanotrophs, are crucial in mitigating emissions of methane as they oxidise most of the methane produced in soils and the...

    journal_title：Microbiome

    pub_type： 杂志文章

    doi：10.1186/s40168-018-0500-x

    authors： Farhan Ul Haque M,Crombie AT,Ensminger SA,Baciu C,Murrell JC

    更新日期：2018-06-28 00:00:00

  • Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants.

    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

    authors： Stanislawski MA,Dabelea D,Wagner BD,Sontag MK,Lozupone CA,Eggesbø M

    更新日期：2017-09-04 00:00:00

  • Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility.

    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

    authors： Seto CT,Jeraldo P,Orenstein R,Chia N,DiBaise JK

    更新日期：2014-11-25 00:00:00

  • A comparison of methods used to unveil the genetic and metabolic pool in the built environment.

    abstract：BACKGROUND:A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribo...

    journal_title：Microbiome

    pub_type： 杂志文章

    doi：10.1186/s40168-018-0453-0

    authors： Gomez-Silvan C,Leung MHY,Grue KA,Kaur R,Tong X,Lee PKH,Andersen GL

    更新日期：2018-04-16 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

  • The human gut archaeome: identification of diverse haloarchaea in Korean subjects.

    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

    authors： Kim JY,Whon TW,Lim MY,Kim YB,Kim N,Kwon MS,Kim J,Lee SH,Choi HJ,Nam IH,Chung WH,Kim JH,Bae JW,Roh SW,Nam YD

    更新日期：2020-08-04 00:00:00

  • Correction to: Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons.

    abstract：:Following publication of the original article [1], the authors reported an error in Figure 1 and a text on page 13. In Figure 1, some areas are missing and the correct figure is presented here. On page 13, the sentence should be updated to the following (change has been indicated in bold italics). ...

    journal_title：Microbiome

    pub_type： 已发布勘误

    doi：10.1186/s40168-019-0763-x

    authors： Chen W,Ren K,Isabwe A,Chen H,Liu M,Yang J

    更新日期：2019-11-14 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

  • Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence.

    abstract：BACKGROUND:High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, "Royal Gala," "Golden Delicious," and "Honey Crisp," and two rootstocks, M.9 and M.M.111. The obje...

    journal_title：Microbiome

    pub_type： 杂志文章

    doi：10.1186/s40168-018-0403-x

    authors： Liu J,Abdelfattah A,Norelli J,Burchard E,Schena L,Droby S,Wisniewski M

    更新日期：2018-01-27 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

  • 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

  • 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

  • Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community.

    abstract：:Recent studies have conflicting data regarding the presence of intra-amniotic microbiota. Viral communities are increasingly recognized as important although overlooked components of the human microbiota. It is unknown if the developing fetus is exposed to a community of viruses (virome). Given the debate over the exi...

    journal_title：Microbiome

    pub_type： 杂志文章

    doi：10.1186/s40168-018-0475-7

    authors： Lim ES,Rodriguez C,Holtz LR

    更新日期：2018-05-11 00:00:00

  • Interactive effects of temperature, organic carbon, and pipe material on microbiota composition and Legionella pneumophila in hot water plumbing systems.

    abstract：BACKGROUND:Several biotic and abiotic factors have been reported to influence the proliferation of microbes, including Legionella pneumophila, in hot water premise plumbing systems, but their combined effects have not been systematically evaluated. Here, we utilize simulated household water heaters to examine the effec...

    journal_title：Microbiome

    pub_type： 杂志文章

    doi：10.1186/s40168-017-0348-5

    authors： Proctor CR,Dai D,Edwards MA,Pruden A

    更新日期：2017-10-04 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

  • Dichotomous development of the gut microbiome in preterm infants.

    abstract：BACKGROUND:Preterm infants are at risk of developing intestinal dysbiosis with an increased proportion of Gammaproteobacteria. In this study, we sought the clinical determinants of the relative abundance of feces-associated Gammaproteobacteria in very low birth weight (VLBW) infants. Fecal microbiome was characterized ...

    journal_title：Microbiome

    pub_type： 杂志文章

    doi：10.1186/s40168-018-0547-8

    authors： Ho TTB,Groer MW,Kane B,Yee AL,Torres BA,Gilbert JA,Maheshwari A

    更新日期：2018-09-12 00:00:00

  • Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons.

    abstract：BACKGROUND:The vaginal microbiome is an important site of bacterial-mammalian symbiosis. This symbiosis is currently best characterized for humans, where lactobacilli dominate the microbial community and may help defend women against infectious disease. However, lactobacilli do not dominate the vaginal microbiota of an...

    journal_title：Microbiome

    pub_type： 杂志文章

    doi：10.1186/s40168-017-0228-z

    authors： Miller EA,Livermore JA,Alberts SC,Tung J,Archie EA

    更新日期：2017-01-19 00:00:00

  • Organophosphorus pesticide chlorpyrifos intake promotes obesity and insulin resistance through impacting gut and gut microbiota.

    abstract：BACKGROUND:Disruption of the gut microbiota homeostasis may induce low-grade inflammation leading to obesity-associated diseases. A major protective mechanism is to use the multi-layered mucus structures to keep a safe distance between gut epithelial cells and microbiota. To investigate whether pesticides would induce ...

    journal_title：Microbiome

    pub_type： 杂志文章

    doi：10.1186/s40168-019-0635-4

    authors： Liang Y,Zhan J,Liu D,Luo M,Han J,Liu X,Liu C,Cheng Z,Zhou Z,Wang P

    更新日期：2019-02-11 00:00:00

  • Context and the human microbiome.

    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

    authors： McDonald D,Birmingham A,Knight R

    更新日期：2015-11-04 00:00:00

  • The unsolved problem of otitis media in indigenous populations: a systematic review of upper respiratory and middle ear microbiology in indigenous children with otitis media.

    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

    authors： Coleman A,Wood A,Bialasiewicz S,Ware RS,Marsh RL,Cervin A

    更新日期：2018-11-05 00:00:00

  • 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 (geocaulo...

    journal_title：Microbiome

    pub_type： 杂志文章

    doi：10.1186/s40168-019-0629-2

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

    更新日期：2019-02-01 00:00:00

  • The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids.

    abstract：BACKGROUND:Sub-therapeutic antibiotics are widely used as growth promoters in the poultry industry; however, the resulting antibiotic resistance threatens public health. A plant-derived growth promoter, Macleaya cordata extract (MCE), with effective ingredients of benzylisoquinoline alkaloids, is a potential alternativ...

    journal_title：Microbiome

    pub_type： 杂志文章

    doi：10.1186/s40168-018-0590-5

    authors： Huang P,Zhang Y,Xiao K,Jiang F,Wang H,Tang D,Liu D,Liu B,Liu Y,He X,Liu H,Liu X,Qing Z,Liu C,Huang J,Ren Y,Yun L,Yin L,Lin Q,Zeng C,Su X,Yuan J,Lin L,Hu N,Cao H,Huang S,Guo Y,Fan W,Zeng J

    更新日期：2018-11-27 00:00:00

  • Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants.

    abstract：BACKGROUND:Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little information is available on the potential roles of chronic urban PAH pollutant exposure on the cutaneous micr...

    journal_title：Microbiome

    pub_type： 杂志文章

    doi：10.1186/s40168-020-00874-1

    authors： Leung MHY,Tong X,Bastien P,Guinot F,Tenenhaus A,Appenzeller BMR,Betts RJ,Mezzache S,Li J,Bourokba N,Breton L,Clavaud C,Lee PKH

    更新日期：2020-06-26 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

  • Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences.

    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

    authors： Miletto M,Lindow SE

    更新日期：2015-12-10 00:00:00

  • Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing.

    abstract：BACKGROUND:Wastewater treatment plants (WWTPs) are recognized as hotspots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our understanding of the composition and distribution of ARGs in WWTPs, the genetic location, host, and fate of ARGs remain largely unknown. RESULTS:In this study,...

    journal_title：Microbiome

    pub_type： 杂志文章

    doi：10.1186/s40168-019-0663-0

    authors： Che Y,Xia Y,Liu L,Li AD,Yang Y,Zhang T

    更新日期：2019-03-21 00:00:00

  • Transplanted human fecal microbiota enhanced Guillain Barré syndrome autoantibody responses after Campylobacter jejuni infection in C57BL/6 mice.

    abstract：BACKGROUND:Campylobacter jejuni is the leading antecedent infection to the autoimmune neuropathy Guillain-Barré syndrome (GBS), which is accompanied by an autoimmune anti-ganglioside antibody attack on peripheral nerves. Previously, we showed that contrasting immune responses mediate C. jejuni induced colitis and autoi...

    journal_title：Microbiome

    pub_type： 杂志文章

    doi：10.1186/s40168-017-0284-4

    authors： Brooks PT,Brakel KA,Bell JA,Bejcek CE,Gilpin T,Brudvig JM,Mansfield LS

    更新日期：2017-08-08 00:00:00

  • The vaginal microbiota, human papillomavirus infection and cervical intraepithelial neoplasia: what do we know and where are we going next?

    abstract：:The vaginal microbiota plays a significant role in health and disease of the female reproductive tract. Next-generation sequencing techniques based upon the analysis of bacterial 16S rRNA genes permit in-depth study of vaginal microbial community structure to a level of detail not possible with standard culture-based ...

    journal_title：Microbiome

    pub_type： 杂志文章,评审

    doi：10.1186/s40168-016-0203-0

    authors： Mitra A,MacIntyre DA,Marchesi JR,Lee YS,Bennett PR,Kyrgiou M

    更新日期：2016-11-01 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

  • 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